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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    Predicting the Impact of Alternative Splicing on Plant MADS Domain Protein Function
    Severing, E.I. ; Dijk, A.D.J. van; Morabito, G. ; Busscher-Lange, J. ; Immink, G.H. ; Ham, R.C.H.J. van - \ 2012
    PLoS ONE 7 (2012)1. - ISSN 1932-6203 - 13 p.
    flowering time - box genes - transcription factors - arabidopsis-thaliana - messenger-rna - evolutionary analysis - exon duplication - organ identity - sequence - identification
    Several genome-wide studies demonstrated that alternative splicing (AS) significantly increases the transcriptome complexity in plants. However, the impact of AS on the functional diversity of proteins is difficult to assess using genome-wide approaches. The availability of detailed sequence annotations for specific genes and gene families allows for a more detailed assessment of the potential effect of AS on their function. One example is the plant MADS-domain transcription factor family, members of which interact to form protein complexes that function in transcription regulation. Here, we perform an in silico analysis of the potential impact of AS on the protein-protein interaction capabilities of MIKC-type MADS-domain proteins. We first confirmed the expression of transcript isoforms resulting from predicted AS events. Expressed transcript isoforms were considered functional if they were likely to be translated and if their corresponding AS events either had an effect on predicted dimerisation motifs or occurred in regions known to be involved in multimeric complex formation, or otherwise, if their effect was conserved in different species. Nine out of twelve MIKC MADS-box genes predicted to produce multiple protein isoforms harbored putative functional AS events according to those criteria. AS events with conserved effects were only found at the borders of or within the K-box domain. We illustrate how AS can contribute to the evolution of interaction networks through an example of selective inclusion of a recently evolved interaction motif in the MADS AFFECTING FLOWERING1-3 (MAF1–3) subclade. Furthermore, we demonstrate the potential effect of an AS event in SHORT VEGETATIVE PHASE (SVP), resulting in the deletion of a short sequence stretch including a predicted interaction motif, by overexpression of the fully spliced and the alternatively spliced SVP transcripts. For most of the AS events we were able to formulate hypotheses about the potential impact on the interaction capabilities of the encoded MIKC proteins
    Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction
    Dijk, A.D.J. van; Morabito, G. ; Fiers, M.A. ; Ham, R.C.H.J. van; Angenent, G.C. ; Immink, R.G.H. - \ 2010
    PLoS Computational Biology 6 (2010). - ISSN 1553-734X - 11 p.
    novo structure prediction - organ-identity proteins - box genes - flower development - floral organ - dna-binding - peptide interactions - signal-transduction - arabidopsis - dimerization
    Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of proteins. Knowledge about how protein sequences define interaction specificity is largely missing, in particular for paralogous protein families with high sequence similarity, such as the plant MADS domain transcription factor family. In comparison to the situation in mammalian species, this important family of transcription regulators has expanded enormously in plant species and contains over 100 members in the model plant species Arabidopsis thaliana. Here, we provide insight into the mechanisms that determine protein-protein interaction specificity for the Arabidopsis MADS domain transcription factor family, using an integrated computational and experimental approach. Plant MADS proteins have highly similar amino acid sequences, but their dimerization patterns vary substantially. Our computational analysis uncovered small sequence regions that explain observed differences in dimerization patterns with reasonable accuracy. Furthermore, we show the usefulness of the method for prediction of MADS domain transcription factor interaction networks in other plant species. Introduction of mutations in the predicted interaction motifs demonstrated that single amino acid mutations can have a large effect and lead to loss or gain of specific interactions. In addition, various performed bioinformatics analyses shed light on the way evolution has shaped MADS domain transcription factor interaction specificity. Identified protein-protein interaction motifs appeared to be strongly conserved among orthologs, indicating their evolutionary importance. We also provide evidence that mutations in these motifs can be a source for sub- or neo-functionalization. The analyses presented here take us a step forward in understanding protein-protein interactions and the interplay between protein sequences and network evolution.
    MADS-complexes regulate transcriptome dynamics during pollen maturation
    Verelst, J.S. ; Twell, D. ; Folter, S. de; Immink, G.H. - \ 2007
    Genome Biology 8 (2007)11. - ISSN 1474-7596 - 15 p.
    male gametophyte development - gene-expression map - arabidopsis-thaliana - tube growth - box genes - cell-differentiation - mature pollen - evolution - family - plants
    Background - Differentiation processes are responsible for the diversity and functional specialization of the cell types that compose an organism. The outcome of these processes can be studied at molecular, physiologic, and biochemical levels by comparing different cell types, but the complexity and dynamics of the regulatory processes that specify the differentiation are largely unexplored. Results - Here we identified the pollen-specific MIKC* class of MADS-domain transcription factors as major regulators of transcriptome dynamics during male reproductive cell development in Arabidopsis thaliana. Pollen transcript profiling of mutants deficient in different MIKC* protein complexes revealed that they control a transcriptional switch that directs pollen maturation and that is essential for pollen competitive ability. We resolved the functional redundancy among the MIKC* proteins and uncovered part of the underlying network by identifying the non-MIKC* MADS-box genes AGL18 and AGL29 as downstream regulators of a subset of the MIKC* MADS-controlled genes. Conclusion - Our results provide a first, unique, and compelling insight into the complexity of a transcription factor network that directs cellular differentiation during pollen maturation, a process that is essential for male reproductive fitness in flowering plants.
    Trans meets cis in MADS science
    Folter, S. de; Angenent, G.C. - \ 2006
    Trends in Plant Science 11 (2006)5. - ISSN 1360-1385 - p. 224 - 231.
    floral organ identity - transcriptional regulatory networks - ternary complex-formation - homeotic gene apetala3 - dna-binding specificities - cell-fate determination - box genes - flower development - in-vitro - chromatin immunoprecipitation
    The interaction between a transcription factor and its binding site at the DNA is an integral part of transcriptional regulatory networks, which is fundamental for an understanding of biological processes. An example is the family of MADS domain transcription factors, which represent key regulators of processes in yeast, animals and plants. However, despite our extensive knowledge of these transcription factors, limited information is available on the cis-elements to which these proteins bind or how these elements are defined. Here, we discuss the current understanding of MADS protein binding sites and compare data from various organisms. This information can help us in developing algorithms to predict binding sites for MADS domain transcription factors, which would be a significant step forward in the identification of `down-stream¿ target genes and the elucidation of transcriptional networks
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