Arabidopsis Research Roundup: March 31st.

This bumper edition of the Arabidopsis Research Roundup includes a wide range of research topics. Firstly Mike Roberts leads a study that adds another layer of complexity to our understanding of the factors that control seed dormancy. Secondly a paper from Ottoline Leyser’s lab at SLCU provides more details regarding the role of BRC1 during shoot branching. Next is a paper that continues David Salt’s collaborative work that aims to understand how the root endodermal barrier influences nutrient uptake. Fourthly is work from Bristol that looks at the interaction between viral infection, the structure of the leaf surface and the polarization of reflected light. The fifth paper features a wide collaboration from the Sainsbury lab in Norwich and aims to more fully understand the factors that lead to non-host infection by Phytophthora infestans. The penultimate paper looks at the interaction of aldolase enzymes with the plant actin cytoskeleton and the final paper brings us full circle back to seed dormancy where researchers from University of Warwick investigate the link between this complex growth response and the circadian clock.

Singh P, Dave A, Vaistij FE, Worrall D, Holroyd GH, Wells JG, Kaminski F, Graham IA, Roberts MR (2017) Jasmonic acid-dependent regulation of seed dormancy following maternal herbivory in Arabidopsis. New Phytol http:/​/​dx.​doi.​org/10.1111/nph.14525

Taken from:

Open Access

Mike Roberts (University of Lancaster) kindly provides an audio description of this paper on the GARNet YouTube channel, explaining that, in collaboration with Ian Graham at the University of York, they have identified a new control mechanism that links jasmonic acid, herbivory and seed dormancy. ABA and GA are known to be important hormones in the control of seed dormancy but this study adds complexity to this story by showing that following herbivory (or leaf wounding), the level of JA increases within Arabidopsis seeds. Perhaps counter-intuitively, in the following generation this leads to a reduction in dormancy, causing seed to germinate sooner than those from non-predated parents. The authors show that this is due to an increase in JA within seeds that importantly also alters sensitivity to ABA. Unlike transgenerational defence priming that acts through a epigenetic mechanism and persists for multiple generations , this study shows that the JA effect on seeds is a more direct response. Ultimately the mechanism in which parents prepare their offspring for subsequent generations is a complex trade off between multiple sources of predation and pathogenesis, environmental factors as well as through the effect of interacting hormone signaling pathways.

Seale M, Bennett T, Leyser O (2017) BRC1 expression regulates bud activation potential, but is not necessary or sufficient for bud growth inhibition in Arabidopsis. Development http:/​/​dx.​doi.​org/10.1242/dev.145649 Open Access

This is the latest contribution from Ottoline Leyser’s lab that looks into the hormonal control of shoot branching. A key determinant of this process is the transcription factor, BRANCHED1 (BRC1) yet this study shows that under certain conditions, in this case with varied amount of strigolactone, the controlling effect of BRC1 expression levels can be mitigated. The authors provide evidence for a mechanism for branching control that involves the coordinated activity of BRC1 and an auxin-transport mechanism, both of which are influenced by a separate strigolactone-mediated signaling pathway.

Li B, Kamiya T, Kalmbach L, Yamagami M, Yamaguchi K, Shigenobu S, Sawa S, Danku JM, Salt DE, Geldner N, Fujiwara T (2017) Role of LOTR1 in Nutrient Transport through Organization of Spatial Distribution of Root Endodermal Barriers. Current Biology


Former GARNet chairman David Salt is a co-author on this paper that is lead by Japanese and Swiss colleagues and continues his work on the development of the casparian strip. These rings of lignin polymers are deposited within root endodermal cells and play a key role in the movement of water and nutrients into the vascular tissue. Suberin lamellae have a similar function and surround endodermal cells, likely acting as a barrier to apoplastic movement. This paper documents the identification of the Tolkienesquely-named LOTR1, which is essential for casparian strip formation. Lotr1 mutants show disrupted casparian strips, ectopic suberization and reduced calcium accumulation in the shoot. Further analysis demonstrates that it is this suberized layer substitutes for the CS in regions of lateral root emergence. Utliamtely they show that the relationship between suberization of the endodermal layer is a key determinant of calcium movement into the root and then around the rest of the plant.

Maxwell DJ, Partridge JC, Roberts NW, Boonham N, Foster GD (2017) The effects of surface structure mutations in Arabidopsis thaliana on the polarization of reflections from virus-infected leaves. PLoS One

http:/​/​dx.​doi.​org/10.1371/journal.pone.0174014.g003 Open Access

Gary Foster (University of Bristol) leads this study that continues his labs work on the effect that viral infection has on light polarization when reflected off leaves. This attribute is important to attract insect predators, which in turn increase the possibility of successful viral transmission. Light polarization is affected by structures on the leaf surface such as trichomes or the makeup of the waxy cuticle. Here the authors show that the cer5 wax synthesis mutant alters the polarization of light following infection with Turnip vein clearing virus (TVCV) but not following infection with Cucumber mosaic virus (CMV). The paper provides no mechanism for this difference but the authors do show that leaf viral titre is equivalent in these mutants and therefore speculate that these changes might influence transmission of each virus by a different insect carrier that in turn responses to different patterns of polarized light.

Prince DC, Rallapalli G, Xu D, Schoonbeek HJ, Çevik V,, Asai S,, Kemen E,, Cruz-Mireles N, Kemen A,, Belhaj K, Schornack S,, Kamoun S, Holub EB, Halkier BA, Jones JD (2017) Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana. BMC Biol. 

http:/​/​dx.​doi.​org/10.1186/s12915-017-0360-z  Open Access

This paper is a wide collaboration that features many colleagues from the Sainsbury lab in Norwich. Wildtype Arabidopsis plants are suspectible to Phytophthora infestans only after earlier infection with Albugo laibachii yet the molecular explanation of this complex interaction between plant and microbes remained opaque. This study demonstrates that Albugo infection alters the levels of a set of tryptophan-derived antimicrobial compounds, which were then found to be relevant for infection with P.infestans. This shows that these antimicrobial compounds might be key for the general maintenance of non-host resistance and might provide important information to aid future strategies to improve food security by reducing biomass loss due to plant pathogens.

Garagounis C, Kostaki KI, Hawkins TJ, Cummins I, Fricker MD, Hussey PJ, Hetherington AM2, Sweetlove LJ (2017) Microcompartmentation of cytosolic aldolase by interaction with the actin cytoskeleton in Arabidopsis. J Exp Bot.


This collaboration between the Universities of Oxford, Bristol and Durham looks into the functional role that molecular microcompartments play in the workings of a cell. Animal models have shown that certain aldolase enzymes are able to function as actin-bundling proteins and so this study focuses on a major plant cytosolic aldolase, FBA8, which is predicted to have two actin binding sites. Although the authors could not detect co-localisation of FBA8-RFP with the actin cytoskeleton they provide in vitro evidence that FBA8 can functionally interact with F-actin. In addition in fba8 mutants there is altered arrangement of actin filaments in guard cells that concomitantly results in a reduced rate of stomatal closure. Therefore these findings leads the authors to propose that FBA8 is able to subtly interact with actin in vivo, evidenced by some FRET-FLIM experiments, and that this may modulate actin dependent cell responses.

Footitt S, Ölcer-Footitt H, Hambidge AJ, Finch-Savage WE (2017) A laboratory simulation of Arabidopsis seed dormancy cycling provides new insight into its regulation by clock genes and the dormancy-related genes DOG1, MFT, CIPK23 and PHYA. Plant Cell Environ http:/​/​dx.​doi.​org/10.1111/pce.12940

William Savage-Finch (University of Warwick) is the corresponding author on this paper that investigates mechanisms that control seed dormancy, which has been built from the analysis of a variety of genetic and environmental factors. They test their predictions by testing a range of mutants in both known dormancy related genes and in the function of the circadian clock. This provides a link between the circadian cycle and the daily variation in the level of seed dormancy in Arabidopsis.

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: 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: July 27th

Each of the papers in this Arabidopsis Research Roundup involves the response to different stimuli. Giles Johnson at Manchester provides an audio description of work that has discovered a novel mechanism of cold sensing whilst Gordon Simpson and John Brown from Dundee are contributors to work that has interrogated the sugar signaling pathway. Finally is a study from Warwick that has identified novel loci involved in ABA signaling and seed vigour.

Dyson BC, Miller MA, Feil R, Rattray N, Bowsher C, Goodacre R, Lunn JE, Johnson GN (2016) FUM2, a cytosolic fumarase, is essential for acclimation to low temperature in Arabidopsis thaliana Plant Physiology

Open Access


Giles Johnson (Manchester) is the corresponding author on this UK-German collaboration that looks at the mechanisms by which plants sense the low temperatures that cause significant phenotypic changes. GC-MS showed that fumarate is a key component in the cold tolerance response and that the activity of the FUM2 enzyme is responsible for accumulation of fumaric acid. Plants that lack FUM2 activity show significant alteration in gene expression and metabolite profile following a cold treatment and in particularly are unable to acclimate photosynthesis at lower temperatures. Therefore this study introduces a novel component of the temperature sensing apparatus, which might have broad significance for attempts to develop crops with an improved cold response.

Giles kindly provides an audio description of this work, which includes an overview into cold acclimation of photosynthesis. This includes an excellent ‘stress-ball’ analogy! (Apologies for pen-clicks :/).


Carvalho RF, Szakonyi D, Simpson CG, Barbosa IC, Brown JW, Baena-González E, Duque P (2016) The Arabidopsis SR45 Splicing Factor, a Negative Regulator of Sugar Signaling, Modulates SNF1-Related Protein Kinase 1 (SnRK1) Stability The Plant Cell


Gordon Simpson and John Brown (James Hutton Institute) are contributors to this Portuguese-led study that investigates the role of the SR45 splicing factor in sugar signaling. In sr45-1 mutants they show that glucose-feeding causes increased levels of the energy-sensing SNF1-Related Protein Kinase 1 (SnRK1) yet without increasing its gene expression. Concomitantly the hypersensitivity of sr45-1 mutants is rescued in plants with reduced levels of SnRK1. The authors discovered that the mechanistic link between these genes involves SR45-1 regulating the alternative splicing of the 5PTase13 gene, which encodes an inositol polyphosphate 5-phosphatase that interacts with SnRK1 in vivo. In wildtype plants 5PTase13 modulates proteasomal-mediated degradation of SnRK1 and therefore a perturbation of this process in sr45-1 explains this defect in sugar-sensing.

Morris K, Barker GC, Walley PG, Lynn JR, Finch-Savage WE (2016) Trait to gene analysis reveals that allelic variation in three genes determines seed vigour. New Phytol. Open Access

Bill Finch-Savage is the corresponding author on this study from the Warwick University that uses Brassica oleracea natural variation to identify novel loci involved in seed vigour. The discovered QTL was termed Speed of Germination (SOG1) and contained two genes, BoLCVIG2, a homologue of the alternative-splicing regulator (AtPTB1) and BoLCVIG1, which has unknown function. Transfer of these alleles into Arabdopsis causes alterations in seed germination, which is also observed in mutants of the equivalent Arabidopsis genes (At3g01060, At3g01150). Furthermore an additional discovered QTL encodes the Reduced ABscisic Acid 1 (RABA1) gene, which influences ABA content and seed vigour. Therefore this mapping strategy has discovered three genes that promote seed vigour resulting from alterations in ABA content and sensitivity.

Arabidopsis Research Roundup: June 9th

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

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

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

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

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

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

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

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

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

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

Arabidopsis Research Roundup: February 9th

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Published on: February 9, 2016

It has been a quiet couple of weeks for newly published UK Arabidopsis Research but what might be lacking in quantity is made up for in quality! Firstly the PRESTA consortium use gene regulatory network analysis to identify a key component in the response to drought stress. Secondly is a paper featuring researchers from Rothamstead that identifies a new molecular participant in the control of RNA surveillance. Thirdly is a paper that investigates the function of aquaporins during lateral root emergence and includes researchers from Warwick and Nottingham. Finally is a study from Sheffield that investigates necrotropic and biotropic strategies employed by an ascomycete pathogen. It is also nice to observe that each of these papers are open access.

Bechtold U, Penfold CA, Jenkins DJ, Legaie R, Moore JD, Lawson T, Matthews JS, Vialet-Chabrand SR, Baxter L, Subramaniam S, Hickman R, Florance H, Sambles C, Salmon DL, Feil R, Bowden L, Hill C, Baker NR, Lunn JE, Finkenstadt B, Mead A, Buchanan-Wollaston V, Beynon JL, Rand DA, Wild DL, Denby KJ, Ott S, Smirnoff N, Mullineaux PM (2016) Time-series transcriptomics reveals that AGAMOUS-LIKE22 links primary metabolism to developmental processes in drought-stressed Arabidopsis Plant Cell http:/​/​dx.​doi.​org/​10.​1105/​tpc.​15.​00910 Open Access

This Large Scale Biology article is the result of the PRESTA collaboration that is based at the Universities of Essex, Exeter and Warwick. The research plan of the PRESTA project is based upon the generation of large scale transcriptomic datasets and in this case they investigate changes in gene expression in plants subjected to drought stress. They identified over 1800 differentially expressed genes and the early changes coincided with a drop in carbon assimilation together with a late increase in foliar ABA content. Using Bayesian network modelling of differentially expressed transcription factors they identified the AGAMOUS-LIKE22 (AGL22) gene as a key component in this gene regulatory network. AGL22 had been previously found to play an important role in the change from vegetative to floral development but in this context it influences photosynthetic rates and lifetime water use.

Hématy K, Bellec Y, Podicheti R, Bouteiller N, Anne P, Morineau C, Haslam RP, Beaudoin F, Napier JA, Mockaitis K, Gagliardi D, Vaucheret H, Lange H, Faure JD (2016) The Zinc-Finger Protein SOP1 Is Required for a Subset of the Nuclear Exosome Functions in Arabidopsis PLoS Genetics 12(2):e1005817 Open Access

This Franco-US collaboration also includes a contribution from Johnathan Napier’s group at Rothamstead Research. They investigated the function of the essential Arabidopsis PASTICCINO2 (PAS2) gene by isolating three suppressors of pas2 mutants (termed sop mutants). PAS2 is involved in correct splicing so the sop mutants prevented degradation of mis-spliced pas2 mRNA species. The suppressor genes were either previously characterized as being involved with function of the exosome (SOP2/RRP4, SOP3/HEN2) or as a novel zinc-finger protein (SOP1) that colocalised with HEN2 in nucleoplasmic loci. The authors show additional evidence suggesting that the SOP proteins are involved in RNA quality control and introduce SOP1 as a novel component that is involved in nuclear RNA surveillance.

Reinhardt H, Hachez C, Bienert MD, Beebo A, Swarup K, Voss U, Bouhidel K, Frigerio L, Schjoerring JK, Bennett MJ, Chaumont F (2016) Tonoplast aquaporins facilitate lateral root emergence Plant Physiology. Open Access

This Belgian-led study includes lead-UK representation from Warwick (Lorenzo Frigerio)  and Nottingham (Malcolm Bennett) and investigates the role of tonoplast-localised aquaporin proteins during lateral root emergence. The AtTIP1;1, AtTIP1;2 and AtTIP2;1 are abundant aquaporin proteins and the triple tip mutant shows a reduction in lateral root (LR) number without having a shorter primary root. This effect is not due to a reduction of LR primordia but rather due to a defect in the elongation of emerging LR. The authors show that spatial and temporal variations of TIP isoform expression throughout the root correlates with the tip mutant phenotype. Surprisingly, native expression of TIP2:1, which is found only at the base of the LR, can restore wildtype LR emergence to the triple mutant, suggesting that aquaporin activity in this region is sufficient to set-off LR outgrowth.

Pétriacq P, Stassen JH, Ton J (2016) Spore density determines infection strategy by the plant-pathogenic fungus Plectosphaerella cucumerina Plant Physiology Open Access

Jurriaan Ton (Sheffield) is the lead researcher on this study that investigates the molecular factors that allow pathogens to switch between necrotropy and biotrophy, which elicit different response pathways within the infected plant. They used untargeted metabolomics to investigate the growth of the ascomycete pathogen Plectosphaerella cucumerina on Arabidopsis leaves. Higher spore densities activate a JA-dependent necrotropic defence response whilst lower spore numbers causes hemi-biotrophic SA-dependent responses. This change is reflected in the susceptibility of different Arabidopsis mutants to differing spore densities and allow the authors to conclude that P. cucumerina is able to gain an advantage over the host immunity by switching between different modes of infection.

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: November 25th

This weeks Arabidopsis Research Roundup contains four papers each with a different focus. Firstly is a large-scale investigation that attempts to define the transcriptional changes that occur in response to bacterial infection. Second is a study that investigates a newly proposed role for the chloroplast chaperone Hsp93. Thirdly is another piece of work that also involves University of Oxford researchers and investigates the genetic networks that control leaf morphology. Finally is an updated plant-specific protocol for the commonly used technique of Chromatin Immunoprecipitation.

Lewis LA, Polanski K, de Torres-Zabala M, Jayaraman S, Bowden L, Moore J, Penfold CA, Jenkins DJ, Hill C, Baxter L, Kulasekaran S, Truman W, Littlejohn G, Prusinska J, Mead A, Steinbrenner J, Hickman R, Rand D, Wild DL, Ott S, Buchanan-Wollaston V, Smirnoff N, Beynon J, Denby K, Grant M (2015) Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000 Plant Cell. Open Access

This ‘Large Scale Biology’ publication is a collaboration between the Universities of Exeter and Warwick, led by Murray Grant and current GARNet Advisory board member Katherine Denby. This study investigates the transcriptional changes that occur over a long time course in response to infection by the pathogen Pseudomonas syringae pv tomato DC3000. The authors aim to differentiate between the changes associated with endogenous microbial-associated molecular pattern (MAMP)-triggered immunity (MTI) and those orchestrated by pathogen effectors. The responses to pathogenic and non-pathogenic P.syringae were compared and using novel computational analysis, it was shown that the majority of gene expression changes that contribute to disease or defense responses occurred within 6hour post-infection, well before pathogen multiplication. Broadly it was found that chloroplast-associated genes are suppressed by a MAMP-triggered response, presumably to restrict nutrient availability. Ultimately this manuscript identified specific promotor elements that are involved in either the MTI response or utilised by the infecting bacteria.

Corresponding author Professor Murray Grant kindly takes ten minutes to discuss the finding of this paper and the community resource that it represents. He also discusses another paper involving the Jasmonate response that resulted from this dataset and was recently highlighted in the Research Roundup. Interview end at 11m10s.

Flores-Pérez Ú1, Bédard J1, Tanabe N2, Lymperopoulos P2, Clarke AK3, Jarvis P (2015) Functional analysis of the Hsp93/ClpC chaperone at the chloroplast envelope Plant Physiology. Open Access

Paul Jarvis (Oxford) is the corresponding author on this study in which his lab collaborates with Swedish researchers to investigate the role of the Hsp93/ClpC chaperone protein in protein import into the chloroplast. This recently postulated role for this protein has not yet been experimental tested so they generated a hsp93[P-] mutant that lacked a functional ClpP-binding motif (PBM), which confers the already determined role for Hsp93 in proteolysis that occurs in the chloroplast stroma. The hsp93[P-] mutant localises to the chloroplast envelope and associates with TIC transport machinery but was unable to complement the phenotypes of a hsp93 null mutant. This showed that the PBM domain was essential for its function. Expression of the Hsp93[P-] mutant in the hsp93 null background did not improve protein import so the authors concluded that these results do not confirm this newly postulated role for the protein and they suggest that its functional role occurs immediately after its substrate had been transported into the chloroplast.

Rast-Somssich MI, Broholm S, Jenkins H, Canales C, Vlad D, Kwantes M, Bilsborough G, Dello Ioio R, Ewing RM, Laufs P, Huijser P, Ohno C, Heisler MG, Hay A, Tsiantis M (2015) Alternate wiring of a KNOXI genetic network underlies differences in leaf development of A. thaliana and C. hirsuta Genes Dev. 29(22):2391-404 Open Access

The study includes researchers from Oxford and Southampton Universities in collaboration with those from Italy, France and Germany in work that is led by Angela Hay and Miltos Tsiantis, who were both previously based in Oxford. This is familiar territory for this group as they compare leaf development between Arabidopsis, which has simple leaves, and the related , Cardamine hirsuta, which has dissected leaves. In this new work they transfer the SHOOTMERISTEMLESS (STM) and BREVIPEDICELLUS (BP) homeobox genes between the two species and investigate their ability to modify leaf form. In Cardamine, expression of BP is controlled by crosstalk between the microRNA164A (MIR164A)/ChCUP-SHAPED COTYLEDON (ChCUC) module and ChASYMMETRIC LEAVES1 (ChAS1) gene. However this regulatory network does not function in Arabidopsis and therefore leads to the establishment of differing regulatory networks that the authors propose are responsible for the alterations in organ geometry.

Posé D, Yant L (2016) DNA-Binding Factor Target Identification by Chromatin Immunoprecipitation (ChIP) in Plants Methods Mol Biol. 1363:25-35.

Levi Yant is a new member of faculty at the John Innes Centre and is the lead author on this paper that introduces an updated protocol for Chromatin Immunoprecipitation in Plants (ChIP). They have used this technique in his lab to identify target genes for a number of transcriptional regulators that are involved in Arabidopsis floral development.

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