Andrew Millar talks Open Data at GARNet2018

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Published on: October 2, 2018

Andrew Millar (University of Edinburgh) speaks at the GARNet2018 conference about ‘Being more Open by being more Productive’

GARNet Arabidopsis Roundup: September 13th

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Published on: September 13, 2018

The latest GARNet Research Roundup includes two papers led by Cyril Zipfel from The Sainsbury lab, Norwich (who has since moved his lab to the University of Zurich). The first paper demonstrates the potential for cross-species strategies for developing disease resistance whilst the second is a phosphoproteomic dissection of the BAK1 immune co-receptor. Third is work from the lab of Liam Dolan (University of Oxford) that has discovered a novel type of regulation for RSL Class I bHLH transcription factors in Marchantia. Finally is research from Paul Dupree’s lab in Cambridge that investigates the structure of galactoglucomannan polysaccharides in the Arabidopsis cell wall.

Pfeilmeier S, George J, Morel A, Roy S, Smoker M, Stransfeld L, Downie JA, Peeters N, Malone JG, Zipfel C (2018) Expression of the Arabidopsis thaliana immune receptor EFR in Medicago truncatula reduces infection by a root pathogenic bacterium, but not nitrogen-fixing rhizobial symbiosis. Plant Biotechnol J. doi: 10.1111/pbi.12999

Open Access

Sebastian Pfeilmeier and Jeoffrey George lead this work from the labs of Jacob Malone and Cyril Zipfel at the John Innes Centre and the Sainsbury lab, Norwich. In this study they have expressed the Arabidopsis PRR ELONGATION FACTOR-THERMO UNSTABLE RECEPTOR (EFR) immune reception in Medicago truncatula. They show that these transgenic plants remain able to form root nodules with the bacterial symbiont Sinorhizobium meliloti. However they are resistant to the bacterial pathogen Ralstonia solanacearum. This study shows the potential of cross-species approaches to develop broad-spectrum pathogen resistance. It will be interesting to learn more about future developments in this area.

Perraki A, DeFalco TA, Derbyshire P, Avila J, Séré D, Sklenar J, Qi X, Stransfeld L, Schwessinger B, Kadota Y, Macho AP, Jiang S, Couto D, Torii KU, Menke FLH, Zipfel C (2018) Phosphocode-dependent functional dichotomy of a common co-receptor in plant signalling. Nature doi: 10.1038/s41586-018-0471-x

This second study from the lab of Cyril Zipfel is led by Artemis Perraki and includes wide range of collaborators from across the globe. They have used phosphoproteomics and targeted mutagenesis to perform a detailed characterisation of the immune co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1). This protein interacts with many leucine-rich repeat receptor kinases (LRR-RKs) yet they find that specific phosphosites discriminate between subsets of BAK1 functions that are linked to hormone or immune signaling. This study reveals new complexity in the regulation of this multi-facted protein and has broad importance regarding our understanding of how the phosphocode allows separation of the different signaling outputs.

Honkanen S, Thamm A, Arteaga-Vazquez MA, Dolan L (2018) Negative regulation of conserved RSL class I bHLH transcription factors evolved independently among land plants. Elife. doi: 10.7554/eLife.38529

Open Access

This study looks at the role of RSL class I basic helix-loop-helix transcription factors in the control of development in the lower plant Marchantia polymorpha. This work is led by Suvi Honkanen from Liam Dolan’s lab at the University of Oxford. In Arabidopsis RSL genes are negatively regulated by the GLABRA transcription factor yet in this study the authors identify a novel microRNA-based regulatory mechanism. Although RSL1 class I genes are evolutionarily conserved across land plants the miRNA regulatory module is only present in Marchantia, demonstrating that conserved genes can have divergent modes of regulation to control lineage-specific developmental requirements

Yu L, Lyczakowski JJ, Pereira CS, Kotake T, Yu X, Li A, Mogelsvang S, Skaf MS, Dupree P (2018) The patterned structure of galactoglucomannan suggests it may bind to cellulose in seed mucilage. Plant Physiol. doi: 10.1104/pp.18.00709

Open Access
This work is led by Li Yu from the lab of Paul Dupree at the University of Cambridge. They have investigated the detailed structure of mannose-based (mannan) polysaccharides within the Arabidopsis cell wall. These have previously been shown to be important in maintaining seed mucilage architecture, which has a glucose-mannose (glucomannan) backbone. The authors assess the contribution of the Cellulose Synthase-Like A2 (CSLA2) and Mannan α-Galactosyl Transferase 1 (MAGT1) enzymes in the construction and decoration of a galactoglucomannan backbone and provide data for molecular stimulations to predict as to how these might interact with cellulose microfibrils.

GARNet talks to Ari Sadanandom

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Published on: September 4, 2018

GARNet talked to Professor Ari Sadanandom from Durham University about a recent paper published in The Plant Cell entitled ‘SUMO Suppresses the Activity of the Jasmonic Acid Receptor CORONATINE INSENSITIVE 1

GARNet Research Roundup: August 22nd

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Published on: August 22, 2018

This week’s GARNet research roundup highlights outstanding science from across the UK. First are a group of three papers led by researchers in Cambridge and Bristol that investigate the role of either sugar or calcium signaling on control of the plant circadian clock. Secondly is work from Durham that provides an elegant link between SUMOylation and the jasmonate-responsive arm of the defence response. The biotrophic arm of defence signaling is the focus of the next paper from University of Nottingham that investigates the role of the N-end rule pathway in that response. Finally is a paper from the John Innes Centre that identifies a key determinant of planar cell polarity across the Arabidopsis leaf.

Frank A, Matiolli CC, Viana AJC, Hearn TJ, Kusakina J, Belbin FE, Wells Newman D, Yochikawa A, Cano-Ramirez DL, Chembath A, Cragg-Barber K, Haydon MJ, Hotta CT, Vincentz M, Webb AAR, Dodd AN (2018) Circadian Entrainment in Arabidopsis by the Sugar-Responsive Transcription Factor bZIP63. Current Biol. doi: 10.1016/j.cub.2018.05.092

Open Access

This research comes from the labs of Anthony Dodd (University of Bristol) and Alex Webb (University of Cambridge) and is led equally by Alexander Frank, Cleverson Matioli, Americo Viana, Timothy Hearn and Jelena Kusakina. They investigate how the Arabidopsis circadian clock is entrained to respond to changing metabolic rhythms, measured by assessing sugar signaling. The molecular factors that control changes in the circadian oscillator were previously unknown but they show that the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) is required to alter expression of the oscillator gene PSEUDO RESPONSE REGULATOR7 (PRR7). They also show that the SnRK1 sugar sensing kinase and TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) gene are required for sugar-mediated circadian adjustment. This study provides important information about additional layers of regulation controlling the relationship between the circadian clock and plant metabolism.

Martí Ruiz MC, Hubbard KE, Gardner MJ, Jung HJ, Aubry S, Hotta CT, Mohd-Noh NI, Robertson FC, Hearn TJ, Tsai YC, Dodd AN, Hannah M, Carré IA, Davies JM, Braam J, Webb AAR (2018) Circadian oscillations of cytosolic free calcium regulate the Arabidopsis circadian clock. Nat Plants. 2018 Aug 20. doi: 10.1038/s41477-018-0224-8

This second paper from the labs of Alex Webb and Anthony Dodd also features work from Isabelle Carre’s and Julia Davis’s lab in Warwick and Cambridge respectively. This work led by María Carmen Martí Ruiz, Katharine Hubbard and Michael J. Gardner looks at the how oscillations of cytoplasmic calcium influence the central circadian clock. They show that calcium influences the clock through the activity of the CALMODULIN-LIKE24 (CML24) gene and further genetic analysis links these activities through the action of the central clock gene TIMING OF CAB2 EXPRESSION1 (TOC1). This paper is also a clear lesson in persistence as it was first received by Nature Plants back in May 2016.

Ohara T, Hearn TJ, Webb AAR, Satake A. Gene regulatory network models in response to sugars in the plant circadian system. J Theor Biol. doi: 10.1016/j.jtbi.2018.08.020

The research includes members of Alex Webb’s group and develops a theoretical model to predict the response of the gene regulatory network that links the circadian clock to metabolic signals. This model predicts that the targets of sugar signaling could be both members of the PSEUDO-RESPONSE REGULATOR gene family as well as evening complex components. These findings are experimental confirmed in the paper by Frank et al in this edition of the GARNet response roundup.

Srivastava AK, Orosa B, Singh P, Cummins I, Walsh C, Zhang C, Grant M, Roberts MR, Anand GS, Fitches E, Sadanandom A (2018) SUMO Suppresses the Activity of the Jasmonic Acid Receptor CORONATINE INSENSITIVE 1. Plant Cell. doi: 10.1105/tpc.18.00036

Open Access

Lead author on this paper from the labs of Elaine Fitches and Ari Sadanandom at the Unversity of Durham is Anjil Kumar Srivastava and includes co-authors from Lancaster University. In the study they reveal a feedback loop between the jasmonic acid receptor CORONATINE INSENSITIVE 1 (COI1) and its targets for degradation; the JASMONATE ZIM (JAZ) domain-containing repressor proteins. The authors show that SUMOylated JAZ proteins inhibit the COI1-dependent degradation of non-SUMOylated JAZ proteins. In addition they identify a SUMO-responsive element within the COI1 protein and that necrotrophic bacteria specifically target SUMO protease in order to modulate JA-responsive defense responses.

Vicente J, Mendiondo GM, Pauwels J, Pastor V, Izquierdo Y, Naumann C, Movahedi M, Rooney D, Gibbs DJ, Smart K, Bachmair A, Gray JE, Dissmeyer N, Castresana C, Ray RV, Gevaert K, Holdsworth MJ (2018) Distinct branches of the N-end rule pathway modulate the plant immune response. New Phytol. doi: 10.1111/nph.15387

Open Access
Jorge Vicente leads this work from the lab of Mike Holdsworth in Nottingham that includes collaborators from Belgium, Spain, Germany and Austria. They investigate the role of the N-end rule degradation pathway in the plant immune response. Indeed they show that portions of this response mediated by the E3 ligase PROTEOLYSIS (PRT)6 are important for expression of a specific set of defense-related genes and basal resistance to a biotropic pathogen. They also show this response is also important in the monocot barley where plants with reduced expression of HvPRT6 have enhanced resistance to different pathogens.

Mansfield C, Newman JL, Olsson TSG, Hartley M, Chan J, Coen E (2018) Ectopic BASL Reveals Tissue Cell Polarity throughout Leaf Development in Arabidopsis thaliana. Curr Biol. doi: 10.1016/j.cub.2018.06.019

Open Access
Catherine Mansfield leads this study from the lab of Enrico Coen at the John Innes Centre that investigates the factors that control cell polarity during leaf development. They show that BASL (BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE) is essential for establishment an organ-wide polarity field across the Arabidopsis leaf. They show this polarity field is aligned with the proximodistal axis of the leaf (base to tip) and is independent of stomatal patterning. Like in animals this demonstrates that planar plant organs have a tissue-wide cell polarity field that might be critical for guiding growth and differentiation.

GARNet Research Roundup: August 10th 2018

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Published on: August 10, 2018

There are three papers in this week’s GARNet research roundup. The first paper is led by Jill Harrison’s lab in Bristol and she also provides an audio description of this work that has characterised a role for CLAVATA genes in the transition from 2D to 3D plant growth. The second paper from Ian Graham’s lab in York introduces the role of the MOTHER-OF-FT-AND-TFL1 gene during seed germination whilst the final paper includes co-authors from SLCU and Nottingham and has identified the RALF34 protein as a novel ligand that influences cell wall growth.

Whitewoods CD, Cammarata J, Nemec Venza Z, Sang S, Crook AD, Aoyama T, Wang XY, Waller M, Kamisugi Y, Cuming AC, Szövényi P, Nimchuk ZL, Roeder AHK, Scanlon MJ, Harrison CJ (2018) CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants. Curr Biol. doi: 10.1016/j.cub.2018.05.068

Open Access

Chris Whitewoods and Joe Cammarata are co-first authors in this UK-US-Japan collaboration that is led by GARNet committee member Jill Harrison from the University of Bristol. They have investigated the expression and function of CLAVATA genes during moss development with particular focus on the transition from 2D to 3D growth, showing that these genes are essential for gametophyte development. By showing the presence or absence of CLAVATA genes in different lower plant species they demonstrate that they are important for the transition between different modes of growth.

Jill talks about this work on the GARNet YouTube channel and podcast.

Vaistij FE, Barros-Galvão T, Cole AF, Gilday AD, He Z, Li Y, Harvey D, Larson TR, Graham IA (2018) MOTHER-OF-FT-AND-TFL1 represses seed germination under far-red light by modulating phytohormone responses in Arabidopsis thaliana. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1806460115

Open Access

Fabian Vaistij is the first author on this paper from the lab of Ian Graham at the University of York that investigates the role of the MOTHER-OF-FT-AND-TFL1 (MFT) in the control of seed germination in Arabidopsis. They show that MFT is upregulated by far red light via the previously characterised PIF1/SOM/ABI5/DELLA pathway whilst repressed by red light through the action of the SPATULA (SPT) transcription factor. The activity of MFT alters levels of ABA and GA that ultimately delay germination in conditions with higher levels of FR light.

Gonneau M, Desprez T, Martin M, Doblas VG, Bacete L, Miart F, Sormani R, Hématy K, Renou J, Landrein B, Murphy E, Van De Cotte B, Vernhettes S, De Smet I, Höfte H (2018) Receptor Kinase THESEUS1 Is a Rapid Alkalinization Factor 34 Receptor in Arabidopsis. Curr Biol. doi: 10.1016/j.cub.2018.05.075
This French-led study that has Martine Gonneau and Thierry Desprez as co-lead authors includes Benoit Landrien (SLCU, Cambridge) and Evan Murphy (University of Nottingham) as co-authors. This research adds further detail to a signaling network that coordinates cell wall growth following different stimuli. They show that the rapid peptide alkalinization factor 34 (RALF34) is the ligand for the previously characterized THESEUS1 receptor kinase and that the activity of this signaling module is dependent on FERONIA, which is another RALF receptor.

Jill Harrison talks to GARNet

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Published on: August 6, 2018

Jill Harrison discusses a recent Current Biology paper entitled ‘CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants

GARNet Research Roundup: July 27th

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Published on: July 26, 2018

This GARNet research roundup includes papers that feature a number of different research areas. Firstly is work from Glasgow that investigates the photoactivation of the UVR8 light receptor. Second is work from the University of Cambridge that links the activity of the BIG protein to the circadian oscillator. The next paper has co-authors from Cambridge and looks at promotor sequences needed for expression in bundle sheath cells. The fourth paper from the University of Leeds documents an important role for peroxisomes in the drought response whilst the final manuscript includes co-authors from the University of Birmingham and looks at the role of the ASYNAPTIC4 protein during meiosis.!divAbstract

Díaz-Ramos LA, O’Hara A, Kanagarajan S, Farkas D, Strid Å, Jenkins GI. Difference in the action spectra for UVR8 monomerisation and HY5 transcript accumulation in Arabidopsis (2018) Photochem Photobiol Sci. doi: 10.1039/c8pp00138c

Open Access

Aranzazu Díaz-Ramos and Andrew O’Hara are co-first authors on this research from the University of Glasgow that investigates the activation of photomorphogenic responses by the UVR8 photoreceptor. They show that two distinct UVR8 responses, either the monomerisation of UVR homodimers or accumulation of HY5 responsive transcripts, occurs at different wavelengths.

Hearn TJ, Marti MC, Abdul-Awal SM, Wimalasekera R, Stanton CR, Haydon MJ, Theodoulou FL, Hannah MA, Webb AA (2018) BIG regulates dynamic adjustment of circadian period in Arabidopsis thaliana. Plant Physiology pp.00571.2018. doi: 10.1104/pp.18.00571

Open Access

Timothy Hearn works with Alex Webb at the University of Cambridge and in this paper characterises how the multi-functional BIG protein impacts the circadian clock. This gene was isolated in a forward genetics screen to identify signaling components that alter the response to nicotinamide, which acts as a brake on the circadian oscillator. This finding allows the authors to better understand how altering the circadian oscillator can affect appropriate phasing during different environmental conditions.

Kirschner S, Woodfield H, Prusko K, Koczor M, Gowik U, Hibberd JM, Westhoff P. Expression of SULTR2;2 in the Arabidopsis bundle sheath and vein cells is mediated by a positive regulator. J Exp Bot. 2018 Jul 19. doi: 10.1093/jxb/ery263

Open Access

Sandra Kirschner is first author on this German-led study that includes Helen Woodfield (now Cardiff University) and Julian Hibberd (University of Cambridge). They are interested in the mechanisms that restrict gene expression to bundle sheath cells in C3 plants with a longer view of understanding the biology of these cells in C4 plants. They analyse the vascular-restricted SULTR2;2 promotor and identified a short region that is necessary for its expression pattern. Importantly they show that this sequence is evolutionarily conserved across Brassicaceae and a distantly related C4 plant.

Ebeed HT, Stevenson S, Cuming AC, Baker A. Conserved and differential transcriptional responses of peroxisome associated pathways to drought, dehydration and ABA. J Exp Bot. 2018 Jul 19. doi: 10.1093/jxb/ery266

Open Access

Heba Ebeed is the lead author of this work conducted in Alison Baker’s lab at the University of Leeds. They take a comparative genomics approach to investigate the expression of peroxisome-localised genes in a moss (physcomitrella), monocot (wheat) and a dicot (arabidopsis). They show that members of three gene families are upregulated in each of these organisms following drought stress, demonstrating the importance of peroxisomes in this environmental response throughout plant evolution.

Chambon A, West A, Vezon D, Horlow C, De Muyt A, Chelysheva L, Ronceret A, Darbyshire AR, Osman K, Heckmann S, Franklin FCH, Grelon M (2018) Identification of ASYNAPTIC4, a component of the meiotic chromosome axis. Plant Physiol. pii: pp.01725.2017. doi: 10.1104/pp.17.01725

Chris Franklin and Alice Darbyshire from the University of Birmingham are co-authors on this French-led study that looks into the role of the ASYNAPTIC4 (ASY4) protein in the control of synapsis formation during meiosis. Plants without ASY4 activity have defective chromosomal axis formation and cannot undergo synapsis. Although the initiation of recombination is unaffected in asy4 mutants, later processes are altered, demonstrating the key role for ASY4 during meiosis

ECJ ruling on GE crops: A disappointing verdict

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Published on: July 25, 2018

The European Court GMO directive, published in 2001, makes it extremely challenging to have genetically modified (GM) crops approved for growth in EU member countries. The financial and time-costs required to develop these crop varieties mean that only one such crop, an insect resistant GM maize, is grown in small amounts in Spain. There is little doubt that the GMO Directive has stalled academic innovation and reduced external investment in crop breeding technology in the EU. Although opponents of the technology are pleased by the absence of Monsanto et al’s EU investment, the broader implication is that there is little use of this technology to generate crops that are resistant to biotic and abiotic stress or have improved nutritional qualities.

Over the past few years many parties have been awaiting a ruling from the European Court of Justice on the use of new breeding technologies, such as CRISPR-Cas9 gene editing, in the future development of crops. The case was brought to the ECJ by Confédération paysanne, which is a French agricultural union, who wanted a judgment on the use of crops generated by mutagenesis techniques.

Over a long period mutagenesis techniques have been used in conventional breeding to introduce 1000s of mutations into crop genomes in the hope of finding a beneficial alteration. However this ECJ case is really concerned with the use of gene editing technology, which has the ability to make precise targeted mutations in order to change gene function and subsequently plant phenotypes. Unlike with traditional GM, plants generated by gene editing techniques do not contain any trace of foreign genetic information, therefore leaving a crop that is indistinguishable from those generated by conventional mutagenesis. Importantly a GE crop can just have a single precise mutation whereas crops generated by conventional mutagenesis can have 1000s of unknown and uncharacterised mutations.

Plant scientists have been cautiously awaiting a positive verdict in this case after non-binding advice given in January by Michale Bobek the Advocate General that GE-induced mutagenesis should not be considered differently from conventional mutagenesis. This is also the opinion of US regulators who have set a much lower bar for approval of non-transgenic GE crops rather than GM crops.

However today (July 25th) the ECJ has disappointed both plant scientists and science advocates with a ruling (PDF) indicating that mutagenesis of all types should fall under the rulings of the GMO directive. This goes further than anyone might have imaged as it suggests that even crops produced by conventional mutagenesis might be prevented from being grown across the continent.

However the ECJ draws back from a blanket ban of all mutagenesised crops as they state:

‘however, that it is apparent from the GMO Directive that it does not apply to organisms obtained by means of certain mutagenesis techniques, namely those which have conventionally been used in a number of applications and have a long safety record.

Therefore this ruling specifically targets mutagenesis by…‘techniques that have emerged since its adoption [the GMO directive]’… meaning CRISPR-Cas9 and related gene editing techniques.

Furthermore the court considers that

‘…the risks linked to the use of these new mutagenesis techniques might prove to be similar to those that result from the production and release of a GMO through transgenesis’.

This is ironic as there is a deep bank of evidence indicating that the risk posed by conventional GM crops is essentially zero, so the risk of GE crops could be similarly defined.

Unfortunately the GMO directive was written to respect the precautionary principle and has no consideration for this evidence. Therefore the reading of this statement sadly must be that GE crops pose some as yet unidentified danger to consumers and the environment.

Another unintentionally ironic statement from the ECJ ruling states…

‘and those new techniques make it possible to produce genetically modified varieties at a rate out of all proportion to those resulting from the application of conventional methods of mutagenesis’.

Yes this is true but not as the statement intended.

Indeed the use of GE technology will allow the generation of new crops much more rapidly than with conventional breeding. However the irony comes from the extremely targeted nature of GE technology as opposed to the 1000s of random mutations that are generated by conventional techniques.

For some unstated reason the ECJ considers that the rapid generation of new crop varieties is a negative consequence of this new technology even though there is no suggestion that any new varieties would not go through appropriate levels of regulation.

So what will be the effect of this ruling?

Unfortunately it will be a case of ‘as you were’ for both academics and biotech companies. Preparatory research will be conducted in growth rooms and glasshouses but at that stage there will be a blockage in what will be possible with any GE crop varieties. The UK government recently approved a field trial of both GM and GE crops but this is just an experimental plot with no suggestion that it is for general release.

Therefore the situation will remain the same with new advantageous crop varieties having nowhere to go in the EU after small field trials are concluded.

This blockage will undoubtedly stall scientific innovation in the EU as there will be little incentive for long-term investment if new crops varieties aren’t able to be used either for altruistic or financial gain. Innovation will continue in universities across Europe but any financial benefits will be gained by companies in the USA or elsewhere.

It’s a sad day for science, technology and evidence-based policy making across Europe.

With Brexit looming on the horizon is this a policy area in which the UK could set itself apart from the remainder of the EU?

Only time will tell but even if the UK does develop a more permissive regulatory environment, challenges will remain when moving GE-crops across EU borders.

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