GARNet Research Roundup: August 16th 2019

This holiday-time edition of the GARNet research roundup begins with two papers that include the late Ian Moore from the University of Oxford as a co-author. The first looks at the role of RAB-A5c in the control of cellular growth anisotropy whilst the second characterises the Transport Protein Particle II (TRAPPII) complex.

The third paper is a UK-wide collaboration that assesses the role of UVA signaling on stomatal development. Next is a paper from Cambridge and the JIC that has identified the TAF4b protein as a novel regulator of meiotic crossovers.

The fifth paper is from the University of York and characterizes a role for cis-12-oxo-phytodienoic acid (OPDA) during seed germination.

The next three papers feature scientists from the University of Leeds in research that investigates 1, a peroxisomal ABC transporter; 2, the role of LRR-RLKs in plasmodesmata development and 3, the cell wall characteristics of banana and mango fruit.

The ninth paper is from the University of Edinburgh and investigates the role of S-nitrosylation in the control of SUMO conjugation.

The next two papers include Steve Penfield at the JIC as a corresponding author; the first looks at the role of endosperm-expressed transcriptional factors during seed dormancy and the second, in collaboration with researchers at the University of Warwick, identifies novel QTLs involved in seed dormancy.

The penultimate study is from Lancaster and presents a surprising outcome resulting from the overexpression of the wheat CA1Pase gene. The final paper includes Alison Tidy and Zoe Wilson from University of Nottingham as co-authors on a study that looks at male fertility in Arabidopsis.


Kirchhelle C, Garcia-Gonzalez D, Irani NG, Jérusalem A, Moore I (2019) Two mechanisms regulate directional cell growth in Arabidopsis lateral roots. Elife. pii: e47988. doi: 10.7554/eLife.47988

Open Access

Charlotte Kirchhelle leads this work that was conducted in the lab of the late Ian Moore at the University of Oxford. She investigates the role of the plant-specific small GTPase RAB-A5c during growth anisotropy in lateral roots, which involves coordinated orientations of cellulose microfibrils (CMFs) and by cortical microtubules (CMTs). They identify RAB-A5c dependent and independent mechanisms to control cellular growth anisotropy in this growing tissue.

From https://elifesciences.org/articles/47988

Kalde M, Elliott L, Ravikumar R, Rybak K, Altmann M, Klaeger S, Wiese C, Abele M, Al B, Kalbfuß N, Qi X, Steiner A, Meng C, Zheng H, Kuster B, Falter-Braun P, Ludwig C, Moore I, Assaad FF (2019) Interactions between Transport Protein Particle (TRAPP) complexes and Rab GTPases in Arabidopsis. Plant J. doi: 10.1111/tpj.14442

This German-led study includes Monika Kalde from the University of Oxford as first author as well Ian Moore as co-author. They characterize the components and function of the Transport Protein Particle II (TRAPPII) complex. TRAPPII plays multiple roles in intra-cellular transport and this study identified 13 subunits, including several that were previously uncharacterised.


Isner JC, Olteanu VA, Hetherington AJ, Coupel-Ledru A, Sun P, Pridgeon AJ, Jones GS, Oates M, Williams TA, Maathuis FJM, Kift R, Webb AR, Gough J, Franklin KA, Hetherington AM (2019). Short- and Long-Term Effects of UVA on Arabidopsis Are Mediated by a Novel cGMP Phosphodiesterase. Curr Biol.29(15):2580-2585.e4. doi: 10.1016/j.cub.2019.06.071

Open Access

Jean-Charles Isner is the first author on this collaboration between labs in Bristol, York, Oxford and Cambridge. They show that UVA radiation (which represents 95% of the UV radiation reaching earth) inhibits stomatal opening through a process that involves a reduction in the cytosolic level of cGMP. The AtCN-PDE1 gene (a cGMP-activated phosphodiesterase) is needed to decrease cGMP levels in Arabidopsis. This response is present across the tree of life except in metazoans. They show AtCN-PDE1 is needed for the UVA response and that prolonged UVA exposure causes increased growth yet reduced water use efficiency.


Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR (2019) Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis. Curr Biol. pii: S0960-9822(19)30844-9. doi: 10.1016/j.cub.2019.06.084

Open Access

This work from Ian Henderson’s lab in Cambridge and Xiaoqi Feng’s lab at the JIC is led by Emma Lawrence and isolates a novel modifier of meiotic crossover frequency, TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. They show TAF4b expression is enriched in meiocytes, compared to the more general expression of its paralog TAF4. Ultimately they reveal TAF4b drives a novel mode of meiotic recombination control through its activity as a general transcription factor.


Barros-Galvão T, Dave A, Cole A, Harvey D, Langer S, Larson TR, Vaistij FE, Graham IA (2019) cis-12-oxo-phytodienoic acid represses Arabidopsis thaliana seed germination in shade light conditions. J Exp Bot. pii: erz337. doi: 10.1093/jxb/erz337

Open Access

Thiago Barros-Galvão is first author on this study from Ian Graham’s lab at the University of York. They investigate how the jasmonic acid pre-cursor cis-12-oxo-phytodienoic acid (OPDA) contributes to control of seed germination, particularly under shade conditions. OPDA acts through the activity of the transcription factor MOTHER-OF-FT-AND-TFL1 (MFT).

From https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erz337/5536641

Carrier DJ, van Roermund CWT, Schaedler TA, Rong HL, IJlst L, Wanders RJA, Baldwin SA, Waterham HR, Theodoulou FL, Baker A (2019) Mutagenesis separates ATPase and thioesterase activities of the peroxisomal ABC transporter, Comatose. Sci Rep. 9(1):10502. doi: 10.1038/s41598-019-46685-9

Open Access

Alison Baker at the University of Leeds is the corresponding author of this UK, Dutch collaboration that includes David Carrier as first author. They characterise the peroxisomal ABC transporter, Comatose (CTS) through mutagenesis of key residues responsible for the proteins intrinsic acyl-CoA thioesterase (ACOT) activity. Ultimately they show that ACOT activity depends of endogenous ATPase activity but that these activities could be functional separated by mutagenesis of key residues.


Grison M, Kirk P, Brault M, Wu XN, Schulze WX, Benitez-Alfonso Y, Immel F, Bayer EMF (2019). Plasma membrane-associated receptor like kinases relocalize to plasmodesmata in response to osmotic stress. Plant Physiol. pii: pp.00473.2019. doi: 10.1104/pp.19.00473

Open Access

GARNet advisory committee member Yoselin Benitez-Alfonso and members of her research group are co-authors on the next two studies. This work is led by Magali Grison in Emmanuelle Bayer’s lab in Bordeaux. They show that the PM-localised Leucine-Rich-Repeat Receptor-Like-Kinases (LRR-RLKs), QSK1 and IMK2 relocate and cluster to the plasmodesmata under osmotic stress conditions. Through a variety of assays that focuses on QSK1 the authors show that reorganisation of RLKs can be important for the regulation of callose deposition at plasmodesmata and under osmotic stress this can have a functional effect on lateral root development.


Rongkaumpan G, Amsbury S, Andablo-Reyes E, Linford H, Connell S, Knox JP, Sarkar A, Benitez-Alfonso Y, Orfila C (2019) Cell Wall Polymer Composition and Spatial Distribution in Ripe Banana and Mango Fruit: Implications for Cell Adhesion and Texture Perception. Front Plant Sci. 10:858. doi: 10.3389/fpls.2019.00858

Open Access

Ganittha Rongkaumpan is first author on this interdisciplinary collaborative research from multiple departments at the University of Leeds. They characterise the composition of the cell wall in two fruits, banana and mango, which soften during ripening. The authors compared structural information, obtained using Atomic Force Microscopy and biochemical analysis, with data from rheology and tribology assays to understand why these fruits feel different in the mouth during ingestion.


Skelly MJ, Malik SI, Le Bihan T, Bo Y, Jiang J, Spoel SH, Loake GJ (2019) A role for S-nitrosylation of the SUMO-conjugating enzyme SCE1 in plant immunity Proc Natl Acad Sci U S A. pii: 201900052. doi: 10.1073/pnas.1900052116

Michael Skelly from the University of Edinburgh is the lead author of this study from the labs of Gary Loake and GARNet chairman Steven Spoel. They investigate the mechanism through which nitric oxide signaling after pathogen recognition stimulates inhibitory S-nitrosylation of the Arabidopsis SUMO E2 enzyme, SCE1. S-nitrosylation occurs on the evolutionary conserved Cys139 of SCE1 and they investigate the wider significant of this residue in the control of immune responses across eukaryotes.


MacGregor DR, Zhang N, Iwasaki M, Chen M, Dave A, Lopez-Molina L, Penfield S (2019) ICE1 and ZOU determine the depth of primary seed dormancy in Arabidopsis independently of their role in endosperm development. Plant J. 98(2):277-290. doi: 10.1111/tpj.14211

Open Access

Dana MacGregor (now at Rothamsted Research) leads this work from the lab of Steve Penfield at the JIC that investigates the extent of control on depth of primary dormancy that is mediated by the endosperm-expressed transcription factors ZHOUPI (ZOU) and INDUCER OF CBF EXPRESSION1 (ICE1). These effects are additive and independent of their role in endosperm development since the dormancy defect in ice1 and zou mutants can be ameliorated without altering seed morphology. They show that ICE1 acts primarily through control of ABA INSENSITIVE 3 (ABI3).


Footitt S, Walley PG, Lynn JR, Hambidge AJ, Penfield S, Finch-Savage WE (2019) Trait analysis reveals DOG1 determines initial depth of seed dormancy, but not changes during dormancy cycling that result in seedling emergence timing. New Phytol. doi: 10.1111/nph.16081

This research is a collaboration between the John Innes Centre and the Universities Liverpool and Warwick, from which Steven Footitt is first author. They used two Arabidopsis ecotypes that have differences in the timing of seedling emergence to identify new QTLs involved in depth of seed dormancy and Seedling Emergence Timing (SET). They revealed that DOG1 is important for determining depth of dormancy. In addition they identified three new SET QTLs, which are each physically close to DOG1, that play a role in the control of SET in the field.


Lobo AKM, Orr D, Gutierrez MO, Andralojc J, Sparks C, Parry MAJ, Carmo-Silva E (2019) Overexpression of ca1pase decreases Rubisco abundance and grain yield in wheat. Plant Physiol. pii: pp.00693.2019. doi: 10.1104/pp.19.00693

Open Access

This research from Lancaster Environmental Centre and their Brazilian collaborators is led by Ana Karla Lobo and demonstrates that overexpression of 2-carboxy-D-arabinitol-1-phosphate phosphatase (CA1Pase) in wheat causes a reduction in above ground biomass and compromises wheat grain yields. As CA1Pase is involved in removing inhibitors of Rubisco activity this result is contrary to the anticipated outcome. This suggests that Rubisco inhibitors might actually protect enzyme activity, thus maintaining the number of active sites that the enzyme is able to support.


Zhao SQ, Li WC, Zhang Y, Tidy AC, Wilson ZA (2019) Knockdown of Arabidopsis ROOT UVB SENSITIVE4 Disrupts Anther Dehiscence by Suppressing Secondary Thickening in the Endothecium. Plant Cell Physiol. doi: 10.1093/pcp/pcz127

Shu-Qing Zhao is the lead author on this China-UK collaboration that includes Alison Tidy and Zoe Wilson from the University of Nottingham. They show that using an artificial microRNA to reduce levels of the RUS4 gene in Arabidopsis causes a decline in male fertility. They perform a detailed analysis of the RUS4 expression module and how it impacts fertility.

GARNet Research Roundup: July 26th 2019

This summer-time-reading bumper edition of the GARNet Research Roundup begins with two papers from the University of Sheffield that each use advanced imaging techniques. Firstly Andrew Fleming’s group leads a study on the link between stomatal function and mesophyll space morphology. Second is a study from Matthew Johnson’s group that looks at the dynamic arrangement of thylakoid stacks.

Next are two papers that include Alison Smith from the JIC as a corresponding author. The first also includes Vasilios Andriotis from the University of Newcastle and looks at the role of the plastidial pentose phosphate pathway during post-germination growth. Second uses a gene-editing strategy to generate potatoes with altered starch morphologies.

The fifth paper also looks at starch; researchers from Cambridge and Norwich are involved in a study that characterises the role of the LIKE SEX4 1 protein in starch degradation.

The sixth paper is from Aberystwyth University and identifies a transcription factor that alters secondary cell wall composition in Brachypodium and maize. Next is research from the University of Bath that looks at the role of a protein S-acyl transferase during seed germination.

The eighth and ninth papers are led by Spanish research groups and include contributions from UK-based co-authors in Cambridge and Nottingham, working on photoperiod perception or phosphate signaling respectively.

The tenth paper features work from Cardiff University and looks at the role of heterologous expression of the Arabidopsis WEE1 protein. The Bancroft lab from the University of York leads the next paper that investigates glucosinolate signaling in Brassica napus.

The final three manuscripts are methods papers. The first from Edinburgh introduces a new NanoLUC reporter whilst the other two include techniques involved in the investigation of light-regulated growth processes.


Lundgren MR, Mathers A, Baillie AL, Dunn J, Wilson MJ, Hunt L, Pajor R, Fradera-Soler M, Rolfe S, Osborne CP, Sturrock CJ, Gray JE, Mooney SJ, Fleming AJ (2019) Mesophyll porosity is modulated by the presence of functional stomata. Nat Commun. doi: 10.1038/s41467-019-10826-5

Open Access

This UK-wide study is led from Andrew Fleming’s lab in Sheffield and includes Marjorie Lundgren as first author (now working in Lancaster). They use microCT imaging alongside more traditional measurements linked to analysis of gas exchange to show that mesophyll airspace formation is linked to stomatal function in both Arabidopsis and wheat. This allows the authors to propose that coordination of stomata and mesophyll airspace pattern underpins water use efficiency in crops.

https://www.nature.com/articles/s41467-019-10826-5

Wood WH, Barnett SFH, Flannery S, Hunter CN, Johnson MP (2019) Dynamic thylakoid stacking is regulated by LHCII phosphorylation but not its interaction with photosystem I. Plant Physiol. doi: 10.1104/pp.19.00503

Open Access

William Wood is the first author on this study from the University of Sheffield that uses 3D structured illumination microscopy (3D-SIM) to look at the dynamics of thylakoid stacking in both Arabidopsis and spinach. They show that the processes they observe are dependent on light harvesting complex II phosphorylation.

http://www.plantphysiol.org/content/early/2019/06/11/pp.19.00503.long

Andriotis VME, Smith AM (2019) The plastidial pentose phosphate pathway is essential for postglobular embryo development in Arabidopsis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1908556116

Open Access

Vasilios Andriotis (now at the University of Newcastle) is the lead author of this work performed in Alison Smith’s lab at the JIC. They look at the role of the plastidial oxidative pentose phosphate pathway (OPPP) during embryo development. This involved demonstrating that production of ribose-5-phosphate (R5P), which in turn leads to synthesis of purine nucleotides, is a critical function of the OPPP.


Tuncel A, Corbin KR, Ahn-Jarvis J, Harris S, Hawkins E, Smedley MA, Harwood W, Warren FJ, Patron NJ, Smith AM (2019) Cas9-mediated mutagenesis of potato starch-branching enzymes generates a range of tuber starch phenotypes. Plant Biotechnol J. doi: 10.1111/pbi.13137

Open Access

Alison Smith and Nicola Patron who work in Norwich Research Park are corresponding authors of this study that includes Aytug Tuncel as first author. They have used Cas9-mediated gene editing to generate potato plants that have a range of different tuber starch structures. This shows that gene-editing techniques allows the transgene-free alteration to generate potentially healthier crops.


Schreier TB, Umhang M, Lee SK, Lue WL, Shen Z, Silver D, Graf A, Müller A, Eicke S, Stadler M, Seung D, Bischof S, Briggs SP, Kötting O, Moorhead GB, Chen J, Zeeman SC (2019) LIKE SEX4 1 acts as a β-amylase-binding scaffold on starch granules during starch degradation. Plant Cell. doi: 10.1105/tpc.19.00089

Open Access

Tina Schreier from the University of Cambridge is the first author on this international study led from Switzerland that also includes Alexander Graf and David Seung from the JIC as co-authors. This study defines a precise role for the LIKE SEX FOUR 1 (LSF1) protein that binds starch and is required for normal starch degradation. Through a variety of experiments they show that the glucan binding, rather than phosphatase activity, is required for LSF1 function during starch degradation.


Bhatia R, Dalton S, Roberts LA, Moron-Garcia OM, Iacono R, Kosik O, Gallagher JA, Bosch M (2019) Modified expression of ZmMYB167 in Brachypodium distachyon and Zea mays leads to increased cell wall lignin and phenolic content. Sci Rep. doi: 10.1038/s41598-019-45225-9

Open Access

Rakesh Bhatia is the first author on this work from the lab of Maurice Bosch at Aberystwyth University. They overexpress the maize MYB transcription factor ZmMYB167 in both Brachypodium and maize. Both species show increased lignin content with Brachypodium but not maize showing a biomass deficit. This indicates that ZmMYB167 could be a useful molecular tool for the alteration of secondary cell wall biosynthesis.

https://www.nature.com/articles/s41598-019-45225-9

Li Y, Xu J, Li G, Wan S, Batistic O, Sun M, Zhang Y, Scott R, Qi B (2019) Protein S-acyl Transferase 15 is Involved in Seed Triacylglycerol Catabolism during Early Seedling Growth in Arabidopsis (2019) J Exp Bot. doi: 10.1093/jxb/erz282

First author on this UK-Chinese collaboration is Yaxiao Li who works with Baoxiu Qi at the University of Bath. The authors characterise the function of Arabidopsis Protein Acyl Transferase 15, AtPAT15. This protein is involved in essential β-oxidation of triacylglycerols during post-germination growth.


Ramos-Sánchez JM, Triozzi PM, Alique D, Geng F, Gao M, Jaeger KE, Wigge PA, Allona I, Perales M (2019) LHY2 Integrates Night-Length Information to Determine Timing of Poplar Photoperiodic Growth. Curr Biol. doi: 10.1016/j.cub.2019.06.003

Open Access

This Spanish-led study includes co-authors from the Sainsbury Laboratory in Cambridge and attempts to define the factors that control photoperiod perception in trees, using poplar as a model system. FLOWERING LOCUS T2 (FT2) has been previously shown to be involved in this process and this study builds on that work to show that night-length information is transmitted by the clock gene LATE ELONGATED HYPOCOTYL 2 (LHY2) and is able to control FT2 expression.

https://www.cell.com/current-biology/fulltext/S0960-9822(19)30696-7?

Silva-Navas J, Conesa CM, Saez A, Navarro-Neila S, Garcia-Mina JM, Zamarreño AM, Baigorri R, Swarup R, Del Pozo JC (2019) Role of cis-zeatin in root responses to phosphate starvation. New Phytol. doi: 10.1111/nph.16020

Ranjan Swarup from the University of Nottingham is a co-author on this Spanish-led study that has Javier Silva-Navas as first author. Through analysis of dark-grown seedlings they have identified a set of new genes involved in root phosphate signaling. In addition they provide evidence of a links between cytokinin and phosphate signaling through modulation of the cell cycle.


Siciliano I, Lentz Grønlund A, Ševčíková H, Spadafora ND, Rafiei G, Francis D, Herbert RJ, Bitonti MB, Rogers HJ, Lipavská H (2019) Expression of Arabidopsis WEE1 in tobacco induces unexpected morphological and developmental changes. Sci Rep. 2019 Jun 18;9(1):8695. doi: 10.1038/s41598-019-45015-3

Open Access

Ilario Siciliano leads this work that includes colleagues from Hilary Rogers’ lab at Cardiff University. The WEE1 protein regulates the cell cycle across eukaryote lineages. In this work they show that overexpression of AtWEE1 in tobacco causes precocious flowering and increased shoot morphogenesis of stem explants whilst in cell culture this WEE1 OX causes smaller cell sizes.


Kittipol V, He Z, Wang L, Doheny-Adams T, Langer S, Bancroft I (2019) Genetic architecture of glucosinolate variation in Brassica napus. J Plant Physiol. doi: 10.1016/j.jplph.2019.06.001

Open Access

This study from the Bancroft lab at the University of York is led by Varanya Kittipol. Through use of Associative Transcriptomics (AT) across a diversity panel of 288 Brassica napus genotypes they are able to identify a set of genes involved in synthesis of glucosinate hydrolysis products.


Urquiza-García U, Millar AJ (2019). Expanding the bioluminescent reporter toolkit for plant science with NanoLUC. Plant Methods. doi: 10.1186/s13007-019-0454-4

Open Access

This study from the University of Edinburgh introduces NanoLUC, a new more stable luciferase-based reporter for use by the plant community.

The final two papers are methods papers that focus on different aspects of light-regulated growth. These are from the University of Southampton and University of York.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0454-4

Terry MJ, Kacprzak SM (2019) A Simple Method for Quantification of Protochlorophyllide in Etiolated Arabidopsis Seedlings. Methods Mol Biol. doi: 10.1007/978-1-4939-9612-4_14

Oakenfull RJ, Ronald J, Davis SJ (2019) Measuring Phytochrome-Dependent Light Input to the Plant Circadian Clock. Methods Mol Biol. doi: 10.1007/978-1-4939-9612-4_15

GARNet Research Roundup: May 27th 2019

This bumper edition of the GARNet research roundup begins with a set of papers from the John Innes Centre. Anne Osbourn’s group is involved with two papers; firstly they discover how altering metabolic networks in the Arabidopsis root can cause changes in the associated microbiota. Second they characterise the role of a light-induced transcription factor in Artemisia. Next Caroline Dean’s group leads a global consortium that investigates the role of liquid-liquid phase separation in the formation of nuclear bodies. The final paper from the JIC is from Philippa Borrill and Cristobal Uauy, in which they identify novel transcription factors in wheat.

The fourth paper is led by Peter Etchells at Durham and characterises receptor kinase activity involved in vascular patterning in Arabidopsis.

The next two papers focus on stomatal patterning; firstly Julie Gray’s group at Sheffield looks at the stomatal responses to long-term pathogen infections. The second paper is from Glasgow and describes improvements in the OnGuard2 software, which models the factors controlling stomatal density.

Jose Gutierrez-Marcos is a co-author on a paper that uses FACS/ATAC-seq to define chromatin changes within cells of the shoot apical meristem. Richard Harrison leads the next paper that is also method-focused; describing use of CRISPR-Cas9 gene editing in Strawberry.

Andrew Miller at the University of Edinburgh is the corresponding author of the penultimate paper, which presents a whole-life-cycle, multi-model Framework that links many aspects of the Arabidopsis life cycle. The final paper is Seth Davies’s group at York and investigates the role of sucrose in the control of the circadian clock.


Huang AC, Jiang T, Liu YX, Bai YC, Reed J, Qu B, Goossens A, Nützmann HW, Bai Y, Osbourn A (2019) A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science. doi: 10.1126/science.aau6389

Ancheng Huang and Ting Jiang are first authors on this UK, Chinese and Belgian collaboration led by Anne Osbourn at the John Innes Centre. They reconstitute three biosynthesic pathways in the Arabidopsis roots and show how this affects the associated microbiota.


Hao X, Zhong Y, Nützmann HW, Fu X, Yan T, Shen Q, Chen M, Ma Y, Zhao J, Osbourn A, Li L, Tang K (2019) Light-induced artemisinin biosynthesis is regulated by the bZIP transcription factor AaHY5 in Artemisia annua. Plant Cell Physiol. doi: 10.1093/pcp/pcz084

Anne Osbourn is a co-author on this Chinese-led study that has identified that the basic leucine zipper transcription factor (TF) AaHY5 regulated of light-induced biosynthesis of artemisinin in Artemisia annua.


Fang X, Wang L, Ishikawa R, Li Y, Fiedler M, Liu F, Calder G, Rowan B, Weigel D, Li P, Dean C (2019) Arabidopsis FLL2 promotes liquid-liquid phase separation of polyadenylation complexes. Nature. doi: 10.1038/s41586-019-1165-8

Xiaofeng Fang, Liang Wang and Ryo Ishikawa are first authors of this UK, German and Chinese collaboration led by Caroline Dean’s lab at the John Innes Centre. They characterise the molecular factors that are required for the formation of nuclear bodies through liquid-liquid phase separation (PDF). These proteins are the Arabidopsis RNA-binding protein FCA and the coiled-coil protein FLL2.

From https://www.nature.com/articles/s41586-019-1165-8

Borrill P, Harrington SA, Simmonds J, Uauy C (2019) Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling. Plant Physiol. doi: 10.1104/pp.19.00380

Open Access

Philippa Borrill, now a faculty member at the University of Birmingham, conducted this work with Cristobal Uauy at the John Innes Centre. They have developed a range of research tools for use in wheat and this paper describes the identification of novel transcription factors involved in senescence.


Wang N, Bagdassarian KS, Doherty RE, Kroon JT, Connor KA, Wang XY, Wang W, Jermyn IH, Turner SR, Etchells JP (2019) Organ-specific genetic interactions between paralogues of the PXY and ER receptor kinases enforce radial patterning in Arabidopsis vascular tissue. Development. doi: 10.1242/dev.177105

Ning Wang works with Peter Etchells at Durham University where they have characterised the interactions between the receptor kinase gene families that regulate radial patterning in the development of vascular tissue.


Dutton C, Hõrak H, Hepworth C, Mitchell A, Ton J, Hunt L, Gray JE (2019) Bacterial infection systemically suppresses stomatal density. Plant Cell Environ. doi: 10.1111/pce.13570

Christian Dutton leads this work conducted at the University of Sheffield. They have investigated the longer-term systemic response to the presence of pathogens that involves reducing stomatal density. This process is mediated via salicylic acid signaling and slows disease progression.

From https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.13570

Jezek M, Hills A, Blatt MR, Lew VL (2019) A constraint-relaxation-recovery mechanism for stomatal dynamics. Plant Cell Environ. doi: 10.1111/pce.13568

Mareike Jezek leads this work from the University of Glasgow in which they have updated the OnGuard2 modelling software that has demonstrated substantial predictive power to describe stomatal dynamics. Their improvements allow for the development of models that are more similar to in vivo observations.


Frerichs A, Engelhorn J, Altmüller J, Gutierrez-Marcos J, Werr W (2019) Specific chromatin changes mark lateral organ founder cells in the Arabidopsis thaliana inflorescence meristem. J Exp Bot. doi: 10.1093/jxb/erz181

Jose Gutierrez-Marcos from the University of Warwick is a co-author on this German study led by Anneke Frerichs in which they analysed the chromatin state of lateral organ founder cells (LOFCs) in the peripheral zone of the Arabidopsis inflorescence meristem in wildtype and apetala1-1 cauliflower-1 double mutants. Importantly they showed that the combined application of FACS/ATAC-seq is able to detect chromatin changes in a cell-type specific manner.


Wilson FM, Harrison K, Armitage AD, Simkin AJ, Harrison RJ (2019) CRISPR/Cas9-mediated mutagenesis of phytoene desaturase in diploid and octoploid strawberry. Plant Methods. doi: 10.1186/s13007-019-0428-6. eCollection 2019

Open Access

This paper is lead by Fiona Wilson at NIAB-EMR in which they present their methods to undertake gene editing in the challenging experimental system of diploid and octoploid strawberries.

From https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0428-6

Zardilis A, Hume A, Millar AJ (2019) A multi-model framework for the Arabidopsis life cycle. J Exp Bot. doi: 10.1093/jxb/ery394

Open Access

Argyris Zardilis conducted this modeling-focussed research at University of Edinburgh. The authors present a whole-life-cycle, multi-model Framework that links vegetative, inflorescence as fruit growth as well as seed dormancy in Arabidopsis. This Framework allows the authors to simulate at the population level in various genotype × environment scenarios.

From https://academic.oup.com/jxb/article/70/9/2463/5336616

Philippou K, Ronald J, Sánchez-Villarreal A, Davis AM, Davis SJ (2019) Physiological and Genetic Dissection of Sucrose Inputs to the Arabidopsis thaliana Circadian System. Genes (Basel). doi: 10.3390/genes10050334

Open Access

Koumis Philippou from Seth Davis’ research group the University of York leads this work that investigates the role of sucrose into the function of the circadian clock.

GARNet Research Roundup: March 7th 2019

This edition of the GARNet research roundup begins with a study into the genetic basis of fertility in barley led by Sarah McKim from Dundee. Second is a study from Oxford and Leicester that characterizes the proteolytic control of chloroplast import. The third paper from Levi Yant’s group at JIC and Nottingham that attempts to discover the influence of polyploidism on population genomic effects whilst the fourth paper from Juliet Coates’ lab in Birmingham uses the growth of Arabidopsis to assess the potential of algal biomass as a biofertiliser. The next two papers include co-authors from Oxford and Warwick respectively and investigate different factors that control seed viability in Arabidopsis and Brassica oleracea. The final paper includes Seth Davies from York as a co-author on a study that looks at control of the circadian clock in field-grown Arabidopsis.


Zwirek M, Waugh R, McKim SM (2019) Interaction between row-type genes in barley controls meristem determinacy and reveals novel routes to improved grain. New Phytol. doi: 10.1111/nph.15548

Open Access

Current GARNet committee members Sarah McKim is the leader of this study in which first author is Monica Zwirek. They investigate the mechanism through which the barley VRS genes contribute to spikelet fertility. They undercover the epistatic relationship between five VRS genes that explains how they contribute to controlling fertility of lateral spikelets. Importantly they demonstrate that various vrs mutant combinations improve fertility in a variety of ways, information that will be useful during the generation of new varieties of barley.

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15548

Ling Q, Broad W, Trösch R, Töpel M, Demiral Sert T, Lymperopoulos P, Baldwin A, Jarvis RP (2019) Ubiquitin-dependent chloroplast-associated protein degradation in plants. Science. doi: 10.1126/science.aav4467

Qihua Ling and William Broad are the first authors on this study from the Universities of Oxford and Leicester. They investigate the role of proteolysis in the functional control of chloroplast-envelope translocases, which are required for the transport of proteins from nucleus-encoded genes into the chloroplast. They identify two newly characterised proteins that function in the same pathway as the known ubiquitin E3 ligase SP1. These novel proteins, SP2 and CDC48, are both required for the movement of ubiquitinated proteins from the chloroplast outer envelope membrane (OEM) into the cytosol, where they are degraded by the proteolytic machinery. This process of chloroplast-associated protein degradation (CHLORAD) maintains tight control of the activity of OEM proteins and is essential for organelle function.

http://science.sciencemag.org/content/363/6429/eaav4467.long

Monnahan P, Kolář F, Baduel P, Sailer C, Koch J, Horvath R, Laenen B, Schmickl R, Paajanen P, Šrámková G, Bohutínská M, Arnold B, Weisman CM, Marhold K, Slotte T, Bomblies K, Yant L (2019) Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa. Nat Ecol Evol. doi: 10.1038/s41559-019-0807-4.

Patrick Monnahan at the John Innes Centre is first author on this study from the Yant lab that has recently moved to the University of Nottingham. In this collaboration with colleagues in the US, Austria, Sweden, the Czech Republic and Slovakia, they have performed large scale sequencing on 39 populations of Arabidopsis arenosa. These plants have differing levels of ploidy and they are attempting to understand how ploidy effects population genomics. They demonstrate that the ploidy effects are subtle but significant and that masking of deleterious mutations, faster substitution rates and interploidy introgression will likely impact the evolution of populations where polyploidy is common.


Ghaderiardakani F, Collas E, Damiano DK, Tagg K, Graham NS, Coates J (2019) Effects of green seaweed extract on Arabidopsis early development suggest roles for hormone signalling in plant responses to algal fertilisers. Sci Rep. doi: 10.1038/s41598-018-38093-2

Open Access

This work from the Coates lab at the University of Birmingham is led by Fatemeh Ghaderiardakani and looked into the potential of algal extracts as biofertiliser. They showed that at >0.1%, extracts taken from the common green seaweed Ulva intestinalis inhibit Arabidopsis seed germination and root elongation. At lower concentrations primary root elongation was promoted albeit with a complete loss of lateral root formation. Elemental analysis allows the authors to suggest that this effect was mediated via a novel mechanism involving aluminium. Overall the authors caution against the use of algal biofertilisers due to potential unforeseen negative effects on plant growth.


Viñegra de la Torre N, Kaschani F, Kaiser M, van der Hoorn RAL, Soppe WJJ, Misas Villamil JC (2019) Dynamic hydrolase labelling as a marker for seed quality in Arabidopsis seeds. Biochem J. doi: 10.1042/BCJ20180911.

GARNet Committee member Renier van der Hoorn is a co-author on this German-led study that investigates how the activity of seed-localised proteases can affect Arabidopsis seed germination. This study has clear real-world application regarding the storage of economically important seed stocks. They show that vacuolar processing enzymes (VPEs) become more active during aging whilst the activity of serine hydrolases declines alongside seed quality. This information has allowed the authors to develop protease-activity-based markers that will provide information about seed quality.


Schausberger C, Roach T, Stöggl WM, Arc E, Finch-Savage WE, Kranner I (2019) Abscisic acid-determined seed vigour differences do not influence redox regulation during ageing. Biochem J. doi: 10.1042/BCJ20180903

William Finch-Savage from the University of Warwick is a co-author on this Austrian-led study that looks at the effect of aging on the quality of Brassica oleracea seeds stored at two oxygen concentrations. Higher O2 causes a more rapid decrease in seed quality through aging yet in contrast aging did not alter the impact of the hormone ABA on seed viability. This study enables the authors to uncover two mechanisms that control seed quality that appear to act through different mechanisms.


Rubin MJ, Brock MT, Davis SJ, Weinig C (2019) QTL Underlying Circadian Clock Parameters Under Seasonally Variable Field Settings in Arabidopsis thaliana G3 (Bethesda). doi: 10.1534/g3.118.200770

Open Access

Seth Davies from the University of York is a co-author on this study led by Matthew Rubin from the University of Wyoming. They looked at the growth of Arabidopsis thaliana recombinant inbred lines grown in field conditions and found an extremely nuanced relationship regarding how QTLs that influence the circadian clock respond to environmental conditions. For example the authors showed that plant growth in June, July and September is controlled by different QTL architecture, demonstrating the complex regulation of the circadian clock in these field growth plants.

GARNet Research Roundup: February 14th 2019

This GARNet research Roundup includes a broad range of topics and contributing institutions. First is a study from TSL that investigates the molecular basis of Arabidopsis and Brassica responses to white rust disease. Second is work from Warwick that uses Arabidopsis as a tool to test genes involved in the evolution of Flax domestication.

The third paper is work from Cambridge that models the response of the circadian oscillator to nicotinamide whilst the fourth paper is a study from the University of Dundee that compares differential gene expression software in the analysis of RNAseq data from a complex organism. The penultimate paper includes a co-author from the University of Oxford and has generated an extended phylogeny of the Brassicaceae family. The final paper compares the growth and metabolite profiles of Arabidopsis and Eutrema salsugineum following drought stress.


Cevik V, Boutrot F, Apel W, Robert-Seilaniantz A, Furzer OJ, Redkar A, Castel B, Kover PX, Prince DC, Holub EB, Jones JDG (2019) Transgressive segregation reveals mechanisms of Arabidopsis immunity to Brassica-infecting races of white rust (Albugo candida). Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1812911116

Open Access

https://www.pnas.org/content/116/7/2767.long

Volkan Cevik is the lead author on this international collaboration that is led by Jonathan Jones at the Sainsbury Lab, Norwich. They have taken advantage of Arabidopsis resistance to white rust (Albugo candida) and used the Multiparent Advanced Generation InterCross (MAGIC) lines to identity the genes responsible for this resistance. This is important as related crop species Brassica juncea and Brassica oleracea are sensitive to this economically important pathogen. They identified a range of nucleotide-binding, leucine-rich repeat (NLR)-encoding genes that were involved in resistance to the pathogen.


Gutaker RM, Zaidem M, Fu YB, Diederichsen A, Smith O, Ware R, Allaby RG (2019) Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fiber production. Sci Rep. doi: 10.1038/s41598-018-37086-5

Open Access

https://www.nature.com/articles/s41598-018-37086-5

Rafal Gutaker is the lead author on this collaborative study between the University of Warwick and colleagues in Germany, Canada and Denmark, which investigated the route of domestication of the cultivated crop Flax. At northern european latitudes flax evolved to become a fibre crop rather than an oil crop by stem expansion and reduction of seed size. The authors investigated the role in this adaptation of PEBP family genes in the flax genome, LuTFL1 and LuTFL2. LuTFL1 was heterologously expressed in Arabidopsis, demonstrating that it is able to perform roles in flowering time and plant architecture. This research highlights the importance of Arabidopsis as a tool for testing the function of genes from less-easily transformed organisms.


Mombaerts L, Carignano A, Robertson FR, Hearn TJ, Junyang J, Hayden D, Rutterford Z, Hotta CT, Hubbard KE, Maria MRC, Yuan Y, Hannah MA, Goncalves J, Webb AAR (2019) Dynamical differential expression (DyDE) reveals the period control mechanisms of the Arabidopsis circadian oscillator. PLoS Comput Biol. doi: 10.1371/journal.pcbi.1006674

Open Access

Laurents Mombarts is the first author in this collaboration between the departments of Plant science and Engineering at the University of Cambridge that looked at the mechanistic effect on nicotinamide on the timing of the circadian oscillation. They developed a systematic and practical modeling framework for the gene regulatory circuits that respond to nicotinamide. They initially developed a mathematical model and then experimentally confirmed their predictions to uncover a role for blue light signalling in this response. Overall their approach could be adapted to predict mechanisms of drug action in other complex biological systems.


Froussios K, Schurch NJ, Mackinnon K, Gierlinski M, Duc C, Simpson GG, Barton GJ (2019) How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in A. thaliana. Bioinformatics. doi: 10.1093/bioinformatics/btz089

Open Access

Gordon Simpson and colleagues at the University of Dundee collaborate with researchers in Clermont-Ferrand with Kimon Froussios as first author. They use Arabidopsis as a model to test a set of Differential Gene Expression (DGE) tools for the effective analysis of RNAseq data generated with three or fewer biological replicates. They tested nine widely used DGE tools and ultimately recommend the use of tools that are based on the negative binomial distribution.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006674

Nikolov LA, Shushkov P, Nevado B, Gan X, Al-Shehbaz IA, Filatov D, Bailey CD, Tsiantis M (2019) Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity. New Phytol. doi: 10.1111/nph.15732.

https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15732

This German, US and UK collaboration is led by Lachezar Nikolov and includes Dmitry Filatov from the University of Oxford as a co-author. They generated a phylogeny of the Brassicaceae, the family that contains Arabidopsis and a number of economically important crops. They used a mixture of fresh tissue and herbarium samples to perform the analysis on almost 80 species; enabling the resolution of new relationships between family members. This work represents an important tool for phylogenetic and comparative studies to maximise future outputs.


Pinheiro C, Dickinson E, Marriott A, Ribeiro IC, Pintó-Marijuan M, António C, Zarrouk O, Chaves MM, Dodd IC, Munné-Bosch S, Thomas-Oates J, Wilson J (2019) Distinctive phytohormonal and metabolic profiles of Arabidopsis thaliana and Eutrema salsugineum under similar soil drying. Planta. doi: 10.1007/s00425-019-03095-5

This collaboration between the UK and Portugal is led by Carla Pinheiro and the corresponding author is Julie Wilson from the University of York. Eutrema salsugineum is a stress-tolerance relative of Arabidopsis and in this study the authors have compared the response of these plants following growth on drying soils. Whereas stomatal sensitivity was similar in both species there were significant differences in metabolite profiles and water usage following drought stress. This analysis allowed the authors to conclude that Arabidopsis is indeed a good model for analysis of responses to commonly encountered levels of drought stress.

GARNet Research Roundup: November 1st 2018

This week’s GARNet research roundup again features papers on a variety of topics. First is work from the University of Leeds that investigates the physical properties of callose:cellulose hydrogels and the implication for cell wall formation. Second is work from the University of York that assesses the role of the HSP90.2 protein in control of the circadian clock. The third paper features GARNet committee member Sarah McKim and looks at the genetic control of petal number whilst the next paper from the Universities of Warwick and Glasgow includes a proteomic analysis of different types of secretory vesicles.

The next two papers look at different aspects of hormone signaling. Firstly Alistair Hetherington from the University of Bristol is a co-author on a study that looks at the role of the BIG protein whilst Simon Turner’s lab in Manchester investigates the role of ABA in xylem fibre formation.

The penultimate paper includes Lindsey Turnbull from the University of Oxford and looks at the stability of epialleles across 5 generations of selection. Finally is a paper that includes researchers from TSL in Norwich who have contributed to a phosphoproteomic screen to identify phosphorylated amino acids that influence the defence response.


Abou-Saleh R, Hernandez-Gomez M, Amsbury S, Paniagua C, Bourdon M, Miyashima S, Helariutta Y, Fuller M, Budtova T, Connell SD, Ries ME, Benitez-Alfonso Y (2018) Interactions between callose and cellulose revealed through the analysis of biopolymer mixtures. Nature Communications DOI: 10.1038/s41467-018-06820-y

https://www.nature.com/articles/s41467-018-06820-y

Open Access
Radwa Abou-Saleh is lead author on this work from Yoselin Benitez-Alfonso’s lab at the University of Leeds. (1,3)-β-glucans such as callose play an important role in plant development yet their physical properties are largely unknown. This study analyses a set of callose:cellulose hydrogel mixtures as a proxy for different cell wall conditions. They show that callose:cellulose hydrogels are more elastic than those composed of only cellulose, providing evidence that the interactions between cellulose and callose are important for the structural features of cell walls.


Davis AM, Ronald J, Ma Z, Wilkinson AJ, Philippou K, Shindo T, Queitsch C, Davis SJ (2018) HSP90 Contributes To Entrainment of the Arabidopsis Circadian Clock via the Morning Loop. Genetics. doi: 10.1534/genetics.118.301586

http://www.genetics.org/content/early/2018/10/18/genetics.118.301586.long

Open Access
Amanda Davies is the first author on this study from Seth Davies’ lab at the University of York in which they assess the role of the molecular chaperone HSP90.2 on function of the circadian clock. The show hsp90.2-3 mutant plants have a lengthened circadian period with a specific defect in the morning. This data allows the authors to better understand the pathway through which HSP90.2 functions to entrain the circadian clock.


Monniaux M, Pieper B, McKim SM, Routier-Kierzkowska AL, Kierzkowski D, Smith RS, Hay A. The role of APETALA1 in petal number robustness. Elife. doi: 10.7554/eLife.39399

https://elifesciences.org/articles/39399

Open Access
GARNet committee member Sarah McKim is a co-author on this paper, that is led by Marie Monniaux, which includes research from her time at the University of Oxford. This work from the Hay lab in Cologne compares petal number in Arabidopsis thaliana, in which the number is invariant, and Cardamine hirsute, in which it varies. They show that petal number robustness can be attributed to the activity of the APETALA1 (AP1) floral regulator and that AP1 masks the activity of several genes in Arabidopsis but not in Cardamine.


Waghmare S, Lileikyte E, Karnik RA, Goodman JK, Blatt MR, Jones AME (2018) SNAREs SYNTAXIN OF PLANTS 121 (SYP121) and SYP122 mediate the secretion of distinct cargo subsets . Plant Physiol. doi: 10.1104/pp.18.00832

http://www.plantphysiol.org/content/early/2018/10/23/pp.18.00832.long

Open Access

This collaboration between the Universities of Glasgow and Warwick is led by Sakharam Waghmare, who works with Mike Blatt in Glasgow. This study uses proteomic approaches to characterise the secretory cargos within vesicles decorated with either of the SNARE proteins SYNTAXIN OF PLANTS 121 (SYP121) or SYP122. Genetic analysis suggests that SYP121 and SYP122 have redundant functions but this new research is able to identify cargo proteins that are either contained within both types of vesicle or that are specific to one or the other.


Zhang RX, Ge S, He J, Li S, Hao Y, Du H, Liu Z, Cheng R, Feng YQ, Xiong L, Li C, Hetherington AM, Liang YK (2018) BIG regulates stomatal immunity and jasmonate production in Arabidopsis. New Phytol. doi: 10.1111/nph.15568

Alistair Hetherington is a co-author on this China-based study led by Ruo‐Xi Zhang from Wuhan. This work adds to some recent interest in the BIG protein; in this study showing that it is involved in the interaction between JA and ethylene signaling during stress responses. In a complex set of interactions they show that the BIG protein differently alters opposing arms of the JA signaling pathway providing additional evidence that this protein is a key regulator of plant hormone signaling, albeit by a set of as yet unknown mechanisms.


Campbell L, Etchells JP, Cooper M, Kumar M, Turner SR. An essential role for Abscisic acid in the regulation of xylem fibre differentiation. Development. doi: 10.1242/dev.161992

This work from Simon Turner’s lab at the University of Manchester is led by Liam Campbell and identifies a novel role for ABA in the formation of xylem fibres during secondary thickening of the Arabidopsis hypocotyl. The action of ABA doesn’t alter the xylem:phloem ratio but rather the activity focuses on the formation of fibres within the already defined xylem tissue.


Schmid MW, Heichinger C, Coman Schmid D, Guthörl D, Gagliardini V, Bruggmann R, Aluri S, Aquino C, Schmid B, Turnbull LA, Grossniklaus U (2018) Contribution of epigenetic variation to adaptation in Arabidopsis. Nat Commun. doi: 10.1038/s41467-018-06932-5

https://www.nature.com/articles/s41467-018-06932-5

Open Access
Lindsey Turnbull (University of Oxford) is a co-author on this paper from Ueli Grossniklaus’ group in Zurich. Marc Schmid is lead author of the study that investigates the inheritance of Arabidopsis epialleles over 5 generations during conditions of simulated selection. The authors show that variations in methylation state are subject to selection and do indeed contribute to adaptive responses


Kadota Y, Liebrand TWH, Goto Y, Sklenar J, Derbyshire P, Menke FLH, Torres MA, Molina A, Zipfel C, Coaker G, Shirasu K (2018) Quantitative phosphoproteomic analysis reveals common regulatory mechanisms between effector- and PAMP-triggered immunity in plants. New Phytol. doi: 10.1111/nph.15523

Members of Cyril Zipfel’s group at The Sainsbury lab in Norwich are co-authors on this paper led by Yasuhiro Kadota from the RIKEN in Yokohama. They use a phosphoproteomic screen to identify a set of newly identified phosphorylation sites on membrane-associated proteins involved in effector-triggered immunity (ETI). Some of these phosphosites overlap with those known to be important for pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI), indicating a convergence of signaling control of both these pathways to certain key residues.

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

GARNet Research Roundup: June 4th

This weeks GARNet Research Roundup begins with a paper from researchers at the University of Dundee, James Hutton Institute, Durham University and the University of Glasgow that characterises a functional role for alternative splicing during the cold response. Second is a paper from Newcastle University that investigates the role of the OXI1 kinase during aphid predation. Third is a paper that includes University of Bristol co-authors that looks at strigolactone signaling in moss whilst the fourth paper from researchers at Leeds and QMUL studies the role of ascorbate during photosynthesis. The final paper from Warwick and York uses gene expression data from pathogen-infected plants to generate a model for predicting a strategy for synthetic engineering of the defence response.


Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo H, Zhang R, Brown JWS (2018) Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome. Plant Cell doi: 10.1105/tpc.18.00177.

www.plantcell.org/content/early/2018/05/15/tpc.18.00177.long

Open Access

Cristiane Calixto and Wenbin Guo work with John Brown at University of Dundee and the James Hutton Institute and in this large-scale biology paper they characterise the role of alternative splicing (AS) during a stress response. RNAseq was performed on plants exposed to cold stress and they showed that hundreds of genes undergo AS just a few hours after temperature decrease and that this response is sensitive to small changes. The authors propose that AS is a mechanism to fine-tune changes in thermo-plasticity of gene expression and in addition they investigate the activity of the novel splicing factor U2B”-LIKE.

Christiane will discuss this research at the upcoming GARNet2018 meeting held at the University of York in September 2018.


Shoala T, Edwards MG, Knight MR, Gatehouse AMR. OXI1 kinase plays a key role in resistance of Arabidopsis towards aphids (Myzus persicae) (2018) Transgenic Res. doi: 10.1007/s11248-018-0078-x.

Open Access

This work is led by Tahsin Shoala in the lab of Angharad Gatehouse at Newcastle University and demonstrates a novel role for MAPK cascades in resistance to aphid predation. They investigate mutants in OXI1 kinase, a gene that activates MAPK signaling and demonstrate a reduction in the aphid population build-up. Furthermore they show that the effect of OXI works through a mechanism that involves callose deposition, demonstrated as oxi1 mutants lack the upregulation of a set of β-1,3-glucanase genes following predation.


Lopez-Obando M, de Villiers R, Hoffmann B, Ma L, de Saint Germain A, Kossmann J, Coudert Y, Harrison CJ, Rameau C, Hills P, Bonhomme S (2018) Physcomitrella patens MAX2 characterization suggests an ancient role for this F-box protein in photomorphogenesis rather than strigolactone signalling. New Phytol. doi: 10.1111/nph.15214

GARNet committee member Jill Harrison is a co-author on this paper that is led by Mauricio Lopez‐Obando working at Université Paris-Saclay. In Physcomitrella patens development they investigate the role of the moss ortholog of the Arabidopsis strigolactone signaling mutant MAX2. Previous work had shown that moss does response to SL signaing but they find that although Ppmax2 mutants showed defects in early development and photomorphogenesis they do not show changes in the SL response. Fascinatingly this indicates that the molecular components that control SL signaling have diverged in vascular plants and seemingly co-opted a role for MAX2 that was previously not required in mosses.


https://academic.oup.com/jxb/article/69/11/2823/4991886

Plumb W, Townsend AJ, Rasool B, Alomrani S, Razak N, Karpinska B, Ruban AV, Foyer CH. Ascorbate-mediated regulation of growth, photoprotection and photoinhibition in Arabidopsis thaliana (2018) J Exp Bot. doi: 10.1093/jxb/ery170

William Plumb (Leeds) and Alexandra Townsend (QMUL) are the lead authors on this study that investigates the importance of ascorbate during photosynthesis. In this work they analysed the growth of ascorbate synthesis mutants that are smaller and have less biomass than wildtype plants. However these plants have normal levels of non-photoinhibiton, allowing the authors to conclude that ascorbate is needed for growth but not photoprotection.


Foo M, Gherman I, Zhang P, Bates DG, Denby K (2018) A Framework for Engineering Stress Resilient Plants using Genetic Feedback Control and Regulatory Network Rewiring. ACS Synth Biol. doi: 10.1021/acssynbio.8b00037
Mathias Foo and Iulia Gherman (University of Warwick) are lead authors on work that analyses gene expression data taken from Botrytis cinerea-infected Arabidopsis. They have identified a network of genes involved in the defence response. They validate their model against previously obtained time series data and then perturb the model in two differences ways, focused on the transcription factor CHE. This analysis demonstrates the potential of combining feedback control theory with synthetic engineering in order to generate plants that are resistant to biotic stress.

https://pubs.acs.org/doi/10.1021/acssynbio.8b00037

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