Tom Beeckman

Ghent University, Gand, Flemish, Belgium

Are you Tom Beeckman?

Claim your profile

Publications (138)1170.28 Total impact

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the de novo identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (http://bioinformatics.psb.ugent.be/webtools/PlantSSP/). Looking for putative regulators of root development, Arabidopsis thaliana SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.
    Journal of Experimental Botany 07/2015; DOI:10.1093/jxb/erv346 · 5.79 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Small peptides of the Arabidopsis GLV/RGF/CLEL family are involved in different developmental programmes, including meristem maintenance and gravitropic responses. In addition, our previous report suggested that they also participate in the formation of lateral roots. Specifically, GLV6 is transcribed during the first stages of primordium development and GLV6 overexpression results in a strong reduction of emerged lateral roots. To investigate the cause of this phenotype we analysed primordium development in gain-of-function (gof) mutants and found that GLV6 induces supernumerary pericycle divisions, hindering the formation of a dome-shaped primordium, a prerequisite for successful emergence. The GLV6 phenotype could be reproduced by ectopic expression of the gene only in xylem-pole pericycle cells. Furthermore, GLV6 seems to function at the very beginning of lateral root initiation because GLV6 excess-either gene overexpression or peptide treatment-disrupts the first asymmetric cell divisions required for proper primordium formation. Our results suggest that GLV6 acts during lateral root initiation controlling the patterning of the first pericycle divisions. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.
    Journal of Experimental Botany 07/2015; DOI:10.1093/jxb/erv329 · 5.79 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Upward leaf movement (hyponastic growth) is frequently observed in response to changing environmental conditions and can be induced by the phytohormone ethylene. Hyponasty results from differential growth; i.e. enhanced cell elongation at the proximal abaxial side of the petiole relative to the adaxial side. Here we characterise Enhanced Hyponasty-D (EHY-D), an activation-tagged Arabidopsis thaliana line with exaggerated hyponasty. This phenotype is associated with overexpression of the mitotic cyclin CYCLINA2;1 (CYCA2;1), which hints at a role for cell divisions in regulating hyponasty. Indeed, mathematical analysis suggested that the observed changes in abaxial cell elongation rates during ethylene treatment should result in a larger hyponastic amplitude than observed, unless a decrease in cell proliferation rate at the proximal abaxial side of the petiole relative to the adaxial side was implemented. Our model predicts that when this differential proliferation mechanism is disrupted by either ectopic overexpression or mutation of CYCA2;1, the hyponastic growth response becomes exaggerated. This is in accordance with experimental observations on CYCA2;1 overexpression lines and cyca2;1 knock-outs. We therefore propose a bipartite mechanism controlling leaf movement; Ethylene induces longitudinal cell expansion in the abaxial petiole epidermis to induce hyponasty and simultaneously affects its amplitude by controlling cell proliferation through CYCA2;1. Further corroborating the model, we found that ethylene treatment results in transcriptional down regulation of A2-type CYCLINs and propose that this, and possibly other regulatory mechanisms affecting CYCA2;1, may contribute to this attenuation of hyponastic growth. Copyright © 2015, Plant Physiology.
    Plant physiology 06/2015; DOI:10.1104/pp.15.00343 · 7.39 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: During the exploration of the soil by plant roots, uptake of water and nutrients can be greatly fostered by a regular spacing of lateral roots (LRs). In the Arabidopsis root, a regular branching pattern depends on oscillatory gene activity to create prebranch sites, patches of cells competent to form LRs. Thus far, the molecular components regulating the oscillations still remain unclear. Here, we show that a local auxin source in the root cap, derived from the auxin precursor indole-3-butyric acid (IBA), modulates the oscillation amplitude, which in turn determines whether a prebranch site is created or not. Moreover, transcriptome profiling identified novel and IBA-regulated components of root patterning, such as the MEMBRANE-ASSOCIATED KINASE REGULATOR4 (MAKR4) that converts the prebranch sites into a regular spacing of lateral organs. Thus, the spatiotemporal patterning of roots is fine-tuned by the root cap-specific conversion pathway of IBA to auxin and the subsequent induction of MAKR4. Copyright © 2015 Elsevier Ltd. All rights reserved.
    Current biology: CB 05/2015; DOI:10.1016/j.cub.2015.03.046 · 9.92 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Cell polarity is a fundamental property of pro- and eukaryotic cells. It is necessary for coordination of cell division, cell morphogenesis and signaling processes. How polarity is generated and maintained is a complex issue governed by interconnected feed-back regulations between small GTPase signaling and membrane tension-based signaling that controls membrane trafficking, and cytoskeleton organization and dynamics. Here, we will review the potential role for calcium as a crucial signal that connects and coordinates the respective processes during polarization processes in plants. This article is part of a Special Issue entitled: 13th European Symposium on Calcium. This article is part of a Special Issue entitled: 13th European Symposium on Calcium. Copyright © 2015. Published by Elsevier B.V.
    Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 02/2015; DOI:10.1016/j.bbamcr.2015.02.017 · 5.30 Impact Factor
  • Source
    Kenny A. Bogaert · Tom Beeckman · Olivier De Clerck
    [Show abstract] [Hide abstract]
    ABSTRACT: Fucoid zygotes have been extensively used to study cell polarization and asymmetrical cell division. Fertilized eggs are responsive to different environmental cues (e.g., light, gravity) for a long period before the polarity is fixed and the cells germinate accordingly. First, it is commonly believed that the direction and sense of the polarization vector are established simultaneously as indicated by the formation of an F-actin patch. Secondly, upon reorientation of the zygote, a new polar gradient is formed and it is assumed that the position of the future rhizoid pole is only influenced by the latter. Here we tested these two hypotheses investigating photopolarization in Fucus zygotes by reorienting zygotes 90° relative to a unilateral light source at different time points during the first cell cycle. We conclude that fixation of direction and sense of the polarization vector is indeed established simultaneously. However, the experiments yielded a distribution of polarization axes that cannot be explained if only the last environmental cue is supposed to determine the polarization axis. We conclude that our observations, together with published findings, can only be explained by assuming imprinting of the different polarization vectors and their integration as a vectorial sum at the moment of axis fixation. This way cells will average different serially perceived cues resulting in a polarization vector representative of the dynamic intertidal environment, instead of betting exclusively on the perceived vector at the moment of axis fixation.
    Frontiers in Plant Science 02/2015; 6. DOI:10.3389/fpls.2015.00026 · 3.95 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Variations in size and shape of multicellular organs depend on spatio-temporal regulation of cell division and expansion. Here, cell division and expansion rates were quantified relative to the three spatial axes in the first leaf pair of Arabidopsis thaliana. The results show striking differences in expansion rates: the expansion rate in the petiole is higher than in the leaf blade; expansion rates in the lateral direction are higher than longitudinal rates between 5 and 10 days after stratification, but become equal at later stages of leaf blade development; and anticlinal expansion co-occurs with, but is an order of magnitude slower than periclinal expansion. Anticlinal expansion rates also differed greatly between tissues: the highest rates occurred in the spongy mesophyll and the lowest in the epidermis. Cell division rates were higher and continued for longer in the epidermis compared with the palisade mesophyll, causing a larger increase of palisade than epidermal cell area over the course of leaf development. The cellular dynamics underlying the effect of shading on petiole length and leaf thickness were then investigated. Low light reduced leaf expansion rates, which was partly compensated by increased duration of the growth phase. Inversely, shading enhanced expansion rates in the petiole, so that the blade to petiole ratio was reduced by 50%. Low light reduced leaf thickness by inhibiting anticlinal cell expansion rates. This effect on cell expansion was preceded by an effect on cell division, leading to one less layer of palisade cells. The two effects could be uncoupled by shifting plants to contrasting light conditions immediately after germination. This extended kinematic analysis maps the spatial and temporal heterogeneity of cell division and expansion, providing a framework for further research to understand the molecular regulatory mechanisms involved.
    Journal of Experimental Botany 09/2014; 65(22). DOI:10.1093/jxb/eru358 · 5.79 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Photoassimilates such as sugars are transported through phloem sieve element cells in plants. Adapted for effective transport, sieve elements develop as enucleated living cells. We used electron microscope imaging and three-dimensional reconstruction to follow sieve element morphogenesis in Arabidopsis. We show that sieve element differentiation involves enucleation, in which the nuclear contents are released and degraded in the cytoplasm at the same time as other organelles are rearranged and the cytosol is degraded. These cellular reorganizations are orchestrated by the genetically redundant NAC domain–containing transcription factors, NAC45 and NAC86 (NAC45/86). Among the NAC45/86 targets, we identified a family of genes required for enucleation that encode proteins with nuclease domains. Thus, sieve elements differentiate through a specialized autolysis mechanism.
    Science 08/2014; 345(6199):933-937. DOI:10.1126/science.1253736 · 31.48 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: 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.
    Science 08/2014; 342(6197):UNSP 1255215. DOI:10.1126/science.1255215 · 31.48 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Overall root architecture is the combined result of primary and lateral root growth and is influenced by both intrinsic genetic programs and external signals. One of the main questions for root biologists is how plants control the number of lateral root primordia and their emergence through the main root. We recently identified SKP2B as a new early marker for lateral root development. Here, we took advantage of its specific expression pattern in a cell sorting and transcriptomic approach to generate a lateral root specific cs-SKP2B dataset that represents the endogenous genetic developmental program. We first validated this dataset by showing that many of the identified genes have a function during root growth or lateral root development. Importantly, genes encoding PEROXIDASES were highly represented in our dataset. We thus next focused on this class of enzymes and showed, using genetic and chemical inhibitor studies, that peroxidase activity and ROS signalling is specifically required during lateral root emergence, but intriguingly not for primordium specification itself.
    Plant physiology 05/2014; 165(3). DOI:10.1104/pp.114.238873 · 7.39 Impact Factor
  • Article: Pericycle
    Tom Beeckman · Ive De Smet
    [Show abstract] [Hide abstract]
    ABSTRACT: Cells in the pericycle play an important role in plant development and physiology.
    Current Biology 05/2014; 24(10):R378-9. DOI:10.1016/j.cub.2014.03.031 · 9.92 Impact Factor
  • Marlies J. F. Demeulenaere · Tom Beeckman
    [Show abstract] [Hide abstract]
    ABSTRACT: The essential role of auxin for cell proliferation in plants is well known. Both auxin signaling and cell cycle regulation have been studied elaborately, but less is known about the connection between these processes. Recent studies report on the first molecular pathways that have been found to directly link auxin levels to the regulation of cell cycle activity. Here, we discuss the general effect of auxin on cell cycle progression and then zoom in on the interplay between auxin and the cell cycle during root development in Arabidopsis thaliana. At the root tip, an auxin gradient maintains the correct organization of the ground tissue layers and controls the size of the root apical meristem. During auxin-induced lateral root initiation LATERAL ORGAN BOUNDARIES-DOMAIN transcription factors are upregulated and control reactivation of the cell cycle and cell specification, both of which are needed for proper lateral root initiation. Auxin-induced lateral root initiation-like pathways are also involved in cell cycle reactivation during the formation of nematode feeding sites, nitrogen-fixing nodules and callus tissue, pointing to the existence of one common auxin–cell cycle module to initiate new organs in plants.
    Auxin and Its Role in Plant Development, 04/2014: pages 119-141; , ISBN: 978-3-7091-1525-1
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: In plants, roots are essential for water and nutrient acquisition. MicroRNAs (miRNAs) regulate their target mRNAs by transcript cleavage and/or inhibition of protein translation and are known as major post-transcriptional regulators of various developmental pathways and stress responses. In Arabidopsis thaliana, four isoforms of miR169 are encoded by 14 different genes and target diverse mRNAs, encoding subunits A of the NF-Y transcription factor complex. These miRNA isoforms and their targets have previously been linked to nutrient signalling in plants. By using mimicry constructs against different isoforms of miR169 and miR-resistant versions of NF-YA genes we analysed the role of specific miR169 isoforms in root growth and branching. We identified a regulatory node involving the particular miR169defg isoform and NF-YA2 and NF-YA10 genes that acts in the control of primary root growth. The specific expression of MIM169defg constructs altered specific cell type numbers and dimensions in the root meristem. Preventing miR169defg-regulation of NF-YA2 indirectly affected laterial root initiation. We also showed that the miR169defg isoform affects NF-YA2 transcripts both at mRNA stability and translation levels. We propose that a specific miR169 isoform and the NF-YA2 target control root architecture in Arabidopsis.
    New Phytologist 02/2014; 202(4). DOI:10.1111/nph.12735 · 7.67 Impact Factor
  • Source
    Kun Yue · Tom Beeckman
    Molecular Plant 02/2014; 7(5). DOI:10.1093/mp/ssu012 · 6.61 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Stomata are two-celled valves that control epidermal pores whose spacing optimizes shoot-atmosphere gas exchange. They develop from protodermal cells after unequal divisions followed by an equal division and differentiation. The concentration of the hormone auxin, a master plant developmental regulator, is tightly controlled in time and space, but its role, if any, in stomatal formation is obscure. Here dynamic changes of auxin activity during stomatal development are monitored using auxin input (DII-VENUS) and output (DR5:VENUS) markers by time-lapse imaging. A decrease in auxin levels in the smaller daughter cell after unequal division presages the acquisition of a guard mother cell fate whose equal division produces the two guard cells. Thus, stomatal patterning requires auxin pathway control of stem cell compartment size, as well as auxin depletion that triggers a developmental switch from unequal to equal division.
    Nature Communications 01/2014; 5:3090. DOI:10.1038/ncomms4090 · 10.74 Impact Factor
  • Source
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The phytohormone auxin is a key developmental signal in plants. To date, only auxin perception has been described to trigger the release of transcription factors termed AUXIN RESPONSE FACTORs (ARFs) from their AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) repressor proteins. Here, we show that phosphorylation of ARF7 and ARF19 via BRASSINOSTEROID-INSENSITIVE2 (BIN2) can also potentiates auxin signalling output during lateral root organogenesis. BIN2-mediated phosphorylation of ARF7 and ARF19 suppresses their interaction with AUX/IAAs, and subsequently enhances the transcriptional activity to their target genes LATERAL ORGAN BOUNDARIES-DOMAIN16 (LBD16) and LBD29. In this context, BIN2 is under the control of the TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF) - TDIF RECEPTOR (TDR) module. TDIF-initiated TDR signalling directly acts on BIN2-mediated ARF phosphorylation, leading to the regulation of auxin signalling during lateral root development. In summary, this study delineates a TDIF-TDR-BIN2 signalling cascade controlling auxin perception-independent regulation of ARF and AUX/IAA interaction during lateral root development.
    Nature Cell Biology 01/2014; 16(1):66–76. DOI:10.1038/ncb2893 · 20.06 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: High-throughput small molecule screenings in model plants are of great value to identify compounds that interfere with plant developmental processes. In academic research, the plant Arabidopsis thaliana is the most commonly used model organism for this purpose. However, compared to plant cellular systems, A. thaliana plants are less amenable to develop high-throughput screening assays. In this chapter, we describe a screening procedure that is compatible with liquid handling systems and increases the throughput of compound screenings in A. thaliana seedlings.
    Methods in molecular biology (Clifton, N.J.) 01/2014; 1056:3-9. DOI:10.1007/978-1-62703-592-7_1 · 1.29 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The development of a multicellular embryo from a single zygote is a complex and highly organized process that is far from understood. In higher plants, apical–basal patterning mechanisms are crucial to correctly specify root and shoot stem cell niches that will sustain and drive post-embryonic plant growth and development. The auxin-responsive AtWRKY23 transcription factor is expressed from early embryogenesis onwards and the timing and localization of its expression overlaps with the root stem cell niche. Knocking down WRKY23 transcript levels or expression of a dominant-negative WRKY23 version via a translational fusion with the SRDX repressor domain affected both apical–basal axis formation as well as installation of the root stem cell niche. WRKY23 expression is affected by two well-known root stem cell specification mechanisms, that is, SHORTROOT and MONOPTEROS–BODENLOS signalling and can partially rescue the root-forming inability of mp embryos. On the basis of these results, we postulate that a tightly controlled WRKY23 expression is involved in the regulation of both auxin-dependent and auxin-independent signalling pathways towards stem cell specification.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The establishment of a pre-pattern or competence to form new organs is a key feature of the postembryonic plasticity of plant development, and the elaboration of such pre-patterns leads to remarkable heterogeneity in plant form. In root systems, many of the differences in architecture can be directly attributed to the outgrowth of lateral roots. In recent years, efforts have focused on understanding how the pattern of lateral roots is established. Here, we review recent findings that point to a periodic mechanism for establishing this pattern, as well as roles for plant hormones, particularly auxin, in the earliest steps leading up to lateral root primordium development. In addition, we compare the development of lateral root primordia with in vitro plant regeneration and discuss possible common molecular mechanisms.
    Development 11/2013; 140(21):4301-4310. DOI:10.1242/dev.090548 · 6.27 Impact Factor

Publication Stats

10k Citations
1,170.28 Total Impact Points

Institutions

  • 1994–2015
    • Ghent University
      • • Department of Plant Biotechnology and Bioinformatics
      • • VIB Department of Plant Systems Biology
      • • Laboratory of Microbiology
      Gand, Flemish, Belgium
  • 2001–2014
    • Vlaams Instituut voor Biotechnologie
      • Department of Plant Systems Biology, UGent
      Gand, Flemish, Belgium
  • 2013
    • University of Nottingham
      • Division of Plant and Crop Sciences
      Nottigham, England, United Kingdom
    • University of Leuven
      Louvain, Flemish, Belgium
    • Universitair Ziekenhuis Ghent
      Gand, Flanders, Belgium
  • 2011
    • University of Lausanne
      • Department of Plant Molecular Biology
      Lausanne, Vaud, Switzerland