Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Understanding plant immunity as a surveillance system to detect invasion
    Cook III, D.E. ; Mesarich, C.H. ; Thomma, B.P.H.J. - \ 2015
    Annual Review of Phytopathology 53 (2015). - ISSN 0066-4286 - p. 541 - 563.
    disease-resistance gene - bacterial elicitor flagellin - syringae effectors avrb - host-selective toxins - innate immunity - arabidopsis-thaliana - molecular-patterns - microbe interactions - durable resistance - necrotrophic pathogens
    Various conceptual models to describe the plant immune system have been presented. The most recent paradigm to gain wide acceptance in the field is often referred to as the zigzag model, which reconciles the previously formulated gene-for-gene hypothesis with the recognition of general elicitors in a single model. This review focuses on the limitations of the current paradigm of molecular plant-microbe interactions and how it too narrowly defines the plant immune system. As such, we discuss an alternative view of plant innate immunity as a system that evolves to detect invasion. This view accommodates the range from mutualistic to parasitic symbioses that plants form with diverse organisms, as well as the spectrum of ligands that the plant immune system perceives. Finally, how this view can contribute to the current practice of resistance breeding is discussed.
    DOG1-imposed dormancy mediates germination responses to temperature cues
    Murphey, M. ; Kovach, K. ; Elnacash, T. ; He, H. ; Bentsink, L. ; Donohue, K. - \ 2015
    Environmental and Experimental Botany 112 (2015). - ISSN 0098-8472 - p. 33 - 43.
    seed-maturation environment - quantitative trait locus - recent climate-change - arabidopsis-thaliana - life-history - ectopic expression - niche construction - natural-selection - dog1-like genes - dog1
    Seed dormancy and environment-dependent germination requirements interact to determine the timing of germination in natural environments. This study tested the contribution of the dormancy gene Delay Of Germination 1 (DOG1) to primary and secondary dormancy induction in response to environmental cues, and evaluated how DOG1-mediated dormancy influenced germination responses to different temperature cues. We verified that DOG1 is involved in the induction of primary dormancy in response to cool seed-maturation temperature experienced by maternal plants, and we found that it is also involved in secondary dormancy in response to warm and prolonged cold stratification experienced by seeds during imbibition. DOG1-imposed dormancy can also mediate germination responses to environmental conditions, including cold stratification and germination temperatures experienced by imbibing seeds. Specifically, germination responsiveness to temperature cues is most apparent when seeds exhibit an intermediate degree of dormancy. However, DOG1 itself does not seem to directly regulate the response to cold stratification nor does it determine the function of temperature-dependent germination, since DOG1 mutants were capable of exhibiting increased germination after cold stratification as well as temperature-dependent germination. Instead, DOG1 has major effects on germination behavior primarily by exposing or masking underlying environmental sensitivity, and thereby strongly influences how environmentally responsive germination can be, and when during a season, it is likely to exhibit environmental sensitivity.
    Organizer-Derived WOX5 Signal Maintains Root Columella Stem Cells through Chromatin-Mediated Repression of CDF4 Expression.
    Pi, L. ; Graaff, E. van der; Llavata Peris, C.I. ; Weijers, D. ; Henning, L. ; Groot, E. de; Laux, T. - \ 2015
    Developmental Cell 33 (2015)5. - ISSN 1534-5807 - p. 576 - 588.
    histone deacetylase - arabidopsis-thaliana - transcriptional repression - gene-expression - wuschel - meristem - shoot - topless - protein - fate
    Stem cells in plants and animals are maintained pluripotent by signals from adjacent niche cells. In plants, WUSCHEL HOMEOBOX (WOX) transcription factors are central regulators of stem cell maintenance in different meristem types, yet their molecular mode of action has remained elusive. Here we show that in the Arabidopsis root meristem, the WOX5 protein moves from the root niche organizer, the quiescent center, into the columella stem cells, where it directly represses the transcription factor gene CDF4. This creates a gradient of CDF4 transcription, which promotes differentiation opposite to the WOX5 gradient, allowing stem cell daughter cells to exit the stem cell state. We further show that WOX5 represses CDF4 transcription by recruiting TPL/TPR co-repressors and the histone deacetylase HDA19, which consequently induces histone deacetylation at the CDF4 regulatory region. Our results show that chromatin-mediated repression of differentiation programs is a common strategy in plant and animal stem cell niches.
    Large-Scale Phenomics Identifies Primary and Fine-Tuning Roles for CRKs in Responses Related to Oxidative Stress.
    Bourdais, G. ; Burdiak, P. ; Gauthier, A. ; Nitsch, L.M.C. ; Salojärvi, J. ; Rayapuram, C. ; Idänheimo, N. ; Hunter, K. ; Kimura, S. ; Merilo, E. ; Vaattovaara, A. ; Oracz, K. ; Kaufholdt, D. ; Pallon, A. ; Anggoro, D.T. ; Glów, D. ; Lowe, J. ; Zhou, J. ; Mohammadi, O. ; Puukko, T. ; Albert, A. ; Lang, H. ; Ernst, D. ; Kollist, H. ; Brosché, M. ; Durner, J. ; Borst, J.W. ; Collinge, D.B. ; Karpinski, S. ; Lyngkjær, M.F. ; Robatzek, S. ; Wrzaczek, M. ; Kangasjärvi, J. - \ 2015
    Plos Genetics 11 (2015)7. - ISSN 1553-7404
    receptor-like kinase - multiple sequence alignment - arabidopsis-thaliana - cell-death - protein-kinase - transcriptional regulation - pseudomonas-syringae - flagellin perception - light acclimation - stomatal immunity
    Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins characterized by the presence of two domains of unknown function 26 (DUF26) in their ectodomain. The CRKs form one of the largest groups of receptor-like protein kinases in plants, but their biological functions have so far remained largely uncharacterized. We conducted a large-scale phenotyping approach of a nearly complete crk T-DNA insertion line collection showing that CRKs control important aspects of plant development and stress adaptation in response to biotic and abiotic stimuli in a non-redundant fashion. In particular, the analysis of reactive oxygen species (ROS)-related stress responses, such as regulation of the stomatal aperture, suggests that CRKs participate in ROS/redox signalling and sensing. CRKs play general and fine-tuning roles in the regulation of stomatal closure induced by microbial and abiotic cues. Despite their great number and high similarity, large-scale phenotyping identified specific functions in diverse processes for many CRKs and indicated that CRK2 and CRK5 play predominant roles in growth regulation and stress adaptation, respectively. As a whole, the CRKs contribute to specificity in ROS signalling. Individual CRKs control distinct responses in an antagonistic fashion suggesting future potential for using CRKs in genetic approaches to improve plant performance and stress tolerance.
    Strigolactones, a Novel Carotenoid-Derived Plant Hormone
    Al-Babili, S. ; Bouwmeester, H.J. - \ 2015
    Annual Review of Plant Biology 66 (2015). - ISSN 1543-5008 - p. 161 - 186.
    arbuscular mycorrhizal symbiosis - low phosphorus availability - abscisic-acid biosynthesis - in-vitro characterization - cytochrome b(6)f complex - root-system architecture - tiller bud outgrowth - box protein max2 - germination stimulants - arabidopsis-thaliana
    Strigolactones (SLs) are carotenoid-derived plant hormones and signaling molecules. When released into the soil, SLs indicate the presence of a host to symbiotic fungi and root parasitic plants. In planta, they regulate several developmental processes that adapt plant architecture to nutrient availability. Highly branched/tillered mutants in Arabidopsis, pea, and rice have enabled the identification of four SL biosynthetic enzymes: a cis/trans-carotene isomerase, two carotenoid cleavage dioxygenases, and a cytochrome P450 (MAX1). In vitro and in vivo enzyme assays and analysis of mutants have shown that the pathway involves a combination of new reactions leading to carlactone, which is converted by a rice MAX1 homolog into an SL parent molecule with a tricyclic lactone moiety. In this review, we focus on SL biosynthesis, describe the hormonal and environmental factors that determine this process, and discuss SL transport and downstream signaling as well as the role of SLs in regulating plant development.
    Large-scale evolutionary analysis of genes and supergene clusters from terpenoid modular pathways provides insights into metabolic diversification in flowering plants.
    Hofberger, J.A. ; Ramirez, A.M. ; Bergh, E. van den; Zhu, X. ; Bouwmeester, H.J. ; Schuurink, R.C. ; Schranz, M.E. - \ 2015
    PLoS ONE 10 (2015)6. - ISSN 1932-6203 - 37 p.
    isopentenyl diphosphate isomerases - disease resistance genes - arabidopsis-thaliana - genome sequence - whole-genome - protein families - draft genome - isoprenoid biosynthesis - secondary metabolism - oxidosqualene cyclase
    An important component of plant evolution is the plethora of pathways producing more than 200,000 biochemically diverse specialized metabolites with pharmacological, nutritional and ecological significance. To unravel dynamics underlying metabolic diversification, it is critical to determine lineage-specific gene family expansion in a phylogenomics framework. However, robust functional annotation is often only available for core enzymes catalyzing committed reaction steps within few model systems. In a genome informatics approach, we extracted information from early-draft gene-space assemblies and non-redundant transcriptomes to identify protein families involved in isoprenoid biosynthesis. Isoprenoids comprise terpenoids with various roles in plant-environment interaction, such as pollinator attraction or pathogen defense. Combining lines of evidence provided by synteny, sequence homology and Hidden-Markov-Modelling, we screened 17 genomes including 12 major crops and found evidence for 1,904 proteins associated with terpenoid biosynthesis. Our terpenoid genes set contains evidence for 840 core terpene-synthases and 338 triterpene-specific synthases. We further identified 190 prenyltransferases, 39 isopentenyl-diphosphate isomerases as well as 278 and 219 proteins involved in mevalonate and methylerithrol pathways, respectively. Assessing the impact of gene and genome duplication to lineage-specific terpenoid pathway expansion, we illustrated key events underlying terpenoid metabolic diversification within 250 million years of flowering plant radiation. By quantifying Angiosperm-wide versatility and phylogenetic relationships of pleiotropic gene families in terpenoid modular pathways, our analysis offers significant insight into evolutionary dynamics underlying diversification of plant secondary metabolism. Furthermore, our data provide a blueprint for future efforts to identify and more rapidly clone terpenoid biosynthetic genes from any plant species.
    The epigenetic footprint of poleward range-expanding plants in apomictic dandelions
    Preite, V. ; Snoek, L.B. ; Oplaat, C. ; Biere, A. ; Putten, W.H. van der; Verhoeven, K.J.F. - \ 2015
    Molecular Ecology 24 (2015)17. - ISSN 0962-1083 - p. 4406 - 4418.
    dna methylation polymorphism - arabidopsis-thaliana - geographic parthenogenesis - ecological epigenetics - phenotypic plasticity - cytosine methylation - population-structure - japanese knotweed - common dandelion - taraxacum
    Epigenetic modifications, such as DNA methylation variation, can generate heritable phenotypic variation independent of the underlying genetic code. However, epigenetic variation in natural plant populations is poorly documented and little understood. Here, we test if northward range expansion of obligate apomicts of the common dandelion (Taraxacum officinale) is associated with DNA methylation variation. We characterized and compared patterns of genetic and DNA-methylation variation in greenhouse-reared offspring of T. officinale that were collected along a latitudinal transect of northward range expansion in Europe. Genetic AFLP and epigenetic MS-AFLP markers revealed high levels of local diversity and modest but significant heritable differentiation between sampling locations and between the Southern, Central and Northern regions of the transect. Patterns of genetic and epigenetic variation were significantly correlated, reflecting the genetic control over epigenetic variation and/or the accumulation of lineage-specific spontaneous epimutations, which may be selectively neutral. In addition, we identified a small component of DNA methylation differentiation along the transect that is independent of genetic variation. This epigenetic differentiation might reflect environment-specific induction or, in case the DNA methylation variation affects relevant traits and fitness, selection of heritable DNA methylation variants. Such generated epigenetic variants might contribute to the adaptive capacity of individual asexual lineages under changing environments. Our results highlight the potential of heritable DNA methylation variation to contribute to population differentiation along ecological gradients. Further studies are needed using higher-resolution methods to understand the functional significance of such natural occurring epigenetic differentiation.
    Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber
    Zhang, Z. ; Mao, L. ; Chen, Junshi ; Bu, F. ; Li, G. ; Sun, J. ; Li, S. ; Sun, H. ; Jiao, C. ; Blakely, R. ; Pan, J. ; Cai, R. ; Luo, R. ; Peer, Y. Van de; Jacobsen, E. ; Fei, Z. ; Huang, S. - \ 2015
    The Plant Cell 27 (2015)6. - ISSN 1040-4651 - p. 1595 - 1604.
    indel-associated mutation - tuberculate fruit gene - false discovery rate - arabidopsis-thaliana - population-scale - functional impact - sequencing data - synthase gene - paired-end - sativus l.
    Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber.
    Immune activation mediated by the late blight resistance protein R1 requires nuclear localization of R1 and AVR1
    Du, Y. ; Berg, J. ; Govers, F. ; Bouwmeester, K. - \ 2015
    New Phytologist 207 (2015)3. - ISSN 0028-646X - p. 735 - 747.
    disease-resistance - phytophthora-infestans - arabidopsis-thaliana - innate immunity - plant immunity - receptor - recognition - potato - gene - component
    Resistance against oomycete pathogens is mainly governed by intracellular nucleotide-binding leucine-rich repeat (NLR) receptors that recognize matching avirulence (AVR) proteins from the pathogen, RXLR effectors that are delivered inside host cells. Detailed molecular understanding of how and where NLR proteins and RXLR effectors interact is essential to inform the deployment of durable resistance (R) genes. Fluorescent tags, nuclear localization signals (NLSs) and nuclear export signals (NESs) were exploited to determine the subcellular localization of the potato late blight protein R1 and the Phytophthora infestans RXLR effector AVR1, and to target these proteins to the nucleus or cytoplasm. Microscopic imaging revealed that both R1 and AVR1 occurred in the nucleus and cytoplasm, and were in close proximity. Transient expression of NLS- or NES-tagged R1 and AVR1 in Nicotiana benthamiana showed that activation of the R1-mediated hypersensitive response and resistance required localization of the R1/AVR1 pair in the nucleus. However, AVR1-mediated suppression of cell death in the absence of R1 was dependent on localization of AVR1 in the cytoplasm. Balanced nucleocytoplasmic partitioning of AVR1 seems to be a prerequisite. Our results show that R1-mediated immunity is activated inside the nucleus with AVR1 in close proximity and suggest that nucleocytoplasmic transport of R1 and AVR1 is tightly regulated.
    Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856
    Thompson, O.A. ; Snoek, L.B. ; Nijveen, H. ; Sterken, M.G. ; Volkers, R.J.M. ; Brenchley, R. ; Hof, A. van 't; Bevers, R.P.J. ; Cossins, A.R. ; Yanai, I. ; Hajnal, A. ; Schmid, T. ; Perkins, J.D. ; Spencer, D. ; Kruglyak, L. ; Andersen, E.C. ; Moerman, D.G. ; Hillier, L.W. ; Kammenga, J.E. ; Waterston, R.H. - \ 2015
    Genetics 200 (2015)3. - ISSN 0016-6731 - p. 975 - 989.
    natural variation data - c. elegans - arabidopsis-thaliana - gene - polymorphism - populations - diversity - nematodes - dna - evolutionary
    The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. The CB4856 genome when compared against the N2 reference has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels) that result in a total of 3.3 megabasepairs (Mb) of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, that have a greatly elevated SNV density, ranging from 2% to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.
    Variation in plant-mediated interactions between rhizobacteria and caterpillars: potential role of soil composition
    Pangesti, N.P.D. ; Pineda Gomez, A.M. ; Dicke, M. ; Loon, J.J.A. van - \ 2015
    Plant Biology 17 (2015)2. - ISSN 1435-8603 - p. 474 - 483.
    induced systemic resistance - arbuscular mycorrhizal symbiosis - arabidopsis-thaliana - insect herbivores - gene-expression - jasmonic acid - pseudomonas-fluorescens - microbes - bacteria - immunity
    Selected strains of non-pathogenic rhizobacteria can trigger induced systemic resistance (ISR) in plants against aboveground insect herbivores. However, the underlying mechanisms of plant-mediated interactions between rhizobacteria and herbivorous insects are still poorly understood. Using Arabidopsis thaliana Col-0-Pseudomonas fluorescens WCS417r as a model system, we investigated the performance and the molecular mechanisms underlying plant-mediated effects of rhizobacteria on the generalist caterpillar Mamestra brassicae and the specialist Pieris brassicae. Rhizobacteria colonisation of Arabidopsis roots resulted in decreased larval weight of M. brassicae, whereas no effect was observed on larval weight of P. brassicae. Using a jasmonic acid (JA)-impaired mutant (dde2-2), we confirmed the importance of JA in rhizobacteria-mediated ISR against M. brassicae. Interestingly, in some experiments we also observed rhizobacteria-induced systemic susceptibility to M. brassicae. The role of soil composition in the variable outcomes of microbe-plant-insect interactions was then assessed by comparing M. brassicae performance and gene transcription in plants grown in potting soil or a mixture of potting soil and sand in a 1:1 ratio. In a mixture of potting soil and sand, rhizobacteria treatment had a consistent negative effect on M. brassicae, whereas the effect was more variable in potting soil. Interestingly, at 24 h post-infestation (hpi) rhizobacteria treatment primed plants grown in a mixture of potting soil and sand for stronger expression of the JA- and ethylene-regulated genes PDF1.2 and HEL, respectively. Our study shows that soil composition can modulate rhizobacteria-plant-insect interactions, and is a factor that should be considered when studying these belowground-aboveground interactions.
    Genetic basis and detection of unintended effects in genetically modified crop plants
    Ladics, G.S. ; Bartholomaeus, A. ; Bregitzer, P. ; Doerrer, N.G. ; Gray, A. ; Holzhauzer, T. ; Jordan, M. ; Keese, P. ; Kok, E.J. ; Macdonald, P. ; Parrott, W. ; Privalle, L. ; Raybould, A. ; Rhee, S.Y. ; Rice, E. ; Romeis, J. ; Vaughn, J. ; Wal, J.M. ; Glenn, K. - \ 2015
    Transgenic Research 24 (2015)4. - ISSN 0962-8819 - p. 587 - 603.
    weed risk-assessment - biochemical pathway database - engineered breeding stacks - multiple fungal pathogens - metabolic flux analysis - somaclonal variation - safety assessment - intellectual disability - arabidopsis-thaliana - transgenic barley
    In January 2014, an international meeting sponsored by the International Life Sciences Institute/Health and Environmental Sciences Institute and the Canadian Food Inspection Agency titled “Genetic Basis of Unintended Effects in Modified Plants” was held in Ottawa, Canada, bringing together over 75 scientists from academia, government, and the agro-biotech industry. The objectives of the meeting were to explore current knowledge and identify areas requiring further study on unintended effects in plants and to discuss how this information can inform and improve genetically modified (GM) crop risk assessments. The meeting featured presentations on the molecular basis of plant genome variability in general, unintended changes at the molecular and phenotypic levels, and the development and use of hypothesis-driven evaluations of unintended effects in assessing conventional and GM crops. The development and role of emerging “omics” technologies in the assessment of unintended effects was also discussed. Several themes recurred in a number of talks; for example, a common observation was that no system for genetic modification, including conventional methods of plant breeding, is without unintended effects. Another common observation was that “unintended” does not necessarily mean “harmful”. This paper summarizes key points from the information presented at the meeting to provide readers with current viewpoints on these topics.
    A complex interplay of tandem- and whole genome duplication drives expansion of the L-type lectin receptor kinase gene family in the brassicaceae
    Hofberger, J.A. ; Nsibo, D.L. ; Govers, F. ; Bouwmeester, K. ; Schranz, M.E. - \ 2015
    Genome Biology and Evolution 7 (2015)3. - ISSN 1759-6653 - p. 720 - 734.
    disease resistance genes - arabidopsis-thaliana - phylogenetic analysis - triggered immunity - provides insight - wide analysis - evolution - plants - diversification - expression
    The comparative analysis of plant gene families in a phylogenetic framework has greatly accelerated due to advances in next generation sequencing. In this study, we provide an evolutionary analysis of the L-type lectin receptor kinase and L-type lectin domain proteins (L-type LecRKs and LLPs) that are considered as components in plant immunity, in the plant family Brassicaceae and related outgroups. We combine several lines of evidence provided by sequence homology, HMM-driven protein domain annotation, phylogenetic analysis and gene synteny for large-scale identification of L-type LecRK and LLP genes within nine core-eudicot genomes. We show that both polyploidy and local duplication events (tandem duplication and gene transposition duplication) have played a major role in L-type LecRK and LLP gene family expansion in the Brassicaceae. We also find significant differences in rates of molecular evolution based on the mode of duplication. Additionally, we show that LLPs share a common evolutionary origin with L-type LecRKs and provide a consistent gene family nomenclature. Finally, we demonstrate that the largest and most diverse L-type LecRK clades are lineage-specific. Our evolutionary analyses of these plant immune components provide a framework to support future plant resistance breeding.
    Isolation and identification of 4-a-rhamnosyloxy benzyl glucosinolate in Noccaea caerulescens showing intraspecific variation
    Graaf, R.M. de; Krosse, S. ; Swolfs, A.E.M. ; Brinke, E. te; Prill, N. ; Leimu, R. ; Galen, P.M. van; Wang, Y. ; Aarts, M.G.M. ; Dam, N.M. van - \ 2015
    Phytochemistry 110 (2015). - ISSN 0031-9422 - p. 166 - 171.
    hyperaccumulator thlaspi-praecox - moringa-oleifera l. - mustard oil bomb - arabidopsis-thaliana - plants - isothiocyanates - stenopetala - accumulation - brassicaceae - profiles
    Glucosinolates are secondary plant compounds typically found in members of the Brassicaceae and a few other plant families. Usually each plant species contains a specific subset of the ~130 different glucosinolates identified to date. However, intraspecific variation in glucosinolate profiles is commonly found. Sinalbin (4-hydroxybenzyl glucosinolate) so far has been identified as the main glucosinolate of the heavy metal accumulating plant species Noccaea caerulescens (Brassicaceae). However, a screening of 13 N. caerulescens populations revealed that in 10 populations a structurally related glucosinolate was found as the major component. Based on nuclear magnetic resonance (NMR) and mass spectrometry analyses of the intact glucosinolate as well as of the products formed after enzymatic conversion by sulfatase or myrosinase, this compound was identified as 4-a-rhamnosyloxy benzyl glucosinolate (glucomoringin). So far, glucomoringin had only been reported as the main glucosinolate of Moringa spp. (Moringaceae) which are tropical tree species. There was no apparent relation between the level of soil pollution at the location of origin, and the presence of glucomoringin. The isothiocyanate that is formed after conversion of glucomoringin is a potent antimicrobial and antitumor agent. It has yet to be established whether glucomoringin or its breakdown product have an added benefit to the plant in its natural habitat
    AIL and HDG proteins act antagonistically to control cell proliferation
    Horstman, A. ; Fukuoka, H. ; Muino Acuna, J.M. ; Nitsch, L.M.C. ; Guo, Changhao ; Passarinho, P.A. ; Sanchez Perez, G.F. ; Immink, R.G.H. ; Angenent, G.C. ; Boutilier, K.A. - \ 2015
    Development 142 (2015). - ISSN 0950-1991 - p. 454 - 464.
    arabidopsis-thaliana - transcription factors - plant transformation - ectopic expression - quantitative pcr - chip-seq - differentiation - genes - plethora - growth
    AINTEGUMENTA-LIKE (AIL) transcription factors are key regulators of cell proliferation and meristem identity. Although AIL functions have been well described, the direct signalling components of this pathway are largely unknown.We show that BABY BOOM(BBM) and other AIL proteins physically interact with multiple members of the L1-expressed HOMEODOMAIN GLABROUS (HDG) transcription factor family, including HDG1, HDG11 and HDG12. Overexpression of HDG1, HDG11 and HDG12 restricts growth due to root and shoot meristem arrest, which is associated with reduced expression of genes involved in meristem development and cell proliferation pathways, whereas downregulation of multiple HDG genes promotes cell overproliferation. These results suggest a role for HDG proteins in promoting cell differentiation. We also reveal a transcriptional network in which BBM andHDG1regulate several common target genes, and whereBBM/AIL and HDG regulate the expression of each other. Taken together, these results suggest opposite roles for AIL and HDG proteins, with AILs promoting cell proliferation and HDGs stimulating cell differentiation, and that these functions are mediated at both the protein-protein interaction and transcriptional level.
    Marker-Based Estimation of Heritability in Immortal Populations
    Kruijer, W.T. ; Boer, M.P. ; Malosetti, M. ; Flood, P.J. ; Engel, B. ; Kooke, R. ; Keurentjes, J.J.B. ; Eeuwijk, F.A. van - \ 2015
    Genetics 199 (2015)2. - ISSN 0016-6731 - p. 379 - 398.
    genome-wide association - multi-environment trials - quantitative trait loci - plant-breeding trials - linear mixed models - arabidopsis-thaliana - missing heritability - complex traits - selection - prediction
    Heritability is a central parameter in quantitative genetics, both from an evolutionary and a breeding perspective. For plant traits heritability is traditionally estimated by comparing within and between genotype variability. This approach estimates broad-sense heritability, and does not account for different genetic relatedness. With the availability of high-density markers there is growing interest in marker based estimates of narrow-sense heritability, using mixed models in which genetic relatedness is estimated from genetic markers. Such estimates have received much attention in human genetics but are rarely reported for plant traits. A major obstacle is that current methodology and software assume a single phenotypic value per genotype, hence requiring genotypic means. An alternative that we propose here, is to use mixed models at individual plant or plot level. Using statistical arguments, simulations and real data we investigate the feasibility of both approaches, and how these affect genomic prediction with G-BLUP and genome-wide association studies. Heritability estimates obtained from genotypic means had very large standard errors and were sometimes biologically unrealistic. Mixed models at individual plant or plot level produced more realistic estimates, and for simulated traits standard errors were up to 13 times smaller. Genomic prediction was also improved by using these mixed models, with up to a 49% increase in accuracy. For GWAS on simulated traits, the use of individual plant data gave almost no increase in power. The new methodology is applicable to any complex trait where multiple replicates of individual genotypes can be scored. This includes important agronomic crops, as well as bacteria and fungi.
    Fruit illumination stimulates cell division but has no detectable effect on fruit size in tomato (Solanum lycopersicum)
    Okello, R.C. ; Heuvelink, E. ; Visser, P.H.B. de; Lammers, M. ; Maagd, R.A. de; Marcelis, L.F.M. ; Struik, P.C. - \ 2015
    Physiologia Plantarum 154 (2015)1. - ISSN 0031-9317 - p. 114 - 127.
    arabidopsis-thaliana - elongation growth - plant development - seed development - sink metabolism - cucumber fruits - gene-expression - hormone-levels - abscisic-acid - phytochrome-b
    Light affects plant growth through assimilate availability and signals regulating development. The effects of light on growth of tomato fruit were studied using cuvettes with light-emitting diodes providing white, red or blue light to individual tomato trusses for different periods during daytime. Hypotheses tested were as follows: (1) light-grown fruits have stronger assimilate sinks than dark-grown fruits, and (2) responses depend on light treatment provided, and fruit development stage. Seven light treatments [dark, 12-h white, 24-h white, 24-h red and 24-h blue light, dark in the first 24 days after anthesis (DAA) followed by 24-h white light until breaker stage, and its reverse] were applied. Observations were made between anthesis and breaker stage at fruit, cell and gene levels. Fruit size and carbohydrate content did not respond to light treatments while cell division was strongly stimulated at the expense of cell expansion by light. The effects of light on cell number and volume were independent of the combination of light color and intensity. Increased cell division and decreased cell volume when fruits were grown in the presence of light were not clearly corroborated by the expression pattern of promoters and inhibitors of cell division and expansion analyzed in this study, implying a strong effect of posttranscriptional regulation. Results suggest the existence of a complex homeostatic regulatory system for fruit growth in which reduced cell division is compensated by enhanced cell expansion.
    The Top 10 oomycete pathogens in molecular plant pathology
    Kamoun, S. ; Furzer, O. ; Jones, J.D.G. ; Judelson, H.S. ; Ali, G.S. ; Dalio, R.J.D. ; Roy, S.G. ; Schena, L. ; Zambounis, A. ; Panabières, F. ; Cahill, D. ; Ruocco, M. ; Figueiredo, A. ; Chen, X.R. ; Hulvey, J. ; Stam, R. ; Lamour, K. ; Gijzen, M. ; Tyler, B.M. ; Grünwald, N.J. ; Mukhtar, M.S. ; Tomé, D.F.A. ; Tör, M. ; Ackerveken, G. van den; McDowell, J. ; Daayf, F. ; Fry, W.E. ; Lindqvist-Kreuze, H. ; Meijer, H.J.G. ; Petre, B. ; Ristaino, J. ; Yoshida, K. ; Birch, P.R.J. ; Govers, F. - \ 2015
    Molecular Plant Pathology 16 (2015)4. - ISSN 1464-6722 - p. 413 - 434.
    grapevine downy mildew - irish potato famine - sudden oak death - blister rusts albuginaceae - eastern united-states - 3 clonal lineages - nb-lrr gene - phytophthora-infestans - plasmopara-viticola - arabidopsis-thaliana
    Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens that threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. The article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.
    On selection for flowering time plasticity in response to density
    Vermeulen, P.J. - \ 2015
    New Phytologist 205 (2015)1. - ISSN 0028-646X - p. 429 - 439.
    arabidopsis-thaliana - phenotypic plasticity - shade-avoidance - adaptive plasticity - impatiens-capensis - dependent selection - plant-populations - genetic-variation - local adaptation - life-history
    Different genotypes often exhibit opposite plastic responses in the timing of the onset of flowering with increasing plant density. In experimental studies, selection for accelerated flowering is generally found. By contrast, game theoretical studies predict that there should be selection for delayed flowering when competition increases. Combining different optimality criteria, the conditions under which accelerated or delayed flowering in response to density would be selected for are analysed with a logistic growth simulation model. To maximize seed production at the whole-stand level (simple optimization), selection should lead to accelerated flowering at high plant density, unless very short growing seasons select for similar onset of flowering at all densities. By contrast, selection of relative individual fitness will lead to delayed flowering when season length is long and/or growth rates are high. These different results give a potential explanation for the observed differences in direction of the plastic responses within and between species, including homeostasis, as a result of the effect of the variation in season length on the benefits of delayed flowering. This suggests that limited plasticity can evolve without the costs and limits that are currently thought to constrain the evolution of plasticity.
    The Cellulase KORRIGAN Is Part of the Cellulose Synthase Complex
    Vain, T. ; Crowell, E.F. ; Timpano, H. ; Biot, E. ; Desprez, T. ; Mansoori Zangir, N. ; Trindade, L.M. ; Pagant, S. ; Robert, S. ; Hofte, H. ; Gonneau, M. ; Vernhettes, S. - \ 2014
    Plant Physiology 165 (2014)4. - ISSN 0032-0889 - p. 1521 - 1532.
    secondary cell-wall - arabidopsis-thaliana - genetic-evidence - plasma-membrane - higher-plants - endo-1,4-beta-glucanase - microtubules - trafficking - elongation - endo-1,4-beta-d-glucanase
    Plant growth and organ formation depend on the oriented deposition of load-bearing cellulose microfibrils in the cell wall. Cellulose is synthesized by a large relative molecular weight cellulose synthase complex (CSC), which comprises at least three distinct cellulose synthases. Cellulose synthesis in plants or bacteria also requires the activity of an endo-1,4-beta-D-glucanase, the exact function of which in the synthesis process is not known. Here, we show, to our knowledge for the first time, that a leaky mutation in the Arabidopsis (Arabidopsis thaliana) membrane-bound endo-1,4-beta-D-glucanase KORRIGAN1 (KOR1) not only caused reduced CSC movement in the plasma membrane but also a reduced cellulose synthesis inhibitor-induced accumulation of CSCs in intracellular compartments. This suggests a role for KOR1 both in the synthesis of cellulose microfibrils and in the intracellular trafficking of CSCs. Next, we used a multidisciplinary approach, including live cell imaging, gel filtration chromatography analysis, split ubiquitin assays in yeast (Saccharomyces cerevisiae NMY51), and bimolecular fluorescence complementation, to show that, in contrast to previous observations, KOR1 is an integral part of the primary cell wall CSC in the plasma membrane.
    Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity
    Debernardi, J.M. ; Mecchia, M.A. ; Vercruyssen, L. ; Smaczniak, C. ; Kaufmann, K. ; Inze, D. ; Rodriguez, R.E. ; Palatnik, J.F. - \ 2014
    The Plant Journal 79 (2014)3. - ISSN 0960-7412 - p. 413 - 426.
    chromatin-remodeling complexes - tandem affinity purification - arabidopsis-thaliana - gene-expression - organ size - cell-division - protein complexes - shoot development - small rnas - growth
    The growth-regulating factors (GRFs) are plant-specific transcription factors. They form complexes with GRF-interacting factors (GIFs), a small family of transcriptional co-activators. In Arabidopsis thaliana, seven out of the nine GRFs are controlled by microRNA miR396. Analysis of Arabidopsis plants carrying a GRF3 allele insensitive to miR396 revealed a strong boost in the number of cells in leaves, which was further enhanced synergistically by an additional increase of GIF1 levels. Genetic experiments revealed that GRF3 can still increase cell number in gif1 mutants, albeit to a much lesser extent. Genome-wide transcript profiling indicated that the simultaneous increase of GRF3 and GIF1 levels causes additional effects in gene expression compared to either of the transgenes alone. We observed that GIF1 interacts in vivo with GRF3, as well as with chromatin-remodeling complexes, providing a mechanistic explanation for the synergistic activities of a GRF3-GIF1 complex. Interestingly, we found that, in addition to the leaf size, the GRF system also affects the organ longevity. Genetic and molecular analysis revealed that the functions of GRFs in leaf growth and senescence can be uncoupled, demonstrating that the miR396-GRF-GIF network impinges on different stages of leaf development. Our results integrate the post-transcriptional control of the GRF transcription factors with the progression of leaf development.
    Conserved histidine of metal transporter AtNRAMP1 is crucial for optimal plant growth under manganese deficiency at chilling temperatures
    Ihnatowicz, A. ; Siwinska, J. ; Meharg, A.A. ; Carey, M. ; Koornneef, M. ; Reymond, M. - \ 2014
    New Phytologist 202 (2014)4. - ISSN 0028-646X - p. 1173 - 1183.
    yeast saccharomyces-cerevisiae - barley hordeum-vulgare - arabidopsis-thaliana - drosophila-melanogaster - iron transport - ion transporters - diploid strains - calcareous soil - nramp family - environment
    Manganese (Mn) is an essential nutrient required for plant growth, in particular in the process of photosynthesis. Plant performance is influenced by various environmental stresses including contrasting temperatures, light or nutrient deficiencies. The molecular responses of plants exposed to such stress factors in combination are largely unknown. Screening of 108 Arabidopsis thaliana (Arabidopsis) accessions for reduced photosynthetic performance at chilling temperatures was performed and one accession (Hog) was isolated. Using genetic and molecular approaches, the molecular basis of this particular response to temperature (GxE interaction) was identified. Hog showed an induction of a severe leaf chlorosis and impaired growth after transfer to lower temperatures. We demonstrated that this response was dependent on the nutrient content of the soil. Genetic mapping and complementation identified NRAMP1 as the causal gene. Chlorotic phenotype was associated with a histidine to tyrosine (H239Y) substitution in the allele of Hog NRAMP1. This led to lethality when Hog seedlings were directly grown at 4 degrees C. Chemical complementation and hydroponic culture experiments showed that Mn deficiency was the major cause of this GxE interaction. For the first time, the NRAMP-specific highly conserved histidine was shown to be crucial for plant performance.
    Drought stress provokes the down-regulation of methionine and ethylene biosynthesis pathways in Medicago truncatula roots and nodules
    Larrainzar, E. ; Molenaar, J.A. ; Wienkoop, S. ; Gil-Quintana, E. ; Alibert, B. ; Limami, A.M. ; Arrese-Igor, C. ; Gonzalez, E.M. - \ 2014
    Plant, Cell & Environment 37 (2014)9. - ISSN 0140-7791 - p. 2051 - 2063.
    cystathionine gamma-synthase - signal-transduction pathway - acetylene-reduction assay - nitrogen-fixation - n-2 fixation - arabidopsis-thaliana - sucrose synthase - soybean nodules - atp sulfurylase - water-deficit
    Symbiotic nitrogen fixation is one of the first physiological processes inhibited in legume plants under water-deficit conditions. Despite the progress made in the last decades, the molecular mechanisms behind this regulation are not fully understood yet. Recent proteomic work carried out in the model legume Medicago truncatula provided the first indications of a possible involvement of nodule methionine (Met) biosynthesis and related pathways in response to water-deficit conditions. To better understand this involvement, the drought-induced changes in expression and content of enzymes involved in the biosynthesis of Met, S-adenosyl-L-methionine (SAM) and ethylene in M.truncatula root and nodules were analyzed using targeted approaches. Nitrogen-fixing plants were subjected to a progressive water deficit and a subsequent recovery period. Besides the physiological characterization of the plants, the content of total sulphur, sulphate and main S-containing metabolites was measured. Results presented here show that S availability is not a limiting factor in the drought-induced decline of nitrogen fixation rates in M.truncatula plants and provide evidences for a down-regulation of the Met and ethylene biosynthesis pathways in roots and nodules in response to water-deficit conditions.
    KORRIGAN1 Interacts Specifically with Integral Components of the Cellulose Synthase Machinery
    Mansoori Zangir, N. ; Timmers, J.F.P. ; Desprez, T. ; Lessa Alvim Kamei, C. ; Dees, D.C.T. ; Vincken, J.P. ; Visser, R.G.F. ; Höfte, H. ; Vernhettes, S. ; Trindade, L.M. - \ 2014
    PLoS ONE 9 (2014)11. - ISSN 1932-6203
    secondary cell-wall - arabidopsis-thaliana - endo-1,4-beta-glucanase - expression - membranes - protein - system - plants - gene - endo-1,4-beta-d-glucanase
    Cellulose is synthesized by the so called rosette protein complex and the catalytic subunits of this complex are the cellulose synthases (CESAs). It is thought that the rosette complexes in the primary and secondary cell walls each contains at least three different non-redundant cellulose synthases. In addition to the CESA proteins, cellulose biosynthesis almost certainly requires the action of other proteins, although few have been identified and little is known about the biochemical role of those that have been identified. One of these proteins is KORRIGAN (KOR1). Mutant analysis of this protein in Arabidopsis thaliana showed altered cellulose content in both the primary and secondary cell wall. KOR1 is thought to be required for cellulose synthesis acting as a cellulase at the plasma membrane–cell wall interface. KOR1 has recently been shown to interact with the primary cellulose synthase rosette complex however direct interaction with that of the secondary cell wall has never been demonstrated. Using various methods, both in vitro and in planta, it was shown that KOR1 interacts specifically with only two of the secondary CESA proteins. The KOR1 protein domain(s) involved in the interaction with the CESA proteins were also identified by analyzing the interaction of truncated forms of KOR1 with CESA proteins. The KOR1 transmembrane domain has shown to be required for the interaction between KOR1 and the different CESAs, as well as for higher oligomer formation of KOR1.
    Genetic dissection of leaf development in Brassica rapa using a ‘geneticalgenomics’ approach
    Xiao, D. ; Wang, H. ; Basnet, R.K. ; Jianjun Zhao, Jianjun ; Lin, K. ; Hou, X. ; Bonnema, A.B. - \ 2014
    Plant Physiology 164 (2014)3. - ISSN 0032-0889 - p. 1309 - 1325.
    quantitative trait loci - flowering time - arabidopsis-thaliana - morphological traits - functional divergence - natural variation - duplicated genes - organ growth - expression - cell
    The paleohexaploid crop Brassica rapa harbors an enormous reservoir of morphological variation, encompassing leafy vegetables, vegetable and fodder turnips (Brassica rapa, ssp. campestris), and oil crops, with different crops having very different leaf morphologies. In the triplicated B. rapa genome, many genes have multiple paralogs that may be regulated differentially and contribute to phenotypic variation. Using a genetical genomics approach, phenotypic data from a segregating doubled haploid population derived from a cross between cultivar Yellow sarson (oil type) and cultivar Pak choi (vegetable type) were used to identify loci controlling leaf development. Twenty-five colocalized phenotypic quantitative trait loci (QTLs) contributing to natural variation for leaf morphological traits, leaf number, plant architecture, and flowering time were identified. Genetic analysis showed that four colocalized phenotypic QTLs colocalized with flowering time and leaf trait candidate genes, with their cis-expression QTLs and cis- or trans-expression QTLs for homologs of genes playing a role in leaf development in Arabidopsis (Arabidopsis thaliana). The leaf gene BRASSICA RAPA KIP-RELATED PROTEIN2_A03 colocalized with QTLs for leaf shape and plant height; BRASSICA RAPA ERECTA_A09 colocalized with QTLs for leaf color and leaf shape; BRASSICA RAPA LONGIFOLIA1_A10 colocalized with QTLs for leaf size, leaf color, plant branching, and flowering time; while the major flowering time gene, BRASSICA RAPA FLOWERING LOCUS C_A02, colocalized with QTLs explaining variation in flowering time, plant architectural traits, and leaf size. Colocalization of these QTLs points to pleiotropic regulation of leaf development and plant architectural traits in B. rapa.
    Prioritization of candidate genes in QTL regions based on associations between traits and biological processes
    Bargsten, J.W. ; Nap, J.P.H. ; Sanchez Perez, G.F. ; Dijk, A.D.J. van - \ 2014
    BMC Plant Biology 14 (2014). - ISSN 1471-2229
    genome-wide association - protein function prediction - arabidopsis-thaliana - nucleotide polymorphisms - enrichment analysis - flowering time - complex traits - oryza-sativa - rice - architecture
    Background Elucidation of genotype-to-phenotype relationships is a major challenge in biology. In plants, it is the basis for molecular breeding. Quantitative Trait Locus (QTL) mapping enables to link variation at the trait level to variation at the genomic level. However, QTL regions typically contain tens to hundreds of genes. In order to prioritize such candidate genes, we show that we can identify potentially causal genes for a trait based on overrepresentation of biological processes (gene functions) for the candidate genes in the QTL regions of that trait. Results The prioritization method was applied to rice QTL data, using gene functions predicted on the basis of sequence- and expression-information. The average reduction of the number of genes was over ten-fold. Comparison with various types of experimental datasets (including QTL fine-mapping and Genome Wide Association Study results) indicated both statistical significance and biological relevance of the obtained connections between genes and traits. A detailed analysis of flowering time QTLs illustrates that genes with completely unknown function are likely to play a role in this important trait. Conclusions Our approach can guide further experimentation and validation of causal genes for quantitative traits. This way it capitalizes on QTL data to uncover how individual genes influence trait variation.
    Regulatory Network of Secondary Metabolism in Brassica rapa: Insight into the Glucosinolate Pathway
    Pino del Carpio, D. ; Kumar, R. ; Arends, D. ; Lin, K. ; Vos, R.C.H. de; Muth, D. ; Kodde, J. ; Boutilier, K.A. ; Bucher, J. ; Wang, X. ; Jansen, R.C. ; Bonnema, G. - \ 2014
    PLoS ONE 9 (2014)9. - ISSN 1932-6203 - 11 p.
    arabidopsis-thaliana - mass-spectrometry - coexpression networks - genomics approach - genetic genomics - biosynthesis - metabolomics - identification - plants - fruit
    Brassica rapa studies towards metabolic variation have largely been focused on the profiling of the diversity of metabolic compounds in specific crop types or regional varieties, but none aimed to identify genes with regulatory function in metabolite composition. Here we followed a genetical genomics approach to identify regulatory genes for six biosynthetic pathways of health-related phytochemicals, i.e carotenoids, tocopherols, folates, glucosinolates, flavonoids and phenylpropanoids. Leaves from six weeks-old plants of a Brassica rapa doubled haploid population, consisting of 92 genotypes, were profiled for their secondary metabolite composition, using both targeted and LC-MS-based untargeted metabolomics approaches. Furthermore, the same population was profiled for transcript variation using a microarray containing EST sequences mainly derived from three Brassica species: B. napus, B. rapa and B. oleracea. The biochemical pathway analysis was based on the network analyses of both metabolite QTLs (mQTLs) and transcript QTLs (eQTLs). Colocalization of mQTLs and eQTLs lead to the identification of candidate regulatory genes involved in the biosynthesis of carotenoids, tocopherols and glucosinolates. We subsequently focused on the well-characterized glucosinolate pathway and revealed two hotspots of co-localization of eQTLs with mQTLs in linkage groups A03 and A09. Our results indicate that such a large-scale genetical genomics approach combining transcriptomics and metabolomics data can provide new insights into the genetic regulation of metabolite composition of Brassica vegetables.
    Morphology, Carbohydrate Composition and Vernalization Response in a Genetically Diverse Collection of Asian and European Turnips (Brassica rapa subsp. rapa)
    Zhang, N. ; Jianjun Zhao, Jianjun ; Lens, F. ; Visser, J. de; Menamo, T. ; Fang, W. ; Xiao, D. ; Bucher, J. ; Basnet, R.K. ; Lin, K. ; Cheng, F. ; Wang, X. ; Bonnema, A.B. - \ 2014
    PLoS ONE 9 (2014)12. - ISSN 1932-6203 - 29 p.
    storage root-formation - sucrose metabolizing enzymes - raphanus-sativus l - sugar-beet - flowering-time - gene-expression - transcriptome analysis - arabidopsis-thaliana - organ development - tuber development
    Brassica rapa displays enormous morphological diversity, with leafy vegetables, turnips and oil crops. Turnips (Brassica rapa subsp. rapa) represent one of the morphotypes, which form tubers and can be used to study the genetics underlying storage organ formation. In the present study we investigated several characteristics of an extensive turnip collection comprising 56 accessions from both Asia (mainly Japanese origin) and Europe. Population structure was calculated using data from 280 evenly distributed SNP markers over 56 turnip accessions. We studied the anatomy of turnip tubers and measured carbohydrate composition of the mature turnip tubers of a subset of the collection. The variation in 16 leaf traits, 12 tuber traits and flowering time was evaluated in five independent experiments for the entire collection. The effect of vernalization on flowering and tuber formation was also investigated. SNP marker profiling basically divided the turnip accessions into two subpopulations, with admixture, generally corresponding with geographical origin (Europe or Asia). The enlarged turnip tuber consists of both hypocotyl and root tissue, but the proportion of the two tissues differs between accessions. The ratio of sucrose to fructose and glucose differed among accessions, while generally starch content was low. The evaluated traits segregated in both subpopulations, with leaf shape, tuber colour and number of shoots per tuber explaining most variation between the two subpopulations. Vernalization resulted in reduced flowering time and smaller tubers for the Asian turnips whereas the European turnips were less affected by vernalization.
    Enhancing crop resilience to combined abiotic and biotic stress through the dissection of physiological and molecular crosstalk
    Kissoudis, C. ; Wiel, C.C.M. van de; Visser, R.G.F. ; Linden, C.G. van der - \ 2014
    Frontiers in Plant Science 5 (2014). - ISSN 1664-462X - 20 p.
    systemic acquired-resistance - activated protein-kinase - programmed cell-death - regulated gene-expression - plant immune-responses - abscisic-acid - salicylic-acid - disease resistance - arabidopsis-thaliana - transcription factor
    Plants growing in their natural habitats are often challenged simultaneously by multiple stress factors, both abiotic and biotic. Research has so far been limited to responses to individual stresses, and understanding of adaptation to combinatorial stress is limited, but indicative of non-additive interactions. Omics data analysis and functional characterization of individual genes has revealed a convergence of signaling pathways for abiotic and biotic stress adaptation. Taking into account that most data originate from imposition of individual stress factors, this review summarizes these findings in a physiological context, following the pathogenesis timeline and highlighting potential differential interactions occurring between abiotic and biotic stress signaling across the different cellular compartments and at the whole plant level. Potential effects of abiotic stress on resistance components such as extracellular receptor proteins, R-genes and systemic acquired resistance will be elaborated, as well as crosstalk at the levels of hormone, reactive oxygen species, and redox signaling. Breeding targets and strategies are proposed focusing on either manipulation and deployment of individual common regulators such as transcription factors or pyramiding of non- (negatively) interacting components such as R-genes with abiotic stress resistance genes. We propose that dissection of broad spectrum stress tolerance conferred by priming chemicals may provide an insight on stress cross regulation and additional candidate genes for improving crop performance under combined stress. Validation of the proposed strategies in lab and field experiments is a first step toward the goal of achieving tolerance to combinatorial stress in crops.
    Apoplastic Venom Allergen-like Proteins of Cyst Nematodes Modulate the Activation of Basal Plant Innate Immunity by Cell Surface Receptors
    Lozano Torres, J.L. ; Wilbers, R.H.P. ; Warmerdam, S. ; Finkers-Tomczak, A.M. ; Diaz Granados Muñoz, A. ; Schaik, C.C. van; Helder, J. ; Bakker, J. ; Goverse, A. ; Schots, A. ; Smant, G. - \ 2014
    PLoS Pathogens 10 (2014)12. - ISSN 1553-7366 - 18 p.
    root-knot nematode - cf-2-dependent disease resistance - pamp-triggered immunity - arabidopsis-thaliana - globodera-rostochiensis - heterodera-schachtii - ancylostoma-caninum - parasitic nematodes - extracellular-matrix - functional-analysis
    Despite causing considerable damage to host tissue during the onset of parasitism, nematodes establish remarkably persistent infections in both animals and plants. It is thought that an elaborate repertoire of effector proteins in nematode secretions suppresses damage-triggered immune responses of the host. However, the nature and mode of action of most immunomodulatory compounds in nematode secretions are not well understood. Here, we show that venom allergen-like proteins of plant-parasitic nematodes selectively suppress host immunity mediated by surface-localized immune receptors. Venom allergen-like proteins are uniquely conserved in secretions of all animal- and plant-parasitic nematodes studied to date, but their role during the onset of parasitism has thus far remained elusive. Knocking-down the expression of the venom allergen-like protein Gr-VAP1 severely hampered the infectivity of the potato cyst nematode Globodera rostochiensis. By contrast, heterologous expression of Gr-VAP1 and two other venom allergen-like proteins from the beet cyst nematode Heterodera schachtii in plants resulted in the loss of basal immunity to multiple unrelated pathogens. The modulation of basal immunity by ectopic venom allergen-like proteins in Arabidopsis thaliana involved extracellular protease-based host defenses and non-photochemical quenching in chloroplasts. Non-photochemical quenching regulates the initiation of the defense-related programmed cell death, the onset of which was commonly suppressed by venom allergen-like proteins from G. rostochiensis, H. schachtii, and the root-knot nematode Meloidogyne incognita. Surprisingly, these venom allergen-like proteins only affected the programmed cell death mediated by surface-localized immune receptors. Furthermore, the delivery of venom allergen-like proteins into host tissue coincides with the enzymatic breakdown of plant cell walls by migratory nematodes. We, therefore, conclude that parasitic nematodes most likely utilize venom allergen-like proteins to suppress the activation of defenses by immunogenic breakdown products in damaged host tissue.
    Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis
    Zhang, Y. ; Dijk, A.D.J. van; Scaffidi, A. ; Flematti, G.R. ; Hofmann, M. ; Charnikhova, T. ; Verstappen, F.W.A. ; Hepworth, J. ; Krol, A.R. van der; Leyser, O. - \ 2014
    Nature Chemical Biology 10 (2014). - ISSN 1552-4450 - p. 1028 - 1033.
    arbuscular mycorrhizal fungi - structural requirements - germination stimulants - biological-activities - arabidopsis-thaliana - crystal-structures - plant hormones - protein - inhibition - expression
    Strigolactones (SLs) are a class of phytohormones and rhizosphere signaling compounds with high structural diversity. Three enzymes, carotenoid isomerase DWARF27 and carotenoid cleavage dioxygenases CCD7 and CCD8, were previously shown to convert all-trans-¿-carotene to carlactone (CL), the SL precursor. However, how CL is metabolized to SLs has remained elusive. Here, by reconstituting the SL biosynthetic pathway in Nicotiana benthamiana, we show that a rice homolog of Arabidopsis MORE AXILLARY GROWTH 1 (MAX1), encodes a cytochrome P450 CYP711 subfamily member that acts as a CL oxidase to stereoselectively convert CL into ent-2'-epi-5-deoxystrigol (B-C lactone ring formation), the presumed precursor of rice SLs. A protein encoded by a second rice MAX1 homolog then catalyzes the conversion of ent-2'-epi-5-deoxystrigol to orobanchol. We therefore report that two members of CYP711 enzymes can catalyze two distinct steps in SL biosynthesis, identifying the first enzymes involved in B-C ring closure and a subsequent structural diversification step of SLs.
    Control of anthocyanin and non-flavonoid compounds by anthocyanin-regulating MYB and bHLH transcription factors in Nicotiana benthamiana leaves
    Outchkourov, N.S. ; Carollo, C.A. ; Gomez Roldan, M.V. ; Vos, C.H. de; Bosch, H.J. ; Hall, R.D. ; Beekwilder, M.J. - \ 2014
    Frontiers in Plant Science 5 (2014). - ISSN 1664-462X - 9 p.
    r2r3-myb gene family - mass-spectrometry - tomato fruit - arabidopsis-thaliana - biosynthesis - tobacco - accumulation - metabolomics - plants - health
    Coloration of plant organs such as fruit, leaves and flowers through anthocyanin production is governed by a combination of MYB and bHLH type transcription factors (TFs). In this study we introduced Rosea1 (ROS1, a MYB type) and Delila (DEL, a bHLH type), into Nicotiana benthamiana leaves by agroinfiltration. ROS1 and DEL form a pair of well-characterized TFs from Snapdragon (Antirrhinum majus), which specifically induce anthocyanin accumulation when expressed in tomato fruit. In N. benthamiana, robust induction of a single anthocyanin, delphinidin-3-rutinoside (D3R) was observed after expression of both ROS1 and DEL. Surprisingly in addition to D3R, a range of additional metabolites were also strongly and specifically up-regulated upon expression of ROS1 and DEL. Except for the D3R, these induced compounds were not derived from the flavonoid pathway. Most notable among these are nornicotine conjugates with butanoyl, hexanoyl, and octanoyl hydrophobic moieties, and phenylpropanoid-polyamine conjugates such as caffeoyl putrescine. The defensive properties of the induced molecules were addressed in bioassays using the tobacco specialist lepidopteran insect Manduca sexta. Our study showed that the effect of ROS1 and DEL expression in N. benthamiana leaves extends beyond the flavonoid pathway. Apparently the same transcription factor may regulate different secondary metabolite pathways in different plant species.
    A novel approach for multi-domain and multi-gene famliy identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants
    Hofberger, J.A. ; Zhou, B. ; Tang, H. ; Jones, J. ; Schranz, M.E. - \ 2014
    BMC Genomics 15 (2014). - ISSN 1471-2164
    genome-wide analysis - nb-arc domain - arabidopsis-thaliana - whole-genome - draft genome - phylogenetic analysis - triggered immunity - mildew resistance - defense responses - encoding genes
    Background Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity. Results To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection acting on all identified genes and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR "gatekeeper" loci sharing syntenic orthologs across all analyzed genomes. Conclusion By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.
    A roadmap to embryo identity in plants
    Radoeva, T.M. ; Weijers, D. - \ 2014
    Trends in Plant Science 19 (2014)11. - ISSN 1360-1385 - p. 709 - 716.
    microspore-derived embryos - somatic embryogenesis - arabidopsis-thaliana - pattern-formation - transcription factor - leafy cotyledon1 - seed development - gene-expression - wuschel gene - cell
    Although plant embryogenesis is usually studied in the context of seed development, there are many alternative roads to embryo initiation. These include somatic embryogenesis in tissue culture and microspore embryogenesis, both widely used in breeding and crop propagation, but also include other modes of ectopic embryo initiation. In the past decades several genes, mostly transcription factors, were identified that can induce embryogenesis in somatic cells. Because the genetic networks in which such regulators operate to promote embryogenesis are largely unknown, a key question is how their activity relates to zygotic and alternative embryo initiation. We describe here the many roads to plant embryo initiation and discuss a framework for defining the developmental roles and mechanisms of plant embryogenesis regulators.
    Group VII Ethylene Response Factor diversification and regulation in four species from flood-prone environments.
    Veen, H. van; Akman, M. ; Jamar, D.C.L. ; Vreugdenhil, D. ; Kooiker, M. ; Tienderen, P.H. van; Voesenek, L.A.C.J. ; Schranz, M.E. ; Sasidharan, R. - \ 2014
    Plant, Cell & Environment 37 (2014)10. - ISSN 0140-7791 - p. 2421 - 2432.
    end rule pathway - submergence tolerance - transcription factors - arabidopsis-thaliana - comparative genomics - rorippa-sylvestris - gene-expression - rice - hypoxia - plants
    Flooding events negatively affect plant performance and survival. Flooding gradients thereby determine the dynamics in vegetation composition and species abundance. In adaptation to flooding, the group VII Ethylene Response Factor genes (ERF-VIIs) play pivotal roles in rice and Arabidopsis through regulation of anaerobic gene expression and antithetical survival strategies. We investigated if ERF-VIIs have a similar role in mediating survival strategies in eudicot species from flood-prone environments. Here, we studied the evolutionary origin and regulation of ERF-VII transcript abundance and the physiological responses in species from two genera of divergent taxonomic lineages (Rumex and Rorippa). Synteny analysis revealed that angiosperm ERF-VIIs arose from two ancestral loci and that subsequent diversification and duplication led to the present ERF-VII variation. We propose that subtle variation in the regulation of ERF-VII transcript abundance could explain variation in tolerance among Rorippa species. In Rumex, the main difference in flood tolerance correlated with the genetic variation in ERF-VII genes. Large transcriptional differences were found by comparing the two genera: darkness and dark submergence-induced Rumex ERF-VIIs, whereas HRE2 expression was increased in submerged Rorippa roots. We conclude that the involvement of ERF-VIIs in flooding tolerance developed in a phylogenetic-dependent manner, with subtle variations within taxonomic clades.
    Effect of sequential induction by Mamestra brassicae L. and Tetranychus urticae Koch on Lima bean plant indirect defense
    Menzel, T.R. ; Huang, T.Y. ; Weldegergis, B.T. ; Gols, R. ; Loon, J.J.A. van; Dicke, M. - \ 2014
    Journal of Chemical Ecology 40 (2014)9. - ISSN 0098-0331 - p. 977 - 985.
    induced volatile emission - host-plant - jasmonic acid - mediated interactions - arabidopsis-thaliana - methyl salicylate - induced responses - predatory mite - herbivores - prey
    Attack by multiple herbivores often leads to modification of induced plant defenses compared to single herbivory, yet little is known about the effects on induced indirect plant defense. Here, we investigated the effect of sequential induction of plant defense by Mamestra brassicae caterpillar oral secretion and an infestation by Tetranychus urticae spider mites on the expression of indirect plant defense in Lima bean plants. The effect on indirect defense was assessed using behavior assays with the specialist predatory mite Phytoseiulus persimilis in an olfactometer, headspace analysis of 11 major herbivore-induced plant volatiles (HIPVs) including (E)-ß-ocimene, and transcript levels of the corresponding gene Phaseolus lunatus (E)-ß-ocimene synthase (PlOS). Predatory mites were found to distinguish between plants induced by spider mites and caterpillar oral secretion but not between plants with single spider mite infestation and plants induced by caterpillar oral secretion prior to spider mite infestation. Indeed, the volatile blends emitted by plants induced by spider mites only and the sequential induction treatment of caterpillar oral secretion followed by spider mite infestation, were similar. Our results suggest that plant indirect defense is not affected by previous treatment with oral secretion of M. brassicae caterpillars.
    Synergism in the effect of prior jasmonic acid application on herbivore-induced volatile emission by Lima bean plants: transcription of a monoterpene synthase gene and volatile emission
    Menzel, T.R. ; Weldegergis, B.T. ; David, A. ; Boland, W. ; Gols, R. ; Loon, J.J.A. van; Dicke, M. - \ 2014
    Journal of Experimental Botany 65 (2014)17. - ISSN 0022-0957 - p. 4821 - 4831.
    induced resistance - arabidopsis-thaliana - brassica-oleracea - phytoseiulus-persimilis - attract parasitoids - signaling pathway - methyl salicylate - predatory mite - corn plants - host-plant
    Jasmonic acid (JA) plays a central role in induced plant defence e.g. by regulating the biosynthesis of herbivore-induced plant volatiles that mediate the attraction of natural enemies of herbivores. Moreover, exogenous application of JA can be used to elicit plant defence responses similar to those induced by biting-chewing herbivores and mites that pierce cells and consume their contents. In the present study, we used Lima bean (Phaseolus lunatus) plants to explore how application of a low dose of JA followed by minor herbivory by spider mites (Tetranychus urticae) affects transcript levels of P. lunatus (E)-ß-ocimene synthase (PlOS), emission of (E)-ß-ocimene and nine other plant volatiles commonly associated with herbivory. Furthermore, we investigated the plant’s phytohormonal response. Application of a low dose of JA increased PlOS transcript levels in a synergistic manner when followed by minor herbivory for both simultaneous and sequential infestation. Emission of (E)-ß-ocimene was also increased, and only JA, but not SA, levels were affected by treatments. Projection to latent structures-discriminant analysis (PLS-DA) of other volatiles showed overlap between treatments. Thus, a low-dose JA application results in a synergistic effect on gene transcription and an increased emission of a volatile compound involved in indirect defence after herbivore infestation.
    Caterpillar-induced plant volatiles remain a reliable signal for foraging wasps during dual attack with a plant pathogen or non-host insect herbivore
    Ponzio, C.A.M. ; Gols, R. ; Weldegergis, B.T. ; Dicke, M. - \ 2014
    Plant, Cell & Environment 37 (2014)8. - ISSN 0140-7791 - p. 1924 - 1935.
    interspecific interactions - pseudomonas-syringae - arabidopsis-thaliana - phytophagous insects - multiple herbivory - cotesia-glomerata - pieris-brassicae - fungal-infection - natural enemies - damaged plants
    Plants respond to herbivory with the emission of plant volatiles, which can be used by the herbivores' natural enemies to locate their hosts or prey. In nature, plants are often simultaneously confronted with insect herbivores and phytopathogens, potentially interfering with the attraction of the herbivores' enemies as a result of modifications of the induced volatile blend. Here, we investigated parasitoid (Cotesia glomerata) attraction to volatiles of plants challenged by different attackers, either alone or in combination with Pieris brassicae caterpillars, hosts of C.¿glomerata. We used a natural system consisting of Brassica nigra plants, eggs and larvae of P.¿brassicae, Brevicoryne brassicae aphids and the bacterial phytopathogen Xanthomonas campestris pv. campestris. In all cases, parasitoids successfully located host-infested plants, and wasp foraging behaviour was unaffected by the simultaneous presence of a non-host attacker or host eggs. Analysis of the volatile emissions show that the volatile blends of caterpillar-infested treatments were different from those without caterpillars. Furthermore, dually attacked plants could not be separated from those with only caterpillars, regardless of non-host identity, supporting the behavioural data. Our results suggest that, in this system, indirect plant defences may be more resistant to interference than is generally assumed, with volatiles induced during dual attack remaining reliable indicators of host presence for parasitoids.
    Ecology of plant volatiles: taking a plant community perspective
    Pierik, R. ; Ballaré, C.L. ; Dicke, M. - \ 2014
    Plant, Cell & Environment 37 (2014)8. - ISSN 0140-7791 - p. 1845 - 1853.
    shade-avoidance - nicotiana-attenuata - neighbor detection - methyl jasmonate - associational resistance - arabidopsis-thaliana - defense responses - natural enemies - predatory mites - canopy light
    Although plants are sessile organisms, they can modulate their phenotype so as to cope with environmental stresses such as herbivore attack and competition with neighbouring plants. Plant-produced volatile compounds mediate various aspects of plant defence. The emission of volatiles has costs and benefits. Research on the role of plant volatiles in defence has focused primarily on the responses of individual plants. However, in nature, plants rarely occur as isolated individuals but are members of plant communities where they compete for resources and exchange information with other plants. In this review, we address the effects of neighbouring plants on plant volatile-mediated defences. We will outline the various roles of volatile compounds in the interactions between plants and other organisms, address the mechanisms of plant neighbour perception in plant communities, and discuss how neighbour detection and volatile signalling are interconnected. Finally, we will outline the most urgent questions to be addressed in the future.
    Identification of quantitative trait loci and a candidate locus for freezing tolerance in controlled and outdoor environments in the overwintering crucifer Boechera stricta.
    Heo, J. ; Feng, D. ; Niu, X. ; Mitchell-Olds, T. ; Tienderen, P.H. van; Tomes, D. ; Schranz, M.E. - \ 2014
    Plant, Cell & Environment 37 (2014)11. - ISSN 0140-7791 - p. 2459 - 2469.
    cold-acclimation - arabidopsis-thaliana - chlorophyll fluorescence - transcription factor - natural variation - frost tolerance - genes - temperature - wheat - expression
    Development of chilling and freezing tolerance is complex and can be affected by photoperiod, temperature and photosynthetic performance; however, there has been limited research on the interaction of these three factors. We evaluated 108 recombinant inbred lines of Boechera stricta, derived from a cross between lines originating from Montana and Colorado, under controlled long day (LD), short-day (SD) and in an outdoor environment (OE). We measured maximum quantum yield of photosystem II, lethal temperature for 50% survival and electrolyte leakage of leaves. Our results revealed significant variation for chilling and freezing tolerance and photosynthetic performance in different environments. Using both single- and multi-trait analyses, three main-effect quantitative trait loci (QTL) were identified. QTL on linkage group (LG)3 were SD specific, whereas QTL on LG4 were found under both LD and SD. Under all conditions, QTL on LG7 were identified, but were particularly predictive for the outdoor experiment. The co-localization of photosynthetic performance and freezing tolerance effects supports these traits being co-regulated. Finally, the major QTL on LG7 is syntenic to the Arabidopsis C-repeat binding factor locus, known regulators of chilling and freezing responses in Arabidopsis thaliana and other species.
    The tomato phosphatidylinositol-phospholipase C2 (SlPLC2) is required for defense gene induction by the fungal elicitor xylanase
    Gonorazky, G. ; Ramirez, L. ; Abd-El-Haliem, A. ; Vossen, J.H. ; Lamattina, L. ; Have, A. ten; Joosten, M.H.A.J. ; Laxalt, A.M. - \ 2014
    Journal of Plant Physiology 171 (2014)11. - ISSN 0176-1617 - p. 959 - 965.
    phosphatidic-acid accumulation - cultured rice cells - nitric-oxide - disease resistance - c/diacylglycerol kinase - arabidopsis-thaliana - signaling pathways - activation - responses - plants
    The tomato [Solanum lycopersicum (Sl)] phosphatidylinositol-phospholipase C (PI-PLC) gene family is composed of six members, named SlPLC1 to SlPLC6, differentially regulated upon pathogen attack. We have previously shown that the fungal elicitor xylanase rapidly induces nitric oxide (NO), which is required for PI-PLCs activity and downstream defense responses in tomato cell suspensions. Here, we show that all six SlPLC genes are expressed in tomato cell suspensions. Treatment of the cells with xylanase induces an early increase in SlPLC5 transcript levels, followed by a raise of the amount of SlPLC2 transcripts. The production of NO is required to augment SlPLC5 transcript levels in xylanase-treated tomato cells. Xylanase also induces SlPLC2 and SlPLC5 transcript levels in planta. We knocked-down the expression of SlPLC2 and SlPLC5 by virus-induced gene silencing. We found that SlPLC2 is required for xylanase-induced expression of the defense-related genes PR1 and HSR203J.
    Functional analysis of the tomato immune receptor Ve1 through domain swaps with Its non-functional homolog Ve2
    Fradin, E.F. ; Zhang, Z. ; Rövenich, H. ; Song, Y. ; Liebrand, T.W.H. ; Masini, L. ; Berg, G.C.M. van den; Joosten, M.H.A.J. ; Thomma, B.P.H.J. - \ 2014
    PLoS ONE 9 (2014)2. - ISSN 1932-6203 - 14 p.
    leucine-rich repeat - disease resistance protein - cladosporium-fulvum - arabidopsis-thaliana - endoplasmic-reticulum - hypersensitive response - verticillium resistance - plasma-membrane - innate immunity - kinase bri1
    Resistance in tomato against race 1 strains of the fungal vascular wilt pathogens Verticillium dahliae and V. albo-atrum is mediated by the Ve locus. This locus comprises two closely linked inversely oriented genes, Ve1 and Ve2, which encode cell surface receptors of the extracellular leucine-rich repeat receptor-like protein (eLRR-RLP) type. While Ve1 mediates Verticillium resistance through monitoring the presence of the recently identified V. dahliae Ave1 effector, no functionality for Ve2 has been demonstrated in tomato. Ve1 and Ve2 contain 37 eLRRs and share 84% amino acid identity, facilitating investigation of Ve protein functionality through domain swapping. In this study it is shown that Ve chimeras in which the first thirty eLRRs of Ve1 were replaced by those of Ve2 remain able to induce HR and activate Verticillium resistance, and that deletion of these thirty eLRRs from Ve1 resulted in loss of functionality. Also the region between eLRR30 and eLRR35 is required for Ve1-mediated resistance, and cannot be replaced by the region between eLRR30 and eLRR35 of Ve2. We furthermore show that the cytoplasmic tail of Ve1 is required for functionality, as truncation of this tail results in loss of functionality. Moreover, the C-terminus of Ve2 fails to activate immune signaling as chimeras containing the C-terminus of Ve2 do not provide Verticillium resistance. Furthermore, Ve1 was found to interact through its C-terminus with the eLRR-containing receptor-like kinase (eLRR-RLK) interactor SOBIR1 that was recently identified as an interactor of eLRR-RLP (immune) receptors. Intriguingly, also Ve2 was found to interact with SOBIR1.
    Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family
    Resjö, S. ; Ali, A. ; Meijer, H.J.G. ; Seidl, M.F. ; Snel, B. ; Sandin, M. ; Levander, F. ; Govers, F. ; Andreasson, E. - \ 2014
    Journal of Proteome Research 13 (2014)4. - ISSN 1535-3893 - p. 1848 - 1859.
    tandem mass-spectrometry - protein-kinases - arabidopsis-thaliana - in-vitro - proteomics - identification - expression - potato - organization - specificity
    The oomycete Phytophthora infestans is the causal agent of late blight in potato and tomato. Since the underlying processes that govern pathogenicity and development in P. infestans are largely unknown, we have performed a large-scale phosphoproteomics study of six different P. infestans life stages. We have obtained quantitative data for 2922 phosphopeptides and compared their abundance. Life-stage-specific phosphopeptides include ATP-binding cassette transporters and a kinase that only occurs in appressoria. In an extended data set, we identified 2179 phosphorylation sites and deduced 22 phosphomotifs. Several of the phosphomotifs matched consensus sequences of kinases that occur in P. infestans but not Arabidopsis. In addition, we detected tyrosine phosphopeptides that are potential targets of kinases resembling mammalian tyrosine kinases. Among the phosphorylated proteins are members of the RXLR and Crinkler effector families. The latter are phosphorylated in several life stages and at multiple positions, in sites that are conserved between different members of the Crinkler family. This indicates that proteins in the Crinkler family have functions beyond their putative role as (necrosis-inducing) effectors. This phosphoproteomics data will be instrumental for studies on oomycetes and host–oomycete interactions. The data sets have been deposited to ProteomeXchange (identifier PXD000433).
    The Brassicaceae-Specific EWR1 Gene Provides Resistance to Vascular Wilt Pathogens
    Yadeta, K.A. ; Valkenburg, D.J. ; Hanemian, M. ; Marco, Y. ; Thomma, B.P.H.J. - \ 2014
    PLoS ONE 9 (2014)2. - ISSN 1932-6203 - 11 p.
    asymmetric interlaced pcr - arabidopsis-thaliana - verticillium wilt - antimicrobial peptides - defense peptides - tomato ve1 - plant - dahliae - disease - proteins
    Soil-borne vascular wilt diseases caused by Verticillium spp. are among the most destructive diseases worldwide in a wide range of plant species. The most effective means of controlling Verticillium wilt diseases is the use of genetic resistance. We have previously reported the identification of four activation-tagged Arabidopsis mutants which showed enhanced resistance to Verticillium wilt. Among these, one mutant also showed enhanced resistance to Ralstonia solanacearum, a bacterial vascular wilt pathogen. Cloning of the activation tag revealed an insertion upstream of gene At3g13437, which we designated as EWR1 (for Enhancer of vascular Wilt Resistance 1) that encodes a putatively secreted protein of unknown function. The search for homologs of Arabidopsis EWR1 (AtEWR1) in public databases only identified homologs within the Brassicaceae family. We subsequently cloned the EWR1 homolog from Brassica oleracea (BoEWR1) and show that over-expression in Arabidopsis results in V. dahliae resistance. Moreover, over-expression of AtEWR1 and BoEWR1 in N. benthamiana, a member of the Solanaceae family, results in V. dahliae resistance, suggesting that EWR1 homologs can be used to engineer Verticillium wilt resistance in non-Brassicaceae crops as well.
    A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens
    Lin, Y.F. ; Severing, E.I. ; Lintel Hekkert, B. te; Schijlen, E.G.W.M. ; Aarts, M.G.M. - \ 2014
    Frontiers in Plant Science 5 (2014). - ISSN 1664-462X - 15 p.
    gene copy number - thlaspi-caerulescens - arabidopsis-thaliana - expression differences - glucosinolate biosynthesis - elevated expression - zinc accumulation - stress-response - cd tolerance - plants
    Noccaea caerulescens is an extremophile plant species belonging to the Brassicaceae family. It has adapted to grow on soils containing high, normally toxic, concentrations of metals such as nickel, zinc, and cadmium. Next to being extremely tolerant to these metals, it is one of the few species known to hyperaccumulate these metals to extremely high concentrations in their aboveground biomass. In order to provide additional molecular resources for this model metal hyperaccumulator species to study and understand the mechanism of adaptation to heavy metal exposure, we aimed to provide a comprehensive database of transcript sequences for N. caerulescens. In this study, 23,830 transcript sequences (isotigs) with an average length of 1025 bp were determined for roots, shoots and inflorescences of N. caerulescens accession “Ganges” by Roche GS-FLEX 454 pyrosequencing. These isotigs were grouped into 20,378 isogroups, representing potential genes. This is a large expansion of the existing N. caerulescens transcriptome set consisting of 3705 unigenes. When translated and compared to a Brassicaceae proteome set, 22,232 (93.2%) of the N. caerulescens isotigs (corresponding to 19,191 isogroups) had a significant match and could be annotated accordingly. Of the remaining sequences, 98 isotigs resembled non-plant sequences and 1386 had no significant similarity to any sequence in the GenBank database. Among the annotated set there were many isotigs with similarity to metal homeostasis genes or genes for glucosinolate biosynthesis. Only for transcripts similar to Metallothionein3 (MT3), clear evidence for an additional copy was found. This comprehensive set of transcripts is expected to further contribute to the discovery of mechanisms used by N. caerulescens to adapt to heavy metal exposure
    Competing neighbors: light perception and root function
    Gundel, P.E. ; Pierik, R. ; Mommer, L. ; Ballare, L. - \ 2014
    Oecologia 176 (2014)1. - ISSN 0029-8549 - p. 1 - 10.
    far-red light - self/non-self discrimination - shade-avoidance responses - below-ground competition - scots pine-seedlings - blue-light - arabidopsis-thaliana - kin recognition - regulated gravitropism - environmental-control
    Plant responses to competition have often been described as passive consequences of reduced resource availability. However, plants have mechanisms to forage for favorable conditions and anticipate competition scenarios. Despite the progresses made in understanding the role of light signaling in modulating plant–plant interactions, little is known about how plants use and integrate information gathered by their photoreceptors aboveground to regulate performance belowground. Given that the phytochrome family of photoreceptors plays a key role in the acquisition of information about the proximity of neighbors and canopy cover, it is tempting to speculate that changes in the red:far-red (R:FR) ratio perceived by aboveground plant parts have important implications shaping plant behavior belowground. Exploring data from published experiments, we assess the neglected role of light signaling in the control of root function. The available evidence indicates that plant exposure to low R:FR ratios affects root growth and morphology, root exudate profiles, and interactions with beneficial soil microorganisms. Although dependent on species identity, signals perceived aboveground are likely to affect root-to-root interactions. Root systems could also be guided to deploy new growth predominantly in open areas by light signals perceived by the shoots. Studying interactions between above- and belowground plant–plant signaling is expected to improve our understanding of the mechanisms of plant competition.
    Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida
    Thorpe, P. ; Mantelin, S. ; Cock, P.J.A. ; Blok, V.C. ; Coke, M.C. ; Evers-van den Akker, S. ; Guzeeva, E. ; Lilley, C.J. ; Smant, G. ; Reid, A.J. ; Wright, K.M. ; Urwin, P.E. ; Jones, J.T. - \ 2014
    BMC Genomics 15 (2014). - ISSN 1471-2164 - 15 p.
    plant-parasitic nematodes - esophageal gland-cells - heterodera-glycines - meloidogyne-incognita - phytophthora-infestans - arabidopsis-thaliana - chorismate mutase - giant-cells - protein - sequence
    Background The potato cyst nematode Globodera pallida has biotrophic interactions with its host. The nematode induces a feeding structure – the syncytium – which it keeps alive for the duration of the life cycle and on which it depends for all nutrients required to develop to the adult stage. Interactions of G. pallida with the host are mediated by effectors, which are produced in two sets of gland cells. These effectors suppress host defences, facilitate migration and induce the formation of the syncytium. Results The recent completion of the G. pallida genome sequence has allowed us to identify the effector complement from this species. We identify 128 orthologues of effectors from other nematodes as well as 117 novel effector candidates. We have used in situ hybridisation to confirm gland cell expression of a subset of these effectors, demonstrating the validity of our effector identification approach. We have examined the expression profiles of all effector candidates using RNAseq; this analysis shows that the majority of effectors fall into one of three clusters of sequences showing conserved expression characteristics (invasive stage nematode only, parasitic stage only or invasive stage and adult male only). We demonstrate that further diversity in the effector pool is generated by alternative splicing. In addition, we show that effectors target a diverse range of structures in plant cells, including the peroxisome. This is the first identification of effectors from any plant pathogen that target this structure. Conclusion This is the first genome scale search for effectors, combined to a life-cycle expression analysis, for any plant-parasitic nematode. We show that, like other phylogenetically unrelated plant pathogens, plant parasitic nematodes deploy hundreds of effectors in order to parasitise plants, with different effectors required for different phases of the infection process.
    Comparative transcriptome analysis of the metal hyperaccumulator Noccaea caerulescens
    Halimaa, P. ; Blande, D. ; Aarts, M.G.M. ; Tuomainen, M. ; Tervahauta, A. ; Karenlampi, S. - \ 2014
    Frontiers in Plant Science 5 (2014). - ISSN 1664-462X
    gene copy number - thlaspi-caerulescens - arabidopsis-thaliana - expression differences - zinc accumulation - topology prediction - tobacco plants - cadmium - tolerance - populations
    The metal hyperaccumulator Noccaea caerulescens is an established model to study the adaptation of plants to metalliferous soils. Various comparators have been used in these studies. The choice of suitable comparators is important and depends on the hypothesis to be tested and methods to be used. In high-throughput analyses such as microarray, N. caerulescens has been compared to non-tolerant, non-accumulator plants like Arabidopsis thaliana or Thlaspi arvense rather than to the related hypertolerant or hyperaccumulator plants. An underutilized source is N. caerulescens populations with considerable variation in their capacity to accumulate and tolerate metals. Whole transcriptome sequencing (RNA-Seq) is revealing interesting variation in their gene expression profiles. Combining physiological characteristics of N. caerulescens accessions with their RNA-Seq has a great potential to provide detailed insight into the underlying molecular mechanisms, including entirely new gene products. In this review we will critically consider comparative transcriptome analyses carried out to explore metal hyperaccumulation and hypertolerance of N. caerulescens, and demonstrate the potential of RNA-Seq analysis as a tool in evolutionary genomics
    Expression profiling reveals functionally redundant multiple-copy genes related to zinc, iron and cadmium responses in Brassica rapa
    Li, J. ; Liu, B. ; Cheng, F. ; Wang, X. ; Aarts, M.G.M. ; Wu, J. - \ 2014
    New Phytologist 203 (2014)1. - ISSN 0028-646X - p. 182 - 194.
    hyperaccumulator thlaspi-caerulescens - ferric-chelate reductase - arabidopsis-thaliana - metal homeostasis - human-nutrition - deficiency - tolerance - plants - toxicity - protein
    Genes underlying environmental adaptability tend to be over-retained in polyploid plant species. Zinc deficiency (ZnD) and iron deficiency (FeD), excess Zn (ZnE) and cadmium exposure (CdE) are major environmental problems for crop cultivation, but little is known about the differential expression of duplicated genes upon these stress conditions. Applying Tag-Seq technology to leaves of Brassica rapa grown under FeD, ZnD, ZnE or CdE conditions, with normal conditions as a control, we examined global gene expression changes and compared the expression patterns of multiple paralogs. We identified 812, 543, 331 and 447 differentially expressed genes under FeD, ZnD, ZnE and CdE conditions, respectively, in B. rapa leaves. Genes involved in regulatory networks centered on the transcription factors bHLH038 or bHLH100 were differentially expressed under (ZnE-induced) FeD. Further analysis revealed that genes associated with Zn, Fe and Cd responses tended to be over-retained in the B. rapa genome. Most of these multiple-copy genes showed the same direction of expression change under stress conditions. We conclude that the duplicated genes involved in trace element responses in B. rapa are functionally redundant, making the regulatory network more complex in B. rapa than in Arabidopsis thaliana
    Soybean SAT1 (Symbiotic Ammonium Transporter 1) encodes a bHLH transcription factor involved in nodule growth and NH4+ transport
    Chiasson, D.M. ; Loughlin, P.C. ; Mazurkiewicz, D. ; Mohammadidehcheshmeh, M. ; Fedorova, E.E. ; Okamoto, M. ; McLean, E. ; Glass, A.D.M. ; Smith, S.E. ; Bisseling, T. ; Tyerman, S.D. ; Day, D.A. ; Kaiser, B.N. - \ 2014
    Proceedings of the National Academy of Sciences of the United States of America 111 (2014)13. - ISSN 0027-8424 - p. 4814 - 4819.
    arabidopsis-thaliana - circadian clock - lotus-japonicus - stress-response - er stress - membrane - protein - expression - domain - gene
    Glycine max symbiotic ammonium transporter 1 was first documented as a putative ammonium (NH4+) channel localized to the symbiosome membrane of soybean root nodules. We show that Glycine max symbiotic ammonium transporter 1 is actually a membrane-localized basic helix–loop–helix (bHLH) DNA-binding transcription factor now renamed Glycine max bHLH membrane 1 (GmbHLHm1). In yeast, GmbHLHm1 enters the nucleus and transcriptionally activates a unique plasma membrane NH4+ channel Saccharomyces cerevisiae ammonium facilitator 1. Ammonium facilitator 1 homologs are present in soybean and other plant species, where they often share chromosomal microsynteny with bHLHm1 loci. GmbHLHm1 is important to the soybean rhizobium symbiosis because loss of activity results in a reduction of nodule fitness and growth. Transcriptional changes in nodules highlight downstream signaling pathways involving circadian clock regulation, nutrient transport, hormone signaling, and cell wall modification. Collectively, these results show that GmbHLHm1 influences nodule development and activity and is linked to a novel mechanism for NH4+ transport common to both yeast and plants.
    A single locus confers tolerance to continuous light and allows substantial yield increase in tomato
    Vélez Ramírez, A.I. ; Ieperen, W. van; Vreugdenhil, D. ; Poppel, P.M.J.A. van; Heuvelink, E. ; Millenaar, F.F. - \ 2014
    Nature Communications 5 (2014). - ISSN 2041-1723
    differential expression analysis - photosystem-ii - lycopersicon-esculentum - greenhouse tomato - dependent phosphorylation - chlorophyll fluorescence - arabidopsis-thaliana - gene-expression - air humidity - plants
    An important constraint for plant biomass production is the natural day length. Artificial light allows for longer photoperiods, but tomato plants develop a detrimental leaf injury when grown under continuous light—a still poorly understood phenomenon discovered in the 1920s. Here, we report a dominant locus on chromosome 7 of wild tomato species that confers continuous light tolerance. Genetic evidence, RNAseq data, silencing experiments and sequence analysis all point to the type III light harvesting ¿chlorophyll a/b binding protein 13 (¿CAB-13) gene as a major factor responsible for the tolerance. In Arabidopsis thaliana, this protein is thought to have a regulatory role balancing light harvesting by photosystems I and II. Introgressing the tolerance into modern tomato hybrid lines, results in up to 20% yield increase, showing that limitations for crop productivity, caused by the adaptation of plants to the terrestrial 24-h day/night cycle, can be overcome.
    Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factorsin flower development
    Pajoro, A. ; Madrigal, P. ; Muiño, J.M. ; Tomas Matus, J. ; Jin, J. ; Mecchia, M.A. ; Debernardi, J.M. ; Palatnik, J.F. ; Balazadeh, S. ; Arif, M. ; Ó’Maoiléidigh, D.S. ; Wellmer, F. ; Krajewski, P. ; Riechmann, J.L. ; Angenent, G.C. - \ 2014
    Genome Biology 15 (2014)3. - ISSN 1474-7596
    floral organ identity - arabidopsis-thaliana - chip-seq - genomic regions - molecular-basis - target genes - zinc-finger - expression - protein - dna
    Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility.
    Identification, cloning and characterization of the tomato TCP transcription factor family
    Parapunova, V.A. ; Busscher, M. ; Busscher-Lange, J. ; Lammers, M. ; Karlova, R.B. ; Bovy, A.G. ; Angenent, G.C. ; Maagd, R.A. de - \ 2014
    BMC Plant Biology 14 (2014). - ISSN 1471-2229
    mads-box gene - arabidopsis-thaliana - fruit-development - leaf development - high-throughput - plant-growth - dna-binding - expression - time - interference
    Background: TCP proteins are plant-specific transcription factors, which are known to have a wide range of functions in different plant species such as in leaf development, flower symmetry, shoot branching, and senescence. Only a small number of TCP genes has been characterised from tomato (Solanum lycopersicum). Here we report several functional features of the members of the entire family present in the tomato genome. Results: We have identified 30 Solanum lycopersicum SlTCP genes, most of which have not been described before. Phylogenetic analysis clearly distinguishes two homology classes of the SlTCP transcription factor family - class I and class II. Class II differentiates in two subclasses, the CIN-TCP subclass and the CYC/TB1 subclass, involved in leaf development and axillary shoots formation, respectively. The expression patterns of all members were determined by quantitative PCR. Several SlTCP genes, like SlTCP12, SlTCP15 and SlTCP18 are preferentially expressed in the tomato fruit, suggesting a role during fruit development or ripening. These genes are regulated by RIN (RIPENING INHIBITOR), CNR (COLORLESS NON-RIPENING) and SlAP2a (APETALA2a) proteins, which are transcription factors with key roles in ripening. With a yeast one-hybrid assay we demonstrated that RIN binds the promoter fragments of SlTCP12, SlTCP15 and SlTCP18, and that CNR binds the SlTCP18 promoter. This data strongly suggests that these class I SlTCP proteins are involved in ripening. Furthermore, we demonstrate that SlTCPs bind the promoter fragments of members of their own family, indicating that they regulate each other. Additional yeast one-hybrid studies performed with Arabidopsis transcription factors revealed binding of the promoter fragments by proteins involved in the ethylene signal transduction pathway, contributing to the idea that these SlTCP genes are involved in the ripening process. Yeast two-hybrid data shows that SlTCP proteins can form homo and heterodimers, suggesting that they act together in order to form functional protein complexes and together regulate developmental processes in tomato.
    Research on floral timing by ambient temperature comes into blossom
    Verhage, D.S.L. ; Angenent, G.C. ; Immink, R.G.H. - \ 2014
    Trends in Plant Science 19 (2014)9. - ISSN 1360-1385 - p. 583 - 591.
    flowering-locus-c - transcription factor pif4 - mads-box genes - arabidopsis-thaliana - negative regulator - membrane-fluidity - light quality - phytochrome-b - time - expression
    The floral transition is an essential process in the life cycle of flower-bearing plants, because their reproductive success depends on it. To determine the right moment of flowering, plants respond to many environmental signals, including day length, light quality, and temperature. Small changes in ambient temperature also affect the flowering process, although our knowledge of the genetic and molecular mechanisms underlying this flowering pathway is limited. However, recent advances in Arabidopsis (Arabidopsis thaliana) have uncovered multiple molecular mechanisms controlling ambient temperature regulation of flowering, which modulate both repressing and activating factors of flowering time. At a time when temperatures are rising worldwide, understanding how plants integrate ambient temperature signals can be crucial for crop production.
    Transcriptional coordination between leaf cell differentiation and chloroplast development established by TCP20 and theand chloroplast development established by TCP20 and theand chloroplast development established by TCP20 and the subgroup Ib bHLH transcription factors
    Andriankaja, M.E. ; Danisman, S.D. ; Mignolet-Spruyt, L.F. ; Claeys, H. ; Kochanke, I. ; Vermeersch, M. ; Milde, L. De; Bodt, S. De; Storme, V. ; Skirycz, A. ; Maurer, F. ; Bauer, P. ; Mühlenbock, P. ; Breusegem, F. Van; Angenent, G.C. ; Immink, R.G.H. ; Inzé, D. - \ 2014
    Plant Molecular Biology 85 (2014)3. - ISSN 0167-4412 - p. 233 - 245.
    iron-deficiency responses - arabidopsis-thaliana - plant-growth - gene-expression - chromatin immunoprecipitation - metal transporter - oxidative stress - circadian clock - pale cress - in-vivo
    The establishment of the photosynthetic apparatus during chloroplast development creates a high demand for iron as a redox metal. However, iron in too high quantities becomes toxic to the plant, thus plants have evolved a complex network of iron uptake and regulation mechanisms. Here, we examined whether four of the subgroup Ib basic helix-loop-helix transcription factors (bHLH38, bHLH39, bHLH100, bHLH101), previously implicated in iron homeostasis in roots, also play a role in regulating iron metabolism in developing leaves. These transcription factor genes were strongly up-regulated during the transition from cell proliferation to expansion, and thus sink-source transition, in young developing leaves of Arabidopsis thaliana. The four subgroup Ib bHLH genes also showed reduced expression levels in developing leaves of plants treated with norflurazon, indicating their expression was tightly linked to the onset of photosynthetic activity in young leaves. In addition, we provide evidence for a mechanism whereby the transcriptional regulators SAC51 and TCP20 antagonistically regulate the expression of these four subgroup Ib bHLH genes. A loss-offunction mutant analysis also revealed that single mutants of bHLH38, bHLH39, bHLH100, and bHLH101 developed smaller rosettes than wild-type plants in soil. When grown in agar plates with reduced iron concentration, triple bhlh39 bhlh100 bhlh101 mutant plants were smaller than wildtype plants. However, measurements of the iron content in single and multiple subgroup Ib bHLH genes, as well as transcript profiling of iron response genes during early leaf development, do not support a role for bHLH38, bHLH39, bHLH100, and bHLH101 in iron homeostasis during early leaf development.
    The Activation and Suppression of Plant Innate Immunity by Parasitic Nematodes
    Goverse, A. ; Smant, G. - \ 2014
    Annual Review of Phytopathology 52 (2014). - ISSN 0066-4286 - p. 243 - 265.
    root-knot nematode - potato cyst-nematode - cf-2-dependent disease resistance - expressed sequence tags - globodera-rostochiensis - heterodera-glycines - arabidopsis-thaliana - mi-1-mediated resistance - meloidogyne-incognita - signaling pathway
    Plant-parasitic nematodes engage in prolonged and intimate relationships with their host plants, often involving complex alterations in host cell morphology and function. It is puzzling how nematodes can achieve this, seemingly without activating the innate immune system of their hosts. Secretions released by infective juvenile nematodes are thought to be crucial for host invasion, for nematode migration inside plants, and for feeding on host cells. In the past, much of the research focused on the manipulation of developmental pathways in host plants by plant-parasitic nematodes. However, recent findings demonstrate that plant-parasitic nematodes also deliver effectors into the apoplast and cytoplasm of host cells to suppress plant defense responses. In this review, we describe the current insights in the molecular and cellular mechanisms underlying the activation and suppression of host innate immunity by plant-parasitic nematodes along seven critical evolutionary and developmental transitions in plant parasitism.
    Intra-specific variation in wild Brassica oleracea for aphid-induced plant responses and consequences for caterpillar-parasitoid interactions
    Li, Y. ; Dicke, M. ; Harvey, J.A. ; Gols, R. - \ 2014
    Oecologia 174 (2014)3. - ISSN 0029-8549 - p. 853 - 862.
    phloem-feeding insect - induced resistance - defense responses - interspecific interactions - multitrophic interactions - arabidopsis-thaliana - phytophagous insects - nicotiana-attenuata - jasmonic acid - host plants
    Herbivore-induced plant responses not only influence the initiating attackers, but also other herbivores feeding on the same host plant simultaneously or at a different time. Insects belonging to different feeding guilds are known to induce different responses in the host plant. Changes in a plant's phenotype not only affect its interactions with herbivores but also with organisms higher in the food chain. Previous work has shown that feeding by a phloem-feeding aphid on a cabbage cultivar facilitates the interaction with a chewing herbivore and its endoparasitoid. Here we study genetic variation in a plant's response to aphid feeding using plants originating from three wild Brassica oleracea populations that are known to differ in constitutive and inducible secondary chemistry. We compared the performance of two different chewing herbivore species, Plutella xylostella and M. brassicae, and their larval endoparasitoids Diadegma semiclausum and M. mediator, respectively, on plants that had been infested with aphids (Brevicoryne brassicae) for 1 week. Remarkably, early infestation with B. brassicae enhanced the performance of the specialist P. xylostella and its parasitoid D. semiclausum, but did not affect that of the generalist M. brassicae, nor its parasitoid M. mediator. Performance of the two herbivore-parasitoid interactions also varied among the cabbage populations and the effect of aphid infestation marginally differed among the three populations. Thus, the effect of aphid infestation on the performance of subsequent attackers is species specific, which may have concomitant consequences for the assembly of insect communities that are naturally associated with these plants.
    Plant interactions with multiple insect herbivores: from community to genes
    Stam, J.M. ; Kroes, A. ; Li, Y. ; Gols, R. ; Loon, J.J.A. van; Poelman, E.H. ; Dicke, M. - \ 2014
    Annual Review of Plant Biology 65 (2014). - ISSN 1543-5008 - p. 689 - 713.
    milkweed asclepias-syriaca - primrose oenothera-biennis - indirect interaction webs - top-down forces - salicylic-acid - jasmonic acid - brassica-oleracea - bottom-up - arabidopsis-thaliana - phytophagous insects
    Every plant is a member of a complex insect community that consists of tens to hundreds of species that belong to different trophic levels. The dynamics of this community are critically influenced by the plant, which mediates interactions between community members that can occur on the plant simultaneously or at different times. Herbivory results in changes in the plant's morphological or chemical phenotype that affect interactions with subsequently arriving herbivores. Changes in the plant's phenotype are mediated by molecular processes such as phytohormonal signaling networks and transcriptomic rearrangements that are initiated by oral secretions of the herbivore. Processes at different levels of biological complexity occur at timescales ranging from minutes to years. In this review, we address plant-mediated interactions with multiple species of the associated insect community and their effects on community dynamics, and link these to the mechanistic effects that multiple attacks have on plant phenotypes.
    State transitions in Chlamydomonas reinhardtii strongly modulate the functional size of photosystem II but not of photosystem I
    Ünlü, C. ; Drop, B. ; Croce, R. ; Amerongen, H. van - \ 2014
    Proceedings of the National Academy of Sciences of the United States of America 111 (2014)9. - ISSN 0027-8424 - p. 3460 - 3465.
    light-harvesting-complex - excitation-energy transfer - resolved chlorophyll fluorescence - alga scenedesmus-obliquus - protein-phosphorylation - thylakoid membrane - charge separation - supramolecular organization - arabidopsis-thaliana - angstrom resolution
    Plants and green algae optimize photosynthesis in changing light conditions by balancing the amount of light absorbed by photosystems I and II. These photosystems work in series to extract electrons from water and reduce NADP+ to NADPH. Light-harvesting complexes (LHCs) are held responsible for maintaining the balance by moving from one photosystem to the other in a process called state transitions. In the green alga Chlamydomonas reinhardtii, a photosynthetic model organism, state transitions are thought to involve 80% of the LHCs. Here, we demonstrate with picosecond-fluorescence spectroscopy on C. reinhardtii cells that, although LHCs indeed detach from photosystem II in state 2 conditions, only a fraction attaches to photosystem I. The detached antenna complexes become protected against photodamage via shortening of the excited-state lifetime. It is discussed how the transition from state 1 to state 2 can protect C. reinhardtii in high-light conditions and how this differs from the situation in plants.
    Impact of light on leaf initiation: a matter of photosynthate availability in the apical bud?
    Savvides, A. ; Ntagkas, N. ; Ieperen, W. van; Dieleman, J.A. ; Marcelis, L.F.M. - \ 2014
    Functional Plant Biology 41 (2014)5. - ISSN 1445-4408 - p. 547 - 556.
    arabidopsis-thaliana - thermal-time - shade-avoidance - air-temperature - young tomato - blue-light - shoot apex - growth - expansion - responses
    Radiation substantially affects leaf initiation rate (LIR), a key variable for plant growth, by influencing the heat budget and therefore the temperature of the shoot apical meristem. The photosynthetically active component of solar radiation (photosynthetic photon flux density; PPFD) is critical for plant growth and when at shade to moderate levels may also influence LIR via limited photosynthate availability. Cucumber and tomato plants were subjected to different PPFDs (2.5–13.2 mol m–2 day–1) and then LIR, carbohydrate content and diel net CO2 uptake of the apical bud were quantified. LIR showed saturating response to increasing PPFD in both species. In this PPFD range, LIR was reduced by 20% in cucumber and by 40% in tomato plants. Carbohydrate content and dark respiration were substantially reduced at low PPFD. LIR may be considered as an adaptive trait of plants to low light levels, which is likely to be determined by the local photosynthate availability. In tomato and cucumber plants, LIR can be markedly reduced at low PPFD in plant production systems at high latitudes, suggesting that models solely based on thermal time may not precisely predict LIR at low PPFD.
    Identification and mapping of a novel dominant resistance gene, TuRB07 to Turnip mosaic virus in Brassica rapa
    Jin, M. ; Lee, S.S. ; Ke, L. ; Kim, J.S. ; Seo, M.S. ; Sohn, S.H. ; Park, B.S. ; Bonnema, A.B. - \ 2014
    Theoretical and Applied Genetics 127 (2014). - ISSN 0040-5752 - p. 509 - 519.
    quantitative trait loci - chinese-cabbage - arabidopsis-thaliana - signal-transduction - linkage maps - host-defense - protein rx - binding - nucleotide - napus
    The inheritance of resistance to Turnip mosaic virus in Brassica rapa was investigated by crossing the resistant line, VC1 with the susceptible line, SR5, and genotyping and phenotyping diverse progenies derived from this cross. Both a doubled haploid population, VCS3M-DH, an F2 and two BC1 (F1 × VC1 and F1 × SR5) populations were created. Population tests revealed that the resistance to the TuMV C4 isolate in B. rapa is controlled by a single dominant gene. This resistance gene, TuRB07 was positioned on the top of linkage group A06 of the B. rapa genome through bulk segregation analysis and fine mapping recombinants in three doubled haploid- and one backcross population using microsatellite markers developed from BAC end sequences. Within the region between the two closely linked markers flanking TuRB07, H132A24-s1, and KS10960, in the Chiifu reference genome, two genes encoding nucleotide-binding site and leucine-rich repeat proteins with a coiled-coil motif (CC-NBS-LRR), Bra018862 and Bra018863 were identified as candidate resistance genes. The gene Bra018862 is truncated, but the gene Bra018863 has all the domains to function. Furthermore, the analysis of structural variation using resequencing data of VC1 and SR5 revealed that Bra018863 might be a functional gene because the gene has no structural variation in the resistant line VC1 when compared with Chiifu, whereas at the other NBS-LRR genes large deletions were identified in the resistant line. Allelic differences of Bra018863 were found between VC1 and SR5, supporting the notion that this gene is a putative candidate gene for the virus resistance.
    The quantitative genetics of indirect genetic effects: a selective review of modelling issues : Review
    Bijma, P. - \ 2014
    Heredity 112 (2014). - ISSN 0018-067X - p. 61 - 69.
    average daily gain - multilevel selection - incorporating interaction - ecological interactions - interacting phenotypes - arabidopsis-thaliana - variance-components - heritable variation - biological groups - sexual selection
    Indirect genetic effects (IGE) occur when the genotype of an individual affects the phenotypic trait value of another conspecific individual. IGEs can have profound effects on both the magnitude and the direction of response to selection. Models of inheritance and response to selection in traits subject to IGEs have been developed within two frameworks; a trait-based framework in which IGEs are specified as a direct consequence of individual trait values, and a variance-component framework in which phenotypic variance is decomposed into a direct and an indirect additive genetic component. This work is a selective review of the quantitative genetics of traits affected by IGEs, with a focus on modelling, estimation and interpretation issues. It includes a discussion on variance-component vs trait-based models of IGEs, a review of issues related to the estimation of IGEs from field data, including the estimation of the interaction coefficient ¿ (psi), and a discussion on the relevance of IGEs for response to selection in cases where the strength of interaction varies among pairs of individuals. An investigation of the trait-based model shows that the interaction coefficient ¿ may deviate considerably from the corresponding regression coefficient when feedback occurs. The increasing research effort devoted to IGEs suggests that they are a widespread phenomenon, probably particularly in natural populations and plants. Further work in this field should considerably broaden our understanding of the quantitative genetics of inheritance and response to selection in relation to the social organisation of populations.
    The Histone Deacetylase Inhibitor Trichostatin A Promotes Totipotency in the Male Gametophyte
    Li, H. ; Soriano, M. ; Cordewener, J.H.G. ; Muino Acuna, J.M. ; Riksen-Bruinsma, T. ; Fukuoka, H. ; Angenent, G.C. ; Boutilier, K.A. - \ 2014
    The Plant Cell 26 (2014)1. - ISSN 1040-4651 - p. 195 - 209.
    brassica-napus l - polycomb-group proteins - plant-cell cycle - somatic embryogenesis - arabidopsis-thaliana - embryo development - retinoblastoma protein - in-vitro - microspore embryogenesis - pollen embryogenesis
    The haploid male gametophyte, the pollen grain, is a terminally differentiated structure whose function ends at fertilization. Plant breeding and propagation widely use haploid embryo production from in vitro–cultured male gametophytes, but this technique remains poorly understood at the mechanistic level. Here, we show that histone deacetylases (HDACs) regulate the switch to haploid embryogenesis. Blocking HDAC activity with trichostatin A (TSA) in cultured male gametophytes of Brassica napus leads to a large increase in the proportion of cells that switch from pollen to embryogenic growth. Embryogenic growth is enhanced by, but not dependent on, the high-temperature stress that is normally used to induce haploid embryogenesis in B. napus. The male gametophyte of Arabidopsis thaliana, which is recalcitrant to haploid embryo development in culture, also forms embryogenic cell clusters after TSA treatment. Genetic analysis suggests that the HDAC protein HDA17 plays a role in this process. TSA treatment of male gametophytes is associated with the hyperacetylation of histones H3 and H4. We propose that the totipotency of the male gametophyte is kept in check by an HDAC-dependent mechanism and that the stress treatments used to induce haploid embryo development in culture impinge on this HDAC-dependent pathway.
    Epigenetic variation in asexually reproducing organisms
    Verhoeven, K.J.F. ; Preite, V. - \ 2014
    Evolution 68 (2014)3. - ISSN 0014-3820 - p. 644 - 655.
    dna methylation - arabidopsis-thaliana - japanese knotweed - transgenerational plasticity - phenotypic plasticity - transposable elements - natural-populations - fallopia-japonica - mutation-rates - clonal plants
    The role that epigenetic inheritance can play in adaptation may differ between sexuals and asexuals because (1) the dynamics of adaptation differ under sexual and asexual reproduction and the opportunities offered by epigenetic inheritance may affect these dynamics differently; and (2) in asexual reproduction epigenetic reprogramming mechanisms that are associated with meiosis can be bypassed, which could promote the buildup of epigenetic variation in asexuals. Here, we evaluate current evidence for an epigenetic contribution to adaptation in asexuals. We argue that two aspects of epigenetic variation should have particular relevance for asexuals, namely epigenetics-mediated phenotypic plasticity within and between generations, and heritable variation via stochastic epimutations. An evaluation of epigenetic reprogramming mechanisms suggests that some, but not all, forms of asexual reproduction enhance the likelihood of stable transmission of epigenetic marks across generations compared to sexual reproduction. However, direct tests of these predicted sexual–asexual differences are virtually lacking. Stable transmission of DNA methylation, transcriptomes, and phenotypes from parent to clonal offspring are demonstrated in various asexual species, and clonal genotypes from natural populations show habitat-specific DNA methylation. We discuss how these initial observations can be extended to demonstrate an epigenetic contribution to adaptation.
    Actin dynamics in Phytophthora infestans; rapidly reorganizing cables and immobile, long-lived plaques
    Meijer, H.J.G. ; Hua, C. ; Kots, K. ; Ketelaar, T. ; Govers, F. - \ 2014
    Cellular Microbiology 16 (2014)6. - ISSN 1462-5814 - p. 948 - 961.
    oomycete achlya-bisexualis - f-actin - hyphal growth - tip growth - quantitative-analysis - aspergillus-nidulans - arabidopsis-thaliana - neurospora-crassa - saprolegnia-ferax - patch movement
    The actin cytoskeleton is a dynamic but well organized intracellular framework that is essential for proper functioning of eukaryotic cells. Here, we use the actin binding peptide Lifeact to investigate the in vivo actin cytoskeleton dynamics in the oomycete plant pathogen Phytophthora infestans. Lifeact-eGFP labelled thick and thin actin bundles and actin filament plaques allowing visualization of actin dynamics. All actin structures in the hyphae were cortically localized. In growing hyphae actin filament cables were axially oriented in the sub-apical region whereas in the extreme apex in growing hyphae, waves of fine F-actin polymerization were observed. Upon growth termination, actin filament plaques appeared in the hyphal tip. The distance between a hyphal tip and the first actin filament plaque correlated strongly with hyphal growth velocity. The actin filament plaques were nearly immobile with average lifetimes exceeding one hour, relatively long when compared to the lifetime of actin patches known in other eukaryotes. Plaque assembly required ~30 seconds while disassembly was accomplished in ~10 sec. Remarkably, plaque disassembly was not accompanied with internalization and the formation of endocytic vesicles. These findings suggest that the functions of actin plaques in oomycetes differ from those of actin patches present in other organisms.
    Two for all: receptor-associated kinases SOBIR1 and BAK1
    Liebrand, T.W.H. ; Burg, H.A. van den; Joosten, M.H.A.J. - \ 2014
    Trends in Plant Science 19 (2014)2. - ISSN 1360-1385 - p. 123 - 132.
    plant innate immunity - pattern-recognition receptors - ethylene-inducing xylanase - arabidopsis-thaliana - cladosporium-fulvum - defense responses - cell-death - signaling pathways - plasma-membrane - protein-kinase
    Leucine-rich repeat-receptor-like proteins (LRR-RLPs) are ubiquitous cell surface receptors lacking a cytoplasmic signalling domain. For most of these LRR-RLPs, it remained enigmatic how they activate cellular responses upon ligand perception. Recently, the LRR-receptor-like kinase (LRR-RLK) SUPPRESSOR OF BIR1-1 (SOBIR1) was shown to be essential for triggering defence responses by certain LRR-RLPs that act as immune receptors. In addition to SOBIR1, the regulatory LRR-RLK BRI1-ASSOCIATED KINASE-1 (BAK1) is also required for LRR-RLP function. Here, we compare the roles of SOBIR1 and BAK1 as regulatory LRR-RLKs in immunity and development. BAK1 has a general regulatory role in plasma membrane-associated receptor complexes comprising LRR-RLPs and/or LRR-RLKs. By contrast, SOBIR1 appears to be specifically required for the function of receptor complexes containing LRR-RLPs.
    More cells, bigger cells or simply reorganization? Alternative mechanisms leading to changed internode architecture under contrasting stress regimes
    Huber, H. ; Brouwer, J.H.F. de; Wettberg, E.J. von; During, H.J. ; Anten, N.P.R. - \ 2014
    New Phytologist 201 (2014)1. - ISSN 0028-646X - p. 193 - 204.
    shade-avoidance responses - impatiens-capensis balsaminaceae - phenotypic plasticity - population differentiation - arabidopsis-thaliana - nutrient availability - morphogenic responses - adaptive plasticity - stoloniferous herb - trifolium-repens
    Shading and mechanical stress (MS) modulate plant architecture by inducing different developmental pathways. Shading results in increased stem elongation, often reducing whole-plant mechanical stability, while MS inhibits elongation, with a concomitant increase in stability. Here, we examined how these organ-level responses are related to patterns and processes at the cellular level by exposing Impatiens capensis to shading and MS. Shading led to the production of narrower cells along the vertical axis. By contrast, MS led to the production of fewer, smaller and broader cells. These responses to treatments were largely in line with genetic differences found among plants from open and closed canopy sites. Shading- and MS-induced plastic responses in cellular characteristics were negatively correlated: genotypes that were more responsive to shading were less responsive to MS and vice versa. This negative correlation, however, did not scale to mechanical and architectural traits. Our data show how environmental conditions elicit distinctly different associations between characteristics at the cellular level, plant morphology and biomechanics. The evolution of optimal response to different environmental cues may be limited by negative correlations of stress-induced responses at the cellular level.
    Prenatal plumbing – Vascular tissue formation in the plant embryo
    Rybel, B. De; Breda, A.S. ; Weijers, D. - \ 2014
    Physiologia Plantarum 151 (2014)2. - ISSN 0031-9317 - p. 126 - 133.
    zipper gene family - arabidopsis-thaliana - transcription factor - cell specification - pattern-formation - lonesome-highway - apical meristem - primary root - auxin - differentiation
    The first vascular tissue precursors are specified early during embryogenesis. These precursors give rise to the multi-layered cylinder of hypocotyl and root through controlled, oriented divisions. Concomitant with its growth, the bundle is patterned into xylem and phloem tissues, and intervening procambial cells. These patterns are later maintained during post-embryonic growth and vascular cells will eventually differentiate, displaying characteristic secondary cell wall modifications. Given that the vascular system forms de novo in a simple yet predictable fashion, the embryo provides an excellent model system to study early developmental aspects of vascular tissue formation. However, the benefits of this model are only beginning to be exploited, and most knowledge about the vascular development is derived from growing post-embryonic tissues. Importantly, it is unclear how much of these established post-embryonic mechanisms can be extrapolated to tissue formation during embryogenesis. Here we review concepts established in the model plant Arabidopsis thaliana and focus on recent advances made in understanding embryonic vascular development.
    SCFTIR1/AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism
    Baster, P. ; Robert, S. ; Kleine-Vehn, J. ; Vanneste, S. ; Kania, U. ; Grunewald, W. ; Rybel, B.P.M. de; Beeckman, T. ; Friml, J. - \ 2013
    The EMBO Journal 32 (2013)2. - ISSN 0261-4189 - p. 260 - 274.
    yucca flavin monooxygenases - efflux carrier polarity - factor gene family - box protein tir1 - arabidopsis-thaliana - plant development - plasma-membrane - binding-protein - dependent endocytosis - ubiquitin ligase
    The distribution of the phytohormone auxin regulates many aspects of plant development including growth response to gravity. Gravitropic root curvature involves coordinated and asymmetric cell elongation between the lower and upper side of the root, mediated by differential cellular auxin levels. The asymmetry in the auxin distribution is established and maintained by a spatio-temporal regulation of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights into the complex regulation of PIN abundance and activity during root gravitropism. We show that PIN2 turnover is differentially regulated on the upper and lower side of gravistimulated roots by distinct but partially overlapping auxin feedback mechanisms. In addition to regulating transcription and clathrin-mediated internalization, auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar targeting and degradation. This effect of elevated auxin levels requires the activity of SKP-Cullin-F-box(TIR1/AFB) (SCFTIR1/AFB)-dependent pathway. Importantly, also suboptimal auxin levels mediate PIN degradation utilizing the same signalling pathway. These feedback mechanisms are functionally important during gravitropic response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating asymmetric growth. The EMBO Journal (2013) 32, 260-274. doi:10.1038/emboj.2012.310; Published online 4 December 2012
    Producing more with less: Strategies and novel technologies for plant-based food biofortification
    Carvalho, S.M.P. ; Vasconcelos, M.W. - \ 2013
    Food Research International 54 (2013)1. - ISSN 0963-9969 - p. 961 - 971.
    nicotianamine synthase genes - arabidopsis-thaliana - metal homeostasis - developing seeds - micronutrient malnutrition - oligopeptide transporters - membrane transporter - sucrose metabolism - mass-spectrometry - mineral elements
    About half of the world population suffers from the malnutrition of iron, zinc, calcium, iodine and selenium. Most of the major staple crops of the world, such as rice, wheat, cassava, beans, sweet potato, pearl millet or maize are often deficient in some of these mineral elements. Hence, increasing the concentration of bioavailable micronutrients in edible crop tissues (biofortification) has become a promising strategy in modern agriculture, allowing the access of more nutritious foods, to more people, with the use of fewer resources. Traditional agricultural practices can partly enhance the nutritional value of plant foods, but the advances in the 'omics' technologies are rapidly being exploited to engineer crops with enhanced key nutrients. Ionomics, or the study of the ionome (which can be defined as the mineral trace element composition of a particular organism), is a modern functional genomics tool that can provide high throughput information about the broad spectrum nutrient composition of a given plant food. In alliance with other 'omics' technologies, such as genomics, transcriptomics and proteomics it can be used to identify numerous genes with important roles in the uptake, transport and accumulation of mineral nutrients in plant foods, in particular in their edible parts. This review provides a critical comparison of the strategies that have been developed to diminish nutrient deficiencies in plant-based foods (SWOT analysis) and a summary of the gene families involved in the mineral nutrient pathways. Finally, it also discusses how 'omics' techniques can be used in genetic engineering programs to increase mineral levels and bioavailability in the most important staple food crops and the socioeconomic implications of plant-based biofortified foods. (C) 2013 Elsevier Ltd. All rights reserved.
    Involvement of phospholipase D-related signal transduction in chemical-induced programmed cell death in tomato cell cultures
    Iakimova, E.T. ; Michaeli, R. ; Woltering, E.J. - \ 2013
    Protoplasma 250 (2013)5. - ISSN 0033-183X - p. 1169 - 1183.
    phosphatidic-acid accumulation - g-protein activation - suspension cells - plasma-membrane - nitric-oxide - chlamydomonas-reinhardtii - arabidopsis-thaliana - aerenchyma formation - disease resistance - defense responses
    Phospholipase D (PLD) and its product phosphatidic acid (PA) are incorporated in a complex metabolic network in which the individual PLD isoforms are suggested to regulate specific developmental and stress responses, including plant programmed cell death (PCD). Despite the accumulating knowledge, the mechanisms through which PLD/PA operate during PCD are still poorly understood. In this work, the role of PLD alpha 1 in PCD and the associated caspase-like proteolysis, ethylene and hydrogen peroxide (H2O2) synthesis in tomato suspension cells was studied. Wild-type (WT) and PLD alpha 1-silenced cell lines were exposed to the cell death-inducing chemicals camptothecin (CPT), fumonisin B1 (FB1) and CdSO4. A range of caspase inhibitors effectively suppressed CPT-induced PCD in WT cells, but failed to alleviate cell death in PLD alpha 1-deficient cells. Compared to WT, in CPT-treated PLD alpha 1 mutant cells, reduced cell death and decreased production of H2O2 were observed. Application of ethylene significantly enhanced CPT-induced cell death both in WT and PLD alpha 1 mutants. Treatments with the PA derivative lyso-phosphatidic acid and mastoparan (agonist of PLD/PLC signalling downstream of G proteins) caused severe cell death. Inhibitors, specific to PLD and PLC, remarkably decreased the chemical-induced cell death. Taken together with our previous findings, the results suggest that PLD alpha 1 contributes to caspase-like-dependent cell death possibly communicated through PA, reactive oxygen species and ethylene. The dead cells expressed morphological features of PCD such as protoplast shrinkage and nucleus compaction. The presented findings reveal novel elements of PLD/PA-mediated cell death response and suggest that PLD alpha 1 is an important factor in chemical-induced PCD signal transduction.
    Model of how plants sense zinc deficiency
    Assuncao, A.G.L. ; Persson, D.P. ; Husted, S. ; Schjorring, J.K. ; Alexander, R.D. ; Aarts, M.G.M. - \ 2013
    Metallomics 5 (2013)9. - ISSN 1756-5901 - p. 1110 - 1116.
    bzip transcription factors - hyperaccumulator thlaspi-caerulescens - genetically encoded sensors - iron-deficiency - arabidopsis-thaliana - response element - dna recognition - cellular zinc - zip family - genes
    Plants are capable of inducing a range of physico-chemical and microbial modifications of the rhizosphere which can mobilize mineral nutrients or prevent toxic elements from entering the roots. Understanding how plants sense and adapt to variations in nutrient availability is essential in order to develop plant-based solutions addressing nutrient-use-efficiency and adaptation to nutrient-limited or -toxic soils. Recently two transcription factors of the bZIP family (basic-region leucine zipper) have been identified in Arabidopsis and shown to be pivotal in the adaptation response to zinc deficiency. They represent not only the first regulators of zinc homeostasis identified in plants, but also a very promising starting-point that can provide new insights into the molecular basis of how plants sense and adapt to the stress of zinc deficiency. Considering the available information thus far we propose in this review a putative model of how plants sense zinc deficiency.
    Genetic Analysis of Health-Related Secondary Metabolites in a Brassica rapa Recombinant Inbred Line Population
    Bagheri, H. ; Soda, M. El; Kim, H.K. ; Fritsche, S. ; Jung, C. ; Aarts, M.G.M. - \ 2013
    International Journal of Molecular Sciences 14 (2013)8. - ISSN 1661-6596 - p. 15561 - 15577.
    synechocystis sp pcc-6803 - quantitative trait loci - vitamin-e content - arabidopsis-thaliana - hydroxyphenylpyruvate dioxygenase - tocopherol biosynthesis - plastoquinone synthesis - functional-analysis - natural variation - alpha-tocopherol
    The genetic basis of the wide variation for nutritional traits in Brassica rapa is largely unknown. A new Recombinant Inbred Line (RIL) population was profiled using High Performance Liquid Chromatography (HPLC) and Nuclear Magnetic Resonance (NMR) analysis to detect quantitative trait loci (QTLs) controlling seed tocopherol and seedling metabolite concentrations. RIL population parent L58 had a higher level of glucosinolates and phenylpropanoids, whereas levels of sucrose, glucose and glutamate were higher in the other RIL population parent, R-o-18. QTL related to seed tocopherol (-, -, -, -, -/- and total tocopherol) concentrations were detected on chromosomes A3, A6, A9 and A10, explaining 11%-35% of the respective variation. The locus on A3 co-locates with the BrVTE1gene, encoding tocopherol cyclase. NMR spectroscopy identified the presence of organic/amino acid, sugar/glucosinolate and aromatic compounds in seedlings. QTL positions were obtained for most of the identified compounds. Compared to previous studies, novel loci were found for glucosinolate concentrations. This work can be used to design markers for marker-assisted selection of nutritional compounds in B. rapa.
    Disease resistance or growth: the role of plant hormones in balancing immune responses and fitness costs
    Denance, N. ; Sanchez Vallet, A. ; Goffner, D. ; Molina, A. - \ 2013
    Frontiers in Plant Science 4 (2013). - ISSN 1664-462X
    systemic acquired-resistance - pattern-recognition receptors - mediated defense responses - syringae pv. tomato - abscisic-acid - pseudomonas-syringae - salicylic-acid - arabidopsis-thaliana - botrytis-cinerea - ustilago-maydis
    Plant growth and response to environmental cues are largely governed by phytohormones. The plant hormones ethylene, jasmonic acid, and salicylic acid (SA) play a central role in the regulation of plant immune responses. In addition, other plant hormones, such as auxins, abscisic acid (ABA), cytokinins, gibberellins, and brassinosteroids, that have been thoroughly described to regulate plant development and growth, have recently emerged as key regulators of plant immunity. Plant hormones interact in complex networks to balance the response to developmental and environmental cues and thus limiting defense-associated fitness costs. The molecular mechanisms that govern these hormonal networks are largely unknown. Moreover, hormone signaling pathways are targeted by pathogens to disturb and evade plant defense responses. In this review, we address novel insights on the regulatory roles of the ABA, SA, and auxin in plant resistance to pathogens and we describe the complex interactions among their signal transduction pathways. The strategies developed by pathogens to evade hormone-mediated defensive responses are also described. Based on these data we discuss how hormone signaling could be manipulated to improve the resistance of crops to pathogens.
    Auxin reflux between the endodermis and pericycle promotes lateral root initiation
    Marhavy, P. ; Vanstraelen, M. ; Rybel, B.P.M. de; Ding, Z.J. ; Bennett, M.J. ; Beeckman, T. ; Benkova, E. - \ 2013
    The EMBO Journal 32 (2013)1. - ISSN 0261-4189 - p. 149 - 158.
    arabidopsis-thaliana - gene-expression - cell-cycle - efflux - transport - family - organization - gradients - proteins - meristem
    Lateral root (LR) formation is initiated when pericycle cells accumulate auxin, thereby acquiring founder cell (FC) status and triggering asymmetric cell divisions, giving rise to a new primordium. How this auxin maximum in pericycle cells builds up and remains focused is not understood. We report that the endodermis plays an active role in the regulation of auxin accumulation and is instructive for FCs to progress during the LR initiation (LRI) phase. We describe the functional importance of a PIN3 (PIN-formed) auxin efflux carrier-dependent hormone reflux pathway between overlaying endodermal and pericycle FCs. Disrupting this reflux pathway causes dramatic defects in the progress of FCs towards the next initiation phase. Our data identify an unexpected regulatory function for the endodermis in LRI as part of the fine-tuning mechanism that appears to act as a check point in LR organogenesis after FCs are specified. The EMBO Journal (2013) 32, 149-158. doi:10.1038/emboj.2012.303; Published online 23 November 2012
    Genetic control of interactions among individuals: contrasting outcomes of indirect genetic effects arising from neighbour disease infection and competition in a forest tree
    Costa e Silva, J. ; Potts, B.M. ; Bijma, P. ; Kerr, R.J. ; Pilbeam, D.J. - \ 2013
    New Phytologist 197 (2013)2. - ISSN 0028-646X - p. 631 - 641.
    eucalyptus-globulus - multilevel selection - mycosphaerella-nubilosa - ecological interactions - arabidopsis-thaliana - heritable variation - evolution - model - life - consequences
    Indirect genetic effects (IGEs) are heritable effects of individuals on trait values of their conspecifics. IGEs may substantially affect response to selection, but empirical studies on IGEs are sparse and their magnitude and correlation with direct genetic effects are largely unknown in plants. Here we used linear mixed models to estimate genetic (co)variances attributable to direct and indirect effects for growth and foliar disease damage in a large pedigreed population of Eucalyptus globulus. We found significant IGEs for growth and disease damage, which increased with age for growth. The correlation between direct and indirect genetic effects was highly negative for growth, but highly positive for disease damage, consistent with neighbour competition and infection, respectively. IGEs increased heritable variation by 71% for disease damage, but reduced heritable variation by 85% for growth, leaving nonsignificant heritable variation for later age growth. Thus, IGEs are likely to prevent response to selection in growth, despite a considerable ordinary heritability. IGEs change our perspective on the genetic architecture and potential response to selection. Depending on the correlation between direct and indirect genetic effects, IGEs may enhance or diminish the response to natural or artificial selection compared with that predicted from ordinary heritability.
    Transfer of knowledge about flowering and vegetative propagation from model species to bulbous plants
    Leeggangers, H.A.C.F. ; Moreno Pachón, N.M. ; Gude, H. ; Immink, G.H. - \ 2013
    International Journal of Developmental Biology 57 (2013)6-8. - ISSN 0214-6282 - p. 611 - 620.
    mads-box genes - axillary meristem formation - tulip tulipa-gesneriana - crocus-sativus l. - agrobacterium-mediated transformation - lily lilium-longiflorum - wild-type - heterotopic expression - arabidopsis-thaliana - stalk elongation
    The extensive characterization of plant genes and genome sequences summed to the continuous development of biotechnology tools, has played a major role in understanding biological processes in plant model species. The challenge for the near future is to generate methods and pipelines for an efficient transfer of this knowledge to economically important crops and other plant species. In the case of flower bulbs, which are economically very important for the ornamental industry, flowering time control and vegetative propagation constitute the most relevant processes for agronomical improvements. Those processes have been reasonably studied in reference species, making them excellent candidates for translational investigations in bulbous plant species. The approaches that can be taken for the transfer of biological knowledge from model to non-model species can be roughly categorized as "bottom-up" or "top-down". The former approach usually goes from individual genes to systems, also known as a "gene-by-gene" approach. It assumes conservation of molecular pathways and therefore makes use of sequence homology searches to identify candidate genes. "Top-down" methodologies go from systems to genes, and are e.g. based on large scale transcriptome profiling via heterologous microarrays or RNA sequencing, followed by the identification of associations between phenotypes, genes, and gene expression patterns and levels. In this review, examples of the various knowledge-transfer approaches are provided and pros and cons are discussed. Due to the latest developments in transgenic research and next generation sequencing and the emerging of systems biology as a matured research field, transfer of knowledge concerning flowering time and vegetative propagation capacity in bulbous species are now within sight
    Morphological and biochemical characterization of Erwinia amylovora-induced hypersensitive cell death in apple leaves
    Iakimova, E.T. ; Sobiczewski, P. ; Michalczuk, L. ; Wegrzynowicz-Lesiak, E. ; Mikicinski, A. ; Woltering, E.J. - \ 2013
    Plant Physiology and Biochemistry 63 (2013). - ISSN 0981-9428 - p. 292 - 305.
    vacuolar-processing-enzyme - 1-aminocyclopropane-1-carboxylic acid synthase - mitochondrial permeability transition - arabidopsis-thaliana - fire blight - oxidative stress - defense responses - salicylic-acid - host plants - disease resistance
    In attached apple leaves, spot-inoculated with Erwinia amylovora, the phenotypic appearance of the hypersensitive response (HR) and the participation of ethylene, reactive oxygen species (ROS) and of vacuolar processing enzyme (VPE) (a plant caspase-1-like protease) were analysed. The HR in both the resistant and susceptible genotypes expressed a similar pattern of distinguishable micro HR lesions that progressed into confined macro HR lesions. The HR symptoms in apple were compared to those in non-host tobacco. The morphology of dead cells (protoplast shrinkage and retraction from cell wall) in apple leaves resembled necrotic programmed cell death (PCD). Lesion formation in both cv. Free Redstar (resistant) and cv. Idared (highly susceptible) was preceded by ROS accumulation and elevation of ethylene levels. Treatment of infected leaves with an inhibitor of ethylene synthesis led to a decrease of ethylene emission and suppression of lesion development in both cultivars. In the resistant but not in the susceptible apple cultivar an early and late increase in VPE gene expression was detected. This suggests that VPE might be an underlying component of the response to E. amylovora in resistant apple cultivars. The findings show that in the studied pathosystem the cell death during the HR proceeds through a signal transduction cascade in which ROS, ethylene and VPE pathways play a role.
    The actin cytoskeleton in root hairs: all is fine at the tip
    Ketelaar, T. - \ 2013
    Current Opinion in Plant Biology 16 (2013)6. - ISSN 1369-5266 - p. 749 - 756.
    class-xi myosins - depolymerizing-factor - pollen tubes - arabidopsis-thaliana - binding proteins - arp2/3 complex - cell expansion - plant-cells - organ growth - small gtpase
    Filamentous actin forms characteristic bundles in plant cells that facilitate cytoplasmic streaming. In contrast, networks of actin exhibiting fast turnover are found especially near sites of rapid cell expansion. These networks may serve various functions including delivering and retaining vesicles while preventing penetration of organelles into the area where cell growth occurs thereby allowing fast turnover of vesicles to and from the plasma membrane. Root hairs elongate by polarized growth at their tips and the local accumulation of fine F-actin near the tip has provided valuable insight into the organization of these networks. Here we will sequentially focus on the role of the actin cytoskeleton in root hair tip growth and on how activities of different actin binding proteins in the apical part of growing root hairs contribute to build the fine F-actin configuration that correlates with tip growth.
    Control of the meiotic cell division program in plants
    Wijnker, T.G. ; Schnittger, A. - \ 2013
    Plant Reproduction 26 (2013)3. - ISSN 2194-7953 - p. 143 - 158.
    anaphase-promoting complex/cyclosome - cyclin-dependent-kinases - genome-wide analysis - phd-finger protein - arabidopsis-thaliana - male meiosis - chromosome synapsis - fission yeast - molecular characterization - developmental defects
    While the question of why organisms reproduce sexually is still a matter of controversy, it is clear that the foundation of sexual reproduction is the formation of gametes with half the genomic DNA content of a somatic cell. This reduction in genomic content is accomplished through meiosis that, in contrast to mitosis, comprises two subsequent chromosome segregation steps without an intervening S phase. In addition, meiosis generates new allele combinations through the compilation of new sets of homologous chromosomes and the reciprocal exchange of chromatid segments between homologues. Progression through meiosis relies on many of the same, or at least homologous, cell cycle regulators that act in mitosis, e.g., cyclin-dependent kinases and the anaphase-promoting complex/cyclosome. However, these mitotic control factors are often differentially regulated in meiosis. In addition, several meiosis-specific cell cycle genes have been identified. We here review the increasing knowledge on meiotic cell cycle control in plants. Interestingly, plants appear to have relaxed cell cycle checkpoints in meiosis in comparison with animals and yeast and many cell cycle mutants are viable. This makes plants powerful models to study meiotic progression and allows unique modifications to their meiotic program to develop new plant-breeding strategies
    Root transcript profiling of two Rorippa (brassicaceae) species reveals gene clusters associated with extreme submergence tolerance.
    Sasidharan, R. ; Mustroph, A. ; Boonman, A. ; Akman, M. ; Ammerlaan, A.M.H. ; Breit, T.M. ; Schranz, M.E. ; Voesenek, L.A.C.J. ; Tienderen, P.H. van - \ 2013
    Plant Physiology 163 (2013)3. - ISSN 0032-0889 - p. 1277 - 1292.
    ethylene response factors - transgenic potato plants - genome-wide analysis - end rule pathway - arabidopsis-thaliana - oxygen deficiency - expression profile - wheat seedlings - stress - hypoxia
    Complete submergence represses photosynthesis and aerobic respiration, causing rapid mortality in most terrestrial plants. However, some plants have evolved traits allowing them to survive prolonged flooding, such as species of the genus Rorippa, close relatives of Arabidopsis (Arabidopsis thaliana). We studied plant survival, changes in carbohydrate and metabolite concentrations, and transcriptome responses to submergence of two species, Rorippa sylvestris and Rorippa amphibia. We exploited the close relationship between Rorippa species and the model species Arabidopsis by using Arabidopsis GeneChip microarrays for whole-genome transcript profiling of roots of young plants exposed to a 24-h submergence treatment or air. A probe mask was used based on hybridization of genomic DNA of both species to the arrays, so that weak probe signals due to Rorippa species/Arabidopsis mismatches were removed. Furthermore, we compared Rorippa species microarray results with those obtained for roots of submerged Arabidopsis plants. Both Rorippa species could tolerate deep submergence, with R. sylvestris surviving much longer than R. amphibia. Submergence resulted in the induction of genes involved in glycolysis and fermentation and the repression of many energy-consuming pathways, similar to the low-oxygen and submergence response of Arabidopsis and rice (Oryza sativa). The qualitative responses of both Rorippa species to submergence appeared roughly similar but differed quantitatively. Notably, glycolysis and fermentation genes and a gene encoding sucrose synthase were more strongly induced in the less tolerant R. amphibia than in R. sylvestris. A comparison with Arabidopsis microarray studies on submerged roots revealed some interesting differences and potential tolerance-related genes in Rorippa species.
    Whole Genome and Tandem Duplicate Retention facilitated Glucosinolate Pathway Diversification in the Mustard Family.
    Hofberger, J.A. ; Lyons, E. ; Edger, P.P. ; Pires, J.C. ; Schranz, M.E. - \ 2013
    Genome Biology and Evolution 5 (2013). - ISSN 1759-6653 - p. 2155 - 2173.
    quantitative trait locus - arabidopsis-thaliana - gene duplication - secondary metabolism - insect resistance - natural variation - provides insight - biosynthesis - evolution - plants
    Plants share a common history of successive whole genome duplication (WGD) events retaining genomic patterns of duplicate gene copies (ohnologs) organized in conserved syntenic blocks. Duplication was often proposed to affect the origin of novel traits during evolution. However, genetic evidence linking WGD to pathway diversification is scarce. We show that WGD and Tandem Duplication (TD) accelerated genetic versatility of plant secondary metabolism, exemplified with the glucosinolate (GS) pathway in the Mustard Family. GS biosynthesis is a well-studied trait, employing at least 52 biosynthetic and regulatory genes in the model plant Arabidopsis. In a phylogenomics approach, we identified 67 GS loci in Aethionema arabicum of the tribe Aethionemae, sister group to all Mustard Family members. All but one of the Arabidopsis GS gene families evolved orthologs in Aethionema and all but one of the orthologous sequence pairs exhibit synteny. The 45% fraction of duplicates among all protein-coding genes in Arabidopsis was increased to 95 and 97% for Arabidopsis and Aethionema GS pathway inventory, respectively. Compared to the 22% average for all protein-coding genes in Arabidopsis, 52 and 56% of Aethionema and Arabidopsis GS loci align to ohnolog copies dating back to the last common WGD event. While 15% of all Arabidopsis genes are organized in tandem arrays, 45% and 48% of GS loci in Arabidopsis and Aethionema descend from TD, respectively. We describe a sequential combination of tandem- and whole genome duplication events driving gene family extension, thereby expanding the evolutionary playground for functional diversification and thus potential novelty and success.
    Two-way plant mediated interactions between root-associated microbes and insects: from ecology to mechanisms
    Pangesti, N.P.D. ; Pineda Gomez, A.M. ; Pieterse, C.M.J. ; Dicke, M. ; Loon, J.J.A. van - \ 2013
    Frontiers in Plant Science 4 (2013). - ISSN 1664-462X - 11 p.
    induced systemic resistance - arbuscular mycorrhizal fungi - below-ground interactions - arabidopsis-thaliana - rhizosphere microbiome - defense responses - salicylic-acid - bacterial communities - jasmonic acid - pathogenic microorganisms
    Plants are members of complex communities and function as a link between above- and below-ground organisms. Associations between plants and soil-borne microbes commonly occur and have often been found beneficial for plant fitness. Root-associated microbes may trigger physiological changes in the host plant that influence interactions between plants and aboveground insects at several trophic levels. Aboveground, plants are under continuous attack by insect herbivores and mount multiple responses that also have systemic effects on belowground microbes. Until recently, both ecological and mechanistic studies have mostly focused on exploring these below- and above-ground interactions using simplified systems involving both single microbe and herbivore species, which is far from the naturally occurring interactions. Increasing the complexity of the systems studied is required to increase our understanding of microbe-plant-insect interactions and to gain more benefit from the use of non-pathogenic microbes in agriculture. In this review, we explore how colonization by either single non-pathogenic microbe species or a community of such microbes belowground affects plant growth and defense and how this affects the interactions of plants with aboveground insects at different trophic levels. Moreover, we review how plant responses to foliar herbivory by insects belonging to different feeding guilds affect interactions of plants with non-pathogenic soil-borne microbes. The role of phytohormones in coordinating plant growth, plant defenses against foliar herbivores while simultaneously establishing associations with non-pathogenic soil microbes is discussed.
    An ecogenomic analysis of herbivore-induced plant volatiles in Brassica juncea
    Mathur, V. ; Tytgat, T.O.G. ; Hordijk, C.A. ; Harhangi, H.R. ; Jansen, J.J. ; Reddy, A.S. ; Harvey, J.A. ; Vet, L.E.M. ; Dam, N.M. van - \ 2013
    Molecular Ecology 22 (2013)24. - ISSN 0962-1083 - p. 6179 - 6196.
    parasitoids cotesia-glomerata - brussels-sprouts plants - green leaf volatiles - arabidopsis-thaliana - glucosinolate hydrolysis - secondary metabolism - nicotiana-attenuata - insect herbivores - natural enemies - jasmonic acid
    Upon herbivore feeding, plants emit complex bouquets of induced volatiles that may repel insect herbivores as well as attract parasitoids or predators. Due to differences in the temporal dynamics of individual components, the composition of the herbivore-induced plant volatile (HIPV) blend changes with time. Consequently, the response of insects associated with plants is not constant either. Using Brassica juncea as the model plant and generalist Spodoptera spp. larvae as the inducing herbivore, we investigated herbivore and parasitoid preference as well as the molecular mechanisms behind the temporal dynamics in HIPV emissions at 24, 48 and 72 h after damage. In choice tests, Spodoptera litura moth preferred undamaged plants, whereas its parasitoid Cotesia marginiventris favoured plants induced for 48 h. In contrast, the specialist Plutella xylostella and its parasitoid C. vestalis preferred plants induced for 72 h. These preferences matched the dynamic changes in HIPV blends over time. Gene expression analysis suggested that the induced response after Spodoptera feeding is mainly controlled by the jasmonic acid pathway in both damaged and systemic leaves. Several genes involved in sulphide and green leaf volatile synthesis were clearly up-regulated. This study thus shows that HIPV blends vary considerably over a short period of time, and these changes are actively regulated at the gene expression level. Moreover, temporal changes in HIPVs elicit differential preferences of herbivores and their natural enemies. We argue that the temporal dynamics of HIPVs may play a key role in shaping the response of insects associated with plants.
    Silencing an N-Acyltransferase-Like Involved in Lignin Biosynthesis in Nicotiana attenuata Dramatically Alters Herbivory-Induced Phenolamide Metabolism
    Gaquerel, E. ; Kotkar, H. ; Onkokesung, N. ; Galis, I. ; Baldwin, I.T. - \ 2013
    PLoS ONE 8 (2013)5. - ISSN 1932-6203
    arabidopsis-thaliana - jasmonic acid - insect herbivores - mediated defenses - down-regulation - pathway - tobacco - accumulation - evolution - shikimate
    In a transcriptomic screen of Manduca sexta-induced N-acyltransferases in leaves of Nicotiana attenuata, we identified an N-acyltransferase gene sharing a high similarity with the tobacco lignin-biosynthetic hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyl transferase (HCT) gene whose expression is controlled by MYB8, a transcription factor that regulates the production of phenylpropanoid polyamine conjugates (phenolamides, PAs). To evaluate the involvement of this HCT-like gene in lignin production as well as the resulting crosstalk with PA metabolism during insect herbivory, we transiently silenced (by VIGs) the expression of this gene and performed non-targeted (UHPLC-ESI/TOF-MS) metabolomics analyses. In agreement with a conserved function of N. attenuata HCT-like in lignin biogenesis, HCT-silenced plants developed weak, soft stems with greatly reduced lignin contents. Metabolic profiling demonstrated large shifts (up to 12% deregulation in total extracted ions in insect-attacked leaves) due to a large diversion of activated coumaric acid units into the production of developmentally and herbivory-induced coumaroyl-containing PAs (N',N''-dicoumaroylspermidine, N',N''-coumaroylputrescine, etc) and to minor increases in the most abundant free phenolics (chlorogenic and cryptochlorogenic acids), all without altering the production of well characterized herbivory-responsive caffeoyl- and feruloyl-based putrescine and spermidine PAs. These data are consistent with a strong metabolic tension, exacerbated during herbivory, over the allocation of coumaroyl-CoA units among lignin and unusual coumaroyl-containing PAs, and rule out a role for HCT-LIKE in tuning the herbivory-induced accumulation of other PAs. Additionally, these results are consistent with a role for lignification as an induced anti-herbivore defense.
    Phenotypic plasticity of plant response to herbivore eggs: effects on resistance to caterpillars and plant development
    Pashalidou, F.G. ; Lucas-Barbosa, D. ; Loon, J.J.A. van; Dicke, M. ; Fatouros, N.E. - \ 2013
    Ecology 94 (2013)3. - ISSN 0012-9658 - p. 702 - 713.
    insect herbivores - pieris-brassicae - specialist herbivores - arabidopsis-thaliana - mamestra-brassicae - defense responses - bunias orientalis - chemical defense - pinus-sylvestris - getting ready
    Herbivory induces direct resistance responses in plants that negatively affect subsequently colonizing herbivores. Moreover, eggs of herbivorous insects can also activate plant resistance, which in some cases prevents hatching larvae from feeding. Until now, plant-mediated effects of eggs on subsequent herbivory, and the specificity of such responses, have remained poorly understood. We studied the specificity and effects of plant resistance induced by herbivore egg deposition against lepidopteran larvae of species with different dietary breadths, feeding on a wild annual plant, the crucifer Brassica nigra. We examined whether this plant-mediated response affects the growth of caterpillars of a specialist (Pieris brassicae) that feeds on B. nigra leaves and flowers, and a generalist (Mamestra brassicae) that rarely attacks this wild crucifer. We measured growth rates of neonate larvae to the end of their second instar after the larvae had hatched on plants exposed to eggs vs. plants without eggs, under laboratory and semi-field conditions. Moreover, we studied the effects of egg deposition by the two herbivore species on plant height and flowering rate before and after larval hatching. Larvae of both herbivore species that developed on plants previously infested with eggs of the specialist butterfly P. brassicae gained less mass compared with larvae that developed on egg-free plants. Plants exposed to butterfly eggs showed accelerated plant growth and flowering compared to egg-free plants. Egg deposition by the generalist moth M. brassicae, in contrast, had no effect on subsequent performance by either herbivore species, or on plant development. Our results demonstrate that B. nigra plants respond differently to eggs of two herbivore species in terms of plant development and induced resistance to caterpillar attack. For this annual crucifer, the retardation of caterpillar growth in response to deposition of eggs by P. brassicae in combination with enhanced growth and flowering likely result in reproductive assurance, after being exposed to eggs from an herbivore whose larvae rapidly reduce the plant's reproductive potential through florivory.
    Comparative analysis of Solanum stoloniferum responses to probing by the green peach aphid Myzus persicae and the potato aphid Macrosiphum euphorbiae
    Alvarez, A.E. ; Broglia, V.G. ; Amato, A.M.A. D'; Wouters, D. ; Vossen, E. ; Garzo, E. ; Tjallingii, W.F. ; Dicke, M. ; Vosman, B. - \ 2013
    Insect Science 20 (2013)2. - ISSN 1672-9609 - p. 207 - 227.
    manduca-sexta lepidoptera - host nicotiana-attenuata - phloem-feeding insects - resistance gene mi - plant defense - arabidopsis-thaliana - brevicoryne-brassicae - molecular-interactions - salivary secretions - microarray analysis
    Plants protect themselves against aphid attacks by species-specific defense mechanisms. Previously, we have shown that Solanum stoloniferum Schlechtd has resistance factors to Myzus persicae Sulzer (Homoptera: Aphididae) at the epidermal/mesophyll level that are not effective against Macrosiphum euphorbiae Thomas (Homoptera: Aphididae). Here, we compare the nymphal mortality, the pre-reproductive development time, and the probing behavior of M. persicae and M. euphorbiae on S. stoloniferum and Solanum tuberosum L. Furthermore, we analyze the changes in gene expression in S. stoloniferum 96 hours post infestation by either aphid species. Although the M. euphorbiae probing behavior shows that aphids encounter more probing constrains on phloem activitieslonger probing and salivation time on S. stoloniferum than on S. tuberosum, the aphids succeeded in reaching a sustained ingestion of phloem sap on both plants. Probing by M. persicae on S. stoloniferum plants resulted in limited feeding only. Survival of M. euphorbiae and M. persicae was affected on young leaves, but not on senescent leaves of S. stoloniferum. Infestation by M. euphorbiae changed the expression of more genes than M. persicae did. At the systemic level both aphids elicited a weak response. Infestation of S. stoloniferum plants with a large number of M. persicae induced morphological changes in the leaves, leading to the development of pustules that were caused by disrupted vascular parenchyma and surrounding tissue. In contrast, an infestation by M. euphorbiae had no morphological effects. Both plant species can be regarded as good host for M. euphorbiae, whereas only S. tuberosum is a good host for M. persicae and S. stoloniferum is not. Infestation of S. stoloniferum by M. persicae or M. euphorbiae changed the expression of a set of plant genes specific for each of the aphids as well as a set of common genes.
    Gomphrena claussenii, the first South-American metallophyte species with indicator-like Zn and Cd accumulation and extreme metal tolerance
    Tomaz Villafort Carvalho, M. ; Amaral, D.C. ; Guilherme, L.R. ; Aarts, M.G.M. - \ 2013
    Frontiers in Plant Science 4 (2013). - ISSN 1664-462X - 10 p.
    sedum-alfredii hance - hyperaccumulator thlaspi-caerulescens - arabidopsis-thaliana - molecular-mechanisms - copper tolerance - zinc tolerance - plants - cadmium - soils - phytoremediation
    Plant species with the capacity to tolerate heavy metals are potentially useful for phytoremediation since they have adapted to survive and reproduce under toxic conditions and to accumulate high metal concentrations. Gomphrena claussenii Moq., a South-American species belonging to the Amaranthaceae, is found at a zinc (Zn) mining area in the state of Minas Gerais, Brazil. Through soil and hydroponic experiments, the metal tolerance and accumulation capacities of G. claussenii were assessed and the effects on physiological characteristics were compared with a closely related non-tolerant species, G. elegans Mart. G. claussenii plants grown in soil sampled at the Zn smelting area accumulated up to 5318µgg-1 of Zn and 287 µg g-1 of cadmium (Cd) in shoot dry biomass after 30 days of exposure. Plants were grown in hydroponics containing up to 3000 µM of Zn and 100 µM of Cd for G. claussenii and 100 µM of Zn and 5 µM of Cd for G. elegans. G. claussenii proved to be an extremely tolerant species to both Zn and Cd, showing only slight metal toxicity symptoms at the highest treatment levels, without significant decrease in biomass and no effects on root growth, whereas the non-tolerant species G. elegans showed significant toxicity effects at the highest exposure levels. Both species accumulated more Zn and Cd in roots than in shoots. In G. elegans, over 90% of the Cd remained in the roots, but G. claussenii showed a root:shoot concentration ratio of around 2, with shoots reaching 0.93% Zn and 0.13% Cd on dry matter base. In G. claussenii shoots, the concentrations of other minerals, such as iron (Fe) and manganese (Mn), were only affected by the highest Zn treatment while in G. elegans the Fe and Mn concentrations in shoots decreased drastically at both Zn and Cd treatments. Taking together, these results indicate that G. claussenii is a novel metallophyte, extremely tolerant of high Zn and Cd exposure and an interesting species for further phytoremediation studies Keywords: phytoremediation, Zn/Cd hypertolerance, hyperaccumulation, metal contamination, Gomphrena claussenii, Gomphrena elegans
    The Brassica rapa FLC homologue FLC2 is a key regulator of flowering time, identified through transcriptional co-expression networks
    Xiao, D. ; Jianjun Zhao, Jianjun ; Hou, X.L. ; Basnet, R.K. ; Carpio, D.P. ; Zhang, N. ; Bucher, J. ; Lin, K. ; Cheng, F. ; Wang, X.W. ; Bonnema, A.B. - \ 2013
    Journal of Experimental Botany 64 (2013)14. - ISSN 0022-0957 - p. 4503 - 4516.
    quantitative trait loci - gene-expression - circadian clock - arabidopsis-thaliana - morphological traits - chinese-cabbage - ssp pekinensis - duplication - evolution - architecture
    The role of many genes and interactions among genes involved in flowering time have been studied extensively in Arabidopsis, and the purpose of this study was to investigate how effectively results obtained with the model species Arabidopsis can be applied to the Brassicacea with often larger and more complex genomes. Brassica rapa represents a very close relative, with its triplicated genome, with subgenomes having evolved by genome fractionation. The question of whether this genome fractionation is a random process, or whether specific genes are preferentially retained, such as flowering time (Ft) genes that play a role in the extreme morphological variation within the B. rapa species (displayed by the diverse morphotypes), is addressed. Data are presented showing that indeed Ft genes are preferentially retained, so the next intriguing question is whether these different orthologues of Arabidopsis Ft genes play similar roles compared with Arabidopsis, and what is the role of these different orthologues in B. rapa. Using a genetical-genomics approach, co-location of flowering quantitative trait loci (QTLs) and expression QTLs (eQTLs) resulted in identification of candidate genes for flowering QTLs and visualization of co-expression networks of Ft genes and flowering time. A major flowering QTL on A02 at the BrFLC2 locus co-localized with cis eQTLs for BrFLC2, BrSSR1, and BrTCP11, and trans eQTLs for the photoperiod gene BrCO and two paralogues of the floral integrator genes BrSOC1 and BrFT. It is concluded that the BrFLC2 Ft gene is a major regulator of flowering time in the studied doubled haploid population.
    Computational modeling of the BRI1-receptor system
    Esse, G.W. van; Harter, K. ; Vries, S.C. de - \ 2013
    Plant, Cell & Environment 36 (2013)9. - ISSN 0140-7791 - p. 1728 - 1737.
    brassinosteroid signal-transduction - plasma-membrane - plant-growth - arabidopsis-thaliana - auxin transport - root-growth - fluorescence microscopy - gsk3-like kinases - egf receptors - protein
    Computational models are useful tools to help understand signalling pathways in plant cells. A systems biology approach where models and experimental data are combined can provide experimentally verifiable predictions and novel insights. The brassinosteroid insensitive 1 (BRI1) receptor is one of the best-understood receptor systems in Arabidopsis with clearly described ligands, mutants and associated phenotypes. Therefore, BRI1-mediated signalling is attractive for mathematical modelling approaches to understand and interpret the spatial and temporal dynamics of signal transduction cascades in planta. To establish such a model, quantitative data sets incorporating local protein concentration, binding affinity and phosphorylation state of the different pathway components are essential. Computational modelling is increasingly employed in studies of plant growth and development. In this section, we have focused on the use of quantitative imaging of fluorescently labelled proteins as an entry point in modelling studies
    A mathematical model for the co-receptors SERK1 and SERK3 in BRI1 mediated signaling
    Esse, G.W. van; Mourik, S. van; Albrecht, C. ; Leeuwen, J. ; Vries, S.C. de - \ 2013
    Plant Physiology 163 (2013)3. - ISSN 0032-0889 - p. 1472 - 1481.
    innate immunity - arabidopsis-thaliana - tyrosine kinases - plant-growth - bri1 - bak1 - pathways - autophosphorylation - transduction - endocytosis
    Brassinosteroids (BRs) are key regulators in plant growth and development. The main BR perceiving receptor in Arabidopsis is Brassinosteroid Insensitive 1 (BRI1). Seedling root growth and hypocotyl elongation can be accurately predicted using a model for BRI1 receptor activity. Genetic evidence shows that non ligand-binding co-receptors of the Somatic Embryogenesis Receptor-like Kinase (SERK) family are essential for BRI1 signal transduction. A relatively simple biochemical model based on the properties of SERK loss-of-function alleles explains complex physiological responses of the BRI1 mediated BR pathway. The model uses BRI1-BR occupancy as the central estimated parameter and includes BRI1-SERK interaction based on mass action kinetics and accurately describes wild type root growth and hypocotyl elongation. Simulation studies suggest that the SERK co-receptors primarily act to increase the magnitude of the BRI1 signal. The model predicts that only a small number of active BRI1-SERK complexes are required to carry out BR signaling at physiological ligand concentration. Finally, when calibrated with single mutants, the model predicts that roots of the serk1serk3 double mutant are almost completely BL-insensitive, while the double mutant hypocotyls remain sensitive. This points to residual BRI1 signaling or to a different co-receptor requirement in shoots.
    The PIN family of proteins in potato and their putative role in tuberisation
    Roumeliotis, E. ; Kloosterman, B.A. ; Oortwijn, M.E.P. ; Visser, R.G.F. ; Bachem, C.W.B. - \ 2013
    Frontiers in Plant Science 4 (2013). - ISSN 1664-462X
    arabidopsis-thaliana - auxin biosynthesis - root gravitropism - tuber initiation - expression - transport - growth - identification - transformation - tissues
    The PIN family of trans-membrane proteins mediates auxin efflux throughout the plant and during various phases of plant development. In Arabidopsis thaliana, the PIN family comprised of 8 members, divided into ‘short’ and ‘long’ PINs according to the length of the hydrophilic domain of the protein. Based on sequence homology using the recently published potato genome sequence (Solanum tuberosum group Phureja) we identified ten annotated potato StPIN genes. Mining the publicly available gene expression data, we constructed a catalogue tissue specificity of StPIN gene expression, focusing on the process of tuberization. A total of four StPIN genes exhibited increased expression four days after tuber induction, prior to the onset of stolon swelling. For two PIN genes, StPIN4 and StPIN2, promoter sequences were cloned and fused to the GUS reporter protein to study tissue specificity in more detail. StPIN4 promoter driven GUS staining was detected in the flower stigma, in the flower style, below the ovary and petals, in the root tips, in the vascular tissue of the stolons and in the tuber parenchyma cells. StPIN2 promoter driven GUS staining was detected in flower buds, in the vascular tissue of the swelling stolons and in the storage parenchyma of the growing tubers. Based on our results, we postulate a role for the StPINs in redistributing auxin in the swelling stolon during early events in tuber development.
    Foraging behaviour by parasitoids in multiherbivore communities
    Rijk, M. de; Dicke, M. ; Poelman, E.H. - \ 2013
    Animal Behaviour 85 (2013)6. - ISSN 0003-3472 - p. 1517 - 1528.
    induced plant volatiles - tritrophic interaction webs - host-searching behavior - cabbage plants - mediated interactions - arabidopsis-thaliana - patch exploitation - cotesia-glomerata - natural enemies - herbivore complexes
    Parasitoid foraging decisions are often affected by community characteristics such as community diversity and complexity. As part of a complex habitat, the presence of unsuitable hosts may affect foraging behaviour of parasitoids. First, unsuitable herbivores may affect the localization of patches where hosts are present. Second, encounters with unsuitable herbivores in the food plant patch may affect parasitoid decisions during their searching behaviour in the patch. In this review, we outline the importance of the presence of unsuitable herbivores on the behavioural responses of parasitoids during both these foraging phases. Nonhosts feeding on a neighbouring plant or on the same plant individual the host is feeding from may affect odour-based searching by parasitoids in a way specific for the species combination studied. Feeding by specific host and nonhost-herbivore combinations may induce volatiles that are more, less or equally attractive compared to those from plants infested by the host only. Within the food patch, mixed presence of host and nonhost may reduce the number of hosts parasitized per time unit and reduce parasitoid foraging efficiency. Importantly, we show that a single nonhost species may have contrasting effects in terms of its effects on odour-based searching and patch residence decisions. We conclude that studying host searching behaviour at both phases of foraging is essential for our understanding of parasitoid foraging behaviour in natural and agricultural settings. We further speculate on the ecological context in which unsuitable herbivores affect either of the two phases of parasitoid foraging.
    Communication between L-galactono-¿-lactone dehydrogenase and cytochrome c.
    Hervas, M. ; Bashir, Q. ; Leferink, N.G.H. ; Ferreira, P. ; Moreno-Beltran, J.B. ; Westphal, A.H. ; Diaz Moreno, I. ; Medina, M. ; La Rosa, M.A. De; Ubbink, M. ; Navarro, J.A. ; Berkel, W.J.H. van - \ 2013
    FEBS Journal 280 (2013)8. - ISSN 1742-464X - p. 1830 - 1840.
    electron-transfer - nmr-spectroscopy - vitamin-c - yeast iso-1-cytochrome-c - arabidopsis-thaliana - protein interactions - kinetic-analysis - viologen analog - complex - plastocyanin
    l-galactono-1,4-lactone dehydrogenase (GALDH) catalyzes the terminal step of vitamin C biosynthesis in plant mitochondria. Here we investigated the communication between Arabidopsis thaliana GALDH and its natural electron acceptor cytochrome c (Cc). Using laser-generated radicals we observed the formation and stabilization of the GALDH semiquinone anionic species (GALDHSQ ). GALDHSQ oxidation by Cc exhibited a nonlinear dependence on Cc concentration consistent with a kinetic mechanism involving protein-partner association to form a transient bimolecular complex prior to the electron transfer step. Oxidation of GALDHSQ by Cc was significantly impaired at high ionic strength, revealing the existence of attractive charge-charge interactions between the two reactants. Isothermal titration calorimetry showed that GALDH weakly interacts with both oxidized and reduced Cc. Chemical shift perturbations for (1) H and (15) N nuclei of Cc, arising from the interactions with unlabeled GALDH, were used to map the interacting surface of Cc. For Arabidopsis Cc and yeast Cc, similar residues are involved in the interaction with GALDH. These residues are confined to a single surface surrounding the heme edge. The range of chemical shift perturbations for the physiological Arabidopsis Cc-GALDH complex is larger than that of the non-physiological yeast Cc-GALDH complex, indicating that the former complex is more specific. In summary, the results point to a relatively low affinity GALDH-Cc interaction, similar for all partner redox states, involving protein-protein dynamic motions. Evidence is also provided that Cc utilizes a conserved surface surrounding the heme edge for the interaction with GALDH and other redox partners.
    Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes
    Basnet, R.K. ; Moreno Pachón, N.M. ; Lin, K. ; Bucher, J. ; Visser, R.G.F. ; Maliepaard, C.A. ; Bonnema, A.B. - \ 2013
    BMC Genomics 14 (2013). - ISSN 1471-2164
    gene-expression profiles - false discovery rate - arabidopsis-thaliana - network analysis - prolamin-box - napus - germination - embryo - maize - plant
    Brassica seeds are important as basic units of plant growth and sources of vegetable oil. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. We conducted a global microarray gene co-expression analysis by measuring transcript abundance of developing seeds from two diverse B. rapa morphotypes: a pak choi (leafy-type) and a yellow sarson (oil-type), and two of their doubled haploid (DH) progenies, (1) to study the timing of metabolic processes in developing seeds, (2) to explore the major transcriptional differences in developing seeds of the two morphotypes, and (3) to identify the optimum stage for a genetical genomics study in B. rapa seed.
    Stepwise artificial evolution of a plant disease resistance gene
    Harris, J.H. ; Slootweg, E.J. ; Goverse, A. ; Baulcombe, D.C. - \ 2013
    Proceedings of the National Academy of Sciences of the United States of America 110 (2013)52. - ISSN 0027-8424 - p. 21189 - 21194.
    nb-lrr protein - tobacco-mosaic-virus - rich repeat domains - cell-death - arabidopsis-thaliana - immune receptors - coiled-coil - hypersensitive response - mediated resistance - pathogen effectors
    Genes encoding plant nucleotide-binding leucine-rich repeat (NB-LRR) proteins confer dominant resistance to diverse pathogens. The wild-type potato NB-LRR protein Rx confers resistance against a single strain of potato virus X (PVX), whereas LRR mutants protect against both a second PVX strain and the distantly related poplar mosaic virus (PopMV). In one of the Rx mutants there was a cost to the broad-spectrum resistance because the response to PopMV was transformed from a mild disease on plants carrying wild-type Rx to a trailing necrosis that killed the plant. To explore the use of secondary mutagenesis to eliminate this cost of broad-spectrum resistance, we performed random mutagenesis of the N-terminal domains of this broad-recognition version of Rx and isolated four mutants with a stronger response against the PopMV coat protein due to enhanced activation sensitivity. These mutations are located close to the nucleotide-binding pocket, a highly conserved structure that likely controls the “switch” between active and inactive NB-LRR conformations. Stable transgenic plants expressing one of these versions of Rx are resistant to the strains of PVX and the PopMV that previously caused trailing necrosis. We conclude from this work that artificial evolution of NB-LRR disease resistance genes in crops can be enhanced by modification of both activation and recognition phases, to both accentuate the positive and eliminate the negative aspects of disease resistance.
    Plants Know Where It Hurts: Root and Shoot Jasmonic Acid Induction Elicit Differential Responses in Brassica oleracea.
    Tytgat, T. ; Verhoeven, K.J.F. ; Janssen, J.J. ; Raaijmakers, C.E. ; Bakx-Schotman, J.M.T. ; McIntyre, L.M. ; Putten, W.H. van der; Biere, A. ; Dam, N.M. van - \ 2013
    PLoS ONE 8 (2013)6. - ISSN 1932-6203
    gene-expression - arabidopsis-thaliana - jaz repressors - multitrophic interactions - 12-oxo-phytodienoic acid - stress responses - herbivory - dynamics - defenses - carbon
    Plants respond to herbivore attack by rapidly inducing defenses that are mainly regulated by jasmonic acid (JA). Due to the systemic nature of induced defenses, attack by root herbivores can also result in a shoot response and vice versa, causing interactions between above- and belowground herbivores. However, little is known about the molecular mechanisms underlying these interactions. We investigated whether plants respond differently when roots or shoots are induced. We mimicked herbivore attack by applying JA to the roots or shoots of Brassica oleracea and analyzed molecular and chemical responses in both organs. In shoots, an immediate and massive change in primary and secondary metabolism was observed. In roots, the JA-induced response was less extensive and qualitatively different from that in the shoots. Strikingly, in both roots and shoots we also observed differential responses in primary metabolism, development as well as defense specific traits depending on whether the JA induction had been below- or aboveground. We conclude that the JA response is not only tissue-specific but also dependent on the organ that was induced. Already very early in the JA signaling pathway the differential response was observed. This indicates that both organs have a different JA signaling cascade, and that the signal eliciting systemic responses contains information about the site of induction, thus providing plants with a mechanism to tailor their responses specifically to the organ that is damaged.
    Visualization of BRI1 and BAK1(SERK3) membrane receptor heterooligomers during brassinosteroid signaling.
    Bücherl, C.A. ; Esse, G.W. van; Kruis, A. ; Luchtenberg, J. ; Westphal, A.H. ; Aker, J.C.M. ; Hoek, A. van; Albrecht, C. ; Borst, J.W. ; Vries, S.C. de - \ 2013
    Plant Physiology 162 (2013)2. - ISSN 0032-0889 - p. 1911 - 1925.
    agrobacterium-mediated transformation - growth-factor receptors - gsk3-like kinase bin2 - transcription factors - plant-growth - arabidopsis-thaliana - extracellular domain - chemokine receptors - plasma-membrane - gene-expression
    The leucine-rich repeat receptor-like kinase BRASSINOSTEROID-INSENSITIVE1 (BRI1) is the main ligand-perceiving receptor for brassinosteroids (BRs) in Arabidopsis (Arabidopsis thaliana). Binding of BRs to the ectodomain of plasma membrane (PM)-located BRI1 receptors initiates an intracellular signal transduction cascade that influences various aspects of plant growth and development. Even though the major components of BR signaling have been revealed and the PM was identified as the main site of BRI1 signaling activity, the very first steps of signal transmission are still elusive. Recently, it was shown that the initiation of BR signal transduction requires the interaction of BRI1 with its SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK) coreceptors. In addition, the resolved structure of the BRI1 ectodomain suggested that BRI1-ASSOCIATED KINASE1 [BAK1](SERK3) may constitute a component of the ligand-perceiving receptor complex. Therefore, we investigated the spatial correlation between BRI1 and BAK1(SERK3) in the natural habitat of both leucine-rich repeat receptor-like kinases using comparative colocalization analysis and fluorescence lifetime imaging microscopy. We show that activation of BR signaling by exogenous ligand application resulted in both elevated colocalization between BRI1 and BAK1(SERK3) and an about 50% increase of receptor heterooligomerization in the PM of live Arabidopsis root epidermal cells. However, large populations of BRI1 and BAK1(SERK3) colocalized independently of BRs. Moreover, we could visualize that approximately 7% of the BRI1 PM pool constitutively heterooligomerizes with BAK1(SERK3) in live root cells. We propose that only small populations of PM-located BRI1 and BAK1(SERK3) receptors participate in active BR signaling and that the initiation of downstream signal transduction involves preassembled BRI1-BAK1(SERK3) heterooligomers.
    An integrative model of the control of ovule primordia formation
    Galbiati, F. ; Sihna Roy, D. ; Simonini, S. ; Cucinotta, M. ; Ceccato, L. ; Cuesta, C. ; Simaskova, M. ; Benkova, E. ; Kamiuchi, Y. ; Aida, M. ; Weijers, D. ; Simon, R. ; Masiero, S. ; Colombo, L. - \ 2013
    The Plant Journal 76 (2013)3. - ISSN 0960-7412 - p. 446 - 455.
    dependent auxin gradients - arabidopsis-thaliana - transcription factor - pattern-formation - early sporogenesis - direct target - gene - cytokinin - gynoecium - aintegumenta
    Upon hormonal signaling, ovules develop as lateral organs from the placenta. Ovule numbers ultimately determine the number of seeds that develop, and thereby contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule primordia formation. We show that expression of the CUC1 and CUC2 genes is required to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required for ovule primordia formation. Furthermore, our results suggest that the auxin response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and promote their transcription. Based on our findings, we propose an integrative model to describe the molecular mechanisms of the early stages of ovule development.
    The rhizosphere microbiome: significance of plant beneficial, plant pathogenic and human pathogenic microorganisms
    Mendes, R. ; Garbeva, P. ; Raaijmakers, J.M. - \ 2013
    FEMS Microbiology Reviews 37 (2013)5. - ISSN 0168-6445 - p. 634 - 663.
    growth-promoting rhizobacteria - pseudomonas-aeruginosa 7nsk2 - bacterial community structure - disease-suppressive bacteria - induced systemic resistance - tobacco necrosis virus - barley hordeum-vulgare - max l merr - arabidopsis-thaliana - salicylic-acid
    Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members of the rhizosphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protective microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when introduced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizosphere microbiome and what they are doing. Here, we review the main functions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight several strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health.
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