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 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

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


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

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.

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.

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.

SLS ’16: An Undergraduate’s View

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Published on: April 26, 2016

Guest Post from Sam Downs, 2nd Year Undergraduate at Cambridge University.

This April, the Sainsbury Laboratory at Cambridge university (SLCU) held its first large meeting – SLS ’16 – on Induced Plant Development. The keynote speakers were Prof. Sofie Goormachtig on root strigolactone signalling to Prof. Christian Fankhauser on growth changes in response to light, with others addressing topics ranging from large scale morphological studies to cell and molecular biology.

It was a first for me too; like most undergraduates, I hadn’t yet attended an academic conference. As I imagine many find at their first conference, it was slightly intimidating to be in a room half-full of PIs – the rest being PhD students, with their own research projects underway, wasn’t much better. There was nothing for it but to get stuck in though, and talking to people about their talks and posters proved easier than I had thought. It’s a testament to the friendliness of the plant science community that everyone was willing to explain their work from the bottom up to a passing undergrad!

As an outsider to research, it was interesting to note what people felt was important to communicate in talks and posters. They seemed to be broadly results-driven or process-driven, and I found this was especially marked in the posters; many were reporting new techniques, such as growing Arabidopsis roots on microfluidics chips, or laser imaging of cell movements, whilst others (such as Dr Dana MacGregor’s prize-winning poster on seed dormancy) drew their main interest from the phenomenon they showed. This is quite different to the way that I’ve mainly engaged with science – essentially, as an interested member of the public. This year I’ve been helping to run the Cambridge student biological society, and we’ve hosted a number of talks by UK scientists. Their talks are mainly of the former kind; essentially reporting new results, suitable for a lay audience. It was thus quite new to me to hear technique-driven presentations, and exciting too – a look above the parapet of summer exam revision (driven, of course, by an entirely different sort of result!).

What struck me most of all, though, was the hearing the questions people asked at the end of each talk. Through these, I got a stronger sense of how active researchers think about science than even the talks or the posters could. As an undergraduate, I’m used to hearing researchers talk about results, and sometimes about methods too; but the biggest difference was how the audience parsed what they heard. The questions focused on the experimental process and the physiology of the whole plant (“What happens to Rorippa aquatica if it’s in warm water, [when heat and submersion have opposite effects]?” “Is the plant’s response to UV-B modulated in the diurnal cycle?”). This is a different way of thinking (perhaps regrettably) to that taken at undergraduate level; we tend to focus more on isolated details, so the bigger picture of how a result came about in the lab and in the organism can be missed. It was a reminder to me of the challenge of getting across this gap from obsession with facts to obsession with science.

Overall, I learnt a lot in the short duration of the SLS, both about what’s going on in plant development and about life in science. I would life to thank the organisers, the speakers, and especially Geraint Parry from GARNet who offered me the opportunity to attend it.

Rorippa                   Temperature mediated developmental changes in Rorippa aquatica

Arabidopsis Research Roundup: April 1st.

This weeks Arabidopsis Research Roundup contains an eclectic mix of investigations. Firstly is a study from Peter Unwin that investigates the molecular factors that control interactions between plants and nematode parasites. Secondly is a study led by John Christie that investigates the factors that control hypocotyl curvature. Thirdly is a fascinating proof-of-concept synbio-style study from Rothamstead Research where an algal gene is transferred into Arabidopsis in the hope of developing a phytomediation-based solution to heavy metal contamination. Fourthly is a study from David Bass that catalogues protist species that feed on leaf-microorganisms whilst finally John Carr heads a study that compares RNA-dependent RNA polymerases from Arabidopsis and Potato.

Eves-van den Akker S, Lilley CJ, Yusup HB, Jones JT, Urwin PE (2016) Functional C-terminally encoded plant peptide (CEP) hormone domains evolved de novo in the plant parasite Rotylenchulus reniformis. Mol Plant Pathol.

This study is a collaboration between researchers at the Universities of Dundee and Leeds, led by Peter Unwin. The focus of the paper is the interaction of Plant-Parasitic Nematodes (PPNs) with their plant hosts. PPNs stimulate redifferentiation of vascular tissues to form ‘feeding structures’ that benefit the parasite. This process is mediated by a diverse family of effector proteins termed C-terminally Encoded Peptide plant hormone mimics (CEPs). This study investigates the CEPs from the nematode Rotylenchulus reniformis and suggests that these peptides evolved de novo in this organism. They show that the activity of a synthetic peptide corresponding to RrCEPs causes a reduction in primary root elongation whilst upregulating a set of genes including the nitrate transporter AtNRT2.1. The authors propose that CEPs evolved in R. reniformis to allow sustained biotrophy by upregulating a specific set of feeding-responsive genes and by limiting the size of the feeding site produced. This study represents an exciting introduction to a currently under-researched area within plant-pathogen interactions.

Sullivan S, Hart JE, Rasch P, Walker CH, Christie JM (2016) Phytochrome A Mediates Blue-Light Enhancement of Second-Positive Phototropism in Arabidopsis. Front Plant Sci. 7:290 Open AccessFrontiersPHOT1

John Christie (Glasgow) is the corresponding author on this investigation into the role of the blue-light receptor phototropin 1 (phot1) during hypocotyl phototropism. Curvature of this organ is enhanced by treatment by red-light mediated by the phytochromeA receptor. However this study shows that pre-treatment with blue-light can also enhance this hypocotyl curvature although this did not occur at higher light intensities. In addition phototropic enhancement was also lacking when PHOT1 is expressed only in the hypocotyl epidermis. Therefore the study shows that the phyA impact on phot1 signaling is restricted to low light intensities and in tissues other than the epidermis.

Zhong Tang, Yanling Lv, Fei Chen, Wenwen Zhang, Barry P. Rosen, and Fang-Jie Zhao (2016) Arsenic Methylation in Arabidopsis thaliana Expressing an Algal Arsenite Methyltransferase Gene Increases Arsenic Phytotoxicity J. Agric. Food Chem. Open Access ArsM

This synthetic biology-focused study is led by Fang-Jie Zhao at Rothamstead Research. The authors take an algal gene (arsM) that allows the transformation of inorganic arsenic to a more volatile methylated version. The biological activity of this enzyme was successfully transferred to two different Arabidopsis ecotypes. However interestingly these transgenic plants became more sensitive to arsenic in growth media suggesting that the new methylated arsenic intermediate is more phytotoxic than inorganic arsenic. Therefore this study demonstrates a negative consequence of this project that attempted to engineer arsenic tolerance in plants. Once again this demonstrates that nature rarely acts predictably and any great ideas usually need to be tested in vivo.

Ploch S, Rose L, Bass D, Bonkowski M (2016) High Diversity Revealed in Leaf Associated Protists (Rhizaria: Cercozoa) of Brassicaceae J Eukaryot Microbiol.

After a fantastic opening line in the abstract, ‘The largest biological surface on earth is formed by plant leaves’, this study includes the work of David Bass from the Natural History Museum in London. They investigate the abundance of protists that associate with leaf-inhabiting microorganisms, the “phyllosphere microbiome“. Their findings demonstrate that protists should be considered an important part of the diversity of plant-interacting microbial organisms.

Hunter LJ, Brockington SF, Murphy AM, Pate AE, Gruden K, MacFarlane SA, Palukaitis P, Carr JP (2016) RNA-dependent RNA polymerase 1 in potato (Solanum tuberosum) and its relationship to other plant RNA-dependent RNA polymerases Sci Rep. 6:23082 Open Access

John Carr (Cambridge) is the UK-lead on this collaboration with Slovenian and Korean researchers. They primarily investigate the role of the RDR1 RNA-dependent RNA polymerase (RDRs) in potato. In Arabidopsis the RDR1 gene contributes to basal viral resistance but potato plants deficient in StRDR1 do not show altered susceptibility to three different plant viruses. In addition they perform a phylogenetic analysis on the RDR genes and identify a novel RDR7 gene that is only found in Rosids (but not Arabidopsis.

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 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.


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.

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 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. 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: 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 Open Access
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 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.

Monitoring Alternative Splicing Changes in Arabidopsis Circadian Clock Genes’ from the group of John Brown at the James Hutton in Dundee

Assessing the Impact of Photosynthetic Sugars on the Arabidopsis Circadian Clock’ from the lab of Alex Webb in Cambridge.

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. 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

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.

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.

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. 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. 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.

Arabidopsis Research Roundup: January 22nd 2016

A mixed selection of research in this UK Arabidopsis Roundup. Firstly a study from Stefan Kepinski and Mark Estelle that adds another layer of understanding to the regulation of the auxin response. Enrique Lopez-Juez leads a study into signaling between the nucleus and chloroplast while Tracey Lawson contributes to an investigation into role of starch metabolism in guard cells. Fran Maathuis and co-worker looks at differences in vacuolar transport between Arabidopsis ecotypes while Alan Marchant is involved in a study of cell wall pectins. Finally William Amos has uses the 1001genomes project to investigate heterozygote instability (HI).

Wang R, Zhang Y, Kieffer M, Yu H, Kepinski S, Estelle M (2016) HSP90 regulates temperature-dependent seedling growth in Arabidopsis by stabilizing the auxin co-receptor F-box protein TIR1. Nat Commun. 5;7:10269. Open Access

Stefan Kepinski (Leeds) is the UK lead on this collaboration with Mark Estelle from UCSD and it continues their previous work that investigates the much-studied auxin receptor TIR1. Arabidopsis seedlings grown at 29C show auxin-dependent hypocotyl elongation although the molecular mechanism behind this response has remained opaque. In this study they show that in high temperatures TIR1 accumulates in a manner dependent on the molecular chaperone, HSP90. In addition HSP90 and the co-chaperone SGT1 directly interact with TIR1. Inhibition of HSP90 results in degradation of the TIR1 and causes a range of auxin-mediated growth processes at both high and low temperatures. This study adds another level of complexity to the molecular basis of the auxin response.

Hills AC, Khan S, López-Juez E (2015) Chloroplast Biogenesis-Associated Nuclear Genes: Control by Plastid Signals Evolved Prior to Their Regulation as Part of Photomorphogenesis. Front Plant Sci. 10;6:1078. Open Access

The work comes exclusively from the lab of Enrique Lopez-Juez at Royal Holloway and investigates at the expression of photosynthesis-associated nuclear genes (PhANGs). This expression is dependent on light as well as plastid-to-nucleus “biogenic” communication signals and causes the assembly of photosynthesis component chloroplasts. The authors investigate the factors that control the activity of the Lhcb promotor in the light and the dark, both in angiosperms and gymnosperms. They propose that suppression of PhANG responses has contributed to the evolution of light-controlled chloroplast biogenesis.

Horrer D, Flütsch S, Pazmino D, Matthews JS, Thalmann M, Nigro A, Leonhardt N, Lawson T, Santelia D (2015) Blue Light Induces a Distinct Starch Degradation Pathway in Guard Cells for Stomatal Opening. Current Biology
Graphical Abstract
Tracey Lawson (University of Essex) is the UK lead on this UK-French-Swiss study that uses the stomatal guard cell experimental system to investigate the role of carbon metabolism in the response to blue light. Interestingly guard cells differ from other leave tissues in that they contain starch at the end of the night. However this starch store is rapidly degraded within 30minutes of light and is important for stomatal opening and subsequent biomass production. This starch degradation involves action of two enzymes, β-amylase 1 (BAM1) and α-amylase 3 (AMY3) that do not function during night time starch degradation in other tissues. This process is coordinated by blue light signalling and correlates with the activity of a plasma membrane ATPase. This study adds yet another level of our understanding into the mechanism of stomatal opening. See image for a proposed model of this process (from Cell Press).

Hartley TN, Maathuis FJ (2015) Allelic variation in the vacuolar TPK1 channel affects its calcium dependence and may impact on stomatal conductance. FEBS Lett. 90(1):110-7

Fran Maathuis (University of York) is the leader on this study that assesses the transport properties of two different vacuolar-localised AtTPK1 alleles identified for a study of natural variation in Arabidopsis. They use patch-clamping the interrogate the difference between these proteins from Lansberg (Ler) and Kas-2 ecotypes, when they showed different levels of Ca(2+) dependence. This coincided with lower water loss in either the presence of absence of ABA and higher Ler AtTPK1 activity at similar cytoplasmic [Ca]. The authors present a model that helps to explain their findings.

Dumont M, Lehner A, Vauzeilles B,, Malassis J, Marchant A, Smyth K, Linclau B, Baron A, Mas Pons J, Anderson CT, Schapman D, Galas L, Mollet JC, Lerouge P (2015) Plant cell wall imaging by metabolic click-mediated labelling of rhamnogalacturonan II using azido 3-deoxy-D-manno-oct-2-ulosonic acid. Plant Journal.

The majority of the authors on this Technical Advance are from French institutions but also includes UK plant scientist Alan Marchant (University of Southampton). They investigate the chemistry of Arabidopsis and tobacco cell walls, specifically looking at the incorperation of 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo), a monosaccharide that is only found the cell wall pectin rhamnogalacturonan-II (RG-II). They show that RG-II is found in the primary cell wall including within the root elongation zone. Finally they show that monitoring of Kdo is an effective way to study the synthesis and redistribution of RG-II during root growth.

Amos W (2015) Heterozygosity increases microsatellite mutation rate. Biol Lett. Open Access

This study is led by Professor William Amos who is based in the Zoology department at Cambridge. He is not usually a plant science researcher but used the excellent 1001genome project to investigate heterozygote instability (HI) in Arabidopsis. He looked at AC microsatellite sequences from over 1100 genome sequences and used rare alleles as a surrogate for more recent mutations, ultimately showing that rare alleles are more likely to occur at locus-population combinations with higher heterozygosity even when all populations carry exactly the same number of alleles. This shows that local heterozygosity causes more mutations and represents a positive feedback loop.

Arabidopsis Research Roundup: December 18th

The final Arabidopsis Research Roundup of 2015 contains a bumper crop of papers that again highlights the diversity of research occuring in UK plant science. Justin Goodrich from the University of Edinburgh kindly provides an audio description of work that identifies a novel role for a member of a transposon gene family. Elsewhere are studies about a specific aspect of the biochemistry of crytochromes as well as confirmation of a role for DNA gyrases in Arabidopsis. Paul Dupree (Cambridge) leads a study into the mechanism of ascorbic acid production while Heather Knight is the UK representative in a study about cell wall composition. We also present an investigation into the mechanism and subsequent expression changes that occur following infection with different isolates of the Turnip Mosaic Potyvirus. Finally are two short studies from Ive de Smet (Nottingham) and Matt Jones (Essex).

Liang SC, Hartwig B, Perera P, Mora-García S, de Leau E, Thornton H, de Alves FL, Rapsilber J, Yang S, James GV, Schneeberger K, Finnegan EJ, Turck F, Goodrich J (2015) Kicking against the PRCs – A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2. PLoS Genet. 11 e1005660. Open Access

Justin Goodrich (Edinburgh) is the lead of this collaborative study between UK, German and Australian researchers that investigates the role of the evolutionarily conserved Polycomb group (PcG) and trithorax group (trxG) genes during plant development. These homeotic genes influence gene expression by causing epigenetic chromatin changes, usually in the form of histone methylation. Previously the ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN1 (ALP1) gene was found to act as a genetic suppressor the Arabidopsis PcG gene, LIKE HETEROCHROMATIN PROTEIN1 (LHP1). In this study ALP1 is shown to genetically interact with members of these two gene families and its activity is necessary for the activation of several floral homeotic genes. Surprisingly the ALP1 gene is shown to encode for a transposase of the PIF/Harbinger class, which is conserved throughout land plants. The authors suspect that the transposase activity has been lost in the angiosperm lineage, where the gene obtained a novel function. Interestingly ALP1 can interact with the core PrC complex, which most notably participates in H3K27me3 methylation and therefore appears to act, along with other proteins such as EMBRYONIC FLOWER 1 (EMF1), as a plant-specific accessory component that controls histone modification. The authors speculate that this novel function might have arisen as a “means for the cognate transposon to evade host surveillance or for the host to exploit features of the transposition machinery beneficial for epigenetic regulation of gene activity”. Over the coming years it will be interesting to discover if other transposon-encoded genes share novel functions and this study represents an important lesson for researchers not to ignore transposon sequences as ‘junk’ DNA that they might feel can clutter up their analysis!

Justin Goodrich kindly provides an audio summary of this paper:

van Wilderen LJ, Silkstone G, Mason M, van Thor JJ, Wilson MT (2015) Kinetic studies on the oxidation of semiquinone and hydroquinone forms of Arabidopsis cryptochrome by molecular oxygen FEBS Open Bio. 5:885-892 Open Access

This study is a collaborative effort between researchers from Imperial College and the University of Essex, led by emeritus biochemistry Professor Michael Wilson and is an in vitro analysis of the oxidation of the Arabidopsis cryptochrome (CRY) photoreceptor in the presence and absence of an external electron donor. They show that a more complex model than previously thought is required to explain the mechanism by which the CRY-associated flavin molecule is oxidised. The authors propose that the final steps in this reaction require cooperative interaction between partners in a CRY homodimer or between separate CRY molecules.

Evans-Roberts KM, Mitchenall LA, Wall MK, Leroux J, Mylne JS, Maxwell A (2015) DNA Gyrase is the Target for the Quinolone Drug Ciprofloxacin in Arabidopsis thaliana. J Biol Chem. Open Access

Antony Maxwell from the Biological Chemistry department from the John Innes Centre is the UK academic lead on this UK-Australian study. This group has previously shown that Arabidopsis contains three proteins thought to function as DNA Gyrases (AtGYRA, ATGYRB1, ATGYRB2) although they could not provide direct evidence that are were involved in DNA supercoiling. This study moves the work on by identifying mutant plants that are resistant to the drug ciprofloxacin and contain a point mutation in AtGYRA. Furthermore ATGYRA heterologously expressed in insect cells has supercoiling activity. Therefore the authors unequivocally show that plants encode an organellar-targeted DNA gyrase that, like bacterial gyrases, is a  target for ciprofloxacin. This work has important consequences for our understanding of plant physiology and in the future development of novel herbicides.

Sawake S, Tajima N, Mortimer JC, Lao J, Ishikawa T, Yu X, Yamanashi Y, Yoshimi Y, Kawai-Yamada M, Dupree P, Tsumuraya Y, Kotake T (2015) KONJAC1 and 2 Are Key Factors for GDP-Mannose Generation and Affect l-Ascorbic Acid and Glucomannan Biosynthesis in Arabidopsis The Plant Cell

Paul Dupree (Cambridge) is the British lead on the UK-Japanese collaboration that investigates the role of the GDP-mannose pyrophosphorylase (GMPP), VITAMIN C DEFECTIVE1 (VTC1) enzyme in catalysis of the rate-limiting step in the production of ascorbic acid (AsA). They identify two novel pyrophosphorylase-like proteins, KONJAC1 (KJC1) and KJC2 that stimulate VTC1. Mutant analysis showed that these proteins are necessary for normal growth that coincides with control of AsA production via stimulating GMPP activity. Yeast 2 Hybrid  analysis is indicative of a direct interactin between KJC and VTC1 proteins. In future, it will be interesting to investigate the role of these proteins in plants that are more relevant to human consumption of AsA.

Sorek N, Szemenyei H, Sorek H, Landers A, Knight H, Bauer S, Wemmer DE, Somerville CR (2015) Identification of MEDIATOR16 as the Arabidopsis COBRA suppressor MONGOOSE1. PNAS

Heather Knight (Durham) is the sole UK representative on this manuscript that is led by the lab of Chris Somerville from the University of California. In this work the authors identified suppressors of the Arabidopsis cobra mutant, which have defects in cellulose formation. The appropriately named mongoose (mon1) mutant partially restored cellulose levels and also restored the esterification ratio of pectin to wild-type levels. MON1 was cloned to the MEDIATOR16 (MED16)/ SENSITIVE TO FREEZING6 (SFR6) locus and single mon1 mutants are resistant to cellulose biosynthesis inhibitors. Concomitantly, transcriptome analysis demonstrated that a set of ‘cell wall’ genes are misregulated in mon1/med16/sfr6, including two encoding pectin methylesterase inhibitors. Overall the authors suggest that cellulose biosynthesis is closely linked to esterification levels of pectin and offer a number of possible explanations for this functional relationship.

Sánchez F, Manrique P, Mansilla C, Lunello P, Wang X, Rodrigo G, López-González S, Jenner C, González-Melendi P, Elena SF, Walsh J, Ponz F (2015) Viral Strain-Specific Differential Alterations in Arabidopsis Developmental Patterns Mol Plant Microbe Interact.

The UK contributor to this Spanish-led study is Carol Jenner, who at the time was a research fellow at the University of Warwick. This study highlights the morphological changes that occur in Arabidopsis plants infected by different isolates of Turnip mosaic virus (TuMW). The UK1 and JPN1 versions of TuMW were shown to have highest levels of sequence divergence in the P3 cistron and following the generation and use of viral chimeras, it is this region that was identified as the major viral determinant of plant developmental changes. However when the P3 gene was constitutively expressed in Arabidopsis it did not cause any development effects, which highlights the importance of performing infection studies in a whole-plant context. Latterly the authors performed transcriptomic and interactomic analysis, showing that infection with the most severe UK1 strain primarily causes changes, perhaps unsurprisingly, in genes involved in transport and in the stress response.

Czyzewicz N, De Smet I (2015) The Arabidopsis thaliana CLAVATA3/EMBRYO-SURROUNDING REGION 26 (CLE26) peptide is able to alter root architecture of Solanum lycopersicum and Brassica napus. Plant Signal Behav

This work was performed in the lab of Ive De Smet, who is a BBSRC research fellow at the University of Nottingham. In this short communication they show that overexpression of the Arabidopsis AtCLE26 peptide is able to induce architectural change in the agriculturally important crops, Brassica napus and Solanum lycopersicum. Having previously shown that AtCLE26 is similarly active in Arabidopsis, Brachypodium and Triticum, these experiments further demonstrate that small peptide signaling plays an important role in root development across plant lineages.

Litthauer S1, Battle MW1, Jones MA (2015) Phototropins do not alter accumulation of evening-phased circadian transcripts under blue light. Plant Signal Behav.

Matt Jones (Essex) leads this accompanying study to the more substantial project previously published in Plant Journal. This manuscript reports that phototropin photoreceptors are not involved in the nuclear accumulation of evening-phased circadian transcripts. In addition they show that even in phototropin mutants, the rhythms of nuclear clock transcript accumulation are maintained under fluctuating light regimes.

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