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: June 12th 2019

In another big edition of the GARNet Research Roundup we cover many different areas of research that utilise a varied group of experimental organisms!

The first paper from the Feng lab at the John Innes Centre performs an assessment of the factors influencing heterochromatin activity in sperm companion cells. Second is work from the JIC and Cardiff University that looks at the role of an auxin minima during fruit valve margin differentiation.

The next two papers have authors from Edinburgh. Firstly the McCormick lab has developed a stereo-based 3D imaging system for plants while Steven Spoel is a co-author on a study that looks at the pathogen responsive gene NPR1.

Coming from across the M8 is a paper from the Christie lab in Glasgow that looks into using phototropin genes as potential targets for crop improvement.

The next paper is from Oxford Brookes University where they visualise the movement of protein nanodomain clusters within the plasma membrane. Elsewhere in Oxford is a paper from the van der Hoorn group that characterises the effect of a novel triazine herbicide.

Two papers from the University of Durham also identify and characterise the role of novel herbicides, in this case on the activity of inositol phosphorylceramide synthases.

The final five papers feature research that each use different experimental organisms. Firstly a paper from the Earlham Institute uses delayed fluorescence to investigate the circadian clock in wheat and OSR. Second is a paper from Warwick that assesses the role of nodulation during nitrogen uptake in Medicago. The next paper features the Yant lab at University of Nottingham looks at growth of two species of Arabidopsis in challenging environments.

The penultimate paper includes authors from the University of Oxford and provides a detailed analysis of the factors controlling leaf shape in Cardamine and Arabidopsis thaliana. The final paper uses the imaging facility at the Hounsfield facility in Nottingham to image the roots of date palms.


He S, Vickers M, Zhang J, Feng X (2019) Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. Elife. doi: 10.7554/eLife.42530

Open Access

Lead author on his paper is Shengbo He from Xiaoqi Feng’s lab at the John Innes Centre. This work looks at activation of Transposable elements (TEs) in the sperm companion cell of Arabidopsis. This is catalyzed by the DEMETER-catalyzed DNA demethylation in regions depleted of histone H1, demonstrating a key role for H1 in determining heterochromatin activity.

https://elifesciences.org/articles/42530

Li XR, Vroomans RMA, Fox S, Grieneisen VA, Østergaard L, Marée AFM (2019) Systems Biology Approach Pinpoints Minimum Requirements for Auxin Distribution during Fruit Opening. Mol Plant. doi: 10.1016/j.molp.2019.05.003

Open Access

Xin-Ran Li and Renske Vroomans are co-lead authors on this work from the Ostergaard, Grieneisen and Maree labs from the John Innes Centre and (now) Cardiff University.They look at the role of an auxin minima in the control of valve margin differentiation in Arabidopsis fruit. They used a cycle of experimental-modeling to develop a model that predicts the maturation of the auxin minimum to ensure timely fruit opening and seed dispersal.


Bernotas G, Scorza LCT, Hansen MF, Hales IJ, Halliday KJ, Smith LN, Smith ML, McCormick AJ (2019) A photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth. Gigascience. doi: 10.1093/gigascience/giz056

Open Access

Gytis Bernotas from UWE and Livia Scorza from the McCormick lab at the University of Edinburgh lead this work that is the result of a 2+ year collaboration with the Melvyn Smith and others at the Computer Machine Vision (CMV) facility at UWE. The authors have developed hardware and software (including a deep neural network) to automate the 3D imaging and segmentation of rosettes and individual leaves using a photometric stereo approach.

https://academic.oup.com/gigascience/article/8/5/giz056/5498634

Chen J, Mohan R, Zhang Y, Li M, Chen H, Palmer IA, Chang M, Qi G, Spoel SH, Mengiste T, Wang D, Liu F, Fu ZQ (2019) NPR1 promotes its own and target gene expression in plant defense by recruiting CDK8. Plant Physiol. doi: 10.1104/pp.19.00124

GARNet chairman Steven Spoel is a co-author on this US-led study with Jian Chen as lead author. The paper investigates the interacting partners of NPR1 (NONEXPRESSER OF PR GENES 1), which is a master regulator of salicyclic signaling and therefore an important regulation of plant defense response.


Hart JE, Sullivan S, Hermanowicz P, Petersen J, Diaz-Ramos LA, Hoey DJ, Łabuz J, Christie JM (2019) Engineering the phototropin photocycle improves photoreceptor performance and plant biomass production. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1902915116

Open Access

Jaynee Hart is first author on this research from Christie lab at the University of Glasgow in which they target the phototropin blue light receptor as a candidate for crop improvement. They showed plants that engineered to have a slow-photocycling version of PHOT1 or PHOT2 had increased biomass under low light conditions, due to their increased sensitivity to low light.


McKenna JF, Rolfe DJ, Webb SED, Tolmie AF, Botchway SW, Martin-Fernandez ML, Hawes C, Runions J (2019) The cell wall regulates dynamics and size of plasma-membrane nanodomains in Arabidopsis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1819077116

Open Access

Joe McKenna from Oxford Brookes University leads this work that takes advantage of their superb imaging facilities to assess the dynamic regulation of specific protein clusters in the Arabidopsis plasma membrane. They show that the cytoskeleton (both actin and microtubule) and the cell wall play roles in the control of intra-PM moment of the pathogen receptor FLS2 and the auxin transporter PIN3.

https://www.pnas.org/content/early/2019/06/07/1819077116

Morimoto K, Cole KS, Kourelis J, Witt CH, Brown D, Krahn D, Stegmann M, Kaschani F, Kaiser M, Burton J, Mohammed S, Yamaguchi-Shinozaki K, Weerapana E, van der Hoorn RAL (2019) Triazine probes targeting ascorbate peroxidases in plants. Plant Physiol. doi: 10.1104/pp.19.00481

Open Access

Kyoko Morimoto is first author on this UK-German-Japanese collaboration led from the lab of GARNet committee member Renier van der Hoorn. They characterise the herbicidal effect of the small 1,3,5-triazine KSC-3 on ascorbate peroxidases (APXs) across a range of plant species.


Pinneh EC, Stoppel R, Knight H, Knight MR, Steel PG, Denny PW (2019) Expression levels of inositol phosphorylceramide synthase modulate plant responses to biotic and abiotic stress in Arabidopsis thaliana. PLoS One. doi: 10.1371/journal.pone.0217087

Open Access

Pinneh EC, Mina JG, Stark MJR, Lindell SD, Luemmen P, Knight MR, Steel PG, Denny PW (2019) The identification of small molecule inhibitors of the plant inositol phosphorylceramide synthase which demonstrate herbicidal activity. Sci Rep. doi: 10.1038/s41598-019-44544-1

Open Access

Elizabeth Pinneh leads these two papers from the Denny lab in Durham. In the first paper they use RNAseq data and analysis of overexpression transgenic lines to define the role of inositol phosphorylceramide synthase (IPCS) during abiotic and biotic stress responses.

Secondly they screened a panel of 11000 compounds for their activity against the AtIPCS2 in a yeast two-hybrid assay. Successful hits from the screen were confirmed with in vitro enzyme assays and in planta against Arabidopsis.


Rees H, Duncan S, Gould P, Wells R, Greenwood M, Brabbs T, Hall A (2019) A high-throughput delayed fluorescence method reveals underlying differences in the control of circadian rhythms in Triticum aestivum and Brassica napus. Plant Methods. doi: 10.1186/s13007-019-0436-6

Open Access

Hannah Rees from Anthony Hall’s lab at the Earlham Institute leads this methods paper that introduces the use of delayed fluorescence to investigate the circadian rhythms in wheat and oil seed rape.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0436-6

Lagunas B, Achom M, Bonyadi-Pour R, Pardal AJ, Richmond BL, Sergaki C, Vázquez S, Schäfer P, Ott S, Hammond J, Gifford ML (2019) Regulation of Resource Partitioning Coordinates Nitrogen and Rhizobia Responses and Autoregulation of Nodulation in Medicago truncatula. Mol Plant. doi: 10.1016/j.molp.2019.03.014

Open Access

Beatriz Lagunas is lead author on this paper from the University of Warwick that investigates the role of nodulation in actual nitrogen uptake by the roots of Medicago truncatula. They use integrated molecular and phenotypic analysis to determine that the respond to nitrogen flux are processed on a whole plant level through multiple developmental processes.

https://www.cell.com/molecular-plant/fulltext/S1674-2052(19)30127-3?

Preite V, Sailer C, Syllwasschy L, Bray S, Ahmadi H, Krämer U, Yant L (2019) Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils Philos Trans R Soc Lond B Biol Sci. doi: 10.1098/rstb.2018.0243

Open Access

Veronica Preite is first author on this UK-German collaboration led by Ute Kraemer and Levi Yant in Nottingham. They performed whole genome resequenced of 64 individuals of two Arabidopsis species that grow on calamine metalliferous sites (which have toxic levels of the zinc and cadmium). They revealed a modest amount of gene and network convergence in plants that have colonised these challenging environments.


Kierzkowski D, Runions A, Vuolo F, Strauss S, Lymbouridou R, Routier-Kierzkowska AL, Wilson-Sánchez D, Jenke H, Galinha C, Mosca G, Zhang Z, Canales C, Dello Ioio R, Huijser P, Smith RS, Tsiantis M (2019) A Growth-Based Framework for Leaf Shape Development and Diversity. doi: 10.1016/j.cell.2019.05.011

Open Access

Claudia Canales and Carla Galinha from Oxford are co-authors on this German-led study from Miltos Tsiantis’ lab that performs a detailed dissection of the growth parameters that control differences in leaf-shape in Cardamine and Arabidopsis. They show critical roles for the SHOOTMERISTEMLESS and REDUCED COMPLEXITY homeobox proteins to define differences in shape determination.


Xiao T, Raygoza AA, Pérez JC, Kirschner G, Deng Y, Atkinson B, Sturrock C, Lube V, Wang JY, Lubineau G, Al-Babili S, Ramírez LAC, Bennett MJ, Blilou I (2019) Emergent Protective Organogenesis in Date Palms: A Morpho-devo-dynamic Adaptive Strategy During Early Development. Plant Cell. doi: 10.1105/tpc.19.00008

Open Access

Members of the Hounsfield CT Imaging Facility 
at the University of Nottingham are co-authors on this paper that is led by Tingting Xiao from KAUST in Saudi Arabia. The paper takes a detailed look at root morphology in Date Palm.

GARNet Research Roundup: April 29th 2019

This edition of the GARNet research roundup features fundamental plant science research conducted in a range of experimental organisms. Firstly Liam Dolan’s lab in Oxford looks at the function of bHLHs proteins in cell differentiation across land plant evolution. Secondly Anthony Hall’s group at the Earlham Institute have identified a novel RecQ helicase involved in work exclusively conducted in wheat. Thirdly researchers from Nottingham work with Arabidopsis to characterise an EXPANSIN protein essential for lateral root development.

The fourth paper is the first of two that look at germination and uses a new model, Aethionema arabicum, to study the role of light in seed dormancy. This work includes research from Royal Holloway. The second ‘dormancy’ paper is from Peter Eastmond’s lab at Rothamsted and further characterises the DOG1 gene in Arabidopsis. The penultimate paper includes co-authors from Warwick and Leeds and introduces a novel chemical inhibitor of auxin transport. The final paper from researchers in Birmingham introduces the 3DCellAtlas Meristem, a powerful tool for cellular annotation of the shoot apical meristem.


Bonnot C, Hetherington AJ, Champion C, Breuninger H, Kelly S, Dolan L (2019) Neofunctionalisation of basic helix loop helix proteins occurred when embryophytes colonised the land. New Phytol. doi: 10.1111/nph.15829 https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15829

Clemence Bonnot is lead author on this study from Liam Dolan’s lab at the University of Oxford in which the authors assess the role of ROOT HAIR DEFECTIVE SIX-LIKE (RSL) genes during evolution of plant development. They look at the function of a member of this bHLH transcription factor family called CbbHLHVIII identified in the charophyceaen alga Chara braunii. This gene is expressed at specific morphologically important regions in the algae and cannot rescue the function of related RSL genes in Marchantia or Arabidopsis. This suggests that the function of RSL proteins in cell differentiation has evolved by neofunctionalisation through land plant lineages.


Gardiner LJ, Wingen LU, Bailey P, Joynson R, Brabbs T, Wright J, Higgins JD, Hall N, Griffiths S, Clavijo BJ, Hall A (2019) Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency. Genome Biol. 20(1):69. doi: 10.1186/s13059-019-1675-6 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1675-6

Open Access

Laura Gardiner and Anthony Hall lead this work that was conducted at the Earlham Institute and uses a bespoke set of bioinformatic tools that allow fundamental questions to be asked in hexaploid wheat. They looked at crossover and gene conversion frequencies in 13 recombinant inbred mapping populations and were able to identity an important QTL and confirm functionality for a novel RecQ helicase gene. This gene does not exist in Arabidopsis and therefore this discovery-motivated research needed to be conducted in wheat. They hope that this identification will provide future opportunities to tackle the challenge of linkage drag when attempting to develop new crops varieties.


Ramakrishna P, Ruiz Duarte P, Rance GA, Schubert M, Vordermaier V, Vu LD, Murphy E, Vilches Barro A, Swarup K, Moirangthem K, Jørgensen B, van de Cotte B, Goh T, Lin Z, Voβ U, Beeckman T, Bennett MJ, Gevaert K, Maizel A, De Smet I (2019) EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation. Proc Natl Acad Sci U S A. 2019 Apr 3. pii: 201820882. doi: 10.1073/pnas.1820882116 https://www.pnas.org/content/early/2019/04/02/1820882116.long

Open Access

This pan-European study is led by Priya Ramakrishna at the University of Nottingham and includes co-authors from the UK, Belgium, Germany and Denmark. The authors look at the lateral root development and characterise the function of the EXPANSIN A1 protein. This protein influences the physical changes in the cell wall that are needed to enable the asymmetry cell divisions that define the location of a new lateral root. Plants lacking EXPA1 function do not properly form lateral roots and are unable to correctly respond to an inductive auxin signal. This clearly demonstrates an important requirement for the activity of genes that transmit cell signals into the physical relationships that exist between cells.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0413-0

Mérai Z, Graeber K, Wilhelmsson P, Ullrich KK, Arshad W, Grosche C, Tarkowská D, Turečková V, Strnad M, Rensing SA, Leubner-Metzger G, Scheid OM (2019) Aethionema arabicum: a novel model plant to study the light control of seed germination. J Exp Bot. pii: erz146. doi: 10.1093/jxb/erz146

https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erz146/5428144

Open Access

This paper includes authors from the UK, Germany, Austria and the Czech Republic including Kai Graeber and Gerhard Leubner-Metzger at Royal Holloway. They introduce the Brassica Aethionema arabicum as a new model to investigate the mechanism of germination inhibition by light as they have identified accessions that are either light-sensitive or light-neutral. In contrast germination in Arabidopsis is stimulated by light. Transcriptome analysis of Aethionema arabicum accessions reveal expression changes in key hormone-regulated genes. Overall they show that largely the same module of molecular components are involved in control of of seed dormancy irrespective of the effect of light on germination. Therefore any phenotypic changes likely result from changes in the activity organisms-specific of these genes.

https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erz146/5428144

Bryant FM, Hughes D, Hassani-Pak K, Eastmond PJ (2019) Basic LEUCINE ZIPPER TRANSCRIPTION FACTOR 67 transactivates DELAY OF GERMINATION 1 to establish primary seed dormancy in Arabidopsis. Plant Cell. pii: tpc.00892.2018. doi: 10.1105/tpc.18.00892 http://www.plantcell.org/content/early/2019/04/08/tpc.18.00892.long

Open Access

http://www.plantcell.org/content/early/2019/04/08/tpc.18.00892.long

Fiona Bryant is lead author on this research from Rothamsted Research that investigates the factors that control expression of the DOG1 gene, which is a key regulator of seed dormancy. They show that LEUCINE ZIPPER TRANSCRIPTION FACTOR67 (bZIP67) regulates DOG1 expression and have uncovered a mechanism that describes the temperature-dependent regulation of DOG1 expression. Finally they identity a molecular change that explains known allelic difference in DOG1 function, which informs different levels of dormancy in different accessions.


Oochi A, Hajny J, Fukui K, Nakao Y, Gallei M, Quareshy M, Takahashi K, Kinoshita T, Harborough SR, Kepinski S, Kasahara H, Napier RM, Friml J, Hayashi KI (2019) Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiol. 2019 Apr 1. pii: pp.00201.2019. doi: 10.1104/pp.19.00201 http://www.plantphysiol.org/content/early/2019/04/01/pp.19.00201.long

Open Access

http://www.plantphysiol.org/content/early/2019/04/01/pp.19.00201.long

This Japanese-led study includes co-authors from the Universities of Warwick and Leeds and describes the identification of a novel positive chemical modulator of auxin cellular efflux. This aptly named PInStatic Acid (PISA) prevents PIN protein internalization yet does not impact the SCFTIR1/AFB signaling cascade. Therefore the authors hope that PISA will be a useful tool for unpicking the cellular mechanisms that control auxin transport.


Montenegro-Johnson T, Strauss S, Jackson MDB, Walker L, Smith RS, Bassel GW. (2019) 3D Cell Atlas Meristem: a tool for the global cellular annotation of shoot apical meristems. Plant Methods. 15:33. doi: 10.1186/s13007-019-0413-0

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0413-0

Open Access

Thomas Montenegro-Johnson, Soeren Strauss, Matthew Jackson and Liam Walker lead this methods paper that was prepared following research that took place at the University of Birmingham and the Max Planck Institute for Plant Breeding Research in Cologne. They describe the 3DCellAtlas Meristem, a tool allows the complete cellular annotation of cells within a shoot apical meristem (SAM), which they have successfully tested in both Arabidopsis and tomato. The authors state that ‘this provides a rapid and robust means to perform comprehensive cellular annotation of SAMs and digital single cell analyses, including cell geometry and gene expression’.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0413-0

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: Jan 11th 2019

The inaugural GARNet Research Roundup of 2019 firstly includes a paper from the University of Sheffield that has identified new pericentromeric epigenetic loci that affect the pathogen response. Secondly is a collaboration between researchers in Birmingham, Nottingham and Oxford that has identified a new mode of regulation of the VRN2 protein. Next are two papers from Jonathan Jones’ lab at The Sainsbury Laboratory in Norwich that firstly provides a toolkit for gene editing in Arabidopsis and secondly characterise the role of the NRG1 gene in the defense response. The penultimate paper is from Paul Devlin’s lab at RHUL and investigates the role of the circadian clock in the control of leaf overtopping whilst the final paper is a meeting report from a recent GARNet workshop on gene editing.


Furci L, Jain R, Stassen J, Berkowitz O, Whelan J, Roquis D, Baillet V, Colot V, Johannes F, Ton J (2019) Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis. Elife. doi: 10.7554/eLife.40655.

Open Access

Leonardo Furci and Ritushree Jain are the lead authors on this study conducted at the University of Sheffield. The authors used a population of epigenetic recombinant inbred lines (epiRILs) to screen for resistance to the oomycete pathogen Hyaloperonospora arabidopsidis. These lines each share genetic information but have varied epigenetic changes. This analysis enabled the identification of plants with hypomethylated pericentromeric regions that were primed to better respond to the presence of this pathogen. The authors discuss the mechanism through which this might affect the defence response albeit without altering other aspects of plant growth.

https://elifesciences.org/articles/40655

Gibbs DJ, Tedds HM, Labandera AM, Bailey M, White MD, Hartman S, Sprigg C, Mogg SL, Osborne R, Dambire C, Boeckx T, Paling Z, Voesenek LACJ, Flashman E, Holdsworth MJ (2018) Oxygen-dependent proteolysis regulates the stability of angiosperm polycomb repressive complex 2 subunit VERNALIZATION 2. Nat Commun. doi: 10.1038/s41467-018-07875-7

Open Access

This collaboration between the Universities of Birmingham, Nottingham, Oxford and colleagues in Utrecht is led by Daniel Gibbs. They demonstrate that the amount of VRN2 protein, which is a member of the Polycomb Repressive Complex2, is controlled by the N-end rule pathway and that this regulation responses to both cold and hypoxia stress. Whilst the VRN2 gene is expressed throughout the plant, the N-end rule degradation pathway ensures that the protein is restricted to meristematic regions until the plant senses the appropriate abiotic stress. Classically VRN2 has been linked to the regulation of flowering time by altering gene expression at the FLC locus so this study introduces new complexity into this process through the involvement of the N-end rule pathway. More information on this linkage will undoubtedly follow over the coming years.

Daniel kindly discusses this paper on the GARNet YouTube channel.


Castel B, Tomlinson L, Locci F, Yang Y, Jones JDG (2019) Optimization of T-DNA architecture for Cas9-mediated mutagenesis in Arabidopsis. PLoS One. doi: 10.1371/journal.pone.0204778

Open Access

Baptiste Castel is lead author of this work conducted at the Sainsbury Laboratory, Norwich in Jonathan Jones’ group. They have conducted a detailed analysis of the factors that contribute to successful gene editing by CRISPR-Cas9, specifically in Arabidopsis. This includes assessing the efficacy of different promotor sequences, guideRNAs, versions of Cas9 enzyme and associated regulatory sequences in the editing of a specific locus. Given that researchers are finding that different plants have different requirements when it comes to successful gene editing, this type of analysis will be invaluable for anyone who plans to conduct a gene editing experiment in Arabidopsis.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0204778

Castel B, Ngou PM, Cevik V, Redkar A, Kim DS, Yang Y, Ding P, Jones JDG (2018) Diverse NLR immune receptors activate defence via the RPW8-NLR NRG1. New Phytol. doi: 10.1111/nph.15659

In this second paper led by Baptiste Castel, they used the techniques outlined in the paper above to generate a set of CRISPR mutants deficient in NRG1, which is a RPW8-NLR resistance (R) gene. These nrg1 mutants have compromised signalling in all tested downstream TIR-NLR resistance genes. In addition the authors demonstrate that this signalling is needed for resistance to oomycete but not bacterial infection. Therefore this study reveals some significant details regarding the components of the disease response that are influenced by the activity of NRG1.


Woodley Of Menie MA, Pawlik P, Webb MT, Bruce KD, Devlin PF (2018) Circadian leaf movements facilitate overtopping of neighbors. Prog Biophys Mol Biol. doi: 10.1016/j.pbiomolbio.2018.12.012

This work is led by Michael Woodley Of Menie from Paul Devlin’s lab at Royal Holloway College and investigates the role of circadian leaf movements during shade avoidance and overtopping. Arabidopsis plants were grow in a grid system that meant leaves would interact with their neighbours and the authors show that plants with a normal circadian rhythm gained an advantage over those adapted to a longer period in which they were grown. This overtopping was additive to the advantage gained through shade avoidance and overall this paper shows that maintainance of clock-aligned leaf movements are beneficial to growth.


Parry G, Harrison CJ (2019) GARNet gene editing workshop. New Phytol. doi: 10.1111/nph.15573

Open Access

GARNet advisory committee member Jill Harrison and GARNet coordinator Geraint Parry are authors on this meeting report resulting from a GARNet organised workshop on gene editing that took place in March 2018 at the University of Bristol. Coincidentally part of the paper discusses the work that was presented at the meeting by Baptiste Castel, which is published in the paper described above.

GARNet Research Roundup: July 16th

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

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

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

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

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

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


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

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

Open Access

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


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

Open Access

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


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

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


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

Open Access

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

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


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

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

Open Access

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


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

Open Access

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


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

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

Open Access

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


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

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

Open Access

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


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

doi: 10.1074/jbc.RA118.003496

Open Access

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


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

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


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

doi: 10.1371/journal.pgen.1007510 Open Access

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

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