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

https://onlinelibrary.wiley.com/doi/abs/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

https://elifesciences.org/articles/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.

http://www.plantphysiol.org/content/early/2018/09/05/pp.18.00709.long

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

https://www.sciencedirect.com/science/article/pii/S0960982218307620

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

www.plantcell.org/content/early/2018/08/16/tpc.18.00036.long

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.

https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15387

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.

https://www.cell.com/current-biology/fulltext/S0960-9822(18)30810-8?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982218308108%3Fshowall%3Dtrue

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.


http://pubs.rsc.org/en/Content/ArticleLanding/2018/PP/C8PP00138C#!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.

https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/ery263/5056055

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.

GARNet Research Roundup: July 16th

This week’s GARNet research roundup begins with a set of papers looking at aspects of the plant defence response with a focus on the cell wall. Firstly work from Mike Deeks’ lab in Exeter assesses the role of FORMIN4 during pre-invasion cell wall apposition. Secondly Sara Pose and Paul Knox (Leeds) are involved with a study looking at how altered cell wall lignin composition alters the defense response. Finally Joe McKenna and Cyril Zipfel are co-authors on a Norwegian-led study that looks at the influence of plant cell wall integrity maintenance in immune signalling.

Relatedly is a study from the Devoto lab at RHUL looks at the role of the defence hormone methyl jasmonate in Arabidopsis cell culture.

Next are two papers that research different aspects of the plant ER. Verena Kriechbaumer (Oxford Brookes) looks at plant ER-localised Lunapark proteins whilst a study from the University of Warwick provides a preliminary structural analysis of the RTNLB13 reticulon protein.

The seventh and eight papers are involved with the plant response to different growth conditions. Research from University of Nottingham looks at the response of the cortical cell layer of the root meristem to low phosphate conditions whilst work from University of Southampton investigates the relationship between nitrate and copper signaling.

The next paper is from Emily Flashman’s lab at the University of Oxford and looks at the role of plant cysteine oxidases as oxygen sensors whilst the tenth paper features John Doonan (Aberystwyth University) as a co-author and investigates how a histone acetyltransferase affects trichome development.

Finally is a paper from Pierre Baudal and Kirsten Bomblies (John Innes Centre) that uses Arabidopsis arenosa as a model to investigate the emergence of novel flowering time alleles in populations that have colonised along railway corridors.


Sassmann S, Rodrigues C, Milne SW, Nenninger A, Allwood E, Littlejohn GR, Talbot NJ, Soeller C, Davies B, Hussey PJ, Deeks MJ (2018) An Immune-Responsive Cytoskeletal-Plasma Membrane Feedback Loop in Plants. Curr Biol. doi: 10.1016/j.cub.2018.05.014

https://www.sciencedirect.com/science/article/pii/S096098221830616X?via%3Dihub

Open Access

Stefan Sassmann is the lead author of this paper from Mike Deeks’s lab in Exeter. They investigate the role of the membrane-integrated FORMIN4 protein in the process of cell wall apposition, which occurs as part of the plant immune response and is dependent on actin dynamics. FORMIN4 is stably localised apart from the active traffic of the endomembrane system and removing its function compromises the defense response, presumably by altering actin distribution at sites of cell wall apposition. This work demonstrates that FORMIN4 acts as a key component of the pre-invasion defense response.


Gallego-Giraldo L, Posé S, Pattathil S, Peralta AG, Hahn MG, Ayre BG, Sunuwar J, Hernandez J, Patel M, Shah J, Rao X, Knox JP, Dixon RA (2018) Elicitors and defense gene induction in plants with altered lignin compositions. New Phytol. doi: 10.1111/nph.15258

Open Access

Sara Pose and Paul Knox (University of Leeds) are co-authors on this US-led study that investigates how lignin composition can influence the defence response. Plants with the same lignin content but changed lignin compositions show altered expression in genes involved with different arms of the defense response. This indicates that cell wall lignin composition plays a significant role in the plants ability to response to different sources of pathogen attack.


Engelsdorf T, Gigli-Bisceglia N, Veerabagu M, McKenna JF, Vaahtera L, Augstein F, Van der Does D, Zipfel C, Hamann T (2018) The plant cell wall integrity maintenance and immune signaling systems cooperate to control stress responses in Arabidopsis thaliana. Sci Signal. doi: 10.1126/scisignal.aao3070

Joe McKenna (Imperial College, now Oxford Brookes University) and Cyril Zipfel (The Sainsbury Laboratory, Norwich) are co-authors on this Norwegian-led study that looks at the plant cell wall integrity maintenance mechanism and how it responses to the challenges of growth, development and environmental stresses. They identified a set of receptor-like kinases that are key for the responses elicted by cell wall damage (CWD). Conversely they showed that the components of the pattern-triggered immunity (PTI) signaling pathway repress responses to CWD. This study provides insights into how cell wall responses interact with downstream gene expression changes following pathogen challenge.


Bömer M, O’Brien JA, Pérez-Salamó I, Krasauskas J, Finch P, Briones A, Daudi A, Souda P, Tsui TL, Whitelegge JP, Paul Bolwell G, Devoto A (2018) COI1-dependent jasmonate signalling affects growth, metabolite production and cell wall protein composition in Arabidopsis. Ann Bot. doi: 10.1093/aob/mcy109

Open Access

Moritz Bömer works with Alessandra Devoto at Royal Holloway University of London and leads this research that looks at the effect of MeJA treatment on growth and gene expression in Arabidopsis cell culture. They demonstrate that both MeJA treatment or COI1 overexpression causes changes in the abundance of proteins involved in cell wall loosening as well as altered levels of primary metabolites alanine, serine and succinic acid. This work demonstrates a close link between hormone signaling, the defence response and the metabolic profile of Arabidopsis cells.

Dr Devoto and her academic colleagues at RHUL are profiled in the latest GARNish newsletter available for download from the GARNet website.


Kriechbaumer V, Breeze E, Pain C, Tolmie F, Frigerio L, Hawes C (2018) Arabidopsis Lunapark proteins are involved in ER cisternae formation. New Phytol. doi: 10.1111/nph.15228

https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15228

Open Access

Verena Kriechbaumer from Oxford Brookes University leads this research that investigates the in planta function of novel ER network-shaping proteins called Lunaparks (LNP). They show that these proteins localise to the entire ER network in Arabidopsis. They use confocal microscopy to show that altering the level of LNP gene expression changes ER morphology, possibly by regulating the formation of ER cisternae.


Chow M, Sklepari M, Frigerio L, Dixon AM (2018) Bacterial expression, purification and biophysical characterization of the smallest plant reticulon isoform, RTNLB13 Protein Expr Purif. doi: 10.1016/j.pep.2018.06.015

Open Access

Michael Chow worked with Lorenzo Frigerio and Ann Dixon at the University of Warwick to provide a preliminary structure and topology analysis of the plant RTNLB13 reticulon protein. This ER-associated integral membrane protein was expressed in bacteria and then a variety of analysis techniques were used to suggest that RTNLB13 has a high level of self-association and protein-membrane interactions.


Janes G, von Wangenheim D, Cowling S, Kerr I, Band L, French AP, Bishopp A (2018) Cellular Patterning of Arabidopsis Roots Under Low Phosphate Conditions Front Plant Sci. doi: 10.3389/fpls.2018.00735

https://www.frontiersin.org/articles/10.3389/fpls.2018.00735/full

Open Access

George Janes works with Anthony Bishopp at the University of Nottingham and leads this study that looks at root meristem development under low phosphate conditions. They show that in phosphate-limiting conditions the cortex layer of the root meristem contains almost double the number of cells, which results in a greater number of root hair-forming epidermal cells. As this change can occur within 24hrs the rapidity of the response represents a significant adaptation to a changing root environment.


Hippler FWR, Mattos-Jr D, Boaretto RM, Williams LE (2018) Copper excess reduces nitrate uptake by Arabidopsis roots with specific effects on gene expression J Plant Physiol. doi: 10.1016/j.jplph.2018.06.005

https://www.sciencedirect.com/science/article/pii/S0176161718302888

Open Access

Franz Hippler (University of Southampton) leads this UK-Brazil collaboration showing that growth of Arabidopsis plants in excess copper conditions causes a downregulation in nitrate uptake. This is due to both direct and indirect changes on the gene expression of nitrate transporters as well as a reduction in transcript level of the plasma membrane proton pump, AHA2. This effect was altered when copper levels were reduced demonstrating that copper toxicity acts at the level of nitrate transport and homeostasis.


White MD, Kamps JJAG, East S, Taylor Kearney LJ, Flashman E (2018) The Plant Cysteine Oxidases from Arabidopsis thaliana are kinetically tailored to act as oxygen sensors J Biol Chem.

doi: 10.1074/jbc.RA118.003496

Open Access

Mark White is the lead author on this work from the lab of Emily Flashman at the University of Oxford in which they look at the role of plant cysteine oxidases (PCOs) as oxygen sensors. They assessed the kinetics of each of AtPCO1 to AtPCO5 proteins and show that the most catalytically competent isoform is AtPCO4, in terms of both responding to O2, and oxidizing hypoxic responsive proteins. This work validates an O2-sensing role for the PCOs and provides evidence for functional differences between members of this enzyme family.


Kotak J, Saisana M, Gegas V, Pechlivani N, Kaldis A, Papoutsoglou P, Makris A, Burns J, Kendig AL, Sheikh M, Kuschner CE, Whitney G, Caiola H, Doonan JH, Vlachonasios KE, McCain ER, Hark AT (2018) The histone acetyltransferase GCN5 and the transcriptional coactivator ADA2b affect leaf development and trichome morphogenesis in Arabidopsis. Planta. doi: 10.1007/s00425-018-2923-9 Open Access

John Doonan (Aberystwyth University) is a co-author on this manuscript led by Jenna Kotak and Amy Herd in the USA. They investigate plants that have mutations in the histone acetyltransferase GCN5 and associated transcriptional coactivator ADA2b. These genes have been previously demonstrated as being involved in endoreduplication and trichome branching. They show that these mutants have alterations in the number and patterning of trichome-branches and that ADA2b and GCN5 are required to couple nuclear content with cell growth and morphogenesis.


Baduel P, Hunter B, Yeola S, Bomblies K. Genetic basis and evolution of rapid cycling in railway populations of tetraploid Arabidopsis arenosa (2018) PLoS Genet.

doi: 10.1371/journal.pgen.1007510 Open Access

Pierre Baduel and Kirsten Bomblies (John Innes Centre) lead this work that was conducted prior to Kirsten’s move to Norwich. In this study they follow the colonization of populations of Arabidopsis arenosa along mountain railway corridors. They demonstrate that selective pressure has occurred on novel alleles of flowering time genes and discuss the implications for ruderal communities linked to railways as allele conduits linked to local adaptations.

Monogram 2018 Report: Matthew Dale

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Published on: June 13, 2018

By Matthew Dale Rothamsted Research

The Monogram meeting is an annual conference where people from all parts of the UK cereal and grass community come together to share the latest advances discovered by academic researchers. The meeting attracts the interest of industrial scientists and plant breeders who are keen to learn about the latest exciting results that have been uncovered. As with every year the diverse program provides something of interest for everyone, having entire sessions dedicated to research themes, from genomic technological advances to grain development and crop end use. PhD students and post-docs, who did not give a presentation could present a poster during the poster sessions. This offered some amazing insights into the research which is being undertaken by young researchers in the UK.

This year the conference was held at the John Innes Centre, in Norwich Research Park. JIC is a fitting venue for this event, producing fantastic research for the plant science community, and contributing greatly to the presentations at Monogram.

The meeting started with the cereal bioinformatics session, during which we were updated on the advances to the various bioinformatic resources. This session highlighted the amazing advancements in the wheat genome annotation and gave a quick overview on the publicly available resources. The bioinformatics workshop was well structured and made the complexity of cereal genetics less daunting. The workshop discussed the advances in genome labelling and the transcriptome resources available, these are the key tools as a starting point for cereal molecular biologists and lay down the foundations for fascinating research to come. As this is a rapidly changing area, the session recognised this by featuring a number of presentations on new technologies and resources, such as KNetMiner, which will soon become available to us.


The conference flowed seamlessly thanks to the careful organisation of Scott Boden, Wendy Forsdick and Brande Wulff. Despite the formal nature of the presentations, interspersed with the science was an abundance of tea breaks and lunches, which allowed plenty of time for mingling with other people with common research interests. As is tradition, a large part of the socialising was done at the conference meal on the second night. The conference meal took place at the beautiful Assembly House in Norwich City Centre which was the perfect setting for yet more discussion over a delicious three course meal and drinks.

The conference was concluded with a more applied session focusing on technologies for crop improvement. This has been yet another successful Monogram and I am looking forward to seeing the advances of this ambitious cereal community in 2019.

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