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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    Organizer-Derived WOX5 Signal Maintains Root Columella Stem Cells through Chromatin-Mediated Repression of CDF4 Expression.
    Pi, L. ; Graaff, E. van der; Llavata Peris, C.I. ; Weijers, D. ; Henning, L. ; Groot, E. de; Laux, T. - \ 2015
    Developmental Cell 33 (2015)5. - ISSN 1534-5807 - p. 576 - 588.
    histone deacetylase - arabidopsis-thaliana - transcriptional repression - gene-expression - wuschel - meristem - shoot - topless - protein - fate
    Stem cells in plants and animals are maintained pluripotent by signals from adjacent niche cells. In plants, WUSCHEL HOMEOBOX (WOX) transcription factors are central regulators of stem cell maintenance in different meristem types, yet their molecular mode of action has remained elusive. Here we show that in the Arabidopsis root meristem, the WOX5 protein moves from the root niche organizer, the quiescent center, into the columella stem cells, where it directly represses the transcription factor gene CDF4. This creates a gradient of CDF4 transcription, which promotes differentiation opposite to the WOX5 gradient, allowing stem cell daughter cells to exit the stem cell state. We further show that WOX5 represses CDF4 transcription by recruiting TPL/TPR co-repressors and the histone deacetylase HDA19, which consequently induces histone deacetylation at the CDF4 regulatory region. Our results show that chromatin-mediated repression of differentiation programs is a common strategy in plant and animal stem cell niches.
    WOX5 Suppresses CYCLIN D Activity to Establish Quiescence at the Center of the Root Stem Cell Niche
    Forzani, C. ; Aichinger, E. ; Willemsen, V. ; Murray, J.A. - \ 2014
    Current Biology 24 (2014)16. - ISSN 0960-9822 - p. 1939 - 1944.
    arabidopsis-thaliana root - division - meristem - differentiation - organization - transition - expression - complex - protein
    In Arabidopsis, stem cells maintain the provision of new cells for root growth. They surround a group of slowly dividing cells named the quiescent center (QC), and, together, they form the stem cell niche (SCN). The QC acts as the signaling center of the SCN, repressing differentiation of the surrounding stem cells [1] and providing a pool of cells able to replace damaged stem cells [2, 3]. Maintenance of the stem cells depends on the transcription factor WUSCHEL-RELATED HOMEOBOX 5 (WOX5), which is specifically expressed in the QC [4]. However, the molecular mechanisms by which WOX5 promotes stem cell fate and whether WOX5 regulates proliferation of the QC are unknown. Here, we reveal a new role for WOX5 in restraining cell division in the cells of the QC, thereby establishing quiescence. In contrast, WOX5 and CYCD3;3/CYCD1;1 both promote cell proliferation in the nascent columella. The additional QC divisions occurring in wox5 mutants are suppressed in mutant combinations with the D type cyclins CYCD3;3 and CYCD1;1. Moreover, ectopic expression of CYCD3;3 in the QC is sufficient to induce cell division in the QC. WOX5 thus suppresses QC divisions that are otherwise promoted by CYCD3;3 and CYCD1;1, in part by interacting with the CYCD3;3 promoter to repress CYCD3;3 expression in the QC. Therefore, we propose a specific role for WOX5 in initiating and maintaining quiescence of the QC by excluding CYCD activity from the QC.
    Precise control of plant stem cell activity through parallel regulatory inputs
    Bennett, T. ; Toorn, A. van; Willemsen, V. ; Scheres, B. - \ 2014
    Development 141 (2014). - ISSN 0950-1991 - p. 4055 - 4064.
    arabidopsis-thaliana root - transcription factor - shoot apex - meristem - gene - differentiation - organization - maintenance - homeostasis - sombrero
    The regulation of columella stem cell activity in the Arabidopsis root cap by a nearby organizing centre, the quiescent centre, has been a key example of the stem cell niche paradigm in plants. Here, we investigate interactions between transcription factors that have been shown to regulate columella stem cells using a simple quantification method for stem cell activity in the root cap. Genetic and expression analyses reveal that the RETINOBLASTOMA-RELATED protein, the FEZ and SOMBRERO NAC-domain transcription factors, the ARF10 and ARF16 auxin response factors and the quiescent centre-expressed WOX5 homeodomain protein each provide independent inputs to regulate the number of columella stem cells. Given the tight control of columella development, we found that these inputs act in a surprisingly parallel manner. Nevertheless, important points of interaction exist; for example, we demonstrate the repression of SMB activity by non-autonomous action of WOX5. Our results suggest that the developmental progression of columella stem cells may be quantitatively regulated by several more broadly acting transcription factors rather than by a single intrinsic stem cell factor, which raises questions about the special nature of the stem cell state in plants.
    Inferring the Gene Network Underlying the Branching of Tomato Inflorescence
    Astola, L. ; Stigter, J.D. ; Dijk, A.D.J. van; Daelen, R. van; Molenaar, J. - \ 2014
    PLoS ONE 9 (2014)4. - ISSN 1932-6203 - 7 p.
    flowering time - reproductive structure - regulatory networks - abscission zone - inference - meristem - lycopersicon - falsiflora - jointless
    The architecture of tomato inflorescence strongly affects flower production and subsequent crop yield. To understand the genetic activities involved, insight into the underlying network of genes that initiate and control the sympodial growth in the tomato is essential. In this paper, we show how the structure of this network can be derived from available data of the expressions of the involved genes. Our approach starts from employing biological expert knowledge to select the most probable gene candidates behind branching behavior. To find how these genes interact, we develop a stepwise procedure for computational inference of the network structure. Our data consists of expression levels from primary shoot meristems, measured at different developmental stages on three different genotypes of tomato. With the network inferred by our algorithm, we can explain the dynamics corresponding to all three genotypes simultaneously, despite their apparent dissimilarities. We also correctly predict the chronological order of expression peaks for the main hubs in the network. Based on the inferred network, using optimal experimental design criteria, we are able to suggest an informative set of experiments for further investigation of the mechanisms underlying branching behavior
    A SCARECROW-RETINOBLASTOMA Protein Network Controls Protective Quiescence in the Arabidopsis Root Stem Cell Organizer
    Cruz-Ramirez, A. ; Diaz Trivino, S. ; Wachsman, G. ; Du, Y. ; Arteága-Vázquez, M. ; Zhang Hongtao, ; Benjamins, R. ; Blilou, I. ; Neef, A.B. ; Chandler, V. ; Scheres, B. - \ 2013
    PloS Biology 11 (2013)11. - ISSN 1545-7885 - 12 p.
    thaliana root - replication stress - cycle progression - clonal analysis - self-renewal - dna-damage - in-vivo - division - meristem - gene
    Quiescent long-term somatic stem cells reside in plant and animal stem cell niches. Within the Arabidopsis root stem cell population, the Quiescent Centre (QC), which contains slowly dividing cells, maintains surrounding short-term stem cells and may act as a long-term reservoir for stem cells. The RETINOBLASTOMA-RELATED (RBR) protein cell-autonomously reinforces mitotic quiescence in the QC. RBR interacts with the stem cell transcription factor SCARECROW (SCR) through an LxCxE motif. Disruption of this interaction by point mutation in SCR or RBR promotes asymmetric divisions in the QC that renew short-term stem cells. Analysis of the in vivo role of quiescence in the root stem cell niche reveals that slow cycling within the QC is not needed for structural integrity of the niche but allows the growing root to cope with DNA damage
    Rooting plant development
    Scheres, B. - \ 2013
    Development 140 (2013)5. - ISSN 0950-1991 - p. 939 - 941.
    arabidopsis root - cell fate - meristem - differentiation - mechanism - shoot - framework - epidermis - division - pattern
    In 1993, we published a paper in Development detailing the anatomical structure of the Arabidopsis root. The paper described how root growth was maintained by the precisely tuned activity of a small set of 'initials', which acted as the source of dividing and differentiating cells, and how these stem cell-like cells surrounded a few infrequently dividing cells. This work underpinned subsequent research on root developmental biology and sparked a detailed molecular analysis of how stem cell groups are positioned and maintained in plants.
    Auxin reflux between the endodermis and pericycle promotes lateral root initiation
    Marhavy, P. ; Vanstraelen, M. ; Rybel, B.P.M. de; Ding, Z.J. ; Bennett, M.J. ; Beeckman, T. ; Benkova, E. - \ 2013
    The EMBO Journal 32 (2013)1. - ISSN 0261-4189 - p. 149 - 158.
    arabidopsis-thaliana - gene-expression - cell-cycle - efflux - transport - family - organization - gradients - proteins - meristem
    Lateral root (LR) formation is initiated when pericycle cells accumulate auxin, thereby acquiring founder cell (FC) status and triggering asymmetric cell divisions, giving rise to a new primordium. How this auxin maximum in pericycle cells builds up and remains focused is not understood. We report that the endodermis plays an active role in the regulation of auxin accumulation and is instructive for FCs to progress during the LR initiation (LRI) phase. We describe the functional importance of a PIN3 (PIN-formed) auxin efflux carrier-dependent hormone reflux pathway between overlaying endodermal and pericycle FCs. Disrupting this reflux pathway causes dramatic defects in the progress of FCs towards the next initiation phase. Our data identify an unexpected regulatory function for the endodermis in LRI as part of the fine-tuning mechanism that appears to act as a check point in LR organogenesis after FCs are specified. The EMBO Journal (2013) 32, 149-158. doi:10.1038/emboj.2012.303; Published online 23 November 2012
    A PHABULOSA/Cytokinin feedback loop controls root growth in Arabidopsis
    Dello loio, R. ; Galinha, C. ; Fletcher, A.G. ; Grigg, S.P. ; Molnar, A. ; Willemsen, V. ; Scheres, B. - \ 2012
    Current Biology 22 (2012)18. - ISSN 0960-9822 - p. 1699 - 1704.
    stem-cell niche - gene family - cytokinin - meristem - auxin - differentiation - expression - polarity - biosynthesis - nitrate
    The hormone cytokinin (CK) controls root length in Arabidopsis thaliana by defining where dividing cells, derived from stem cells of the root meristem, start to differentiate. However, the regulatory inputs directing CK to promote differentiation remain poorly understood. Here, we show that the HD-ZIPIII transcription factor PHABULOSA (PHB) directly activates the CK biosynthesis gene ISOPENTENYL TRANSFERASE 7 (IPT7), thus promoting cell differentiation and regulating root length. We further demonstrate that CK feeds back to repress both PHB and microRNA165, a negative regulator of PHB. These interactions comprise an incoherent regulatory loop in which CK represses both its activator and a repressor of its activator. We propose that this regulatory circuit determines the balance of cell division and differentiation during root development and may provide robustness against CK fluctuations.
    A new whole-mount DNA quantification method and the analysis of nuclear DNA content in the stem-cell niche of Arabidopsis roots
    Willemse, J. ; Kulikova, O. ; Jong, H. de; Bisseling, T. - \ 2008
    The Plant Journal 55 (2008)5. - ISSN 0960-7412 - p. 886 - 894.
    flow-cytometry - thaliana root - fluorescence - division - meristem - growth
    A semi-automated method to quantify fluorescence intensity of objects in intact organs and tissues, composed of several cell layers, has been designed. The method has been developed on whole-mount propidium-iodide stained Arabidopsis thaliana (Arabidopsis) root tips, in which the DNA content of individual nuclei could be quantified. A diameter of less than 150 microm makes this organ most appropriate for whole-mount imaging. Further advantages are the lack of chlorophyll and transparent cell walls, with only a little background fluorescence. The method has a great advantage over flow cytometry, as the information regarding the positions of nuclei is maintained, and nuclei with aberrant DNA content can be re-assessed individually, which facilitates the efficient distinction between technical artefact and aberrant DNA content. Our averaging 3D method calculates the average of the summed fluorescence intensities of all sections of a nucleus and interpolates the missing sections, thereby allowing for the correction of detection problems. Furthermore, this method has the advantage of detecting objects in tissues covering multiple cell layers. The results of our method in Arabidopsis root tips showed that the quiescent centre cells, which rarely divide, are diploid, and are arrested in G1 or G0. Most stem cells, with the exception of those of the vascular tissue, are diploid cells, and their rather low division rate is caused by an elongated G1 phase. In contrast, the majority of the vascular stem cells are tetraploid.
    Cytokinins act directly on lateral root founder cells to inhibit root initiation
    Laplaze, L. ; Benkova, E. ; Casimiro, I. ; Maes, L. ; Vanneste, S. ; Swarup, R. ; Weijers, D. ; Calvo, V. ; Parizot, B. ; Herrera-Rodriguez, M.B. ; Offringa, R. ; Graham, N. ; Doumas, P. ; Friml, J. ; Bogusz, D. ; Beeckman, T. ; Bennett, M. - \ 2007
    The Plant Cell 19 (2007)12. - ISSN 1040-4651 - p. 3889 - 3900.
    arabidopsis-thaliana - response regulators - tobacco plants - pea roots - auxin - shoot - gene - expression - pericycle - meristem
    In Arabidopsis thaliana, lateral roots are formed from root pericycle cells adjacent to the xylem poles. Lateral root development is regulated antagonistically by the plant hormones auxin and cytokinin. While a great deal is known about how auxin promotes lateral root development, the mechanism of cytokinin repression is still unclear. Elevating cytokinin levels was observed to disrupt lateral root initiation and the regular pattern of divisions that characterizes lateral root development in Arabidopsis. To identify the stage of lateral root development that is sensitive to cytokinins, we targeted the expression of the Agrobacterium tumefaciens cytokinin biosynthesis enzyme isopentenyltransferase to either xylem-pole pericycle cells or young lateral root primordia using GAL4-GFP enhancer trap lines. Transactivation experiments revealed that xylem-pole pericycle cells are sensitive to cytokinins, whereas young lateral root primordia are not. This effect is physiologically significant because transactivation of the Arabidopsis cytokinin degrading enzyme cytokinin oxidase 1 in lateral root founder cells results in increased lateral root formation. We observed that cytokinins perturb the expression of PIN genes in lateral root founder cells and prevent the formation of an auxin gradient that is required to pattern lateral root primordia.
    Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action
    Welch, D. ; Hassan, H. ; Blilou, I. ; Immink, G.H. ; Heidstra, R. - \ 2007
    Genes and Development 21 (2007). - ISSN 0890-9369 - p. 2196 - 2204.
    radial organization - gene - scarecrow - thaliana - movement - meristem - plants - expression - endodermis - efficient
    In the Arabidopsis root, the SHORT-ROOT transcription factor moves outward to the ground tissue from its site of transcription in the stele and is required for the specification of the endodermis and the stem cell organizing quiescent center cells. In addition, SHORT-ROOT and the downstream transcription factor SCARECROW control an oriented cell division in ground tissue stem cell daughters. Here, we show that the JACKDAW and MAGPIE genes, which encode members of a plant-specific family of zinc finger proteins, act in a SHR-dependent feed-forward loop to regulate the range of action of SHORT-ROOT and SCARECROW. JACKDAW expression is initiated independent of SHORT-ROOT and regulates the SCARECROW expression domain outside the stele, while MAGPIE expression depends on SHORT-ROOT and SCARECROW. We provide evidence that JACKDAW and MAGPIE regulate tissue boundaries and asymmetric cell division and can control SHORT-ROOT and SCARECROW activity in a transcriptional and protein interaction network.
    Arabidopsis thaliana Somatic Embryogenesis Receptor Kinase I protein is present in sporophytic and gametophytic cells and undergoes endocytosis
    Kwaaitaal, M.A.C.J. ; Vries, S.C. de; Russinova, E.T. - \ 2005
    Protoplasma 226 (2005)1-2. - ISSN 0033-183X - p. 55 - 65.
    leucine-rich repeat - signal-transduction - gene family - phosphatase - meristem - embryos - interacts - pathway - shoot - bak1
    Arabidopsis thaliana plants expressing AtSERK1 fused to yellow-fluorescent protein were generated. Fluorescence was detected predominantly at the cell periphery, most likely the plasma membrane, of cells in ovules, embryo sacs, anthers, and embryos and in seedlings. The AtSERK1 protein was detected in diverse cell types including the epidermis and the vascular bundles. In some cells, fluorescent receptors were seen in small vesicle-like compartments. After application of the fungal toxin Brefeldin A, the fluorescent receptors were rapidly internalized in the root meristem and root vascular tissue. We conclude that the AtSERK1 receptor functions in a common signalling pathway employed in both sporophytic and gametophytic cells.
    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.
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