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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    Revisiting the Role of Master Regulators in Tomato Ripening
    Wang, Rufang ; Angenent, Gerco C. ; Seymour, Graham ; Maagd, Ruud A. de - \ 2020
    Trends in Plant Science 25 (2020)3. - ISSN 1360-1385 - p. 291 - 301.
    CRISPR- mutagenesis - gain-of-function - mutants - ripening - tomato - transcription factors

    The study of transcriptional regulation of tomato ripening has been led by spontaneous mutations in transcription factor (TF) genes that completely inhibit normal ripening, suggesting that they are ‘master regulators’. Studies using CRISPR/Cas9 mutagenesis to produce knockouts of the underlying genes indicate a different picture, suggesting that the regulation is more robust than previously thought. This requires us to revisit our model of the regulation of ripening and replace it with one involving a network of partially redundant components. At the same time, the fast rise of CRISPR/Cas mutagenesis, resulting in unexpectedly weak phenotypes, compared with knockdown technology, suggests that compensatory mechanisms may obscure protein functions. This emphasises the need for assessment of these mechanisms in plants and for the careful design of mutagenesis experiments.

    Auxin Response Factors : Output control in auxin biology
    Roosjen, Mark ; Paque, Sébastien ; Weijers, Dolf - \ 2018
    Journal of Experimental Botany 69 (2018)2. - ISSN 0022-0957 - p. 179 - 188.
    Auxin - auxin response - gene regulation - plant development - signal transduction - transcription factors
    The phytohormone auxin is involved in almost all developmental processes in land plants. Most, if not all, of these processes are mediated by changes in gene expression. Auxin acts on gene expression through a short nuclear pathway that converges upon the activation of a family of DNA-binding transcription factors. These AUXIN RESPONSE FACTORS (ARFs) are thus the effector of auxin response and translate the chemical signal into the regulation of a defined set of genes. Given the limited number of dedicated components in auxin signaling, distinct properties among the ARF family probably contribute to the establishment of multiple unique auxin responses in plant development. In the two decades following the identification of the first ARF in Arabidopsis, much has been learnt about how these transcription factors act, and how they generate unique auxin responses. Progress in genetics, biochemistry, genomics, and structural biology has helped to develop mechanistic models for ARF action. However, despite intensive efforts, many central questions are yet to be addressed. In this review, we highlight what has been learnt about ARF transcription factors, and identify outstanding questions and challenges for the near future.
    MADS evolution : insights into evolutionary changes in transcription factors and their binding sites
    Bruijn, Suze-Annigje de - \ 2017
    Wageningen University. Promotor(en): G.C. Angenent, co-promotor(en): K. Kaufmann. - Wageningen : Wageningen University - ISBN 9789463436700 - 195
    plants - evolution - mads-box proteins - transcription factors - flowers - molecular biology - planten - evolutie - mads-box eiwitten - transcriptiefactoren - bloemen - moleculaire biologie

    Although most flowers follow a conserved 'bauplan' consisting of sepals, petals, stamens and carpels, there is a remarkable amount of morphological diversity. Interestingly, all flowers are specified by the conserved (A)BCE-model. Most of the transcription factors in this model belong to the MADS-domain family. We examined how these transcription factors and their binding sites in the genome evolved, as a first step to elucidate how diversity in flower morphology has been created.

    We analyzed the evolution of transcription factor binding sites by comparing binding sites of the major floral regulator SEPALLATA3 between two closely related Arabidopsis species, as well as between A. thaliana ecotypes. We found substantial overlap in transcription factor binding profiles between ecotypes, but limited overlap between the related species.

    We also assessed how transcription factors themselves can change in their properties by analyzing the divergence between paralogs. We examined how the PISTILLATA paralogs in Tarenaya hassleriana diverged, as this species occupies an interesting position in the eudicot phylogeny. We also studied whether divergence of the APETALA3 paralogs in Aquilegia could explain the specification of an additional floral organ in this genus. In both cases, we conclude that the paralogs diverged from each other in their biochemical properties.

    In the future, it would be interesting to assess how these changes in transcription factors and their binding sites affect floral regulatory networks and ultimately floral shape.

    MADS specificity : Unravelling the dual function of the MADS domain protein FRUITFULL
    Mourik, Hilda van - \ 2017
    Wageningen University. Promotor(en): G.C. Angenent, co-promotor(en): K. Kaufmann. - Wageningen : Wageningen University - ISBN 9789463436724 - 199
    transcription factors - dna binding proteins - arabidopsis thaliana - mads-box proteins - protein-protein interactions - gene regulation - transcriptiefactoren - dna-bindende eiwitten - arabidopsis thaliana - mads-box eiwitten - eiwit-eiwit interacties - genregulatie

    Encrypted in the DNA lays most information needed for the development of an organism. The transcription of this information into precise patterns of gene activity results in the development of different cell types, organs, and developmental structures. Moreover, transcriptional regulation enables an organism to respond to changing environmental conditions. Essential for the regulation of transcription are DNA-binding transcription factors (TFs). TFs bind the DNA in a sequence-specific fashion. Upon binding of a TF to its DNA binding site, TFs typically activate or repress the transcription of nearby genes. To better understand transcriptional regulation it is essential to study DNA binding specificity of TFs.

    In the last decades, technological advances allowed the development of high-throughput methods to study protein-DNA interactions. Traditional in vitro methods study one or a few interactions, while new high-throughput methods can determine TF specificity by measuring relative DNA-binding affinities against a large collection or even all possible binding sites. Several high-throughput techniques to study TF-DNA interactions are discussed in Chapter 1 of this thesis. These new technologies and methods resulted in a fast growing number of studies on DNA binding specificities of TFs, expanding the knowledge about TF specificity. A review on the current knowledge of TF DNA binding specificity is described in Chapter 1.

    One aspect that influences DNA binding of TFs are differences in ability to form protein-protein interactions. The aim of this thesis was to study the role of protein-protein interactions in determining DNA binding specificity of a developmental regulatory MADS domain TF in Arabidopsis thaliana. While the members of the MADS-box protein family have many, diverse in vivo functions, all members bind in vitro to a 10-bp motif called the CArG-box. Moreover, studies demonstrated that closely related MADS proteins are expressed in the same cells, therefore encountering the same DNA accessibility and DNA methylation patterns, but bind different in vivo targets. Interestingly, MADS domain proteins bind DNA obligatorily as homo- and heterodimers and the interactions between MADS domain proteins are highly protein specific. Hence, MADS domain proteins are a perfect model system to study the influence of intra-family protein interactions on DNA binding specificity.

    To study the influence of protein-protein interactions on DNA-binding specificity this work focusses on one specific MADS domain protein, FRUITFULL (FUL). FUL is expressed at two stages during flower development and, in both stages FUL has highly diverse functions. In Chapter 2 we demonstrate using RNA-seq that FUL regulates different sets of target genes in the two stages. Moreover, using ChIP-seq we show that FUL genomic DNA binding is partly tissue-specific. These tissue-specifically bound and regulated genes are in line with the known dual functions of FUL during development. Interestingly, using protein complex immunoprecipitation for the two studied tissues/stages we show that the interactions of FUL with other MADS domain proteins are also tissue-specific. To determine whether the tissue-specific in vivo binding pattern are due to differences in DNA binding specificity of the FUL-MADS dimers, we studied the DNA binding specificities of the different protein complexes using SELEX-seq. The SELEX-seq results show that although all tested dimers preferably bind the canonical binding motif of MADS domain proteins, different dimers have different preferences for nucleotides within and surrounding the canonical binding site. Hence, different MADS domain dimers have different in vitro DNA binding specificities. By mapping the SELEX-seq affinities to the genome we were able to compare these results with in vivo tissue-specific ChIP-seq data. This analysis revealed a strong correlation between tissue-specific dimer affinities and tissue-specific genomic binding sites of FUL. Hence, we show that the choice of MADS dimerization partner influences DNA binding specificity, highlighting the role of intra-family protein interactions in defining DNA binding specificity.

    To allow other researchers to determine genome-wide DNA binding of TFs Chapter 3 provides a step-by-step guide for ChIP-seq experiments and computational analysis. The protocol is designed for wet-lab biologists to perform ChIP-seq experiments and analyse their own ChIP-seq data.

    Using the genome-wide DNA binding patterns determined by ChIP-seq, Chapter 4 and Chapter 5 take a more detailed look at some of the genes directly bound by FUL. In Chapter 4, we demonstrate a connection between developmentally and environmentally regulated growth programs. We studied a gene directly bound by FUL in pistil tissue, SMALL AUXIN UPREGULATED RNA 10 (SAUR10). SAUR10 expression is regulated by FUL in multiple tissues, among others cauline leaves, stems, and branches. The results show that the expression of SAUR10 at the abaxial side of branches is influenced by a combination of environmental and developmental regulated growth programs: hormones, light conditions, and FUL binding. This spatial regulation possibly affects the angle between the side branches and the main inflorescence stem. Additionally, we discuss several other FUL target genes involved in hormone pathways and light conditions.

    Chapter 5 focusses on the putative direct targets of FUL in IM tissue. Among the putative direct targets two genes involved in flavonoid synthesis were identified, FLAVONOID SYNTHESE 1 (FLS1) and UDP-GLUCOSYL TRANSFERASE 78D3 (UGT78D3). Interestingly, similar to the ful-7 mutant, the fls1 mutant is late flowering. Moreover, expression data exposed an increased gene expression for both FLS1 and UGT78D3 in developing meristems and showed FLS1 expression to be influenced by light conditions. We report the first link between the MADS domain protein FUL and flavonoid synthesis in Arabidopsis. Moreover, our results indicate a possible link between flavonoids and flowering time.

    In Chapter 6 I discuss the findings of this thesis and make suggestions for further research. Taken together, the work in this thesis shows that intra-family protein interactions can influence DNA-binding specificity of a protein. Thereby these protein-protein interactions can influence genome-wide binding patterns and, as a result, the function of a protein. Moreover, by studying several putative direct targets of FUL in more detail, we demonstrated a connection between development and environment in growth-regulated programs. Interestingly, the FUL target SAUR10 is repressed by FUL in several tissues, including cauline leaves, inflorescence stems, and branches. However, no influence of FUL on SAUR10 expression could be detected in the pistil. So, despite the binding of FUL to the promotor of SAUR10 in the pistil, this binding does not result in gene regulation. This finding reflects the complex relation between TF occupancy and gene regulation, further research is needed to better understand this relation. Moreover, besides MADS domain protein interactions, we found FUL to interact with several proteins of other families. The role of these cross-family protein interactions in cooperative gene regulation is not fully understood and will be an important research topic in the coming years.

    Studies on global transcriptional regulator EBR1 and genome-wide gene expression in the fungal plant pathogen Fusarium graminearum
    Zhao, C. - \ 2015
    Wageningen University. Promotor(en): Pierre de Wit; D. Tang, co-promotor(en): Theo van der Lee. - Wageningen : Wageningen University - ISBN 9789462575998 - 167
    plant pathogenic fungi - gibberella zeae - transcription factors - gene expression - gene mapping - genomics - plantenziekteverwekkende schimmels - gibberella zeae - transcriptiefactoren - genexpressie - genkartering - genomica

    Abstract of PhD thesis

    Fusarium graminearum is a destructive plant pathogen that causes Fusarium head blight (FHB) on many crops, such as wheat, barley, rye and oat. In the first part of this thesis, we studied a transcription factor EBR1 that is required for radial growth and virulence in F. graminearum. Mutant ebr1 shows reduced apical dominance of the hyphal tip and loses its ability to penetrate the rachis of the spikelets. Subcellular localization analysis showed that EBR1 protein is exclusively localized in the nucleus of both conidia and hyphae. In the second part of thesis, by using RNA-Seq data, we revised 655 incorrectly predicted gene models and identified 231 genes with two or more alternative splice variants in F. graminearum. Furthermore, we analyzed the genome-wide gene expression pattern and found that genes locate in non-conserved regions of chromosomes showed relatively lower expression level. We further provided evidence showing that the non-conserved regions are full of gene relocations in F. graminearum.

    Applied and fundamental aspects of BABY BOOM-mediated regeneration
    Heidmann, I.A. - \ 2015
    Wageningen University. Promotor(en): Gerco Angenent, co-promotor(en): Kim Boutilier. - Wageningen : Wageningen University - ISBN 9789462574663 - 180
    nicotiana tabacum - capsicum annuum - verjonging - transcriptiefactoren - somatische embryogenese - auxinen - moleculaire biologie - nicotiana tabacum - capsicum annuum - regeneration - transcription factors - somatic embryogenesis - auxins - molecular biology

    Keywords: Somatic embryogenesis, Transcription factor, AINTEGUMENTA-LIKE, BABY BOOM, BBM, Sweet Pepper Transformation

    Title: Applied and Fundamental Aspects of BBM-mediated Regeneration

    Author: Iris Heidmann

    Catergories: Plant regeneration, Plant transformation, transcription factor, somatic embryogenesis

    Plant regeneration from tissues or single cells is essential for plant propagation. Efficient regeneration can be archieved through somatic embryogenesis using the plant growth regulator auxin or overexpression of specific transcription factors, but the underlying mechanisms are poorly understood. The potency of the BABY BOOM (BBM) AINTEGUMENTA-LIKE transcription factor to induce somatic embryogenesis in crop (sweet pepper) and model species (tobacco) was investigated. It was found that the introduction of BBM into sweet pepper, which is recalcitrant for transformation, enhanced the regeneration of transgenic plants. Exogenous cytokinin was necessary to induce somatic embryogenesis in both tobacco and sweet pepper. The mechanism underlying BBM-mediated somatic embryogenesis was studied in Arabidopsis by identifying BBM target genes (ChIPSeq). Genes controlling zygotic embryo identity and maturation (LAFL), as well as auxin biosynthesis (TAA1, YUCCA) and transport (PIN) are BBM targets. Mutant analysis and chemical inhibition studies showed that these genes play positive roles in BBM-induced somatic embryogenesis.

    Functional Divergence of Two Secreted Immune Proteases of Tomato
    Ilyas, M. ; Hörger, A.C. ; Bozkurt, T.O. ; Burg, H.A. van den; Kaschani, F. ; Kaiser, M. ; Belhaj, K. ; Smoker, M. ; Joosten, M. ; Kamoun, S. ; Hoorn, R.A.L. van der - \ 2015
    Current Biology 25 (2015)17. - ISSN 0960-9822 - p. 2300 - 2306.
    cf-2-dependent disease resistance - pathogen effectors - transcription factors - provides insights - genome sequence - plant-pathogens - gene - defense - target - specialization
    Rcr3 and Pip1 are paralogous secreted papain-like proteases of tomato. Both proteases are inhibited by Avr2 from the fungal pathogen Cladosporium fulvum, but only Rcr3 acts as a co-receptor for Avr2 recognition by the tomato Cf-2 immune receptor [ 1, 2, 3 and 4]. Here, we show that Pip1-depleted tomato plants are hyper-susceptible to fungal, bacterial, and oomycete plant pathogens, demonstrating that Pip1 is an important broad-range immune protease. By contrast, in the absence of Cf-2, Rcr3 depletion does not affect fungal and bacterial infection levels but causes increased susceptibility only to the oomycete pathogen Phytophthora infestans. Rcr3 and Pip1 reside on a genetic locus that evolved over 36 million years ago. These proteins differ in surface-exposed residues outside the substrate-binding groove, and Pip1 is 5- to 10-fold more abundant than Rcr3. We propose a model in which Rcr3 and Pip1 diverged functionally upon gene duplication, possibly driven by an arms race with pathogen-derived inhibitors or by coevolution with the Cf-2 immune receptor detecting inhibitors of Rcr3, but not of Pip1.
    A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds
    Dias Costa, M.C. ; Righetti, K. ; Nijveen, H. ; Yazdanpanah, F. ; Ligterink, W. ; Buitink, J. ; Hilhorst, H.W.M. - \ 2015
    Planta 242 (2015)2. - ISSN 0032-0935 - p. 435 - 449.
    medicago-truncatula seeds - transcription factors - expression data - abiotic stress - dormancy - drought - identification - maturation - longevity - software
    Main conclusion During re-establishment of desiccation tolerance (DT), early events promote initial protection and growth arrest, while late events promote stress adaptation and contribute to survival in the dry state. Mature seeds of Arabidopsis thaliana are desiccation tolerant, but they lose desiccation tolerance (DT) while progressing to germination. Yet, there is a small developmental window during which DT can be rescued by treatment with abscisic acid (ABA). To gain temporal resolution and identify relevant genes in this process, data from a time series of microarrays were used to build a gene co-expression network. The network has two regions, namely early response (ER) and late response (LR). Genes in the ER region are related to biological processes, such as dormancy, acquisition of DT and drought, amplification of signals, growth arrest and induction of protection mechanisms (such as LEA proteins). Genes in the LR region lead to inhibition of photosynthesis and primary metabolism, promote adaptation to stress conditions and contribute to seed longevity. Phenotyping of 12 hubs in relation to re-establishment of DT with T-DNA insertion lines indicated a significant increase in the ability to re-establish DT compared with the wild-type in the lines cbsx4, at3g53040 and at4g25580, suggesting the operation of redundant and compensatory mechanisms. Moreover, we show that re-establishment of DT by polyethylene glycol and ABA occurs through partially overlapping mechanisms. Our data confirm that co-expression network analysis is a valid approach to examine data from time series of transcriptome analysis, as it provides promising insights into biologically relevant relations that help to generate new information about the roles of certain genes for DT.
    Characterization of the modes of action of deoxynivalenol (DON) in the human Jurkat T-cell line
    Katika, M.R. ; Hendriksen, P.J.M. ; Loveren, H. van; Peijnenburg, A.A.C.M. - \ 2015
    Journal of Immunotoxicology 12 (2015)3. - ISSN 1547-691X - p. 206 - 216.
    activated protein-kinases - endoplasmic-reticulum stress - kappa-b activation - gene-expression - trichothecene deoxynivalenol - vomitoxin deoxynivalenol - transcription factors - cytokine production - induced apoptosis - wheat products
    Deoxynivalenol (DON) is one of the most abundant mycotoxins worldwide and mostly detected in cereals and grains. As such, DON poses a risk for many adverse health effects to human and animals. In particular, immune cells are very sensitive to DON, with the initiating step leading to toxicity being a binding to the eukaryotic 60S ribosomal subunit and induction of ribotoxic stress. The present study aimed to: (1) extend insight into the mechanism of action (MOA) of DON in immune cells; and (2) understand why immune cells are more sensitive to DON than most other cell types. Previously published microarray studies have described the effects of DON on immune cells. To build upon these findings, here, immunocytological and biochemical studies were performed using human T-lymphocyte Jurkat cells that were exposed for 3¿h to 0.5¿µM DON. Induction of ER stress by DON was confirmed by immunocytology demonstrating increased protein expression of two major ER stress markers ATF3 and DDIT3. T-cell activation was confirmed by induction of phosphorylation of protein kinases JNK and AKT, activation of NF-¿B (p65), and increased expression of NFAT target gene NUR77; each of these are known inducers of the T-cell activation response. Induction of an oxidative stress response was also confirmed by monitoring the nuclear translocation of major oxidative stress markers NRF2 and KEAP1, as well as by changes (i.e. decreases) in cell levels of reduced glutathione. Lastly, this study showed that DON induced cleavage of caspase-3, an event known to mediate apoptosis. Taken together, these results allowed us to formulate a potential mechanism of action of DON in immune cells, i.e. binding to eukaryotic 60S ribosomal subunit¿¿¿ribotoxic stress¿¿¿ER stress¿¿¿calcium release from the ER into cytoplasm¿¿¿T-cell activation and oxidative stress¿¿¿apoptosis. It is proposed that immune cells are more sensitive to DON than other cell types due to the induction of a T-cell activation response by increased intracellular calcium levels.
    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.
    PLETHORA gradient formation mechanism separates auxin responses
    Mahonen, A.P. ; Tusscher, K. ten; Diaz Trivino, S. ; Heidstra, R. ; Scheres, B. - \ 2014
    Nature 515 (2014). - ISSN 0028-0836 - p. 125 - 129.
    monocyte chemoattractant protein-1 - inflammatory breast-cancer - arabidopsis root apex - stem-cell niche - transcription factors - genomics browser - carcinoma cells - tumor - angiogenesis - expression
    During plant growth, dividing cells in meristems must coordinate transitions from division to expansion and differentiation, thus generating three distinct developmental zones: the meristem, elongation zone and differentiation zone1. Simultaneously, plants display tropisms, rapid adjustments of their direction of growth to adapt to environmental conditions. It is unclear how stable zonation is maintained during transient adjustments in growth direction. In Arabidopsis roots, many aspects of zonation are controlled by the phytohormone auxin and auxin-induced PLETHORA (PLT) transcription factors, both of which display a graded distribution with a maximum near the root tip2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12. In addition, auxin is also pivotal for tropic responses13, 14. Here, using an iterative experimental and computational approach, we show how an interplay between auxin and PLTs controls zonation and gravitropism. We find that the PLT gradient is not a direct, proportionate readout of the auxin gradient. Rather, prolonged high auxin levels generate a narrow PLT transcription domain from which a gradient of PLT protein is subsequently generated through slow growth dilution and cell-to-cell movement. The resulting PLT levels define the location of developmental zones. In addition to slowly promoting PLT transcription, auxin also rapidly influences division, expansion and differentiation rates. We demonstrate how this specific regulatory design in which auxin cooperates with PLTs through different mechanisms and on different timescales enables both the fast tropic environmental responses and stable zonation dynamics necessary for coordinated cell differentiation.
    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.
    Aanwezigheid van een gen is nog lang geen garantie : Moleculaire en genetische kennis maakt sprongen
    Angenent, G.C. ; Kierkels, T. ; Heuvelink, E. - \ 2014
    Onder Glas 11 (2014)9. - p. 18 - 19.
    glastuinbouw - plantenveredeling - genetica - rassen (planten) - resistentieveredeling - dna - transcriptiefactoren - genexpressie - eiwitten - greenhouse horticulture - plant breeding - genetics - varieties - resistance breeding - dna - transcription factors - gene expression - proteins
    Plantenveredeling staat tegenwoordig heel ver van de teler af. De reden is dat de moleculaire en genetische kennis enorme sprongen heeft gemaakt. Er is bovendien een hele geheimtaal ontstaan, waardoor de veredelaar vooral goed kan praten met vakgenoten en veel minder met de teler. Hier een aantal recente inzichten op een rij.
    Safety aspects of genetically modified crops with abiotic stress tolerance
    Liang, C. ; Prins, T.W. ; Wiel, C.C.M. van de; Kok, E.J. - \ 2014
    Trends in Food Science and Technology 40 (2014)1. - ISSN 0924-2244 - p. 115 - 122.
    risk-assessment - salt tolerance - transcription factors - salinity tolerance - transgenic plants - drought tolerance - gene flow - vegetable crops - gm crops - ipt gene
    Abiotic stress, such as drought, salinity, and temperature extremes, significantly reduce crop yields. Hence, development of abiotic stress-tolerant crops by modern biotechnology may contribute to global food security. Prior to introducing genetically modified crops with abiotic stress tolerance to the market, a food and environmental safety assessment is generally required. Although worldwide harmonised comparative approach is currently provided, risk assessors still face challenges to assess genetically modified crops with abiotic stress-tolerance. Here, we discuss current developments of abiotic stress tolerance as well as issues concerning food and environmental safety assessment of these crops, including current approaches, challenges and future directions.
    Transcriptional regulation of nodule development and senescence in Medicago truncatula
    Karmarkar, V.M. - \ 2014
    Wageningen University. Promotor(en): Ton Bisseling, co-promotor(en): Rene Geurts. - Wageningen : Wageningen University - ISBN 9789462570214 - 110
    medicago truncatula - plantenontwikkeling - veroudering - wortelknolletjes - stikstoffixatie - genexpressie - symbiose - transcriptie - transcriptiefactoren - medicago truncatula - plant development - senescence - root nodules - nitrogen fixation - gene expression - symbiosis - transcription - transcription factors
    AINTEGUMENTA-LIKE proteins: hubs in a plethora of networks
    Horstman, A. ; Willemsen, V. ; Boutilier, K.A. ; Heidstra, R. - \ 2014
    Trends in Plant Science 19 (2014)3. - ISSN 1360-1385 - p. 146 - 157.
    stem-cell niche - ethylene-responsive element - lateral root initiation - homeodomain finger proteins - actin-depolymerizing factor - homeotic gene apetala2 - shoot apical meristem - dna-binding proteins - transcription factors - arabidopsis root
    Members of the AINTEGUMENTA-LIKE (AIL) family of APETALA 2/ETHYLENE RESPONSE FACTOR (AP2/ERF) domain transcription factors are expressed in all dividing tissues in the plant, where they have central roles in developmental processes such as embryogenesis, stem cell niche specification, meristem maintenance, organ positioning, and growth. When overexpressed, AIL proteins induce adventitious growth, including somatic embryogenesis and ectopic organ formation. The Arabidopsis (Arabidopsis thaliana) genome contains eight AIL genes, including AINTEGUMENTA, BABY BOOM, and the PLETHORA genes. Studies on these transcription factors have revealed their intricate relationship with auxin as well as their involvement in an increasing number of gene regulatory networks, in which extensive crosstalk and feedback loops have a major role.
    Understanding and identifying amino acid repeats
    Luo, H. ; Nijveen, H. - \ 2014
    Briefings in Bioinformatics 15 (2014)4. - ISSN 1467-5463 - p. 582 - 591.
    low-complexity regions - protein homology detection - intragenic tandem repeats - hidden markov-models - statistical significance - biological sequences - transcription factors - scoring schemes - evolution - identification
    Amino acid repeats (AARs) are abundant in protein sequences. They have particular roles in protein function and evolution. Simple repeat patterns generated by DNA slippage tend to introduce length variations and point mutations in repeat regions. Loss of normal and gain of abnormal function owing to their variable length are potential risks leading to diseases. Repeats with complex patterns mostly refer to the functional domain repeats, such as the well-known leucine-rich repeat and WD repeat, which are frequently involved in protein–protein interaction. They are mainly derived from internal gene duplication events and stabilized by ‘gate-keeper’ residues, which play crucial roles in preventing inter-domain aggregation. AARs are widely distributed in different proteomes across a variety of taxonomic ranges, and especially abundant in eukaryotic proteins. However, their specific evolutionary and functional scenarios are still poorly understood. Identifying AARs in protein sequences is the first step for the further investigation of their biological function and evolutionary mechanism. In principle, this is an NP-hard problem, as most of the repeat fragments are shaped by a series of sophisticated evolutionary events and become latent periodical patterns. It is not possible to define a uniform criterion for detecting and verifying various repeat patterns. Instead, different algorithms based on different strategies have been developed to cope with different repeat patterns. In this review, we attempt to describe the amino acid repeat-detection algorithms currently available and compare their strategies based on an in-depth analysis of the biological significance of protein repeats.
    Insight into the Genetic Components of Community Genetics: QTL Mapping of Insect Association in a Fast-Growing Forest Tree
    DeWoody, J. ; Viger, M. ; Lakatos, F. ; Tuba, K. ; Taylor, G. ; Smulders, M.J.M. - \ 2013
    PLoS ONE 8 (2013)11. - ISSN 1932-6203
    quantitative trait loci - genome-wide analysis - x populus-deltoides - plant hybrid zones - glutamate-receptor - arthropod community - molecular-genetics - short-rotation - segregation distortion - transcription factors
    Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common garden experiment. The F2 offspring of a hybrid poplar (Populus trichocarpa x P. deltoides) cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive and negative correlations were detected among damage categories and between sampling times. For example, sap suckers on leaves in June were positively correlated with sap suckers on leaves (P
    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.
    Resistant Starch Induces Catabolic but Suppresses Immune and Cell Division Pathways and Changes the Microbiome in Proximal Colon of Male Pigs
    Haenen, D. ; Souza Da Silva, C. ; Zhang, J. ; Koopmans, S.J. ; Bosch, G. ; Vervoort, J.J.M. ; Gerrits, W.J.J. ; Kemp, B. ; Smidt, H. ; Müller, M.R. ; Hooiveld, G.J.E.J. - \ 2013
    The Journal of Nutrition 143 (2013)12. - ISSN 0022-3166 - p. 1889 - 1898.
    chain fatty-acids - inflammatory-bowel-disease - endoplasmic-reticulum stress - butyrate-producing bacteria - activated receptor-gamma - human large-intestine - gene-expression - gastrointestinal-tract - transcription factors - gut microbiota
    Consumption of resistant starch (RS) has been associated with various intestinal health benefits, but knowledge on its effects on global gene expression in the colon is limited. The main objective of the current study was to identify genes affected by RS in the proximal colon to infer which biologic pathways were modulated. Ten 17-wk-old male pigs, fitted with a cannula in the proximal colon for repeated collection of tissue biopsy samples and luminal content, were fed a digestible starch (DS) diet or a diet high in RS (34%) for 2 consecutive periods of 14 d in a crossover design. Analysis of the colonic transcriptome profiles revealed that, upon RS feeding, oxidative metabolic pathways, such as the tricarboxylic acid cycle and ß-oxidation, were induced, whereas many immune response pathways, including adaptive and innate immune system, as well as cell division were suppressed. The nuclear receptor peroxisome proliferator-activated receptor ¿ (PPARG) was identified as a potential key upstream regulator. RS significantly (P <0.05) increased the relative abundance of several butyrate-producing microbial groups, including the butyrate producers Faecalibacterium prausnitzii and Megasphaera elsdenii, and reduced the abundance of potentially pathogenic members of the genus Leptospira and the phylum Proteobacteria. Concentrations in carotid plasma of the 3 main short-chain fatty acids acetate, propionate, and butyrate were significantly higher with RS consumption compared with DS consumption. Overall, this study provides novel insights on effects of RS in proximal colon and contributes to our understanding of a healthy diet.
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