Arabidopsis Research Roundup: February 12th

This weeks Arabidopsis Research Roundup begins with a study from SLCU that investigates the interaction between nitrate and cytokinin signaling in the shoot meristem. Next is research from Sheffield that studies changes to the macromolecular composition of the photosynthetic apparatus following the transition from dark to light. Third are three papers that include University of Edinburgh faculty members as co-authors; Gary Loake is involved in a global study on NO signaling, Karen Halliday is included on a study into the relationship between clock components and the PIF-mediated hypocotyl elongation and Naomi Nakayama contributes to the development of a model that explains PIN protein localisation. Cyril Zipfel (TSL) is a co-author on the fifth paper, which introduces a new signaling component in the defence response and whilst the penultimate paper includes Denis Murphy (University of South Wales) and investigates the effect of dioxins on seed development. The final paper documents research from Manchester and Nottingham that uses a cress endosperm as a model to test the elastic properties of thin biological membranes.


Landrein B, Formosa-Jordan P, Malivert A,, Schuster C, Melnyk CW,, Yang W, Turnbull C, Meyerowitz EM, Locke JCW,, Jönsson H (2018) Nitrate modulates stem cell dynamics in Arabidopsis shoot meristems through cytokinins. PNAS doi: 10.1073/pnas.1718670115.

Open Access

http://www.pnas.org/content/early/2018/01/22/1718670115

Henrik Jonsson and James Locke (SLCU) are corresponding authors on this investigation into the relationship between nitrate and cytokinin signalling in the Arabidopsis shoot meristem (SAM). They show that nitrate availability determines the size of the SAM, which is controlled by the transport of cytokinin precursors from the root to the shoot. A discussion about this paper with lead author Benoit Landrien and Professor Jonsson is available on the GARNet YouTube and iTunes channels.


Wood WHJ, MacGregor-Chatwin C, Barnett SFH, Mayneord GE, Huang X, Hobbs JK, Hunter CN, Johnson MP (2018) Dynamic thylakoid stacking regulates the balance between linear and cyclic photosynthetic electron transfer. Nature Plants. doi: 10.1038/s41477-017-0092-7

Open with this link

This research in this manuscript has come from the University of Sheffield with Matthew Johnson as the corresponding author. They have used atomic force microscopy (AFM) to investigate how the transition from dark to light affects the macromolecular architecture of the photosynthetic apparatus within the thylakoid membrane. This transition does not alter the antenna size of either photosystem yet increases the number of thylakoid grana. Overall these changes serve to regulate the balance between light harvesting, CO2 fixation and enabling the protection of PSII activity from the destructive effects of non-photochemical quenching.


Imran QM, Hussain A, Lee SU, Mun BG, Falak N, Loake GJ, Yun BW (2018) Transcriptome profile of NO-induced Arabidopsis transcription factor genes suggests their putative regulatory role in multiple biological processes. Sci Rep. doi: 10.1038/s41598-017-18850-5.

https://www.nature.com/articles/s41598-017-18850-5

Open Access

Gary Loake (University of Edinburgh) is a contributor to this Korean-led manuscript that has performed expression analysis on plants treated with S-nitrosocysteine (CySNO). They have identified many novel NO-responsive transcription factors and were able to confirm the role of three random TFs in this response following analysis of loss of function mutants. This paper provides new insights into the molecular components that contribute to NO signalling during plant defence and immunity.


Martín G, Rovira A, Veciana N, Soy J, Toledo-Ortiz G, Gommers CMM, Boix M, Henriques R, Minguet EG, Alabadí D, Halliday KJ, Leivar P, Monte E Circadian Waves of Transcriptional Repression Shape PIF-Regulated Photoperiod-Responsive Growth in Arabidopsis. Curr Biol. doi: 10.1016/j.cub.2017.12.021

Karen Halliday (University of Ediburgh) is a co-author on this Spanish-led study that investigates how the expression of PHYTOCHROME-INTERACTING FACTORS (PIFs) genes is controlled. The activity of PIFs are responsible for determining the rate of hypocotyl elongation in different light conditions and this paper demonstrates that PSEUDO-RESPONSE REGULATORS PRR9/7/5 proteins act antagonistically to the PIFs by interacting at the promotor of the CDF5 transcription factor. This provides a mechanism to explain the circadian-controlled regulation of hypocotyl cell elongation.


Hernandez V, Barrio RA, Benítez M, Nakayama N, Romero-Arias JR, Villarreal Lujan C (2018) A physico-genetic module for the polarisation of auxin efflux carriers PIN-FORMED (PIN). Phys Biol. doi: 10.1088/1478-3975/aaac99

Naomi Nakayama (University of Edinburgh) is a co-author on this Mexican-led study that proposes a physico-genetic model that explains the localization of PIN auxin transporter proteins to the Arabidopsis plasma membrane. This model confirms experimental observations and allows the prediction that mechanical forces can predominate over molecular components.


www.cell.com/molecular-cell/fulltext/S1097-2765(17)30983-8

Wang J, Grubb LE, Wang J, Liang X, Li L, Gao C, Ma M, Feng F, Li M, Li L, Zhang X, Yu F, Xie Q, Chen S, Zipfel C, Monaghan J, Zhou JM (2018) A Regulatory Module Controlling Homeostasis of a Plant Immune Kinase. Mol Cell. doi: 10.1016/j.molcel.2017.12.026

This Chinese-led paper includes Cyril Zipfel (TSL) as a co-author and identifies the U-box proteins PUB25 and PUB26 as E3 ligases for the cytoplasmic kinase BIK1, which is a key rate limiting component of the plant defence response. This multi-protein regulatory module provides another level of complexity to our understanding of the molecular factors involved in plant immunity.


Hanano A, Almousally I, Shaban M, Murphy DJ (2018) Exposure of Arabidopsis Plants to Dioxin Results in a Wrinkled Seed Phenotype that is likely due to 20S Proteasomal Degradation of WRI1. J Exp Bot. doi: 10.1093/jxb/ery027

Denis Murphy (University of South Wales) is a co-author on this Syrian-led study that uses Arabidopsis seeds to test the negative effects of dioxins. Seeds treated with dioxins have a wrinked phenotype that corresponds to changes in the expression of genes related to lipid and carbohydrate metabolism. Overall this study reveals a novel set of genetic changes effects caused by dioxins that explain the profound effects on seed development.


S. P. Pearce, J. R. King, T. Steinbrecher, G. Leubner-Metzger, N. M. Everitt, M. J. Holdsworth (2018) Finite indentation of highly curved elastic shells Proceedings of the Royal Society A doi: 10.1098/rspa.2017.0482

Open Access

Plant scientist Mike Holdsworth (University of Nottingham) is a co-author on this paper that has used the endosperm from garden cress (Lepidium sativum) as the experimental model to define the elastic properties of a thin biological surface. Indentation experiments have been classically used to measure these properties and then develop mathematically models that explain their characteristics. These models rely on an assumed flat surface whereas in reality any surface will often be curved. By obtaining measurements from identations studies on the cress endosperm they are able to better refine the models that explain the properties of the membrane in this context.

Arabidopsis Research Roundup: December 8th.

This weeks Research Roundup begins with two papers from the University of Edinburgh on very different topics of Arabidopsis research. Firstly Alistair McCormick and Sofirtios Tsaftaris introduce a new low-cost phenotyping platform whilst Gerben Ooijen’s group has analysed the role of SUMOylation in the control of the circadian clock. The next three papers each involve wide UK collaborations and either look at plant nutrient composition (Nottingham, Dundee, York), the role of N-end rule pathway in the control of seed storage mobilisation (Rothamsted, Nottingham, Oxford, Birmingham, Cambridge) or the development of a new tool for the study of phloem sieve elements (Leeds, Rothamsted, Cambridge, Newcastle). The penultimate paper from Daniel Zilbermann (JIC) highlights the global mechanisms of methyltransferase function in Arabidopsis and mice whilst the final paper from Alexandre Ruban (QMUL) and co-authors continues his groups work to unpick the specifics of NPQ.


Dobrescu A, Scorza LCT, Tsaftaris SA, McCormick AJ (2017) A “Do-It-Yourself” phenotyping system: measuring growth and morphology throughout the diel cycle in rosette shaped plants. Plant Methods. doi: 10.1186/s13007-017-0247-6

Open Access

University of Edinburgh colleagues Alistair McCormick and Sofirtios Tsaftaris lead this work that presents a low cost phenotyping system for the analysis of the growth rate and phenotypic characteristics of Arabidopsis thaliana rosettes. The software that they have developed allows the accurate segmentation of multiple rosettes within a single image and overall offers a straightforward solution for automated phenotyping across a range of growth environments.


Hansen LL, van den Burg HA, van Ooijen G (2017) Sumoylation Contributes to Timekeeping and Temperature Compensation of the Plant Circadian Clock. J Biol Rhythms. doi: 10.1177/0748730417737633

Gerben van Ooijen (University of Edinburgh) is the corresponding author of this work that has identified SUMOylation as a novel mechanism of regulating circadian clock genes in Arabidopsis. Plants with defects in sumoylation have altered circadian periods that exhibit incorrect temperature compensation. Overall these results indicate that sumoylation importantly buffers clock function in response to changing temperatures.


Alcock TD, Havlickova L, He Z, Bancroft I, White PJ, Broadley MR, Graham NS (2017) Identification of Candidate Genes for Calcium and Magnesium Accumulation in Brassica napus L. by Association Genetics. Front Plant Sci. doi: 10.3389/fpls.2017.01968

Open Access

Neil Graham and Martin Broadley (University of Nottingham) are the corresponding authors of this study that has taken advantage of the Brassica napus Associative Transcriptomes RIPR diversity panel developed by Ian Bancroft’s lab in York. Novel loci involved with an altered response to calcium and magnesium were identified in B.napus before mineral composition was analysed in Arabidopsis mutants defective in orthologous genes. The analysed plants exhibited alteration in mineral composition, meaning that the associated Brassica loci might be targets for future breeding strategies aimed at improving plant nutrient compositions.


Zhang H, Gannon L, Hassall KL, Deery MJ, Gibbs DJ, Holdsworth MJ, van der Hoorn RAL, Lilley KS, Theodoulou FL (2017) N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway. New Phytol. doi: 10.1111/nph.14909

Freddie Theodoulou (Rothamsted Research) is the corresponding author of this research that involved a collaboration with colleagues in Cambridge, Birmingham, Nottingham and Oxford. They have performed a proteomic analysis on etiolated seedlings to identify those proteins designated for degradation by the N-end rule pathway. They analysed prt6 mutant plants that lack the function of the E3 ligase PROTEOLYSIS6 (PRT6) and discovered that N-terminal peptides from 45 protein groups were upregulated in this mutant, corresponding to the equivalent downregulation of several known N-end rule proteases. Overall the authors show that PRT6 plays an important role in the regulation of seed storage mobilisation in young seedlings and is therefore a possible future target to manipulate the plant responses to adverse environmental conditions. Dr Kirsty Hassall, a statistician at Rothamsted, is an author on this paper and in the latest edition of the GARNish newsletter explains how she interacts with plant scientists during her work.


Torode TA, O’Neill RE, Marcus SE, Cornuault V, Pose-Albacete S, Lauder RP, Kracun SK, Gro Rydahl M, Andersen MCF, Willats WGT, Braybrook SA, Townsend BJ, Clausen MH, Knox JP (2017) Branched pectic galactan in phloem-sieve-element cell walls: implications for cell mechanics. Plant Physiol. doi: 10.1104/pp.17.01568 Open Access

Paul Knox (University of Leeds) is the corresponding author of this study that includes contributions from researchers at SLCU, Newcastle and Rothamsted. This work is based around the development of a monoclonal antibody, LM26 that is able to recognize a β-1,6-galactosyl substitution of β-1,4-galactan. LM26 has allowed the identification of this unusual branched galactan that is specific to phloem elements and the authors hope that it can be a useful tool in future studies on the biology of phloem elements


Lyons DB, Zilberman D (2017) DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. Elife. doi: 10.7554/eLife.30674 Open Access

Daniel Zilberman has recently moved to the John Innes Centre and is the lead author of this work that was conducted when he was working in US. This research is a cross-kingdom analysis showing that nucleosome-free DNA is the preferred target for methyltransferases in both Arabidopsis and mice, and that nucleosomes appear to be a barrier to the function of these enzymes. Furthermore they demonstrate that linker-specific methylation that is usually absent in Arabidopsis can be introduced by removal of histone H1. This shows that flowering plants still possess this ability despite its loss, during the evolution of H1, over a billion years ago.


Tutkus M, Chmeliov J, Rutkauskas D, Ruban AV, Valkunas L (2017) Influence of the Carotenoid Composition on the Conformational Dynamics of Photosynthetic Light-Harvesting Complexes. J Phys Chem Lett. doi: 10.1021/acs.jpclett.7b02634

Alexandre Ruban (QMUL) is a co-author on this study that investigates the role that carotenoid composition plays in the control of Non-photochemical quenching (NPQ), a mechanism that protects the photosynthetic apparatus from light-damage. Arabidopsis mutants with differing carotenoid compositions were analysed for the dynamics of the conformation switches that occur during NPQ. Interestingly they show that LHCII has robust function  that is resistant to different carotenoid concentrations.

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: rdcu.be/wnOh

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: https://www.youtube.com/watch?v=gYdL6eddOcA


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

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


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

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


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

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


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

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


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

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


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

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


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

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


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

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


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

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


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

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


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

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

Arabidopsis Research Roundup: 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 14th

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Published on: August 14, 2017

This weeks UK Arabidopsis Research Roundup includes a study from the lab of GARNet Chairman Steven Spoel that describes their work on the control of ROS signaling. The other two papers looks at different aspects of photosynthetic control. Firstly Giles Johnson (University of Manchester) investigates the proteomic changes that occur during dynamic acclimation. Finally Alex Webb’s lab (University of Cambridge) investigate how the products of photosynthesis feed into ethylene-dependent control of the circadian clock.


Kneeshaw S, Keyani R, Delorme-Hinoux V, Imrie L, Loake GJ, Le Bihan T, Reichheld JP, Spoel SH (2017) Nucleoredoxin guards against oxidative stress by protecting antioxidant enzymes.

PNAS https://doi.org/10.1073/pnas.1703344114 Open Access

GARNet Chairman Steven Spoel (University of Edinburgh) leads this Franco-UK collaboration that investigated the role of the pathogen-induced oxidoreductase Nucleoredoxin 1 (NRX1) during the response to oxidative stress. They show that NRX1 targets a range of enzymes that are responsible for scavenging damaging cellular H2O2 and subsequently protect these enzymes from damage. This unexpected regulatory mechanism demonstrates a key role for NRX1 in protecting plants from the oxidative stress, which is an important component of the plants defence response.

Steven discussed this paper below. This audio is also on GARNet YouTube and iTunes channels.


Miller MAE, O’Cualain R, Selley J, Knight D, Karim MF, Hubbard SJ, Johnson GN (2017) Dynamic Acclimation to High Light in Arabidopsis thaliana Involves Widespread Reengineering of the Leaf Proteome Front Plant Sci. https://doi.org/10.3389/fpls.2017.01239 Open Access

Giles Johnson leads this collaborations between two departments from the University of Manchester that has looked at changes to the leaf proteome that occur under differing light conditions. Transferring leaves from low to high light conditions causes a process called dynamic acclimation, which is perturbed in gpt2 mutants. Proteomic analysis of wildtype and gpt2 leaves reveals that a similar number of proteins are changed during dynamic acclimation but the identify of these is altered, with a reduced abundance of proteins involved in photosynthesis. Interestingly gpt2 showed an increase in the number of proteins involved in the stress response.

In 2016 Giles talked to GARNet about a different paper that looks at cold acclimation in Arabidopsis.


Haydon MJ, Mielczarek O, Frank A, Román Á, Webb AA (2017) Sucrose and ethylene signaling interact to modulate the circadian clock. Plant Physiol. https://doi.org/10.1104/pp.17.00592 Open Access

Alex Webb (University of Cambridge) collaborates with Mike Laydon (previously at York, now at the University of Melbourne) on this study that links photosynthesis with circadian and hormone signalling. Previous work showed that GIGANTEA (GI) is necessary to maintain sucrose-dependent circadian oscillations in the dark. This extension of that work demonstrates that sucrose stabilises GI by altering the activity of the ZEITLUPE (ZTL) F-box protein, which is surprisingly dependent on the key ethylene signalling intermediate CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1). Over recent times the role of ethylene on control of the circadian clock has been overlooked but this study shows that the hormone can shorten the circadian period through the activity of sucrose and GI. This study integrates another signal into our understanding of the exquisite regulatory relationships that control clock function.


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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

http:/​/​dx.​doi.​org/10.1073/pnas.1704745114

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.

http:/​/​dx.​doi.​org/10.1038/nplants.2017.87

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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.

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