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.

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