Arabidopsis Research Roundup: October 5th

After a brief hiatus the UK Arabidopsis Research Roundup returns with eight papers that focus on different aspects of Arabidopsis cell biology.

Firstly GARNet PI Jim Murray leads a study that performs a genome-wide analysis of sub-nucleosomal particles whilst Phil Wigge’s lab at SLCU conducts a more focused study on G-box regulatory sequences.

Thirdly Veronica Grieneisen (JIC) and co-workers have modelled the process of boron transport in the root, revealing exciting insights into how traffic jams might form.

Fourthly is a large scale biology paper led by Miriam Gifford (University of Warwick) that looks at the temporal and spatial expression patterns that control lateral root development.

Next Alexander Ruban (QMUL) investigates how low-light acclimated plants respond to high light.

The sixth and seventh studies are led by Alison Baker (Leeds) or Bill Davies (Lancaster) and look at phosphate or hormone signaling respectively.

Finally Gareth Jenkins (University of Glasgow) compares the UV-B signaling module in lower plants with that in Arabidopsis.


Pass DA, Sornay E, Marchbank A, Crawford MR, Paszkiewicz K, Kent NA, Murray JAH (2017) Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PLoS Genet. doi: 10.1371/journal.pgen.1006988

Open Access

GARNet PI Jim Murray is the corresponding author on this study that performs a whole-genome scan of sub-nucleosomal particles (subNSPs) that have been identified using differential micrococcal nuclease (MNase) digestion. They link the position of subNSPs with RNAseq data taken from plants grown in different light conditions. They show that this new technique is able to discriminate regulatory regions that have been obscured by previous experimental procedures and therefore represents a very useful experimental method.


Ezer D, Shepherd SJ, Brestovitsky A, Dickinson P, Cortijo S, Charoensawan V, Box MS, Biswas S, Jaeger K, Wigge PA (2017) The G-box transcriptional regulatory code in Arabidopsis. Plant Physiol. 10.1104/pp.17.01086

Open Access

Phil Wigge (SLCU) is the corresponding author of this study that investigates the sequence elements that are linked to the conserved G-box regulatory motifs. They identify a set of bZIP and bHLH transcription factors that predict the expression of genes downstream of perfect G-boxes. In addition they have developed a website that provide visualisations of the G-box regulatory network (araboxcis.org).


Sotta N, Duncan S, Tanaka M, Takafumi S, Marée AF, Fujiwara T, Grieneisen VA (2017) Rapid transporter regulation prevents substrate flow traffic jams in boron transport. Elife. doi: 10.7554/eLife.27038

Open Access

Veronica Grieneisen (JIC) is the lead author on this detailed analysis of the regulatory circuits that are established during boron uptake in Arabidopsis roots. They used mathematical modelling to show that during boron uptake, swift regulation of transport activity is needed to prevent toxic accumulation of the metal. This system has analogy to the way in which traffic jams of nutrient flow might form and has relevance for regulatory systems outside of plant science. https://www.sciencedaily.com/releases/2017/09/170905104358.htm


Walker L, Boddington C, Jenkins D, Wang Y, Grønlund JT, Hulsmans J, Kumar S, Patel D, Moore JD, Carter A, Samavedam S, Bomono G, Hersh DS, Coruzzi GM, Burroughs NJ, Gifford ML (2017) Root architecture shaping by the environment is orchestrated by dynamic gene expression in space and time. Plant Cell. doi: 10.1105/tpc.16.00961

Open Access

Miriam Gifford (University of Warwick) leads this broad consortium that has taken a systems biology approach to better define the environmental factors that control dynamic root architecture. They track transcriptional responses during lateral root development in remarkable detail, looking at individual transcripts. They confirm the idea that the activity of a gene is not simply a function of its amino acid sequence but rather the temporal and spatial regulation of its expression.


Tian Y, Sacharz J, Ware MA, Zhang H, Ruban AV (2017) Effects of periodic photoinhibitory light exposure on physiology and productivity of Arabidopsis plants grown under low light. J Exp Bot. doi: 10.1093/jxb/erx213. Open Access

Alexander Ruban (QMUL) is the corresponding author on this collaboration with Chinese colleagues that examined the effect of high-light stress on low-light acclimated Arabidopsis plants. Initially these plants showed significant photo-inhibition but that they recovered rapidly and after 2 weeks of treatment there was no change in photosynthetic yield. In addition high light acclimated plants showed accelerated reproductive phase change that coincided with higher seed yield.


Qi W, Manfield IW, Muench SP, Baker A (2017) AtSPX1 affects the AtPHR1 -DNA binding equilibrium by binding monomeric AtPHR1 in solution. Biochem J. doi: 10.1042/BCJ20170522 Open Access

Alison Baker (University of Leeds) leads this research that focusses on the binding of the Phosphate Starvation Response 1 (PHR1) transcription factor to regulatory P1BS DNA sequences. They show a tandem P1BS sequence is bound more strongly than a single P1BS site. Ultimately they demonstrate tight regulation of phosphate signaling both by the concentration of phosphate as well as the activity of the interacting SPX protein.


Li X, Chen L, Forde BG, Davies WJ (2017) The Biphasic Root Growth Response to Abscisic Acid in Arabidopsis Involves Interaction with Ethylene and Auxin Signalling Pathways. Front Plant Sci. doi: 10.3389/fpls.2017.01493 Open Access

Bill Davies and Brian Forde (Lancaster University) lead this work that investigates the effect on ethylene and auxin on the biphasic response to ABA during root elongation. They used a range of hormone signalling mutants to show that the response to high ABA is via both ethylene and auzin signalling. In contrast the response to low ABA does not require ethylene signalling.


Soriano G, Cloix C, Heilmann M, Núñez-Olivera E, Martínez-Abaigar J, Jenkins GI (2017) Evolutionary conservation of structure and function of the UVR8 photoreceptor from the liverwort Marchantia polymorpha and the moss Physcomitrella patens. New Phytol. doi: 10.1111/nph.14767

Gareth Jenkins (University of Glasgow) is the corresponding author of this work that looks at the role of the UVR8 UV-B receptor in lower plants. They expressed the versions of UVR8 from a moss or a liverwort in Arabidopsis and showed that although there appears to be differences in the regulation of this protein, the mechanism of UV-B signaling is evolutionarily conserved

Arabidopsis Research Roundup: September 6th

This largest ever Arabidopsis Research Roundup (ARR) includes 6 papers from Norwich Research Park (NRP), including three featuring Cyril Zipfel (TSL) as a co-author on papers that investigate different aspects of plant immune signaling. Elsewhere on the NRP site Veronica Grieneisen (JIC) is a co-author on a study that defines the root auxin maximum whilst Dale Sanders and Saskia Hogenhout lead a paper that defines a method for the analysis of calcium signaling. Finally Robert Sablowski’s group at the JIC investigates the role of the DELLA proteins during meristem development.

Elsewhere investigators from Kew Gardens and Bangor University have used nanopore sequencing for the facile characterisation of field populations of Arabidopsis. Similarly Seth Davies (University of York) is part of a collaboration that looks how alterations in the circadian clock might affect plant fitness.

Verena Kriechbaumer (Oxford Brookes) leads a phylogenetic study into the conservation of auxin biosynthesis genes whilst Hilary Rodgers (Cardiff University) is a co-author on a Chinese-led study that looks into role of cadmium on the Arabidopsis cell cycle.

This ARR is full of examples of UK researchers involved in global collaborations. This includes Cambridge researchers involved in a proteomic analysis of microsomes, Justin Goodrich from the University of Edinburgh as part of a US-led study that defines the regulation of the PRC2 complex and Katherine Denby (University of York) as a member of a consortium that has performed a network analysis of jasmonic acid signaling.

Finally are two studies in which the research takes place within a single institution. Malcolm Hawksford (Rothamsted Research) looks at the effect of wheat transcription factors in the response to the heavy metal zinc whilst Emily Larson and Mike Blatt (University of Glasgow) investigate the role of clathrin on plant vesicular transport.


D’Ambrosio JM, Couto D, Fabro G, Scuffi D, Lamattina L, Munnik T, Andersson MX, Alvarez ME, Zipfel C, Laxalt AM (2017) PLC2 Regulates MAMP-Triggered Immunity by Modulating ROS Production in Arabidopsis. Plant Physiol 10.1104/pp.17.00173

This Argentinian-led study includes Cyril Zipfel (TSL) as a co-author on this work that uses miRNA-mediated gene silencing to assess the role of the phosphoinositide-specific phospholipase C (PI-PLC) in plant immune signaling.


Imkampe J, Halter T, Huang S, Schulze S, Mazzotta S, Schmidt N, Manstretta R, Postel S, Wierzba M, Yang Y, vanDongen WM, Stahl M, Zipfel C, Goshe MB, Clouse S, de Vries SC, Tax F, Wang X, Kemmerling B (2017) The Arabidopsis Leucine-rich Repeat Receptor Kinase BIR3 Negatively Regulates BAK1 Receptor Complex Formation and Stabilizes BAK1. Plant Cell. 10.1105/tpc.17.00376

Cyril Zipfel (TSL) is a co-author on this global collaboration that further defines the role of the BAK1 receptor in hormone and immune signaling through its interaction with two LRR-RK proteins (BIR2 and BIR3).


Singh V, Perraki A, Kim SY, Shrivastava S, Lee JH, Zhao Y, Schwessinger B, Oh MH, Marshall-Colon A, Zipfel C, Huber SC (2017) Tyrosine-610 in the Receptor Kinase BAK1 Does Not Play a Major Role in Brassinosteroid Signaling or Innate Immunity. Front Plant Sci. 10.3389/fpls.2017.01273

Cyril Zipfel (TSL) is a co-author on this US-led manuscript that again looks into the role of the BRI1-ASSOCIATED KINASE1 (BAK1) on plant immune signaling. Importantly they show that the phosphorylation of tyrosine-610 is actually not necessary for this proteins role in brassinosteroid or immune signaling


Di Mambro R, De Ruvo M,,, Pacifici E, Salvi E, Sozzani R, Benfey PN,, Busch W, Novak O, Ljung K, Di Paola L, Marée AFM, Costantino P, Grieneisen VA, Sabatini S (2017) Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root. Proc Natl Acad Sci U S A 10.1073/pnas.1705833114

Veronica Grieneisen (JIC) is a co-corresponding author on this work with Sabrina Sabatini from the University of Rome. They define the auxin minimum, a newly characterised determinat of root patterning that delineates the separation of root division and the differentiation zones. This is defined by the interaction between cytokinin and auxin signaling cascades.

Veronica discusses this paper on the GARNet YouTube channel: https://www.youtube.com/watch?v=gYdL6eddOcA


Vincent TR, Canham J, Toyota M, Avramova M, Mugford ST, Gilroy S, Miller AJ, Hogenhout S, Sanders D (2017) Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor. J Vis Exp. 10.3791/56142

Dale Sanders and GARNet committee member Saskia Hogenhout (JIC) lead this study that describes an imaging technique that allows for the real time assessment of calcium dynamics using a fluorescently tagged sensor.


Serrano-Mislata A, Bencivenga S, Bush M, Schiessl K, Boden S, Sablowski R (2017) DELLA genes restrict inflorescence meristem function independently of plant height. Nature Plants. 10.1038/s41477-017-0003-y

Robert Sablowski (JIC) leads this paper that investigates the role of DELLA proteins in the control of cell cycle regulators and how this impacts meristem size in both barley and Arabidopsis. Read more about it on the John Innes Centre website.


Parker J, Helmstetter AJ, Devey D, Wilkinson T, Papadopulos AST (2017) Field-based species identification of closely-related plants using real-time nanopore sequencing. Sci Rep. 10.1038/s41598-017-08461-5 Open Access

This investigation led by researchers at Kew Gardens and at the Bangor University use Real Time Nanopore Sequencing (RTnS) that allows for rapid species identification in the field and that combining RTnS and laboratory-based high-throughput sequencing leads to a significant improvement in genome assembly.


Rubin MJ, Brock MT, Davis AM, German ZM, Knapp M, Welch SM, Harmer SL, Maloof JN7, Davis SJ, Weinig C (2017) Circadian rhythms vary over the growing season and correlate with fitness components. Mol Ecol. 10.1111/mec.14287 Open Access

Seth Davies (University of York) is a co-author on this US-led work that conducts a study of field-growth Arabidopsis to evaluate the contribution of the circadian clock toward survival and fecundity. They show that variation in clock function correlates with growth performance in a natural environment.


Poulet A, Kriechbaumer V (2017) Bioinformatics Analysis of Phylogeny and Transcription of TAA/YUC Auxin Biosynthetic Genes. Int J Mol Sci. 10.3390/ijms18081791 Open Access

The paper from Oxford Brookes University provides a phylogenetic analysis of TAA/TAR (tryptophan aminotransferase related) and YUCCA proteins that are involved in auxin biosynthesis. In addition they provide tissue and cell-specific information about the function of these proteins and that their function is conserved in lower plant species.


Cui W, Wang H, Song J, Cao X, Rogers HJ, Francis D, Jia C, Sun L, Hou M, Yang Y, Tai P, Liu W (2017) Cell cycle arrest mediated by Cd-induced DNA damage in Arabidopsis root tips. Ecotoxicol Environ Saf. 10.1016/j.ecoenv.2017.07.074 Open Access

Hilary Rodgers (Cardiff University) is a co-author on this Chinese-led study that looks into the effect of cadmium treatment on the regulation of the cell cycle and DNA damage repair. They show that different cadmium concentrations effect different phases of the cell cycle.


Alqurashi M, Thomas L, Gehring C, Marondedze C (2017) A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses. Proteomes. 10.3390/proteomes5030022 Open Access

This international collaboration includes members of the Cambridge Centre for Proteomics and conducts a quantitative analysis of the Arabidopsis microsomal proteome following treatment with hydrogen peroxide or ABA. Perhaps unsurprisingly a high number of proteins characterized as ‘responsing to stress’ were found upregulated following treatment with H2O2 or ABA.


Xiao J, Jin R, Yu X, Shen M, Wagner JD, Pai A, Song C, Zhuang M, Klasfeld S, He C, Santos AM, Helliwell C, Pruneda-Paz JL, Kay SA, Lin X, Cui S, Garcia MF, Clarenz O, Goodrich J, Zhang X, Austin RS,, Bonasio R, Wagner D (2017) Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nature Genet 10.1038/ng.3937

Justin Goodrich (University of Edinburgh) is a co-author on this US-led study that looks into the role of Polycomb response element (PREs) in directing the placement of the Polycomb repressive complex 2 (PRC2) via their interaction with a newly identified transcription factors. Justin has recently discussed a paper on a similar topic on the GARNet YouTube channel.


Hickman R, van Verk MC, Van Dijken AJH, Pereira Mendes M, Vroegop-Vos IA, Caarls L, Steenbergen M, Van Der Nagel I, Wesselink GJ, Jironkin A, Talbot A, Rhodes J, de Vries M, Schuurink RC, Denby K, Pieterse CMJ, Van Wees SCM (2017) Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network. The Plant Cell 10.1105/tpc.16.00958 Open Access

GARNet committee member Katherine Denby (University of York) is a member of this large consortium of researchers who have performed a network analysis on the dynamics of jasmonic acid signaling


Evens NP, Buchner P, Williams LE, Hawkesford MJ (2017) The role of ZIP transporters and group F bZIP transcription factors in the Zn-deficiency response of wheat (Triticum aestivum) Plant J. 10.1111/tpj.13655 Open Access

Malcolm Hawkesford (Rothamsted Research) leads this study that investigate a set of wheat bZIP transcription factors and ZIP transporters that are involved in the uptake and transport of zinc. As part of this work they use Arabidopsis to test the conserved function of these wheat proteins.


Larson ER, Van Zelm E, Roux C, Marion-Poll A, Blatt MR (2017) Clathrin Heavy Chain subunits coordinate endo- and exocytic traffic and affect stomatal movement. Plant Physiol. 10.1104/pp.17.00970 Open Access

Mike Blatt and Emily Larson (University of Glasgow) are the co-corresponding authors on this study that looks into the role of clathrin heavy chain on vesicular transport in Arabidopsis. They looked at clathrin mutants to show that the protein plays an unsurprisingly important role in both endo- and exocytosis.

Arabidopsis Research Roundup: March 6th.

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Published on: March 6, 2017

This weeks Arabidopsis Research Roundup includes four papers that focus on different aspects of plant cell biology. Firstly Ian Henderson’s research group in Cambridge defines the role of a critical component that determines crossover frequency in plants and other eukaryotes. Secondly Karl Oparka (Edinburgh) leads a broad collaboration that defines the mechanism of unloading of solutes and macromolecules from the root phloem. Thirdly Keith Lindsey (Durham) has developed a model that describes how auxin patterns the Arabidopsis root. Finally Mike Blatt (Glasgow) is part of a group that uses Arabidopsis as a framework for the study of ABA-signaling during stomatal movement in ferns.


Ziolkowski PA, Underwood CJ, Lambing C, Martinez-Garcia M, Lawrence EJ, Ziolkowska L, Griffin C, Choi K, Franklin FC, Martienssen RA, Henderson IR (2017) Natural variation and dosage of the HEI10 meiotic E3 ligase control Arabidopsis crossover recombination. Genes Dev

http:/​/​dx.​doi.​org/10.1101/gad.295501.116

Open Access

GARNet committee member Ian Henderson (University of Cambridge) leads this work that features collaborators from the UK, US and Poland. They use an experimental technique that allows facile analysis of recombination rates alongside a study of Arabidopsis natural variation to isolate a QTL that is critical for maintaining the correct number of crossovers during meiosis. This HEI10 gene codes for an E3 ligase (the targets of which are currently unknown) whose copy number is a key component in the control of recombination rate. Hei10 mutants have less crossovers whilst plants with extra copies of HEI10 have an increased number, especially in sub-telomeric regions of the genome. HEI10 is a highly conserved protein, demonstrating its important role to ensure appropriate levels of recombination throughout the evolution of eukaryotes.

Ian kindly takes ten minutes to discuss this paper with GARNet on our YouTube Channel.


Ross-Elliott TJ, Jensen KH, Haaning KS, Wager BM, Knoblauch J, Howell AH, Mullendore DL, Monteith AG, Paultre D, Yan D, Otero-Perez S, Bourdon M, Sager R, Lee JY, Helariutta Y, Knoblauch M, Oparka KJ (2017) Phloem unloading in Arabidopsis roots is convective and regulated by the phloem-pole pericycle. Elife.

http:/​/​dx.​doi.​org/10.7554/eLife.24125

Open Access

Karl Oparka (University of Edinburgh) is the corresponding author of this study that includes researchers from the UK, US and Denmark. Movement of solutes and macromolecules through the plant phloem is key for the correct distribution of nutrients allowing for optimal growth. In this paper they discover that unloading of molecules from the phloem occurs via a set of specialized funnel plasmodesmata that link the phloem to adjacent pericycle cells. Remarkably they find that whereas solutes are constantly unloaded, larger proteins are released through these plasmodesmata in discrete pulses, which they describe as ‘batch unloading’. Overall this study provides evidence of a major role for the phloem-pericycle cells in the process of moving essential nutrients from the phloem into surrounding tissues.


Moore S, Liu J, Zhang X, Lindsey K (2017) A recovery principle provides insight into auxin pattern control in the Arabidopsis root. Sci Rep. http:/​/​dx.​doi.​org/10.1038/srep43004

Open Access

The work comes from the lab of Keith Lindsey (University of Durham) and developes a data-driven model that predicts the role of auxin patterning in the recovery of an Arabidopsis root following a perturbation of polar auxin transport. They demonstrate three main principles that define the role of auxin influx and efflux carriers in this process and also provide experimental validation for their predictions.


Cai S, Chen G, Wang Y, Huang Y, Marchant B, Wang Y, Yang Q, Dai F, Hills A, Franks PJ, Nevo E, Soltis D, Soltis P, Sessa E, Wolf PG, Xue D, Zhang G, Pogson BJ, Blatt MR, Chen ZH (2017)

Evolutionary Conservation of ABA Signaling for Stomatal Closure in Ferns Plant Physiol

http:/​/​dx.​doi.​org/10.1104/pp.16.01848

Open Access

Mike Blatt (University of Glasgow) is a co-author on this global study that looks into the evolution of ABA-signaling in the control of stomatal closure. Although this study is focused on this process in ferns they build their findings on the analysis of transcriptional networks from Arabidopsis. Ultimately they find that the evolution of ABA-controlled guard cells movements are important in the adaptation of ferns to a terrestrial environment.

Arabidopsis Research Roundup: January 11th

The first Arabidopsis Research Roundup of 2017 includes a wide range of studies that use our favourite model organism.

Firstly Kerry Franklin (University of Bristol) is the corresponding author on a paper that describes the complex interaction between the responses to sunlight and heat. Secondly Paul Dupree (University of Cambridge) leads a study that defines the important structural relationship between xylan and cellulose. Thirdly members of Gos Micklem’s group in Cambridge are part of the Araport team that present their ThaleMine tool.

Richard Napier (University of Warwick) is a co-author on the fourth paper that introduces a new chemical tool for study of the auxin response. The penultimate paper includes Matthew Terry (University of Southampton) on a paper that investigates the role of a Fe-S-containing protein cluster in chlorophyll biosynthesis and finally there is a methods paper from Stefanie Rosa in Caroline Dean’s lab at the John Innes Centre that describes the use of FISH to detect single molecules of RNA.


Hayes S, Sharma A, Fraser DP, Trevisan M, Cragg-Barber CK, Tavridou E, Fankhauser C, Jenkins GI, Franklin KA (2016) UV-B Perceived by the UVR8 Photoreceptor Inhibits Plant Thermomorphogenesis. Current Biology http:/​/​dx.​doi.​org/10.1016/j.cub.2016.11.004

Open Access

This collaboration between the research groups of Kerry Franklin (University of Bristol) and Gareth Jenkins (University of Glasgow) looks at how the perception of UV-B light inhibits the morphological changes that occur in response to increased temperatures (thermomorphogenesis). This response includes induced hypocotyl elongation, which is mediated via PIF4 and various players in the auxin response. Interestingly the authors show that UV-B light perceived by UVR8 attenautes this response by preventing PIF4 abundance and by stabilising the the bHLH protein LONG HYPOCOTYL IN FAR RED (HFR1) protein. These results suggest that there exists a precise mechanism for fine-tuning the growth responses that occur in sunlight that would usually include both increased temperature and UV-B irradiation.
UVB_pic


Simmons TJ, Mortimer JC, Bernardinelli OD, Pöppler AC, Brown SP, deAzevedo ER, Dupree R, Dupree P (2016) Folding of xylan onto cellulose fibrils in plant cell walls revealed by solid-state NMR. Nat Commun.

http:/​/​dx.​doi.​org/10.1038/ncomms13902 Open Access
In this paper Paul Dupree (University Cambridge) collaborates both with colleagues in Spain and with his father Ray, who is a physicist at the University of Warwick. They use NMR to perform a structural analysis of xylan, which is the most prevalent non-cellulosic polysaccharide in the cell wall matrix and binds to cellulose microfibrils. Whereas in solution xylan forms a threefold helical screw, it flattens into a twofold helical screw ribbon to closely bind to cellulose when in the cell wall. They used the cellulose-deficient Arabidopsis irx3 mutant to show that the xylan two-fold screw confirmation breaks down when it cannot bind cellulose. The authors state that this finding has important implications in our understanding of the formation of the cell wall and perhaps more importantly how it might be broken down during attempts to maximise economic usages of plant biomass.

A local Cambridge newspaper reported that this finding could ‘pave the way for wooden skyscrapers’
XylanPic


Krishnakumar V, Contrino S, Cheng CY, Belyaeva I, Ferlanti ES, Miller JR, Vaughn MW, Micklem G, Town CD, Chan AP (2016) ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery. Plant Cell Physiol http:/​/​dx.​doi.​org/10.1093/pcp/pcw200 Open Access

This paper is presented by the Araport team, which is based in the USA but includes representatives from Gos Micklem’s lab in University of Cambridge. They outline the functionality of the ThaleMine data warehouse which is an important component of the tools included on Araport (https://www.araport.org/). ThaleMine collects a wide variety of data from public datasets and presents it in a easy-to-interrogate form, facilitating the experiments of both lab-based researchers or bioinformaticians. This tool is build upon the InterMine software framework, which has been widely adopted across other model organisms.

Chris Town and Sergio Contrino provided a hands-on workshop describing the tools on Araport in last year GARNet2016 meeting and their workshop materials can be downloaded here.


Steenackers WJ, Klíma P, Quareshy M, Cesarino I, Kumpf RP, Corneillie S, Araújo P, Viaene T, Goeminne G, Nowack MK, Ljung K, Friml J, Blakeslee JJ, Novák O, Zažímalová E, Napier RM, Boerjan WA, Vanholme B (2016) cis-cinnamic acid is a novel, natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiol. http:/​/​dx.​doi.​org/pp.00943.2016 Open Access
cCApic
This pan-european collaboration includes members of Richard Napier’s lab at the University of Warwick. They outline the activity of a novel inhibitor of auxin efflux transport called cis-cinnamic acid (c-CA). When c-CA is applied to growth media plants appears to exhibit an auxin-response phenotype yet these experiments show that c-CA is neither an auxin or anti-auxin and in fact blocks local auxin efflux, thus causing buildup of cellular auxin. This effect does not occur with t-CA showing specificity for c-CA and it does not affect long distance auxin transport, which occurs through the phloem. Therefore this paper presents a new pharamolgical tool for the study of in planta auxin transport and homeostasis.


Hu X, Page MT, Sumida A, Tanaka A, Terry MJ, Tanaka R (2016) The iron-sulfur cluster biosynthesis protein SUFB is required for chlorophyll synthesis, but not phytochrome signaling. Plant J.

http:/​/​dx.​doi.​org/10.1111/tpj.13455

Matthew Terry and Mike Page (University of Southampton) are co-authors on this Japanese-led study that investigates the function of the SUFB subunit of the SUFBCD iron-sulfur cluster. These Fe-S protein clusters play roles in many metabolic processes and the SUFB mutant hmc1 exhibits a defect in chlorophyll biosynthesis due to an accumulation of Mg-containing biosynthetic intermediates. In addition both SUFC- and SUFD-deficient RNAi lines accumulated the same Mg intermediate indicating that the SUFBCD cluster is responsible for this step necessary for chlorophyll production.


Duncan S, Olsson TS, Hartley M, Dean C, Rosa S (2016) A method for detecting single mRNA molecules in Arabidopsis thaliana. Plant Methods. http:/​/​dx.​doi.​org/10.1186/s13007-016-0114-x

Open Access
This paper from is lead by Stefanie Rosa in Caroline Dean’s lab at the John Innes Centre describes a novel method for imaging single molecules of RNA by smFISH. They analyse the localisation of both nascent and mature mRNAs, allowing for analysis of the location of RNA processing and translation.<
RosaPic

Arabidopsis Research Roundup: August 26th

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Published on: August 26, 2016

This weeks Arabidopsis Research Roundup includes three papers across a wide range of topics. Firstly is a widely-reported study, described here with an audio description by Nik Cunniffe and Sanjie Ziang, of the evolutionary relationship between viral infection, pollinator attraction, plant fertility and miRNA-regulated gene expression. Secondly, Gordon Simpson is a co-author on a paper that has elucidated the crystal structure of the FPA proteins and finally Gareth Jenkins leads an investigation into the relationship between UV light, the UVR8 protein and histone modifications.

Groen SC, Jiang S, Murphy AM, Cunniffe NJ, Westwood JH, Davey MP, Bruce TJ, Caulfield JC, Furzer OJ, Reed A, Robinson SI, Miller E, Davis CN, Pickett JA, Whitney HM, Glover BJ, Carr JP (2016) Virus Infection of Plants Alters Pollinator Preference: A Payback for Susceptible Hosts? PLoS Pathog. 12(8):e1005790

http:/​/​dx.​doi.​org/10.1371/journal.ppat.1005790

Open Access
BumbleBee
This pan-UK collaboration is led by John Carr, Beverly Glover and Nik Cunniffe at the University of Cambridge and has received wide attention in the general press. Nik Cunniffe also kindly provides an audio description of this work that looked into the effect of viral infection on the attraction of pollinators. The authors used GC-MS to look at the volatiles produced in virally infected Arabidopsis and tomato plants, showing that infection can alter the foraging behavior of bumblebees. Mutational analysis of both cucumber mosaic virus (CMV) and Arabidopsis showed that the microRNA pathway is involved in regulating the emission of these pollinator-perceivable volatiles. When virus-infected tomato plants were not pollinated there was a clear reduction in seed yield, indicating that the plant requires the volatile production following viral infection to attract pollinators, leading to reproductive success. Importantly the authors model the possible trade-off between viral infection and reproductive success in the wild, which might oppose the strong selective pressure for the establishment of disease-resistance genes. The authors speculate that this is a co-beneficial relationship for both virus and plant.

Nick Cunniffe and Sanjie Jiang kindly provide an audio description of this work.


 

Zhang Y, Rataj K, Simpson GG, Tong L (2016) Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA PLoS One 11(8):e0160694

http:/​/​dx.​doi.​org/10.1371/journal.pone.0160694

Open Access

Gordon Simpson (University of Dundee) in a co-author on this US-led study that has elucidated the crystal structure of the SPOC domain of the FPA floral regulator protein. FPA contains a N-terminal RNA recognition motif and a C-terminal SPEN paralog and ortholog C-terminal (SPOC) domain. This SPOC domain is highly conserved throughout plant species and this crystal structure is an important development in our understanding of the regulation of RNA 3’-end formation and how much the plant SPOC domains compare with an equivalent from metazoans.

 

Velanis CN, Herzyk P, Jenkins GI (2016) Regulation of transcription by the Arabidopsis UVR8 photoreceptor involves a specific histone modification Plant Mol Biol.

http:/​/​dx.​doi.​org/10.1007/s11103-016-0522-3

Open Access

Gareth Jenkins (Glasgow) leads this study that continues his groups work on the Arabidopsis UVR8 photoreceptor. They show that UV-B exposure increases histone lysine acetylation on UVR8-regulated genes in a UVR8 dependent manner. In fact all of the histone enrichments throughout the genome following UV-B required UVR8 activity. However the authors could find no direct interaction between UVR8 and the known enzymes involved in light-mediated histone modification indicating that UVR8 either interacts with a novel set of proteins or the UVR8 effect is mediated via a currently unknown signaling intermediate.
UVRpic

Arabidopsis Research Roundup: July 19th

There are six papers in this weeks Arabidopsis Research Roundup. Two of these include research on the stomatal patterning gene TMM. Firstly a White Rose consortium investigates the ancestral basis of stomatal patterning, whilst a Glasgow-based study investigates the relationship between patterning and the dynamics of guard cell opening. The GARNet committee is represented by work from Cardiff that looks at the relationship between seed size and shoot branching and also from Cambridge in research that studies meiotic recombination in genomic regions important for pathogen defense. Finally are two studies that look into aspects of root and shoot patterning and include co-authors from CPIB in Nottingham or the John Innes Centre.

Caine R, Chater CC, Kamisugi Y, Cuming AC, Beerling DJ, Gray JE, Fleming AJ (2016) An ancestral stomatal patterning module revealed in the non-vascular land plant Physcomitrella patens Development

http://dx.doi.org/10.1242/dev.135038 Open Access

This study is a collaboration between labs in Sheffield and Leeds, led by Andrew Fleming (Sheffield). They investigate the role that the signalling module comprised of Epidermal Patterning Factors (EPFs), ERECTA and TMM play during the evolution of stomatal patterning. This module is known to play an important role in Arabidopsis and in this study the authors show that the moss Physcomitrella patens contains homologs of each of the genes and that they perform the same function. When P.paten versions of these genes are transferred to equivalent Arabidopsis mutants they show conserved function demonstrating that this module is an example of an ancestral patterning system.

Andrew Fleming provides a brief audio description of this manuscript:

Papanatsiou M, Amtmann A, Blatt MR (2016) Stomatal spacing facilitates guard cell ion transport independent of the epidermal solute reservoir. Plant Physiol. http://dx.doi.org/10.1104/pp.16.00850 Open Access

Mike Blatt and Anna Amtmann (University of Glasgow) are the co-supervisors for this study into the relationshop between ion transport in stomatal guard cells and their physical positioning within a leaf. They used a genetic approach to assess the effect of stomatal clustering, showing that too many mouths (tmm) mutant plants have reduced stomatal movements associated with alterations in K+ channel gating and coincident with a surprising reduction in the level of K+ ions in guard cells. These results underline the importance of stomatal spacing in this process but do not provide a full explanation into the alteration in K+ ion dynamics.

Sornay E, Dewitte W, Murray JAH (2016) Seed size plasticity in response to embryonic lethality conferred by ectopic CYCD activation is dependent on plant architecture Plant Signaling and Behaviour e1192741

http://dx.doi.org/10.1080/15592324.2016.1192741 Open Access

From http://dx.doi.org/10.1080/15592324.2016.1192741
From http://dx.doi.org/10.1080/15592324.2016.1192741

This research comes from the lab of GARNet PI Jim Murray (Cardiff) and investigates cell proliferation and growth within a developing seed. They previously have shown that targeting of D-type cyclin CYCD7;1 to the central cell and early endosperm can trigger nuclear divisions and ovule abortion, which leads to a smaller number of larger seed. In this study they show that development of larger seed in transgenic plants is influenced by the architecture of the mother, as plants with increased side branches, caused by pruning of the main stem, do not generate this phenotype. This is indicative of a close relationship between the amount of resources allocated to different parts of the plant and that a transgenic effect was altered by a different plant morphology. This should provide an important insight into future work that aims to define the effect of any particular transgenic alteration.

Choi K, Reinhard C, Serra H, Ziolkowski PA,, Underwood CJ,, Zhao X, Hardcastle TJ, Yelina NE, Griffin C, Jackson M, Mézard C, McVean G, Copenhaver GP,, Henderson IR (2016) Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes. PLoS Genet. 12(7):e1006179.

http://dx.doi.org/10.1371/journal.pgen.1006179 Open Access

GARNet advisory board member Ian Henderson (Cambridge) is the corresponding author of this study that involves contributions from the UK, US, Poland and France. They investigate genomic regions that show increased meiotic recombination, which is predicted to occur coincident with genes involved in pathogen defence given their requirement to adapt to new external challenges. This study focuses on NBS-LRR domain proteins that tend to physically cluster in the Arabidopsis genome. Interesting they discovered both hot and coldspots for meiotic recombination that associate with NBS-LRR clusters, the later often correlating with structural heterozygosity. In a more detailed dissection of 1000 crossovers in the RESISTANCE TO ALBUGO CANDIDA1 (RAC1) R hotspot, they discovered higher recombination frequencies associating with known sequence motifs important for the pathogen response, which were influenced by ecotype-specific factors. Ultimately the authors note that there is a complex relationship between regions of meiotic recombination, structural heterozygosity and the evolutionary pressures that occurs with host-pathogen relationships.

Orman-Ligeza B, Parizot B, de Rycke R, Fernandez A, Himschoot E, Van Breusegem F, Bennett MJ, Périlleux C, Beeckman T, Draye X (2016) RBOH-mediated ROS production facilitates lateral root emergence in Arabidopsis. Development http://dx.doi.org/10.1242/dev.136465 Open Access

From http://dx.doi.org/10.1242/dev.136465
From http://dx.doi.org/10.1242/dev.136465

 Malcolm Bennett (CPIB) is the sole UK-based co-author on this study led by Belgian collaborators and investigates the role of reactive oxygen species (ROS) in auxin-regulated lateral root (LR) formation. They show that ROS can reactivate LR primordia and pre-branch sites, resulting in increased LR numbers. This occurs in both wildtype and in auxin mutants that have reduced numbers due to changes in auxin-mediated cell wall remodeling. ROS is deposited in the apoplast of emerging LR cells in a pattern that is coincident with the expression of the RESPIRATORY BURST OXIDASE HOMOLOGS (RBOH) genes. Concomitantly the altered expression of RBOH was shown to affect the development and emergence of LRs. This adds a further level of complexity to the current understanding of the signaling factors that converge to facilitate LR growth.

 

Shi B,, Zhang C, Tian C, Wang J,, Wang Q,, Xu T,, Xu Y, Ohno C, Sablowski R, Heisler MG, Theres K, Wang Y, Jiao Y (2016) Two-Step Regulation of a Meristematic Cell Population Acting in Shoot Branching in Arabidopsis. PLoS Genet. http://dx.doi.org/10.1371/journal.pgen.1006168 Open Access

This Chinese-led study includes Robert Sablowski (JIC) as a co-author and studies the factors that influence the development of axillary meristems. They use innovative live imaging to show that SHOOT MERISTEMLESS (STM) is continuously expressed and that this dependent on a leaf axil auxin minimum. Once STM expression is lost then the axil is unable to form a meristem even if STM is switched back later in development, indicating that cells undergo an irreversible developmental commitment. The expression domain of STM is under cell-type specific control of REVOLUTA (REV) DNA binding. Overall this study demonstrates that meristematic competence and initiation is dependent on differing levels of the key regulator STM.

From http://dx.doi.org/10.1371/journal.pgen.1006168
From http://dx.doi.org/10.1371/journal.pgen.1006168

Arabidopsis Research Roundup: March 24th

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Published on: March 24, 2016

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

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

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

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

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

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

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

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

Arabidopsis Research Roundup: February 17th

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Published on: February 16, 2016

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

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

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

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

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

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

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

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

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