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: February 24th

Just three papers in this weeks Arabidopsis Research Roundup and they each cover fundamental aspects of the hormone and environmental control of gene expression. First Keith Lindsey provides an audio description of work that aims to dissect the complex hormonal regulation of root growth while secondly, Nick Harberd is involved in a study that investigates the HY5 shoot-root signaling protein. Finally Ian Graham leads a study into factors that regulate seed dormancy.

Rowe JH, Topping JF, Liu J, Lindsey K (2016) Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin New Phytol. 10.1111/nph.13882 Open Access
Keith Lindsey (Durham) is the corresponding author for this study that investigates the complex hormonal network that regulates the Arabidopsis root response to osmotic stress. The effect of ABA, cytokinin and ethylene on auxin transport are assessed through changes in the dynamics of PIN protein expression. Unsurprisingly they discover a wide range of effects transmitted via crosstalk between these four hormones and that these effects act in a tissue specific manner, as the expression of PIN1 (in the vascular tissue) and PIN2 (in the lateral root cap and epidermis) are altered in different ways. Ultimately the authors conclude that the classic ‘stress hormone’ ABA regulates the root response to drought together with auxin, ethylene and cytokinin in a complex signaling network.

Keith has kindly supplied a brief audio description of this work.

Chen X, Yao Q, Gao X, Jiang C, Harberd NP, Fu X (2016) Shoot-to-Root Mobile Transcription Factor HY5 Coordinates Plant Carbon and Nitrogen Acquisition
GARNet committee member Nick Harberd (Oxford) is the UK representative on this Chinese-led study that investigates the mode of action of the mobile transcription factor ELONGATED HYPOCOTYL5 (HY5). It has been long known that HY5, a bZIP TF, regulates growth responses to light and in this study the authors demonstrate that HY5 controls light-regulated root growth and nitrate uptake. Remarkably, HY5 from the shoot can activate root-derived HY5, in turn switching on the nitrate transporter NRT2.1. This response involves a mechanism that senses carbon:nitrogen balance across different light conditions, thus placing HY5 as a key regulator in the whole-plant response to changing environmental conditions.

Dave A, Vaistij FE, Gilday AD, Penfield SD, Graham IA (2016) Regulation of Arabidopsis thaliana seed dormancy and germination by 12-oxo-phytodienoic acid Journal of Experimental Botany Open Access

This paper results from a collaboration between the labs of Ian Graham (CNAP, York) and Steve Penfield (John Innes Centre) and features an investigation into factors that regulate seed germination. Previously it was known that oxylipin 12-oxo-phytodienoic acid (OPDA) acts together with ABA to regulate germination but this study elucidates that OPDA specifically acts via the ABI5 and RGL2 hormone-regulated proteins. Furthermore the OPDA-ABA signal also acts via another dormancy promoting factor, MOTHER-OF-FT-AND-TFL1 (MFT). Therefore maintenance of dormancy in Arabidopsis seedlings is regulated by ABA and MFT promoting the accumulation of OPDA, highlighting this as a critical control point in this complex process.

Arabidopsis Research Roundup: January 29th

This weeks Arabidopsis Research Roundup features a paper from David Baulcombe and Joe Ecker that further deciphers mechanisms of RNA silencing and is kindly discussed by postdoc Mat Lewsey in a short audio description. Elsewhere there are three studies that include researchers from CPIB in Nottingham. Leah Band contributes to a study that links environment sensing, cell death and auxin signaling whilst Ive De Smet leads a study that finds new proteins involved in cell division. Malcolm Bennett and John King take a modeling approach to describe auxin signaling via the GH3 protein family. Finally Frank Menke leads a study that provides more detail into Pattern Recognition Receptor (PRR) mediated immune signaling and then Jim Dunwell participates in a paper that describes a new method of analyzing GWAS data.

Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker JR (2016) Mobile small RNAs regulate genome-wide DNA methylation. Proc Natl Acad Sci U S A. Open Access

Over the past few years RNA-mediated silencing has emerged a key mechanism for the control of gene expression. This study is a collaboration between the lab of Sir David Balcombe (Cambridge) and Joe Ecker at the SALK institute in California. Mat Lewsey, who is a British postdoc working with Professor Ecker, kindly provided a short audio description of the paper.

These groups have previously shown that sRNAs are highly mobile throughout the plant. This study shows that thousands of loci expressed in roots are dependent on mobile sRNAs generated from the shoot. They unpick the genetic basis of this response showing that it is largely dependent on the DOMAINS REARRANGED METHYLTRANSFERASES 1/2 (DRM1/DRM2) but not CHROMOMETHYLASE (CMT)2/3 DNA methyltransferases. They also show that mobile sRNAs are resposible for the silencing of TEs that are found in gene-rich regions, although this is not a physiologically important response in Arabidopsis, which contains a relatively small amount of transposon tissue. Interestingly they a show that sRNAs generated from different Arabidopsis ecotypes are able to move across graft junctions and can cause methylation in usually unmethylated regions.

PNASpicXuan W, Band LR, Kumpf RP, Van Damme D, Parizot B, De Rop G, Opdenacker D, Möller BK, Skorzinski N, Njo MF, De Rybel B, Audenaert D, Nowack MK, Vanneste S, Beeckman T (2016) Cyclic programmed cell death stimulates hormone signaling and root development in Arabidopsis. Science . 351(6271):384-7

This study is led by Tom Beeckman from Gent University and features Leah Band from CPIB in Nottingham. They reveal an exciting relationship between cell death in root cap cells and hormone signaling. The root cap is a protective tissue that overlies the Arabidopsis root tip and might be considered as an ‘inactive’ tissue. However this study shows that an auxin signal released from root cap cells sets the spacing of lateral organs along the root. As root cap cells move up the root they undergo programmed cell death, which in turn releases a pulse of auxin and establishes a pattern of lateral root formation. The authors suggest that this relationship might integrate external soil conditions so that lateral roots will develop to optimise uptake of water and nutrients. It is well known that an auxin signal simulates lateral root formation but this study provides an explanation as to the genesis of this signal and its integration with external environmental factors.

Yue K, Sandal P, Williams EL, Murphy E, Stes E, Nikonorova N, Ramakrishna P, Czyzewicz N, Montero-Morales L, Kumpf R, Lin Z, van de Cotte B, Iqbal M, Van Bel M, Van De Slijke E, Meyer MR, Gadeyne A, Zipfel C, De Jaeger G, Van Montagu M, Van Damme D, Gevaert K, Rao AG, Beeckman T, De Smet I (2016) PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root. Proc Natl Acad Sci U S A.

This broad collaboration between US-UK and Belgian researchers is led by Tom Beeckman and Ive De Smet, who works at CPIB in Nottingham. In addition it includes a contribution from Cyril Zipfel at TSL. This study aimed to identify proteins that interact with the plasma membrane-localized receptor kinase ARABIDOPSIS CRINKLY 4 (ACR4), which plays a role in the control of cell division in the Arabidopsis root. They find that PROTEIN PHOSPHATASE 2A-3 (PP2A-3), a catalytic subunit of PP2A holoenzymes interacts with ACR4 and has a previous uncharacterised role in control of formative cell divisions. The authors show that the biochemical network that links ACR4 and PP2A-3 is regulated by phosphorylation.

Mellor N, Bennett MJ, King JR (2016) GH3-Mediated Auxin Conjugation Can Result in Either Transient or Oscillatory Transcriptional Auxin Responses. Bull Math Biol.

This paper led by Professor Malcolm Bennett and John King from CPIB is an example of the growing number of multi-disciplinary interactions between biologists and mathematicians. Here a model is developed that interrogates auxin signaling and homeostasis through the GH3 gene family. This includes a parameter that considers auxin transport via the LAX3 influx protein, which, together with the activity of GH3 proteins can facilitate a positive feedback loop that allows cells to response to excess auxin.

Mithoe SC, Ludwig C, Pel MJ, Cucinotta M, Casartelli A, Mbengue M, Sklenar J, Derbyshire P, Robatzek S, Pieterse CM, Aebersold R, Menke FL (2016) Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase. EMBO Rep. Open Access

Frank Menke (TSL, Norwich) is the leader on this collaboration between UK, Dutch and Swiss researchers that investigates innate immunity signaling mediated via Pattern Recognition Receptors (PRRs). Tight control of this signalling is very important to prevent spurious activation of the immune response. These authors find that the differentially phosphorylated MKKK7 can interact with the FLS2 protein, which is key in the perception of bacterial flagellin. In turn MKKK7 attenuates the signalling of a downstream MAPK that contributes to defence-related gene expression. Therefore the show that the FLS2-MKKK7 signaling module is critical for control of innate immunity.

Wang SB, Feng JY, Ren WL, Huang B, Zhou L, Wen YJ, Zhang J, Dunwell JM, Xu S, Zhang YM (2016) Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology. Sci Rep. Open Access

Professor Jim Dunwell (Reading) is a UK contributor to this largely Chinese publication that introduces a new method to analysis GWAS-style data. They propose an analysis based on random-SNP-effect MLM (RMLM) and a multi-locus RMLM (MRMLM) and using stimulations show that their new method can be powerful than conventional types of analysis. To test the method they analysed flowering time traits in Arabidopsis and detected more genes that were involved in the process.

For those interested in different-types of GWAS analysis, Professor David Salt introduced another new method during a recent ARR.

Arabidopsis Research Roundup: November 13th.

This weeks Arabidopsis Research Roundup presents a wide range of topics from researchers across the UK. Firstly we highlight a study that documents the early stages of a potential biotechnological/synthetic biology approach to improve higher plant photosynthesis using algal components. Corresponding author Alistair McCormick also takes five minutes to discuss this work. Secondly a team based mostly at Bath introduces the function of the PAT14 gene, which is involved in S-palmitoylation. Thirdly is a study that successfully transfers SI components between evolutionary diverged plant species and the final paper documents research that adds additional complexity to the signalling pathway that responses to strigolactones.

Atkinson N, Feike D, Mackinder LC, Meyer MT, Griffiths H, Jonikas MC, Smith AM, McCormick AJ (2015) Introducing an algal carbon-concentrating mechanism into higher plants: location and incorporation of key components. Plant Biotechnol J. Open Access

This work results from a collaborative effort between the four groups that make up the Combining Algal and Plant Photosynthesis (CAPP) consortium and include Howard Griffiths (Cambridge), Martin Jonikas (Carnegie Institute for Science), Alison Smith (JIC) and Alistair McCormick (Edinburgh). Here they attempt to express in higher plants a range of algal proteins that are involved in carbon-concentrating mechanisms (CCM). They initially confirmed the intracellular locations of ten algal CCM components and showed that these locations were largely conserved when the proteins were expressed transiently in tobacco or stably in Arabidopsis. Although the expression of these CCMs components in Arabidopsis didn’t enhance growth, the authors suggest that stacking of multiple CCM proteins might be needed to confer an increase in productivity.

Alistair takes five minutes to discuss this paper here:

Li Y, Scott RJ, Doughty J, Grant M, Qi B (2015) Protein S-acyltransferase 14: a specific role for palmitoylation in leaf senescence in Arabidopsis. Plant Physiology Open Access

This Southwest-based study is led by Baoxiu Qi from the Plant-Lab at Bath University with input from Murray Grant (Exeter). They investigate Protein S-Acyl Transferase (PATs) protein, which are multi-pass transmembrane proteins that catalyze S-acylation (commonly known as S-palmitoylation). This process both confers correct protein localisation and is involved in signalling. These are 24 PATs in Arabidopsis and this study focuses on the novel PAT14, which they show has its predicted enzymatic role. Pat14 mutant plants show accelerated senescence that is associated with SA, but not JA or ABA-signaling. Therefore the authors suggest that AtPAT14 plays a pivotal role in regulating senescence via SA pathways and that this is the first published linkage between palmitoylation and leaf senescence.

Lin Z1, Eaves DJ1, Sanchez-Moran E1, Franklin FC1, Franklin-Tong VE1 (2015) The Papaver rhoeas S determinants confer self-incompatibility to Arabidopsis thaliana in planta Science 350(6261):684-7 http:/​/​dx.​doi.​org/​10.1126/science.aad2983

University of Birmingham researchers led by Noni Franklin- Tong publish this study in Science in which they transfer the elements that confer self-incompatibility (SI) in Papever rhoeas (Poppy) to Arabidopsis. They find that Arabidopsis pistils that express the self-determinant PrsS protein reject pollen that expresses the PrpS protein. This leads to a robust SI response in these plants, demonstrating that these two components are sufficient for the establishment of this interaction. Poppy and Arabidopsis are evolutionarily separated by 140million years so the authors suggest that the successful transfer of SI determinants between these divergent species will have potential utility in future crop production strategies.

Soundappan I, Bennett T, Morffy N, Liang Y, Stanga JP, Abbas A, Leyser O, Nelson DC (2015) SMAX1-LIKE/D53 Family Members Enable Distinct MAX2-Dependent Responses to Strigolactones and Karrikins in Arabidopsis The Plant Cell

Ottoline Leyser (SLCU) is the UK lead on this US-UK collaboration that investigates the plant response to butenolide signals, namely the plant hormone strigolactones and smoke-derived karrikins. It is known that these molecules are perceived by the F-box protein MORE AXILLARY GROWTH2 (MAX2) and that the Arabidopsis SUPPRESSOR OF MAX2 1 (SMAX1) protein acts downstream of this perception. This study documents an extensive genetic study that shows that the activity of the SMAX1-LIKE genes, SMXL6, SMXL7, and SMXL8 promote shoot branching. smxl6,7,8 mutant plants suppress several strigolactone-related phenotypes in max2, that focus on the response to auxin but not on germination or hypocotyl elongation responses, which are only suppressed in smax1 mutants. On a molecular level these responses are controlled by the MAX2-dependant degradation of the SMAX1/SMXL proteins, which result in changes in gene expression. Therefore this shows that the diversity of SMAX1/SMXL proteins allows the signaling pathway that responses to butenolide signals to bifurcate downstream of the initial perception.

Arabidopsis Research Roundup: November 5th

Academics from the John Innes Centre lead two of the papers featured in this week Arabidopsis Research Roundup. Firstly Veronica Grieneisen leads a study that combines modeling and experimental work to assess the factors that establish the root auxin maximum and secondly the structural biologist David Lawson heads up an investigation into the plastid-localised enzyme, DPE1. Seemingly a common theme in UK-Arabidopsis research focuses on the factors that control the dynamics of stomatal opening and this week Mike Blatt from Glasgow heads a team that investigates the role of potassium and nitric oxide in this process. Finally we present a paper that investigates proteins that interact within the ER.

El-Showk S, Help-Rinta-Rahko H, Blomster T, Siligato R, Marée AF, Mähönen AP, Grieneisen VA (2015) Parsimonious Model of Vascular Patterning Links Transverse Hormone Fluxes to Lateral Root Initiation: Auxin Leads the Way, while Cytokinin Levels Out PLoS Comput Biol. e1004450Picture Open Access

Veronica Grieneisen (JIC) is the UK-based leader of this work that was performed with her Finnish collaborators. They work on the modeling the processes that define the auxin maximum in the root meristem. This patterning is defined by the activity of the PIN-formed auxin efflux transport proteins and the AHP6 protein, an inhibitor of cytokinin signaling. The authors implement a parsimonious computational model of auxin transport that considers hormonal regulation of the auxin transporters within a spatial context, explicitly taking into account cell shape and polarity and the presence of cell walls. They initially find that variation in cytokinin signaling, mediated by diffusion of the hormone is insufficient for patterning but rather it is an auxin-dependent modification of the cytokinin signal that can define the auxin maximum. Although the role that the PIN proteins play in root vascular patterning is well established, the authors experimentally verify a role for the AUX/LAX auxin influx carrier family of proteins. They also show that polar PIN localisation generates a flux of auxin flow that ultimately causes its own accumulation in the pericycle cells that signal for lateral root initiation. Finally their model confirms the supposition that these pericycle cells compete for auxin accumulation, therefore ensuring that lateral roots develop in the correct localisation. The associated figure is from this paper.

O’Neill EC, Stevenson CE, Tantanarat K, Latousakis D, Donaldson MI, Rejzek M, Nepogodiev SA, Limpaseni T, Field RA, Lawson DM (2015) Structural Dissection of the Maltodextrin Disproportionation Cycle of the Arabidopsis Plastidial Enzyme DPE1. Journal of Biological Chemistry Open Access

This is another paper led by JIC researchers, this time in collaboration with Thai partners. This focuses on determining the structure of the Arabidopsis Plastidial Disproportionating Enzyme 1 (DPE1) that acts to convert two maltotriose molecules to a molecule of maltopentaose and a molecule of glucose, which, for different reasons, are both more functional useful molecules for the plant. They have used ligand soaking techniques to trap the DPE1 in a different set of conformational states and have found that it exists as a homodimer with a variety of interesting features. This includes a dynamic ‘gate’ loop that may play a role in substrate capture, subtle changes in which could alter the efficacy of the active site. The structural insights provided by this study allow the authors to confidently delineate the complete AtDPE1 disproportionation cycle

Chen ZH, Wang Y, Wang JW, Babla M, Zhao C, García-Mata C, Sani E, Differ C, Mak M, Hills A, Amtmann A, Blatt MR (2015) Nitrate reductase mutation alters potassium nutrition as well as nitric oxide-mediated control of guard cell ion channels in Arabidopsis New Phytol. Open Access

<a href="http://www.gla cialis vente en” onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘’, ‘Mike Blatt’]);” target=”_blank”>Mike Blatt (Glasgow) is the lead on this UK-Sino-Australino-Argentine collaboration that investigates the role of nitrate reductase enzyme in potassium flux in guard cells. This flux is necessary for a plants adaption to the environment and is controlled by the activity of ABA via the activity of H2O2 and Nitric Oxide (NO). The authors showed that multiple responses to ABA were impaired in nia1nia2 nitrate reductase mutants, which includes the K+ IN current in guard cells, required for stomatal closure. This response was rescued by exogenous NO and allowed the authors to demonstrate that there exists a complex interaction involving ABA, NO, potassium nutrition and nitrogen metabolism that is necessary to ensure correct stomatal responses.

Kriechbaumer V, Botchway SW, Slade SE, Knox K, Frigerio L, Oparka K, Hawes C (2015) Reticulomics: Protein-Protein Interaction Studies with Two Plasmodesmata-Localized Reticulon Family Proteins Identify Binding Partners Enriched at Plasmodesmata, Endoplasmic Reticulum, and the Plasma Membrane Plant Physiol. 169(3):1933-45

This proteomic analysis of endoplasmic reticulum components is a collaboration between the Central Laser Facility at Didcot, Warwick, Edinburgh and Oxford Brookes Universities, led by Professor Chris Hawes. Plant Reticulon proteins (RTNLB) specifically populate and tubulate the ER, mediated by their varied multi-meric interactions. In addition, certain RTNLB are also present in plasmodesmata (PD) and two of these proteins, RTNLB3 and RTNLB6 were GFP-tagged, Co-IPed and interacting proteins were analysed by MS. This identified a range of known PD-localised proteins, and these interactions were experimentally verified in tobacco cells using FRET-microscopy. The authors suggest that this data shows that RTNLB proteins may play important roles in linking the cortical ER to the plasma membrane. This paper is the ‘sister’ to another manuscript in Plant Physiology that was highlighted in a recent Arabidopsis Research Roundup.

Arabidopsis Research Roundup: October 12th

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Published on: October 11, 2015

The Arabidopsis Research Roundup is ‘defense-focused’ this week. We present three papers that highlight different aspects of plant immunity, two of which result from UK-US-China collaborations. Firstly a team from the Sainsbury Lab, Norwich looks at two molecular mechanisms that control stomatal closure. There are then two studies that involve University of Exeter researchers that investigate either the role of plant hormones in the response to bacterial pathogens or the role that the physical barrier of the cell wall plays in the prevention of infection. Next a group of JIC researchers present a Large Scale Biology investigation of microtubule interacting proteins. Finally a study from QMUL looks at the interaction between NPQ and photoinhibition in controlling the activity of Photosystem II.

Gou M, Zhang Z, Zhang N, Huang Q, Monaghan J, Yang H, Shi Z, Zipfel C, Hua J (2015) Opposing effects on two phases of defense responses from concerted actions of HSC70 and BON1 in Arabidopsis. Plant Physiol.

GARNet Advisory Board Member Cyril Zipfel is the UK lead on this US-China-UK collaboration that looks at two aspects of the plant immune response that are regulated by the same proteins, albeit in an antagonistic way. The heat shock protein HSC70 and the calcium binding protein BON1 both are involved in stomatal closure, the formers effect mediated by the SNC1 protein and the latter (BON1) via the activitation of SGT1 that in turn inhibits HSC70. These new functions demonstrate opposing roles for HSC80 and BON1 in the immune response and further highlight the complexity of the signaling pathways that ultimately feed into the gross phenotypic change of stomatal closure.

de Torres Zabala M, Zhai B, Jayaraman S, Eleftheriadou G, Winsbury R, Yang R, Truman W, Tang S, Smirnoff N, Grant M (2015) Novel JAZ co-operativity and unexpected JA dynamics underpin Arabidopsis defence responses to Pseudomonas syringae infection New Phytol.

This is another UK-USA-China collaboration led by Murray Grant at the University of Exeter, in which the role of the plant hormones is assessed in the response to bacterial pathogens. The defence response is mediated by both the hormones salicylic acid (SA) and jasmonic acid (JA) which antagnise many of each others activity. Pathogens have been shown to produce a JA-mimic cornatine (COR) in order to stall SA-mediated effects. In this study the authors use a systems-biology based approach that involved targeted hormone profiling, high-temporal-resolution micro-array analysis, reverse genetics and mRNA-seq to introduce a complex network of regulation that involves JAZ proteins, which are repressors of the JA signal. In short they show that JAZ5 and JAZ10 specifically co-operate to inhibit pathogen growth by restricting COR cytotoxicity by novel mechanisms, which do not involve previously well-defined signaling proteins.

Marcos R, Izquierdo Y, Vellosillo T, Kulasekaran S, Cascón T, Hamberg M, Castresana C (2015) 9-Lipoxygenase-derived oxylipins activate brassinosteroid signaling to promote cell wall-based defense and limit pathogen infection Plant Physiol.

This work was performed in Madrid under the supervision of Carmen Castresana but includes the work of Satish Kulasekaran who is now at the Exeter. The focus of the work is the oxylipins, which are oxygenated lipid derivatives that regulate plant development and immunity. Using a variety of noxy mutants (non-responding to oxylipins) they show that the effect of the oxylipins is mediated via changes in the cell wall and this is signalled via the Brassinosteriod response pathway. Suspectibility to bacterial and fungal infection was enhanced in noxy mutants but plants were resistance when BR signalling was switched on. Therefore this manuscript introduces an important interaction between the oxylipins and BR signalling and helps to clarify their role in modulating plant defense.

Derbyshire P, Ménard D, Green P, Saalbach G, Buschmann H, Lloyd CW, Pesquet E (2015) Proteomic Analysis of Microtubule Interacting Proteins over the Course of Xylem Tracheary Element Formation in Arabidopsis Plant Cell.

The experiments in this Large Scale Biology paper were performed in the lab of Clive Lloyd (John Innes Centre) which included the work of Eduoard Pesquet, who now has his own lab in Sweden. They looked the microtubule patterning that defines the nature of tracheary element (TEs) thickening in plant vascular tissues. They used Arabidopsis cell suspension culture to isolate microtubule interacting proteins present during TE differentiation. One protein of interest was CELLULOSE SYNTHASE-INTERACTING PROTEIN1, associated with primary wall synthesis, which was enriched during secondary cell wall formation of TEs. The authors knocked-down the expression of some of their identified proteins and indeed showed that they were important for this differentiation. A take-home message is that the proteins that interact with microtubules and link them to different metabolic compartments do indeed specifically vary during TE differentiation, regulating different aspects of cell wall patterning.

Giovagnetti V, Ruban AV (2015) Discerning the effects of photoinhibition and photoprotection on the rate of oxygen evolution in Arabidopsis leaves J Photochem Photobiol B.

Arabidopsis Research Roundup Regular Alexandre Ruban (QMUL) again looks at the mechanisms that lessen the amount of photoinhibition (when photosystem II is damaged by being exposed to too much light). An opposing response is Non-photochemical quenching (NPQ) of chlorophyll a fluorescence which serves to protect PSII from high light conditions. In this study they confirm that a recently devised procedure that aims to discern between the effect of NPQ and photoinhibition works well as a measurement for the efficiency of PSII activity.

Arabidopsis Research Roundup: August 12th

The UK Arabidopsis Research Roundup this week includes a couple of EVO-DEVO-type studies that compare processes within different organisms (Physcomitrella and Cardamine) to those occurring in Arabidopsis. These include the evolution of both hormone signaling and leaf development. Elsewhere a cell-biological focused study looks at the factors that control formation of plasmodesmata whilst another manuscript investigates the details of a plants mechanism to avoid photoinhibition.

Yasumura Y1, Pierik R2, Kelly S3, Sakuta M4, Voesenek LA5, Harberd NP (2015) An Ancestral Role for Constitutive Triple Response 1 (CTR1) Proteins in Both Ethylene and Abscisic Acid Signaling Plant Physiology

GARNet Advisory Board Member Nick Harberd leads this study that investigates the evolution of the CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1) protein, which has known to be involved in ethylene signalling for two decades. CTR1 is compared between mosses, lycophytes and angiosperms, showing that PpCTR1 from moss Physcomitrella patens has the same function and the Arabidopsis equivalent, indicating that this signaling pathway predates the land plant lineage. However PpCTR1 is also involved in ABA signaling, which is not the case with AtCTR1 and may be explained by the presence of an AtCTR1 homolog in angiosperms. The authors state that this work provides new insights into the molecular events that contributed to the adaptive evolution of regulatory mechanisms across plant species

Kirsten Knox, Pengwei Wang, Verena Kriechbaumer, Jens Tilsner, Lorenzo Frigerio, Imogen Sparkes, Chris Hawes, Karl Oparka (2015) Putting the Squeeze on Plasmodesmata: A Role for Reticulons in Primary Plasmodesmata Formation Plant Physiology

This study is led by Karl Oparka (Edinburgh) and Chris Hawes (Oxford Brookes) as well as including PIs from Exeter (Sparkes), Warwick (<a href="http://www2.warwick cialis professional 20” onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘’, ‘Frigerio’]);” target=”_blank”>Frigerio) and St Andrews (Tilsner). The manuscript investigates formation of plasmodesmata (PD), which are known to form from endoplasmic reticulum (ER) via an intermediant termed the desmotubule. Members of the Reticulon (RTNLB) family of ER-tubulating proteins are found in the PD proteome are are associated with developing PD following cell division. The authors use super-resolution imaging to show that RTNLB6 colocalises with desmotubules. The mobility of these RTNLB proteins was show, using FRAP, to vary dependent on their positioning within a developing cell plate. Mutant studies show that RTNLB proteins act as important regulators of the formation of PDs and the authors discuss the wider potential roles of these proteins in this process.

Ware MA, Giovagnetti V, Belgio E, Ruban AV (2015) PsbS protein modulates non-photochemical chlorophyll fluorescence quenching in membranes depleted of photosystems J Photochem Photobiol B

Alexander Ruban (QMUL) continues a fine run of recent publications with this study that investigates plants that express increased levels of the photosynthetic PsbS protein, in the context of a subsequent increase in levels of non-photochemical fluorescence quenching (NPQ). In these PsbS overexpressors, there is increased amplitude of the irreversible NPQ component, qI, which likely results from aggregation of the LHCII antenna complex. Use of freeze-fracture electron microscopy show that quenched thylakoids have 3x more aggregated LHCII particles compared to those that are dark-adapted. Overall, these results demonstrate the importance of this LHCII aggregation in the NPQ mechanism whilst showing that structure of the PSII supercomplex plays no role in formation in process of quenching.

Cartolano M, Pieper B, Lempe J, Tattersall A, Huijser P, Tresch A, Darrah PR, Hay A, Tsiantis M (2015) Heterochrony underpins natural variation in Cardamine hirsuta leaf form Proc Natl Acad Sci U S A. 2015 Aug 4.

The study is a continuation of many years of work led by Miltos Tsiantis (who maintains links with Oxford University), aimed at increasing the understanding of how different morphological patterns develop. They compare leaf patterning in Arabidopsis (which has a simple leaf) and in the related plant, Cardamine (that has a complex leaf). They have identified a novel QTL from Cardamine that shows that age-dependent progression of leaf form underlies variation in this trait within species. Interestingly the QTL mapped to a cis-acting region controlling expression of the floral regulator FLC. Genotypes expressing low levels of FLC show early flowering and accelerated changes in leaf form, including faster leaflet production. These findings link reproductive timing with leaf development and the authors speculate that this may help to optimize resource allocation to the next generation.

Arabidopsis Research Roundup: July 11th

A couple of weeks since the last update as it’s been quiet for UK Arabidopsis Research publications. However we now see a variety of publications that address some important questions in different signaling pathways. Firstly a multinational collaboration performs a genome-wide analysis of DELLA binding, followed by two studies looking different aspects of light signaling, specifically the link with the production of protective carotenoids and also with the tight control of protein degradation. Elsewhere there is the description of a systems biology approach developed to aid the definition of signaling pathways in non-model organisms and finally a commentary piece about some work on Arabidopsis Arenosa.


Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins (2015) Marín-de la Rosa N, Pfeiffer A, Hill K, Locascio A, Bhalerao RP, Miskolczi P, Grønlund AL, Wanchoo-Kohli A, Thomas SG, Bennett MJ, Lohmann JU, Blázquez MA, Alabadí D PLoS Genet. 11(7):e1005337.

The Centre for Integrative Biology in Nottingham and Rothamstead Plant Science partner with groups from Sweden, Germany, Spain and Saudi Arabia in this truly international collaboration. They investigate the role of DELLA proteins in the relay of environmental cues to multiple transcriptional circuits. The primary experimentation in this study uses ChIP-Seq to analyse the DNA-binding sites of one DELLA protein. Perhaps as expected the DELLA protein binds multiple promotor regions yet with a particular enrichment in regions upstream of cytokinin-regulated genes, where they interact with type-B ARABIDOPSIS RESPONSE REGULATOR (ARR) proteins. The biological relevance of this mechanism is underpinned by the requirement for both DELLAs and B-type ARRs in the control of root growth and photomorphogenesis.


Regulation of carotenoid biosynthesis by shade relies on specific subsets of antagonistic transcription factors and co-factors (2015) Bou-Torrent J, Toledo-Ortiz G, Ortiz-Alcaide M, Cifuentes-Esquivel N, Halliday KJ, Martinez-Garcia JF, Rodriguez-Concepcion M Plant Physiol.

Karen Halliday at the University of Edinburgh is part of this UK-Spanish team that studied the regulation of carotenoid biosynthesis via a light signaling module formed by PIF1 and HY5. In shade conditions, PIF proteins signal for a decrease in carotenoid accumulation, thus saving the plant unneeded energy consumption. The PIF1 response focusses on the phytoene synthase (PSY) biosynthetic gene and is antagonised by the PAR1 transcriptional co-factor. However this is not a universal response carried out by known antagonisers of PIF1 function, demonstrating that carotenoid biosynthesis is finely regulated by a precise subset of regulatory proteins.


High-level expression and phosphorylation of phytochrome B modulates flowering time in Arabidopsis (2015) Hajdu A, Ádám É, Sheerin DJ, Dobos O, Bernula P, Hiltbrunner A,, Kozma-Bognár L, Nagy F Plant Journal

Professor Ferenc Nagy has dual appointments in Edinburgh and in Hungary and this output results from work performed in Hungary. This study looks at control of flowering via phytochrome B signalling, which has been previously shown to rely on the degradation of the CONSTANS (CO) protein that in turn delays flowering by attenuating FLOWERING LOCUS T (FT) expression. Therefore phyB mutants show accelerated flowering, yet this is unexpectedly also true following PHYB overexpression. The novelty of this study comes from showing that PHYB overexpression induces FT without affecting CO transcription but rather acts by causing accumulation of the CO protein, due to an affect on a COP1-ubiquitin ligase complex. This article adds further detail to the already complex relationship between light signaling, the circadian clock, protein degradation and de novo transcription in the control of flowering in Arabidopsis.


Inferring orthologous gene regulatory networks using interspecies data fusion (2015) Penfold CA, Millar JB, Wild DL. Bioinformatics. 31(12):i97-i105.

This study was led by David Wild from Warwick Systems Biology Centre. The authors have used two related Bayesian approaches to network inference that allow Gene Regulatory Networks (GRN) to be jointly inferred in, or leveraged between, several related species, for example between Arabidopsis and related crop species. Inferring gene function is achieved with more accuracy when GRNs are compared between species rather than attempting to use stand alone inference. The manuscript uses data from the yeast S.pombe but the broader principles could be applied to other experimental systems.


The High Life: Alpine Dwarfism in Arabidopsis (2015) Bomblies K Plant Physiol. 168(3):767.

This commentary piece about high altitude growth of Arabidopsis aernosa is the first published work from Kristen Bomblies since she moved her lab to the John Innes Centre from Havard (together with the lab of Levi Yant). Having these two talented young researchers relocate to the UK is be great for UK plant science so I sure everyone in the community wishes them all the best. Watch Kristen talk about her work at a New Phytologist conference from 2014.

Levi Yant also has two postdoctoral posts currently available in his lab.


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