Arabidopsis Research Roundup: February 20th

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Published on: February 19, 2017

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

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

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

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

Open Access

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

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

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

Open Access

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

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


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

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

Open Access

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

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

Open Access

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

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

Open Access

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

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: January 11th

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

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

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

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

Open Access

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

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

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

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

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

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

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

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

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


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

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

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

Arabidopsis Research Roundup: December 29th

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Published on: December 28, 2016

The final Research Roundup of 2016 includes two papers that take different strategies toward the ultimate aim of crop improvement and use Arabidopsis as a tool for their initial discoveries. Firstly Christine Raines (University of Essex) uses a transgenic approach to upregulate enzymes of the calvin cycle while researchers from Rothamstead and Oxford use a chemical intervention strategy. Both of these strategies are successful in increasing yield.

Second are a set of back-to-back papers featuring Xiaoqi Feng (JIC) that investigate DNA methylation patterns in both male and female gametes.

Finally Henrik Jonsson (SLCU) leads a paper that precisely defines the parameters that are important in determining the relationship between cell size, location and cytokinesis.


Simkin AJ, Lopez-Calcagno PE, Davey PA, Headland LR, Lawson T, Timm S, Bauwe H, Raines CA (2016) Simultaneous stimulation of the SBPase, FBP aldolase and the photorespiratory GDC-H protein increases CO2 assimilation, vegetative biomass and seed yield in Arabidopsis. Plant Biotechnol J

Open Access
GARNet Committee Member Christine Raines leads this UK-German study that alters the amounts of three calvin cycle enzymes and assesses the subsequent change in photosynthetic rate in Arabidopsis plants. These enzymes sedoheptulose 1,7-bisphosphatase (SBPase), fructose 1,6-bisphophate aldolase (FBPA) and the glycine decarboxylase H-protein (GDC-H) were overexpressed either individually or together and each plant shows an increase in the quantum efficiency of photosystem II. This results in improved CO2 fixation and a concomitant increase in leaf area and biomass. Overall the authors have shown that this transgenic gene stacking approach can have potential for improving plant productivity.

Griffiths CA, Sagar R, Geng Y, Primavesi LF, Patel MK, Passarelli MK, Gilmore IS, Steven RT, Bunch J,, Paul MJ, Davis BG (2016) Chemical intervention in plant sugar signalling increases yield and resilience. Nature

This study is a collaboration between Rothamstead Research and the University of Oxford and has been featured in a recent Nature podcast. This paper outlines a chemical intervention strategy to improve crop productivity and includes some fundamental work performed in Arabidopsis. They used a ”signaling-precursor concept” to design and synthesise a plant permeable version of Trehalose-6-phosphate (T6P), which could readily be uptaken and activated by sunlight in planta. Addition of T6P to wheat increases grain yield whilst when applied to leaf tissue it improves recovery from drought stress. This is an exciting test case to show the potential of chemical intervention yet the authors are rightly cautious when considering the general use of the compound given the variability of field conditions.

Hsieh PH, He S,, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X (2016) Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. PNAS

Xiaoqi Feng (John Innes Centre) is the corresponding author on this study that investigates the transgenerational maintenance of methylation through the male germline. They undertook the challenging purification of Arabidopsis pollen sperm and vegetative cells from both wildtype plants and plants that contains mutations within different DNA methytransferases. They show that background methylation is equivalent in sperm, vegetative and somatic cells but that specific CG methylation is higher in pollen sperm and vegetative cells than in somatic cells. The authors suggest that this allows more accurate inheritance of methylation patterns across successive generations.

Park K, Kim MY, Vickers M, Park JS, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S (2016) DNA demethylation is initiated in the central cells of Arabidopsis and rice. PNAS

In this second of back-to-back papers, Xiaoqi Feng is a co-author on an international study that looks into the role of the DEMETER DNA demethylase on the control of gene expression in the endosperm. This tissue results from the fusion of a male pollen sperm cell and the female central cell and is associated with significant demethylation. This study documents the first genome-wide analysis of DNA methylation in the female central cell in Arabidopsis. They show that DNA demethylation requires DEMETER function but that it is likely not associated with the downregulation of the MET1 methytransferase. Therefore the authors suggest that characteristic endospermal DNA demethylation occurs through locus-specific activity.

Willis L,, Refahi Y, Wightman R, Landrein B, Teles J, Huang KC,, Meyerowitz EM,,, Jönsson H (2016) Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche. PNAS

Henrik Jonsson (Sainsbury Lab Cambridge) is the corresponding author on this UK-US collaboration that uses a 4D imaging pipeline to track the growth of epidermal cells in the Arabidopsis shoot apical meristem (SAM). They suggest that neither cell size or cell age are determinants for progression to cytokinesis, which is also independent of cell contact topologies and the cell position within the SAM. However they find that a more complex mix of parameters determine the constraints on determination of cell size. Following cell division they also show that a smaller daughter cell will grow at a faster rather than its larger sister, a finding that the authors suggest challenges present models of growth regulation.Jonsson

Arabidopsis Research Roundup: August 19th

This weeks Arabidopsis Research Roundup includes broad representation from Norwich Research Park with Caroline Dean, Enrico Coen and Cyril Zipfel each leading studies that focus respectively on the regulation of transcriptional state, auxin patterning that defines leaf shape or the molecular basis of the PAMP response.

Elsewhere Liam Dolan (Oxford) leads, and Malcolm Bennett (CPIB) is the principal UK contributor on studies that look into different aspects of the key molecular signals in either root hair or lateral root development.

Finally Richard Napier is a co-author on a study that better characterises the molecular basis of the well-used plant growth inhibitor MDCA.

Yang H, Howard M, Dean C (2016) Physical coupling of activation and derepression activities to maintain an active transcriptional state at FLC PNAS

Dame Caroline Dean and Martin Howard (JIC) lead this follow-on work from a paper highlighted in an ARR from the start of 2016. Here they use the FLOWERING LOCUS C (FLC) locus as a model to study the trans factors that control methylation state. They find a physical interaction between the H3K36 methyltransferase SDG8 (which promotes the active H3K36me3 mark) and the H3K27me3 demethylase ELF6 (which removes the silencing H3K27me3 mark). SDG8 also associated with RNA polymerase II and the PAF1 transcriptional regulatory complex. Therefore the authors suggest that the addition of active histone marks coincides with transcription at the locus whilst SDG8 and ELF6 exhibit co-dependent localisation to FLC chromatin. Therefore this interaction links activation and derepression and coordinates active transcription whilst preventing ectopic silencing.

Abley K, Sauret-Güeto S, Marée AF, Coen E (2016) Formation of polarity convergences underlying shoot outgrowths. Elife.

Open Access
Enrico Coen (JIC) is the corresponding author on this investigation that had generated models that predict locations of leaf outgrowth linked to auxin biosynthesis and transport. They use live imaging in wildtype and kanadi1kanadi2 mutants to show that the cellular polarity of the PIN1 auxin transporter is orientated so as to move auxin away from regions with high levels of biosynthesis. In turn, this moves auxin toward regions with high expression of AUX/LAX auxin importers. This data allows the generation of detailed models that describe the processes that control auxin-mediated tissue-patterning (and are impossible to describe in a single paragraph).

Couto D, Niebergall R, Liang X, Bücherl CA, Sklenar J, Macho AP, Ntoukakis V, Derbyshire P, Altenbach D, Maclean D, Robatzek S, Uhrig J, Menke F, Zhou JM, Zipfel C (2016) The Arabidopsis Protein Phosphatase PP2C38 Negatively Regulates the Central Immune Kinase BIK1 PLoS Pathog.

Open Access

Cyril Zipfel is the lead investigator on this study that links researchers at TSL with colleagues in China and Germany. The focus of this work is the cytoplasmic kinase BIK1, which is a target of several pattern recognition receptors (PRRs) that are involved in the defence response, and the novel protein phosphatase PP2C38, which acts as a negative regulator of BIK1. Under non-inductive conditions PP2C38 prevents BIK1 activity but following pathogen-associated molecular patterns (PAMP) perception, it is phosphorylated and dissociates from BIK1, allowing full activity. This study provides another layer of detail into the complex central immune response that allows plants to response to a vast array of pathogenic microorganisms.

Goh T, Toyokura K, Wells DM, Swarup K, Yamamoto M, Mimura T, Weijers D, Fukaki H, Laplaze L, Bennett MJ, Guyomarc’h S (2016) Quiescent center initiation in the Arabidopsis lateral root primordia is dependent on the SCARECROW transcription factor Development.

Open Access

Malcolm Bennett and Darren Wells (CPIB) are authors on this international collaboration that links UK, Japanese, French and Dutch researchers. The essential role of the central organizer center (the quiescent center, QC) is well known in primary root meristem development but its role during lateral root (LR) formation remained unclear. LR formation is characterised by biphasic growth that involves early morphogenesis from the central stele and subsequent LR meristem formation. This study uses 3D imaging to demonstrate that LR QC cells originate from outer cell layers of early primordial, in a SCARECROW (SCR) dependent manner. Perturbing SCR function causes incorrect formation of the LR QC and prevents wildtype LR patterning. The manuscript also contains some excellent videos of growing LRs that are very informative.
AUX1-YFPKim CM, Dolan L (2016) ROOT HAIR DEFECTIVE SIX-LIKE Class I Genes Promote Root Hair Development in the Grass Brachypodium distachyon PLoS Genet. Open Access

This study comes from Liam Dolan’s lab at the University of Oxford and moves their research focus on root hair development from Arabidopsis into the grass Brachypodium distachyon. ROOT HAIR DEFECTIVE SIX-LIKE (RSL) class I basic helix loop helix genes are expressed in cells that develop root hair fate in Arabidopsis and this study indentifies 3 RSl1 genes in Brachypodium which, when ecoptically expressed, are sufficient for the development of root hairs in all cell files. The function of these RSL proteins is conserved as the Brachypodium versions are able to restore a wildtype phenotype to root hair-less Arabidopsis mutants. Even though root hair patterning is significantly different in Brachypodium and Arabidopsis, this study shows the role of the RSL genes is conserved.
Steenackers WJ, Cesarino I, Klíma P, Quareshy M, Vanholme R, Corneillie S, Kumpf RP, Van de Wouwer D, Ljung K, Goeminne G, Novak O, Zažímalová E, Napier RM, Boerjan WA, Vanholme B (2016) The allelochemical MDCA inhibits lignification and affects auxin homeostasis. Plant Physiology

Open Access

Richard Napier (Warwick) is the UK PI on this pan-European study that investigates the molecular basis behind the physiological role of the compound phenylpropanoid 3,4-(methylenedioxy)cinnamic acid (MDCA), which inhibits the phenylpropanoid pathway, important in lignin formation. MDCA causes inhibition of primary root growth and increase proliferation of lateral roots, not through lignin perturbation but due to a disruption in auxin homeostasis. MS analysis demonstrates that MDCA causes overall changes in auxin biosynthesis, conjugation and catabolism, similar to changes observed in mutants involved in the phenylpropanoid pathways. These result link auxin and phenylpropanoid biosynthesis pathways and provide a new explanation for the well demonstrated phytotoxic properties of MDCA.

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: July 19th

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

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

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

Andrew Fleming provides a brief audio description of this manuscript:

Papanatsiou M, Amtmann A, Blatt MR (2016) Stomatal spacing facilitates guard cell ion transport independent of the epidermal solute reservoir. Plant Physiol. Open Access

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

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


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

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

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

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


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


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

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


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
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