Arabidopsis Research Roundup: July 11th

After a conference break the Arabidopsis Research Roundup returns with an outstanding selection of papers from UK (and mostly Scotland-based) researchers. Firstly Levi Yant provides an audio description of work that has identified important loci for adaption to harsh environments. Secondly John Doonan leads a multi-national group investigating the role of eiF4A phosphorylation within proliferating cells. Next two Scottish-based studies both investigate aspects of light signalling on different scales: a Glasgow-based consortium dissects the UVR8 signaling module while the role of phytochrome on global carbon allocation is studied by Karen Halliday’s group in Edinburgh. The final paper also involves significant Scottish involvement with Piers Hemsley at Dundee together with Simon Turner at Manchester investigating the role of s-acylation in the activity of the cellulose synthase complex.

Arnold BJ, Lahner B, DaCosta JM, Weisman CM, Hollister JD, Salt DE, Bomblies K, Yant L (2016) Borrowed alleles and convergence in serpentine adaptation. PNAS Open Access

New investigator at the John Innes Centre, Levi Yant, is the corresponding author on this study that also includes contributions from the labs of Kristen Bomblies and current GARNet Chairman David Salt. This investigation uses GWAS techniques to identify loci in Arabidopsis Arenosa that are important for growth on serpentine barrens, which are characterised by drought, mineral paucity and high levels of heavy metals. They showed that polygenic multi-trait genomic locations are important for serpentine adaptation. The authors reassessed previous independent datasets and showed that 11 loci have been identified across these studies and are therefore good candidates as drivers of convergent evolution. This study provides evidence that certain A.arenosa alleles have been introgressed from A.lyrata and that these may facilitate adaptation to a multi-hazard environment.

Levi kindly provides a short audio description of this work, that also touches on ionomics and data reuse!

Bush MS, Pierrat O, Nibau C, Mikitova V, Zheng T, Corke FM, Vlachonasios K, Mayberry LK, Browning KS, Doonan JH (2016) eIF4A RNA Helicase Associates with Cyclin-Dependent Protein Kinase A in Proliferating Cells and is Modulated by Phosphorylation Plant Physiol. Open Access

Growth of phospho-null or phospho-mimetic mutants of eif4a1

John Doonan (Aberystwyth) is the leader of this wide collaboration of UK, US, Czech, Greek and Chinese researchers that investigate the interaction of the eIF4A RNA helicase with cyclin-dependent protein kinase A (CDKA). This interaction only occurs in proliferating cells where CDKA acts by phosphorylating specific amino acids on eIF4A. Throughout in vivo and in vitro experiments using phospho-null and phosphor-mimetic version of eIF4A, the authors show that phosphorylation acts to downregulate eIF4A activity, subsequently altering the efficacy of translation.


Heilmann M, Velanis CN, Cloix C, Smith BO, Christie JM, Jenkins GI (2016) Dimer/monomer status and in vivo function of salt-bridge mutants of the plant UV-B photoreceptor UVR8. Plant J Open Access

This exclusively University of Glasgow study is led by John Christie and Gareth Jenkins. Dimeric UVR8 is a UV photoreceptor that after UV-B interaction dissociates into monomers, which interact with COP1 to begin signal transduction. The UVR8 dimer develops through the formation of salt-bridges between individual UVR8 proteins. In this study the details of the dimerization are dissected, showing that several salt-bridge amino acids are necessary for the multiple functions of both the UVR8 dimer and monomer. Interestingly the authors show that UVR8 with conservative mutations of Asp96 and Asp107 to Asn96 and Asn107 are unable to form dimers yet retain wildtype responses to UV-B. This shows that monomeric UVR8 has the ability to normally initiate a signal transduction pathway and complicates our understanding of the in vivo role of the UVR8 dimer.

Phy mutants have reduced biomass. Taken from:

Yang D, Seaton DD, Krahmer J, Halliday KJ (2016) Photoreceptor effects on plant biomass, resource allocation, and metabolic state. PNAS 113(27):7667-72

Karen Halliday (Edinburgh) is the corresponding author on this investigation into the broader impact of Arabidopsis phytochromes on carbon allocation and biomass production. Even though phytochrome mutants have reduced CO2 uptake they overaccumulate resources into sucrose and starch and show altered day:night growth rates. Overall this leads to reduced growth coincident with reduced expression of CELLULOSE SYNTHASE-LIKE genes. The authors demonstrate that phytochromes play a significant role in the control of biomass allocation and that they additionally differentially respond to external stresses. Evolutionarily this indicates that modification of phytochrome expression might be an important mechanism for responding to changing environments.

Kumar M, Wightman R, Atanassov I, Gupta A, Hurst CH, Hemsley PA, Turner S (2016) S-Acylation of the cellulose synthase complex is essential for its plasma membrane localization. Science. 353(6295):166-9

Simon Turner (Manchester) and Piers Hemsley (James Hutton Institute, University of Dundee) lead this research which amalgamates the work from their individual labs and assesses the role of S-acylation on the activity of cellulose synthase complex (CSC). They show that core subunits of the CSC, cellulose synthase A (CESA) proteins, require s-acylation for their localisation to the plasma membrane, which is necessary for their in vivo activity. The authors estimate that a CSC might contain over 100 S-acyl groups, which could significantly alter its hydrophobicity and its interactions within the membrane environment.

CES localisation: Taken from

Arabidopsis Research Roundup: December 9th.

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

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

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

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

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

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

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

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

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

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

Arabidopsis Research Roundup: August 27th

The Arabdopsis Research Roundup broadens its remit this week. As well as including three original research papers, which look at casparian strip formation, light and hormone signaling, we also highlight an important viewpoint article that aims to set standards for synthetic biology parts. In addition we include a meeting report from a plant synthetic biology summer school and interviews with plant scientists at the JIC, Caroline Dean and Anne Osbourn.

Kamiya T, Borghi M, Wang P, Danku JM, Kalmbach L, Hosmani PS, Naseer S, Fujiwara T, Geldner N, Salt DE (2015) The MYB36 transcription factor orchestrates Casparian strip formation Proc Natl Acad Sci USA Open Access

GARNet Advisory Board Chairman David Salt (Aberdeen) leads this international collaboration that looks at the (relatively) poorly understood Casparian strip (CS), a lignin-based filter that lies in root endodermal cells. Formation of the CS is initiated by Casparian strip domain proteins (CASPs) that recruit other proteins, which begin the process of lignin deposition. In this study the authors look upstream this process and identify the transcription factor MYB36 that directly regulates expression of CASPs and is essential for CS formation. Ectopic expression of MYB36 in root cortical tissues is sufficient to stimulate expression of CASP1-GFP and subsequent deposit a CS-like structure in the cell wall of cortex cells. These results have implications for the design of future experiments that aim to control how nutrients are taken up by the plant as even though myb36 mutants have a ‘root-defect’, they also have changes to their leaf ionome.

Sadanandom A, Ádám É, Orosa B, Viczián A, Klose C, Zhang C, Josse EM, Kozma-Bognár L, Nagy F (2015) SUMOylation of phytochrome-B negatively regulates light-induced signaling in Arabidopsis thaliana Proc Natl Acad Sci USA Open Access

Ari Sadanandom (Durham) and Ferenc Nagy (Edinburgh) are the leaders of this study that investigates the precise function of the PhyB photoreceptor protein. PhyB interacts with a wide range of downstream signaling partners including the PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors. The small ubiquitin-like modifier (SUMO) peptide is conjugated to larger proteins to bring about a variety of signaling outcomes. In this case the authors find that SUMO is preferentially attached to the C-term of PhyB under red light conditions, a relationship that occurs in a diurnal pattern. SUMOylation of PhyB prevents interaction with PIF5 whilst the OVERLY TOLERANT TO SALT 1 (OTS1) protein likely de-SUMOlyates PhyB in vivo. Altered levels of PhyB SUMOylation cause distinct light-responsive phenotypes and as such this paper adds another level of regulation to the already complex known network that controls light signaling.

Schuster C, Gaillochet C, Lohmann JU (2015) Arabidopsis HECATE genes function in phytohormone control during gynoecium development Development. Open Access

Christopher Schuster who is now a postdoc based at the Sainsbury lab in Cambridge is the lead author on this investigation into the role of the HECATE (HEC) family of bHLH transcription factors on fruit development in Arabidopsis. During this process HEC proteins are involved in the response to both the phytohormones auxin and cytokinin, the authors proposing that HEC1 plays an essential role in Arabidopsis gynoecium formation.

Patron N et al (2015) Standards for plant synthetic biology: a common syntax for exchange of DNA parts New Phytologist Open Access

Carmichael RE, Boyce A, Matthewman C Patron N (2015) An introduction to synthetic biology in plant systems New Phytologist Open Access

Although not strictly based on Arabdopsis work, there are a couple of articles in New Phytologist that have broad relevance to plant scientists who are interested in plant synthetic biology. In the first of these Nicola Patron (The Sainsbury Laboratory) leads a wide consortium that aims to set parameters for the standardisation of parts in plant synthetic biology. It is hoped that as the principles of synbio are used more widley in the plant sciences that the proposals in this paper will serve as a useful guide to standidise part production. GARNet has recently written a blog post on this topic.
The associated meeting report looks at the use of plant synthetic biology in a teaching context with a synopsis of the ERASynBio summer school hosted by John Innes Centre. In this event, young researchers from a range of backgrounds were introduced to the power and potential of plant synthetic biology through a diverse course of lectures, practical session and group projects.


Vicente C (2015) An interview with Caroline Dean Development Open Access

An interview with Anne Osbourn (2015) New Phytologist <a href="http://dx.doi acheter″ onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘’, ‘ ‘]);” target=”_blank”> Open Access

These are interviews with eminent female plant molecular biologists who both work at the John Innes Centre. Caroline Dean’s lab focuses on the epigenetic mechanisms that regulate vernalisation whilst Anne Osbourn is interested in using synthetic biology approaches to engineer metabolic pathways for the production of novel compounds.

Arabidopsis Research Roundup: June 10th.

This weeks UK Arabidopsis Research Roundup features work from two members of the GARNet advisory board who are working on very different aspects of how plants response to external stimuli. In addition there is a genetic and biochemical dissection of primary cell wall formation as well as a comment piece that questions recent findings concerning the relationship between auxin, ABP1 and cortical microtubules.

Busoms S, Teres J, Huang X, Bomblies K, Danku J, Douglas A, Weigel D, Poschenrieder C, Salt DE (2015) Salinity is an agent of divergent selection driving local adaptation of Arabidopsis thaliana to coastal habitats Plant Physiology

Current GARNet Chairman David Salt from Aberdeen has collaborated with researchers from Spain, Germany and the USA in this study that looks at the drivers of adaptive evolution of Arabidopsis plants grown in saline conditions. Unusually this is a field-based study using Arabidopsis that naturally grow in coastal or inland areas of NE Span. Plants taken from coastal areas outperform inland plants when grown on highly saline soils, indicating local adaptation to salt tolerance. The authors conclude that the variation in sodium concentration is causing divergent selection between these two populations.

Monaghan J, Matschi S, Romeis T, Zipfel C (2015) The calcium-dependent protein kinase CPK28 negatively regulates the BIK1-mediated PAMP-induced calcium burst Plant Signaling and Behaviour June 2015

GARNet advisory board member Cyril Zipfel from the Sainsbury lab led this study looking at the role of the cytoplasmic kinase BIK1 in the plants response to microbial infection. In plants that are mutant for the Ca2+-dependent protein kinase CPK28, BIK1 accumulates, which leads to enhancing immune signaling. In this study the authors add to these previous finding from their lab by showing that CPK28 also contributes to a burst of Ca2+ production following exposure to pathogens.

Mortimer JC, Faria-Blanc N, Yu X, Tryfona T, Sorieul M, Ng YZ, Zhang Z, Stott K, Anders N, Dupree P (2015) An unusual xylan in Arabidopsis primary cell walls is synthesised by GUX3, IRX9L, IRX10L and IRX14 Plant Journal

Paul Dupree from the Biochemistry department at the University of Cambridge led this work that investigated a newly characterised form of Xylan, a little studied component of the plant primary cell wall. Genetic analysis indicates that the IRX9L, IRX10L and IRX14 proteins are necessary for xylan backbone synthesis. Importantly this new xylan is contains GlcA side chains, whose addition only requires the glucuronyltransferase GUX3. This type of xylan has not been observed in secondary cell walls so the authors comment on how differences in xylan structure assist in the formation of primary vs secondary cell walls.

Taken from wikipedia.
Taken from wikipedia.






T Baskin (2015) Auxin inhibits expansion rate independently of cortical microtubules. Trends in Plant Science

Visiting scholar at CPIB in Nottingham, Tobias Baskin provides a short reply to a publication in Nature that claimed that the control of cell expansion by auxin is caused by reorientation of cortical microtubules. In this paper, Tobias provides evidence from both a simple experiment and from the literature that this might not be the paradigm-shifting observation that it initially appears.

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