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

https://linkinghub.elsevier.com/retrieve/pii/S0960982218307048

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

www.pnas.org/content/early/2018/07/25/1806460115

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.

https://www.cell.com/current-biology/abstract/S0960-9822(18)30711-5#%20

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 is first author 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.

One switch to control them all – unravelling seasonality in plants

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Published on: June 7, 2018

Written by Marie-Anne Robertson and Andrew J. Millar, of the School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland.


Plants make drastic changes to their biology to survive the changing seasons. Yet we know little about how they do this – despite the important clues it could give us on how plants adapt to harsh environments. It is only by studying a long-known anomaly in patterns of gene expression that we discover one answer has been there all along.

Plants are masters at adapting to the changing world around them. Dramatic shifts from day to night, and from season to season, can bring harsh frosts or long droughts that stretch a plant’s survival abilities to its limits. The secret to success is not simply adapting to a change in conditions, instead plants anticipate predictable changes.

Over the last 30 years, molecular genetics has revealed the intricate working of plant’s circadian clock. This molecular circuitry acts as a 24 hour timekeeper, controlling over a third of their genome. It allows plants to make multiple adjustments from day to night, including the movement of leaves, flower opening and their use of nutrients and energy.

The changing seasons, however, require more dramatic biological shifts to guarantee survival. Yet we are still largely in the dark when it comes to understanding the underlying processes. What we know so far comes from detailed studies of the most obvious and visible changes, such as the flowering of many plants in spring. Flowering time is important for agriculture, because it controls when some crops can be harvested.

Plants have a surprisingly simple way of anticipating when spring is on the way. The genes controlling flowering are only expressed at particular points in the day. When this coincides with the right environmental trigger, such as longer daylight hours, it alters the behaviour of the proteins controlled by that gene, triggering flowering. In engineering, this process is called coincidence detection. It ensures that these plants avoid harsh winter conditions and risk their delicate flowers only in longer days.

Beyond beautiful spring blooms, plants must also make big shifts to many, less visible, parts of their biology, such as metabolism and energy use. The question is could a coincidence detector explain these other adjustments? This wasn’t obvious, because the best-known detector was specialised for flowering.

Plants produce a vast number of proteins with different roles in their biology. Studying changes in their levels should provide us with clues into the specific ways plants adapt. Scientists have known for a long time that although the level of some proteins are stable across the day, curiously the genes that dictate their production are still expressed in a rhythmic way. This was long seen as a biological anomaly but it turns out that we have missed the bigger picture by only studying daily rhythms.

In a new publication from Seaton et al (2018), looked at how levels of proteins change in response to the seasons – recreating seasonal daylight hours for the plant Arabidopsis, a commonly used model for other plant species. We studied the proteins involved in the most important aspects of plant biology, those involved in photosynthesis – the conversion of sunlight into energy – and those involved in the storage and use of that energy.

In all over a third of genes in Arabidopsis show a rhythm in their expression and around 1700 proteins changed their levels according to seasonal daylight hours. By simply adjusting our focus, what was once seen as a biological anomaly was revealed to be a master key, which promises to open the door to understanding seasonal change.

Many of the proteins we identified were involved in photosynthesis and energy use, but interestingly some were involved in the plant’s secondary metabolism. This has a wider range of functions including toxic and repellent chemicals that act as the plants defence system and could help to ward off seasonal pests.

The experiments also revealed that the timing of gene expression is key. Those genes with a daily peak of activity in the evening had most effect during long days whereas those that peak in the morning were more effective during short days. As so many plant genes have rhythmic expression, this type of coincidence detection, termed translational coincidence, affected hundreds of proteins in this study.

This simple, yet remarkably powerful, global ‘switching’ mechanism allows plants to make sweeping changes to their biology. Like high street shops stocking up for the upcoming season – whether it is swimwear or winter coats – plants must also select the right options from their extensive protein catalogue. When daily rhythms in gene expression work together with the newly discovered process of translational coincidence it provides plants with a powerful way of mixing and matching vast numbers of proteins to boost their survival.

Further analysis reveals that these findings may not be unique to plants. Analysing data from cyanobacteria and algae indicates translational coincidence could be applied to all photosynthetic organisms. This is starting to provide us with vital insights into how plants, and perhaps other photosynthetic organisms, cope with change. In the future, these fundamental discoveries may pave the way to fine tuning plants biology to make them better suited to harsh environments or even help to expand their geographical boundaries.

Take a look at a video about this work here:
Seaton_IMG_0346_final

Seaton DD, Graf A, Baerenfaller K, Stitt M, Millar AJ, Gruissem W (2018) Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism. Mol Syst Biol. doi: 10.15252/msb.20177962 Open Access


This article is licensed under the Creative Commons License: Attribution 4.0 International, http://creativecommons.org/licenses/by/4.0/legalcodeCC-BY4.0.

The study is reported in the following paper, which is free online: Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism (2018) Seaton, D. D., Graf, A., Baerenfaller, K., Stitt, M., Millar, A. J. & Gruissem, W. Molecular Systems Biology. 14, 3, p. e7962. Link: http://dx.doi.org/10.15252/msb.20177962

All the published data, analysis scripts and results are also freely available on the FAIRDOMHub, http://doi.org/10.15490/fairdomhub.1.investigation.163.2

The study involved researchers from the University of Edinburgh, Scotland; the Max Planck Institute in Golm, Germany and the ETH in Zurich, Switzerland.

The study was funded by the European Union FP7 project TiMet (award 245143).

Monogram 2018 Report: Patrycja Sokolowska

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Published on: June 5, 2018

By Patrycja Sokolowska, PhD student at Rothamsted Research

Monogram 2018 at John Innes Centre in Norwich was the first, and so far the only conference I have been to since I have started my PhD. Monogram has the established reputation to be the best cereal research meeting in the UK, and it gathers the most experienced wheat scientists and breeders, as well as PhD students and young postdoctoral researchers. My colleagues who went to the Monogram last year said it was great, so I was very excited to go and experience it for myself. I was not disappointed!

The conference venue was located in a lovely surroundings of Norwich and the conference itself was brilliantly organised. Morning and afternoon sessions were grouped into focus blocks with clear themes, and although I found all the sessions interesting, due to the nature of my research, the Cereals Bioinformatics Session and Grain Development and Crop End Use Session were most useful for me. Apart from the variety of talks from invited speakers and PhD students, we also had a poster session, during which I had a chance to present my work. The session meant to last for one afternoon, but it extended into the whole duration of the conference (!), which was great, because we could talk about our work for longer!

But Monogram is not only hard work! Our hosts in Norwich made sure that we have time to relax and have a chat with other attendees over a meal too. On the first day we enjoyed the barbeque and a drink, and the second day ended with a bit more formal dinner in the beautiful Assembly House.

Monogram meeting proved to be a great place to meet peers working in a very similar field. Usually, even though I am lucky enough to be doing my PhD in a crop sciences-based research institute, where quite a lot of people work on wheat, I do not get a chance to exchange my experiences with students, simply because the project we are working on are very different. Monogram gave me an amazing opportunity to meet PhD students who use similar laboratory techniques and work on organisms closely related to wheat. We had a chance to talk about our research and exchange valuable experiences. I hope we will keep in touch and I am looking forward to reading their first publications.

Overall, these were very intense but informative and fruitful three days. I am very happy that I could be a part of this year’s Monogram and I would recommend going to anyone working in the field of cereal research. I would like to thank GARNet for awarding me the travel grant to attend this conference, and making my expenses budget a little less tight! I am looking forward to the Monogram meeting in Nottingham next year! Who knows, maybe I will have a chance to present next year!

Me during my flash talk presentation, trying to lure people into visiting my poster
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