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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    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.
    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.
    Epistatic natural allelic variation reveals a function of AGAMOUS-LIKE6 in axillary bud formation in Arabidopsis
    Huang, X. ; Effgen, S. ; Meyer, R.C. ; Theres, K. ; Koornneef, M. - \ 2012
    The Plant Cell 24 (2012)6. - ISSN 1040-4651 - p. 2364 - 2379.
    mads-box gene - quantitative trait loci - organ-identity proteins - inbred line population - transcription factor - meristem development - ectopic expression - apical dominance - flowering time - complex-formation
    In the Arabidopsis Multiparent Recombinant Inbred Line mapping population, a limited number of plants were detected that lacked axillary buds in most of the axils of the cauline (stem) leaves, but formed such buds in almost all rosette axils. Genetic analysis showed that polymorphisms in at least three loci together constitute this phenotype, which only occurs in late-flowering plants. Early flowering is epistatic to two of these loci, called REDUCED SHOOT BRANCHING1 (RSB1) and RSB2, which themselves do not affect flowering time. Map-based cloning and confirmation by transformation with genes from the region where RSB1 was identified by fine-mapping showed that a specific allele of AGAMOUS-Like6 from accession C24 conferred reduced branching in the cauline leaves. Site-directed mutagenesis in the Columbia allele revealed the causal amino acid substitution, which behaved as dominant negative, as was concluded from a loss-of-function mutation that showed the same phenotype in the late-flowering genetic background. This causal allele occurs at a frequency of 15% in the resequenced Arabidopsis thaliana accessions and correlated with reduced stem branching only in late-flowering accessions. The data show the importance of natural variation and epistatic interactions in revealing gene function
    Characterization of SOC1’s Central Role in Flowering by the Identification of Its Upstream and Downstream Regulators1[C][W]
    Immink, R.G.H. ; Posé, D. ; Ferrario, S.I.T. ; Ott, F. ; Kaufmann, K. ; Valentim, F.L. ; Folter, S. de; Wal, F. van der; Dijk, A.D.J. van; Schmid, M. ; Angenent, G.C. - \ 2012
    Plant Physiology 160 (2012)1. - ISSN 0032-0889 - p. 433 - 449.
    floral organ identity - mads domain proteins - time gene soc1 - arabidopsis-thaliana - transcription factor - homeotic gene - target genes - negative regulator - ectopic expression - meristem identity
    The transition from vegetative to reproductive development is one of the most important phase changes in the plant life cycle. This step is controlled by various environmental signals that are integrated at the molecular level by so-called floral integrators. One such floral integrator in Arabidopsis (Arabidopsis thaliana) is the MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Despite extensive genetic studies, little is known about the transcriptional control of SOC1, and we are just starting to explore the network of genes under the direct control of SOC1 transcription factor complexes. Here, we show that several MADS domain proteins, including SOC1 heterodimers, are able to bind SOC1 regulatory sequences. Genome-wide target gene analysis by ChIP-seq confirmed the binding of SOC1 to its own locus and shows that it also binds to a plethora of flowering-time regulatory and floral homeotic genes. In turn, the encoded floral homeotic MADS domain proteins appear to bind SOC1 regulatory sequences. Subsequent in planta analyses revealed SOC1 repression by several floral homeotic MADS domain proteins, and we show that, mechanistically, this depends on the presence of the SOC1 protein. Together, our data show that SOC1 constitutes a major hub in the regulatory networks underlying floral timing and flower development and that these networks are composed of many positive and negative autoregulatory and feedback loops. The latter seems to be crucial for the generation of a robust flower-inducing signal, followed shortly after by repression of the SOC1 floral integrator.
    Intercellular transport of epidermis-expressed MADS domain transcription factors and their effect on plant morphology and floral transition
    Urbanus, S.L. ; Martinelli, A.P. ; Dinh, Q.D. ; Aizza, L.C.B. ; Dornelas, M. ; Angenent, G.C. ; Immink, G.H. - \ 2010
    The Plant Journal 63 (2010)3. - ISSN 0960-7412 - p. 60 - 72.
    homeotic gene apetala3 - stem-cell maintenance - organ identity - arabidopsis-thaliana - flower development - homeobox genes - ectopic expression - meristem identity - ovule development - pound-foolish
    During the lifetime of an angiosperm plant various important processes such as floral transition, specification of floral organ identity and floral determinacy, are controlled by members of the MADS domain transcription factor family. To investigate the possible non-cell-autonomous function of MADS domain proteins, we expressed GFP-tagged clones of AGAMOUS (AG), APETALA3 (AP3), PISTILLATA (PI) and SEPALLATA3 (SEP3) under the control of the MERISTEMLAYER1 promoter in Arabidopsis thaliana plants. Morphological analyses revealed that epidermal overexpression was sufficient for homeotic changes in floral organs, but that it did not result in early flowering or terminal flower phenotypes that are associated with constitutive overexpression of these proteins. Localisations of the tagged proteins in these plants were analysed with confocal laser scanning microscopy in leaf tissue, inflorescence meristems and floral meristems. We demonstrated that only AG is able to move via secondary plasmodesmata from the epidermal cell layer to the subepidermal cell layer in the floral meristem and to a lesser extent in the inflorescence meristem. To study the homeotic effects in more detail, the capacity of trafficking AG to complement the ag mutant phenotype was compared with the capacity of the non-inwards-moving AP3 protein to complement the ap3 mutant phenotype. While epidermal expression of AG gave full complementation, AP3 appeared not to be able to drive all homeotic functions from the epidermis, perhaps reflecting the difference in mobility of these proteins
    Tagging of MADS domain proteins for chromatin immunoprecipitation
    Folter, S. de; Urbanus, S.L. ; Zuijlen, L. ; Kaufmann, K. ; Angenent, G.C. - \ 2007
    BMC Plant Biology (2007). - ISSN 1471-2229 - p. 7 - 47.
    floral homeotic gene - arabidopsis fruit-development - box gene - recombinant proteins - regulatory elements - negative regulation - ectopic expression - flower development - organ identity - purification
    Most transcription factors fulfill their role in complexes and regulate their target genes upon binding to DNA motifs located in upstream regions or introns. To date, knowledge about transcription factor target genes and their corresponding transcription factor binding sites are still very limited. Two related methods that allow in vivo identification of transcription factor binding sites are chromatin immunoprecipitation (ChIP) and chromatin affinity purification (ChAP). For ChAP, the protein of interest is tagged with a peptide or protein, which can be used for affinity purification of the protein-DNA complex and hence, the identification of the target gene.
    Heterologous expression of the BABY BOOM AP2/ERF transcription factor enhances the regeneration capacity of tobacco (Nicotiana tabacum L.)
    Srinivasan, C. ; Liu, Z. ; Heidmann, I. ; Supena, E.D.J. ; Fukuoka, H. ; Joosen, R.V.L. ; Lambalk, J. ; Angenent, G.C. ; Scorza, R. ; Custers, J.B.M. ; Boutilier, K.A. - \ 2007
    Planta 225 (2007)2. - ISSN 0032-0935 - p. 341 - 351.
    inducible gene-expression - transgenic tobacco - somatic embryogenesis - arabidopsis-thaliana - ectopic expression - apetala2-like gene - plant-regeneration - embryo development - hormone-levels - homeotic gene
    Gain-of-function studies have shown that ectopic expression of the BABY BOOM (BBM) AP2/ERF domain transcription factor is sufficient to induce spontaneous somatic embryogenesis in Arabidopsis (Arabidopsis thaliana (L.) Heynh) and Brassica napus (B. napus L.) seedlings. Here we examined the effect of ectopic BBM expression on the development and regenerative capacity of tobacco (Nicotiana tabacum L.) through heterologous expression of Arabidopsis and B. napus BBM genes. 35S::BBM tobacco lines exhibited a number of the phenotypes previously observed in 35S::BBM Arabidopsis and B. napus transgenics, including callus formation, leaf rumpling, and sterility, but they did not undergo spontaneous somatic embryogenesis. 35S::BBM plants with severe ectopic expression phenotypes could not be assessed for enhanced regeneration at the seedling stage due to complete male and female sterility of the primary transformants, therefore fertile BBM ectopic expression lines with strong misexpression phenotypes were generated by expressing a steroid-inducible, post-translationally controlled BBM fusion protein (BBM:GR) under the control of a 35S promoter. These lines exhibited spontaneous shoot and root formation, while somatic embryogenesis could be induced from in-vitro germinated seedling hypocotyls cultured on media supplemented with cytokinin. Together these results suggest that ectopic BBM expression in transgenic tobacco also activates cell proliferation pathways, but differences exist between Arabidopsis/B. napus and N. tabacum with respect to their competence to respond to the BBM signalling molecule
    Isolation and characterization of an AGAMOUS homologue from cocoa
    Chaidamsari, T. ; Sugiarit, H. ; Santoso, D. ; Angenent, G.C. ; Maagd, R.A. de - \ 2006
    Plant Science 170 (2006)5. - ISSN 0168-9452 - p. 968 - 975.
    mads-box genes - ectopic expression - flower development - transcription factors - arabidopsis - plants - transformation - theobroma - evolution - cacao
    We report the cloning of a cDNA from TcAG, an AG (Arabidopsis thaliana MADS-box C-type transcription factor gene AGAMOUS) homologue from cocoa (Theobroma cacao L.). TcAG was in the cocoa flower expressed primarily in stamens and ovaries, comparable to AG in Arabidopsis. Additionally, we found that TcAG is also expressed in the fruit (pod) wall and during its entire development, as well as in the fruit pulp. Ectopic expression of TcAG in transgenic A. thaliana plants resulted in a range of weak to strong apetala2 (ap2) mutant-like phenotypes as well as early flowering and curly leaves, as observed in other studies of plants overexpressing a functional AG homologue. The severity of the phenotypes correlated positively with the TcAG transcript level in the transgenic plants.
    Comprehensive interaction map of the Arabidopsis MADS box transcription factors
    Folter, S. de; Immink, R.G.H. ; Kieffer, M. ; Parenicová, L. ; Henz, S.R. ; Weigel, D. ; Busscher, M. ; Kooiker, K. ; Colombo, L. ; Kater, M.M. ; Davis, B. ; Angenent, G.C. - \ 2005
    The Plant Cell 17 (2005)5. - ISSN 1040-4651 - p. 1424 - 1433.
    protein-protein interactions - bimolecular fluorescence complementation - living plant-cells - saccharomyces-cerevisiae - flower development - homeotic gene - meristem identity - floral organ - ectopic expression - mass-spectrometry
    Interactions between proteins are essential for their functioning and the biological processes they control. The elucidation of interaction maps based on yeast studies is a first step toward the understanding of molecular networks and provides a framework of proteins that possess the capacity and specificity to interact. Here, we present a comprehensive plant protein–protein interactome map of nearly all members of the Arabidopsis thaliana MADS box transcription factor family. A matrix-based yeast two-hybrid screen of >100 members of this family revealed a collection of specific heterodimers and a few homodimers. Clustering of proteins with similar interaction patterns pinpoints proteins involved in the same developmental program and provides valuable information about the participation of uncharacterized proteins in these programs. Furthermore, a model is proposed that integrates the floral induction and floral organ formation networks based on the interactions between the proteins involved. Heterodimers between flower induction and floral organ identity proteins were observed, which point to (auto)regulatory mechanisms that prevent the activity of flower induction proteins in the flower.
    The Petunia ortholog of Arabidopsis SUPERMAN plays a distinct role in floral morphogenesis
    Nakagawa, H. ; Ferrario, S.I.T. ; Angenent, G.C. ; Kobayashi, A. ; Takatsuji, H. - \ 2004
    The Plant Cell 16 (2004). - ISSN 1040-4651 - p. 920 - 932.
    mads box - ectopic expression - homeotic genes - cell-proliferation - transgenic petunia - flower development - meristem - protein - identity - domain
    Arabidopsis (Arabidopsis thaliana) SUPERMAN (SUP) plays a role in establishing a boundary between whorls 3 and 4 of flowers and in ovule development. We characterized a Petunia hybrida (petunia) homolog of SUP, designated PhSUP1, to compare with SUP. Genomic DNA of the PhSUP1 partially restored the stamen number and ovule development phenotypes of the Arabidopsis sup mutant. Two P. hybrida lines of transposon (dTph1) insertion mutants of PhSUP1 exhibited increased stamen number at the cost of normal carpel development, and ovule development was defective owing to aberrant growth of the integument. Unlike Arabidopsis sup mutants, phsup1 mutants also showed extra tissues connecting stamens, a petal tube and an ovary, and aberrancies in the development of anther and placenta. PhSUP1 transcripts occurred in the basal region of wild-type flowers around developing organ primordia in whorls 2 and 3 as well as in the funiculus of the ovule, concave regions of the placenta, and interthecal regions of developing anthers. Overexpression of PhSUP1 in P. hybrida resulted in size reduction of petals, leaves, and inflorescence stems. The shortening of inflorescence stems and petal tubes was primarily attributable to suppression of cell elongation, whereas a decrease in cell number was mainly responsible for the size reduction of petal limbs.
    Expression Patterns of a putative homolog of AGAMOUS, STAG1, from Strawberry
    Rosin, F.M.A. ; Aharoni, A. ; Salentijn, E.M.J. ; Schaart, J.G. ; Boone, M.J. ; Hannapel, D.J. - \ 2003
    Plant Science 165 (2003). - ISSN 0168-9452 - p. 959 - 968.
    controlling flower development - ectopic expression - transcription factors - floral organ - gene - petunia - plants - identity - transformation - identification
    MADS box genes function to regulate vegetative, floral, and fruit development in plants. Here we characterize the expression pattern of a MADS box gene from strawberry (Fragariaxananassa), designated STAG1. Sequence analysis revealed that STAG1 shared 68-91 mino acid sequence identity to AGAMOUS homologs from a variety of plant species. STAG1 transcripts were detected in stamens, carpels, and developing fruit. In situ hybridization revealed that STAG1 mRNA expression was restricted to the endothelium and the vascular bundles connecting the achenes to the inner part of the receptacle and was not evident in the receptacle of the fruit. Analysis of the expression of a GUS marker gene driven by the STAG1 promoter showed that during floral development, STAG1 was active in stamens, the base of the receptacle and the petals, and in the central pith and vascular tissue. During the ripening stage of fruit development, STAG1 activity was detected in achenes, pith cells, and cortical cells. Sequence analysis and expression patterns indicate that STAG1 is an AGAMOUS homolog of strawberry
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