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.

MASC Annual Report: 2019-20

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Published on: June 17, 2020

Over the past thirty years the Multinational Arabidopsis Steering Committee (MASC) has represented the global Arabidopsis community through its collaborative oversight of the annual International Conference on Arabidopsis Research (ICAR), production of a MASC annual report and preparation of the series of decadal Roadmaps that have helped coordinate the future activities of the community.


The 2019-2020 MASC Annual Report includes reports from three stakeholder groups:

  1. Subject-area-specific subcommittees
    Bioinformatics 💻
    ORFoemics 🧬
    Epigenetics 🧬
    Immunity 🦠
    Metabolomics 🍕
    Natural Variation and Comparative Genomics 🌞☔️🧂
    Proteomics 💪
    Systems Biology 🧪
  2. Community projects
    @tair_news
    @BAR_PlantBio
    @GrameneDatabase
    @GlobalPlantGPC
    @ABRC_OSU
    @NascArabidopsis
    @EMPHASIS_EU
    @I_P_P_N
    International Arabidopsis Informatics Consortium
    RIKEN BioResource Center!
  3. Individual MASC member countries from thirty countries
    🇦🇷🇦🇺🇦🇹🇧🇪🇧🇷🇨🇦🇨🇱🇨🇳🇨🇿🇩🇰🇪🇪🇫🇮🇫🇷🇬🇷🇮🇳🇮🇪🇮🇱🇮🇹🇯🇵🇳🇿🇳🇴🇵🇱🇸🇦🇰🇷🇪🇸🇨🇭🇹🇼🇹🇷🇬🇧🇺🇸

The report is attached and you can download this PDF below.
http://arabidopsisresearch.org/images/publications/mascreports/MASC_Report_2020_Online_.pdf

Nicol Caplin discusses ionising radiation and plants in space!

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Published on: June 17, 2020

Nicol Caplin who worked at the University of the West of England discusses a paper in Frontier in Plant Science entitled ‘Developmental, Morphological and Physiological Traits in Plants Exposed for Five Generations to Chronic Low-Level Ionising Radiation‘. Nicol nows work for the European Space Agency so we also speculate about the relevance of her work to interplanetary Terraforming!

Sam Wilson talks to GARNet about Photosynthesis and NPQ.

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Published on: June 10, 2020

Sam Wilson from Queen Mary University of London discusses a recent paper in Plant Physiology entitled ‘Rethinking the influence of chloroplast movements on non-photochemical quenching and photoprotection‘. In this research they take a fresh look at the relationship between chloroplast movements and photoprotection.

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