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  • ItemOpen AccessAccepted version Peer-reviewed
    Cytokinin Targets Auxin Transport to Promote Shoot Branching.
    (Oxford University Press (OUP), 2018-06) Waldie, Tanya; Leyser, Ottoline; Waldie, Tanya [0000-0001-7760-0950]; Leyser, Ottoline [0000-0003-2161-3829]
    Cytokinin promotes shoot branching by activating axillary buds, but its mechanism of action in Arabidopsis (Arabidopsis thaliana) in this process is unclear. We have shown previously that a hextuple mutant lacking a clade of type-A Arabidopsis Response Regulators (ARRs) known to act in cytokinin signaling has reduced shoot branching compared with the wild type. Since these proteins typically act as negative regulators of cytokinin signaling, this is an unexpected result. To explore this paradox more deeply, we characterized the effects of loss of function of the type-B ARR, ARR1, which positively regulates cytokinin-induced gene expression. The arr1 mutant has increased branching, consistent with a role antagonistic to the type-A ARRs but in apparent conflict with the known positive role for cytokinin in bud activation. We show that the arr branching phenotypes correlate with increases in stem auxin transport and steady-state levels of the auxin export proteins PIN3 and PIN7 on the plasma membrane of xylem-associated cells in the main stem. Cytokinin treatment results in an increased accumulation of PIN3, PIN7, and the closely related PIN4 within several hours, and loss of PIN3, PIN4, and PIN7 can partially rescue the arr1 branching phenotype. This suggests that there are multiple signaling pathways for cytokinin in bud outgrowth; one of these pathways regulates PIN proteins in shoots, independently of the canonical signaling function of the ARR genes tested here. A hypothesis consistent with the arr shoot phenotypes is that feedback control of biosynthesis leads to altered cytokinin accumulation, driving cytokinin signaling via this pathway.
  • ItemOpen AccessAccepted version Peer-reviewed
    Transcription factors PRE3 and WOX11 are involved in the formation of new lateral roots from secondary growth taproot in A. thaliana.
    (Wiley, 2018-05) Baesso, B; Chiatante, D; Terzaghi, M; Zenga, D; Nieminen, K; Mahonen, AP; Siligato, R; Helariutta, YE; Scippa, GS; Montagnoli, A; Helariutta, Yrjo [0000-0002-7287-8459]
    The spatial deployment of lateral roots determines the ability of a plant to interact with the surrounding environment for nutrition and anchorage. This paper shows that besides the pericycle, the vascular cambium becomes active in Arabidopsis thaliana taproot at a later stage of development and is also able to form new lateral roots. To demonstrate the above, we implemented a two-step approach in which the first step leads to development of a secondary structure in A. thaliana taproot, and the second applies a mechanical stress on the vascular cambium to initiate formation of a new lateral root primordium. GUS staining showed PRE3, DR5 and WOX11 signals in the cambial zone of the root during new lateral root formation. An advanced level of wood formation, characterized by the presence of medullar rays, was achieved. Preliminary investigations suggest the involvement of auxin and two transcription factors (PRE3/ATBS1/bHLH135/TMO7 and WOX11) in the transition of some vascular cambium initials from a role as producers of xylem/phloem mother cells to founder cells of a new lateral root primordium.
  • ItemOpen AccessPublished version Peer-reviewed
    A Gene Regulatory Network for Cellular Reprogramming in Plant Regeneration.
    (Oxford University Press (OUP), 2018-04-01) Ikeuchi, Momoko; Shibata, Michitaro; Rymen, Bart; Iwase, Akira; Bågman, Anne-Maarit; Watt, Lewis; Coleman, Duncan; Favero, David S; Takahashi, Tatsuya; Ahnert, Sebastian E; Brady, Siobhan M; Sugimoto, Keiko; Ikeuchi, Momoko [0000-0001-9474-5131]; Shibata, Michitaro [0000-0002-7008-8437]; Favero, David S [0000-0002-6879-0323]; Brady, Siobhan M [0000-0001-9424-8055]
    Wounding triggers organ regeneration in many plant species, and application of plant hormones, such as auxin and cytokinin, enhances their regenerative capacities in tissue culture. Recent studies have identified several key players mediating wound- and/or plant hormone-induced cellular reprogramming, but the global architecture of gene regulatory relationships underlying plant cellular reprogramming is still far from clear. In this study, we uncovered a gene regulatory network (GRN) associated with plant cellular reprogramming by using an enhanced yeast one-hybrid (eY1H) screen systematically to identify regulatory relationships between 252 transcription factors (TFs) and 48 promoters. Our network analyses suggest that wound- and/or hormone-invoked signals exhibit extensive cross-talk and regulate many common reprogramming-associated genes via multilayered regulatory cascades. Our data suggest that PLETHORA 3 (PLT3), ENHANCER OF SHOOT REGENERATION 1 (ESR1) and HEAT SHOCK FACTOR B 1 (HSFB1) act as critical nodes that have many overlapping targets and potentially connect upstream stimuli to downstream developmental decisions. Interestingly, a set of wound-inducible APETALA 2/ETHYLENE RESPONSE FACTORs (AP2/ERFs) appear to regulate these key genes, which, in turn, form feed-forward cascades that control downstream targets associated with callus formation and organ regeneration. In addition, we found another regulatory pathway, mediated by LATERAL ORGAN BOUNDARY/ASYMMETRIC LEAVES 2 (LOB/AS2) TFs, which probably plays a distinct but partially overlapping role alongside the AP2/ERFs in the putative gene regulatory cascades. Taken together, our findings provide the first global picture of the GRN governing plant cell reprogramming, which will serve as a valuable resource for future studies.
  • ItemOpen AccessPublished version Peer-reviewed
    Developmental Restriction of Retrotransposition Activated in Arabidopsis by Environmental Stress.
    (Oxford University Press (OUP), 2017-10) Gaubert, Hervé; Sanchez, Diego H; Drost, Hajk-Georg; Paszkowski, Jerzy; Drost, Hajk-Georg [0000-0002-1567-306X]
    Retrotransposons (RTs) can rapidly increase in copy number due to periodic bursts of transposition. Such bursts are mutagenic and thus potentially deleterious. However, certain transposition-induced gain-of-function or regulatory mutations may be of selective advantage. How an optimal balance between these opposing effects arises is not well characterized. Here, we studied transposition bursts of a heat-activated retrotransposon family in Arabidopsis We recorded a high inter and intraplant variation in the number and chromosomal position of new insertions, which usually did not affect plant fertility and were equally well transmitted through male and female gametes, even though 90% of them were within active genes. We found that a highly heterogeneous distribution of these new retroelement copies result from a combination of two mechanisms, of which the first prevents multiple transposition bursts in a given somatic cell lineage that later contributes to differentiation of gametes, and the second restricts the regulatory influence of new insertions toward neighboring chromosomal DNA. As a whole, such regulatory characteristics of this family of RTs ensure its rapid but stepwise accumulation in plant populations experiencing transposition bursts accompanied by high diversity of chromosomal sites harboring new RT insertions.
  • ItemOpen AccessPublished version Peer-reviewed
    Leaf margin organisation and the existence of vaterite-producing hydathodes in the alpine plant Saxifraga scardica
    (Elsevier BV, 2018) Wightman, R; Wallis, S; Aston, P; Wightman, Raymond [0000-0003-1295-4875]
    Some sections of species within the genus Saxifraga deposit a chalky crust on the surface of their leaves, originating from the guttation medium produced by the sunken hydathodes found generally at or near the leaf margin. The organisation of the hydathode tissues, that of the rest of the leaf and the physiology of the crust is poorly understood. We have used cryo-SEM and cryo-fracture to study leaf tissue organisation and structure in Saxifraga scardica and compared it to the imaging data with the previously characterised Saxifraga cochlearis. We find S. scardica contains a transparent and tapered leaf margin containing thick walled cylindrical cells that may serve to deflect light to the adjacent palisade mesophyll tissue. Raman microscopy reveals the S. scardica leaf crust contains the rare and metastable calcium carbonate polymorph vaterite whereas the crust from S. cochlearis contains only calcite. Vaterite-crust is also observed on the leaves of some species within the section Porphyrion but is not found on members of the section Ligulatae. The implications of these findings are discussed.
  • ItemOpen AccessPublished version Peer-reviewed
    Molecular ​​time-sharing ​​through​​ dynamic ​​pulsing ​​in ​​single ​​cells
    (Elsevier, 2018-02-28) Locke, JCW
    n cells, specific regulators often compete for limited amounts of a core enzymatic resource. It is typically assumed that competition leads to partitioning of core enzyme molecules among regulators at constant levels. Alternatively, however, different regulatory species could time share, or take turns utilizing, the core resource. Using quantitative time-lapse microscopy, we analyzed sigma factor activity dynamics, and their competition for RNA polymerase, in individual Bacillus subtilis cells under energy stress. Multiple alternative sigma factors were activated in ∼1-hr pulses in stochastic and repetitive fashion. Pairwise analysis revealed that two sigma factors rarely pulse simultaneously and that some pairs are anti-correlated, indicating that RNAP utilization alternates among different sigma factors. Mathematical modeling revealed how stochastic time-sharing dynamics can emerge from pulse-generating sigma factor regulatory circuits actively competing for RNAP. Time sharing provides a mechanism for cells to dynamically control the distribution of cell states within a population. Since core molecular components are limiting in many other systems, time sharing may represent a general mode of regulation.
  • ItemOpen AccessPublished version Peer-reviewed
    The self-organization of plant microtubules inside the cell volume yields their cortical localization, stable alignment, and sensitivity to external cues.
    (Public Library of Science (PLoS), 2018-02) Mirabet, Vincent; Krupinski, Pawel; Hamant, Olivier; Meyerowitz, Elliot M; Jönsson, Henrik; Boudaoud, Arezki; Hamant, Olivier [0000-0001-6906-6620]; Boudaoud, Arezki [0000-0002-2780-4717]
    Many cell functions rely on the ability of microtubules to self-organize as complex networks. In plants, cortical microtubules are essential to determine cell shape as they guide the deposition of cellulose microfibrils, and thus control mechanical anisotropy of the cell wall. Here we analyze how, in turn, cell shape may influence microtubule behavior. Building upon previous models that confined microtubules to the cell surface, we introduce an agent model of microtubules enclosed in a three-dimensional volume. We show that the microtubule network has spontaneous aligned configurations that could explain many experimental observations without resorting to specific regulation. In particular, we find that the preferred cortical localization of microtubules emerges from directional persistence of the microtubules, and their interactions with each other and with the stiff wall. We also identify microtubule parameters that seem relatively insensitive to cell shape, such as length or number. In contrast, microtubule array anisotropy depends on local curvature of the cell surface and global orientation follows robustly the longest axis of the cell. Lastly, we find that geometric cues may be overcome, as the network is capable of reorienting toward weak external directional cues. Altogether our simulations show that the microtubule network is a good transducer of weak external polarity, while at the same time, easily reaching stable global configurations.
  • ItemOpen AccessPublished version Peer-reviewed
    The pea branching RMS2 gene encodes the PsAFB4/5 auxin receptor and is involved in an auxin-strigolactone regulation loop
    (Public Library of Science (PLoS)) Leyser, HMO; ligerot, Yasmine; de Saint Germain, Alexandre; Waldie, Tanya; Troadec, Christelle; Citerne, Sylvie; Kadakia, Nikita; Pillot, Jean-Paul; Prigge, Michael; Aubert, Gregoire; Bendahmane, Abdelhafid; Estelle, Mark; Debelle, Frederic; Rameau, Catherine; Leyser, Ottoline [0000-0003-2161-3829]
    Strigolactones (SLs) are well known for their role in repressing shoot branching. In pea, increased transcript levels of SL biosynthesis genes are observed in stems of highly branched SL deficient (ramosus1 (rms1) and rms5) and SL response (rms3 and rms4) mutants indicative of negative feedback control. In contrast, the highly branched rms2 mutant has reduced transcript levels of SL biosynthesis genes. Grafting studies and hormone quantification led to a model where RMS2 mediates a shoot-to-root feedback signal that regulates both SL biosynthesis gene transcript levels and xylem sap levels of cytokinin exported from roots. Here we cloned RMS2 using synteny with Medicago truncatula and demonstrated that it encodes a putative auxin receptor of the AFB4/5 clade. Phenotypes similar to rms2 were found in Arabidopsis afb4/5 mutants, including increased shoot branching, low expression of SL biosynthesis genes and high auxin levels in stems. Moreover, afb4/5 and rms2 display a specific resistance to the herbicide picloram. Yeast-two-hybrid experiments supported the hypothesis that the RMS2 protein functions as an auxin receptor. SL root feeding using hydroponics repressed auxin levels in stems and down-regulated transcript levels of auxin biosynthesis genes within one hour. This auxin down-regulation was also observed in plants treated with the polar auxin transport inhibitor NPA. Together these data suggest a homeostatic feedback loop in which auxin up-regulates SL synthesis in an RMS2-dependent manner and SL down-regulates auxin synthesis in an RMS3 and RMS4- dependent manner.
  • ItemOpen AccessAccepted version Peer-reviewed
    Cell Cycle Control by Nuclear Sequestration of CDC20 and CDH1 mRNA in Plant Stem Cells.
    (Elsevier BV, 2017-12-21) Yang, Weibing; Wightman, Raymond; Meyerowitz, Elliot M; Yang, Weibing [0000-0002-2379-5729]; Wightman, Raymond [0000-0003-1295-4875]
    In eukaryotes, most RNA molecules are exported into the cytoplasm after transcription. Long noncoding RNAs (lncRNAs) reside and function primarily inside the nucleus, but nuclear localization of mRNAs has been considered rare in both animals and plants. Here we show that Arabidopsis anaphase-promoting complex/cyclosome (APC/C) coactivator genes CDC20 and CCS52B (CDH1 ortholog) are co-expressed with their target cyclin B genes (CYCBs) during mitosis. CYCB transcripts can be exported and translated; however, CDC20 and CCS52B mRNAs are confined to the nucleus at prophase, and the cognate proteins are not translated until the redistribution of the mRNAs to the cytoplasm after nuclear envelope breakdown (NEBD) at prometaphase. The 5' untranslated region (UTR) plays dual roles in CDC20 mRNA nuclear localization and translation. Mitotic accumulation of CDC20 and CCS52B transcripts enables the timely and rapid activation of APC/C, while the nuclear sequestration of these transcripts at prophase appears to protect cyclins from precocious degradation.
  • ItemOpen AccessPublished version Peer-reviewed
    myTAI: evolutionary transcriptomics with R.
    (Oxford University Press (OUP), 2018-05-01) Drost, Hajk-Georg; Gabel, Alexander; Liu, Jialin; Quint, Marcel; Grosse, Ivo; Drost, Hajk-Georg [0000-0002-1567-306X]
    MOTIVATION: Next Generation Sequencing (NGS) technologies generate a large amount of high quality transcriptome datasets enabling the investigation of molecular processes on a genomic and metagenomic scale. These transcriptomics studies aim to quantify and compare the molecular phenotypes of the biological processes at hand. Despite the vast increase of available transcriptome datasets, little is known about the evolutionary conservation of those characterized transcriptomes. RESULTS: The myTAI package implements exploratory analysis functions to infer transcriptome conservation patterns in any transcriptome dataset. Comprehensive documentation of myTAI functions and tutorial vignettes provide step-by-step instructions on how to use the package in an exploratory and computationally reproducible manner. AVAILABILITY AND IMPLEMENTATION: The open source myTAI package is available at and CONTACT: SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
  • ItemOpen AccessPublished version Peer-reviewed
    Nitrate modulates stem cell dynamics in Arabidopsis shoot meristems through cytokinins
    (National Academy of Sciences, 2018-02-06) Jonsson, Henrik; Meyerowitz; Landrein, BPM; Formosa-Jordan; Malivert; Schuster, C; Melnyk, CW; Yang, W; Turnbull; Locke, JCW; Jonsson, Henrik [0000-0003-2340-588X]; Landrein, Benoit [0000-0002-2371-9996]; Schuster, Christoph [0000-0002-1948-2367]; Yang, Weibing [0000-0002-2379-5729]
    The shoot apical meristem (SAM) is responsible for the generation of all of the aerial parts of plants. Given its critical role, dynamical changes in SAM activity should play a central role in the adaptation of plant architecture to the environment. Using quantitative microscopy, grafting experiments and genetic perturbations, we connect the plant environment to the SAM, by describing the molecular mechanism by which cytokinins signal the level of nutrient availability to the SAM. We show that a systemic signal of cytokinin precursors mediates the adaptation of SAM size and organogenesis rate to the availability of mineral nutrients by modulating the expression of WUSCHEL, a key regulator of stem cell homeostasis. In time- lapse experiments, we further show that this mechanism allows meristems to adapt to rapid changes in nitrate concentration, and thereby modulate their rate of organ production to the availability of mineral nutrients within a few days. Our work sheds new light on the role of the stem cell regulatory network, by showing that it does not only maintain meristem homeostasis but also allows plants to adapt to rapid changes in the environment.
  • ItemOpen AccessAccepted version Peer-reviewed
    SecretSanta: flexible pipelines for functional secretome prediction.
    (Oxford University Press (OUP), 2018-07-01) Gogleva, Anna; Drost, Hajk-Georg; Schornack, Sebastian; Drost, Hajk-Georg [0000-0002-1567-306X]; Schornack, Sebastian [0000-0002-7836-5881]
    MOTIVATION: The secretome denotes the collection of secreted proteins exported outside of the cell. The functional roles of secreted proteins include the maintenance and remodelling of the extracellular matrix as well as signalling between host and non-host cells. These features make secretomes rich reservoirs of biomarkers for disease classification and host-pathogen interaction studies. Common biomarkers are extracellular proteins secreted via classical pathways that can be predicted from sequence by annotating the presence or absence of N-terminal signal peptides. Several heterogeneous command line tools and web-interfaces exist to identify individual motifs, signal sequences and domains that are either characteristic or strictly excluded from secreted proteins. However, a single flexible secretome-prediction workflow that combines all analytic steps is still missing. RESULTS: To bridge this gap the SecretSanta package implements wrapper and parser functions around established command line tools for the integrative prediction of extracellular proteins that are secreted via classical pathways. The modularity of SecretSanta enables users to create tailored pipelines and apply them across the whole tree of life to facilitate comparison of secretomes across multiple species or under various conditions. AVAILABILITY AND IMPLEMENTATION: SecretSanta is implemented in the R programming language and is released under GPL-3 license. All functions have been optimized and parallelized to allow large-scale processing of sequences. The open-source code, installation instructions and vignette with use case scenarios can be downloaded from SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
  • ItemOpen AccessPublished version Peer-reviewed
    Cross-species functional diversity within the PIN auxin efflux protein family.
    (eLife Sciences Publications, Ltd, 2017-10-24) O'Connor, Devin Lee; Elton, Samuel; Ticchiarelli, Fabrizio; Hsia, Mon Mandy; Vogel, John P; Leyser, Ottoline; O'Connor, Devin Lee [0000-0003-4071-8626]; Elton, Samuel [0000-0003-4470-4758]; Ticchiarelli, Fabrizio [0000-0001-5744-2393]; Vogel, John P [0000-0003-1786-2689]; Leyser, Ottoline [0000-0003-2161-3829]
    In Arabidopsis, development during flowering is coordinated by transport of the hormone auxin mediated by polar-localized PIN-FORMED1 (AtPIN1). However Arabidopsis has lost a PIN clade sister to AtPIN1, Sister-of-PIN1 (SoPIN1), which is conserved in flowering plants. We previously proposed that the AtPIN1 organ initiation and vein patterning functions are split between the SoPIN1 and PIN1 clades in grasses. Here we show that in the grass Brachypodium sopin1 mutants have organ initiation defects similar to Arabidopsis atpin1, while loss of PIN1 function in Brachypodium has little effect on organ initiation but alters stem growth. Heterologous expression of Brachypodium SoPIN1 and PIN1b in Arabidopsis provides further evidence of functional specificity. SoPIN1 but not PIN1b can mediate flower formation in null atpin1 mutants, although both can complement a missense allele. The behavior of SoPIN1 and PIN1b in Arabidopsis illustrates how membrane and tissue-level accumulation, transport activity, and interaction contribute to PIN functional specificity.
  • ItemOpen AccessPublished version Peer-reviewed
    Manipulation of Bryophyte Hosts by Pathogenic and Symbiotic Microbes.
    (Oxford University Press (OUP), 2018-04-01) Carella, Philip; Schornack, Sebastian; Schornack, Sebastian [0000-0002-7836-5881]
    The colonization of plant tissues by pathogenic and symbiotic microbes is associated with a strong and directed effort to reprogram host cells in order to permit, promote and sustain microbial growth. In response to colonization, hosts accommodate or sequester invading microbes by activating a set of complex regulatory programs that initiate symbioses or bolster defenses. Extensive research has elucidated a suite of molecular and physiological responses occurring in plant hosts and their microbial partners; however, this information is mostly limited to model systems representing evolutionarily young plant lineages such as angiosperms. The extent to which these processes are conserved across land plants is therefore poorly understood. In this review, we outline key aspects of host reprogramming that occur during plant-microbe interactions in early diverging land plants belonging to the bryophytes (liverworts, hornworts and mosses). We discuss how further knowledge of bryophyte-microbe interactions will advance our understanding of how plants and microbes co-operated and clashed during the conquest of land.
  • ItemOpen AccessAccepted version Peer-reviewed
    Mechanochemical Polarization of Contiguous Cell Walls Shapes Plant Pavement Cells.
    (Elsevier BV, 2017-11-06) Majda, Mateusz; Grones, Peter; Sintorn, Ida-Maria; Vain, Thomas; Milani, Pascale; Krupinski, Pawel; Zagórska-Marek, Beata; Viotti, Corrado; Jönsson, Henrik; Mellerowicz, Ewa J; Hamant, Olivier; Robert, Stéphanie; Jonsson, Henrik [0000-0003-2340-588X]
    The epidermis of aerial plant organs is thought to be limiting for growth, because it acts as a continuous load-bearing layer, resisting tension. Leaf epidermis contains jigsaw puzzle piece-shaped pavement cells whose shape has been proposed to be a result of subcellular variations in expansion rate that induce local buckling events. Paradoxically, such local compressive buckling should not occur given the tensile stresses across the epidermis. Using computational modeling, we show that the simplest scenario to explain pavement cell shapes within an epidermis under tension must involve mechanical wall heterogeneities across and along the anticlinal pavement cell walls between adjacent cells. Combining genetics, atomic force microscopy, and immunolabeling, we demonstrate that contiguous cell walls indeed exhibit hybrid mechanochemical properties. Such biochemical wall heterogeneities precede wall bending. Altogether, this provides a possible mechanism for the generation of complex plant cell shapes.
  • ItemOpen AccessPublished version Peer-reviewed
    LYS12 LysM receptor decelerates Phytophthora palmivora disease progression in Lotus japonicus.
    (Wiley, 2018-01) Fuechtbauer, Winnie; Yunusov, Temur; Bozsóki, Zoltán; Gavrin, Aleksandr; James, Euan K; Stougaard, Jens; Schornack, Sebastian; Radutoiu, Simona; Yunusov, Temur [0000-0001-9936-4354]; Gavrin, Aleksandr [0000-0003-0179-8491]; Schornack, Sebastian [0000-0002-7836-5881]
    Phytophthora palmivora is a devastating oomycete plant pathogen. We found that P. palmivora induces disease in Lotus japonicus and used this interaction to identify cellular and molecular events in response to this oomycete, which has a broad host range. Transcript quantification revealed that Lys12 was highly and rapidly induced during P. palmivora infection. Mutants of Lys12 displayed accelerated disease progression, earlier plant death and a lower level of defence gene expression than the wild type, while the defence program after chitin, laminarin, oligogalacturonide or flg22 treatment and the root symbioses with nitrogen-fixing rhizobia and arbuscular mycorrhiza were similar to the wild type. On the microbial side, we found that P. palmivora encodes an active chitin synthase-like protein, and mycelial growth is impaired after treatment with a chitin-synthase inhibitor. However, wheat germ agglutinin-detectable N-acetyl-glucosamine (GlcNAc) epitopes were not identified when the oomycete was grown in vitro or while infecting the roots. This indicates that conventional GlcNAc-mers are unlikely to be produced and/or accumulate in P. palmivora cell walls and that LYS12 might perceive an unknown carbohydrate. The impact of Lys12 on progression of root rot disease, together with the finding that similar genes are present in other P. palmivora hosts, suggests that LYS12 might mediate a common early response to this pathogen.
  • ItemOpen AccessPublished version Peer-reviewed
    The Medicago truncatula GRAS protein RAD1 supports arbuscular mycorrhiza symbiosis and Phytophthora palmivora susceptibility.
    (Oxford University Press (OUP), 2017-12-16) Rey, Thomas; Bonhomme, Maxime; Chatterjee, Abhishek; Gavrin, Aleksandr; Toulotte, Justine; Yang, Weibing; André, Olivier; Jacquet, Christophe; Schornack, Sebastian; Gavrin, Aleksandr [0000-0003-0179-8491]; Yang, Weibing [0000-0002-2379-5729]; Schornack, Sebastian [0000-0002-7836-5881]
    The roots of most land plants are colonized by symbiotic arbuscular mycorrhiza (AM) fungi. To facilitate this symbiosis, plant genomes encode a set of genes required for microbial perception and accommodation. However, the extent to which infection by filamentous root pathogens also relies on some of these genes remains an open question. Here, we used genome-wide association mapping to identify genes contributing to colonization of Medicago truncatula roots by the pathogenic oomycete Phytophthora palmivora. Single-nucleotide polymorphism (SNP) markers most significantly associated with plant colonization response were identified upstream of RAD1, which encodes a GRAS transcription regulator first negatively implicated in root nodule symbiosis and recently identified as a positive regulator of AM symbiosis. RAD1 transcript levels are up-regulated both in response to AM fungus and, to a lower extent, in infected tissues by P. palmivora where its expression is restricted to root cortex cells proximal to pathogen hyphae. Reverse genetics showed that reduction of RAD1 transcript levels as well as a rad1 mutant are impaired in their full colonization by AM fungi as well as by P. palmivora. Thus, the importance of RAD1 extends beyond symbiotic interactions, suggesting a general involvement in M. truncatula microbe-induced root development and interactions with unrelated beneficial and detrimental filamentous microbes.
  • ItemOpen AccessPublished version Peer-reviewed
    Sequence-independent identification of active LTR retrotransposons in Arabidopsis
    (Elsevier (Cell Press), 2018-03-05) Griffiths, J; Catoni, M; Iwaski, M; Paszkowski, J
    Detection of retrotransposons capable of contemporary transposition is hampered by the replicative nature of their movement and is usually limited to fortuitous observations of new integration events causing visible phenotypes. To circumvent this shortcoming, we developed a screening strategy for novel active retrotransposons containing long terminal repeats (LTR-TEs). Our approach is based on specific recovery of an LTR region that is part of the linear extrachromosomal DNA (ecDNA) synthetized in the reverse transcription step of the LTR-TE replication/transposition cycle. The method is inexpensive and straightforward and does not require prior knowledge of the retroelement sequence. Here we demonstrate the high sensitivity and specificity of this approach using Arabidopsis mutants with known retrotransposon activities. Using this method, we then identified a novel and mobile retroelement in the Landsberg erecta Arabidopsis ecotype that is absent in the annotated reference genome of Col-0. The cost-effective procedure presented here can be used to identify transposition-competent LTR-retrotransposons in a broad variety of biological specimens, independent of their sequence annotation.
  • ItemOpen AccessAccepted version Peer-reviewed
    Plant Vasculature: Selective Membrane-to-Microtubule Tethering Patterns the Xylem Cell Wall.
    (Elsevier BV, 2017-09-11) Bourdon, Matthieu; Kalmbach, Lothar; Helariutta, Yrjö; Bourdon, Matthieu [0000-0001-7243-5642]; Helariutta, Yrjo [0000-0002-7287-8459]
    To introduce pits into a cell wall, plants depolymerize cortical microtubules, which prevents subsequent secondary cell wall thickening. A newly identified protein tethers microtubules to the plasma membrane and contains this breakdown to defined regions, thereby shaping these holes.
  • ItemOpen AccessPublished version Peer-reviewed
    High-frequency recombination between members of an LTR retrotransposon family during transposition bursts.
    (Springer Science and Business Media LLC, 2017-11-03) Sanchez, Diego H; Gaubert, Hervé; Drost, Hajk-Georg; Zabet, Nicolae Radu; Paszkowski, Jerzy; Drost, Hajk-Georg [0000-0002-1567-306X]
    Retrotransposons containing long terminal repeats (LTRs) form a substantial fraction of eukaryotic genomes. The timing of past transposition can be estimated by quantifying the accumulation of mutations in initially identical LTRs. This way, retrotransposons are divided into young, potentially mobile elements, and old that moved thousands or even millions of years ago. Both types are found within a single retrotransposon family and it is assumed that the old members will remain immobile and degenerate further. Here, we provide evidence in Arabidopsis that old members enter into replication/transposition cycles through high rates of intra-family recombination. The recombination occurs pairwise, resembling the formation of recombinant retroviruses. Thus, each transposition burst generates a novel progeny population of chromosomally integrated LTR retrotransposons consisting of pairwise recombination products produced in a process comparable the sexual exchange of genetic information. Our observations provide an explanation for the reported high rates of sequence diversification in retrotransposons.