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: July 20th

There is a bumper crop of publications in high quality journals in this weeks UK Arabidopsis Research Roundup, including manuscripts in PNAS, Nature Communications, PLoS Genetics , PloS One and Plant Physiology. Malcolm Bennett, Alex Webb and Anthony Hall lead a major collaborative effort that links the circadian clock with lateral root formation whilst Ottoline Leyser (SLCU) and Mike Bevan (JIC) participate in a similarly broad consortium in a study linking organ size and MAPK signaling. Liam Dolan’s group from Oxford looks at mechanisms of tip-growth across the plant kingdoms whilst elsewhere three members of faculty at the University of Birmingham are involved in two papers looking at the regulation of meiosis. Finally there are two US-led studies that include significant contributions from UK-based researchers, including Matthew Jones from the University of Essex.


Voß U, Wilson MH, Kenobi K, Gould PD, Robertson FC, Peer WA, Lucas M, Swarup K, Casimiro I, Holman TJ, Wells DM, Péret B, Goh T, Fukaki H, Hodgman TC, Laplaze L, Halliday KJ, Ljung K, Murphy AS, Hall AJ, Webb AA, Bennett MJ (2015) The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana Nature Communication 6:7641.

Once again Malcolm Bennett (CPIB) leads a multi-Institute collaboration that includes Alex Webb (Cambridge) and current GARNet board member Anthony Hall (Liverpool). This is also an extremely international effect with groups from the UK, USA, Sweden, Japan, Spain and France. The science looks at lateral root stems cells and how the circadian clock is rephased during LR emergence. They show that the clock controls auxin levels and auxin-related genes. The conclusion is that the circadian clock acts to gate auxin signalling during LR development to facilitate organ emergence and adds to a growing portfolio of evidence that suggest the circadian clock might act in a cell autonomous manner. Anthony Hall, James Locke and Peter Gould currently have a grant that is looking at this phenomenon in Arabidopsis root cells.


Johnson KL, Ramm S, Kappel C, Ward S, Leyser O, Sakamoto T, Kurata T, Bevan MW, Lenhard M (2015) The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis PLoS One.10(7):e0131103.

Ottoline Leyser, Sally Ward (Sainsbury lab, Cambridge) and Mike Bevan (JIC) are the UK contributors to this joint UK-German-Japanese-Australian collaboration. This study follows a screen for plants with reduced organ size and introduces a novel allele of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5), named Tinkerbell (tink). This mutation reveals that IBR5 is a novel regulator of organ size by changing the growth rate in petals and leaves although this occurs independent of the previously characterised KLU pathway. The authors use microarray data to suggest an additional role for TINK/IBR5 during male gametophyte development. Ultimately they conclude that IBR5 might influence organ size through auxin and TCP growth regulatory pathways.


Tam TH, Catarino B, Dolan L (2015) Conserved regulatory mechanism controls the development of cells with rooting functions in land plants Proc Natl Acad Sci U S A.

Liam Dolan’s lab at the University of Oxford is a world leader in the study of root hair development. Previously it has been shown the group XI basic helix-loop-helix (bHLH) transcription factor (LOTUS JAPONICUS ROOTHAIRLESS1-LIKE (LRL) regulates root hair growth in Arabidopsis, Lotus or rice. This study investigates the equivalent proteins in the moss Phycomitrella patens and show that they are involved in an auxin signaling pathway that promotes cell outgrowth albeit via a different set of signaling intermediates. Overall the authors show that a core auxin network that supports cellular ‘tip-growth’ exists throughout land plant lineages even though the specificity of this signaling has diverged over the course of the ~420million years that separates angiosperms and mosses.


Varas J, Sánchez-Morán E, Copenhaver GP, Santos JL, Pradillo M (2015) Analysis of the Relationships between DNA Double-Strand Breaks, Synaptonemal Complex and Crossovers Using the Atfas1-4 Mutant. PLoS Genet.11(7): e1005301.

The work led by Monica Pradillo at the University of Madrid includes a contribution from Eugenio Sanchez-Moran from the University of Birmingham. This work focuses on the hetero-trimeric Chromatin Assembly Factor 1 (CAF-1), which is a histone chaperone that assembles acetylated histones H3/H4 onto newly synthesized DNA. In Arabidopsis the CAF1 complex is composed of the FAS1, FAS2 and MSI1 proteins. Atfas1 mutant plants are less fertility, have a higher number of double stranded breaks (DSB) and show a higher gene conversion frequency. The authors investigate how DSBs can influence meiotic recombination and synaptonemal complex (SC) formation by genetic analysis of Atfas1-containing double mutants. Ultimately their experiments provide new insights into the relationships between different recombinase proteins in Arabidopsis. Overall an increase in the number of DSBs does not translate to an increase in the number of crossovers (COs) but instead in a higher GC frequency. The authors provide different theories to explain this mechanism, including the possible existence of CO homeostasis in plants.


Lambing C, Osman K, Nuntasoontorn K, West A, Higgins JD, Copenhaver GP, Yang J, Armstrong SJ, Mechtler K, Roitinger E, Franklin FC (2015) Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers PLoS Genetics 11(7):e1005372

The University of Birmingham is the lead Instiution in this study that also investigates regulation of meiosis. The groups of Chris Franklin and Sue Armstrong collaborate with US and Austrian partners to study the organization of meiotic chromosomes during prophase I. Using structured illumination microscopy (SIM) they show that dynamic changes in chromosome axis is coincident with synaptonemal complex (SC) formation and depletion of the ASY1 protein, which requires the function of the PCH2 ATPase. Using a pch2 mutant the authors are able to tease apart different aspects of ‘crossover’ (CO) biology and that the pch2 defect occurs precisely during CO maturation, not during designation. In addition, CO distribution is also affected in some chromosome regions showing that failure to deplete ASY1 can result in downstream events that include disruption of CO patterning.


Jones MA, Hu W, Litthauer S, Lagarias JC, Harmer S (2015) A Constitutively Active Allele of Phytochrome B Maintains Circadian Robustness in the Absence of Light Plant Physiology.

Matthew Jones (University of Essex) is the primary author of this work that comes from a collaboration from his time in the lab of Stacey Harmer in UC Davis. Since 2012 Matthew has been a lecturer at the University of Essex where he continues with work of this nature. In this study they introduce a constitutively active allele of the PHYB photoreceptor that is able to phenoopy red-light input into the circadian clock. In these mutants the pace of the clock is insensitive to light-intensity and this response is dependant on its PHYB nuclear localisation. Finally they show that fine tuning of PHYB signalling requires PHYC and overall they conclude that nuclear phytocrome signalling is necessary for sustaining clock function under red light.


Chakravorty D, Gookin TE, Milner M, Yu Y, Assmann SM (2015) Extra-Large G proteins (XLGs) expand the repertoire of subunits in Arabidopsis heterotrimeric G protein signalling Plant Physiol.

Sally Assman from Penn State University leads this study that includes a contribution from Matthew Milner who now works at NIAB. The number of proposed G protein subunits is greatly reduced in diploid plant genomes yet this study shows that a family of Arabidopsis GPA-related proteins (XLG1-3) can increase the repertoire of potential G proteins interactions by interacting with beta and gamma subunits. The authors propose they have uncovered a new plant-specific paradigm in cell signaling.

Arabidopsis Research Roundup: June 10th.

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

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

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

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

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

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

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

Taken from wikipedia.
Taken from wikipedia.






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

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

Arabidopsis Research Roundup: May 27th

This weeks Arabidopsis Research Roundup sees a small number of high quality publications driven by UK-based researchers together with a couple of collaborative efforts that highlight the international aspect of research. Topics include two greatly different descriptions of how a plant responds to attack, an investigation into the intersection of vesicle and potassium transport as well as descriptions of auxin and sugar signaling.

Sarris PF, Duxbury Z, Huh SU, Ma Y, Segonzac C, Sklenar J, Derbyshire P, Cevik V, Rallapalli G, Saucet SB, Wirthmueller L, Menke FL, Sohn KH, Jones JD (2015) A Plant Immune Receptor Detects Pathogen Effectors that Target WRKY Transcription Factors. Cell 161, p1089-1100

Jonathan Jones at the Sainsbury lab collaborated with his ex-PhD student Kee Hoon Sohn (now at Massey University in NZ) to produce this high profile publication in Cell. Professor Jones’s group has been in the vanguard of research into the response to bacterial pathogens and this paper adds a further layer of understanding as they show that the plant uses a bacteria’s own ‘attack mechanism’ against itself. Many bacterial effector proteins target WRKY DNA-binding protein domains in order to interfere with transcription. This work shows that the plant defence factor RRS1 also contains a WRKY domain, enabling it to ‘sense’ when the bacteria is in the cell and act as a decoy that makes the bacteria subsequently open to attack.


Jaouannet M, Morris JA, Hedley PE, Bos JI (2015) Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance. PLos Pathogens 11: e1004918.

The group of Jorunn Bos at the James Hutton Institute in Dundee looked at a different aspect of the defence response whereby they investigated transcriptional responses to aphid predation on Arabidopsis. Host and non-host responses to aphids show a high degree of overlap in expression but interestingly the host response included repressive of genes involved in metabolism and oxidative response. This type of study will pave the way for the future development of aphid control strategies in crop plants and once again highlights the utility of Arabidopsis as a model system.


Zhang B, Karnik R, Wang Y, Wallmeroth N, Blatt MR, Grefen C (2015) The Arabidopsis R-SNARE VAMP721 Interacts with KAT1 and KC1 K+ Channels to Moderate K+ Current at the Plasma Membrane Plant Cell [Epub]

Control of potassium channels is the focus of this work from Mike Blatt’s lab at the University of Glasgow. They identify a subset of SNARE proteins (that are involved in vesicle trafficing) that control K+ channels, albeit in an unconventional manner. The vesicle-associated membrane proteins 721 (VAMP721) is able to target vesicles as well as supressing the actitivty of the K+ channels KAT1 and KC. This leads to a model whereby different subsets of SNARE proteins opposingly effect K+ channel activity alongside having an effect on vesicular transport.


Panoli A, Martin MV, Alandete-Saez M, Simon M, Neff C, Swarup R, Bellido A, Yuan L, Pagnussat GC, Sundaresan V. (2015) Auxin Import and Local Auxin Biosynthesis Are Required for Mitotic Divisions, Cell Expansion and Cell Specification during Female Gametophyte Development in Arabidopsis thaliana. PLoS One. 10:e0126164.

The primary interest of Ranjan Swarup’s group at the University of Nottingham is in hormone signalling and root development yet he is included as a collaborator in this publication led from UC-Davies that focusses on auxin signalling during female gametophyte development. The paper shows that the YUCCA family of the auxin biosynthetic genes are asymmetrically expressed during embryo sac development and that the AUX1 and LAX1 auxin influx carriers are expressed only at both the micropylar pole of the embryo sac and in adjacent cells of the ovule. In addition aux1lax1lax2 triple mutants show numerous gametophytic developmental defects.  Given the importance of auxin in most aspects of plant development, this paper highlights the specific manner in which auxin is required for mitotic divisions, cell expansion and patterning during embryo sac development.


Zheng L, Shang L, Chen X, Zhang L, Xia Y, Smith C, Bevan MW, Li Y, Jing HC (2015) TANG, Encoding a Symplekin_C Domain-contained Protein, Influences Sugar Responses in Arabidopsis Plant Physiol [Epub]

Mike Bevan at the JIC is a collaborator on this Chinese driven project that investigates Arabidopsis tang1 mutants. These plants are hypersensitive to sugar amd following a classic map-based cloning approach, the TANG1 gene was found to encode a novel protein with a predicted Symplekin tight junction protein C-terminal. As TANG1 is ubquitiously expressed and has little effect on known sugar signalling pathways, the precise in vivo role of the protein remains somewhat opaque even though it is clearly an important player in the response to sugar in Arabidopsis.

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