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: Feb 9th

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Published on: February 14, 2017

This weeks Arabidopsis Roundup again includes a broad selection of research topics. Firstly researchers at SLCU are involved in work that describes Arabidopsis sepal development. Secondly Cyril Zipfel from TSL leads a study that adds a layer of complexity to our knowledge of cellular pathogen perception. Thirdly the group of Reiner van der Hoorn from Oxford introduces the use of a novel set of inhibitors that reveals differential activity of proteosomal subunits during bacterial infection. Finally Hugh Pritchard from Kew Gardens is a co-author on a lipidomic study of the seed dessication-stress response.

Meyer HM, Teles J, Formosa-Jordan P, Refahi Y, San-Bento R, Ingram G, Jönsson H, Locke JC, Roeder AH (2017) Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal. Elife.


Open Access

James Locke and Henrik Jonsson (SLCU) are authors on this paper that is led by Adrienne Roeder at Cornell in the USA. The Roeder lab largely focused their research on development of the sepal. The SLCU researchers provided modeling support for this investigation into the critical role of the ATML1 gene in the differentiation of initially identical cells into giant or regular sized sepal cells. They show that there it is a threshold level of differential ATML1 expression that is key in determining cell fate. If this threshold is met during the G2 phase of the cell cycle the cells enter endoreduplication and become giant. If the threshold isn’t reached then the cells divide and remain at a ‘normal’ size. Ultimately they demonstrate a fluctuation-driven patterning mechanism that determines cell fate.

Stegmann M, Monaghan J, Smakowska-Luzan E, Rovenich H, Lehner A, Holton N, Belkhadir Y, Zipfel C (2017) The receptor kinase FER is a RALF-regulated scaffold controlling plant immune signaling Science


Cyril Zipfel (The Sainsbury Lab, Norwich) is the lead author of this study that builds upon his labs work into mechanisms of pathogen perception by cell-surface receptor kinases. In this latest work they show that the SITE-1 PROTEASE (ST1P) cleaves endogenous RAPID ALKALINIZATION FACTOR (RALF) propeptides to inhibit plant immunity, a response mediated via the receptor kinase FERONIA (FER). The FER protein is also involved in the formation of other immune complexes. The authors have discovered a mechanism by which FER reglates RALK signaling, indicating that they might have uncovered a more general mechanism for this key control point of immune signaling.

Misas-Villamil JC,, van der Burgh AM, Grosse-Holz F, Bach-Pages M, Kovács J,, Kaschani F, Schilasky S, Emon AE, Ruben M, Kaiser M, Overkleeft HS, van der Hoorn RA (2017) Subunit-selective proteasome activity profiling uncovers uncoupled proteasome subunit activities during bacterial infections. Plant Journal


Reiner van der Hoorn (University of Oxford) lead this cross-Europe collaboration that introduces a range of inhibitors and probes that can discriminate between catalytic subunits of the proteasome. These tools were studied in both Arabidopsis and Nicotiana benthamiana and the authors used the plant-microbe interactions to further validate their specificity. They show that proteasomal subunits have separate paralogs that are differentiatially incorperated into the larger complex depending on an interaction with pathogenic bacteria. Aliquots of these probes are available on request from

The authors encourage their usage so as to increase the chance that they might become commercially available. More information from the Plant Chemetics lab.

Chen H, Yu X, Zhang X, Yang L, Huang X, Zhang J, Pritchard HW, Li W (2017) Phospholipase Dα1-mediated phosphatidic acid change is a key determinant of desiccation-induced viability loss in seeds. Plant Cell Environ.


Hugh Pritchard (Kew Gardens) is a co-author on this Chinese-led study that investigates the role of phosphatidic acid (PA) on seed viability. Higher levels of PA correlated with lower seed viability after a desiccation stress. Using Arabidopsis seeds they showed that the enzyme phospholipase D α1 (PLD α1) localises to the plasma membrane following desiccation, where it produces PA. When PLD α1 was suppressed, seed recovery following desiccation improved. The authors used comparative lipidomics to compare PA levels in eight plant species and from their Arabidopsis work, they propose a new model for the mechanism by which seed desiccation effects germination rates.

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: March 4th

There are six articles in this weeks Arabidopsis Research Roundup that bridge a diverse range of topics. Firstly lead author Deirdre McLachlan provides an audio description of a study that investigates the role of triacylglycerol breakdown in stomatal signaling. Secondly is a study that assesses the role of a Rab GTPase in control of anisotropic cell growth. The third and fourth papers looks into the defence response, focused on either JA or nitric oxide signaling. Finally are two papers that look into the response of Arabidopsis seedlings to growth on either arsenic or cadmium.

McLachlan DH, Lan J, Geilfus CM, Dodd AN, Larson T, Baker A, Hõrak H, Kollist H, He Z, Graham I, Mickelbart MV, Hetherington AM The Breakdown of Stored Triacylglycerols Is Required during Light-Induced Stomatal Opening Current Biology Open Access
Slide 1
The control of stomatal opening is a key environmental response to changes in CO2 levels and water availability. This study, led by Alistair Hetherington (Bristol), demonstrates that triacylglycerols (TAGs), contained in lipid droplets (LD), are critical for light-induced stomatal opening. Following illumination, the number of LDs are reduced through the β-oxidation pathway, a response that requires blue-light receptors. The authors postulate that a reduction in ATP-availability due to delayed fatty acid breakdown contributed to the stomatal phenotype. The lack of available ATP was confirmed following analysis of the activity of a plasma membrane H+-ATPase. Overall the authors suggest that the light-induced breakdown of TAG contributes to an evolutionarily conserved signaling pathway that controls stomatal opening therefore playing a key role in environmental adaptation.

The lead author of this study, Deidre McLachlan kindly provides a brief audio description of this paper.

During our discussion Deidre mentioned some related work that links blue-light signaling and starch degradation during stomatal opening that was included in a recent ARR.


Kirchhelle C, Chow CM, Foucart C, Neto H, Stierhof YD, Kalde M, Walton C, Fricker M, Smith RS, Jérusalem A, Irani N, Moore I (2016) The Specification of Geometric Edges by a Plant Rab GTPase Is an Essential Cell-Patterning Principle During Organogenesis in Arabidopsis. Developmental Cell 36(4):386-400 Open Access
Ian Moore (Oxford) is the corresponding author on this UK-German collaboration that investigates the role of a Rab GTPase in pattern formation during organogenesis. It is known that the endomembrane system controls the asymmetric distribution of cargoes to different ‘geometric edges’ of a plant cell, establishing biochemically distinct domains that are important for anisotropic growth. This study identifies a new type of membrane vesicle that accumulates specifically along geometric edges and that contains the RAB-A5c protein which, when inhibited, distorts the geometry of cells in subsequently formed lateral organs (in this case, lateral roots). Interestingly this effect is independent of changes to general endomembrane trafficking. The precise mechanism of RAB-A5c activity is unknown but loss of its activity reduces cell wall stiffness at domain-specific locations, therefore perturbing cell growth in those directions. Therefore this study provides interesting insight into fundamental mechanisms that control the growth of cells in a developing organ.

Thatcher LF, Cevik V, Grant M, Zhai B, Jones JD, Manners JM, Kazan K (2016) Characterization of a JAZ7 activation-tagged Arabidopsis mutant with increased susceptibility to the fungal pathogen Fusarium oxysporum J Exp Bot. Open Access

Jonathan Jones (TSL) and Murray Grant (Exeter) are collaborators on this research that investigates the role of jasmonic acid signaling in plant resistance to the fungal pathogen Fusarium oxysporum. In this study they show that the JASMONATE ZIM-domain7 (JAZ7) gene is induced by Fusarium oxysporum and that the jaz7-1D mutant has increased suspectibility to infection. This genotype has constitutive JAZ7 expression and also demonstrates sensitivity to a bacterial pathogen. To cause alterations in gene expression, the JAZ7 protein interacts with a range of transcriptional activators and repressors. The authors postulate that in wildtype plants JAZ7 represses the JA-transcriptional network through its interaction with the co-repressor TOPLESS protein and that in the jaz7-1D plants this response network is hyper-activated leading to an inappropriately high response to pathogen attack.

Yun BW, Skelly MJ, Yin M, Yu M, Mun BG, Lee SU, Hussain A, Spoel SH, Loake GJ (2016) Nitric oxide and S-nitrosoglutathione function additively during plant immunity. New Phytol.

Gary Loake and GARNet Advisory board member Steven Spoel (Edinburgh) are the leaders of this UK-Korean collaboration that studies the role of Nitric Oxide (NO) in the plant defence response. NO often undergoes S-nitrosylation to produce S-nitrosothiol (SNO), which is important for its bioactivity. This reaction involves the S-nitrosoglutathione reductase 1 (GSNOR1) enzyme, which serves to turnover the NO donor, S-nitrosoglutathione (GSNO). In this study the authors investigate mutant plants that accumulate NO and some a reduction in the basal defence response due to a reduction in salicylic acid (SA) signaling. This response was not rescued by the overexpression of GSNOR1 even though this was able to reduce phenotypes resulting from SNO accumulation. Mutant plants that have increased NO accumulation but lower activity of GSNOR1, so therefore an increased ratio of NO:SNO, were more suspectible to growth of bacterial pathogens. The authors conclude that the relationship between NO and GSNO is critically for plant immunity and development.

Lindsay ER, Maathuis FJ (2016) Arabidopsis thaliana NIP7;1 is Involved in Tissue Arsenic Distribution and Tolerance in Response to Arsenate FEBS Lett.

Francois Maathuis (York) is the corresponding author of this study that investigates the role of the Arabidopsis aquaglyceroporin NIP7;1 in the uptake of different chemical forms of arsenic. Mutant nip7;1 plants improved the tolerance of arsenic by reducing uptake of the chemical. This is the first demonstration for the role of a NIP transporter in the response to arsenic and highlights the possibility of focussing on these proteins as a target for breeding or genetically-modifying tolerance to this toxic metal.

Wang H, He L, Song J, Cui W, Zhang Y, Jia C, Francis D, Rogers HJ, Sun L, Tai P, Hui X, Yang Y, Liu W (2016) Cadmium-induced genomic instability in Arabidopsis: Molecular toxicological biomarkers for early diagnosis of cadmium stress Chemosphere 150:258-265

Hilary Rodgers (Cardiff) is the sole UK representative on this Chinese study that has developed screening parameters to evaluate the growth of plants on cadmium. The study uses microsatellite instability (MSI) analysis, random-amplified polymorphic DNA (RAPD), and methylation-sensitive arbitrarily primed PCR (MSAP-PCR) to define a range of genomic alterations that occurred after growth of Arabidopsis plants across a range of concentrations of cadmium. They conclude that analysis of genomic methylation polymorphisms were the most sensitive biomarkers to diagnosis early cadmium stress in these plants and provide important insights for future biomonitoring strategies.

Arabidopsis Research Roundup: December 18th

The final Arabidopsis Research Roundup of 2015 contains a bumper crop of papers that again highlights the diversity of research occuring in UK plant science. Justin Goodrich from the University of Edinburgh kindly provides an audio description of work that identifies a novel role for a member of a transposon gene family. Elsewhere are studies about a specific aspect of the biochemistry of crytochromes as well as confirmation of a role for DNA gyrases in Arabidopsis. Paul Dupree (Cambridge) leads a study into the mechanism of ascorbic acid production while Heather Knight is the UK representative in a study about cell wall composition. We also present an investigation into the mechanism and subsequent expression changes that occur following infection with different isolates of the Turnip Mosaic Potyvirus. Finally are two short studies from Ive de Smet (Nottingham) and Matt Jones (Essex).

Liang SC, Hartwig B, Perera P, Mora-García S, de Leau E, Thornton H, de Alves FL, Rapsilber J, Yang S, James GV, Schneeberger K, Finnegan EJ, Turck F, Goodrich J (2015) Kicking against the PRCs – A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2. PLoS Genet. 11 e1005660. Open Access

Justin Goodrich (Edinburgh) is the lead of this collaborative study between UK, German and Australian researchers that investigates the role of the evolutionarily conserved Polycomb group (PcG) and trithorax group (trxG) genes during plant development. These homeotic genes influence gene expression by causing epigenetic chromatin changes, usually in the form of histone methylation. Previously the ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN1 (ALP1) gene was found to act as a genetic suppressor the Arabidopsis PcG gene, LIKE HETEROCHROMATIN PROTEIN1 (LHP1). In this study ALP1 is shown to genetically interact with members of these two gene families and its activity is necessary for the activation of several floral homeotic genes. Surprisingly the ALP1 gene is shown to encode for a transposase of the PIF/Harbinger class, which is conserved throughout land plants. The authors suspect that the transposase activity has been lost in the angiosperm lineage, where the gene obtained a novel function. Interestingly ALP1 can interact with the core PrC complex, which most notably participates in H3K27me3 methylation and therefore appears to act, along with other proteins such as EMBRYONIC FLOWER 1 (EMF1), as a plant-specific accessory component that controls histone modification. The authors speculate that this novel function might have arisen as a “means for the cognate transposon to evade host surveillance or for the host to exploit features of the transposition machinery beneficial for epigenetic regulation of gene activity”. Over the coming years it will be interesting to discover if other transposon-encoded genes share novel functions and this study represents an important lesson for researchers not to ignore transposon sequences as ‘junk’ DNA that they might feel can clutter up their analysis!

Justin Goodrich kindly provides an audio summary of this paper:

van Wilderen LJ, Silkstone G, Mason M, van Thor JJ, Wilson MT (2015) Kinetic studies on the oxidation of semiquinone and hydroquinone forms of Arabidopsis cryptochrome by molecular oxygen FEBS Open Bio. 5:885-892 Open Access

This study is a collaborative effort between researchers from Imperial College and the University of Essex, led by emeritus biochemistry Professor Michael Wilson and is an in vitro analysis of the oxidation of the Arabidopsis cryptochrome (CRY) photoreceptor in the presence and absence of an external electron donor. They show that a more complex model than previously thought is required to explain the mechanism by which the CRY-associated flavin molecule is oxidised. The authors propose that the final steps in this reaction require cooperative interaction between partners in a CRY homodimer or between separate CRY molecules.

Evans-Roberts KM, Mitchenall LA, Wall MK, Leroux J, Mylne JS, Maxwell A (2015) DNA Gyrase is the Target for the Quinolone Drug Ciprofloxacin in Arabidopsis thaliana. J Biol Chem. Open Access

Antony Maxwell from the Biological Chemistry department from the John Innes Centre is the UK academic lead on this UK-Australian study. This group has previously shown that Arabidopsis contains three proteins thought to function as DNA Gyrases (AtGYRA, ATGYRB1, ATGYRB2) although they could not provide direct evidence that are were involved in DNA supercoiling. This study moves the work on by identifying mutant plants that are resistant to the drug ciprofloxacin and contain a point mutation in AtGYRA. Furthermore ATGYRA heterologously expressed in insect cells has supercoiling activity. Therefore the authors unequivocally show that plants encode an organellar-targeted DNA gyrase that, like bacterial gyrases, is a  target for ciprofloxacin. This work has important consequences for our understanding of plant physiology and in the future development of novel herbicides.

Sawake S, Tajima N, Mortimer JC, Lao J, Ishikawa T, Yu X, Yamanashi Y, Yoshimi Y, Kawai-Yamada M, Dupree P, Tsumuraya Y, Kotake T (2015) KONJAC1 and 2 Are Key Factors for GDP-Mannose Generation and Affect l-Ascorbic Acid and Glucomannan Biosynthesis in Arabidopsis The Plant Cell

Paul Dupree (Cambridge) is the British lead on the UK-Japanese collaboration that investigates the role of the GDP-mannose pyrophosphorylase (GMPP), VITAMIN C DEFECTIVE1 (VTC1) enzyme in catalysis of the rate-limiting step in the production of ascorbic acid (AsA). They identify two novel pyrophosphorylase-like proteins, KONJAC1 (KJC1) and KJC2 that stimulate VTC1. Mutant analysis showed that these proteins are necessary for normal growth that coincides with control of AsA production via stimulating GMPP activity. Yeast 2 Hybrid  analysis is indicative of a direct interactin between KJC and VTC1 proteins. In future, it will be interesting to investigate the role of these proteins in plants that are more relevant to human consumption of AsA.

Sorek N, Szemenyei H, Sorek H, Landers A, Knight H, Bauer S, Wemmer DE, Somerville CR (2015) Identification of MEDIATOR16 as the Arabidopsis COBRA suppressor MONGOOSE1. PNAS

Heather Knight (Durham) is the sole UK representative on this manuscript that is led by the lab of Chris Somerville from the University of California. In this work the authors identified suppressors of the Arabidopsis cobra mutant, which have defects in cellulose formation. The appropriately named mongoose (mon1) mutant partially restored cellulose levels and also restored the esterification ratio of pectin to wild-type levels. MON1 was cloned to the MEDIATOR16 (MED16)/ SENSITIVE TO FREEZING6 (SFR6) locus and single mon1 mutants are resistant to cellulose biosynthesis inhibitors. Concomitantly, transcriptome analysis demonstrated that a set of ‘cell wall’ genes are misregulated in mon1/med16/sfr6, including two encoding pectin methylesterase inhibitors. Overall the authors suggest that cellulose biosynthesis is closely linked to esterification levels of pectin and offer a number of possible explanations for this functional relationship.

Sánchez F, Manrique P, Mansilla C, Lunello P, Wang X, Rodrigo G, López-González S, Jenner C, González-Melendi P, Elena SF, Walsh J, Ponz F (2015) Viral Strain-Specific Differential Alterations in Arabidopsis Developmental Patterns Mol Plant Microbe Interact.

The UK contributor to this Spanish-led study is Carol Jenner, who at the time was a research fellow at the University of Warwick. This study highlights the morphological changes that occur in Arabidopsis plants infected by different isolates of Turnip mosaic virus (TuMW). The UK1 and JPN1 versions of TuMW were shown to have highest levels of sequence divergence in the P3 cistron and following the generation and use of viral chimeras, it is this region that was identified as the major viral determinant of plant developmental changes. However when the P3 gene was constitutively expressed in Arabidopsis it did not cause any development effects, which highlights the importance of performing infection studies in a whole-plant context. Latterly the authors performed transcriptomic and interactomic analysis, showing that infection with the most severe UK1 strain primarily causes changes, perhaps unsurprisingly, in genes involved in transport and in the stress response.

Czyzewicz N, De Smet I (2015) The Arabidopsis thaliana CLAVATA3/EMBRYO-SURROUNDING REGION 26 (CLE26) peptide is able to alter root architecture of Solanum lycopersicum and Brassica napus. Plant Signal Behav

This work was performed in the lab of Ive De Smet, who is a BBSRC research fellow at the University of Nottingham. In this short communication they show that overexpression of the Arabidopsis AtCLE26 peptide is able to induce architectural change in the agriculturally important crops, Brassica napus and Solanum lycopersicum. Having previously shown that AtCLE26 is similarly active in Arabidopsis, Brachypodium and Triticum, these experiments further demonstrate that small peptide signaling plays an important role in root development across plant lineages.

Litthauer S1, Battle MW1, Jones MA (2015) Phototropins do not alter accumulation of evening-phased circadian transcripts under blue light. Plant Signal Behav.

Matt Jones (Essex) leads this accompanying study to the more substantial project previously published in Plant Journal. This manuscript reports that phototropin photoreceptors are not involved in the nuclear accumulation of evening-phased circadian transcripts. In addition they show that even in phototropin mutants, the rhythms of nuclear clock transcript accumulation are maintained under fluctuating light regimes.

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.

Arabidopsis Research Roundup: August 21st.

There are a wide array of topics included in this weeks Arabidopsis Research Roundup, ranging from studies on stomatal density, thylakoid transport, metabolic flux analysis, mutant detection and root development. We feature unlinked studies from three researchers from the University of Oxford Plant Science (Paul Jarvis, Lee Sweetlove and Nick Harberd), whilst the papers from Julie Gray and Brian Forde share the broad theme that investigates different mechanisms that might be used to improve nitrogen uptake, either by modifying the expression of a single gene involved in root development or by altering stomatal density.

Hepworth C, Doheny-Adams T, Hunt L, Cameron DD, Gray JE (2015) Manipulating stomatal density enhances drought tolerance without deleterious effect on nutrient uptake New Phytol.

Julie Gray (University of Sheffield) is an expert on both stomatal biology and on the potential for manipulating stomatal density to improve crop production. In this study drought tolerance and soil water retention were measured in four Arabidopsis mutants with defects in epidermal patterning and stomatal density. Nutrient uptake was measured by mass flow of 15N. Plants with less stomata had reduced transpiration and were drought-tolerant yet interestingly showed little reduction in shoot N concentrations, especially when water availability is restricted. In contrast, plants with extra stomata could take up more N except when access to water was reduced. Therefore the authors show that by altering stomatal density they can generate plants that are drought resistance yet maintain nutrient uptake or generate plants with enhancing nutrient uptake is conditions with plentiful water.

Trösch R, Töpel M, Flores-Pérez Ú, Jarvis P (2015) Genetic and Physical Interaction Studies Reveal Functional Similarities between ALB3 and ALB4 in Arabidopsis. Plant Physiol.

This German, Swedish and UK collaboration is led by Paul Jarvis at the University of Oxford and broadly investigates thylakoid protein targeting. The ALB3 complex has previously been shown to target light harvesting complex proteins (LHCP) to the thylakoid. A related Arabidopsis protein, ALB4, had been proposed to interact not the LHCPs but rather with the ATP synthase complex. However this study shows that ALB3 and ALB4 have some overlapping roles in addition to their specific functions and that they can engage with a similar set of interactor proteins to bring their substrates to the thylakoid membrane.

Cheung CY, Ratcliffe RG, Sweetlove LJ (2015) A method of accounting for enzyme costs in flux balance analysis reveals alternative pathways and metabolite stores in an illuminated Arabidopsis leaf Plant Physiol.

Lee Sweetlove (Oxford University) leads this study that looks at the Flux Balance Analysis (FBA) of plant metabolism across several metabolic pathways by attaching ‘flux weighting factors’ to allow for the variable intrinsic cost of supporting each flux. This model has been applied to the Arabidopsis leaf exposed to different light regimes to explore the flexibility of the network in meeting its metabolic requirements. The authors discover interesting trade-offs between use of different carbon storage forms and in the variable consumption of ATP and NADPH by different metabolic pathways.

Belfield EJ, Brown C, Gan X, Jiang C, Baban D, Mithani A, Mott R, Ragoussis J, Harberd NP (2014) Microarray-based optimization to detect genomic deletion mutations Genom Data Dec;2:53-54

GARNet Advisory Board member Nick Harberd (Oxford University) leads this short communication that highlights the development of a tool for detection of genomic deletion mutants in Arabidopsis. Using a NimbleGen whole genome custom tiling array they successfully identify five mutants with deletion ranging from 4bp to 5kb and therefore introduce a powerful tool for analysing this type of genetic lesion in Arabidopsis and other plant species with well-constructed genomes.

Yu C, Liu Y, Zhang A, Su S, Yan A, Huang L, Ali I, Liu Y, Forde BG, Gan Y (2015) MADS-box Transcription Factor OsMADS25 Regulates Root Development through Affection of Nitrate Accumulation in Rice PLoS One

Brian Forde (Lancaster University) is the UK lead on this Chinese collaboration that focuses on nitrate accumulation and how it regulates root development in rice. This occurs via a MADS-box transcription factor OsMADS25 that, when overexpressed in Arabidopsis, promotes primary and lateral root development. Altered expression of this gene also affects root development in transgenic rice and includes significant changes in nitrate accumulation. Therefore this gene might prove to be an important target for future attempts to improve plant growth in regions with altered nitrate concentrations.

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.

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