Arabdopsis Research Roundup: May 11th

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Published on: May 11, 2017

This weeks Arabidopsis Research Roundup is lead by two papers that characterise the relationship between cell size and growth in different Arabidopsis tissues. Firstly the lab of GARNet PI Jim Murray look at how the cell cycle influences cell size progression in the SAM whilst George Bassel’s group from Birmingham investigate cell growth within a developing embryo. Thirdly is a paper from the University of Essex that further defines the role of the CP12 protein in control of photosynthesis. Next is a paper from researchers from the University of Warwick who lead a fascinating piece of rocket science that identifies differences in the vernalisation requirement across Brassica species whilst in the fifth paper, researchers from Lancaster identify environmentally defined QTLs that determine the plant response to glutamate. Finally is a paper that highlights a new software tool that has the self-explanatory title of the ‘UEA small RNA Workbench’ and is applicable for use with plant-derived datasets.

R Jones A, Forero-Vargas M, Withers SP, Smith RS, Traas J, Dewitte W, Murray JAH (2017) Cell-size dependent progression of the cell cycle creates homeostasis and flexibility of plant cell size. Nat Commun http:/​/​dx.​doi.​org/10.1038/ncomms15060

Open Access

This study comes from the lab of current GARNet PI Jim Murray at the Cardiff University. Lead author Angharad Jones kindly provides an audio description of the paper for the GARNet YouTube channel. This  investigation looks at the factors that control the interaction between cell size and cell growth in a developing shoot meristem. They show that the dynamic regulation of this relationship is linked to the activity of two cyclin dependent kinases (CDKs) and that cell size is key in controlling the transition from G1>S and from G2>M phases of the cell cycle. Importantly this work uses precise imaging to track the progression of individual cell lineages and is therefore able to suggest that cell size is an emergent and not a directly determined property.


Souza NM, Topham AT, Bassel GW (2017) Quantitative analysis of the 3D cell shape changes driving soybean germination. J Exp Bot. http:/​/​dx.​doi.​org/10.1093/jxb/erx048

Open Access

George Bassel (University of Birmingham) leads this paper that uses information gained from the study of patterns of cell expansion in Arabidopsis embryos to investigate a similar process in soybean. Indeed as in Arabidopsis they show that there is preferential early cell expansion closest to the soybean radicle and that starting cell size corresponds to different growth rates. In addition they show that the growing hypocotyl has complex regulation and that differential ansiotrophy growth drives forward the process of germination. Ultimately they show that this occurs equivalently in both model and crop species.


Elena López-Calcagno P, Omar Abuzaid A, Lawson T, Anne Raines C (2017) Arabidopsis CP12 mutants have reduced levels of phosphoribulokinase and impaired function of the Calvin-Benson cycle. J Exp Bot http:/​/​dx.​doi.​org/10.1093/jxb/erx084 Open Access
This study from the photosynthesis group at the University of Essex is led by Tracey Lawson and GARNet committee member Christine Raines. They investigate the role of the CP12 multigene family that has three members in Arabidopsis. These are redox-sensitive proteins that facilitate the formation of a complex between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) during the Calvin-Benson cycle. They show that plants with reduced levels of CP12-1 or CP12-2 have lower photosynthetic capacity and subsequently exhibit slower growth. The cell biological explanation for this alteration appears to focus on the PRK protein, which is present at lower levels in plants with reduced CP12-1 or CP12-2. Therefore the authors find that CP12-1 and CP12-2 are the key members of this gene family and they likely show functional redundancy in the tight control of photosynthesis.


Taylor JL, Massiah A, Kennedy S, Hong Y, Jackson SD (2017) FLC expression is down-regulated by cold treatment in Diplotaxis tenuifolia (wild rocket), but flowering time is unaffected. J Plant Physiol.

http:/​/​dx.​doi.​org/10.1016/j.jplph.2017.03.015 Open Access
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Steve Jackson (University of Warwick) leads this work that also features Chinese collaborators and investigates the role of FLOWERING LOCUS C (FLC) in the popular peppery salad plant Rocket (Diplotaxis tenuifolia) that, as a Brassica, is a somewhat closely related to Arabdopsis. The authors studied the vernalisation requirement in this plant so isolated its version of FLC, which was shown to functional compliment an Arabidopsis flc null mutant. However they showed that even though cold treatment reduced levels of DtFLC this did not alter the bolting time of the plant. This somewhat surprising result demonstrates that the link between FLC and flowering time is uncoupled in this species and that other mechanisms may take precedence, a situation different to that observed in Arabidopsis and other Brassicas.


Walch-Liu P, Meyer RC, Altmann T, Forde BG (2017) QTL analysis of the developmental response to L-glutamate in Arabidopsis roots and its genotype-by-environment interactions. J Exp Bot.

http:/​/​dx.​doi.​org/10.1093/jxb/erx132 Open Access Researchers from the groups of Brian Forde (Lancaster University) and Thomas Altmann (Leibniz Institute) collaborate in this research that identifies three novel QTLs (GluS1-3) that are involved in the response of Arabdopsis roots to external L-glutamate. When this experiment was extended they discovered that different environmental factors play a significant role in the control of this trait. The GluS1 locus is located on Chr3 yet is epistatically controlled by loci on Chr1 and Chr5 in response to temperatures. Overall this study demonstrates that the response to glutamate is controlled by multiple environmentally sensitive loci that vary between Arabidopsis ecotypes


Mohorianu I, Stocks MB, Applegate CS, Folkes L, Moulton V (2017) The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis. Methods Mol Biol.

http:/​/​dx.​doi.​org/10.1007/978-1-4939-6866-4_14

This manuscript from the University of East Anglia describes a set of software tools for the analysis of small RNAs. They used an Arabidopsis dataset to demonstrate the utility of the UEA small RNA Workbench, which can be found here: http://srna-workbench.cmp.uea.ac.uk/

Arabidopsis Research Roundup: February 9th

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Published on: February 9, 2016

It has been a quiet couple of weeks for newly published UK Arabidopsis Research but what might be lacking in quantity is made up for in quality! Firstly the PRESTA consortium use gene regulatory network analysis to identify a key component in the response to drought stress. Secondly is a paper featuring researchers from Rothamstead that identifies a new molecular participant in the control of RNA surveillance. Thirdly is a paper that investigates the function of aquaporins during lateral root emergence and includes researchers from Warwick and Nottingham. Finally is a study from Sheffield that investigates necrotropic and biotropic strategies employed by an ascomycete pathogen. It is also nice to observe that each of these papers are open access.

Bechtold U, Penfold CA, Jenkins DJ, Legaie R, Moore JD, Lawson T, Matthews JS, Vialet-Chabrand SR, Baxter L, Subramaniam S, Hickman R, Florance H, Sambles C, Salmon DL, Feil R, Bowden L, Hill C, Baker NR, Lunn JE, Finkenstadt B, Mead A, Buchanan-Wollaston V, Beynon JL, Rand DA, Wild DL, Denby KJ, Ott S, Smirnoff N, Mullineaux PM (2016) Time-series transcriptomics reveals that AGAMOUS-LIKE22 links primary metabolism to developmental processes in drought-stressed Arabidopsis Plant Cell http:/​/​dx.​doi.​org/​10.​1105/​tpc.​15.​00910 Open Access

This Large Scale Biology article is the result of the PRESTA collaboration that is based at the Universities of Essex, Exeter and Warwick. The research plan of the PRESTA project is based upon the generation of large scale transcriptomic datasets and in this case they investigate changes in gene expression in plants subjected to drought stress. They identified over 1800 differentially expressed genes and the early changes coincided with a drop in carbon assimilation together with a late increase in foliar ABA content. Using Bayesian network modelling of differentially expressed transcription factors they identified the AGAMOUS-LIKE22 (AGL22) gene as a key component in this gene regulatory network. AGL22 had been previously found to play an important role in the change from vegetative to floral development but in this context it influences photosynthetic rates and lifetime water use.

Hématy K, Bellec Y, Podicheti R, Bouteiller N, Anne P, Morineau C, Haslam RP, Beaudoin F, Napier JA, Mockaitis K, Gagliardi D, Vaucheret H, Lange H, Faure JD (2016) The Zinc-Finger Protein SOP1 Is Required for a Subset of the Nuclear Exosome Functions in Arabidopsis PLoS Genetics 12(2):e1005817 http://dx.doi.org/10.1371/journal.pgen.1005817 Open Access

This Franco-US collaboration also includes a contribution from Johnathan Napier’s group at Rothamstead Research. They investigated the function of the essential Arabidopsis PASTICCINO2 (PAS2) gene by isolating three suppressors of pas2 mutants (termed sop mutants). PAS2 is involved in correct splicing so the sop mutants prevented degradation of mis-spliced pas2 mRNA species. The suppressor genes were either previously characterized as being involved with function of the exosome (SOP2/RRP4, SOP3/HEN2) or as a novel zinc-finger protein (SOP1) that colocalised with HEN2 in nucleoplasmic loci. The authors show additional evidence suggesting that the SOP proteins are involved in RNA quality control and introduce SOP1 as a novel component that is involved in nuclear RNA surveillance.

Reinhardt H, Hachez C, Bienert MD, Beebo A, Swarup K, Voss U, Bouhidel K, Frigerio L, Schjoerring JK, Bennett MJ, Chaumont F (2016) Tonoplast aquaporins facilitate lateral root emergence Plant Physiology. http://dx.doi.org/10.1104/pp.15.01635 Open Access

This Belgian-led study includes lead-UK representation from Warwick (Lorenzo Frigerio)  and Nottingham (Malcolm Bennett) and investigates the role of tonoplast-localised aquaporin proteins during lateral root emergence. The AtTIP1;1, AtTIP1;2 and AtTIP2;1 are abundant aquaporin proteins and the triple tip mutant shows a reduction in lateral root (LR) number without having a shorter primary root. This effect is not due to a reduction of LR primordia but rather due to a defect in the elongation of emerging LR. The authors show that spatial and temporal variations of TIP isoform expression throughout the root correlates with the tip mutant phenotype. Surprisingly, native expression of TIP2:1, which is found only at the base of the LR, can restore wildtype LR emergence to the triple mutant, suggesting that aquaporin activity in this region is sufficient to set-off LR outgrowth.

Pétriacq P, Stassen JH, Ton J (2016) Spore density determines infection strategy by the plant-pathogenic fungus Plectosphaerella cucumerina Plant Physiology http://dx.doi.org/10.1104/pp.15.00551 Open Access

Jurriaan Ton (Sheffield) is the lead researcher on this study that investigates the molecular factors that allow pathogens to switch between necrotropy and biotrophy, which elicit different response pathways within the infected plant. They used untargeted metabolomics to investigate the growth of the ascomycete pathogen Plectosphaerella cucumerina on Arabidopsis leaves. Higher spore densities activate a JA-dependent necrotropic defence response whilst lower spore numbers causes hemi-biotrophic SA-dependent responses. This change is reflected in the susceptibility of different Arabidopsis mutants to differing spore densities and allow the authors to conclude that P. cucumerina is able to gain an advantage over the host immunity by switching between different modes of infection.

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. http://dx.doi.org/10.1038/ncomms10269 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. http://dx.doi.org/10.3389/fpls.2015.01078 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 http://dx.doi.org/10.1016/j.cub.2015.12.036
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 http://dx.doi.org/10.1002/1873-3468.12035

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. http://dx.doi.org/10.1111/tpj.13104

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. http://dx.doi.org/10.1098/rsbl.2015.0929 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: January 8th

For the inaugural Arabidopsis Research Roundup of 2016 we feature the final publications of UK researchers from 2015. Martin Howard kindly provides an audio description of a paper that looks at a fundamental aspect of transcriptional regulation, through the lense of the FLC gene, whilst his co-author Caroline Dean on that paper is an author on another manuscript that investigates RNA stability in the same FLC locus. Katja Graumann leads a paper that looks into gene expression at the periphery of the nucleus whilst Ian Colbeck looks at the effect of silver nanoparticles on plant growth. Ari Sadanandom is the UK lead of a study that investigates of SUMOylation and Ian Fricker looks at the role of a cytochrome P450 on the defence response. Finally Liam Dolan is involved in a comparative analysis of the genes involved in tip growth in the cells of plants and moss.

Wu Z, Ietswaart R, Liu F, Yang H, Howard M, Dean C (2015) Quantitative regulation of FLC via coordinated transcriptional initiation and elongation. Proc Natl Acad Sci U S A. http://dx.doi.org/10.1073/pnas.1518369112 Open Access

Martin Howard and Caroline Dean lead this study that comes out of the John Innes Centre and is the result of the same collaboration that featured in an ARR earlier in 2015. In this study they investigate the mechanisms that control the quantitative regulation of gene expression by focusing on the complex regulation of the FLOWERING LOCUS C (FLC). FLC expression is controlled by a chromatin silencing mechanism involving alternative polyadenylation of antisense transcripts. However they surprisingly show that the amount of RNA Polymerase II occupancy at FLC does not coincide very well with levels of FLC transcription. They used modeling to predict that there is a tight coordination between transcriptional initiation and elongation, which was validated by detailed measurements of the levels of FLC intronic RNA. Variation within initiation and elongation rates were significantly different and was coincident with changes in H3K36me3 and H3K4me2 levels in the FLC gene. The authors propose that chromatin state can influence transcriptional initiation and elongation rates and may be a general mechanism for quantitative gene regulation in a chromatin context.

Martin Howard kindly provides an audio description of this paper and wider aspects of transcriptional regulation.

Wu Z, Zhu D, Lin X, Miao J, Gu L, Deng X, Yang Q, Sun K, Zhu D, Cao X, Tsuge T, Dean C, Aoyama T, Gu H, Qu LJ (2015) RNA-binding proteins At RZ-1B and At RZ-1C play a critical role in regulation of pre-mRNA splicing and gene expression during Arabidopsis development Plant Cell http://dx.doi.org/10.1105/tpc.15.00949

This study investigates a set of previously mysterious RNA-binding proteins and is led by Chinese researchers with a UK contribution from Caroline Dean (JIC). They look at two Arabidopsis proteins, AtRZ-1B and At RZ-1C that have RNA-binding domains and are localised to the mysterious nuclear speckles. In addition these proteins physically interact with a range of serine/arginine-rich (SR) proteins and disrupting this binding causes a range of growth phenotypes that are similar to that observed in At rz-1b/At rz-1c double mutants. These include delayed seed germination, reduced stature, and serrated leaves and on the cellular level this is accompanied by defective splicing and global changes in gene expression. Interestingly AtRz-1C directly effects the expression of the floral repressor FLC, which links this work with other research in the Dean lab. Overall this highlights the important role of At RZ-1B/1C in RNA splicing and the link to many developmental phenotypes.

Smith S, Galinha C, Desset S, Tolmie F, Evans D, Tatout C, Graumann K (2015) Marker gene tethering by nucleoporins affects gene expression in plants. Nucleus. http://dx.doi.org/10.1080/19491034.2015.1126028

Expression of Seh1-LacI-YFP at the nuclear periphery. From http://dx.doi.org/10.1080/19491034.2015.1126028
Expression of Seh1-LacI-YFP at the nuclear periphery. From http://dx.doi.org/10.1080/19491034.2015.1126028

Katja Graumann and David Evans (Oxford Brookes) are the lead academics on this collaboration with the lab of Christophe Tatout from Clermont Ferrand in France. They are attempting to answer a long standing question in the field of the biology of the nucleus; whether genes that are located close to nuclear pore complexes have increased gene expression. They used the Lac Operator/ Lac Repressor (LacI-LacO) system to assess changes in gene expression when a loci is tethered to the NPC by attaching the LacI domain to the nucleoporins Seh1 or NUP50a. The Seh1 clones localised to the nuclear periphery and showed higher RNA and protein expression of Luc. When this interaction at the periphery was distributed, the higher levels of expression were abolished. The authors therefore show that association with the nuclear periphery is important for the regulation of gene expression.

Sosan A, Svistunenko D, Straltsova D, Tsiurkina K, Smolich I, Lawson T, Subramaniam S, Golovko V, Anderson D, Sokolik A, Colbeck I, Demidchik V (2015) Engineered silver nanoparticles are sensed at the plasma membrane and dramatically modify physiology of Arabidopsis thaliana plants. Plant Journal http://dx.doi.org/10.1111/tpj.13105

Ian Colbeck (Essex) is the UK lead on this study that involves a collaboration between researchers in New Zealand, Belarus and Russia and focuses on the effect of silver nanoparticles (Ag NPs) on the growth of Arabidopsis seedlings. This type of nanoparticle is used for many difference applications so worries exist about the safety of their use. This study looks at the effect of Ag NPs on Arabidopsis root elongation and leaf expansion, both of which were inhibited at over [300mg/l] Ag NPs. In addition there were reductions of photosynthetic efficiency and accumulation of silver in plant tissues. They also showed that these particles altered the influx and efflux of metal ions whilst, although they were unable to catalyse hydroxyl radical generation, they did directly oxidise the major plant antioxidant, L-ascorbic acid. Overall the authors show that silver nanoparticles induce classical stress signalling responses but also illicit specific detrimental effects at the plasma membrane. At the whole plant level this study provides a worrying example for the role of Ag NPs on whole plant growth, even though the concentrations used in food preparation might be lower.

Crozet P, Margalha L, Butowt R, Fernandes N, Elias A, Orosa B, Tomanov K, Teige M, Bachmair A, Sadanandom A, Baena-González E (2015) SUMOylation represses SnRK1 signaling in Arabidopsis. Plant Journal http://dx.doi.org/10.1111/tpj.13096

This pan-European study features researchers from Portugal, Austria and the UK’s Durham University, led by Ari Sadanandom. They investigate the role of the SnRK1 protein kinase, which is a key enzyme for modulating the plant stress response. This paper adds detail to the cellular mechanisms that regulate SnRK1 and they show that SnRK1 is SUMOylated by the SIZ1 E3 SUMO ligase. SnRK1 is ubiquitinated and degraded in a SIZ1-dependent manner that is lacking in siz1 mutants. Interestingly only active SnRK1 is degraded as the inactive SnRK1 protein is stable but can be easily degraded upon SUMOylation. Finally they show that SnRK1 is involved in a negative feedback loop wherein it controls its own SUMOylation and degradation that, in wildtype cells, prevents a potentially detrimental stress response.

Fuchs R, Kopischke M, Klapprodt C, Hause G, Meyer AJ, Schwarzländer M, Fricker MD, Lipka V (2015) Immobilized subpopulations of leaf epidermal mitochondria mediate PEN2-dependent pathogen entry control in Arabidopsis. Plant Cell http://dx.doi.org/10.1105/tpc.15.00887

Mark Fricker (Oxford) is the UK research lead on this study that investigates the role of the atypical myrosinase PEN2 in the response to pathogen attack. PEN2 is targeted to both peroxisomes and mitochondria and can also form homo-oligomer complexes. PEN2 localised to mitochondria are immobilized following fungal invasion and this accompanies mitochondrial arrest. The substrate for PEN2 is produced by the cytochrome P450 monooxygenase CYP81F2, which is localized to the ER and moves toward immobilized mitochondria. The critical function of PEN2 in that organelle was confirmed by the result that showed exclusive mitochondria targeting could rescue pen2 mutant phenotypes. The authors show by live-cell imaging that arrested mitochondria in domains of plant-microbe interaction exhibit a pathogen-induced redox imbalance that may lead to production of intracellular signals.

Ortiz-Ramírez C, Hernandez-Coronado M, Thamm A, Catarino B, Wang M, Dolan L, Feijó JA, Becker JD (2015) A transcriptome atlas of Physcomitrella patens provides insights into the evolution and development of land plants. Mol Plant. http://dx.doi.org/10.1016/j.molp.2015.12.002

Liam Dolan (Oxford) is an author on this study that is led from Portugal and is an investigation of the transcriptome of the model moss Physcomitrella patens throughout its life cycle. They also compare transcriptomes from P.patens and Arabidopsis, allowing the authors to identify transcription factors that are expressed in tip growing cells. Interestingly they identified differences in expression patterns that might account for the differences between tip growth in moss and the Arabidopsis root hairs, an area that is the expertise of the Dolan lab.

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. http://dx.doi.org/10.1371/journal.pgen.1005660 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 http://dx.doi.org/10.1016/j.fob.2015.10.007 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. http://dx.doi.org/10.1074/jbc.M115.689554 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 http://dx.doi.org/10.1105/tpc.15.00379

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 http://dx.doi.org/10.1073/pnas.1521675112

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. http://dx.doi.org/10.1094/MPMI-05-15-0111-R

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 http://dx.doi.org/10.1080/15592324.2015.1118598

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. http://dx.doi.org/10.1080/15592324.2015.1126029

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.

Arabidopsis Research Roundup: December 9th.

This December 9th Arabidopsis Research Roundup includes four rather different studies. Firstly we include an excellent audio description from David Salt about a new type of GWAS analysis that his lab was involved in developing. This allowed identification of new genetic loci involved in molybdenum signalling. Secondly Isabelle Carre’s group from Warwick presents a study into the interactions that define the functioning of the circadian clock. Thirdly Mike Blatt leads a study that models stomatal opening and finally we include an investigation of the DOG1 gene, that includes a contribution from Fuquan Liu.

Forsberg SK, Andreatta ME, Huang XY, Danku J, Salt DE, Carlborg Ö (2015) The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance PLoS Genet. e1005648. http://dx.doi.org/10.1371/journal.pgen.1005648 Open Access.

Current GARNet Chairman David Salt (Aberdeen) is the UK lead on this collaboration with the lab of Orjan Carlborg from Uppsala in Sweden. The novelty of this paper is in the development of a new technique to measure Genome-Wide Association using the variance in SNP differences instead of using the mean. Professor Salt explained this vGWA technique in the attached audio-file, which is especially useful for people not so familiar with GWAS. Using this vGWA technique the authors were able to re-analyse an old dataset to gain additional understanding of how certain genetic loci are regulated to explain differences in the production of the essential nutrient molybdenum. Overall this paper introduces an analysis technique that can hopefully be used by other members of the community to analyse/re-analyse their data with increased rigour.

This is the 10minute audio file where David explains the paper:

Adams S, Manfield I, Stockley P, Carré IA (2015) Revised Morning Loops of the Arabidopsis Circadian Clock Based on Analyses of Direct Regulatory Interactions. PLoS One.10(12):e0143943. http://dx.doi.org/ 10.1371/journal.pone.0143943 Open Access

This collaboration between the Universities of Warwick and Leeds is led by Isabelle Carré and investigates the Arabidopsis circadian clock. They analysed the in vivo interactions of the LATE ELONGATED HYPOCOTYL (LHY) protein with promotors of other clock components. This uncovered a novel regulatory loop between LHY and the CIRCADIAN CLOCK ASSOCIATED-1 (CCA1) gene. Furthermore they show LHY acts as a repressor of all other clock components, clearly placing this protein as a key regulatory component of the Arabidopsis clock.

Minguet-Parramona C, Wang Y, Hills A, Vialet-Chabrand S, Griffiths H, Rogers S, Lawson T, Lew V, Blatt MR (2015) An optimal frequency in Ca2+ oscillations for stomatal closure is an emergent property of ion transport in guard cells. Plant Physiol. http://dx.doi.org/10.1104/pp.15.01607 Open Access

Mike Blatt is the corresponding author for this collaboration between Glasgow, Cambridge and Essex Universities. There are a good number of UK researchers who investigate the factors that regulate stomatal opening and this study looks at the role of calcium oscillations in this process. They have used the Arabidopsis OnGuard model that faithfully reproduces the optimum 10minute period of Ca2+ oscillation in guard cells. They used experimentally derived kinetics to describe the activity of ion transporters in the plasma membrane and tonoplast. Overall they discovered that the calcium oscillations are actually a by-product of the ion transport that determines stomatal aperature and not the overall controlling factor.

Cyrek M, Fedak H, Ciesielski A, Guo Y, Śliwa A, Brzeźniak L, Krzyczmonik K, Pietras Z, Liu F, Kaczanowski S, Swiezewski S (2015) Seed dormancy in Arabidopsis thaliana is controlled by alternative polyadenylation of DOG1 Plant Physiol. http://dx.doi.org/10.1104/pp.15.01483

Fuquan Liu (Queens, Belfast) is the UK contributor to this Polish-led study focused on the DOG1 gene, which is a key regulator of Arabidopsis seed dormancy. Previously it had been shown that the C-terminus of DOG1 is not conserved in many other plant species. The DOG1 transcript is alternatively polyadenylated and the authors show that Arabidopsis mutants that lack current 3’ RNA processing also show defects in seed dormancy. The shorter version of DOG1 is able to rescue the dog1 phenotype, which allows the authors to propose that DOG1 is a key regulator of seed dormancy and that the phenotypes of RNA processing mutants are linked to the incorrect processing of this specific mRNA species.

Arabidopsis Research Roundup: August 5th

This weeks Arabidopsis Research Roundup bucks the recent trend of featuring large consortium-led studies as it contains four studies each from a single UK Institution. Matthew Jones (Essex) looks at the link between photosynthesis, the circadian clock and blue-light signaling whilst Miriam Gifford (Warwick) uses cell sorting to more precisely define the plants response to an oomycete pathogen. Elsewhere Peter Eastmond (Rothamstead) looks at lipid metabolism and Keith Lindsey (Durham) leads a theorectical study on the effectiveness of methods for modelling hormone crosstalk in the root.

Litthauer S, Battle M, Lawson T, Jones MA (2015) Phototropins Maintain Robust Circadian Oscillation of PSII Operating Efficiency Under Blue Light Plant J. http://dx.doi.org/10.1111/tpj.12947

Matt Jones is a Leuverhulme Research Fellow at the University of Essex and this study is his first output as a group leader. It investigates the affect of the circadian clock on the operating efficiency of photosystem II (PSII). Previous this efficiency had been shown to be controlled by transcriptional feedback loops within the nucleus. However this study shows that in blue light it is maintained by phototropin receptors, which do not influence the nucleus. The novel imaging methodology used in this study highlight differences between the modulation of circadian outputs in distinct subcellular compartments.

Coker TL, Cevik V, Beynon JL, Gifford ML (2015) Spatial dissection of the Arabidopsis thaliana transcriptional response to downy mildew using Fluorescence Activated Cell Sorting Front Plant Sci. http://dx.doi.org/10.3389/fpls.2015.00527

Miriam Gifford leads this study from the University of Warwick that looks at the transcriptional response of Arabidopsis to downy mildew infection. The Gifford lab are experts in analysis of transcriptional data from microarrays. This study uses FACS-sorted cells infected with the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis in an attempt to focus-in on infected cells without the diluting effects of non-infected cells within the same tissue. Almost 300 transcripts were differentially expressed between haustoriated and non-haustoriated cells and this technique uncovered novel genes that had previously not been implicated in playing a role in this pathogen response.

Craddock CP, Adams N, Bryant FM, Kurup S, Eastmond PJ (2015) Regulation of endomembrane biogenesis in Arabidopsis by PHOSPATIDIC ACID HYDROLASE Plant Signal Behav. http://dx.doi.org/10.1080/15592324.2015.1065367

This study was wholly undertaken at Rothamsted Research led by Peter Eastmond. They investigate the coordination of lipid biosynthesis by focussing on the activity of two different enzymes, PHOSPHATIDIC ACID PHOSPHOHYDROLASE (PAH) and PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE (CCT). These enzymes participate in a feedback loop to control the biosynthesis of phosphaticylcholine (PC) and phosphatidic acid (PA), which is linked to biogenesis of the endoplasmic reticulum. This work offers a clue that PAH activity may require phosphorylation even though this data is not yet clear.

Simon Moore, Xiaoxian Zhang, Junli Liu & Keith Lindsey (2015) Some fundamental aspects of modelling auxin patterning in the context of auxin-ethylene-cytokinin crosstalk Plant Signalling and Behaviour http://dx.doi.org/10.1080/15592324.2015.1056424

In this manuscript Keith Lindsey and colleagues from Durham University use the paradigm of root-tip auxin-ethylene-cytokinin signaling to discuss the effectiveness of linking experimental data, reaction kinetics and spatiotemporal modelling to dissect hormonal crosstalk. The authors agree that the integration of kinetic equations with spatial root structure can produce powerful models for assessing the crosstalk of multiple hormone interactions in a spatiotemporal manner. Finally the authors come up with key recommendations to be considered when developing models for spatiotemporal hormonal crosstalk in the Arabidopsis root

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