March 2016 - Weeding the Gems

Arabidopsis Research Roundup: March 24th

Categories: Arabidopsis, Audio, Glasgow University, Global, RHUL, Uncategorized, University of Leeds

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Published on: March 24, 2016

Just three papers this week in the UK Arabidopsis Research Roundup. Firstly Professor Anna Amtmann provides an audio description of her groups characterisation of the binding partners of the Histone Deacetylase Complex1 protein. Secondly Dr Carine De Marcos Lousa leads a study that investigates a set of plant-specific proteins involved in the cellular secretory pathway. Finally Dr Paul Devlin is a contributor to a study that characterises the role of a nucleoporin protein in the shade avoidance response.

Perrella G, Carr C, Asensi-Fabado MA, Donald NA, Páldi K, Hannah MA, Amtmann A (2016) The Histone Deacetylase Complex (HDC) 1 protein of Arabidopsis thaliana has the capacity to interact with multiple proteins including histone 3-binding proteins and histone 1 variants. Plant Physiol. http://dx.doi.org/10.1104/pp.15.01760 Open Access

Anna Amtmann (Glasgow) leads this European collaboration that investigates the binding capability of the Histone Deacetylase Complex (HDC) 1 protein, which has been previously shown to regulate multiple growth phenotypes due to its interaction with histone deacetylases. HDC1 proteins are ubiquitously present throughout plant tissues yet their secondary structure offers little clue to their specific binding interactions. Therefore this attempt to dissect the interaction spectrum of HDC1 and discovered that the protein interacts with different histone3 (H3) binding proteins but not H3 itself. Interestingly HDC1 could also interact with different variants of the H1 histone linker protein. The authors show that the ancestral core of HDC1 had a narrower range of interactions indicating that over evolutionary time the protein had developed more promiscuous binding. However even the conserved portion of the protein is able to interact with H3-associated proteins and H1, indicating that HDC1 played an important role in the establishment of interactions between histones and modifying enzymes.

Professor Amtmann kindly provides a short audio description of this paper. Apologies for the variation in sound quality and volume!

de Marcos Lousa C, Soubeyrand E, Bolognese P, Wattelet-Boyer V, Bouyssou G, Marais C, Boutté Y, Filippini F, Moreau P (2016) Subcellular localization and trafficking of phytolongins (non-SNARE longins) in the plant secretory pathway J Exp Bot. http://dx.doi.org/0.1093/jxb/erw094 Open Access

Carine De Marcos Lousa (Leeds Beckett) is the lead author in the UK-French-Italian study that investigates the activity of plant specific R-SNARE proteins, called longins. SNARE proteins are critical for the membrane fusion events that occur during intracellular transport. A new four-member family of longins called ‘phytolongins’ (Phyl) that lack a typical SNARE domain have recently been discovered. These ubiquituosly expressed proteins are distributed throughout the secretory pathway with different members localised at ER, Golgi apparatus or post-Golgi compartments. Furthermore the export of the Phyl1.1 protein from the ER is dependent on a Y48F49 motif as well as the activity of at least three accessory proteins. This manuscript is the first characterisation of Phyl subcellular localisation and adds to our knowledge of specific mechanisms involved in the plant secretory pathway.

Gallemí M, Galstyan A, Paulišić S, Then C, Ferrández-Ayela A, Lorenzo-Orts L, Roig-Villanova I, Wang X, Micol JL, Ponce MR, Devlin PF, Martínez-García JF (2016) DRACULA2, a dynamic nucleoporin with a role in the regulation of the shade avoidance syndrome in Arabidopsis. Development. http://dx.doi.org/10.1242/dev.130211

This Spanish-led study includes Dr Paul Devlin (RHUL) and introduces a new gene that is involved in the shade-avoidance-response in Arabidopsis. The DRACULA2 gene is a homolog of the metazoan nucleoporin NUP98, which is a component of the nuclear pore complex (NPC). The authors find that other members of the NPC are also involved in the control of hypocotyl elongation in response to proximity of other plants. This is likely due to nuclear transport-dependent processes. However the authors suggest that DRA2 also has a transport-independent role that is related to its physical association with the NPC. This demonstrates that nucleoporins play an important role in plant signaling, although assigning specificity to their activity remains difficult given their general role in nucleocytoplasmic transport.

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Arabidopsis Research Roundup: March 18th

by Geraint

Categories: Arabidopsis, Cambridge University, Global, John Innes Centre, RHUL

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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

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 2016

by Geraint

Categories: Arabidopsis, Audio, Bristol University, Cardiff University, Edinburgh University, Exeter University, funding, GARNet, Global, John Innes Centre, New Phytologist, Oxford University, Sainsbury Lab, Uncategorized, University of Oxford, University of York

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Published on: March 3, 2016

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 (2016) 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

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

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.

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