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  • geraintparry
  • GARNet Coordinator @ Cardiff University. Past lecturer in Plant Science and genetics. Researcher into plant nuclear transport and regulation of auxin signalling.
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#UKPlantSciPresents Webinar Series begins September 15th

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Published on: August 21, 2020

The previously awesome #GARNetPresents webinar series is morphing into the #UKPlantSciPresents webinar series. This series has the aim of promoting plant science excellence across the UK! UK plant science research uses many different experimental organisms such as Arabidopsis, Wheat, Brassicas, Brachypodium, Marchantia, Physomitrella and many others.

This webinar series is supported by both GARNet and Monogram Small Grains Network . By expanding the series supporters we aim to promote the webinar to a wider set of the plant science community.


We surveyed the audience at the final webinar before the summer break and the majority of attendees would like a webinar every two weeks that include two speakers presenting their research. Therefore this format will continue from Tuesday September 15th 3pm BST.

We are recruiting speakers so if you want to promote your research to hundreds of interested attendees please contact Geraint Parry with your idea and a possible talk title. The webinar will be recorded so is a fantastic opportunity for you to obtain a YouTube video to promote your research on a personal or lab website!

In the meantime please check out the recording of the past #GARNetPresents webinars.

GARNish Edition 33: GENOMIC ARABIDOPSIS RESEARCH NETWORK: 2000-2020

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Published on: July 31, 2020

Contents:

– Society Updates
– Introducing Quantitative Plant Biology
– Congratulations to Ottoline Leyser
– Conference Updates
– Bacterial Plant Diseases Programme
– Introducing CHAP
– Twenty Years of GARNet
– GARNet Research Roundup
– MASC Publication Update
– Plant RNA Interactome Capture
– Update on new BBSRC Projects
– Spotlight on University of Nottingham

Download here: https://www.garnetcommunity.org.uk/sites/default/files/newsltr/GARNish33_Online_Final_0.pdf

https://www.garnetcommunity.org.uk/sites/default/files/newsltr/GARNish33_Online_Final_0.pdf

Marcel Bach-Pages describes the plant RNA Interactome Capture Method

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Published on: July 22, 2020

Marcel Bach-Pages works with Gail Preston at the University of Oxford and we discuss a new protocol to identify the RNA-Binding Proteome from Arabidopsis leaves. This community-focused work includes full instructions for use of the protocol and they provide an accessible list of proteins that they have identified. This research is published in Biomolecules and is entitled ‘Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method‘.

GARNet Research Roundup: July 17th 2020

This edition of GARNet Research Roundup begins with a remarkable four papers that include work from Caroline Dean’s lab at the John Innes Centre. The first two papers are collaborations with members of Martin Howard’s lab and look at the molecular mechanisms that control long-term cold sensing or the antisense regulation of FLC respectively. The third paper looks at the function of the ICU1-associated PRC2 complex while the final ‘Dean-lab’ paper is a collaboration with Judith Irwin and looks at regulation of flowering time in Brassica napus.

The next three papers also feature authors from the John Innes Centre. The first looks at the role of mRNA methylation in the control of leaf organogenesis; the second paper investigates how AXR1 functions in the methylation of transposable elements and the final paper characterises a new method for the automated measurement of seeds.

The first non-JIC paper in this Roundup is led by Robert Caine from the University of Sheffield and characterises stomatal development in Physcomitrium patens. Andrea Harper at the University of York leads the next paper that applies an associative transcriptomics approach to the genome of Brassica juncea.

The next paper includes co-authors from Aberystwyth and characterises a molecular interaction from pollen tubes that can stimulate ectopic programmed cell death. The final two papers include co-authors from the University of Oxford. Firstly Paul Jarvis is involved with a Japanese study that looks at chloroplast autophagy and ubiquitination. Finally Nick Harberd is co-author on a Chinese study looking at iron accumulation in Arabidopsis seeds.


Zhao Y, Antoniou-Kourounioti RL, Calder G, Dean C, Howard M (2020) Temperature-dependent growth contributes to long-term cold sensing Nature; 10.1038/s41586-020-2485-4. doi:10.1038/s41586-020-2485-4

Yusheng Zhao is first author on this work from the Howard and Dean labs at the John Innes Centre. They reveal a molecular mechanism that underpins the ability of plants to sense the winter period. They show that abundance of the transcription factor NTL8 is critical for the control of expression of the VERNALIZATION INSENSITIVE 3 protein, which in turn epigenetically silences FLC throughout the winter.

https://www.nature.com/articles/s41586-020-2485-4

Fang X, Wu Z, Raitskin O, et al (2020) The 3′ processing of antisense RNAs physically links to chromatin-based transcriptional control Proc Natl Acad Sci U S A. 2020;202007268. doi:10.1073/pnas.2007268117

Open Access

Xiaofeng Feng works with the Howard and Dean labs at the John Innes Centre and is lead author on this research. The authors provide molecular detail to the complex control of antisense RNA regulation of the FLC locus, which provides a link to epigenetic silencing via the Polycomb Repressive Complex 2.


Bloomer RH, Hutchison CE, Bäurle I, et al (2020) The Arabidopsis epigenetic regulator ICU11 as an accessory protein of Polycomb Repressive Complex 2 Proc Natl Acad Sci U S A. 2020;201920621. doi:10.1073/pnas.1920621117 Open Access

Rebecca Bloomer is first author on this collaboration between researchers at the John Innes Centre and the University of Edinburgh. They identify INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 (PRC2) accessory protein that co-localises with the core components of the PRC2. The ICU1-associated PRC2 complex controls H3K36me3 demethylation at the FLC locus, revealing an additional mechanism for the control of flowering time.


Tudor EH, Jones DM, He Z, et al (2020) QTL-seq identifies BnaFT.A02 and BnaFLC.A02 as candidates for variation in vernalization requirement and response in winter oilseed rape (Brassica napus) Plant Biotechnol J. 2020;10.1111/pbi.13421. doi:10.1111/pbi.13421 Open Access

Eleri Tudor is first author on this work from the Dean and Irwin labs at the John Innes Centre. They characterise the key floral regulators FLOWERING LOCUS C (BnaFLC.A02) and FLOWERING LOCUS T (BnaFT.A02) in Brassica napus, showing that allelic variation at these loci is importance for the close-association between vernalisation and flowering time.

https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13421

Arribas-Hernández L, Simonini S, Hansen MH, et al (2020) Recurrent requirement for the m6A-ECT2/ECT3/ECT4 axis in the control of cell proliferation during plant organogenesis Development. doi:10.1242/dev.189134 Open Access

Laura Arribas-Hernández is lead author on this Danish-UK collaboration that includes Sara Simonini and Lars Ostergaard from the John Innes Centre as co-authors. They look at the role of YTH-domain proteins ECT2, ECT3 and ECT4 during leaf development. They show that the methylated mRNA (m6A)-binding site of these proteins is essential for their function, highlighting the m6A-ECT2/ECT3/ECT4 axis as an important module to stimulate plant organogenesis.

https://dev.biologists.org/content/early/2020/06/30/dev.189134.long

Christophorou N, She W, Long J, et al (2020) AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization PLoS Genet. 16(6):e1008894. doi:10.1371/journal.pgen.1008894 Open Access

This collaboration between Université Paris-Saclay and the John Innes Centre includes Nicolas Christophorou as first author. They investigate the role of the well-characterised NEDD8/RUB1 E1 ligase AXR1 in DNA methylation of transposable elements. This links the role of AXR1 with its previously characterised effects in hormone signalling and in the control of the formation of meiotic crossovers.


Colmer J, O’Neill CM, Wells R, et al (2020) SeedGerm: a cost-effective phenotyping platform for automated seed imaging and machine-learning based phenotypic analysis of crop seed germination New Phytol. 10.1111/nph.16736. doi:10.1111/nph.16736 Open Access

This UK-Chinese-Dutch collaboration is led by Joshua Colmer and introduces a new phenotyping platform that was tested against a diverse panel of Brassica napus varieties. This SeedGerm hardware and software measures seed germination, automates seed imaging and is a platform for machine-learning based phenotypic analysis. This will hopefully be a useful tool for the investigation of critical seed phenotypes.

https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.16736

Caine RS, Chater CCC, Fleming AJ, Gray JE (2020) Stomata and Sporophytes of the Model Moss Physcomitrium patens. Front Plant Sci. 2020;11:643. doi:10.3389/fpls.2020.00643 Open Access

Bobby Caine from the University of Sheffield is lead author on this research that characterises stomatal development in the model moss species Physcomitrium patens. Although they show key differences in stomatal development between Physcomitrium and Arabidopsis, key regulators of this process in higher plants also functions in mosses, providing important evolutionary insights.

https://www.frontiersin.org/articles/10.3389/fpls.2020.00643/full

Harper AL, He Z, Langer S, et al (2020) Validation of an Associative Transcriptomics platform in the polyploid crop species Brassica juncea by dissection of the genetic architecture of agronomic and quality traits Plant J. 2020;10.1111/tpj.14876. doi:10.1111/tpj.14876  Open Access

GARNet committee member Andrea Harper from the University of York leads this research that employs associative transcriptomics analysis in Brassica juncea. To generate this analysis platform they mapped transcriptome data from a diverse panel of B. juncea accessions to produce a pan-transcriptome reference. This will be a useful research for the mapping of loci involved in important agronomic traits.


Lin Z, Xie F, Trivino M, et al. (2020) Ectopic expression of a self-incompatibility module triggers growth arrest and cell death in vegetative cells Plant Physiol. doi:10.1104/pp.20.00292 Open Access

Zongcheng Lin is first author on this Belgium-led study that includes Marina Trivino and Maurice Bosch from IBERS, Aberystwyth University as co-authors. They look at the interaction between cognate PrsS and PrpS proteins that are involved in the pollen self-incompatibility response in poppy. By ectopic expression in Arabidopsis roots they show that this interaction can cause programmed cell death (PCD) in vegetative tissues. This signalling module may become an important tool for inducible PCD in other developmental contexts.

http://www.plantphysiol.org/content/early/2020/06/19/pp.20.00292.long

Kikuchi Y, Nakamura S, Woodson JD, et al (2020) Chloroplast autophagy and ubiquitination combine to manage oxidative damage and starvation responses Plant Physiol. 2020;pp.00237.2020. doi:10.1104/pp.20.00237 Open Access

Paul Jarvis from the University of Oxford is a co-author on this Japanese study led by Yuta Kikuchi. This work demonstrates that autophagy and chloroplast-associated ubiquitin ligase E3s cooperate for protein turnover, management of ROS accumulation, and adaptation to starvation.


Sun Y, Li JQ, Yan JY, et al (2020) Ethylene promotes seed iron storage during Arabidopsis seed maturation via ERF95 transcription factor J Integr Plant Biol. 10.1111/jipb.12986. doi:10.1111/jipb.12986

Nick Harberd from the University of Oxford is a co-author on this Chinese study led by Ying Sun at Zhejiang University in Hangzhou. In this work they show that the ERF95 transcription factor regulates Arabidopsis seed Fe accumulation and through a series of investigations they are able to conclude that the gaseous hormone ethylene promotes seed Fe accumulation during seed maturation via an EIN3-ERF95-FER1-dependent signaling pathway.

Christos Velanis discusses the polycomb group complex, domesticated transposons and the future of scientific funding.

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Published on: July 15, 2020

Christos Velanis works at the University of Edinburgh and discusses work published in PloS Genetics entitled ‘The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)‘.

Pumi Perera is co-first author on this work from the Goodrich lab that is the follow-on to research published in PLoS Genetics in 2015 ‘Kicking against the PRCs – A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2‘. At the time GARNet talked to Justin Goodrich about this paper

Plant Science Conference Updates: July 2020

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Published on: July 6, 2020

This has been a challenging time for both conference organisers and conference venues. Most 2020 plant science conferences have cancelled, postponed or majorly changed their events.

Below is a non-exhaustive list of the changes that have been made to different conferences. Up to date as July 6th 2020. (download)

Catriona Walker and Al Ware discuss Arresting Flowers

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Published on: July 1, 2020

Al Ware (University of Nottingham) and Catriona Walker (University of Leeds) discuss a recent paper published in Nature Plants entitled ‘Auxin export from proximal fruits drives arrest in temporally competent inflorescences’. We chat about auxin, mind-numbing phenotyping and local arrest of flowering.

GARNet Research Roundup: June 26th 2020

This edition of the GARNet Research Roundup begins with a study from Nottingham and Leeds that looks at the much-neglected subject of the control of floral arrest. The second paper from Edinburgh identifies a signaling role for the co-opted transposable elements ALP1 and ALP2 in Arabidopsis. Hans-Wilhelm Nützmann from the University of Bath leads the next study that looks at the co-regulation of clustered biosynthetic pathway genes. The fourth paper is from Cambridge and looks at the role of the ASY1 protein during meiotic recombination. The next paper is from Durham and looks at the role of GA-regulated DELLA proteins in the regulation of stomatal aperature.

The next five papers have a methods-type application that should be useful to other researchers. Firstly a research team led from Oxford highlights an improved protocol for the proteome-analysis technique of RNA interactome capture. Secondly researchers from UEA introduce the NATpare tool, which is a pipeline for high-throughput prediction and functional analysis of nat-siRNAs. The third ‘methods’ paper is from the University of Warwick where they have developed novel markers for protoplast-based analyses of hormone signaling. The fourth paper is a protocol for using CRISPR-Cas9 gene editing in Brachypodium. The final ‘methods-type’ paper is from Alison Smith’s group in Cambridge and has developed a riboswitch-based resource for use in the model alga Chlamydomonas reinhardtii.

The eleventh paper is led from the University of Glasgow and looks at the activity of the circadian clock in Arabidopsis roots. The next paper introduces genes from the parasitic plant Striga hermonthica into Arabidopsis to show that strigolactone signaling can replace GA signaling in the control of seed germination. The final two papers are focused on research in wheat, first led from the University of Leicester that looks at recombination in durum wheat and secondly from Rothamsted in which they have identified a whole family of NPF membrane transporter genes.


Ware A, Walker CH, Šimura J, et al (2020) Auxin export from proximal fruits drives arrest in temporally competent inflorescences Nat Plants. 2020;10.1038/s41477-020-0661-z. doi:10.1038/s41477-020-0661-z

Open Access with this link rdcu.be/b4rmT

Al Ware and Catriona Walker are co-first authors on this study from the Universities of Nottingham and Leeds. They have looked at the factors that control the timing of floral arrest in Arabidopsis. They discover that there is a minimum number and optimal positioning of fruits that is necessary for floral arrest, as well as looking into the role of auxin transport in this process.


Velanis CN, Perera P, Thomson B, et al (2020) The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2) PLoS Genet. 2020;16(5):e1008681. doi:10.1371/journal.pgen.1008681

Open Access

Christos Velanis is first author on this research led by the Goodrich group at the University of Edinburgh that looked at the function of the Arabidopsis ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) gene, which has arose by domestication of the Harbinger class of transposable elements (TEs). ALP1 is a component of the POLYCOMB REPRESSIVE COMPLEX 2 (PRC2) but yet its functional significance is not yet known. They also identify the related ALP2 gene and find that it interacts with MULTICOPY SUPPRESSOR OF IRA1 (MSI1) as part of the PRC2.


Nützmann HW, Doerr D, Ramírez-Colmenero A, et al (2020) Active and repressed biosynthetic gene clusters have spatially distinct chromosome states Proc Natl Acad Sci U S A. 2020;201920474. doi:10.1073/pnas.1920474117

Hans-Wilhelm Nützmann is a now a member of faculty at the University of Bath but led this research as a member of the Osbourn group at the John Innes Centre. They use Hi-C and related techniques to study the control of expression of clustered biosynthetic pathway genes in Arabidopsis. This study reveals potential mechanisms that suggest gene clustering in the one-dimensional chromosome is accompanied by compartmentalization of the 3D chromosome.


Lambing C, Kuo PC, Tock AJ, Topp SD, Henderson IR (2020) ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference in Arabidopsis Proc Natl Acad Sci U S A. 2020;201921055. doi:10.1073/pnas.1921055117

Open Access

Christophe Lambing is first author on this study from the Henderson lab at the University of Cambridge that investigates the role of the ASY1 protein in the control of recombination frequency during meiosis. ASY1 is localized in an ascending telomere-to-centromere gradient and this informs the role that it plays to antagonize telomere-recombination to ensure this occurs in more gene-rich regions of the chromosomes.


Sukiran NA, Steel PG, Knight MR (2020) Basal stomatal aperture is regulated by GA-DELLAs in Arabidopsis J Plant Physiol. 2020;250:153182. doi:10.1016/j.jplph.2020.153182

Nur Afiqah Sukiran is the first author of this study from the Durham University that investigates the role of DELLA proteins in the regulation of stomatal aperature. They also find that the GID1 gibberellin receptor is necessary for optimal basal stomatal aperture.

Professor Marc Knight will be discussing his labs work on the #GARNetPresents webinar on June 30th 2020


Bach-Pages M, Homma F, Kourelis J, et al (2020) Discovering the RNA-Binding Proteome of Plant Leaves with an Improved RNA Interactome Capture Method. Biomolecules. 2020;10(4):661 doi:10.3390/biom10040661

Open Access

Marcel Bach-Pages is first author on this research led from the University of Oxford that has improved the proteome-analysis technique of RNA interactome capture (RIC) to identify 717 RNA Binding Proteins (RBP) from Arabidopsis. Many of these RBPs exhibit unconventional modes of RNA binding and uncovered greater diversity in the number of proteins for which RNA binding is an important part of their function.


Thody J, Folkes L, Moulton V (2020) NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs Nucleic Acids Res. 2020;gkaa448. doi:10.1093/nar/gkaa448

Joshua Thody leads this work from the University of East Anglia in which the authors present a new software pipeline, called NATpare, for prediction and functional analysis of Natural antisense transcript-derived small interfering RNAs (nat-siRNAs) using sRNA and degradome sequencing data. Although this tool could be used to analyse data from different experimental systems it is benchmarked using Arabidopsis data and the authors show that it could rapidly identify a comprehensive set of nat-siRNAs from different tissues and that are produced in response to different stresses.


Lehmann S, Dominguez-Ferreras A, Huang WJ, Denby K, Ntoukakis V, Schäfer P (2020) Novel markers for high-throughput protoplast-based analyses of phytohormone signaling. PLoS One. 2020;15(6):e0234154. doi:10.1371/journal.pone.0234154

Open Access

Silke Lehmann leads this work from the University of Warwick that has generated a community-resource of 18 promoter::luciferase constructs that respond to different phytohormones. In addition they suggest an experimental setup for high-throughput analyses in which these new reporter constructs might be used to screen for biological and environmental stimuli that effect hormone-mediated gene expression.


Hus K, Betekhtin A, Pinski A, et al (2020) A CRISPR/Cas9-Based Mutagenesis Protocol for Brachypodium distachyon and Its Allopolyploid Relative, Brachypodium hybridum. Front Plant Sci. 2020;11:614. doi:10.3389/fpls.2020.00614 Open Access

This Polish project is led by Karolina Hus and includes co-authors from Cambridge and Aberystwyth. They have developed a protocols for CRISPR-Cas9 gene editing in Brachypodia species. As proof of concept they target two cyclin-dependent kinases (CDKG1 and CDKG2) that are involved in DNA recombination.


Mehrshahi P, Nguyen GTDT, Gorchs Rovira A, et al (2020) Development of Novel Riboswitches for Synthetic Biology in the Green Alga Chlamydomonas ACS Synth Biol. 2020;10.1021/acssynbio.0c00082. doi:10.1021/acssynbio.0c00082

Open Access

Payam Mehrshahi is the first author on this Academia-Industry collaboration led from the University of Cambrige. They have used a synthetic biology approach to assess the effectiveness of riboswitchs (RNA regulatory elements) in the control of gene expression in the model alga Chlamydomonas reinhardtii.


Nimmo HG, Laird J, Bindbeutel R, Nusinow DA (2020) The evening complex is central to the difference between the circadian clocks of Arabidopsis thaliana shoots and roots Physiol Plant. 2020;10.1111/ppl.13108. doi:10.1111/ppl.13108 Open Access

Hugh Nimmo from the University of Glasgow is lead author on this UK-USA collaboration that has looked at the operation of the circadian clock in root tissues and in particularly how it responds to light quality. They found that plants with mutations in certain genes that make up the circadian clock evening complex have root-specific effects, confirming that the shoot and root clocks response to differently to light signals.


Bunsick M, Toh S, Wong C, et al (2020) SMAX1-dependent seed germination bypasses GA signalling in Arabidopsis and Striga Nat Plants. 2020;10.1038/s41477-020-0653-z. doi:10.1038/s41477-020-0653-z

Michael Bunsick is first author of this Canadian-led study that includes Julie Scholes from the University of Sheffield as a co-author. Leading from a curiosity about the relationship between host root exudates and the parasitic plant Striga hermonthica, they were led to find that expression of Striga strigolactone-hormone receptor proteins in Arabidopsis is able to bypass the requirement for GA in seed germination. This demonstrates both how the Striga might sense host signals and that there is no absolute requirement for GA-during seed germination.


Desjardins SD, Ogle DE, Ayoub MA, et al (2020) MutS homologue 4 and MutS homologue 5 maintain the obligate crossover in wheat despite stepwise gene loss following polyploidization Plant Physiol. 2020;pp.00534.2020. doi:10.1104/pp.20.00534

Open Access

Stuart Desjardins is first author on his research led from the University of Leicester. They work with allotetraploid (AABB) durum wheat and show that this plant undergoes two pathways of meiotic recombination. They show that the class I pathway requires the MSH4 and MSH5 (MutSγ) proteins and the authors show that these genes are absent in hexaploid (AABBDD) wheat. These findings enable the authors to speculate about the function of these proteins in allopolyploid wheat.


Wang H, Wan Y, Buchner P, King R, Ma H, Hawkesford MJ (2020) Phylogeny and gene expression of the complete NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY (NPF) in Triticum aestivum L J Exp Bot. 2020;eraa210. doi:10.1093/jxb/eraa210 Open Access

Huadun Wang is first author on this manuscript that is led from Rothamsted Research and includes Chinese collaborators. They investigate the 331 member family of wheat NPF genes that encode membrane transporters that transport a diverse range of substrates. Phylogenetically these wheat NPF genes are closely clustered with Arabidopsis, Brachypodium and rice orthologs and this study and lays the foundation for their further functional analysis in wheat.

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