Thomas Depuydt

Title: 
PhD student
Project: 
Multi-omics plant gene analysis

Publications

  1. Willems, A., Liang, Y., Heyman, J., Depuydt, T., Eekhout, T., Canher, B., … De Veylder, L. (2023). Plant lineage-specific PIKMIN1 drives APC/CCCS52A2 E3-ligase activity-dependent cell division. Plant Physiology, 191(3), 1574–1595. https://doi.org/10.1093/plphys/kiac528
    The anaphase-promoting complex/cyclosome (APC/C) marks key cell cycle proteins for proteasomal breakdown, thereby ensuring unidirectional progression through the cell cycle. Its target recognition is temporally regulated by activating subunits, one of which is called CELL CYCLE SWITCH 52 A2 (CCS52A2). We sought to expand the knowledge on the APC/C by using the severe growth phenotypes of CCS52A2-deficient Arabidopsis (Arabidopsis thaliana) plants as a readout in a suppressor mutagenesis screen, resulting in the identification of the previously undescribed gene called PIKMIN1 (PKN1). PKN1 deficiency rescues the disorganized root stem cell phenotype of the ccs52a2-1 mutant, whereas an excess of PKN1 inhibits growth of ccs52a2-1 plants, indicating the need for control of PKN1 abundance for proper development. Accordingly, the lack of PKN1 in a wild-type background negatively impacts cell division, while its systemic overexpression promotes proliferation. PKN1 shows a cell cycle phase-dependent accumulation pattern, localizing to microtubular structures, including the preprophase band, the mitotic spindle, and phragmoplast. PKN1 is conserved throughout the plant kingdom, with its function in cell division being evolutionary conserved in the liverwort Marchantia polymorpha. Our data thus demonstrate that PKN1 represents a novel, plant-specific gene with a role in cell division that is likely proteolytically controlled by the CCS52A2-activated APC/C.
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  2. Nguyen, T. H., Thiers, L., Van Moerkercke, A., Bai, Y., Fernandez Calvo, P., Minne, M., … Goossens, A. (2023). A redundant transcription factor network steers spatiotemporal Arabidopsis triterpene synthesis. NATURE PLANTS. https://doi.org/10.1038/s41477-023-01419-8
  3. Depuydt, T., De Rybel, B., & Vandepoele, K. (2022). Charting plant gene functions in the multi-omics and single-cell era. TRENDS IN PLANT SCIENCE, 28(3), 283–296. https://doi.org/10.1016/j.tplants.2022.09.008
    Despite the increased access to high-quality plant genome sequences, the set of genes with a known function remains far from complete. With the advent of novel bulk and single-cell omics profiling methods, we are entering a new era where advanced and highly integrative functional annotation strategies are being developed to elucidate the functions of all plant genes. Here, we review different multi-omics approaches to improve functional and regulatory gene characterization and highlight the power of machine learning and network biology to fully exploit the complementary information embedded in different omics layers. Finally, we discuss the potential of emerging single-cell methods and algorithms to further increase the resolution, allowing generation of functional insights about plant biology.
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  4. Depuydt, T., & Vandepoele, K. (2021). Multi‐omics network‐based functional annotation of unknown Arabidopsis genes. PLANT JOURNAL, 108, 1193–1212. https://doi.org/10.1111/tpj.15507
    Unraveling gene function is pivotal to understanding the signaling cascades that control plant development and stress responses. Since experimental profiling is costly and labor intensive, there is a clear need for high-confidence computational annotation. In contrast to detailed gene-specific functional information, transcriptomics data is widely available for both model and crop species. Here, we describe a novel automated function prediction (AFP) method, which leverages complementary information from multiple expression datasets by analyzing study-specific gene co-expression networks. First, we benchmarked the prediction performance on recently characterized Arabidopsis thaliana genes, and showed that our method outperforms state-of-the-art expression-based approaches. Next, we predicted biological process annotations for known (n=15,790) and unknown (n=11,865) genes in A. thaliana and validated our predictions using experimental protein-DNA and protein-protein interaction data (covering >220 thousand interactions in total), obtaining a set of high-confidence functional annotations. Our method assigned at least one validated annotation to 5,054 (42.6%) unknown genes, and at least one novel validated function to 3,408 (53.0%) genes with computational annotations only. These omics-supported functional annotations shed light on a variety of developmental processes and molecular responses, such as flower and root development, defense responses to fungi and bacteria, and phytohormone signaling, and help fill the information gap on biological process annotations in Arabidopsis. An in-depth analysis of two context-specific networks, modeling seed development and response to water deprivation, shows how previously uncharacterized genes function within the respective networks. Moreover, our AFP approach can be applied in future studies to facilitate gene discovery for crop improvement.
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  5. Vancaester, E., Depuydt, T., Osuna, C., & Vandepoele, K. (2020). Comprehensive and functional analysis of horizontal gene transfer events in diatoms. MOLECULAR BIOLOGY AND EVOLUTION, 37(11), 3243–3257. https://doi.org/10.1093/molbev/msaa182
    Diatoms are a diverse group of mainly photosynthetic algae, responsible for 20% of worldwide oxygen production, which can rapidly respond to favourable conditions and often outcompete other phytoplankton. We investigated the contribution of horizontal gene transfer (HGT) to its ecological success. A large-scale phylogeny-based prokaryotic HGT detection procedure across nine sequenced diatoms showed that 3-5% of their proteome has a horizontal origin and a large influx occurred at the ancestor of diatoms. More than 90% of HGT genes are expressed, and species-specific HGT genes in Phaeodactylum tricornutum undergo strong purifying selection. Genes derived from HGT are implicated in several processes including environmental sensing, and expand the metabolic toolbox. Cobalamin (vitamin B12) is an essential cofactor for roughly half of the diatoms and is only produced by bacteria. Five consecutive genes involved in the final synthesis of the cobalamin biosynthetic pathway, which could function as scavenging and repair genes, were detected as HGT. The full suite of these genes were detected in the cold-adapted diatom Fragilariopsis cylindrus. This might give diatoms originating from the Southern Ocean, a region typically depleted in cobalamin, a competitive advantage. Overall, we show that HGT is a prevalent mechanism that is actively used in diatoms to expand its adaptive capabilities.
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