Arabidopsis Research Roundup: June 9th

This edition of the Arabidopsis Research Roundup pleasingly includes four Open Access articles. Firstly Jose Gutierrez-Marcos leads an investigation into stress-induced memory, secondly Richard Morris is the corresponding author on a study that has developed a new model that explains waves of calcium signalling that response to environmental stresses. Thirdly is a UK-US collaboration that defines the factors that control carotenoid accumulation in seeds. Finally Chris Hawes leads a study that characterises the novel localisation of a subset of auxin biosynthetic enzymes.

Wibowo A, Becker C, Marconi G, Durr J, Price J, Hagmann J, Papareddy R, Putra H, Kageyama J, Becker J, Weigel D, Gutierrez-Marcos J (2016) Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity Elife http://dx.doi.org/10.7554/eLife.13546 Open AccessStress_Model

Jose Gutierrez-Marcos is the corresponding author on this pan-European study that adds to our increasing knowledge about the role of generational memory in the response to stress. Distinct regions of the Arabidopsis genome are susceptible to fluctuations in the level of DNA methylation in response to hyperosmotic stress, a condition that persists into a following generation. This effect is transmitted through the female lineage and the authors investigate this effect in more detail by focussing on a single epigenetically targeted locus. By designing experiments that ran over a series of generations they show that a plants ‘short term memory’ is reliant on the DNA methylation machinery and is able to transmit a distinct developmental response to immediate offspring.

Evans MJ, Choi WG, Gilroy S, Morris RJ (2016) A ROS-assisted Calcium Wave Dependent on AtRBOHD and TPC1 Propagates the Systemic Response to Salt Stress in Arabidopsis Roots. Plant Physiol.

http:/​/​dx.​doi.​org/​10.​1104/​pp.​16.​00215 Open Access

Richard Morris (JIC) leads this US-UK collaboration that investigates the downstream mechanisms that occur after the waves of ROS and Ca2+ signalling that respond to environmental stresses. The authors show that the current model for propagation of this wave, which relies upon a diffusive wave Ca2+ signalling, is unable to explain the speed of transmission of the wave. The authors develop a new model that adds a ROS-signalling component to explain the velocity of the Ca2+ wave and experimentally verify that their model could represent the in vivo situation. In addition they show that the effectiveness of this ROS-release signalling module is dependent on the activity of the vacuolar ion channel TPC1 and the NADPH Oxidase AtRBOHD.
CaWavePic
Gonzalez-Jorge S, Mehrshahi P, Magallanes-Lundback M, Lipka AE, Angelovici R, Gore MA, DellaPenna D (2016) ZEAXANTHIN EPOXIDASE activity potentiates carotenoid degradation in maturing Arabidopsis seed. Plant Physiol.

http:/​/​dx.​doi.​org/​10.​1104/​pp.​16.​00604 Open Access

The lead author of this US-led study is Sabrina Gonzalez-Jorge who is currently a post-doc in GARNet committee member Ian Henderson’s lab in Cambridge. This study elucidates nine loci that are involved in carotenoid homeostasis in Arabidopsis seeds and shows that plants lacking the ZEAXANTHIN EPOXIDASE (ZEP) protein have a six-fold reduction in total seed carotenoids. Natural variation within the ZEP gene is able to account for the fine-tuning of seed carotenoid content and acts upstream of two previously characterised CAROTENOID CLEAVAGE DIOXYGENASE enzymes. Importantly, and somewhat surprisingly, four of the nine Arabidopsis loci are thought to have conserved function in determining the composition of carotenoids in maize kernels. This demonstrates that studying this phenomonen in Arabidopsis is highly relevant for study of the same process in economically important crops.

Kriechbaumer V, Botchway SW, Hawes C (2016) Localization and interactions between Arabidopsis auxin biosynthetic enzymes in the TAA/YUC-dependent pathway J Exp Bot.

http://dx.doi.org/10.1093/jxb/erw195 Open Access

Chris Hawes (Oxford Brookes) leads this study that localised a subset of enzymes involved in auxin biosynthesis to the endoplasmic reticulum. In addition certain of these enzymes appear to physically interact. This localisation is confirmed by showing ER microsomal fractions are able to undertake auxin biosynthesis. The auxin signalling pathway is complex and well characterised yet this finding adds another layer of regulation that might influence the dynamics of auxin activity.

Arabidopsis Research Report: May 26th

This weeks Arabidopsis Research Roundup includes six studies across a range of discplines. Firstly Alison Smith provides an excellent audio description of an investigation into the dynamics of night-time starch degradation.

Secondly three UK institutions (Durham, Exeter and Oxford Brookes) participate in a study of VAP27 membrane network proteins. Next a broad collaboration from CPIB in Nottingham then introduce a multi-scale model that helps describe Arabidopsis root development.

We also include two studies that involve collaborations with Korean researchers: Gary Loake is a contributor on a study that introduces plant RALF genes whilst Ian Henderson’s research group participates in a study into the function of the SWR1 complex in miRNA gene expression. Finally we highlight a new Plant Cell teaching tool put together by UK academics from Hull and Bristol.

Feike D, Seung D, Graf A, Bischof S, Ellick T, Coiro M, Soyk S, Eicke S, Mettler-Altmann T, Lu KJ, Trick M, Zeeman SC, Smith AM (2016) The starch granule-associated protein EARLY STARVATION1 (ESV1) is required for the control of starch degradation in Arabidopsis thaliana leaves Plant Cell

http://dx.doi.org/10.1105/tpc.16.00011 Open Access

This UK and Swiss study is led by Alison Smith from the John Innes Centre and investigates starch degradation that occurs during nighttime. They developed a novel screen to identify an uncharacterized mutant called early starvation 1 (esv1) that more rapidly degraded starch so that it is exhausted earlier in the night. They found that ESV1 and the related LESV1 proteins associated with starch granules within the chloroplast stroma. The authors propose that these proteins influence the organisation of the starch granule matrix, facilitating access for starch-degrading enzymes. In addition they also show that this function appears to be conserved throughout all starch-synthesizing organisms.

Professor Smith provides an audio description of this paper:

Wang P, Richardson C, Hawkins TJ, Sparkes I, Hawes C, Hussey PJ (2016) Plant VAP27 proteins: domain characterization, intracellular localization and role in plant development. New Phytol. 210(4):1311-1326 http://dx.doi.org/10.1111/nph.13857

This cell biology-focused study is a collaboration between the Universities of Exeter, Durham and Oxford Brookes and investigates vesicle-associated membrane protein-associated proteins (VAPs), which form part of the network that links the plasma membrane and ER. The Arabidopsis genome contains 10 VAP homologues (VAP27-1 to -10) split into 3 clades. Members of clades I and II localise to both ER as well as to ER/PM contact sites (EPCSs) whilst clade II members are only found at the PM, all discovered through transient expression experiments in tobacco. Interestingly the localisation to the EPCSs is associated with the cytoskeleton but does not require the presence of that underlying structure. These proteins are expressed in most cell types and when their levels are altered, plants show pleiotropic phenotypes. Overall this study shows that VAP27 proteins are required for ER-cytoskeleton interactions that are critical for normal plant development.

Muraro D, Larrieu A, Lucas M, Chopard J, Byrne H, Godin C, King J (2016) A multi-scale model of the interplay between cell signalling and hormone transport in specifying the root meristem of Arabidopsis thaliana. J Theor Biol. S0022-5193(16)30070-4 http://dx.doi.org/10.1016/j.jtbi.2016.04.036

From http://dx.doi.org/10.1016/j.jtbi.2016.04.036

This investigation was performed at CPIB in Nottingham in collaboration with the Virtual Plant Project in Montpellier and is led by John King. The authors have developed a multi-scale computational model that allows the study of signalling networks that occurs during Arabidopsis root growth. This model was experimentally tested to investigate how it is affected by hormonal changes during root growth. The model was able to identify two novel mutants that significantly alter root length through perturbations in meristem size. In general this study demonstrates the value of multi-scale modeling as part of the process of evaluating the function of the components that define the formation of the root meristem.

Sharma A, Hussain A, Mun BG, Imran QM, Falak N, Lee SU, Kim JY, Hong JK, Loake GJ, Ali A, Yun BW (2016) Comprehensive analysis of plant rapid alkalization factor (RALF) genes Plant Physiol Biochem. 106:82-90

http://dx.doi.org/10.1016/j.plaphy.2016.03.037

This Korean-led study includes a contribution from Gary Loake from the University of Edinburgh and is the first comprehensive investigation of Rapid alkalization factor (RALF) proteins across plant species. These RALF proteins are thought to be important signalling molecules in plant defense and development. This study provides information on gene structure, subcellular locations, conserved motifs, protein structure, protein-ligand interactions and promoter analysis across Arabidopsis, rice, maize and soybean. The RALF genes are phylogenetically divided into 7 clades and their mRNA upregulation following nitrosative and oxidative stresses suggests that they are function in responding to changes in cellular redox status. Overall this manuscript provides a valuable resource to prime future research into the role of RALF genes.

Choi K, Kim J, Müller SY, Oh M, Underwood C, Henderson I, Lee I (2016) Regulation of microRNA-mediated developmental changes by the SWR1 chromatin remodeling complex in Arabidopsis thaliana. Plant Physiol. http://dx.doi.org/10.1104/pp.16.00332

GARNet committee member Ian Henderson (Cambridge) is a contributor on this study that is led by researchers in Seoul, South Korea. In the last ARR, Vinod Kumar described work that looked into the role of the SWR1 chromatin-remodeling complex and this study provides an insight into the role of this same SWR1 complex on microRNA (miRNA)-mediated transcriptional control. In SWR1 complex mutants (arp6, sef, and pie1), deep sequencing revealed that many miRNA types and their target mRNAs are misregulated. This further establishes the role of the SWR1 complex in the control of nucleosome occupancy, likely by mediating the exchange of H2A isoforms, for a range of genes involved in the fine-tuning of numerous developmental processes.

Hubbard, K, Dodd, A. (2016). Rhythms of Life: The Plant Circadian Clock. Teaching Tools in Plant Biology: Lecture Notes. http://dx.doi.org/10.1105/tpc.116.tt0416

Katherine Hubbard and Anthony Dodd have produced a teaching resource focused on the Circadian Clock as part of the increasingly comprehensive Plant Cell Teaching Tools. Most academics are looking to save time and this resource will allow them to do this and provides excellent coverage of the topic.

Arabidopsis Research Roundup: May 13th

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Published on: May 13, 2016

This weeks Arabidopsis Research Roundup includes two peer-reviewed papers and the release of a preprint. Vinod Kumar from the JIC provides an audio description of a study that investigates the role of the SWR1 complex in the defence response. Secondly Jessica Metcalf from Oxford is a contributor on a study that looks at population responses of Arabidopsis to simulated climate change. Finally John Brown (University of Dundee and the James Hutton Institute) is the corresponding authors on a preprint that introduces a new Arabidopsis transcriptome annotation.

Berriri S, Gangappa SN, Kumar SV (2016) SWR1 chromatin-remodelling complex subunits and H2A.Z have non-overlapping functions in immunity and gene regulation in Arabidopsis Molecular Plant http://dx.doi.org/10.1016/j.molp.2016.04.003 Open Access

Vinod Kumar (John Innes Centre) is the corresponding author on this study that investigates the incorporation of the histone variant H2A.Z into Arabidopsis nucleosomes. This histone variant is important in the control of differential gene expression although its role in plant immunity is not well understood. H2A.Z is integrated into nucleosome by the SWR1 chromatin remodelling complex that contains a number of subunits namely PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 (PIE1), ACTIN-RELATED PROTEIN6 (ARP6), and SWR1 COMPLEX 6 (SWC6). Interestingly each subunit plays discrete roles in different pathogen response processes including basal resistance, enhanced resistance, effector-triggered immunity or in altered JA/ET-mediated immunity. Genome wide expression analysis reveals a role for PIE1 in the crosstalk between signalling processes and overall that SWR1c components might have distinct non-overlapping roles during gene regulation and expression.

Dr Kumar kindly provides a brief audio description of this paper:

 

Fournier-Level A, Perry EO, Wang JA, Braun PT, Migneault A, Cooper MD, Metcalf CJ, Schmitt J (2016) Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana PNAS http://dx.doi.org/10.1073/pnas.1517456113 PNASpic

Mathematician Jessica Metcalf (Oxford) is an author on this US-led study that uses Arabidopsis to investigate the effect of climate change on evolution of fitness. Over four seasons plants were grown under four climatic conditions (present day, overall increased temp, winter-warming and poleward-migration temp) and 12 traits were measured as a proxy for fitness evolution. The data was used to simulate evolutionary trajectories over a 50-100 year period. The authors found that each climatic condition resulted in different outcomes where populations with fewer founding genotypes or less initial diversity adapted less well to altered conditions. This suggests that successful adaptation to climate change is linked to the diversity within a given population prior to the change occurring.

Zhang R, Calixto C, Marquez Y, Venhuizen P, Tzioutziou N, Guo W, Spensley M, Frey N, Hirt H, James A, Nimmo H, Barta A, Kalyna M, Brown J (2016) AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data. Preprint BioRxiv http://dx.doi.org/10.1101/051938 Open Access

This preprint includes researchers from the Universities of Dundee (John Brown), Glasgow (Hugh Nimmo) and Vienna and the James Hutton Institute and introduces AtRTD2, a new transcriptome for Arabidopsis and AtRTD2-QUASI for expression analysis and quantification of alternatively spliced isoforms in RNA-seq data.

Arabidopsis Research Roundup: March 18th

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Published on: March 18, 2016

This weeks Arabidopsis Research Roundup includes three papers from the Norwich Research Park on very different topics. Firstly the team of Richard Morris investigates the nature of mRNA sequences that are transported over long-distances. Secondly Kristen Bomblies introduces a set of genes involved in the evolution of weediness whilst finally Cyril Zipfel is involved in research that developed a novel assay for identification of defence signaling components. Elsewhere Paul Devlin’s group from RHUL characterises the interactions between components of a light signaling pathway whilst Alex Webb and co-workers use a novel assay to confirm the activity of plant nucleotide cyclases involved in calcium signaling.

Calderwood A, Kopriva S, Morris RJ (2016) Transcript abundance explains mRNA mobility data in Arabidopsis thaliana. Plant Cell http://dx.doi.org/10.1105/tpc.15.00956 Open Access

Richard Morris (JIC) is the lead author on this ‘Breakthrough Report’ that analyses previously generated data in order to ascertain whether populations of mRNAs that are transported long-distances in the phloem are selected by any mechanism. They showed that in general mobile transcripts can be explained by their abundance and half-life, leading to the conclusion that the majority of transported mRNAs are not selected on the basis of their primary sequence.

Baduel P, Arnold B, Weisman CM, Hunter B, Bomblies K (2016) HABITAT-ASSOCIATED LIFE HISTORY AND STRESS-TOLERANCE VARIATION IN ARABIDOPSIS ARENOSA Plant Physiol. http://dx.doi.org/10.1104/pp.15.01875 Open Access

Recent ECR Research Grant awardee Kristen Bomblies (JIC) leads this investigation into growth variation in Arabidopsis Arenosa. This obligate outbreeding relative of A.thaliana is normally not weedy but can transition to weediness in conditions of high disturbance. This study uses transcriptome sequencing, genome resequencing scans for selection, and stress tolerance assays to investigate a weedy population of A.arenosa that has been discovered growing along railway lines through central and Northern Europe. These plants show constitutive upregulation of genes involved in heat shock and freezing tolerance. Amongst the genes that were strongly selected in the weedy population was LATE ELONGATED HYPOCOTYL (LHY), which is known to regulate many stress-regulated genes in A.thaliana and therefore might be a significant determinant in the evolution of weediness.

Saur IM, Kadota Y, Sklenar J, Holton NJ, Smakowska E, Belkhadir Y, Zipfel C, Rathjen JP (2016) NbCSPR underlies age-dependent immune responses to bacterial cold shock protein in Nicotiana benthamiana Proc Natl Acad Sci U S A. http://dx.doi.org/10.1073/pnas.15118471

This Australian-Austrian-UK collaboration includes work from the lab of Cyril Zipfel (TSL). The initial work in this study uses the Nicotiana benthamiana expression system to identify novel leucine-rich repeat (LRR)-containing pattern recognition receptors (PRR) that interact with the BRI1-ASSOCIATED KINASE1 (BAK1) protein, which is important in recognition of bacterial pathogens. N.benthamiana plants were treated with the effector peptide csp22 and the resulting samples were immunopurified with BAK1. They identified a protein termed RECEPTOR-LIKE PROTEIN REQUIRED FOR CSP22 RESPONSIVENESS (NbCSPR) which, when silenced in tobacco resulted in reduced defence responses to the csp22 peptide. Subsequent expression of NbCSPR in Arabidopsis caused antibacterial resistance. Primarily the authors demonstrate a novel protocol that could be used to identify further novel components in signaling pathways that response to pathogen attack.

Siddiqui H, Khan S, Rhodes BM, Devlin PF (2016) FHY3 and FAR1 Act Downstream of Light Stable Phytochromes Front Plant Sci. 7:175 http://dx.doi.org/10.3389/fpls.2016.00175 Open Access
DevlinPic
Paul Devlin (RHUL) is the lead on this study that looks at the regulation of the ELF4 gene. This gene is a light-dependent target for the transcription factors FHY3 and FAR1 and the authors demonstrate that this signaling acts via not only the phytochrome PhyA but also through phyB, phyD, and phyE. ELF4 induction by FHY3 and FAR1 occurs specifically in the evening, which allows expression of ELF4 beyond dusk during shortening days. Without the action of the two transcription factors, this ELF4 expression is not maintained resulting in further downstream gene expression changes that alters the cycling of the circadian clock.

Abdul-Awal SM, Hotta CT, Dodd AN, Davey MP, Smith AG, Webb AA (2016) NO-mediated [Ca2+]cyt increases depend on ADP-ribosyl cyclase activity in Arabidopsis Plant Physiol. http://dx.doi.org/10.1104/pp.15.01965 Open Access

This study continues Alex Webb’s (Cambridge) work in the area of calcium signaling by investigating the control of cyclic ADP-ribose (cADPR) production in Arabidopsis. Although the role of cADPR in plant signaling is well established there are no ADPR cyclase enzymes with strong similarity to known metazoan enzymes in previously interrogated plant genomes. This argues for either a unique synthesis route for cADPR or for the activity of an enzyme with low sequence similarity to previously characterized cyclases. To test these difference ideas the authors developed two novel fluorescence-based assays to measure ADPR cyclase activity. These assays reveal that indeed there is activity that resembles the characteristics of a cyclase, which additionally is activated by nitric oxide (NO). This potentially links NO signaling activity to increased levels of cADPR and mobilisation of a calcium signal.

Arabidopsis Research Roundup: March 4th

There are six articles in this weeks Arabidopsis Research Roundup that bridge a diverse range of topics. Firstly lead author Deirdre McLachlan provides an audio description of a study that investigates the role of triacylglycerol breakdown in stomatal signaling. Secondly is a study that assesses the role of a Rab GTPase in control of anisotropic cell growth. The third and fourth papers looks into the defence response, focused on either JA or nitric oxide signaling. Finally are two papers that look into the response of Arabidopsis seedlings to growth on either arsenic or cadmium.

McLachlan DH, Lan J, Geilfus CM, Dodd AN, Larson T, Baker A, Hõrak H, Kollist H, He Z, Graham I, Mickelbart MV, Hetherington AM The Breakdown of Stored Triacylglycerols Is Required during Light-Induced Stomatal Opening Current Biology http://dx.doi.org/10.1016/j.cub.2016.01.019 Open Access
Slide 1
The control of stomatal opening is a key environmental response to changes in CO2 levels and water availability. This study, led by Alistair Hetherington (Bristol), demonstrates that triacylglycerols (TAGs), contained in lipid droplets (LD), are critical for light-induced stomatal opening. Following illumination, the number of LDs are reduced through the β-oxidation pathway, a response that requires blue-light receptors. The authors postulate that a reduction in ATP-availability due to delayed fatty acid breakdown contributed to the stomatal phenotype. The lack of available ATP was confirmed following analysis of the activity of a plasma membrane H+-ATPase. Overall the authors suggest that the light-induced breakdown of TAG contributes to an evolutionarily conserved signaling pathway that controls stomatal opening therefore playing a key role in environmental adaptation.

The lead author of this study, Deidre McLachlan kindly provides a brief audio description of this paper.

During our discussion Deidre mentioned some related work that links blue-light signaling and starch degradation during stomatal opening that was included in a recent ARR.

 

Kirchhelle C, Chow CM, Foucart C, Neto H, Stierhof YD, Kalde M, Walton C, Fricker M, Smith RS, Jérusalem A, Irani N, Moore I (2016) The Specification of Geometric Edges by a Plant Rab GTPase Is an Essential Cell-Patterning Principle During Organogenesis in Arabidopsis. Developmental Cell 36(4):386-400 http://dx.doi.org/10.1016/j.devcel.2016.01.020 Open Access
Rab5C
Ian Moore (Oxford) is the corresponding author on this UK-German collaboration that investigates the role of a Rab GTPase in pattern formation during organogenesis. It is known that the endomembrane system controls the asymmetric distribution of cargoes to different ‘geometric edges’ of a plant cell, establishing biochemically distinct domains that are important for anisotropic growth. This study identifies a new type of membrane vesicle that accumulates specifically along geometric edges and that contains the RAB-A5c protein which, when inhibited, distorts the geometry of cells in subsequently formed lateral organs (in this case, lateral roots). Interestingly this effect is independent of changes to general endomembrane trafficking. The precise mechanism of RAB-A5c activity is unknown but loss of its activity reduces cell wall stiffness at domain-specific locations, therefore perturbing cell growth in those directions. Therefore this study provides interesting insight into fundamental mechanisms that control the growth of cells in a developing organ.

Thatcher LF, Cevik V, Grant M, Zhai B, Jones JD, Manners JM, Kazan K (2016) Characterization of a JAZ7 activation-tagged Arabidopsis mutant with increased susceptibility to the fungal pathogen Fusarium oxysporum J Exp Bot. http://dx.doi.org/10.1093/jxb/erw040 Open Access

Jonathan Jones (TSL) and Murray Grant (Exeter) are collaborators on this research that investigates the role of jasmonic acid signaling in plant resistance to the fungal pathogen Fusarium oxysporum. In this study they show that the JASMONATE ZIM-domain7 (JAZ7) gene is induced by Fusarium oxysporum and that the jaz7-1D mutant has increased suspectibility to infection. This genotype has constitutive JAZ7 expression and also demonstrates sensitivity to a bacterial pathogen. To cause alterations in gene expression, the JAZ7 protein interacts with a range of transcriptional activators and repressors. The authors postulate that in wildtype plants JAZ7 represses the JA-transcriptional network through its interaction with the co-repressor TOPLESS protein and that in the jaz7-1D plants this response network is hyper-activated leading to an inappropriately high response to pathogen attack.

Yun BW, Skelly MJ, Yin M, Yu M, Mun BG, Lee SU, Hussain A, Spoel SH, Loake GJ (2016) Nitric oxide and S-nitrosoglutathione function additively during plant immunity. New Phytol. http://dx.doi.org/10.1111/nph.13903

Gary Loake and GARNet Advisory board member Steven Spoel (Edinburgh) are the leaders of this UK-Korean collaboration that studies the role of Nitric Oxide (NO) in the plant defence response. NO often undergoes S-nitrosylation to produce S-nitrosothiol (SNO), which is important for its bioactivity. This reaction involves the S-nitrosoglutathione reductase 1 (GSNOR1) enzyme, which serves to turnover the NO donor, S-nitrosoglutathione (GSNO). In this study the authors investigate mutant plants that accumulate NO and some a reduction in the basal defence response due to a reduction in salicylic acid (SA) signaling. This response was not rescued by the overexpression of GSNOR1 even though this was able to reduce phenotypes resulting from SNO accumulation. Mutant plants that have increased NO accumulation but lower activity of GSNOR1, so therefore an increased ratio of NO:SNO, were more suspectible to growth of bacterial pathogens. The authors conclude that the relationship between NO and GSNO is critically for plant immunity and development.

Lindsay ER, Maathuis FJ (2016) Arabidopsis thaliana NIP7;1 is Involved in Tissue Arsenic Distribution and Tolerance in Response to Arsenate FEBS Lett. http://dx.doi.org/10.1002/1873-3468.12103

Francois Maathuis (York) is the corresponding author of this study that investigates the role of the Arabidopsis aquaglyceroporin NIP7;1 in the uptake of different chemical forms of arsenic. Mutant nip7;1 plants improved the tolerance of arsenic by reducing uptake of the chemical. This is the first demonstration for the role of a NIP transporter in the response to arsenic and highlights the possibility of focussing on these proteins as a target for breeding or genetically-modifying tolerance to this toxic metal.

Wang H, He L, Song J, Cui W, Zhang Y, Jia C, Francis D, Rogers HJ, Sun L, Tai P, Hui X, Yang Y, Liu W (2016) Cadmium-induced genomic instability in Arabidopsis: Molecular toxicological biomarkers for early diagnosis of cadmium stress Chemosphere 150:258-265 http://dx.doi.org/10.1016/j.chemosphere.2016.02.042

Hilary Rodgers (Cardiff) is the sole UK representative on this Chinese study that has developed screening parameters to evaluate the growth of plants on cadmium. The study uses microsatellite instability (MSI) analysis, random-amplified polymorphic DNA (RAPD), and methylation-sensitive arbitrarily primed PCR (MSAP-PCR) to define a range of genomic alterations that occurred after growth of Arabidopsis plants across a range of concentrations of cadmium. They conclude that analysis of genomic methylation polymorphisms were the most sensitive biomarkers to diagnosis early cadmium stress in these plants and provide important insights for future biomonitoring strategies.

Arabidopsis Research Roundup: February 24th

Just three papers in this weeks Arabidopsis Research Roundup and they each cover fundamental aspects of the hormone and environmental control of gene expression. First Keith Lindsey provides an audio description of work that aims to dissect the complex hormonal regulation of root growth while secondly, Nick Harberd is involved in a study that investigates the HY5 shoot-root signaling protein. Finally Ian Graham leads a study into factors that regulate seed dormancy.

Rowe JH, Topping JF, Liu J, Lindsey K (2016) Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin New Phytol. http://dx.doi.org/ 10.1111/nph.13882 Open Access
HormoneSig
Keith Lindsey (Durham) is the corresponding author for this study that investigates the complex hormonal network that regulates the Arabidopsis root response to osmotic stress. The effect of ABA, cytokinin and ethylene on auxin transport are assessed through changes in the dynamics of PIN protein expression. Unsurprisingly they discover a wide range of effects transmitted via crosstalk between these four hormones and that these effects act in a tissue specific manner, as the expression of PIN1 (in the vascular tissue) and PIN2 (in the lateral root cap and epidermis) are altered in different ways. Ultimately the authors conclude that the classic ‘stress hormone’ ABA regulates the root response to drought together with auxin, ethylene and cytokinin in a complex signaling network.

Keith has kindly supplied a brief audio description of this work.

Chen X, Yao Q, Gao X, Jiang C, Harberd NP, Fu X (2016) Shoot-to-Root Mobile Transcription Factor HY5 Coordinates Plant Carbon and Nitrogen Acquisition http://dx.doi.org/10.1016/j.cub.2015.12.066
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GARNet committee member Nick Harberd (Oxford) is the UK representative on this Chinese-led study that investigates the mode of action of the mobile transcription factor ELONGATED HYPOCOTYL5 (HY5). It has been long known that HY5, a bZIP TF, regulates growth responses to light and in this study the authors demonstrate that HY5 controls light-regulated root growth and nitrate uptake. Remarkably, HY5 from the shoot can activate root-derived HY5, in turn switching on the nitrate transporter NRT2.1. This response involves a mechanism that senses carbon:nitrogen balance across different light conditions, thus placing HY5 as a key regulator in the whole-plant response to changing environmental conditions.

Dave A, Vaistij FE, Gilday AD, Penfield SD, Graham IA (2016) Regulation of Arabidopsis thaliana seed dormancy and germination by 12-oxo-phytodienoic acid Journal of Experimental Botany http://dx.doi.org/10.1093/jxb/erw028 Open Access

This paper results from a collaboration between the labs of Ian Graham (CNAP, York) and Steve Penfield (John Innes Centre) and features an investigation into factors that regulate seed germination. Previously it was known that oxylipin 12-oxo-phytodienoic acid (OPDA) acts together with ABA to regulate germination but this study elucidates that OPDA specifically acts via the ABI5 and RGL2 hormone-regulated proteins. Furthermore the OPDA-ABA signal also acts via another dormancy promoting factor, MOTHER-OF-FT-AND-TFL1 (MFT). Therefore maintenance of dormancy in Arabidopsis seedlings is regulated by ABA and MFT promoting the accumulation of OPDA, highlighting this as a critical control point in this complex process.

Arabidopsis Research Roundup: February 17th

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Published on: February 16, 2016

This weeks Arabidopsis Research Roundup features papers that build upon the history of research in each featured lab. Firstly Gareth Jenkins from Glasgow continues to investigate mechanisms of UV-B signaling whilst Laila Moubayidin, now at the JIC, is involved in work that investigates the multiple factors that control root meristem size. Finally we present a three protocol papers that are featured in a new colelction of articles that focus on protocols that can be used to assess different environmental responses.

Findlay KM, Jenkins GI (2016) Regulation of UVR8 photoreceptor dimer/monomer photo-equilibrium in Arabidopsis plants grown under photoperiodic conditions. Plant Cell Environment http://dx.doi.org/10.1111/pce.12724 Open Access
UVBmodel
The research group led by Gareth Jenkins (Glasgow) continues their work on the plant response to UV in this study that investigates the binding patterns of the UVR8 protein. UVR8 mediates the plant response to UV-B light and the protein either exists in a monomeric (active) or dimeric (inactive) form. This study shows that UVR8 maintains dimer/monomer photo-equilibrium through diurnal photoperiods and that the REPRESSOR OF UV-B PHOTOMORPHOGENESIS 1 (RUP1) and RUP2 proteins are necessary for maintaining this equilibrium. Interestingly they show that the UVR8 balance is tipped toward the monomeric form in lower temperatures. This shows that the protein does not act as a simple switch to signal for changes in UV-B as its effect is influenced by environmental parameters outside of the light source.

Moubayidin L, Salvi E, Giustini L, Terpstra I, Heidstra R, Costantino P, Sabatini S (2016) A SCARECROW-based regulatory circuit controls Arabidopsis thaliana meristem size from the root endodermis Planta http://dx.doi.org/10.1007/s00425-016-2471-0 Open Access

Laila Moubayidin now works as a postdoc with Lars Ostergaard at the JIC but this work is the result of research conducted with Sabrina Sabatini in Rome. In this study they continue the labs investigation into the role of the SCARECROW (SCR) protein in the control of root meristem size. They show that SCR, from endodermal cells, sustains a gibberellic acid signal by regulating RGA REPRESSOR OF ga1-3 (RGA) protein stability. This in turn controls the activity of the cytokinin responsive transcription factor ARR1 at the root transition zone. This activity therefore maintains a balance of cell division and differentiation that maintains correct meristem size.

A new edition of ‘Methods in Molecular Biology’ focuses on ‘Environmental Responses in Plants and includes a number of papers featuring UK authors who work on Arabidopsis.

Hydrotropism: Analysis of the Root Response to a Moisture Gradient’ that features Malcolm Bennett from CPIB in Nottingham. http://dx.doi.org/10.1007/978-1-4939-3356-3_1

Monitoring Alternative Splicing Changes in Arabidopsis Circadian Clock Genes’ from the group of John Brown at the James Hutton in Dundee http://dx.doi.org/10.1007/978-1-4939-3356-3_11

Assessing the Impact of Photosynthetic Sugars on the Arabidopsis Circadian Clock’ from the lab of Alex Webb in Cambridge. http://dx.doi.org/10.1007/978-1-4939-3356-3_12

Arabidopsis Research Roundup: January 29th

This weeks Arabidopsis Research Roundup features a paper from David Baulcombe and Joe Ecker that further deciphers mechanisms of RNA silencing and is kindly discussed by postdoc Mat Lewsey in a short audio description. Elsewhere there are three studies that include researchers from CPIB in Nottingham. Leah Band contributes to a study that links environment sensing, cell death and auxin signaling whilst Ive De Smet leads a study that finds new proteins involved in cell division. Malcolm Bennett and John King take a modeling approach to describe auxin signaling via the GH3 protein family. Finally Frank Menke leads a study that provides more detail into Pattern Recognition Receptor (PRR) mediated immune signaling and then Jim Dunwell participates in a paper that describes a new method of analyzing GWAS data.

Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker JR (2016) Mobile small RNAs regulate genome-wide DNA methylation. Proc Natl Acad Sci U S A. http://dx.doi.org/10.1073/pnas.1515072113 Open Access

Over the past few years RNA-mediated silencing has emerged a key mechanism for the control of gene expression. This study is a collaboration between the lab of Sir David Balcombe (Cambridge) and Joe Ecker at the SALK institute in California. Mat Lewsey, who is a British postdoc working with Professor Ecker, kindly provided a short audio description of the paper.

These groups have previously shown that sRNAs are highly mobile throughout the plant. This study shows that thousands of loci expressed in roots are dependent on mobile sRNAs generated from the shoot. They unpick the genetic basis of this response showing that it is largely dependent on the DOMAINS REARRANGED METHYLTRANSFERASES 1/2 (DRM1/DRM2) but not CHROMOMETHYLASE (CMT)2/3 DNA methyltransferases. They also show that mobile sRNAs are resposible for the silencing of TEs that are found in gene-rich regions, although this is not a physiologically important response in Arabidopsis, which contains a relatively small amount of transposon tissue. Interestingly they a show that sRNAs generated from different Arabidopsis ecotypes are able to move across graft junctions and can cause methylation in usually unmethylated regions.

PNASpicXuan W, Band LR, Kumpf RP, Van Damme D, Parizot B, De Rop G, Opdenacker D, Möller BK, Skorzinski N, Njo MF, De Rybel B, Audenaert D, Nowack MK, Vanneste S, Beeckman T (2016) Cyclic programmed cell death stimulates hormone signaling and root development in Arabidopsis. Science . 351(6271):384-7 http://dx.doi.org/10.1126/science.aad2776

This study is led by Tom Beeckman from Gent University and features Leah Band from CPIB in Nottingham. They reveal an exciting relationship between cell death in root cap cells and hormone signaling. The root cap is a protective tissue that overlies the Arabidopsis root tip and might be considered as an ‘inactive’ tissue. However this study shows that an auxin signal released from root cap cells sets the spacing of lateral organs along the root. As root cap cells move up the root they undergo programmed cell death, which in turn releases a pulse of auxin and establishes a pattern of lateral root formation. The authors suggest that this relationship might integrate external soil conditions so that lateral roots will develop to optimise uptake of water and nutrients. It is well known that an auxin signal simulates lateral root formation but this study provides an explanation as to the genesis of this signal and its integration with external environmental factors.

Yue K, Sandal P, Williams EL, Murphy E, Stes E, Nikonorova N, Ramakrishna P, Czyzewicz N, Montero-Morales L, Kumpf R, Lin Z, van de Cotte B, Iqbal M, Van Bel M, Van De Slijke E, Meyer MR, Gadeyne A, Zipfel C, De Jaeger G, Van Montagu M, Van Damme D, Gevaert K, Rao AG, Beeckman T, De Smet I (2016) PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root. Proc Natl Acad Sci U S A. http://dx.doi.org/10.1073/pnas.1525122113

This broad collaboration between US-UK and Belgian researchers is led by Tom Beeckman and Ive De Smet, who works at CPIB in Nottingham. In addition it includes a contribution from Cyril Zipfel at TSL. This study aimed to identify proteins that interact with the plasma membrane-localized receptor kinase ARABIDOPSIS CRINKLY 4 (ACR4), which plays a role in the control of cell division in the Arabidopsis root. They find that PROTEIN PHOSPHATASE 2A-3 (PP2A-3), a catalytic subunit of PP2A holoenzymes interacts with ACR4 and has a previous uncharacterised role in control of formative cell divisions. The authors show that the biochemical network that links ACR4 and PP2A-3 is regulated by phosphorylation.

Mellor N, Bennett MJ, King JR (2016) GH3-Mediated Auxin Conjugation Can Result in Either Transient or Oscillatory Transcriptional Auxin Responses. Bull Math Biol. http://dx.doi.org/10.1007/s11538-015-0137-x

This paper led by Professor Malcolm Bennett and John King from CPIB is an example of the growing number of multi-disciplinary interactions between biologists and mathematicians. Here a model is developed that interrogates auxin signaling and homeostasis through the GH3 gene family. This includes a parameter that considers auxin transport via the LAX3 influx protein, which, together with the activity of GH3 proteins can facilitate a positive feedback loop that allows cells to response to excess auxin.

Mithoe SC, Ludwig C, Pel MJ, Cucinotta M, Casartelli A, Mbengue M, Sklenar J, Derbyshire P, Robatzek S, Pieterse CM, Aebersold R, Menke FL (2016) Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase. EMBO Rep. http://dx.doi.org/10.15252/embr.201540806 Open Access

Frank Menke (TSL, Norwich) is the leader on this collaboration between UK, Dutch and Swiss researchers that investigates innate immunity signaling mediated via Pattern Recognition Receptors (PRRs). Tight control of this signalling is very important to prevent spurious activation of the immune response. These authors find that the differentially phosphorylated MKKK7 can interact with the FLS2 protein, which is key in the perception of bacterial flagellin. In turn MKKK7 attenuates the signalling of a downstream MAPK that contributes to defence-related gene expression. Therefore the show that the FLS2-MKKK7 signaling module is critical for control of innate immunity.

Wang SB, Feng JY, Ren WL, Huang B, Zhou L, Wen YJ, Zhang J, Dunwell JM, Xu S, Zhang YM (2016) Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology. Sci Rep. http://dx.doi.org/10.1038/srep19444 Open Access

Professor Jim Dunwell (Reading) is a UK contributor to this largely Chinese publication that introduces a new method to analysis GWAS-style data. They propose an analysis based on random-SNP-effect MLM (RMLM) and a multi-locus RMLM (MRMLM) and using stimulations show that their new method can be powerful than conventional types of analysis. To test the method they analysed flowering time traits in Arabidopsis and detected more genes that were involved in the process.

For those interested in different-types of GWAS analysis, Professor David Salt introduced another new method during a recent ARR.

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