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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Mediator of tolerance to abiotic stress ERF6 regulates susceptibility of Arabidopsis to Meloidogyne incognita
Warmerdam, Sonja ; Sterken, Mark G. ; Schaik, Casper van; Oortwijn, Marian E.P. ; Lozano-Torres, Jose L. ; Bakker, Jaap ; Goverse, Aska ; Smant, Geert - \ 2019
Molecular Plant Pathology 20 (2019)1. - ISSN 1464-6722 - p. 137 - 152.
abiotic stress - Arabidopsis thaliana - ERF6 - genome-wide association mapping - Meloidogyne incognita - root-knot nematodes - transcription factor

Root-knot nematodes transform vascular host cells into permanent feeding structures to selectively withdraw their nutrients from host plants during the course of several weeks. The susceptibility of host plants to root-knot nematode infections is thought to be a complex trait involving many genetic loci. However, genome-wide association (GWA) analysis has so far revealed only four quantitative trait loci (QTLs) linked to the reproductive success of the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana, which suggests that the genetic architecture underlying host susceptibility could be much simpler than previously thought. Here, we report that, by using a relaxed stringency approach in a GWA analysis, we could identify 15 additional loci linked to quantitative variation in the reproductive success of M. incognita in Arabidopsis. To test the robustness of our analysis, we functionally characterized six genes located in a QTL with the lowest acceptable statistical support and smallest effect size. This led us to identify ETHYLENE RESPONSE FACTOR 6 (ERF6) as a novel susceptibility gene for M. incognita in Arabidopsis. ERF6 functions as a transcriptional activator and suppressor of genes in response to various abiotic stresses independent of ethylene signalling. However, whole-transcriptome analysis of nematode-infected roots of the Arabidopsis erf6-1 knockout mutant line showed that allelic variation at this locus may regulate the conversion of aminocyclopropane-1-carboxylate (ACC) into ethylene by altering the expression of 1-aminocyclopropane-1-carboxylate oxidase 3 (ACO3). Our data further suggest that tolerance to abiotic stress mediated by ERF6 forms a novel layer of control in the susceptibility of Arabidopsis to M. incognita.

A molecular network for functional versatility of HECATE transcription factors
Gaillochet, Christophe ; Jamge, Suraj ; Wal, Froukje van der; Angenent, Gerco ; Immink, Richard ; Lohmann, Jan U. - \ 2018
The Plant Journal 95 (2018)1. - ISSN 0960-7412 - p. 57 - 70.
Arabidopsis thaliana - flowering time - HECATE - NGATHA - regulatory module - shoot apical meristem - transcription factor

During the plant life cycle, diverse signaling inputs are continuously integrated and engage specific genetic programs depending on the cellular or developmental context. Consistent with an important role in this process, HECATE (HEC) basic helix–loop–helix transcription factors display diverse functions, from photomorphogenesis to the control of shoot meristem dynamics and gynoecium patterning. However, the molecular mechanisms underlying their functional versatility and the deployment of specific HEC subprograms remain elusive. To address this issue, we systematically identified proteins with the capacity to interact with HEC1, the best-characterized member of the family, and integrated this information with our data set of direct HEC1 target genes. The resulting core genetic modules were consistent with specific developmental functions of HEC1, including its described activities in light signaling, gynoecium development and auxin homeostasis. Importantly, we found that HEC genes also play a role in the modulation of flowering time, and uncovered that their role in gynoecium development may involve the direct transcriptional regulation of NGATHA1 (NGA1) and NGA2 genes. NGA factors were previously shown to contribute to fruit development, but our data now show that they also modulate stem cell homeostasis in the shoot apical meristem. Taken together, our results delineate a molecular network underlying the functional versatility of HEC transcription factors. Our analyses have not only allowed us to identify relevant target genes controlling shoot stem cell activity and a so far undescribed biological function of HEC1, but also provide a rich resource for the mechanistic elucidation of further context-dependent HEC activities.

Control of oriented cell division in the Arabidopsis embryo
Dop, M. van; Liao, C.Y. ; Weijers, D. - \ 2015
Current Opinion in Plant Biology 23 (2015). - ISSN 1369-5266 - p. 25 - 30.
preprophase band organization - plant development - transcription factor - monopteros - gene - root - differentiation - morphogenesis - cytokinesis - proteins
Multicellular plant development requires strict control of cell division orientation. A key unanswered question is how developmental regulators interact with the generic cell division machinery to trigger oriented divisions. We discuss the Arabidopsis embryo as a model for addressing this question. Recent progress in 3D imaging and computation now allows sketching of a framework for the developmental control of division orientation in which the signaling molecule auxin controls oriented division by preventing a geometrically defined default plane. We expect that the identification of auxin effectors, together with the identification of novel regulators of cell division will help to link developmental regulators to the division machinery.
Building a plant: cell fate specification in the early Arabidopsis embryo
Hove, C.A. ten; Lu, Kuan-Ju ; Weijers, D. - \ 2015
Development 142 (2015). - ISSN 0950-1991 - p. 420 - 430.
homeodomain-leucine-zipper - apical-basal axis - layer-specific gene - box protein tir1 - transcription factor - vascular development - early embryogenesis - pattern-formation - shoot meristem - f-box
Embryogenesis is the beginning of plant development, yet the cell fate decisions and patterning steps that occur during this time are reiterated during development to build the post-embryonic architecture. In Arabidopsis, embryogenesis follows a simple and predictable pattern, making it an ideal model with which to understand how cellular and tissue developmental processes are controlled. Here, we review the early stages of Arabidopsis embryogenesis, focusing on the globular stage, during which time stem cells are first specified and all major tissues obtain their identities. We discuss four different aspects of development: the formation of outer versus inner layers; the specification of vascular and ground tissues; the determination of shoot and root domains; and the establishment of the first stem cells.
Chikungunya virus non-structural protein 2-mediated host shut-off disables the unfolded protein response
Fros, J.J. ; Major, L.D. ; Scholte, F.E. ; Gardner, J. ; Hemert, M.J. van; Suhrbier, A. ; Pijlman, G.P. - \ 2015
Journal of General Virology 96 (2015)3. - ISSN 0022-1317 - p. 580 - 589.
endoplasmic-reticulum stress - semliki-forest-virus - messenger-rna - mammalian-cells - er stress - translational shutoff - transcription factor - gene-expression - insect cells - infection
The unfolded protein response (UPR) is a cellular defence mechanism against high concentrations of misfolded protein in the endoplasmic reticulum (ER). In the presence of misfolded proteins, ER-transmembrane proteins PERK and IRE1a become activated. PERK phosphorylates eIF2a leading to a general inhibition of cellular translation, whilst the expression of transcription factor ATF4 is upregulated. Active IRE1a splices out an intron from XBP1 mRNA, to produce a potent transcription factor. Activation of the UPR increases the production of several proteins involved in protein folding, degradation and apoptosis. Here, we demonstrated that transient expression of chikungunya virus (CHIKV) (family Togaviridae, genus Alphavirus) envelope glycoproteins induced the UPR and that CHIKV infection resulted in the phosphorylation of eIF2a and partial splicing of XBP1 mRNA. However, infection with CHIKV did not increase the expression of ATF4 and known UPR target genes (GRP78/BiP, GRP94 and CHOP). Moreover, nuclear XBP1 was not observed during CHIKV infection. Even upon stimulation with tunicamycin, the UPR was efficiently inhibited in CHIKV-infected cells. Individual expression of CHIKV non-structural proteins (nsPs) revealed that nsP2 alone was sufficient to inhibit the UPR. Mutations that rendered nsP2 unable to cause host-cell shut-off prevented nsP2-mediated inhibition of the UPR. This indicates that initial UPR induction takes place in the ER but that expression of functional UPR transcription factors and target genes is efficiently inhibited by CHIKV nsP2.
Epigenetic Basis of Morphological Variation and Phenotypic Plasticity in Arabidopsis thaliana
Kooke, R. ; Johannes, F. ; Wardenaar, R. ; Becker, F.F.M. ; Etcheverry, M. ; Colot, V. ; Vreugdenhil, D. ; Keurentjes, J.J.B. - \ 2015
The Plant Cell 27 (2015)2. - ISSN 1040-4651 - p. 337 - 348.
quantitative trait loci - dna methylation - transcription factor - qtl analysis - population - plant - inheritance - stability - evolution - performance
Epigenetics is receiving growing attention in the plant science community. Epigenetic modifications are thought to play a particularly important role in fluctuating environments. It is hypothesized that epigenetics contributes to plant phenotypic plasticity because epigenetic modifications, in contrast to DNA sequence variation, are more likely to be reversible. The population of decrease in DNA methylation 1-2 (ddm1-2)-derived epigenetic recombinant inbred lines (epiRILs) in Arabidopsis thaliana is well suited for studying this hypothesis, as DNA methylation differences are maximized and DNA sequence variation is minimized. Here, we report on the extensive heritable epigenetic variation in plant growth and morphology in neutral and saline conditions detected among the epiRILs. Plant performance, in terms of branching and leaf area, was both reduced and enhanced by different quantitative trait loci (QTLs) in the ddm1-2 inherited epigenotypes. The variation in plasticity associated significantly with certain genomic regions in which the ddm1-2 inherited epigenotypes caused an increased sensitivity to environmental changes, probably due to impaired genetic regulation in the epiRILs. Many of the QTLs for morphology and plasticity overlapped, suggesting major pleiotropic effects. These findings indicate that epigenetics contributes substantially to variation in plant growth, morphology, and plasticity, especially under stress conditions
Cisgenic apple trees; development, characterization, and performance
Krens, F.A. ; Schaart, J.G. ; Burgh, A.M. van der; Tinnenbroek-Capel, I.E.M. ; Groenwold, R. ; Kodde, L.P. ; Broggini, G.A.L. ; Gessler, C. ; Schouten, H.J. - \ 2015
Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 11 p.
scab resistance gene - selectable marker - mediated transformation - plant transformation - transcription factor - transgenic apple - agrobacterium - gala - recombinase - expression
Two methods were developed for the generation of cisgenic apples. Both have been successfully applied producing trees. The first method avoids the use of any foreign selectable marker genes; only the gene-of-interest is integrated between the T-DNA border sequences. The second method makes use of recombinase-based marker excision. For the first method we used the MdMYB10 gene from a red-fleshed apple coding for a transcription factor involved in regulating anthocyanin biosynthesis. Red plantlets were obtained and presence of the cisgene was confirmed. Plantlets were grafted and grown in a greenhouse. After 3 years, the first flowers appeared, showing red petals. Pollination led to production of red-fleshed cisgenic apples. The second method used the pM(arker)F(ree) vector system, introducing the scab resistance gene Rvi6, derived from apple. Agrobacterium-mediated transformation, followed by selection on kanamycin, produced genetically modified apple lines. Next, leaves from in vitro material were treated to activate the recombinase leading to excision of selection genes. Subsequently, the leaf explants were subjected to negative selection for marker-free plantlets by inducing regeneration on medium containing 5-fluorocytosine. After verification of the marker-free nature, the obtained plants were grafted onto rootstocks. Young trees from four cisgenic lines and one intragenic line, all containing Rvi6, were planted in an orchard. Appropriate controls were incorporated in this trial. We scored scab incidence for three consecutive years on leaves after inoculations with Rvi6-avirulent strains. One cisgenic line and the intragenic line performed as well as the resistant control. In 2014 trees started to overcome their juvenile character and formed flowers and fruits. The first results of scoring scab symptoms on apple fruits were obtained. Apple fruits from susceptible controls showed scab symptoms, while fruits from cisgenic and intragenic lines were free of scab.
Molecular cloning and characterization of the trichome specificchrysanthemyl diphosphate/chrysanthemol synthase promoter fromTanacetum cinerariifolium
Sultana, S. ; Hu, H. ; Gao, L. ; Mao, J. ; Luo, J. ; Jongsma, M.A. ; Wang, C. - \ 2015
Scientia Horticulturae 185 (2015). - ISSN 0304-4238 - p. 193 - 199.
mosaic virus-35s promoter - artemisia-annua - transcription factor - diphosphate synthase - pyrethrin biosynthesis - transgene expression - plant transformation - glandular trichomes - gene - cinerariaefolium
Natural pyrethrins accumulate to high concentrations in the flower achenes of pyrethrum (Tanacetumcinerariifolium). They are extracted from dried flowers and widely used as a natural pesticide. Chrysanthe-mol synthase (CHS) is the first key enzyme in the biosynthesis of pyrethrins. In this work, a 1128 bp TcCHSpromoter fragment was cloned from pyrethrum genomic DNA. The sequence contained cis-elementspredicted to be responsive to different hormones, light, and environmental stresses. To characterizethe promoter it was fused to the reporter genes green fluorescent protein (GFP) and -glucuronidase(GUS), and respectively transformed into florist’s chrysanthemum (Chrysanthemum morifolium ‘1581’)and tobacco (Nicotiana tabacum). GFP fluorescence in florist’s chrysanthemum ‘1581’and GUS staining oftobacco showed that the TcCHS promoter was exclusively expressed in the glandular secretory trichomes(GSTs) of both plant species. The findings will support research on factors influencing the accumulationof pyrethrins, and can be used for trichome-specific metabolic engineering of plants to ensure minimaladverse effects on plant growth and development.
White adipose tissue reference network: a knowledge resource for exploring potential health-relevant relations
Kelder, T. ; Summer, G. ; Caspers, M. ; Schothorst, E.M. van; Keijer, J. ; Duivenvoorde, Loes ; Klaus, S. ; Volgt, A. ; Bohnert, L. ; Pico, C. ; Palou, A. ; Bonet, M.L. ; Dembinska-Kiec, A. ; Malczewska-Malec, M. ; Kieć-Wilk, Beata ; Bas, J.M. del; Caimari, A. ; Arola, L. ; Erk, M. van; Ommen, Ben van; Radonjic, M. - \ 2015
Genes & Nutrition 10 (2015)1. - ISSN 1555-8932
metabolic syndrome - high-fat - transcription factor - biological networks - insulin-secretion - gene-expression - cell biology - short-term - obesity - diet
Optimal health is maintained by interaction of multiple intrinsic and environmental factors at different levels of complexity-from molecular, to physiological, to social. Understanding and quantification of these interactions will aid design of successful health interventions. We introduce the reference network concept as a platform for multi-level exploration of biological relations relevant for metabolic health, by integration and mining of biological interactions derived from public resources and context-specific experimental data. A White Adipose Tissue Health Reference Network (WATRefNet) was constructed as a resource for discovery and prioritization of mechanism-based biomarkers for white adipose tissue (WAT) health status and the effect of food and drug compounds on WAT health status. The WATRefNet (6,797 nodes and 32,171 edges) is based on (1) experimental data obtained from 10 studies addressing different adiposity states, (2) seven public knowledge bases of molecular interactions, (3) expert's definitions of five physiologically relevant processes key to WAT health, namely WAT expandability, Oxidative capacity, Metabolic state, Oxidative stress and Tissue inflammation, and (4) a collection of relevant biomarkers of these processes identified by BIOCLAIMS ( http://bioclaims.uib.es ). The WATRefNet comprehends multiple layers of biological complexity as it contains various types of nodes and edges that represent different biological levels and interactions. We have validated the reference network by showing overrepresentation with anti-obesity drug targets, pathology-associated genes and differentially expressed genes from an external disease model dataset. The resulting network has been used to extract subnetworks specific to the above-mentioned expert-defined physiological processes. Each of these process-specific signatures represents a mechanistically supported composite biomarker for assessing and quantifying the effect of interventions on a physiological aspect that determines WAT health status. Following this principle, five anti-diabetic drug interventions and one diet intervention were scored for the match of their expression signature to the five biomarker signatures derived from the WATRefNet. This confirmed previous observations of successful intervention by dietary lifestyle and revealed WAT-specific effects of drug interventions. The WATRefNet represents a sustainable knowledge resource for extraction of relevant relationships such as mechanisms of action, nutrient intervention targets and biomarkers and for assessment of health effects for support of health claims made on food products.
Prevalence of transcription factors in ascomycete and basidiomycete fungi
Todd, Richard B. ; Zhou, M. ; Ohm, R.A. ; Leeggangers, H.A.C.F. ; Visser, L. ; Vries, R.P. de - \ 2014
transcription factor - gene regulation - fungal genomes - evolution - zinc binuclear cluster - zinc finger - DNA binding domain
Background: Gene regulation underlies fungal physiology and therefore is a major factor in fungal biodiversity. Analysis of genome sequences has revealed a large number of putative transcription factors in most fungal genomes. The presence of fungal orthologs for individual regulators has been analysed and appears to be highly variable with some regulators widely conserved and others showing narrow distribution. Although genome-scale transcription factor surveys have been performed before, no global study into the prevalence of specific regulators across the fungal kingdom has been presented. Results: In this study we have analysed the number of members for 37 regulator classes in 77 ascomycete and 31 basidiomycete fungal genomes and revealed significant differences between ascomycetes and basidiomycetes. In addition, we determined the presence of 64 regulators characterised in ascomycetes across these 108 genomes. This demonstrated that overall the highest presence of orthologs is in the filamentous ascomycetes. A significant number of regulators lacked orthologs in the ascomycete yeasts and the basidiomycetes. Conversely, of seven basidiomycete regulators included in the study, only one had orthologs in ascomycetes. Conclusions: This study demonstrates a significant difference in the regulatory repertoire of ascomycete and basidiomycete fungi, at the level of both regulator class and individual regulator. This suggests that the current regulatory systems of these fungi have been mainly developed after the two phyla diverged. Most regulators detected in both phyla are involved in central functions of fungal physiology and therefore were likely already present in the ancestor of the two phyla.
Precise control of plant stem cell activity through parallel regulatory inputs
Bennett, T. ; Toorn, A. van; Willemsen, V. ; Scheres, B. - \ 2014
Development 141 (2014). - ISSN 0950-1991 - p. 4055 - 4064.
arabidopsis-thaliana root - transcription factor - shoot apex - meristem - gene - differentiation - organization - maintenance - homeostasis - sombrero
The regulation of columella stem cell activity in the Arabidopsis root cap by a nearby organizing centre, the quiescent centre, has been a key example of the stem cell niche paradigm in plants. Here, we investigate interactions between transcription factors that have been shown to regulate columella stem cells using a simple quantification method for stem cell activity in the root cap. Genetic and expression analyses reveal that the RETINOBLASTOMA-RELATED protein, the FEZ and SOMBRERO NAC-domain transcription factors, the ARF10 and ARF16 auxin response factors and the quiescent centre-expressed WOX5 homeodomain protein each provide independent inputs to regulate the number of columella stem cells. Given the tight control of columella development, we found that these inputs act in a surprisingly parallel manner. Nevertheless, important points of interaction exist; for example, we demonstrate the repression of SMB activity by non-autonomous action of WOX5. Our results suggest that the developmental progression of columella stem cells may be quantitatively regulated by several more broadly acting transcription factors rather than by a single intrinsic stem cell factor, which raises questions about the special nature of the stem cell state in plants.
Irreversible fate commitment in the Arabidopsis stomatal lineage requires a Fama and Retinoblastoma-related module
Matos, J.L. ; Lau, O.S. ; Hachez, C. ; Cruz-Ramirez, A. ; Scheres, B. ; Bergmann, D.C. - \ 2014
eLife 3 (2014). - ISSN 2050-084X
asymmetric cell divisions - gateway binary vectors - transcription factor - secretory peptide - guard-cells - differentiation - expression - genes - transformation - termination
The presumed totipotency of plant cells leads to questions about how specific stem cell lineages and terminal fates could be established. In the Arabidopsis stomatal lineage, a transient self-renewing phase creates precursors that differentiate into one of two epidermal cell types, guard cells or pavement cells. We found that irreversible differentiation of guard cells involves RETINOBLASTOMA-RELATED (RBR) recruitment to regulatory regions of master regulators of stomatal initiation, facilitated through interaction with a terminal stomatal lineage transcription factor, FAMA. Disrupting physical interactions between FAMA and RBR preferentially reveals the role of RBR in enforcing fate commitment over its role in cell-cycle control in this developmental context. Analysis of the phenotypes linked to the modulation of FAMA and RBR sheds new light on the way iterative divisions and terminal differentiation are coordinately regulated in a plant stem-cell lineage. - See more at: http://elifesciences.org/content/3/e03271#sthash.f3srCCrx.dpuf
An O-methyltransferase modifies accumulation of methylated anthocyanins in seedlings of tomato
Gomez Roldan, M.V. ; Outchkourov, N.S. ; Houwelingen, A.M.M.L. van; Lammers, M. ; Romero Fuente, I. ; Ziklo, N. ; Aharoni, A. ; Hall, R.D. ; Beekwilder, M.J. - \ 2014
The Plant Journal 80 (2014)4. - ISSN 0960-7412 - p. 695 - 708.
plant transformation - transcription factor - petunia-hybrida - fruit - biosynthesis - expression - protein - system - metabolome - infection
Anthocyanins contribute to the appearance of fruit by conferring to them a red, blue or purple colour. In a food context, they have also been suggested to promote consumer health. In purple tomato tissues, such as hypocotyls, stems and purple fruits, various anthocyanins accumulate. These molecules have characteristic patterns of modification, including hydroxylations, methylations, glycosylations and acylations. The genetic basis for many of these modifications has not been fully elucidated, and nor has their role in the functioning of anthocyanins. In this paper, AnthOMT, an O-methyltransferase (OMT) mediating the methylation of anthocyanins, has been identified and functionally characterized using a combined metabolomics and transcriptomics approach. Gene candidates were selected from the draft tomato genome, and their expression was subsequently monitored in a tomato seedling system comprising three tissues and involving several time points. In addition, we also followed gene expression in wild-type red and purple transgenic tomato fruits expressing Rosea1 and Delila transcription factors. Of the 57 candidates identified, only a single OMT gene showed patterns strongly correlating with both accumulation of anthocyanins and expression of anthocyanin biosynthesis genes. This candidate (AnthOMT) was compared to a closely related caffeoyl CoA OMT by recombinant expression in Escherichia coli, and then tested for substrate specificity. AnthOMT showed a strong affinity for glycosylated anthocyanins, while other flavonoid glycosides and aglycones were much less preferred. Gene silencing experiments with AnthOMT resulted in reduced levels of the predominant methylated anthocyanins. This confirms the role of this enzyme in the diversification of tomato anthocyanins.
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.
Mathematical Models Light Up Plant Signaling
Chew, Y.H. ; Smith, R.W. ; Jones, H.J. ; Seaton, D.D. ; Grima, R. ; Halliday, K.J. - \ 2014
The Plant Cell 26 (2014)1. - ISSN 1040-4651 - p. 5 - 20.
arabidopsis circadian clock - recombinant inbred lines - flowering-time - transcription factor - hypocotyl growth - floral induction - oryza-sativa - rice genome - cellular interactions - photoperiodic control
Plants respond to changes in the environment by triggering a suite of regulatory networks that control and synchronize molecular signaling in different tissues, organs, and the whole plant. Molecular studies through genetic and environmental perturbations, particularly in the model plant Arabidopsis thaliana, have revealed many of the mechanisms by which these responses are actuated. In recent years, mathematical modeling has become a complementary tool to the experimental approach that has furthered our understanding of biological mechanisms. In this review, we present modeling examples encompassing a range of different biological processes, in particular those regulated by light. Current issues and future directions in the modeling of plant systems are discussed.
Omics and modeling approaches approaches for understanding regulation of asymmetric cell divisions in Arabidopsis and other angiosperm plants.
Kajala, K. ; Ramakrishna, A. ; Fisher, A. ; Bergmann, D.C. ; Smet, I. De; Sozzani, R. ; Weijers, D. ; Brady, S.M. - \ 2014
Annals of Botany 113 (2014)7. - ISSN 0305-7364 - p. 1083 - 1105.
lateral root initiation - receptor-like kinase - vascular-tissue-development - dependent auxin gradients - laser-ablation analysis - of-function mutation - apical-basal axis - iii hd-zip - transcription factor - gene-expression
Background Asymmetric cell divisions are formative divisions that generate daughter cells of distinct identity. These divisions are coordinated by either extrinsic (‘niche-controlled’) or intrinsic regulatory mechanisms and are fundamentally important in plant development. Scope This review describes how asymmetric cell divisions are regulated during development and in different cell types in both the root and the shoot of plants. It further highlights ways in which omics and modelling approaches have been used to elucidate these regulatory mechanisms. For example, the regulation of embryonic asymmetric divisions is described, including the first divisions of the zygote, formative vascular divisions and divisions that give rise to the root stem cell niche. Asymmetric divisions of the root cortex endodermis initial, pericycle cells that give rise to the lateral root primordium, procambium, cambium and stomatal cells are also discussed. Finally, a perspective is provided regarding the role of other hormones or regulatory molecules in asymmetric divisions, the presence of segregated determinants and the usefulness of modelling approaches in understanding network dynamics within these very special cells. Conclusions Asymmetric cell divisions define plant development. High-throughput genomic and modelling approaches can elucidate their regulation, which in turn could enable the engineering of plant traits such as stomatal density, lateral root development and wood formation.
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.
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.
Integration of growth and patterning during vascular tissue formation in Arabidopsis
Rybel, B. De; Adibi, M. ; Breda, A.S. ; Wendrich, J.R. ; Smit, M.E. ; Novák, O. ; Yamaguchi, N. ; Yoshida, S. ; Isterdael, G. van; Palovaara, J. ; Nijsse, B. ; Boekschoten, M.V. ; Hooiveld, G.J.E.J. ; Beeckman, T. ; Wagner, D. ; Ljung, K. ; Fleck, C. ; Weijers, D. - \ 2014
Science 345 (2014)6197. - ISSN 0036-8075 - 9 p.
dependent auxin gradients - solid-phase extraction - shoot apical meristem - transcription factor - root - cytokinins - purification - expression - transport - genes
Coordination of cell division and pattern formation is central to tissue and organ development, particularly in plants where walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these hormones converge upon tissue development. We identify a genetic network that reinforces an early embryonic bias in auxin distribution to create a local, nonresponding cytokinin source within the root vascular tissue. Experimental and theoretical evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions. We further demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue.
Exploring the molecular link between swim-training and caudal fin development in zebrafish (Danio rerio) larvae
Fiaz, A.W. ; Leon, K.M. ; Leeuwen, J.L. van; Kranenbarg, S. - \ 2014
Journal of Applied Ichthyology 30 (2014)4. - ISSN 0175-8659 - p. 753 - 761.
transcription factor - mechanical control - gene-expression - bone - activation - forces - tissue - transhydrogenase - osteoblasts - contributes
In vitro and in vivo studies have shown that mechanical forces play an important role during development. The molecular mechanisms via which mechanical forces regulate development have been extensively investigated by in vitro studies. However, knowledge about the molecular pathways that mediate the effect of mechanical forces during development in vivo is limited. Previously, we showed that swim-training increased maximum normalized curvatures in the caudal fin (suggesting that the caudal fin experienced increased mechanical loads) and prioritized the development of skeletal structures in the caudal fin. Therefore, we used the zebrafish caudal fin to explore the molecular link between an increased swimming activity and development in vivo. Whole genome microarray analysis of caudal fins of zebrafish subjected to swim-training and control fish identified 46 genes which were up-regulated with a fold change of 1.5 or larger at 10 dpf. Fourteen genes were expressed specifically in the following tissues in the caudal fin: the neural tube, the tissue surrounding the hypurals, the finfold, or muscle fibers. Subsequently, we identified two muscle specific genes, aste1 (asteroid homolog 1) and zgc:65811, which showed an increased expression specifically in the caudal fin in response to swim-training. This makes these genes interesting candidate genes for further research on the molecular link between mechanical forces and caudal fin development. Our study is the first to investigate the molecular link between swim-training and caudal fin development and offers a system that can provide a deeper understanding of the link between mechanical and molecular signals during development in vivo.
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