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 (

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.

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:

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: August 23rd

There is a bumper crop of papers in this weeks UK Arabidopsis Research Roundup! First up is a remarkable piece of work from George Bassel’s (University of Birmingham) lab that defines the network of cellular interactions that occur in the hypocotyl. Second and third are papers from the JIC in which Lars Ostergaard’s group uncovers the extent of the ETTIN signaling network and Caroline Dean‘s and Martin Howard’s labs provide evidence for a two step progression toward stable gene silencing following vernalisation at the FLC locus. Fourthly is a study that includes members of Alex Webb’s group (University of Cambridge) as co-authors that investigates the link between the circadian clock and night time starch metabolism. Fifth is a paper from Christine Foyer (University of Leeds) that looks at the effect of commonly used inhibitors on cellular redox state and gene expression. The next paper includes Phillip Carella (SLCU) as a co-author and looks at the role of classic flowering time genes on the phenomenon of Age-Related Resistance and finally Lee Sweetlove’s (University of Oxford) lab has published a methods paper for the analysis of photorespiration in non-photosynthetic tissues.

Jackson MD, Xu H, Duran-Nebreda S, Stamm P, Bassel GW (2017) Topological analysis of multicellular complexity in the plant hypocotyl. Elife http:/​/​dx.​doi.​org/10.7554/eLife.26023

Open Access

George Bassel (University of Birmingham) is the corresponding author on this work that provides fantastic images of the plant hypocotyl taken as part of an analysis on the cell growth dynamics in this organ. They show that Arabidopsis epidermal atrichoblast cells demonstrate a reduced path length that coincides with preferential movement of small molecules through these cells. They analysis this process in various mutants showing which gene activities were necessary for the construction of this pattern. In addition they compared topological features in Arabidopsis, Poppy and Foxglove, showing that cell interactions and path length determinants differ between these organisms. Overall this manuscript defines the network principles that control complex organ construction as well as a function for higher order patterning.

Simonini S, Bencivenga S, Trick M, Ostergaard L (2017) Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis. Plant Cell 10.1105/tpc.17.00389

Open Access

Last year Lars Ostergaard (JIC) discussed a paper from his lab on the GARNet YouTube channel in which they defined a new auxin-signaling paradigm that involved the non-canoical Auxin Response Factor ETTIN. This follow up to that study investigates the genetic network controlled by ETTIN activity and defines a range of developmental processes dependent on ETTIN auxin sensing. Furthermore by looking at direct ETTIN targets they suggest that this protein acts as a central node for the coordination of auxin signaling in the shoot. Finally their analysis of the effect of auxin on interactions between ETTIN and other transcription factors indicates that these are important factors in the diverse set of growth process controlled by auxin.

Yang H, Berry S, Olsson TSG, Hartley M, Howard M, Dean C (2017) Distinct phases of Polycomb silencing to hold epigenetic memory of cold in Arabidopsis. Science 10.1126/science.aan1121

This is another manuscript resulting from the extremely fruitful collaboration between the labs of Caroline Dean and Martin Howard at the John Innes Centre. This paper again focuses on the FLC locus and provides evidence for a new mechanism that defines how the binding of a subset of PRC2 factors nucleates a small region (<500bp) of chromatin at the FLC TSS, causing an increase in the repressive H3K27me2 histone mark. This metastable region serves as the seed for the development of stable epigenetic marks across the length of the locus through the activity of other distinct Polycomb factors. This occurs after a cold treatment and causes the spread of H3K27me2 repression. The novelty of this work is in the distinct temporal separation of phases of silencing, which ultimately result in the repression of FLC expression after a prolonged cold treatment.

Seki M, Ohara T, Hearn TJ, Frank A, da Silva VCH, Caldana C, Webb AAR, Satake A (2017) Adjustment of the Arabidopsis circadian oscillator by sugar signalling dictates the regulation of starch metabolism. Sci Rep. 10.1038/s41598-017-08325-y

Open Access

Research from Alex Webb’s group at the University of Cambridge features in the ARR for the second consecutive week, again on a similar topic. On this occasion they collaborate with Japanese colleagues to investigate the role of the circadian clock on determining the nighttime usage rate of starch that has accumulated during the day. They used a phase oscillator model to explain the link between the speed of the clock, starch breakdown and the maintenance of sucrose homeostasis. In addition they use Arabidopsis sugar response mutants to show that the circadian clock measures amount of cellular sucrose, which then controls the dynamics of starch breakdown.

Karpinska B, Alomrani SO, Foyer CH (2017) Inhibitor-induced oxidation of the nucleus and cytosol in Arabidopsis thaliana: implications for organelle to nucleus retrograde signalling. Philos Trans R Soc Lond B Biol Sci. 10.1098/rstb.2016.0392 Open Access

Christine Foyer (University of Leeds) is the corresponding author on this paper that looks at the effect of cellular oxidation on retrograde signaling between chloroplasts, mitochondria and the nucleus. They use a novel in vivo redox reporter to measure the effect of commonly used organelle inhibitors on cellular redox state. They discovered that these inhibitors cause a variety of effects on redox state and gene expression, which differed dependent on cell type. Researchers should be aware of these effects when they are drawing conclusions from their own experiments using these inhibitors.

Wilson DC, Kempthorne CJ, Carella P, Liscombe DK, Cameron R (2017) Age-Related Resistance in Arabidopsis thaliana Involves the MADS-domain Transcription Factor SHORT VEGETATIVE PHASE and Direct Action of Salicylic Acid on Pseudomonas syringae. Mol Plant Microbe Interact 10.1094/MPMI-07-17-0172-R

Phillip Carella is a Research Fellow at SLCU and this work from this previous lab in Canada investigates Arabidopsis Age-Related Resistance (ARR), a process that requires SA accumulation, which is then thought to act as an antimicrobial agent. The ARR response is lacking in plants containing a mutation in for the SHORT VEGETATIVE PHASE (SVP) gene. These svp plants have reduced SA, thought to be due to uncoupled overactivity of the SUPPRESSOR OF OVEREXPRESSION OF CO 1 gene. Overall this study shows that the flowering time gene SVP plays a complementary role in the control of SA accumulation, which confers ARR to older plants.

Fernie AR, Bauwe H, Sweetlove LJ (2017) Investigating the Role of the Photorespiratory Pathway in Non-photosynthetic Tissues. Methods Mol Biol 10.1007/978-1-4939-7225-8_15

Lee Sweetlove (University of Oxford) describes a protocol for evaluating the role of the photorespiration on the control of growth in non-photosynthetic tissues. This can be scaled for use in both Arabidopsis and in larger plants.

Arabidopsis Research Roundup: August 1st

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Published on: August 1, 2017

This weeks Arabidopsis Research Roundup has a tools-focus as it includes three papers that highlight new tools that are available to the plant science community. Silke Robatzek (TSL) leads research that has developed software for analysis of subcellular fluorescent markers whilst in a broadly similar area Mark Fricker (University of Oxford) is part of an international collaboration that characterises a tool that allows for analysis of intracellular ATP concentrations. Thirdly Phillip White (JHI) leads a consortium that has developed computer-assisted software to aid automated phenotyping. In the fourth paper Silke Robatzek again features as co-corresponding author with Richard Morris (JIC) in a study that mixes plant biology and computational analysis to model stomatal dynamics. Finally Christine Raines (University of Essex) leads research that has overexpressed a member of the photosynthetic apparatus that surprisingly results in plants with larger biomass and seed yield.

Faulkner C, Zhou J, Evrard A, Bourdais G, MacLean D, Häweker H, Eckes P, Robatzek S (2017) An automated quantitative image analysis tool for the identification of microtubule patterns in plants. Traffic. http:/​/​dx.​doi.​org/10.1111/tra.12505 Open Access

This research from The Sainsbury lab, Norwich and John Innes Centre includes Silke Robatzek as corresponding author as well as new faculty member Christine Faulkner as lead author. This paper documents the development of CellArchitect, which is an image analysis tool to track the movement of subcellular microtubule markers obtained using con-focal microscopy. They validated CellArchifect by treating with a variety of chemicals that alter microtubule dynamics. In addition they show that this software can be used to track actin or ER markers and as such should have broad utility for cell biology researchers particularly those that are undertaking often laborious chemical biology screens.

De Col V,, Fuchs P, Nietzel T, Elsässer M, Voon CP, Candeo A, Seeliger I, Fricker MD, Grefen C, Møller IM, Bassi A, Lim BL,, Zancani M, Meyer AJ,, Costa A, Wagner S, Schwarzländer M (2017) ATP sensing in living plant cells reveals tissue gradients and stress dynamics of energy physiology. Elife. http:/​/​dx.​doi.​org/10.7554/eLife.26770 Open Access

Mark Fricker (University of Oxford) is part of this international collaboration that have used a novel technique for visualizing ATP levels using a fluorescent biosensor in vitro, within isolated mitochondria and within intact seedlings. They demonstrate differing ATP concentrations within tissues, highlighting root hair cells. Induced hypoxia shows that there is significant plasticity in the cellular ATP concentrations and that these can be successful monitored using the biosensor tool.

Dupuy LX, Wright G, Thompson JA, Taylor A, Dekeyser S, White CP, Thomas WTB, Nightingale M, Hammond JP, Graham NS, Thomas CL, Broadley MR, White PJ (2017) Accelerating root system phenotyping of seedlings through a computer-assisted processing pipeline. Plant Methods.

http:/​/​dx.​doi.​org/10.1186/s13007-017-0207-1 Open Access

Phillip White (James Hutton Institute) and collaborators at the University of Nottingham have developed this computer-assisted pipeline designed to facilitate the phenotyping of plant roots. This can be scaled up for plants of different sizes and thus has broad utility. This software rapidly extracts root traits from image data, a process that can be a bottleneck in the screening process. This software complements parallel attempts that have developed automated platforms for sample preparation and handling.

Woolfenden HC, Bourdais G, Kopischke M, Miedes E, Molina A, Robatzek S, Morris RJ (2017) A computational approach for inferring the cell wall properties that govern guard cell dynamics. Plant J. http:/​/​dx.​doi.​org/10.1111/tpj.13640 Open Access

Richard Morris (John Innes Centre) and Silke Robatzek (The Sainsbury lab, Norwich) are the corresponding authors on this study in which they collaborate with Spanish colleagues. They investigate how different attributes of guard cell walls are responsible for the opening and closing of stomata. By considering the cell wall as a composite of a pectin rich matrix embedded within cellulose microfibrils they predict the movements that are responsible for stomatal dynamics. They validate their predictions using Arabidopsis mutants and they to show that stomatal opening/closing is brought about by a mix of hoop reinforcement and strain-stiffening resulting in anisotrophic growth.

Simkin AJ, McAusland L, Lawson T, Raines CA (2017) Over-expression of the RieskeFeS protein increases electron transport rates and biomass yield. Plant Physiol.

http:/​/​dx.​doi.​org/10.1104/pp.17.00622 Open Access

GARNet committee member Christine Raines (University of Essex) leads this study in which they have generated plants that overexpress the Rieske FeS protein (PetC), which is a component of the cytochrome b6f (cyt b6f) complex. These plants show equivalent increases in both proteins within the cytochrome b6f complex and more surprisingly within members of PSI and PSII. The mechanisms that explain these changes are currently unknown but these plants offer an exciting tool in order to study multiple aspects of photosynthetic biology. Perhaps more importantly these plants show increased biomass and seed yield indicating that manipulation of these proteins in crop plants might be important for developing higher yielding varieties.

Arabidopsis Research Roundup: July 18th

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Published on: July 18, 2017

This weeks Arabidopsis Research Roundup includes four studies from around the UK. Firstly is a systems-level study of the drought response that includes Alessandra Devoto from RHUL as a co-author. Secondly Anne Osbourn’s group at the JIC investigates sesterterpenoid biosynthesis across plant species. Thirdly Paul Jarvis from Oxford University adds to this groups portfolio of research on the mechanisms that control thylakoid import. Finally Patrick Gallois (University of Manchester) provides further insight into the regulation of programmed cell death.

Kim JM, To TK et al (2017) Acetate-mediated novel survival strategy against drought in plants Nature Plants http:/​/​dx.​doi.​org/10.1038/nplants.2017.97

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Alessandra Devoto (Royal Holloway) is a co-author of this study led by Jong-Myong Kim, Mototaki Seki (RIKEN, Yokohama) and Taiko Kim Ko (University of Toyko) that investigates the system-wide alterations that plants make in response to drought stress. They demonstrate that the histone deacetylase HDA6 is the primary regulator of an epigenetic switch that leads to a metabolic flux conversion from glycolysis into acetate synthesis. This in turn stimulates the jasmonate signaling pathway that causes increased drought tolerance. Importantly the authors show that this critical survival response is evolutionarily conserved through monocots and dicots.

Huang AC, Kautsar SA, Hong YJ, Medema MH, Bond AD, Tantillo DJ, Osbourn A (2017) Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution. PNAS http:/​/​dx.​doi.​org/10.1073/pnas.1705567114

Open Access

Anne Osbourn (JIC) leads this study in which her group works with collaborators from Cambridge, Wageningen and UC Davis to perform a cross-species genome-wide analysis of sesterterpenoid biosynthesis. They use a novel search algorithm to identify paired enzymatic components that comprise sesterterpene synthases (STS). These enzymes were transiently overexpressed in tobacco leaves, resulting in the formation of fungal-like sesterterpenes, suggestive of convergent evolution of plant and fungal STS. This study illuminates possible future strategies for the beneficial use of sesterterpenes through metabolic and protein engineering

Bédard J, Trösch R, Wu F, Ling Q, Flores-Pérez Ú, Töpel M, Nawaz F, Jarvis P (2017) New Suppressors of the Chloroplast Protein Import Mutant tic40 Reveal a Genetic Link between Protein Import and Thylakoid Biogenesis. Plant Cell. http:/​/​dx.​doi.​org/10.1105/tpc.16.00962 Open Access

Paul Jarvis (Oxford University) leads this global collaboration that focuses on the chloroplast protein import protein Tic40. A suppressor screen identified two novel regulators of Tic40, ALB4 and STIC2 that they postulate are involved in the thylakoid targeting of a subset of proteins and that their influence becomes more important in the absence of Tic40.

Cai YM, Yu J, Ge Y, Mironov A, Gallois P (2017) Two proteases with caspase-3-like activity, cathepsin B and proteasome, antagonistically control ER-stress-induced programmed cell death in Arabidopsis. New Phytol.

http:/​/​dx.​doi.​org/10.1111/nph.14676 Open Access

Patrick Gallois is the corresponding author on this study that originates at the University of Manchester. They attempt to establish a role for cathepsin B and proteasome subunit PBA1 in the control of programmed cell death (PCD) and whether their functions interest with those of caspase-3. They reveal a complex system of regulation where aspects of PCD are differentially impacted by each of these proteins. They propose the role of cathepsin B might occur late in PCD following tonoplast rupture.

Arabidopsis Research Roundup: July 3rd.

The Arabidopsis Research Roundup returns this week with selection of publications from institutions across the UK. Firstly George Bassel (Birmingham) leads a study that investigates the integration of inductive signals in the embryonic root. Secondly a group from the Oxford Brookes plant science group look into the literal linkages between the golgi apparatus and ER. Thirdly John Christie (Glasgow) and co-workers define a new variant of the phototropin receptor. Next Caroline Dean and Martin Howard (John Innes Centre) collaborate on work that defines the relationship between FLC, COOLAIR and cell size. The fifth paper is led by members of SLCU and investigates the regulatory influence of the Evening Complex of the circadian clock. The penultimate paper features work from Alison Smith’s group at the JIC that looks at dynamics of starch accumulation and degradation. Lastly is research from NIAB that defines the pathogeniticity of novel UK isolates of the fungal pathogen Verticillium longisporum.

Topham AT, Taylor RE, Yan D, Nambara E, Johnston IG, Bassel GW (2017) Temperature variability is integrated by a spatially embedded decision-making center to break dormancy in Arabidopsis seeds. PNAS


Open Access

George Bassel (University of Birmingham) leads this study that identifies a decision making centre in the embryonic root that is defined by the intimate interaction between the hormones abscisic acid (ABA) and gibberellin (GA). The activity of this ‘decision centre’ is linked to both hormone transport and changes in temperature, the overall output of which is the decision to promotes seed germination or to delay until more favourable environmental conditions.

George discusses this paper on the GARNet YouTube channel.

Osterrieder A, Sparkes IA, Botchway SW, Ward A, Ketelaar T, de Ruijter N, Hawes C (2017) Stacks off tracks: a role for the golgin AtCASP in plant endoplasmic reticulum-Golgi apparatus tethering. J Exp Bot. http:/​/​dx.​doi.​org/10.1093/jxb/erx167

Open Access

Anne Osterrieder and Chris Hawes (Oxford Brookes University) continue their work that looks at  the cellular dynamics of the golgi apparatus with this study that identifies the AtCASP protein as a important component that tethers the golgi to the ER. They use live-cell imaging to visualise golgi formation in cells that have different levels of AtCASP, allowing the authors to confirm that ER-golgi tethering is disrupted without the activity of this protein.

Petersen J, Inoue SI, Kelly SM, Sullivan S, Kinoshita T, Christie JM (2017) Functional Characterization of a Constitutively Active Kinase Variant of Arabidopsis Phototropin 1

J Biol Chem. http:/​/​dx.​doi.​org/10.1074/jbc.M117.799643

Open Access

John Christie (University of Glasgow) collaborates with Japanese colleagues to identify a novel variant of the phototropin receptor. Study of this variant allows a greater understanding regarding the mode of action of this protein under different light conditions, as controlled by phosphorylation.

Ietswaart R, Rosa S, Wu Z, Dean C, Howard M (2017) Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation. Cell Syst. http:/​/​dx.​doi.​org/10.1016/j.cels.2017.05.010

Open Access

Martin Howard and Caroline Dean (John Innes Centre) again collaborate on research that analyses the mode of regulation of FLC. They dissect RNA dynamics of FLC expression by single molecule in situ RNA fluorescence, showing that this is dependent on the presence of the antisense COOLAIR regulatory DNA. In the absence of COOLAIR they show FLC expression has a linear relationship with cell size but in the presence of the antisense transcript, FLC expression decreases with cell size. Overall they demonstrate FLC expression is tightly dependent on the presence of the antisense COOLAIR transcript.

Ezer D, Jung JH, Lan H, Biswas S, Gregoire L, Box MS, Charoensawan V,, Cortijo S, Lai X,, Stöckle D, Zubieta C, Jaeger KE, Wigge PA (2017) The evening complex coordinates environmental and endogenous signals in Arabidopsis. Nat Plants.


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Phil Wigge and Katja Jaeger (SLCU) lead this study that investigates how the evening complex of the circadian clock coordinates the expression of numerous important growth regulators. This genome wide regulation is determined by temperature and concides with the binding of phytochrome B, which provides a cellularly mechanism of this level of environmental control.

Fernandez O, Ishihara H, George GM, Mengin V, Flis A, Sumner D, Arrivault S, Feil R, Lunn JE, Zeeman SC, Smith AM, Stitt M (2017) Foliar starch turnover occurs in long days and in falling light at the end of the day. Plant Physiol. http:/​/​dx.​doi.​org/10.1104/pp.17.00601

Open Access

On this paper Alison Smith (John Innes Centre) is a co-corresponding author together with Mark Stitt from the Max Planck Institute for Molecular Plant Physiology in Potsdam. They continue their work to investigate the dynamics of starch metabolism in Arabidopsis leaves. Broadly they show the rate of starch accumulation corresponds to the photosynthetic rate whilst degradation is linked to correct functioning of the circadian clock. They investigate this process in more detail by determining how the rate of starch degradation alters dependent on the time after dawn.

Depotter J, Rodriguez-Moreno L, Thomma BP, Wood T (2017) The emerging British Verticillium longisporum population consists of aggressive Brassica pathogens. Phytopathology http:/​/​dx.​doi.​org/10.1094/PHYTO-05-17-0184-R

Tom Wood (NIAB) is the corresponding author of this study that characterises four new UK isolates of the fungal pathogen Verticillium longisporum. The pathogenticity of V.longisporum was tested on Arabidopsis alongside three other Brassica crops. They demonstrate that the UK isolates were unusually aggressive yet this was not consistent across all Brassica cultivars with different fungal lineages showing different effects on oil seed rape, cabbage or cauliflower.

Arabidopsis Research Roundup: May 17th

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Published on: May 17, 2017

This weeks Arabidopsis research roundup begins with a paper led by CPIB at the University of Nottingham that discovers a somewhat surprisingly mechanism controling Arabidopsis root hydrotropism. Next are two papers from the University of Leeds that firstly investigate how the JAGGED LATERAL ORGANS gene influences the auxin response and secondly looks at the role of redox regulation in the control of the cell cycle and seed development. Finally are two papers that look at different aspects of the plant pathogen interactions. Jonathan Jones from the John Innes Centre is a co-author on a paper that dissects the multiple gene expression networks that control plant immunity whilst Charles Melnyk at the Sainsbury lab in Cambridge is involved with work that investigates the hormonal control mechanisms that influence the invasion of parasitic plants.

Dietrich D, Pang L, Kobayashi A, Fozard JA, Boudolf V, Bhosale R, Antoni R, Nguyen T, Hiratsuka S, Fujii N, Miyazawa Y, Bae TW, Wells DM,, Owen MR,, Band LR,, Dyson RJ, Jensen OE, King JR, Tracy SR, Sturrock CJ,, Mooney SJ, Roberts JA, Bhalerao RP, Dinneny JR, Rodriguez PL, Nagatani A, Hosokawa Y, Baskin TI, Pridmore TP, De Veylder L, Takahashi H, Bennett MJ (2017) Root hydrotropism is controlled via a cortex-specific growth mechanism. Nature Plants


Open Access via access link:

Malcolm Bennett (University of Nottingham) leads a broad international collaboration that looks at the response of Arabidopsis roots to water. Surprisingly they show that this response occurs not in the root meristem but in the elongation zone and is controlled by a ABA signaling mechanism. They show that hydrotropism is dependent on cell elongation in the cortex but not in any other cell file. This is different to the gravitropic response and demonstrates that these tropisms are controlled by distinct tissue-specific mechanisms. To provide for information about this paper, lead author Daniela Dietrich joins Professor Bennett to discuss this paper on the GARNet YouTube channel and speculate on the function of different root cell layers in water uptake.

Rast-Somssich MI, Žádníková P, Schmid S, Kieffer M, Kepinski S, Simon R (2017) The Arabidopsis JAGGED LATERAL ORGANS (JLO) gene sensitizes plants to auxin. J Exp Bot.

http:/​/​dx.​doi.​org/10.1093/jxb/erx131 Open Access

This German-led study includes Stefan Kepinski (University of Leeds) as a co-author. They investigate the role of the JAGGED LATERAL ORGANS (JLO) transcription factor in the establishment of the stem cell niche in the root meristem. JLO interacts with auxin signaling pathway by influencing the degradation of the key regulator BODENLOS (BDL) via the TIR1-mediated degradation pathway. In jlo mutants BDL remains present in the meristem, which does not correctly develop. They discover a novel regulatory mechanism wherein the dosage of the TIR1 and AFB1 auxin receptors is reduced, which in turn prevents BDL degradation. This shows that the JLO transcription factor is a key upstream regulator of meristem formation by playing a significant role in the fine control of the auxin response.

De Simone A, Hubbard R, Vinegra de la Torre N, Velappan Y, Wilson M, Considine MJ, Soppe W, Foyer CH (2017) Redox changes during the cell cycle in the embryonic root meristem of Arabidopsis thaliana. Antioxid Redox Signal. http:/​/​dx.​doi.​org/10.1089/ars.2016.6959

Open Access

Christine Foyer (University of Leeds) collaborates with Australian and German researchers to unpick the role that redox regulation plays in the control of the plant cell cycle. They use an in vivo redox reporter (roGFP2) to show that a cycle of reduction and oxidation occurs throughout the cell cycle. Their experimental system is Arabidopsis seed germination and they show that vitamin c defective mutants with low redox buffering capacity have altered germination rates that coincide with a changed dry seed transcriptome. Overall this paper demonstrates that the cell cycle and embryo size are linked to redox regulation.

Hillmer RA, Tsuda K, Rallapalli G, Asai S, Truman W, Papke MD, Sakakibara H, Jones JDG, Myers CL, Katagiri F (2017) The highly buffered Arabidopsis immune signaling network conceals the functions of its components. PLoS Genet. http:/​/​dx.​doi.​org/10.1371/journal.pgen.1006639

Open Access

Jonathan Jones (John Innes Centre) is a co-author on this Japanese-led research that studies the signaling networks invovled in plant immunity. They use a systems biology approach to dissect the network of interactions that occur within the transcriptome when plants are exposed to the immune stimulant flagellin-22. This analysis discovers that there are separated networks that represent pathways controlled by different higher-level signals, such as jasmonate or salicylic acid. This provides the entire network with a degree of buffering that allows a more effective response to pathogen attack. This type of network analysis is able to reveal facets of the defence response that would not be possible when using simple null mutant analysis so adds consideration detail to the already complicated story of plant-pathogen interactions

Spallek T, Melnyk CW, Wakatake T, Zhang J, Sakamoto Y, Kiba T, Yoshida S, Matsunaga S, Sakakibara H, Shirasu K (2017) Interspecies hormonal control of host root morphology by parasitic plants. PNAS


Charles Melnyk (Sainsbury Lab, Cambridge) is an author on this study led by Ken Shirasu at RIKEN and uses Arabidopsis to investigate the relationship between parasitic plants and their hosts, specifically at the level of interspecies transport via a structure called the haustorium. Haustoria are structures through which substances, such as RNA and proteins, reciprocally move between host and parasite. In this paper they look at the interaction between Arabidopsis roots and the hemiparasitic plant Phtheirospermum japonicum, demonstrating that movement of molecules between species occurs via haustoria once a vascular connection is made. Arabidopsis secondary root growth is induced under infection, a response that requires the effect of the hormone cytokinin. They look at the genetics of this interaction and show that cytokinin signaling genes are important in establishing root hypertrophy. Overall this study demonstrates the important of cytokinin during infection with parasitic plants and might be an important target to design strategies to combat these negative interactions in systems.

Arabidopsis Research Roundup: February 20th

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Published on: February 19, 2017

This weeks Arabidopsis Research Roundup begins with two papers that look at endogenous and exogenous causes of cell proliferation. Firstly Mike Bevan (JIC) leads a team that looks into the role of controlled protein degradation in this process whilst secondly, Peter Etchells from Durham is a co-author on a study that investigates how nematode pathogens stimulate cell proliferation at the site of infection.

Thirdly is work featuring Cyril Zipfel and colleagues from TSL that looks at how autophosphorylation controls the activity of calcium dependent protein kinases. Fourthly is a broad collaboration led by Richard Mott (UCL) that uses genomic structural variation to identify novel loci. Next Simon Turner from the University of Manchester phylogenetically defines the RALK peptide lineages across plant species. Finally researchers at the University of York conduct a structural analysis of the Arabidopsis AtGSTF2 glutathione transferase.

Dong H, Dumenil J, Lu FH, Na L, Vanhaeren H, Naumann C, Klecker M, Prior R, Smith C, McKenzie N, Saalbach G, Chen L, Xia T, Gonzalez N, Seguela M, Inze D, Dissmeyer N, Li Y, Bevan MW (2017) Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis.

Genes Dev. http:/​/​dx.​doi.​org/10.1101/gad.292235.116

Open Access

Mike Bevan (John Innes Centre) is the corresponding author of this study that also includes researchers from labs in Belgium, Germany and China. They investigate a fundamental determinant of organ shape, the pattern of cell proliferation that leads to final cell size. They show that two RING E3 ligases activate the DA1 peptidase that in turn affects the stabilization and activity of a range of other proteins including the transcription factors TEOSINTE BRANCED 1/CYCLOIDEA/PCF 15 (TCP15) and TCP22. Overall this results in continued cell proliferation and repression of endoreduplication, which ultimately serves to regulate the timing of the transition from cell proliferation to organ differentiation.

Mike discusses the science surrounding this paper on the GARNet YouTube channel.

Guo X,, Wang J, Gardner M, Fukuda H, Kondo Y, Etchells JP, Wang X, Mitchum MG. Identification of cyst nematode B-type CLE peptides and modulation of the vascular stem cell pathway for feeding cell formation. PLoS Pathog. http:/​/​dx.​doi.​org/10.1371/journal.ppat.1006142

Open Access

Peter Etchells (University of Durham) is a co-author on this US-led study that looks at the effect of nematode-delivered CLE-like peptides on cell growth and how that impacts parasitism. This study has identified a new class of peptides from nematodes that are similar to the plant B-type CLE-like peptide TDIF (tracheary element differentiation inhibitory factor). They show that the nematodes alter the activity of the TDIF-TDR (TDIF receptor)-WOX4 signaling module during infection, whose endogenous function acts during procambial meristem cell proliferation. A variety of mutants involved in this process show reduced infection and leading to the hypothesis that WOX4 is a potential target for nematode CLEs. When exogenous nematode CLE peptides are added to Arabidopsis roots they cause massive cell proliferation. This demonstrates that this response is clearly important for the establishment of nematode infection, usually in cambial cell files.

Bender KW, Blackburn RK, Monaghan J, Derbyshire P, Menke FL, Zipfel C, Goshe MB, Zielinski RE, Huber SC (2017) Autophosphorylation-based calcium (Ca2+) sensitivity priming and Ca2+/Calmodulin inhibition of Arabidopsis thaliana Ca2+-dependent protein kinase 28 (CPK28) J Biol Chem.


Cyril Zipfel (The Sainsbury Lab) features for a second consecutive week on the Arabidopsis research roundup, this time as a co-author in a study that investigates the role of autophosphorylation in the regulation of calcium (Ca2+) dependent protein kinases (CPKs). In addition they evaluated the role of Calmodulin (CaM) on the activity of CPKs, something that had been previously overlooked. Indeed they show that CPK28 is a CaM-binding protein and that autophosphorylation causes increased activity, especially in low Ca2+ concentrations. Therefore this research provides a mechanistic insight into how a cell might respond to low levels of Ca2+.

Imprialou M, Kahles A, Steffen JG, Osborne EJ, Gan X, Lempe J, Bhomra A, Belfield E, Visscher A, Greenhalgh R, Harberd NP, Goram R, Hein J, Robert-Seilaniantz A, Jones J, Stegle O, Kover P, Tsiantis M, Nordborg M, Rätsch G, Clark RM, Mott R Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits. Genetics. http:/​/​dx.​doi.​org/10.1534/genetics.116.192823

Open Access

Richard Mott (UCL) is corresponding author on this paper includes authors from throughout the UK, Europe and the US. They provide a new analysis of Arabidopsis populations that relies on the genome structural variation. They treat these structural variants as quantitative traits and subsequently map genetically in the same way as in a gene expression study. When a structural variant locus is linked to a genotype at a distant locus then it is designated as a site of transposition. Remarkably they show 25% of the structural variants can be assigned to the transposition events. This method of assessing structural variant loci is amendable to sequencing at low-coverage and this study identified loci that might be involved in germination and resistant to pathogens. Overall they find that genes within structural variants are more likely to be silenced and that this novel analysis technique is particularly useful when mapping transposition events.

Campbell L, Turner SR1(2017) A Comprehensive Analysis of RALF Proteins in Green Plants Suggests There Are Two Distinct Functional Groups. Front Plant Sci. http:/​/​dx.​doi.​org/10.3389/fpls.2017.00037

Open Access

This study from the lab of Simon Turner (University of Manchester) analyse Rapid Alkalinization Factor (RALFs) cysteine-rich peptides from across 51 plant species. They infer that these plant RALFs originate from four major clades in which the majority of the variation exists in the mature peptide sequence, indicative of clade-specific activities. Clade IV accounts for a third of the total peptides yet these lack a number of sequence features thought to be important for RALF function, which leads the authors to speculate that this clade should be thought of as containing RALF-related peptides instead of regular RALFs. Further experimental work is needed in order to define the true nature of the functional relationship between Clades I-III and Clade IV.

Ahmad L, Rylott EL, Bruce NC, Edwards R, Grogan G (2016) Structural evidence for Arabidopsis glutathione transferase AtGSTF2 functioning as a transporter of small organic ligands. FEBS Open Bio. http:/​/​dx.​doi.​org/10.1002/2211-5463.12168

Open Access

This paper links plant science and structural biology in a study that was undertaken at the University of York. Plant Glutathione transferases (GSTs) have multiple roles including in the detoxification of xenobiotics as well as in various non-catalytic roles. In this work the structure of the Arabidopsis AtGSTF2 is revealed in tandem with a variety of non-catalytic partners including indole-3-aldehyde, camalexin, the flavonoid quercetrin and its non-rhamnosylated analogue quercetin. These are thought to bind to AtGSTF2 by hydrophobic interactions at either one or two symmetrical binding sites. The authors speculate that this non-catalytic binding might have a possible role in ligand transport.

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