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GARNet Research Roundup: April 9th 2020

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Published on: April 9, 2020

This Easter edition of the GARNet Research Roundup begins with research from Aberystwyth University that has developed a system for studying self-incompatability in self-compatible Arabidopsis. Next is an outstanding community-focussed study led from the John Innes Centre that outlines the development of new resources that better enable discovery-led science to be conducted within hexaploid wheat.

Third is a study led by the Dodd group at the JIC that links the circadian clock to water-use efficiency. The fourth paper is from the Edwards group at Bristol investigates the effect of higher temperatures on meiotic recombination in wheat. The fifth paper is from Rothamsted Research and introduces novel molecular tools that will be useful in future studies of the economically important weed Blackgrass.

The next paper includes co-authors from the Sainsbury lab in Norwich and looks at the role of carbonic anhydrases in plant immunity at higher levels of CO2. The seventh paper looks at the integration of light signaling and the circadian clock and includes Paul Devlin from RHUL as a co-author. The penultimate paper includes Gareth Jenkins from Glasgow as a co-author and looks at the perception of different wavelengths of UV light by the photoreceptor UVR8. The final paper includes Marko Hyvönen from Cambridge as a co-author and investigates the organisation of the RALF gene family in strawberry.

Wang L, Triviño M, Lin Z, Carli J, Eaves DJ, Van Damme D, Nowack MK, Franklin-Tong VE, Bosch M (2020) New opportunities and insights into Papaver self-incompatibility by imaging engineered Arabidopsis pollen. J Exp Bot. doi: 10.1093/jxb/eraa092 Open Access

Ludi Wang is first author on this work led from Maurice Bosch’s lab at Aberystwyth University. They have transferred their work on self-incompatability (SI) in Papaver into Arabidopsis, so as to take advantage of its excellent genetic resources. They show that the SI response can be recapitulated in Arabidopsis, even though it is self-compatible. This research has allowed them to discover new roles for clathrin-mediated endocytosis, the actin cytoskeleton and calcium signaling during SI.

Ludi and Maurice discuss this work on the GARNet Community podcast.

Adamski NM, Borrill P, Brinton J, Harrington SA, Marchal C, Bentley AR, Bovill WD, Cattivelli L, Cockram J, Contreras-Moreira B, Ford B, Ghosh S, Harwood W, Hassani-Pak K, Hayta S, Hickey LT, Kanyuka K, King J, Maccaferrri M, Naamati G, Pozniak CJ, Ramirez-Gonzalez RH, Sansaloni C, Trevaskis B, Wingen LU, Wulff BB, Uauy C (2020) A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. Elife. doi: 10.7554/eLife.55646 Open Access

This research is led from the Uauy lab at the John Innes Centre by Nikolai Adamski, Phillippa Borrill (now at Birmingham), Jemima Brinton, Sophie Harrington and Clemence Marchal. This team worked with collaborators based around the UK, in Australia, Canada and Mexico and they outline the resources that they have developed that will promote the use of wheat as an experimental organism for discovery-led research.

https://elifesciences.org/articles/55646

Simon NM, Graham CA, Comben NE, Hetherington AM, Dodd AN (2020) The circadian clock influences the long-term water use efficiency of Arabidopsis. Plant Physiol. doi: 10.1104/pp.20.00030 Open Access

This research is led by Noriane Simon who worked with Anthony Dodd at the University of Bristol and the John Innes Centre. They showed that misregulation of components that control the circadian oscillator causes alterations in water-use efficiency in Arabidopsis plants. This response is linked to the control of transpiration via circadian control of guard cell physiology.

Coulton A, Burridge AJ, Edwards KJ (2020) Examining the Effects of Temperature on Recombination in Wheat. Front Plant Sci. doi: 10.3389/fpls.2020.00230 Open Access

Alexander Coulton is lead author on this study from the University of Bristol that has looked at how temperature changes alter the landscape of meiotic recombination in wheat. Despite showing that high temperature induces movement of recombination events toward centromeres, the overall effect is limited due to the tight linkages of many wheat genes.

Mellado-Sánchez M, McDiarmid F, Cardoso V, Kanyuka K, MacGregor DR (2020) Virus-mediated transient expression techniques enable gene function studies in black-grass. Plant Physiol. doi: 10.1104/pp.20.00205 Open Access

This Letter to the editor of Plant Physiology is led by Macarena Mellado-Sánchez, who works with Dana MacGregor at Rothamsted Research. They demonstrate the first usage of Virus-mediated gene silencing (VIGS) and Virus-mediated protein overexpression (VOX) in Blackgrass, which is a significant crop weed. They use these techniques in genetic gain and loss of function studies that result in changes in herbicide resistance in transformed blackgrass. Hopefully this work can be a prelude to future research in this potentially important experimental system for understanding how weeds effect crop yields.

http://www.plantphysiol.org/content/early/2020/04/01/pp.20.00205.long

Zhou Y, Vroegop-Vos IA, Van Dijken AJH, Van der Does D, Zipfel C, Pieterse CMJ, Van Wees SCM (2020) Carbonic anhydrases CA1 and CA4 function in atmospheric CO(2)-modulated disease resistance. Planta. doi: 10.1007/s00425-020-03370-w

Yeling Zhou is first author on this Dutch-led research that includes Dieuwertje Van der Does and Cyril Zipfel from the Sainsbury lab in Norwich. They show that the Carbonic anhydrases CA1 and CA4 play a role in plant immunity under higher levels of atmospheric CO2. This indicates that these genes might be future targets for improving plant disease resistance.

Liu Y, Ma M, Li G, Yuan L, Xie Y, Wei H, Ma X, Li Q, Devlin PF, Xu X, Wang H (2020) Transcription Factors FHY3 and FAR1 Regulate Light-induced CIRCADIAN CLOCK ASSOCIATED1 Gene Expression in Arabidopsis. Plant Cell. doi: 10.1105/tpc.19.00981

Paul Devlin from RHUL is a co-author on this Chinese-study led by Yang Liu. They show that FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its paralogue FAR-RED IMPAIRED RESPONSE1 (FAR1) are essential for light induction of CCA1, which contracts to the repressive effect of PHYTOCHROME INTERACTING FACTOR 5 (PIF5). They introduce an integrated photosensory signaling pathway that brings together light signalling with control of the circadian clock.

Rai N, O’Hara A, Farkas D, Safronov O, Ratanasopa K, Wang F, Lindfors AV, Jenkins GI, Lehto T, Salojärvi J, Brosché M, Strid Å, Aphalo PJ, Morales LO. (2020) The photoreceptor UVR8 mediates the perception of both UV-B and UV-A wavelengths up to 350 nm of sunlight with responsivity moderated by cryptochromes. Plant Cell Environ. doi: 10.1111/pce.13752 Open Access

Neha Rai is first author on this Finnish-led study that includes Gareth Jenkins from the University of Glasgow as a co-author. They investigated the response of the photoreceptors UV RESISTANCE LOCUS 8 (UVR8) and CRYPTOCHROMES 1 and 2 (CRYs) to UV wavelengths included in sunlight. They show that the wavelength of 350 nm is an important cut-off for the perception of UV-B and UV-A by these different photoreceptors.

https://onlinelibrary.wiley.com/doi/full/10.1111/pce.13752

Negrini F, O’Grady K, Hyvönen M, Folta KM, Baraldi E (2020) Genomic structure and transcript analysis of the Rapid Alkalinization Factor (RALF) gene family during host-pathogen crosstalk in Fragaria vesca and Fragaria x ananassa strawberry. PLoS One. doi: 10.1371/journal.pone.0226448 Open Access

Marko Hyvönen working at the University of Cambridge is a co-author on this Italian-US collaboration led by Francesca Negrini. This work describes the genomic organisation of the family of the Rapid Alkalinization Factors (RALFs) in octoploid strawberry. In addition they describe the upregulation of one family member, FanRALF3-1, during fungal infection. This will lead to future research aimed at defining the precise molecular relationship between FanRALF3-1 expression and the immune response in strawberry.

GARNet Research Roundup: March 13th 2020

by Geraint

Categories: Aberystwyth University, Bristol University, Durham University, Global, Kings College, Lancaster Unversity, Uncategorized, University of Nottingham, University of York

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Published on: March 13, 2020

This edition of the GARNet Research Roundup begins with research from Durham University that links environmental sensing, SUMOylation and BR signaling. The second paper is from the Baulcombe lab in Cambridge and investigates the epigenetic control of transposons. The third paper is from Aberystwyth University and introduces the DeepPod learning framework for the automated counting of Arabidopsis siliques.

The fourth paper includes co-authors from the University of Nottingham in research that conducts a comprehensive analysis of the Arabidopsis auxin receptor gene family. The next paper from the University of Bristol looks at different statistical methods to measure segregation distortion.

The sixth paper is a structural-biology study of an Arabidopsis histone methyltransferase and includes co-authors from King’s College London and the Crick Institute. The penultimate paper includes Brian Forde from Lancaster University as a co-author and analyses the ZmTMM1 transcription factor from maize. The final paper investigates the role of the WRKY6 transcription factor during seed development and includes Ian Bancroft as a co-author.

Srivastava M, Srivastava AK, Orosa-Puente B, Campanaro A, Zhang C, Sadanandom A (2020) SUMO Conjugation to BZR1 Enables Brassinosteroid Signaling to Integrate Environmental Cues to Shape Plant Growth. Curr Biol. doi: 10.1016/j.cub.2020.01.089 Open Access

Moumita Srivastava is first author on this study from Durham University that introduces SUMO regulation of brassinosteroid (BR) signalling through the BZR1 transcription factor. During salt stress Arabidopsis plants arrest growth by upregulating the SUMO protease ULP1a that in turn deSUMOylates BZR1 allowing for its destabilizing interaction with the BIN2 kinase. This study environmental sensing, SUMOylation and the BR response.

https://www.cell.com/current-biology/fulltext/S0960-9822(20)30169-X?_

Wang Z, Baulcombe DC (2020) Transposon age and non-CG methylation. Nat Commun. doi: 10.1038/s41467-020-14995-6 Open Access

Zhengming Wang and David Baulcombe from the University of Cambridge are authors on this research that assesses the ordering of the mechanisms through which transposon-containing chromatin is silenced. They demonstrate that both RNA-directed DNA methylation (RdDM) and RNA-independent silencing through chromodomain DNA methyltransferases (CMTs) occurs to provide long-term control of transposons and concomitant alterations to the transcriptome.

https://www.nature.com/articles/s41467-020-14995-6

Hamidinekoo A, Garzón-Martínez GA, Ghahremani M, Corke FMK, Zwiggelaar R, Doonan JH, Lu C (2020) DeepPod: a convolutional neural network based quantification of fruit number in Arabidopsis. Gigascience doi: 10.1093/gigascience/giaa012 Open Access

This research from Aberystwyth University includes Azam Hamidinekoo as first author in which they have developed the DeepPod deep learning framework for the automated identification of Arabidopsis siliques from complex images. They used a training set of over 2400 images to develop prediction software that had comparable success with manual expert human counting. The project code is available on GitHub.

https://academic.oup.com/gigascience/article/9/3/giaa012/5780255

Prigge MJ, Platre M, Kadakia N, Zhang Y, Greenham K, Szutu W, Pandey BK, Bhosale RA, Bennett MJ, Busch W, Estelle M (2020) Genetic analysis of the Arabidopsis TIR1/AFB auxin receptors reveals both overlapping and specialized functions. Elife doi: 10.7554/eLife.54740 Open Access

Mike Prigge from UCSD in California leads this research that includes co-authors from the University of Nottingham. They analyse the phenotypes of all mutant combinations of the six-member TIR1/AFB family of auxin receptors, demonstrating significant functional overlap but that the presence of a functional TIR1 or AFB2 is needed to maintain growth throughout the life cycle. Interestingly they find that the mysterious AFB1 receptor appears to play a specalised role in processes dependent on more rapid auxin-mediated effects.

https://elifesciences.org/articles/54740

Coulton A, Przewieslik-Allen AM, Burridge AJ, Shaw DS, Edwards KJ, Barker GLA (2020) Segregation distortion: Utilizing simulated genotyping data to evaluate statistical methods. PLoS One. doi: 10.1371/journal.pone.0228951 Open Access

Alexander Coulton is the first author on this study from the University of Bristol that looks at different statistical tests that are used to confirm segregation distortion in high-density SNP data. In this data they find that the false discovery rate correction best fits the traditional p-value threshold of 0.05 and they perform empirical tests using mapping populations generated between different wheat varieties.

Dobrovolska O, Brilkov M, Madeleine N, Ødegård-Fougner Ø, Strømland Ø, Martin SR, De Marco V, Christodoulou E, Teigen K, Isaksson J, Underhaug J, Reuter N, Aalen RB, Aasland R, Halskau Ø (2020) The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection. FEBS J doi: 10.1111/febs.15256

This Norwegian-led study has Olena Dobrovolska as first author and co-authors from King’s College London and the Crick Institute. They have performed a structural analysis using NMR and molecular dynamics of the Arabidopsis Histone lysine methyltransferase ASHH2.

Liu Y, Jia Z, Li X, Wang Z, Chen F, Mi G, Forde B, Takahashi H, Yuan L (2020) Involvement of a truncated MADS-box transcription factor ZmTMM1 in root nitrate foraging. J Exp Bot. doi: 10.1093/jxb/eraa116

Ying Liu leads this Chinese study that includes Brian Forde from Lancaster as a co-author. They show that the maize ZmTMM1 transcription factor is able to rescue the nitrate foraging defect in Arabidopsis anr1agl21 double mutants, demonstrating a link between nitrate-induced transcriptional regulation in grasses and dicots.

https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/eraa116/5781150

Song G, Li X, Munir R, Khan AR, Azhar W, Yasin MU, Jiang Q, Bancroft I, Gan Y (2020) The WRKY6 transcription factor affects seed oil accumulation and alters fatty acid compositions in Arabidopsis thaliana. Physiol Plant. doi: 10.1111/ppl.13082

Ian Bancroft from the University of York is a co-author on this Chinese-led study in which Ge Song is first author. They discovered a high expression level of the WRKY6 transcription factor in developing seeds of Arabidopsis and that wrky6 mutants have larger seeds with altered fatty acid (FA) content and composition. The authors suggest that WRKY6 could be a target for the genetic improvement of FA content in the oil-seed crop of Brassica napus.

GARNet Research Roundup: Jan 24th 2020

by Geraint

Categories: Aberystwyth University, Bristol University, Cardiff University, Durham University, Glasgow University, Global, James Hutton Institute, Rothamsted Research, Uncategorized, University of Bristol, University of Cambridge, University of Dundee, University of Glasgow

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Published on: January 24, 2020

The first GARNet Research Roundup of 2020 begins with a study from the University of Dundee at the James Hutton Institute in which they have adapted nanopore direct sequencing to analyse the Arabidopsis mRNA methylome. The second study is also from Dundee and is an analysis of alternative splicing in C4 sugarcane.

The next two papers look at the control of stomatal development. In the first, researchers from Bristol investigate the integration of temperature and light-induced signals whilst the second paper is from Sheffield and looks at the role, or lack thereof, of the HY5 protein. The fifth paper is also from Sheffield and looks at the role of the MALECTIN DOMAIN KINESIN 2 protein in dividing tissues.

The next two papers investigate the control of lateral root formation. Firstly researchers from Glasgow look at how potassium signaling integrates with both the mechanisms of RNA-directed DNA-methylation and the auxin response. The other paper looks at how auxin signaling integrates with the plasmodesmata development and includes co-authors from the University of Nottingham.

The eighth paper is led from Nottingham and looks at the role of the PROTEOLYSIS (PRT)1 during the plant immune response whilst the next paper, which is from the University of Cambridge, also looks at plant immunity, specifically at how the biosynthesis of phytic acid impacts this response.

The remaining four papers include UK-based co-authors from University of South Wales, Rothamsted and Cardiff, Durham, Oxford and Aberystwyth in international research teams led from Malaysian (the expression of Acyl-CoA-binding proteins in oil palm), China (the effect of silver nanoparticles on plant growth), Japan (convergent evolution of lateral organ formation) and Chile (the factors that influence grain filling in wheat) respectively.

Parker MT, Knop K, Sherwood AV, Schurch NJ, Mackinnon K, Gould PD, Hall AJ, Barton GJ, Simpson GG (2020) Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m(6)A modification. Elife. doi: 10.7554/eLife.49658 Open Access

Matt Parker, Kasia Knop, Anya Sherwood and Nicholas Schurch are co-first authors on this study from the University of Dundee at the James Hutton Institute in which they perform direct RNA sequencing using a nanopore sequencer. They used this technical advance to analyse the mRNA (m6A) methylome and reveal a contribution to the control of the circadian clock. Future use of this technique will undoubtedly allow for an improved annotation of the Arabidopsis genome (and others).

https://elifesciences.org/articles/49658

Dantas LLB, Calixto CPG, Dourado MM, Carneiro MS, Brown JWS, Hotta CT (2019) Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane. Front Plant Sci. doi: 10.3389/fpls.2019.01614 Open Access

This study is led from Brazil with Luiza Dantas as first author and includes co-authors from the University of Dundee at the James Hutton Institute. They investigate the level of alternative splicing (AS) in commercial sugarcane, which is an important C4 crop. Tissue samples were collected in winter and summer and this analysis reveals temperature- and organ-dependent differences in the levels of AS across a set of genes under circadian control.

Kostaki KI, Coupel-Ledru A, Bonnell VC, Gustavsson M, Sun P, Mclaughlin FJ, Fraser DP, McLachlan DH, Hetherington AM, Dodd AN, Franklin KA (2020). Guard cells integrate light and temperature signals to control stomatal aperture. Plant Physiol. doi: 10.1104/pp.19.01528 Open Access

Kalliopi-Ioanna Kostaki is first author on this study from the University of Bristol that begins to unpick the mechanisms that integrate light and temperature signals in the control of stomatal development. These signals converge on phototropin photoreceptors and multiple members of the 14-3-3 protein family. This work also reveals a currently uncharacterised pathway that controls temperature regulation of guard cell movement.

http:// http://www.plantphysiol.org/content/early/2020/01/22/pp.19.01528

Zoulias N, Brown J, Rowe J, Casson SA (2020) HY5 is not integral to light mediated stomatal development in Arabidopsis. PLoS One. doi: 10.1371/journal.pone.0222480 Open Access

Nick Zoulias is first author on this study from the Casson lab at University of Sheffield. ELONGATED HYPOCOTYL 5 (HY5) is a key regulator of light-mediated development yet in this study the authors show that the HY5-signaling cascade does not play a role in stomatal development. This key finding shows that phytochrome and cryptochrome signaling in guard cells is transmitted via non-HY5 signaling components.

Galindo-Trigo S, Grand TM, Voigt CA, Smith LM (2020) A malectin domain kinesin functions in pollen and seed development in Arabidopsis. J Exp Bot doi: 10.1093/jxb/eraa023
This research from the Smith lab at the University of Sheffield is led by Sergio Galindo-Trigo. They show that MALECTIN DOMAIN KINESIN 2 (MDKIN2) is involved in pollen, embryo and endosperm development. Malectin domains bind polysaccharides and peptides when found extracellularly in receptor-like kinases so this might suggest that in dividing tissues MDKIN2 plays a role during the physical division of cells.

Shahzad Z, Eaglesfield R, Carr C, Amtmann A (2020) Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed. Nat Commun. doi: 10.1038/s41467-019-13927-3 Open Access

Zaigham Shahzad at the University of Glasgow is the first author in this study that looks at the relationship between potassium deficiency and lateral root formation. This effect is mediated via the impact of CLSY1, a key component of the RNA-directed DNA-methylation machinery, on the transcriptional repression of the AuxIAA protein IAA27. Interestingly this system appears to act as a backup to the auxin-dependent proteolysis pathway that is primarily responsible for the control of IAA27 activity.

https://www.nature.com/articles/s41467-019-13927-3

Sager R, Wang X, Hill K, Yoo BC, Caplan J, Nedo A, Tran T, Bennett MJ, Lee JY (2020) Auxin-dependent control of a plasmodesmal regulator creates a negative feedback loop modulating lateral root emergence. Nat Commun. doi: 10.1038/s41467-019-14226-7.

This US study is led by Ross Sager and includes co-authors from the University of Nottingham. This research links the role of auxin in lateral root formation with plasmodesmata development through control of the plasmodesmal regulator PDLP5. They present a model wherein molecules required for lateral root emergence transit through plasmodesmata following an inductive auxin signal.

https://www.nature.com/articles/s41467-019-14226-7

Till CJ, Vicente J, Zhang H, Oszvald M, Deery MJ, Pastor V, Lilley KS, Ray RV, Theodoulou FL, Holdsworth MJ (2019) The Arabidopsis thaliana N-recognin E3 ligase PROTEOLYSIS1 influences the immune response. Plant Direct. doi: 10.1002/pld3.194 Open Access

Christopher Till, Jorge Vicente and Hongtao Zhangis are co-first authors on this research led from the University of Nottingham and Rothamsted Research that involves use of quantitative proteomics to define the role of the N-recognin E3 ligase PROTEOLYSIS (PRT)1 during the plant immune response.

https://onlinelibrary.wiley.com/doi/full/10.1002/pld3.194

Poon JSY, Le Fevre RE, Carr JP, Hanke DE, Murphy AM (2019) Inositol hexakisphosphate biosynthesis underpins PAMP-triggered immunity to Pseudomonas syringae pv. tomato in Arabidopsis thaliana but is dispensable for establishment of systemic acquired resistance. Mol Plant Pathol. doi: 10.1111/mpp.12902
This research from the University of Cambridge is led by Jacquelyne Poon and Alex Murphy and looks at the role of the phytic acid (inositol hexakisphosphate, InsP6) biosynthesis in dividing tissues during the plant immune response. They characterize Arabidopsis plants with mutations in biosynthetic enzymes to show that there are multiple mechanisms of basal resistance that are dependent upon InsP6.

Amiruddin N, Chan PL, Azizi N, Morris PE, Chan KL, Ong PW, Rosli R, Masura SS, Murphy DJ, Sambanthamurthi R, Haslam RP, Chye ML, Harwood JL, Low EL (2019) Characterisation of Oil Palm Acyl-CoA-Binding Proteins and Correlation of their Gene Expression with Oil Synthesis. Plant Cell Physiol. doi: 10.1093/pcp/pcz237.
Nadzirah Amiruddin is lead author on this Malaysian-led research that includes collaborators from the University of South Wales, Rothamsted Research and Cardiff University. This paper looks at the expression of Acyl-CoA-binding proteins (ACBPs) in oil palm; providing important information about the role of this protein family during oil synthesis in the world’s most important oil crop.

Wang L, Sun J, Lin L, Fu Y, Alenius H, Lindsey K, Chen C (2019) Silver nanoparticles regulate Arabidopsis root growth by concentration-dependent modification of reactive oxygen species accumulation and cell division. Ecotoxicol Environ Saf. doi: 10.1016/j.ecoenv.2019.110072.

This Chinese-study is led by Likai Wang and includes Keith Lindsey from Durham University as a co-author. They look at the effect of silver nanoparticles (AgNPs) on growth of Arabidopsis. AgNPs are taken up by roots and have opposing effects at either 50 mg L-1 or 100mg mg L-1. This is an important preliminary study to understand how plant growth might be altered if AgNP’s are used as a delivery mechanism.

Naramoto S, Jones VAS, Trozzi N, Sato M, Toyooka K, Shimamura M, Ishida S, Nishitani K, Ishizaki K, Nishihama R, Kohchi T, Dolan L, Kyozuka J (2019) A conserved regulatory mechanism mediates the convergent evolution of plant shoot lateral organs. PLoS Biol. 2019 doi: 10.1371/journal.pbio.3000560 Open Access

This Japanese study is led by Satoshi Naramoto and Junko Kyozuka and includes co-authors from the University of Oxford. They performed a mutant screen in the liverwort Marchantia polymorpha to identify the LATERAL ORGAN SUPRESSOR 1 (MpLOS1) gene, which regulates meristem maintenance and lateral organ development. Remarkably they showed this gene is also functions in the control of lateral organ development in rice, therefore demonstrating convergent evolution across plant lineages in the control of lateral organs.

Del Pozo A, Méndez-Espinoza AM, Romero-Bravo S, Garriga M, Estrada F, Alcaíno M, Camargo-Rodriguez AV, Corke FMK, Doonan JH, Lobos GA (2020) Genotypic variations in leaf and whole-plant water use efficiencies are closely related in bread wheat genotypes under well-watered and water-limited conditions during grain filling. Sci Rep. doi: 10.1038/s41598-019-57116-0 Open Access

Alejandro del Pozo leads this Chilean study that includes co-authors from Aberystwyth and NIAB. This large-scale glasshouse experiment looked at the effect of water deficit on the growth of 14 bread wheat genotypes. Measurement of multiple parameters revealed that plants face limitations to the assimilation process during grain filling due to natural senesce and water stress.

GARNet Research Roundup: October 17th 2019

by Geraint

Categories: Bristol University, Cambridge University, Durham University, Edinburgh University, Global, James Hutton Institute, John Innes Centre, Nottingham University, Rothamsted Research, SLCU, Uncategorized, University of Bristol, University of Cambridge, University of Dundee, University of Edinburgh, University of Nottingham, University of Sheffield

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Published on: October 17, 2019

This edition of the GARNet Research Roundup includes a superb selection of papers by scientists from across the UK. First is work from the Spoel lab in Edinburgh that characterizes the fine-tuning of NPR1 activity during the plant immune response. Second is work from SLCU and the University of Helsinki that is an extensive investigation into the molecular basis of cambial development. Next is research from Nottingham that looks at the importance of soil macro-structures during the growth of wheat roots.

Fourth are three papers that highlight the breadth of research occurring at the John Innes Centre. The first paper is from Enrico Coen’s lab that applies their expertise in computational modeling to leaf development in the carnivorous plant Utricularia gibba. Second is work from Saskia Hogenhout’s lab that looks at immunity to infection by Phytoplasma pathogens. Last is work from Lars Ostergaard’s lab that characterises the role of Auxin Binding promoter elements in floral development.

The seventh paper from Bristol and Glasgow looks at shade avoidance signaling via PIF5, COP1 and UVR8 whilst the eighth paper, which is from Rothamsted, demonstrates how metabolic engineering in Arabidopsis seeds can result in a high proportion of human milk fat substitute. The next paper is from the University of Durham and investigates how the composition of the Arabidopsis cell wall impacts freezing tolerance. The first author of this paper, Dr Paige Panter discusses the paper on the GARNet community podcast.

The tenth paper is from Julia Davies’s lab at the University of Cambridge and introduces an uncharacterised response to extracellular ATP signals in Arabidopsis roots. The next paper is from Mike Blatt’s group at University of Glasgow and characterises a new interaction between vesicular transport and ion channels. The penultimate entry includes co-authors from the JIC on a Chinese-led study that demonstrates improved seed vigour in wheat through overexpression of a NAC transcription factor. Finally are two methods papers taken from a special journal issue on ‘Plant Meiosis’.

Skelly MJ, Furniss JJ, Grey HL, Wong KW, Spoel SH (2019) Dynamic ubiquitination determines transcriptional activity of the plant immune coactivator NPR1. Elife. doi: 10.7554/eLife.47005
Open Access

https://elifesciences.org/articles/47005

Michael Skelly is lead author on this paper from the lab of current GARNet chair Steven Spoel. In it they investigate the mechanisms that fine-tune the function of NPR1, a key player in the plant immune response. Progressive ubiquitination of NPR1 by an E3 ligase causes both its interaction with target genes and its subsequent degradation by an E4 ligase. This latter occurrence is opposed by the deubiquitinase activity of UBP6/7, setting up a complex regulatory environment that allows the plant to rapidly response to pathogen attack.

Zhang J, Eswaran G, Alonso-Serra J, Kucukoglu M, Xiang J, Yang W, Elo A, Nieminen K, Damén T, Joung JG, Yun JY, Lee JH, Ragni L, Barbier de Reuille P, Ahnert SE, Lee JY, Mähönen AP, Helariutta Y (2019) Transcriptional regulatory framework for vascular cambium development in Arabidopsis roots. Nat Plants. doi: 10.1038/s41477-019-0522-9

This pan-European-Korean collaboration has Jing Zhang from the University of Helsinki and the Sainsbury Laboratory, University of Cambridge as first author. They use cambium cell-specific transcript profiling and follow-on network analysis to discover 62 new transcription factors involved in cambial development in Arabidopsis. This information was used to engineer plants with increased radial growth through ectopic cambial activity as well as to generate plants with no cambial activity. This understanding provides a platform for possible future improvements in production of woody biomass.

Atkinson JA, Hawkesford MJ, Whalley WR, Zhou H, Mooney SJ (2019) Soil strength influences wheat root interactions with soil macropores. Plant Cell Environ. doi: 10.1111/pce.13659
This work is led from the University of Nottingham by John Atkinson and Sacha Mooney. They use X-ray Computed Tomography to investigate a trait called trematotropism, which applies to the ability of deep rooting plants to search out macropores and avoid densely packed soil. They show root colonisation of macropores is an important adaptive trait and that strategies should be put in place to increase these structures within the natural soil environment.

Lee KJI, Bushell C, Koide Y, Fozard JA, Piao C, Yu M, Newman J, Whitewoods C, Avondo J, Kennaway R, Marée AFM, Cui M, Coen E (2019) Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism. PLoS Biol. doi: 10.1371/journal.pbio.3000427
Open Access

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000427

Karen Lee, Claire Bushell and Yohei Koide are co-first authors on this work led by Enrico Coen at the John Innes Centre and Minlong Cui at the Zhejiang Agriculture and Forestry University in China. This study uses 3D imaging, cellular and clonal analysis, combined with computational modelling to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. They identify growth ansiotrophies that result in the final leave shape that develops from an initial near-spherical form. These processes have some similarities to the polar growth seen in Arabidopsis leaves. Overall they show that ‘simple modulations of a common growth framework underlie the shaping of a diverse range of morphologies’.

Pecher P, Moro G, Canale MC, Capdevielle S, Singh A, MacLean A, Sugio A, Kuo CH, Lopes JRS, Hogenhout SA (2019) Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize. PLoS Pathog. doi: 10.1371/journal.ppat.1008035
Open Access

This work from Saskia Hogenhout’s lab at the John Innes Centre is led by Pascal Pecher and Gabriele Moro. They look at the effect of SAP11 effectors from Phytoplasma species that infect either Arabidopsis or maize. They demonstrate that although both related versions of SAP11 destabilise plant TCP transcription factors, their modes of action have significant differences. Please look out for Saskia discussing this paper on the GARNet Community podcast next week.

Kuhn A, Runciman B, Tasker-Brown W, Østergaard L 92019) Two Auxin Response Elements Fine-Tune PINOID Expression During Gynoecium Development in Arabidopsis thaliana. Biomolecules. doi: 10.3390/biom9100526
Open Access

Andre Kuhn is first author of this research from Lars Østergaard’s lab at the John Innes Centre. They functional characterise two Auxin-responsive Elements (AuxRE) within the promotor of the PINOID gene, which are bound by the ETITIN/ARF3 Auxin Response Factor. Alteration of this AuxRE causes phenotypic changes during flower development demonstrating that even with a complex regulatory environment, small changes to cis-elements can have significant developmental consequences.

Sharma A, Sharma B, Hayes S, Kerner K, Hoecker U, Jenkins GI, Franklin KA (2019) UVR8 disrupts stabilisation of PIF5 by COP1 to inhibit plant stem elongation in sunlight. Nat Commun. doi: 10.1038/s41467-019-12369-1
Open Access

https://www.nature.com/articles/s41467-019-12369-1

Ashutosh Sharma is first author of this UK-Spanish-Germany collaboration led by Keara Franklin at University of Bristol. They have characterised the interaction between three significant molecular players that function during the shade avoidance response in Arabidopsis; PIF5, UVR8 and COP1. In shaded conditions, UVR8 indirectly promotes rapid degradation of PIF5 through their interactions with the E3 ubiquitin ligase COP1.

van Erp H, Bryant FM, Martin-Moreno J, Michaelson LV, Bhutada G, Eastmond PJ (2019) Engineering the stereoisomeric structure of seed oil to mimic human milk fat. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1907915116

Open Access

https://www.pnas.org/content/early/2019/09/24/1907915116.long

Harrie Van Arp and Peter Eastmond at Rothamsted Research lead this extremely translational study in which they have modified the metabolic pathway for triacylglycerol (TAG) biosynthesis. By modifying the location of one biosynthesis enzyme and removing the activity of another, the fats produced in these Arabidopsis seeds are enriched to contain TAGs that are similar to those found in human milk. They propose that this technology could be used to develop a source of plant-derived human milk fat substitute.

Panter PE, Kent O, Dale M, Smith SJ, Skipsey M, Thorlby G, Cummins I, Ramsay N, Begum RA, Sanhueza D, Fry SC, Knight MR, Knight H (2019) MUR1-mediated cell-wall fucosylation is required for freezing tolerance in Arabidopsis thaliana. New Phytol. doi: 10.1111/nph.16209

Paige Panter led this work as part of her PhD at the University of Durham in the lab of Heather Knight. They characterise the role of the MUR1 protein in the control of cell wall fucosylation and how this contributes to plant freezing tolerance. Paige discusses this paper and the long history of MUR1 on the GARNet Community podcast. Please check it out!

Wang L, Stacey G, Leblanc-Fournier N, Legué V, Moulia B, Davies JM (2019) Early Extracellular ATP Signaling in Arabidopsis Root Epidermis: A Multi-Conductance Process. Front Plant Sci. doi: 10.3389/fpls.2019.01064.

Open Access

The UK-French collaboration is led by Limin Wang from Julia Davies’s lab in Cambridge. They use patch clamp electrophysiology to identify previously uncharacterized channel conductances that respond to extracellular ATP across the root elongation zone epidermal plasma membrane.

Waghmare S, Lefoulon C, Zhang B, Lileikyte E, Donald NA, Blatt MR (2019) K+ channel-SEC11 binding exchange regulates SNARE assembly for secretory traffic. Plant Physiol. doi: 10.1104/pp.19.00919

Open Access

This work from Mike Blatt’s lab in Glasgow is led by Sakharam Waghmare. They look at the interaction between SNARE proteins, which are involved in vesicular fusion and K+ channels, which help control turgor pressure during cell expansion. Through combining analysis of protein-protein interactions and electrophysiological measurement they have found that this interaction requires the activity of the regulatory protein SEC11.

Li W, He X, Chen Y, Jing Y, Shen C, Yang J, Teng W, Zhao X, Hu W, Hu M, Li H, Miller AJ, Tong Y (2019) A wheat transcription factor positively sets seed vigour by regulating the grain nitrate signal. New Phytol. doi: 10.1111/nph.16234
Wenjing Li is first author of this Chinese study that includes Yi Chen and Anthony Miller from the John Innes Centre as co-authors. This research shows that seed vigour and nitrate accumulation in wheat is regulated by the TaNAC2 transcriptions factor through its control of the TaNRT2.5 nitrate transporter. The authors suggest that both genes could be used as potential future targets to increase grain yield and nitrogen use efficiency.

The Special Issue of Methods in Molecular Biology on Plant Meiosis includes papers from the University of Cambridge, led by Christophe Lambing and the James Hutton Institute, led by Benoit Darrier.

Lambing C, Choi K, Blackwell AR, Henderson IR (2019) Chromatin Immunoprecipitation of Meiotically Expressed Proteins from Arabidopsis thaliana Flowers. Methods Mol Biol. doi: 10.1007/978-1-4939-9818-0_16
Darrier B, Arrieta M, Mittmann SU, Sourdille P, Ramsay L, Waugh R, Colas I (2019) Following the Formation of Synaptonemal Complex Formation in Wheat and Barley by High-Resolution Microscopy. Methods Mol Biol. doi: 10.1007/978-1-4939-9818-0_15

GARNet Research Roundup: August 16th 2019

by Geraint

Categories: Bristol University, Cambridge University, Edinburgh University, Global, John Innes Centre, Lancaster University, Nottingham University, Oxford University, Rothamsted Research, Uncategorized, University of Bristol, University of Cambridge, University of Oxford, University of York, Warwick University

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Published on: August 16, 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.

From https://www.cell.com/current-biology/fulltext/S0960-9822(19)30798-5

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.

From https://www.cell.com/current-biology/fulltext/S0960-9822(19)30844-9

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.

From https://www.frontiersin.org/articles/10.3389/fpls.2019.00858/full

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).

From https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.14211

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.

From http://www.plantphysiol.org/content/early/2019/07/31/pp.19.00693.long

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: Jan 11th 2019

by Geraint

Categories: Bristol University, Cardiff University, epigenetics, Global, John Innes Centre, Nottingham University, Oxford University, Plos One, RHUL, Sainsbury Lab, Uncategorized, University of Birmingham, University of Bristol, University of Oxford, University of Sheffield

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Published on: January 11, 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.

https://www.nature.com/articles/s41467-018-07875-7

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: November 1st 2018

by Geraint

Categories: Bristol University, Glasgow University, Global, James Hutton Institute, John Innes Centre, Oxford University, Sainsbury Lab, Uncategorized, University of Bristol, University of Leeds, University of Manchester, University of York, Warwick University

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Published on: November 1, 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: June 4th

by Geraint

Categories: Bristol University, Durham University, Glasgow University, Global, James Hutton Institute, QMUL, University of Bristol, University of Leeds, University of York, Warwick University

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Published on: June 4, 2018

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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