GARNet Research Roundup: August 16th 2019

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

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

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

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

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

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

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


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

Open Access

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

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

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

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


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

Open Access

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


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

Open Access

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


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

Open Access

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

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

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

Open Access

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


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

Open Access

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


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

Open Access

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


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

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


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

Open Access

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


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

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


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

Open Access

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


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

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

Report from Monogram 2019

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Published on: August 12, 2019

by Adeline Sourdille, James Hutton Institute, University of Dundee.

I first attended Monogram in Bristol in 2017 and did not have the opportunity to be there in 2018 in Norwich. After the success that Monogram 2017 had been, the expectations were high for the 2019 edition in Nottingham. Monogram is one of these meetings where its reputation precedes itself and I was particularly looking forward to sharing my work and exchanging with other cereals researchers from the UK and other parts in the world.


My work as a PhD student at the James Hutton Institute in Dundee, Scotland, is focusing on the effect of DNA-Methylation in barley, however I had the chance to work with the University of Cambridge on Arabidopsis material to assess how transferable the effect of the epigenome on meiotic recombination is from a model plant (Arabidopsis) to a rather complex cereal widely cultivated in Scotland (barley). Attending Monogram 2019 in Nottingham highlighted even more how crucial it is to maintain the bridge between model species and crops in order to better understand the mechanisms underlying the sustainable food production of tomorrow. This was particularly highlighted by the wide diversity of talks concerning many different species, from Wheat (obviously) to rice, as well as barley, brachypodium, maize, and so many more.

The JHI crew at #Monogram19 Photo @malcolmacaulay

Having transferred to academia to do my PhD after first working in the breeding world, which is much more applied, I also truly appreciated the perfect balance between fundamental research, such as gene and QTL mapping in wheat, by Jemima Brinton or the role of OsEPF1 in stomatal density, by Umar Mohammed, and applied projects with Alison Lovegrove’s talk about how to improve fibre content into white bread and Simon Orford’s description of how to use the Germplasm resources available at the John Innes Centre for breeders.

Simon Orford introdcues the GRU at the John Innes Centre. Photo @Notts-WRC

The talk which was the most surprising to me and one of the most interesting from the conference was given by Laura Gardiner from IBM research UK about how to use AI and genomics combined to improve crops. It is to me fascinating how much new computing technologies can bring into areas where you would not expect them, especially plant science.

The Poster Session was preceded by a Flash Presentation Session. This exercise is great to force scientist to condensate their research into a 60 seconds talk and a good opportunity to try and lure people to visit your poster. The Poster Session itself was nicely coupled with an outdoor barbecue and allowed for the most interesting discussions with other scientists and breeders, where the outcome mostly was some suggestions of what work could be done to complement the existing results I have generated. It was also a great opportunity to visit other people’s posters and discover the broad variety of science which people from the Monogram network do, from roots to flowers, from Arabidopsis to wheat, or from South to North!

Queuing to present a flash talk. Photo @Amma Simon

Finally, the organising team of Monogram 2019 in Nottingham did an amazing job with the choice of the conference and dinner venues. The Exchange building on the Jubilee Campus in Nottingham is in a charming environment surrounded by water and the conference dinner was held in the Albert Hall in the centre of Nottingham, which has splendid rooms and decors! Not to forget the close proximity to “Ye Old Trip To Jerusalem”, allegedly the oldest pub in the United Kingdom and definitely a place worth a stop if the occasion presents itself!

The University of Nottingham Jubilee Campus. Photo @mscott0106

All in all, I would like to deeply thank GARNet for allowing me to attend this conference and present my work there and will be looking forward to hosting all the Monogram community next year, in Dundee, Scotland!

XV Cell Wall Meeting 2019

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Published on: August 8, 2019

by Sam Amsbury, University of Leeds

In July I attended the XV Cell wall meeting hosted at the University of Cambridge. This was my first time at this meeting, held once every three years, and I was excited to meet so many members of the cell wall research community.


The meeting kicked off on the Sunday with a reception in the beautiful botanic gardens at Cambridge which provided an informal atmosphere to meet other delegates which contributed to a relaxed atmosphere in the sessions. The organising committee did an excellent job in putting together an extensive scientific programme with almost 90 talks and 170 posters to showcase a diversity of cell wall research areas and I felt very privileged to be selected to give a talk.

The Welcome Party. https://cellwall2019.org/

The talks were grouped by different research themes and were full of exciting science with lots of cutting edge unpublished research on display which was great to see. With no parallel sessions I was able to attend all the talks and was particularly interested in the composition, structure and architecture sessions where I learnt about a range of emerging new tools for studying cell wall structure which I hope to incorporate into my future work. I presented my work on the second day and this was my first talk at a major conference, an experience I found both daunting but incredibly valuable. Getting the chance to present my research led to a number of interesting conversations in the coffee/lunch breaks throughout the week both with new people and old collaborators which gave me a valuable different perspective on my data.


It was nice to see sessions specifically focused around equality and diversity and research ethics and it was great that these sessions were about as full as the other sessions. The talk of Professor Dame Athene Donald DBE, FRS was a particular highlight and I would encourage everyone to read her excellent blog (http://occamstypewriter.org/athenedonald/). Putting these issues at the heart of a conference raises their profile and helps to make everyone aware of how we can ensure a diverse and ethical community and all the associated benefits that brings.

Professor Donald provides an inspiration talk. Photo @donohoho

One of the excellent aspects of this meeting was how much time was dedicated to viewing the numerous posters making them an integral part of the meeting. This gave people the chance to engage with as many people as possible and I spoke to a wide range of people during these sessions making new contacts that will hopefully remain contacts as I progress through my career.

Networking is an important part of the Cell Wall meeting. Photo @meninatoxica

It was a pleasure to attend such an interesting meeting and meet so many excellent cell wall researchers. On the back of this meeting I have already embarked upon a new and exciting collaboration and I would like to thank GARNet for the travel grant to help me be able to afford to attend. I am already looking forward to the 2022 meeting in Malaga, Spain.

RMS Botanical Microscopy Meeting 2019

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Published on: August 8, 2019

by Chiara Perico, University of Bristol

The Botanical Microscopy Meeting is an international event organised by the Royal Microscopical Society (RMS). This year’s edition ran from the 14-18th April and was held in the Kenneth Wheare Hall, conference venue at Oxford Brookes University. The format of the meeting consisted of eight sessions: each of which was opened with a lecture from an invited speaker and followed by presentations from selected speakers. The sessions covered a variety of research areas in plant cell biology, ranging from fundamental cell biology to plant-pathogen interactions to new advances in botanical microscopy.


My abstract was selected for a presentation within the “Cytoskeleton” session. I’m particularly happy with the feedback provided during question time and useful discussions that arose, which helped me identify key experiments to be carried out during my future research. I also had the opportunity to discuss the strengths and weaknesses of some of my results with some of the world experts on the plant cytoskeleton who were present at the meeting.


Another highlight was the presentation by Dr. Jordi Chan (JIC, Norwich), whose research combines imaging and computer modelling and aims to unravel the mechanisms responsible for cell wall synthase deposition and how these can modulate cell shape and plant morphogenesis.

An example of Jordi Chan’s research. Link

Overall, the Botanical Microscopy Meeting was extremely relevant not only to present my research to a community of experts but also, as a final year PhD student, as a chance to establish a contact with potential future employers.


I would also like to thank GARNet for providing a travel grant and facilitating my participation in the meeting.

GARNet Workshop on 3D RNA-Seq Analysis Tool

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Published on: August 6, 2019

October 24th-25th 2019. University of Leeds.

Researchers at the James Hutton Institute and the University of Dundee-Plant Sciences have developed the 3D RNA-Seq Analysis Tool for the comprehensive differential expression, alternative splicing analysis and visualisation of RNASeq Data.

https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/

This program runs the analysis through a user-friendly graphical interface, can handle complex experimental designs, allows user setting of statistical parameters, visualizes the results through graphics and tables, and generates publication quality figures and customerised analysis reports.

It is designed to be run by biologists with minimal bioinformatics experience (or by bioinformaticians) allowing lab scientists to take control of the analysis of their RNA-seq data.


In order to provide training in this new software tool GARNet are hosting a workshop at the University of Leeds that is led by the creators of the 3D App, Wenbin Guo and Runxuan Zhang.

This workshop will take places at the University of Leeds and is hosted by GARNet Committee Member Yoselin Benitez-Alfonso.


Workshop Date: Thursday October 24th 12pm until Friday October 25th 5pm.

Location: Leeds Institute for Data Analytics, University of Leeds, Leeds, LS2 9JT

Workshop Cost: £30

Number of Delegates: Around 20

Further details on how to apply can be found on the workshop website:

https://garnet3drnaseqworkshop.weebly.com/

https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/

Workshop Schedule

Thursday October 24th 2019

12pm: Arrival and Lunch

1.15pm: Yoselin Benitez-Alfonso– Welcome to the University of Leeds

1.30pm: Runxuan Zhang– A suite of computational solutions for improved gene and transcript level analysis using RNA-seq.

2.30pm: Presenter fropm Earlham Institute- Data management hands-on session: Taking care of your data.

4.00pm: Tea Break

4.30pm: Pingtao Ding, The Sainsbury Laboratory, Norwich- Proof of Concept: Using the 3D RNA-Seq app to analyse expression changes under different immune activation conditions.

5.30pm: Runxuan Zhang and Wenbin Guo– Preparation for the hands on session: downloading the data, etc

7pm: Evening meal and drinks in Leeds

Friday October 25th 2019

9.00am: Runxuan Zhang and Wenbin Guo- Hands on session with 3D RNA-Seq App

10.30am: Tea Break

11.00am: Hands on session with 3D RNA-Seq App, continued

11.45am: Recapping main features of 3D RNA-Seq App and General Q+A

1.00pm: Lunch and General Meeting end

2.00pm: 1-2-1 sessions on analysis of own data.

https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/
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