GARNet talks to Candida Nibau

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Published on: March 25, 2020

Candida Nibau who works at Aberystwyth University discusses a paper recently published in The Plant Cell entitailed ‘CDKG1 Is Required for Meiotic and Somatic Recombination Intermediate Processing in Arabidopsis‘. We discuss this and plenty of other exciting future work! Please have a listen!

Opening up the Arabidopsis Proteome

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Published on: March 16, 2020

In 2000 the sequencing of the Arabidopsis thaliana genome was the starting gun for a new era in plant biology research. The remarkable community-facing tools that have been developed with a focus on this model organism include TAIR, the BAR and the 1001 Genomes project and have greatly benefited many researchers around the world.

Numerous studies have been investigated the Arabidopsis proteome in various tissues, cells or organelles taken from plants exposed to a range of biotic and abiotic challenges. However a new publication builds upon existing research with their analysis of the linkages that exist between Arabidopsis transcriptomes, proteomes and phosphoproteomes, each of which had be analysed from 30 different tissues types.

Mergner, J., Frejno, M., List, M. et al. (2020) Mass-spectrometry-based draft of the Arabidopsis proteome. Nature

Tissue map and multi-omics dataset

This German-led research team were able to estimate that there are 18000 translated proteins in Arabidopsis, which are phosphorylated at 43000 sites and that their absolute expression ranges over six-orders of magnitude.

Importantly they have provided community-access to this entire resource through the ProteomicsDB and ATHENA databases.

Data exploration in ATHENA and ProteomicsDB

Compared to a now-12 year old whole plant proteomic study, this work significantly increases predicted levels of protein abundance to include 18,210 out of the 27,655 protein-coding genes. No doubt these increases are due to technical improvements as well as improved Arabidopsis genome annotation (from TAIR7 to Araport 11). They confirmed previous information held within the PhosPhAT database that 47% of the proteome is phosphorylated, although the authors think this is likely an underestimation.

They identified fewer proteins that arise from low abundance transcripts, indicating that there are additional findings to be made in the lower protein abundance range and that they may be functionally important as many of these proteins could be involved in key processes of cell signaling and regulation of gene expression regulation.

Interestingly they find that most proteins do not vary in absolute tissue specificity but rather that plant morphological differences are most likely controlled through the differences in the relative abundance of those proteins. The storage protein CRA1 and photosynthetic RuBisco complex were found to have the expectedly high abundance in seeds and green tissues respectively, whilst both the transcriptome and proteome from pollen were found to be the most tissue diverse.

Overall the primary determinant of protein level was the level of transcript yet many other molecular factors were involved. Perhaps most frustratingly, the authors showed that 48% of variation in protein abundance was unexplained, highlighting the enormous amount of research that is still required even in this most well studied of plants.

By investigating the abundance of proteins arising from paralogous genes they showed that often a particular copy showed higher abundance and therefore might be a better target for future mutant studies, although the paper says nothing about any compensatory effects that might occur in mutant plants.

Examining the Phosphoproteome

The amount of phosphorylation within individual proteins was extremely variable with at one end of the spectrum the LEA protein family phosphorylated on every available serine, threonine or tyrosine residue. The authors speculate that this level of phosphorylation in these seed proteins may be important
 to regulate conformational state or phase transi
tion. The authors are careful to state that phosphorylation of a particular amino acid is not necessarily linked to function. However they did generate phosphomimetic mutants
 in the abscisic acid (ABA) receptor RCAR10, demonstrating a previously uncharacterised function for these amino acids during ABA signaling.

Ascribing function to protein phosphorylation

Overall this research provides evidence, if it were needed, that the co-analysis of multiple ‘omic databases can provide experimental insights that will guide future research. The authors hope that their online database and analysis resources will be useful tools for the community. Of course there is plenty to do and as one eminent plant scientist suggested, this is a nice starting-point toward a full 1001 Proteomes project 🙂

….What have you done for me lately. ?

GARNet Research Roundup: March 13th 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.

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.

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.

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.

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.

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 talks to Anne-Marie Labandera

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Published on: March 11, 2020

We talk to Anne-Marie Labandera from the University of Birmingham about a new paper published in New Phytologist entitled ‘The PRT6 N-degron pathway restricts VERNALIZATION 2 to endogenous hypoxic niches to modulate plant development‘.

This adds to the story introduced in a 2019 Nature Communications paper that we discussed with Dan Gibbs on the GARNet YouTube channel.

UK Rice Research Consortium Meeting: February 27-28th 2020

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Published on: March 4, 2020

            Rice is a major global food crop with an estimated 3.5 billion people taking 20% of their calories from different species of this grass. As such there are many scientific and international development reasons why UK researchers should conduct rice research, even though it is very unlikely to be ever grown commercially in this country……unless climate change is much more catastrophic than predicted!

            The UK Rice Research Community is small but growing. The inaugural open meeting took place in 2019 in Nottingham and the 2020 meeting was hosted by Bobby Caine and Andrew Fleming in Sheffield. This meeting focused on early career researchers, with all talks bar two given by PhD students or PDRAs, together with sessions on grant writing and careers advice as well as a horizon-scanning roundtable on what is needed to progress the community.

UKRRC Group Photo from @robertcaine19

            Given the challenges in growing rice in the UK, this community has excellent overseas collaborations with researchers at IRRI in the Philippines, Malaysia, Vietnam, across Africa and in the USA. However one of the highlighted difficulties in progressing this research comes with the required paperwork needed to obtain overseas germplasm!! This delays projects and reduces the impact of UK scientists. Unfortunately there are unlikely to be any quick fixes in this area. UK researchers would also like to see the establishment of a UK stockcentre, although perhaps the current number of active research groups might not make this any more viable than simple sharing germplasm between labs.

            As a new person to this community it was surprising to hear that there are significant difficulties even with growing plants in pots in the UK and that there isn’t a good reproducible source of ‘rice appropriate soil’ and therefore much time is lost troubleshooting even the most basic plant growth requirements. Rice is being grown down the spine of the country from Aberdeen, Durham, Sheffield, Nottingham and Rothamsted amongst other locations so there is the need for information sharing to reduce lost research time. Perhaps the UKRRC website is the place for these resources.

            As mentioned above many of the short talks featured overseas collaborations. Dr Jen Sloan from the Fleming lab in Sheffield introduced a project that generated plenty of interesting conversations. They have used an innovative CO2 priming strategy in an attempt to replicate the increased biomass produced in plants grown at constant elevated CO2. Indeed they showed that a 21day CO2 priming was sufficient to increase adult biomass both in the growth chamber and in the field. They have worked with Malaysian farmers to help the development of a field-priming system that uses fungal mycelium to produce the excess CO2. This technology is accessible for the Malaysian small-holder farmers and therefore might be a simple real world solution for increasing biomass. They will continue with this research program whilst beginning to also investigate the actual mechanism through which the CO2 priming works, which remains a big mystery!

Jen Sloan discusses CO2 priming

            Leonie Luginbuehl works with Julian Hibberd at the University of Cambridge and over the past few years has investigated which fluorescent proteins are the best to use in rice plants. She is developing the type of fundamental resource that will be very important for this research community moving forward. She has expanded this toolkit to develop nucleus-localized fluorescently tagged proteins that she is using for FACS and subsequent tissue-specific gene expression. Look out for that information over the coming years!

Leonie Luginbuehl introduces her work with fluorescent reporters.

            Due to their involvement with the major C4Rice project the Hibberd lab has a rice transformation pipeline but this challenging technique is usually beyond the scope of individual labs. Therefore the crop transformation facility at NIAB is very useful for community-members who wish to assess transgenic germplasm. The second round of applications for this FREE resource is open until March 31st and most applications are accepted given a robust scientific case.

            Most rice is first grown in a nursery and then transplanted into flooded paddy-fields. However direct seeding IS possible and even though it requires more intensive weeding, overall it has a lesser environmental impact. Most rice varieties have not been optimised for direct seeding and this is the focus of the project that Guillaume Menard is working on at Rothamsted. They collaborate with IRRI to conduct high-throughput phenotyping and imaging in their search of traits that can be linked to direct seeding. Although this is work remains in process they intend for their enormous amount of generated data to become publically available on the IRRI servers….watch that space…

            Meeting Co-organiser Bobby Caine has recently obtained a GCRF Global Challenges Research Fellowship from the University of Sheffield where he continues to work with Julie Gray to look at the role of stomatal density on environmental tolerance. This fellowship has given him the outstanding opportunity to interact with Vietnamese farmers to test their varied germplasm for stomatal alterations, with the ultimate aim of transferring beneficial traits into rice elite varieties.

Bobby Caine presenting the importance of stomata!

            Although the UK rice research community is small it was excellent to see that participants from the majority of institutes with this type of research attended this meeting and showed a real willingness to build future resource sharing and collaborative relationships. Hopefully these early career researchers can ‘grow older together‘ with this spirit of collaboration so that they can bring the UK’s excellent research infrastructure and history in discovery-led and applied resource to this globally important research area.

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