GARNet Research Roundup: April 11th 2018

This weeks GARNet research roundup begins with a microscopy-based study led by Lorenzo Frigerio from the University of Warwick that investigates the origin of Protein Storage Vacuoles. The second paper from John Doonan at Aberystwyth University looks at how differential splicing of cyclin-dependent Kinase G1 effects the thermosensory response. Reiner van de Hoorn from Oxford leads the next paper that characterises the use of activity-based protein profiling (ABPP) to identify novel α-glycosidases in model and non-model plants. Simon McQueen-Mason from York is corresponding author of the next paper that identified a new QTL from Brachypodium that is involved in cell wall formation. The fifth paper is led by Anthony Dodd from Bristol and characterises the role of the SnRK1 complex in hypocotyl elongation whilst the penultimate manuscript from Julia Davies’s lab in Cambridge performs patch clamp analysis of dorn1 mutant plants. The final paper from Brendan Davies at the University of Leeds characterises the SMG kinase, a gene that is lacking from the Arabidopsis genome, in Physcomitrella patens.

Feeney M, Kittelmann M, Menassa R, Hawes C, Frigerio L. Protein storage vacuoles originate from remodelled pre-existing vacuoles in Arabidopsis thaliana (2018) Plant Physiol. 2018 Mar 19. pii: pp.00010.2018. doi: 10.1104/pp.18.00010 Open Access

This collaboration between the Universities of Warwick and Oxford Brookes is led by Lorenzo Frigerio and Chris Hawes. They have investigated the origin of seed Protein Storage Vacuoles (PSV) using a two-pronged approach using confocal and immunoelectron microscopy. They looked at embryo development as well as in leaf cells that have been reprogrammed for embryonic cell fate by overexpression of the LEAFY COTYLEDON2 TF. These studies indicate that PSVs are formed following the reprogramming of pre-existing embryonic vacuole (EV) rather than from de novo assembly.

Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan JH. The Cyclin Dependent Kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A (2018) Plant J. doi: 10.1111/tpj.13914 Open Access

John Doonan (Aberystwyth University) is the corresponding author on this UK-Austrian collaboration that presents the role of the cyclin-dependent Kinase G1 (CDKG1) in thermosensing in Arabidopsis. Ambient temperature change causes altered gene expression of the spliceosome component, ATU2AF65A. Interestingly the CDKG1 gene is differentially spliced and to produces two protein isoforms that are both needed to complement the expression of ATU2AF65A across a temperature range. This alternative splicing is dependent on CDKG2 and CYCLIN L1 and is a novel control mechanism in the temperature control response.

Husaini AM, Morimoto K, Chandrasekar B, Kelly S, Kaschani F, Palmero D, Jiang J, Kaiser M, Ahrazem O, Overkleeft HS, van der Hoorn RAL (2018) Multiplex fluorescent, activity-based protein profiling identifies active α-glycosidases and other hydrolases in plants. Plant Physiol. pii: pp.00250.2018. doi: 10.1104/pp.18.00250 Open Access

Renier Van de Hoorn (University of Oxford) leads this pan-european study that uses novel cyclophellitol aziridine probes that label α-glycosidase enzymes. They identified two novel α-glycosidases in Arabidopsis as well as using the technique in non-model saffron crocus. Finally they showed that this multiplex fluorescent labelling in combination with probes for serine hydrolases and cysteine proteases can be used to identify changes in hydrolase activity in response to pathogen infection.

Whitehead C, Ostos Garrido FJ, Reymond M, Simister R, Distelfeld A, Atienza SG, Piston F, Gomez LD, McQueen-Mason SJ (2018) A glycosyl transferase family 43 protein involved in xylan biosynthesis is associated with straw digestibility in Brachypodium distachyon. New Phytol. doi: 10.1111/nph.15089 Open Access

Simon McQueen-Mason (University of York) leads this study that use QTL mapping to identify a gene in Bracypodium that is involved in cell wall architecture, which might then be a target to develop plants with improved cellulose digestibility. This glycosyl transferase family (GT) 43 protein is an orthologue of Arabidopsis IRX14, which is involved in xylan biosynthesis. When RNAi was used to reduce expression of this gene the resulting plants showed increased digestibility, indicating that this BdGT43A will be a good target for future breeding plans.

Wang L, Wilkins KA, Davies JM (2018) Arabidopsis DORN1 extracellular ATP receptor; activation of plasma membrane K(+) -and Ca(2+) -permeable conductances New Phytol. 2018 Mar 25. doi: 10.1111/nph.15111. Open Access

This letter to New Phytologist from the lab of Julia Davis (University of Cambridge) outlines some experiments to determine whether the DORN1 plasma membrane receptor is responsible for transmitting a signal from extracellular ATP (eATP). They performed patch clamp analysis on isolated protoplasts and showed that DORN1 is involved in the activation of Ca+ and K+ pumps by eATP as, in contrast to wildtype, dorn1 mutant protoplast showed no voltage changes after incubation with eATP.

Simon NML, Sawkins E, Dodd AN. Involvement of the SnRK1 subunit KIN10 in sucrose-induced hypocotyl elongation (2018) Plant Signal Behav. 27:1-9. doi: 10.1080/15592324.2018.1457913.

Anthony Dodd (University of Bristol) is the corresponding author of this follow-on study from one that previously featured on the GARNet YouTube channel. This study measures sucrose-induced hypocotyl elongation in two T-DNA mutants of the SnRK1 subunit KIN10 gene. These mutants had altered responses to sucrose leading to the hypothesis that the SnRK1 complex suppresses hypocotyl elongation in the presence of external sugar.

Lloyd JPB, Lang D, Zimmer AD, Causier B, Reski R, Davies B (2018) The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens. Nucleic Acids Res. doi: 10.1093/nar/gky225 Open Access

Brendan Davis (University of Leeds) is the corresponding author on research that investigates the role of the SMG1 kinase during nonsense-mediated mRNA decay (NMD) in the moss Physcomitrella patens. This kinase plays a critical role in animals but as it is not present in Arabidopsis, its function is not well studied in plants. However moss smg mutants show expression changes in genes involved in a variety of processes indicating that NMD is a common control mechanism in moss. In addition these plants have increased susceptibility to DNA damage, which suggests that the SMG1 kinase is a key player in quality control mechanisms in plants.

Arabidopsis Research Roundup: February 22nd 2018

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Published on: February 22, 2018

This edition of the Arabidopsis Research roundup beings with a study from SLCU that provides a molecular context to the changes that occur at graft junctions. Second is a study from Edinburgh that reports on the findings of a citizen science plant phenotyping project. Third are two studies from the John Innes Centre that follow-on from previous studies. These characterise the molecular response to seasonal transitions and the factors that control floral development.

The fifth paper is led by Chris Hawes at Oxford Brookes and characterises a novel sub-group of ER localized reticulon proteins. The next paper from the University of Sheffield looks at the whole plant response to changing global carbon dioxide concentrations. The seventh paper from Bristol and York also broadly looks at CO2 but this time at the molecular factors that control stomatal closure in response to both ABA and CO2 signals. Christine Foyer (Leeds) is a co-author on the penultimate paper that characterises the role of ascorbic acid in hormone signaling whilst the final paper from Julian Hibberd at the University of Cambridge analyses a regulatory element that contributes to the evolutionary transition to C4 photosynthesis.

Melnyk CW, Gabel A, Hardcastle TJ, Robinson S, Miyashima S, Grosse I, Meyerowitz EM (2018) Transcriptome dynamics at Arabidopsis graft junctions reveal an intertissue recognition mechanism that activates vascular regeneration. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1718263115 Open Access
This research was led by Charles Melynk during this time working with Elliot Meyerowitz at SLCU. Grafting is an important classic and contemporary technique in plant biology and this study investigates the gene expression changes that occur on either side of a graft junction. They show asymmetry changes in gene expression on either side of a graft that include an increase in vascular initiation but only in grafted tissues and not in those that are cut and then separated. This study provides an exciting insight into the molecular changes that occur during tissue grafting.

Giuffrida MV, Chen F, Scharr H, Tsaftaris SA (2018) Citizen crowds and experts: observer variability in image-based plant phenotyping. Plant Methods. doi: 10.1186/s13007-018-0278-7 Open Access

This UK, German and Italian study is led by Sotirios Tsaftaris at the University of Edinburgh and reports on a fascinating citizen science study that evaluated the ability of experts and non-experts to use plant phenotyping software. They demonstrate that non-experts can be effectively involved in plant phenotyping annotation tasks given enough statistical power and if the study is suitably designed.

Hepworth J, Antoniou-Kourounioti RL, Bloomer RH, Selga C, Berggren K, Cox D, Collier Harris BR, Irwin JA, Holm S, Säll T,Howard M, Dean C (2018) Absence of warmth permits epigenetic memory of winter in Arabidopsis. Nat Commun. doi: 10.1038/s41467-018-03065-7 Open Access

Caroline Dean and Martin Howard (John Innes Centre) lead this study that further characterise the relationship between the VERNALIZATION INSENSITIVE3 (VIN3) an FLOWERING LOCUS C (FLC) genes in two separate thermosensory processes that monitor long term temperature changes. They suggest that the regulatory strategies currently employed by plants might become less effective as the climate becomes more variable and will have a knock-on effect on plant growth and productivity.

Simonini S, Stephenson P, Østergaard L (2018) A molecular framework controlling style morphology in Brassicaceae. Development. doi: 10.1242/dev.158105 Open Access
Lars Ostergaard (John Innes Centre) leads this study that characterises how the activity of five transcription factors (TF) integrate with auxin signaling in the control of gynoecium development. The auxin response factor ETTIN is a central controller of this relationship across members of the Brassicaceae and that variation in an ETTIN sub-domain effects TF affinities, interaction strength and gynoecium morphology

Kriechbaumer V, Maneta-Peyret L, Fouillen L, Botchway SW, Upson J, Hughes L, Richardson J, Kittelmann M, Moreau P, Hawes C

The odd one out: Arabidopsis reticulon 20 does not bend ER membranes but has a role in lipid regulation. Sci Rep. doi: 10.1038/s41598-018-20840-0

This study is led by Chris Hawes (Oxford Brookes) and continues his labs work on the plant ER. They are working on a subgroup of reticulons, which are ER membrane proteins, that have an extended N-terminal domain. Three members of this subgroup show different localisation patterns that indicates that along their sequences are similar they might play different cellular roles.

Williams A, Pétriacq P, Schwarzenbacher RE, Beerling DJ, Ton J (2018) Mechanisms of glacial-to-future atmospheric CO2 effects on plant immunity. New Phytol. doi: 10.1111/nph.15018 Open Access
This article from the University of Sheffield uses Arabidopsis to investigate the impact that changing climatic CO2 concentrations might have on plant immunity. The authors performed a global analysis on the response to sub-ambient and elevated CO2 and found that both changes causes alterations to salicyclic acid or jasmonic acid response pathways. However these responses are not always opposite, revealing new insights in the response to changing CO2 concentrations.


Isner JC, Begum A, Nuehse T, Hetherington AM, Maathuis FJM (2018) KIN7 Kinase Regulates the Vacuolar TPK1 K+ Channel during Stomatal Closure. Curr Biol. doi: 10.1016/j.cub.2017.12.046.

This is collaborative work between the Universities of York and Bristol and analyses factors that control stomatal closure. They show the TPK1 vacuolar K+ channel is important for ABA and CO2 mediated closure and that the function of this protein is regulated by the KIN7 receptor-like kinase. These activities result in potassium release from the vacuole leading to osmotic changes that contribute to stomatal closure.

Caviglia M, Mazorra Morales LM, Concellón A, Gergoff Grozeff GE, Wilson M, Foyer CH, Bartoli CG (2018) Ethylene signaling triggered by low concentrations of ascorbic acid regulates biomass accumulation in Arabidopsis thaliana. Free Radic Biol Med. doi: 10.1016/j.freeradbiomed.2018.01.032

Christine Foyer (University of Leeds) is a co-author on this research showing that a defect in ascorbic acid production leads to elevated levels of the hormone ethylene as well as having a wider impact on the control of growth-mediating hormone signalling. This result indicates that the cellular redox buffer AA is a significant contributor to hormone signalling pathways.

Reyna-Llorens I, Burgess SJ, Reeves G, Singh P, Stevenson SR, Williams BP, Stanley S, Hibberd JM (2018) Ancient duons may underpin spatial patterning of gene expression in C4 leaves.Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1720576115

Julian Hibberd (University of Cambridge) is the corresponding author on this study that is part of his labs overarching aim of discovering what is necessary to transfer C4 photosynthesis into C3 plants. As part of this work they are searching for master regulator sequences that have allowed for the multiple independent evolution of C4 photosynthesis. They have identified a regulatory duon that is a pair of cis-elements located in coding sequences of genes preferentially expressed in bundle sheath cells of C4 leaves and are also present in C3 plants and algae. Therefore they discuss how C4 plants have co-opted these regulatory elements and how it might be exploited in future molecular engineering projects.

Arabidopsis Research Roundup: October 23rd

Different aspects of plant cell wall biology dominant the first few papers of this weeks Arabidopsis Research Roundup. Firstly Andrew Fleming (University of Sheffield) and colleagues identify that a specific type of cell wall stiffening is important in control of stomatal opening. Secondly are two papers from the lab of Paul Dupree (University of Cambridge) that investigate the role that xylan modifications play in the formation of the cell wall. Finally in this broad area John Runions (Oxford Brookes) and colleagues show that attachment to the cell wall is critical for correct function of the dynamic actin filament network. Elsewhere Jerry Roberts (CPIB) leads a study that looks at proteins that control floral development. Next the group of Alexander Jones  at SLCU has developed an exciting new tool that allows for in vivo visualization of the plant hormone GA. Finally the lab of Phil Wigge (also at SLCU) further expands their work that dissects the signaling pathways that controlling the response to temperature.

Carter R, Woolfenden H, Baillie A, Amsbury S, Carroll S, Healicon E, Sovatzoglou S, Braybrook S, Gray JE, Hobbs J, Morris RJ, Fleming AJ (2017) Stomatal Opening Involves Polar, Not Radial, Stiffening Of Guard Cells. Curr Biol. doi: 10.1016/j.cub.2017.08.006 Open Access

This broad UK collaboration is led by Andrew Fleming at the University of Sheffield and looks into the factors that control stiffening of cell walls in stomatal guard cells. They use Atomic Force Microscopy to show that stiffening of the polar regions of guard cell walls pins down these ends of cells during stomatal opening. This study provides exciting new insights into the importance of cell wall dynamics on stomatal opening and likely has significant agronomic importance.

Grantham NJ, Wurman-Rodrich J, Terrett OM, Lyczakowski JJ, Stott K, Iuga D, Simmons TJ, Durand-Tardif M, Brown SP, Dupree R, Busse-Wicher M, Dupree P (2017) An even pattern of xylan substitution is critical for interaction with cellulose in plant cell walls. Nat Plants doi: 10.1038/s41477-017-0030-8

Lyczakowski JJ,,, Wicher KB,, Terrett OM, Faria-Blanc N, Yu X, Brown D,, Krogh KBRM, Dupree P,,, Busse-Wicher M (2017) Removal of glucuronic acid from xylan is a strategy to improve the conversion of plant biomass to sugars for bioenergy. Biotechnol Biofuels. doi: 10.1186/s13068-017-0902-1

Open Access

Paul Dupree (University of Cambridge) is involved in two papers that investigate the chemical decorations that adorn components of the plant cell wall. In the first paper they demonstrate that the incorrect addition of acetyl esters onto xylan prevents the formation of the secondary cell wall due to a reduced interaction between xylan and cellulose microfibrils. They undertake a genetic study to show that the ESKIMO1/XOAT1/TBL29, a xylan-specific O-acetyltransferase is responsive for correct attachment of acetyl esters to xylan.

In the second paper they show that a reduction in the attachment of the acetyl ester glucuronic acid to xylan allows increased isolation of ethanol following saccharification. This has enormous potential significance in ongoing attempts to generate lignocellulose biomass that is more amenable to conversion into potential biofuels.

Tolmie F, Poulet A, McKenna J, Sassmann S, Graumann K, Deeks M, Runions J (2017) The cell wall of Arabidopsis thaliana influences actin network dynamics. J Exp Bot. doi: 10.1093/jxb/erx269.
This collaboration between Oxford Brookes and Exeter Universities looks in details at the Arabidopsis actin filament network using a set of novel imaging tools. In addition they show that the network is distributed when the link to the cell wall is disrupted. As might be expected this also effects the function of the network as evidenced by changes in Golgi body motility.

González-Carranza ZH, Zhang X, Peters JL, Boltz V, Szecsi J, Bendahmane M, Roberts JA (2017) HAWAIIAN SKIRT controls size and floral organ number by modulating CUC1 and CUC2 expression. PLoS One.

doi: 10.1371/journal.pone.0185106 Open Access

Jerry Roberts (CPIB, Nottingham) leads a collaboration with Dutch and French colleagues to investigate the role of the F-box gene HAWAIIAN SKIRT in control of flower development. This protein acts by interacting with the CUC-SHAPED COTYLEDON 1 (CUC1) and CUC2 transcription factors to restrict petal size by altering cell proliferation and mitotic growth.

Rizza A, Walia A, Lanquar V, Frommer WB, Jones AM (2017) In vivo gibberellin gradients visualized in rapidly elongating tissues. Nat Plants. doi: 10.1038/s41477-017-0021-9

Free with the link:

Alexander Jones (SLCU) collaborates with Wolf Frommers’ lab in Stanford to develop a novel tool to analyse the plant hormone gibberellin in planta. This optogenetic biosensor protein allowed them to show that GA levels correlate with cell length in hypocotyl and root tissues. GA levels are dependent on PIF signalling in a relationship that controls rapid tissue elongation in reponse to favourable environmental conditions. We’re pleased to announce that Alexander will be speaking at next September’s GARNet2018: A Plant Science Showcase at the University of York.

Cortijo S, Charoensawan V, Brestovitsky A, Buning R, Ravarani C, Rhodes D, van Noort J, Jaeger KE, Wigge PA (2017) Transcriptional regulation of the ambient temperature response by H2A.Z-nucleosomes and HSF1 transcription factors in Arabidopsis. Molecular Plant doi: 10.1016/j.molp.2017.08.014

Open Access

Phil Wigge (SLCU) leads this work that investigates how the temperature responsive histone variant H2A.Z interacts with heat shock transcription factors (HSFs). They find that the activity of HSFs is able to evict H2A.Z histones yet at non-inducible temperatures these heat responsive genes show an over-representation of H2A.Z-nucleosomes. They demonstrate that this relationship allows plants to be primed to rapidly response to temperature change whilst preventing leaky transcription in times of low temperature.

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: 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: January 17th

Todays Arabidopsis Research Roundup includes some excellent examples of UK labs engaged in collaborative work with researchers from around the globe. However first up is a study solely from the John Innes Centre, led by Vinod Kumar, that investigates the role of PIF4 during the thermosensory response. Secondly David Evans (Oxford Brookes University) is a co-author on a French-led study that has looked into the role of LINC complexes during interphase heterochromatin patterning. Thirdly is the description of the new PhenoTiki imaging tool that has come from the lab of Sotirios Tsaftaris in Edinburgh. Work from Paul Dupree (University of Cambridge) features in the ARR for the second consecutive week, this time with a study looking at the sugar composition of seed mucilage. The penultimate study is from the lab of Renier van der Hoorn (Oxford University) who investigates the role of Cys proteases during senescence and finally is a study from Seth Davis (University of York) that looks at the link between the circadian clock and the plants energy sensing mechanisms.

Gangappa SN, Berriri S, Kumar SV (2016) PIF4 Coordinates Thermosensory Growth and Immunity in Arabidopsis. Current Biology


Open Access
Vinod Kumar (John Innes Centre) leads this study that looks at the role of the PHYTOCHROME INTERACTING FACTOR 4 (PIF4) transcription factor during the thermosensory response and its effect on plant architecture. They looked at the natural variation of PIF4, demonstrating the role of different varients on the balance between growth and immunity to pathogens. Pertubing PIF4-mediated effects result in temperature-resilient disease resistance. This study links with a paper highlighted in last weeks ARR from Kerry Franklin and co-authors that presented the role of UVR8 on the control of PIF4 heat responsive effects. These studies further confirm the important role of PIF4 in plant development in response to environmental change and biotic challenges.

Vinod discusses this paper and a related manuscript from next weeks ARR. Also available on the GARNet YouTube channel.

Poulet A, Duc C, Voisin M, Desset S, Tutois S, Vanrobays E, Benoit M, Evans DE, Probst AV, Tatout C (2017) The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants. J Cell Science.


Open Access

This study is led by Christophe Tatout from Clermond-Ferrand and includes David Evans and Axel Poulet (Oxford Brookes University) as co-authors. The paper focuses on the role of the nuclear envelope-localised LInker of Nucleoskeleton and Cytoskeleton (LINC) complex on nuclear morphology and interphase chromatin localisation. This work is underpinned by the use of novel 3D imaging tools to define where in the nucleus the chromatin is localised in both wildtype and linc mutant plants. This allows the authors to show that the LINC complex is necessary for proper heterchromatin organisation at the nuclear periphery, which might have broad implications for gene expression and transcriptional silencing.

Minervini M, Giuffrida MV, Perata P, Tsaftaris SA (2017) Phenotiki: An open software and hardware platform for affordable and easy image-based phenotyping of rosette-shaped plants. Plant J. http:/​/​dx.​doi.​org/10.1111/tpj.13472

Open Access
This manuscript describes the PhenoTiki tool that is designed for the automated phenotyping of Arabidopsis rosettes, work which is led by Sofortios Tsaftaris (University of Edinburgh). PhenoTiki describes both the imaging software and also cheap-to-use off-the-shelf hardware that allows for facile imaging at reduced costs. The proof-of-concept study in the paper shows a comprehensive analysis from a range of parameters in 24 Arabidopsis rosettes from different genotypes. This data is compared favourably to more expensive methods of automated phenotyping so the authors hope PhenoTiki can be adopted as a low-cost method for image analysis. Full details can be found at

Saez-Aguayo S, Rautengarten C, Temple H, Sanhueza D, Ejsmentewicz T, Sandoval-Ibañez O, Doñas-Cofré DA, Parra-Rojas JP, Ebert B, Lehner A, Mollet JC, Dupree P, Scheller HV, Heazlewood JL, Reyes FC, Orellana A (2016) UUAT1 Is a Golgi-Localized UDP-Uronic Acid Transporter that Modulates the Polysaccharide Composition of Arabidopsis Seed Mucilage. Plant Cell. http:/​/​dx.​doi.​org/10.1105/tpc.16.00465

Open Access
Paul Dupree (University of Cambridge) is part of this global collaboration with colleagues from Australia, USA and Chile. The study investigates the intracellular movement of the plant cell polysaccharide pre-cursor UDP-glucuronic acid (UDP-GlcA). To identify genes involved in this process they cleverly screened mutants for alteration in seed mucilage, which has high level of other polysaccharides. This strategy identified UUAT1, which is a golgi-localised transporter of UDP-GlcA and UDP-galacturonic acid (UDP-GalA). Uuat1 mutants have altered sugar composition in both the seed coat mucilage and in other plant organs. These changes were also associated with an increase, by a currently unknown mechanism, of homogalacturonan methylation. Overall the authors show that UUAT1 is important for the correct distribution of cell wall polysaccahrides throughout growing embryo and will surely play important developmental roles in the function of the cell wall.

Pružinská A, Shindo T, Niessen S, Kaschani F, Tóth R, Millar AH, van der Hoorn RA (2017) Major Cys protease activities are not essential for senescence in individually darkened Arabidopsis leaves. BMC Plant Biol.


Open Access

In this paper Renier van der Hoorn (University of Oxford) interacts with US, German and Australian colleagues to use the activity-based protein profiling (ABPP) technique to assess the activity of active enzymes during senescence. They show that in Arabidopsis leaves the expression of several Papain-like Cys Proteases (PLCPs) is elevated but the activity of many Vacuolar Processing Enzymes (VPEs) is decreased, even though their transcript level increases. The amount of senescence was assessed in plants with mutations in different members of these protease families and surprisingly did not find any difference when compared to wildtype plants. One exception was in plants containing a mutation in the AALP PLCP which showed a significant, albeit slight, descrease in the rate of senescence.

Shin J, Sánchez-Villarreal A,, Davis AM,, Du SX, Berendzen KW, Koncz C, Ding Z, Li C, Davis SJ (2017) The metabolic sensor AKIN10 modulates the Arabidopsis circadian clock in a light-dependent manner. Plant Cell Environ.

<a href=”” onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘http://onlinelibrary.wiley generic cialis’, ‘http:/​/​dx.​doi.​org/10.1111/pce.12903’]);” target=”_blank”>http:/​/​dx.​doi.​org/10.1111/pce.12903

Seth Davies (University of York) leads this study that includes German, Mexican and Chinese collaborators and looks at the link between the circadian clock and plant metabolism. The energy sensing Snf1 (sucrose non-fermenting 1)-related kinase 1 (SnRK1) complex contains the catalytic AKIN10 protein, which plays an important role in clock function by controlling expression of the key evening element GIGANTEA (GI). This AKIN10 effect requires the clock regulator TIME FOR COFFEE (TIC) demonstrating an important role for the plants energy sensing mechanisms, via the AKIN10, in conditional control of clock gene expression.

Arabidopsis Research Roundup: August 8th

This weeks Arabidopsis Roundup contains a wide breadth of UK research. Firstly the lab of Jurriaan Ton undertakes a global analysis into the role of methylation in the immune response. Jurriaan kindly provides a short audio description of this work. Secondly Dame Caroline Dean’s lab further add to our understanding of the vernalisation response in Arabidopsis. Thirdly is work from Rothamstead that evaluates the fatty acid composition of the seed aleurone while fourthly is a study from Durham and Oxford Brookes that introduces a novel regulator of autophagy. Finally is a study that adds clarity to the phenotypic effects resulting from ascorbic acid deficiency.

López Sánchez A, H M Stassen J, Furci L, Smith LM, Ton J (2016) The role of DNA (de)methylation in immune responsiveness of Arabidopsis Plant Journal Open Access

Jurriaan Ton is the corresponding for study from the University of Sheffield that looks into the role of reversible methylation on the Arabidopsis immune response. Methylation is a well known regulator of gene expression and in this research the authors attempt to interrogate its effect on the immune response. Hypo-methylated mutants are more resistant, whilst hyper-methylated mutants are more suspectible to the biotrophic pathogen Hyaloperonospora arabidopsidis (Hpa). Downstream gene expression changes in these methylation mutants focus at the level of cell-wall modification and salicylic acid (SA)-responses. Oppositely the hypo-methylated mutant nrpe1 is more suspective to the necrotrophic pathogen Plectosphaerella cucumerina whilst the hyper-methylated ros1 mutant is resistant to this organism. The Ton-lab has been involved in the discovery of the exciting phenomon of transgenerational acquired resistance, and both nrpe1 and ros1 fail to develop this response against Hpa. Global gene expression shows that either NRPE1 or ROS1 influence about 50% of the gene expression changes that occur following Hpa infection. Finally since less than 15% of genes with altered gene expression reside close to NRPE1 or ROS1, the authors are able to propose that much of this regulation is due to methylation effects that act in trans- throughout the genome.

Jurriaan kindly provides a comprehensive description of this work:

Qüesta JI, Song J, Geraldo N, An H, Dean C (2016) Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization Science. 353(6298):485-8


Dame Caroline Dean (John Innes Centre) is the lead author of this manuscript that builds upon the portfolio of work from her lab aimed at characterising the vernalization response. This work again uses the FLOWERING LOCUS C (FLC) gene as a model to study the factors that allow gene-silencing mediated by Polycomb silencing complexes. The authors find that a single intragenic point mutation prevents nucleation of the homeodomain-Polycomb repressive complex 2 (PHD-PRC2) to this region, a process that involves the transcriptional repressor VAL1. In the wildtype FLC locus the localisation of VAL1 promotes transcriptional silencing through histone deacylation through interaction with the conserved apoptosis- and splicing-associated protein (ASAP) complex. This study adds an additional layer of molecular complexity to the process of regulating the FLC locus and provides insight into the important role for primary sequence-specific targeting during gene silencing.

Bryant F, Munoz-Azcarate O, Kelly AA, Beaudoin F, Kurup S, Eastmond PJ (2016) Acyl carrier protein DESATURASE 2 and 3 are responsible for making omega-7 fatty acids in the aleurone Plant Physiology Open Access

Peter Eastmond (Rothamstead) leads this work that investigates the components that determine seed fatty acid content. Specifically Omega-7 monounsaturated fatty acids (ω-7s) are enriched in the aleurone of Arabidopsis seeds so this study used a Multiparent Advanced Generation Inter-Cross population to identify a QTL linked to ω-7 content that includes the ACYL-ACYL CARRIER PROTEIN DESATURASE1 (AAD1) and AAD3 genes. AAD family members possess both stearoyl- and palmitoyl-ACP Δ9 desaturase activity and aad3 mutants show a significant reduction in ω-7 content, which is common with mutants in other AAD family members. In addition the authors show that the FATTY ACID ELONGASE1 protein is required for accumulation of long-chain ω-7s in the aleurone. Overall this research provides new insight into the pathway that produces ω-7s in the aleurone, indicating that these genes might represent a target for future strategies to alter seed fatty acid content.

Wang P, Richardson C, Hawes C, Hussey PJ.(2016) Arabidopsis NAP1 Regulates the Formation of Autophagosomes Current Biology


This is collaborative effort between the labs of Patrick Hussey (Durham) and Chris Hawes (Oxford Brookes) investigates the role of the NAP1 protein, which is a member of the SCAR/WAVE complex, on the formation of autophagosomes. These organelles are induced by certain stress conditions and fewer are produced in nap1 mutants after starvation stress. This also corresponds to wildtype NAP1 localisation. Concomitantly nap1 mutants, as well as mutants of other members of SCAR/WAVE complex, are more suspectible to nitrogen starvation and is less tolerant to salt stress. The best characterised role of the SCAR/WAVE complex is during ARP2/3-mediated actin nucleation yet this study demonstrates an addition function as a regulatory of autophagy.

Lim B, Smirnoff N, Cobbett CS, Golz JF (2016) Ascorbate-Deficient vtc2 Mutants in Arabidopsis Do Not Exhibit Decreased Growth Front Plant Sci. 7:1025 Open Access

Nick Smirnoff (Exeter) is a co-author on the Australian-led research into Arabidopsis vtc mutants, which have a significant reduction in ascorbate-acid levels. Ascorbate is synthesized via the L-galactose pathway, the first enzyme of which is encoded by the paralogs VITAMIN C2 (VTC2) and VTC5. This study characterises the growth of a vtc2 T-DNA mutant that has a 30% reduction in ascorbate levels. Surprisingly this does not result in any signficant phenotypic and they suggest that a previously characterised growth reduction in other vtc2 mutant alleles is likely due to unknown genetic lesions.

Arabidopsis Research Roundup: June 9th

This edition of the Arabidopsis Research Roundup pleasingly includes four Open Access articles. Firstly Jose Gutierrez-Marcos leads an investigation into stress-induced memory, secondly Richard Morris is the corresponding author on a study that has developed a new model that explains waves of calcium signalling that response to environmental stresses. Thirdly is a UK-US collaboration that defines the factors that control carotenoid accumulation in seeds. Finally Chris Hawes leads a study that characterises the novel localisation of a subset of auxin biosynthetic enzymes.

Wibowo A, Becker C, Marconi G, Durr J, Price J, Hagmann J, Papareddy R, Putra H, Kageyama J, Becker J, Weigel D, Gutierrez-Marcos J (2016) Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity Elife Open AccessStress_Model

Jose Gutierrez-Marcos is the corresponding author on this pan-European study that adds to our increasing knowledge about the role of generational memory in the response to stress. Distinct regions of the Arabidopsis genome are susceptible to fluctuations in the level of DNA methylation in response to hyperosmotic stress, a condition that persists into a following generation. This effect is transmitted through the female lineage and the authors investigate this effect in more detail by focussing on a single epigenetically targeted locus. By designing experiments that ran over a series of generations they show that a plants ‘short term memory’ is reliant on the DNA methylation machinery and is able to transmit a distinct developmental response to immediate offspring.

Evans MJ, Choi WG, Gilroy S, Morris RJ (2016) A ROS-assisted Calcium Wave Dependent on AtRBOHD and TPC1 Propagates the Systemic Response to Salt Stress in Arabidopsis Roots. Plant Physiol.

http:/​/​dx.​doi.​org/​10.​1104/​pp.​16.​00215 Open Access

Richard Morris (JIC) leads this US-UK collaboration that investigates the downstream mechanisms that occur after the waves of ROS and Ca2+ signalling that respond to environmental stresses. The authors show that the current model for propagation of this wave, which relies upon a diffusive wave Ca2+ signalling, is unable to explain the speed of transmission of the wave. The authors develop a new model that adds a ROS-signalling component to explain the velocity of the Ca2+ wave and experimentally verify that their model could represent the in vivo situation. In addition they show that the effectiveness of this ROS-release signalling module is dependent on the activity of the vacuolar ion channel TPC1 and the NADPH Oxidase AtRBOHD.
Gonzalez-Jorge S, Mehrshahi P, Magallanes-Lundback M, Lipka AE, Angelovici R, Gore MA, DellaPenna D (2016) ZEAXANTHIN EPOXIDASE activity potentiates carotenoid degradation in maturing Arabidopsis seed. Plant Physiol.

http:/​/​dx.​doi.​org/​10.​1104/​pp.​16.​00604 Open Access

The lead author of this US-led study is Sabrina Gonzalez-Jorge who is currently a post-doc in GARNet committee member Ian Henderson’s lab in Cambridge. This study elucidates nine loci that are involved in carotenoid homeostasis in Arabidopsis seeds and shows that plants lacking the ZEAXANTHIN EPOXIDASE (ZEP) protein have a six-fold reduction in total seed carotenoids. Natural variation within the ZEP gene is able to account for the fine-tuning of seed carotenoid content and acts upstream of two previously characterised CAROTENOID CLEAVAGE DIOXYGENASE enzymes. Importantly, and somewhat surprisingly, four of the nine Arabidopsis loci are thought to have conserved function in determining the composition of carotenoids in maize kernels. This demonstrates that studying this phenomonen in Arabidopsis is highly relevant for study of the same process in economically important crops.

Kriechbaumer V, Botchway SW, Hawes C (2016) Localization and interactions between Arabidopsis auxin biosynthetic enzymes in the TAA/YUC-dependent pathway J Exp Bot. Open Access

Chris Hawes (Oxford Brookes) leads this study that localised a subset of enzymes involved in auxin biosynthesis to the endoplasmic reticulum. In addition certain of these enzymes appear to physically interact. This localisation is confirmed by showing ER microsomal fractions are able to undertake auxin biosynthesis. The auxin signalling pathway is complex and well characterised yet this finding adds another layer of regulation that might influence the dynamics of auxin activity.

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