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GARNet Research Roundup: June 26th 2020

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Published on: June 26, 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

https://register.gotowebinar.com/register/4555062676282771981

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.

GARNet Research Roundup: May 7th 2020

by Geraint

Categories: Edinburgh University, Glasgow University, Global, John Innes Centre, Sainsbury Lab, Uncategorized, University of Bristol, University of Cambridge, University of Edinburgh, University of Glasgow

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Published on: May 7, 2020

This edition of GARNet Research Roundup begins with two studies from the John Innes Centre. The first takes a detailed look at meiosis in Arabidopsis arenosa and the second introduces a novel mode of auxin perception.

The third paper from the Grierson lab in Bristol uses innovative methods to assess root-soil cohesion through study of root hairs. The fourth paper is also from Bristol and looks at the evolution of stomata.

The fifth and sixth papers are from Scotland. Firstly researchers at Edinburgh have developed a deep learning approach for plant phenotyping whilst in the second research from Glasgow looks at the role of UVR8 in the UV response of UV-B adapted plants.

The seventh paper is from The Sainsbury lab, Norwich and reveals a new role for phosphorylation in the formation of the RRS1-R/RPS4 immune receptor complex.

The final paper includes co-authors from Cambridge and looks at the role of epigenetic changes in the reponse to an experimentally evolved plant virus.

Morgan C, Zhang H, Henry CE, Franklin FCH, Bomblies K (2020) Derived alleles of two axis proteins affect meiotic traits in autotetraploid Arabidopsis arenosa. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1919459117 Open Access

Chris Morgan works at the John Innes Centre and leads this research that looks at meiosis in Arabidopsis arenosa. They use super resolution microscopy to look in great detail at the intertaction of the ASY1 and ASY3 loci. Chris discussed this work on the GARNet community podcast.

Kuhn A, Ramans Harborough S, McLaughlin HM, Natarajan B, Verstraeten I, Friml J, Kepinski S, Østergaard L (2020) Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. Elife doi: 10.7554/eLife.51787 Open Access

Andre Kuhn works with Lars Ostergaard at the John Innes Centre and leads this research that has identified a novel mode of auxin perception in which the ETTIN transcription factor directly interacts with auxin. This allows a rapid response that does not rely on the canonical mode of auxin perception via protein degradation. Andre discussed this work on the GARNet community podcast.

De Baets S, Denbigh TDG, Smyth KM, Eldridge BM, Weldon L, Higgins B, Matyjaszkiewicz A, Meersmans J, Larson ER, Chenchiah IV, Liverpool TB, Quine TA, Grierson CS (2020) Micro-scale interactions between Arabidopsis root hairs and soil particles influence soil erosion. Commun Biol. doi: 10.1038/s42003-020-0886-4 Open Access

This work from the University of Bristol is led by Sarah De Baets S, Tom Denbigh, Kevin Smyth, Beth Eldridge. They have developed a series o fthree innovative assays to investigate the role of root hairs in the cohesion of the roots-soil interaction. This research shows that root hairs play a significant role in this process. Tom and Beth discussed this work on the GARNet community podcast.

Harris BJ, Harrison CJ, Hetherington AM, Williams TA (2020) Phylogenomic Evidence for the Monophyly of Bryophytes and the Reductive Evolution of Stomata. Curr Biol. doi: 10.1016/j.cub.2020.03.048 Open Access

This paper from the University of Bristol is led by Brogan Harris and investigates the evolutionary origins of genes that specify stomatal development and function in bryophytes. They show that important stomatal lineage genes are present in bryophytes, indicating that their stomata have undergone reductive evolution.

https://linkinghub.elsevier.com/retrieve/pii/S0960-9822(20)30418-8

Dobrescu A, Giuffrida MV, Tsaftaris SA (2020) Doing More With Less: A Multitask Deep Learning Approach in Plant Phenotyping. Front Plant Sci. 2020 Feb 28;11:141. doi: 10.3389/fpls.2020.00141 Open Access

Andrei Dobrescu leads this methods paper from the University of Edinburgh that uses multitask deep learning to develop software for plant phenotying. They test their method on the analysis of Arabidopsis rosettes.

https://www.frontiersin.org/articles/10.3389/fpls.2020.00141/full

Liao X, Liu W, Yang HQ, Jenkins GI (2020) A dynamic model of UVR8 photoreceptor signaling in UV-B-acclimated Arabidopsis. New Phytol. doi: 10.1111/nph.16581 Open Access

Xinyang Liao leads this work from the University of Glasgow that continues the Jenkins’ lab research on the UVR8 photoreceptor. In this paper they analysed the role of UVR8 in UV-B-acclimated plants in which the switch between between monomeric and dimeric states can response to high UV-B without the need for new translation. This response is also alters the interaction of UVR8 with the COP1 and RUP2 proteins.

https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.16581

Guo H, Ahn HK, Sklenar J, Huang J, Ma Y, Ding P, Menke FLH, Jones JDG (2020) Phosphorylation-Regulated Activation of the Arabidopsis RRS1-R/RPS4 Immune Receptor Complex Reveals Two Distinct Effector Recognition Mechanisms. Cell Host Microbe. doi: 10.1016/j.chom.2020.03.008

Hailong Guo and Hee-Kyung Ahn work with Jonathan Jones at the Sainsbury lab, Norwich and lead this work that investigates the role of phosphorylation in the formation of the RRS1-R/RPS4 Immune Receptor Complex. This response is different to the effector-triggered conformational changes of RRS1 and represents a distinct novel route for immune signalling.

https://www.sciencedirect.com/science/article/abs/pii/S1931312820301724?via%3Dihub

Corrêa RL, Sanz-Carbonell A, Kogej Z, Müller SY, Ambrós S, López-Gomollón S, Gómez G, Baulcombe DC, Elena SF (2020) Viral Fitness Determines the Magnitude of Transcriptomic and Epigenomic Reprogramming of Defense Responses in Plants. Mol Biol Evol. doi: 10.1093/molbev/msaa091

This Spanish led study includes Regis Corrêa as lead author and includes David Baulcombe from Cambridge as a co-author. They infected Arabidopsis with an ancestral and experimentally-evolved isolates of turnip mosaic potyvirus (TuMV). The evolved version was more virulent and triggered a greater transcriptomic response in the plant as well inducing other epigenetic changes.

GARNet Research Roundup: April 9th 2020

by Geraint

Categories: Bristol University, Cambridge University, Glasgow University, Global, John Innes Centre, RHUL, Rothamsted Research, Sainsbury Lab, Uncategorized, University of Birmingham, University of Cambridge, University of Glasgow

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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: February 7th 2020

by Geraint

Categories: Aberystwyth University, Glasgow University, Global, James Hutton Institute, John Innes Centre, Rothamsted Research, Uncategorized, University of Dundee, University of Glasgow, University of Nottingham

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Published on: February 7, 2020

This latest edition of the GARNet Research Roundup begins with two studies that look at different aspects of lateral root formation and include members of Malcolm Bennett’s lab in Nottingham. The first investigates a critical role for hydropatterning in the control of lateral root initiation whilst the second looks at how cell death in overlying tissue layers plays an active role in the control of lateral root emergence.

The third paper is from the John Innes Centre and investigates the mechanism through which a small number of noncoding SNPs can alter chromatin dynamics at the FLC locus. The fourth paper is from Glasgow and assesses a link between auxin signaling and proteins involved in membrane trafficking.

The next paper is from Rothamsted Research and looks at how aerial differences in wheat cultivars can affect the root-associated microbiome. The sixth paper is from the James Hutton Institute and investigates the relationship between phosphate and zinc signaling during the growth of Brassica oleracea.

The final three papers focus on some aspect of plant mechanical strength. The first paper is from Aberystwyth and looks at the how mechanical stress impacts growth of Brachypodium. The next two papers are led from the US and Sweden respectively and include UK co-authors from Leeds, the JIC and York. The first looks at how lignin modifications illicits defence responses whilst the second begins to demonstrate how xyloglucan modifications alter secondary cell wall growth.

von Wangenheim D, Banda J, Schmitz A, Boland J, Bishopp A, Maizel A, Stelzer EHK, Bennett M (2020) Early developmental plasticity of lateral roots in response to asymmetric water availability. Nat Plants. doi: 10.1038/s41477-019-0580-z Open Access with link.

This brief communication is led by Daniel von Wangenheim, who worked with Malcolm Bennett and colleagues at the University of Nottingham. They use light sheet fluorescence microscopy to investigate how the local water environment controls the initiation of lateral root primordia. They show that this response is extremely plastic and that the initiation of pericycle cell files is linked to the external hydrological landscape. This study reveals a potential adaptive advantage when roots forage under heterogeneous soil conditions, which of course exists in all ‘real-world’ situations.

BotanyOne has written a nice blog about this paper and Daniel von Wangenheim has produced a superb explanatory video.

Escamez S, André D, Sztojka B, Bollhöner B, Hall H, Berthet B, Voß U, Lers A, Maizel A, Andersson M, Bennett M, Tuominen H (2020) Cell Death in Cells Overlying Lateral Root Primordia Facilitates Organ Growth in Arabidopsis. Curr Biol. doi: 10.1016/j.cub.2019.11.078 Open Access

Ute Voss and Malcolm Bennett from Nottingham are co-authors on this Finnish-led study in which Sacha Escamez is first author. They show that cell death occuring in advance of emerging lateral roots is an active developmental process rather than a passive effect of lateral root initiation. Plants with a cell-death-deficiency show delayed lateral root development, which is rescued through physical or genetic removal of outer cell files.

https://www.cell.com/current-biology/fulltext/S0960-9822(19)31580-5?_

Qüesta JI, Antoniou-Kourounioti RL, Rosa S, Li P, Duncan S, Whittaker C, Howard M, Dean C (2020) Noncoding SNPs influence a distinct phase of Polycomb silencing to destabilize long-term epigenetic memory at Arabidopsis FLC. Genes Dev. doi: 10.1101/gad.333245.119 Open Access

This research from the John Innes Centre is led by Julia Qüesta and Rea Antoniou-Kourounioti. They show that four noncoding SNPs in the Lov-1 Arabidopsis accession are responsible for the reactivation of FLC after only a short cold treatment. They combine experimentation and modelling to also propose that the control of FLC reactivation is linked to the extent of DNA replication during the cold period.

Rea discusses this paper on the GARNet Community podcast. Look out for it on February 19th.

http://genesdev.cshlp.org/content/early/2020/01/28/gad.333245.119.long

Xia L, Marquès-Bueno MM, Karnik RA (2020) Trafficking SNARE SYP132 Partakes in Auxin-associated Root Growth. Plant Physiol. doi: 10.1104/pp.19.01301 Open Access

This short communication is led by Lingfeng Xia in the Karnik lab at the University of Glasgow and looks at the role of auxin in the control of expression of the SNARE protein SYP132 during root growth and the gravitropic response. This linkage is indicative of an important role for membrane trafficking during the auxin response.

Kavamura VN, Robinson RJ, Hughes D, Clark I, Rossmann M, Melo IS, Hirsch PR, Mendes R, Mauchline TH (2020) Wheat dwarfing influences selection of the rhizosphere microbiome. Sci Rep. doi: 10.1038/s41598-020-58402-y
Open Access

Vanessa Kavamura is first author on this study led from Rothamsted Research that looks at how the aerial phenotypes of different wheat cultivars impacts root traits and the soil microbiome. Interestingly they show that taller wheat varieties are predicted to have a more connected bacterial network, which might lead to a more favourably rhizosphere for plant growth.

https://www.nature.com/articles/s41598-020-58402-y

Pongrac P, Fischer S, Thompson JA, Wright G, White PJ (2020) Early Responses of Brassica oleracea Roots to Zinc Supply Under Sufficient and Sub-Optimal Phosphorus Supply. Front Plant Sci. doi: 10.3389/fpls.2019.01645 Open Access

Paula Pongrac is the first author on this study led from the James Hutton Institute in which they investigate how plants respond to their access to environmental phosphate and zinc. They assess gene expression of Brassica oleracea plants grown under different mineral conditions and reveal important relationships between the response to phosphorous and zinc that will inform future nutrient supply strategies and identification of novel germplasm.

Gladala-Kostarz A, Doonan JH, Bosch M (2020) Mechanical stimulation in Brachypodium distachyon: implications for fitness, productivity and cell wall properties. Plant Cell Environ. doi: 10.1111/pce.13724.

Agnieszka Gladala‐Kostarz who works with Maurice Bosch at Aberystwyth University is the first author on this research that looked at the effect of both wind- and mechanical- treatments on growth of two accessions of Brachypodium distachyon. They catalogue the physical changes that occur in this important base-line study that tracks the relevance of these environmental factors on the multiple growth traits.

Gallego-Giraldo L, Liu C, Pose-Albacete S, Pattathil S, Peralta AG, Young J, Westpheling J, Hahn MG, Rao X, Knox JP, De Meester B, Boerjan W, Dixon RA (2020) ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1) releases latent defense signals in stems with reduced lignin content. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1914422117 Open Access

Lina Gallego-Giraldo is the first author on the US-led paper that includes Paul Knox and Sara Pose-Albacete from the University of Leeds. In this work they look at the link between lignin modifications and the inappropriate initiation of plant defence responses. They show that cell wall pectin remodeling mediated by the ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1) protein releases defence elicitors and as such provides important information on the link between these processes.

Kushwah S, Banasiak A, Nishikubo N, Derba-Maceluch M, Majda M, Endo S, Kumar V, Gomez L, Gorzsás A, McQueen-Mason S, Braam J, Sundberg B, Mellerowicz EJ (2020) Arabidopsis XTH4 and XTH9 contribute to wood cell expansion and secondary wall formation. Plant Physiol. doi: 10.1104/pp.19.01529 Open Access

Sunita Kushwah leads this Swedish-study that has co-authors from the JIC and York. They investigate a novel role for the XTH4 and XTH9 xyloglucan endo-transglycosylase/ hydrolases during secondary growth in Arabidopsis. The activity of these enzymes has a significant effect on cell wall composition and in the control of wood formation

https://www.nottingham.ac.uk/biosciences/people/ute.voss

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: November 22nd 2019

by Geraint

Categories: Cambridge University, Durham University, Glasgow University, Global, John Innes Centre, Lancaster Unversity, Nottingham University, SLCU, Uncategorized, University of Birmingham, University of Cambridge, University of Manchester, University of Nottingham, University of York

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Published on: November 22, 2019

This bumper edition of the GARNet Research Roundup begins with three papers that have a focus on the circadian clock. First is from Cambridge and looks at a novel role for TTG1 in control of the clock. The second paper also includes co-authors from Cambridge and looks at the clock Evening Complex. The final clock paper includes co-authors from York and looks at the new roles for EARLY FLOWERING 3 and GIGANTEA.

The next four papers include researchers from the John Innes Centre. Yiling Ding’s lab lead an exciting study into the role of RNA G-quadruplex to define liquid-liquid phase separations. Next David Seung and Alison Baker look at production of amylose starch across Arabidopsis accessions. The third JIC paper is from the Charpentier lab and looks at nuclear calcium signaling in the root. Finally Lars Ostergaard is a co-author on a paper that identifies a novel biostimulant that controls podshatter in Brassica.

The eighth paper is from Glasgow and describes the bioengineering of plants to express a novel antibiotic bacteriocin.

Next are three papers introduce exciting new research tools. 1. Weibei Yang in the Meyerowitz lab introduces a method for co-labeling of RNAs and protein 2. Researchers in Nottingham introduce RootNav2.0 for the automated measurement of root archtiectures 3. The Haydon Lab has developed a GAL4-GFP luciferase system for tissue-specific gene expression analysis.

Two Photosynthesis-based papers come next with firstly an analysis on the link between metabolism and the light response curve (from Manchester) and secondly a look at the role of aquaporins in control of CO2 conductance (Cambridge and Lancaster).

The fourteenth paper is from Durham and characterises an important protein regulator of the autophagy-dependent degradation pathway whilst the fifteenth is from Cambridge and uses cryo-SEM to analyse cell wall structures.

The penultimate paper is from Birmingham and looks at the role of redox signaling in aphid fecundity and the final paper includes co-authors from RHUL and looks at the interaction between the E2FB and RETINOBLASTOMA-RELATED proteins.

Airoldi CA, Hearn TJ, Brockington SF, Webb AAR, Glover BJ (2019) TTG1 proteins regulate circadian activity as well as epidermal cell fate and pigmentation. Nat Plants. doi: 10.1038/s41477-019-0544-3

This study from the University of Cambridge is led by Chiara Airoldi and introduces a new role for the TRANSPARENT TESTA GLABRA 1 (TTG1) WD-repeat (WDR) subfamily in the regulation of the circadian clock. TTG1 regulates epidermal cell differentiation and pigment production, while LIGHT-REGULATED WD1 and LIGHT-REGULATED WD2A are known to regulate the clock. The triple lwd1 lwd2 ttg1 mutant has no detectable circadian rhythym. This suggests that members of this protein family have undergone subfunctionalization to diverge from their core functions. This paper is of interest to those who research evolution of protein function as well as the to those interested in the control of the circadian clock.

https://www.nature.com/articles/s41477-019-0544-3

Tong M, Lee K, Ezer D, Cortijo S, Jung J, Charoensawan V, Box MS, Jaeger K, Takahashi N, Mas P, Wigge PA, Seo PJ (2019) The Evening Complex establishes repressive chromatin domains via H2A.Z deposition. Plant Physiol. doi: 10.1104/pp.19.00881

This collaboration between the UK and South Korea is led by Meixuezi Tong and investigates how the Evening Complex (EC) component of the circadian clock interacts with chromatin to control gene expression at dusk. This occurs through direct interaction with the SWI2/SNF2-RELATED complex and together they bind to the core clock genes PRR7 and PRR9, causing the deposition of H2A.Z at these loci subsequent to causing their repression at dusk.

Anwer MU, Davis A, Davis SJ, Quint M (2019) Photoperiod sensing of the circadian clock is controlled by EARLY FLOWERING 3 and GIGANTEA. Plant J. doi: 10.1111/tpj.14604

Amanda Davies and Seth Davies from the University of York are co-authors on this German-led study with Muhammad Anwer as both first and corresponding author. They look at the role of important circadian regulators ELF3 and GIGANTEA through generation of previously unanalysed elf3gi double mutants. In these plants the circadian oscillator fails to synchronize to light-dark cycles even under diurnal conditions, demonstrating that these genes act together to convey photoperiod sensing to the central oscillator.

Zhang Y, Yang M, Duncan S, Yang X, Abdelhamid MAS, Huang L, Zhang H, Benfey PN, Waller ZAE, Ding Y (2019) G-quadruplex structures trigger RNA phase separation. Nucleic Acids Res. doi: 10.1093/nar/gkz978
Open Access

Yueying Zhang is the first author of this study conducted in the lab of Yiliang Ding at the John Innes Centre, in collaboration with the Benfey lab in the USA. They reveal an exciting mode of regulating RNA activity through the formation of RNA G-quadruplex (GQ) complexes. They use the SHORTROOT mRNA as the model for this study, showing that GQ-mediated complex formation can bring liquid-liquid phase separation. This study is of fundamental importance as it provides the first evidence that RNA can adopt structural motifs to trigger and/or maintain the specificity of RNA-driven phase separation.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz978/5624975?guestAccessKey=d3913912-fdbb-4f35-aa71-625442722842

Seung D, Echevarría-Poza A, Steuernagel B, Smith AM (2019) Natural polymorphisms in Arabidopsis result in wide variation or loss of the amylose component of starch. Plant Physiol. doi: 10.1104/pp.19.01062
Open Access

David Seung at the John Innes Centre the first and corresponding author of this study that used data from the Arabidopsis 1135 Genome project to investigate the prevelance of amylose production. Plants with amylose-free starch have no detrimental phenotypes so the function of this glucose-polymer, that accounts for up to 30% of all natural starch, is unknown. They looked at the polymorphisms within the GRANULE-BOUND STARCH SYNTHASE (GBSS) enzyme, identifying natural accessions that have no GBSS activity yet are viable within their natural environments. This study is a prelude to future research that will discover the adaptive significance of amylose.

Leitão N, Dangeville P, Carter R, Charpentier M (2019) Nuclear calcium signatures are associated with root development. Nat Commun. doi: 10.1038/s41467-019-12845-8
Open Access

Nuno Leitao is first author on this research from the Charpentier lab at the John Innes Centre. They looked at the role of nuclear Ca2+ signalling on primary root meristem development and auxin homeostasis through activity of the nuclear membrane localised ion channel DOES NOT MAKE INFECTIONS 1 (DMI1). This study discovers a previously unappreciated role for intracellular Ca2+ signalling during plant development.

Łangowski Ł, Goñi O, Quille P, Stephenson P, Carmody N, Feeney E, Barton D, Østergaard L, O’Connell S (2019 A plant biostimulant from the seaweed Ascophyllum nodosum (Sealicit) reduces podshatter and yield loss in oilseed rape through modulation of IND expression. Sci Rep. doi: 10.1038/s41598-019-52958-0
Open Access

Lars Ostergaard is a co-author on this Irish-study led by Lukasz Łangowski that investigates the factors that control pod shatter in oil seed rape. They show that the seaweed Ascophyllum nodosum-based biostimulant (Sealicit) is able to reduce podshatter by effecting the expression of the major regulator of pod shattering, INDEHISCENT. This has implications for the use of this compound by farmers wanting to reduce the amount of seed loss due to premature pod shatter.

Rooney WM, Grinter RW, Correia A, Parkhill J, Walker DC, Milner JJ (2019) Engineering bacteriocin-mediated resistance against the plant pathogen Pseudomonas syringae. Plant Biotechnol J. doi: 10.1111/pbi.13294
Open Access

William Rooney at the University of Glasgow is lead author on this study that attempts to combat Pseudomonas syringae infections through expression of a novel protein antibiotic bacteriocin, putidacin. They show that transgenic expression of this bacterial protein provides effective protection against Pseudomonas. This proof of concept opens the possibility for more widespread use of bacteriocins as an effective plant protection strategy.

https://onlinelibrary.wiley.com/doi/epdf/10.1111/pbi.13294

Yang W, Schuster C, Prunet N, Dong Q, Landrein B, Wightman R, Meyerowitz EM (2019) Visualization of Protein Coding, Long Non-coding and Nuclear RNAs by FISH in Sections of Shoot Apical Meristems and Developing Flowers. Plant Physiol. doi: 10.1104/pp.19.00980
This extended methods paper is led by Weibing Yang at the Sainsbury lab in Cambridge. They have adapted RNA fluorescence in situ hybridization (rnaFISH) to explore RNA localization in the shoot apical meristem of Arabidopsis. They are able to label mRNA as well as long ncRNAs and have developed double labeling to assay two separate RNAs in the same cell and to assess nucleo-cytoplasmic separation of RNA species. Finally they link rnaFISH with fluorescence immunocytochemistry for the simultaneous localization of a single genes mRNA and protein.

https://www.frontiersin.org/articles/10.3389/fpls.2019.01398/full

Yasrab R, Atkinson JA, Wells DM, French AP, Pridmore TP, Pound MP (2019) RootNav 2.0: Deep learning for automatic navigation of complex plant root architectures. Gigascience. doi: 10.1093/gigascience/giz123
Open Access

Robail Yasrab is lead author on this work from the University of Nottingham that introduces the RootNav2.0 software tool. This was developed by modern deep-learning approaches and allows the fully automated measurement of vertically growth root systems. RootNav2.0 was favourably compared with its semi-automated predecessor RootNav1.0 and can be used for measurement of root architectures from a range of different plant species.

Román Á, Golz JF, Webb AA, Graham IA, Haydon MJ (2019) Combining GAL4 GFP enhancer trap with split luciferase to measure spatiotemporal promoter activity in Arabidopsis. Plant J. doi: 10.1111/tpj.14603

This technical advance is led by Angela Roman, was in the Haydon lab during its time at the University of York. They have used the GAL4-GFP enhancer trap system, to develop a tissue-specific split luciferase assay for non-invasive detection of spatiotemporal gene expression in Arabidopsis. In this example they use the study to measure dynamics of circadian gene expression but is clearly applicable to answer many other experimental questions.

Herrmann HA, Schwartz JM, Johnson GN (2019) From empirical to theoretical models of light response curves – linking photosynthetic and metabolic acclimation. Photosynth Res. doi: 10.1007/s11120-019-00681-2
Open Access

Helena Herrmann is lead author on this work fro the University of Manchester. In this study they developed and then empirically tested a series of simple kinetic models that explains the metabolic changes that are required to alter light response curves (LRCs) across a range of temperatures. This allowed them to show how changes in NADPH and CO2 utilization respond to environmental changes. This provides useful information as to how a plant adapts its metabolic response to light depending on the growth temperature.

Helena explaining her research

Kromdijk J, Głowacka K, Long SP (2019) Photosynthetic efficiency and mesophyll conductance are unaffected in Arabidopsis thaliana aquaporin knock-out lines. J Exp Bot. doi: 10.1093/jxb/erz442

Open Access
Wanne Kromdijk leads this US-led research that includes contributions from the Universities of Cambridge and Lancaster. They looked at the potential role of membrane-bound aquaporins in the control of diffusion conductance for CO2 transfer from substomatal cavity to chloroplast stroma (gm). They tested three aquaporin mutants across a range of light and CO2 concentrations and surprisingly found that they appear to play no significant contribution to the control of gm. The reporting of this type of ‘negative’ result will prevent unnecessary replication of experiments and help to streamline the research process.

Wang P, Pleskot R, Zang J, Winkler J, Wang J, Yperman K, Zhang T, Wang K, Gong J, Guan Y, Richardson C, Duckney P, Vandorpe M, Mylle E, Fiserova J, Van Damme D, Hussey PJ (2019) Plant AtEH/Pan1 proteins drive autophagosome formation at ER-PM contact sites with actin and endocytic machinery. Nat Commun. doi: 10.1038/s41467-019-12782-6
Open Access

Pengwei Wang is first author in this research led from Durham University that incudes Chinese and Belgian collaborators. They show that the AtEH/Pan1 protein is involved with actin cytoskeleton regulated autophagy and recruits multiple other components to autophagosomes during this process. In addition they show vesicle bound-AtEH/Pan1 interact with VAP27-1 at the ER-PM. This demonstrates that AtEH/Pan1 is a key component of the autophagy-dependent degradation pathway.

Lyczakowski JJ, Bourdon M, Terrett OM, Helariutta Y, Wightman R, Dupree P (2019) Structural Imaging of Native Cryo-Preserved Secondary Cell Walls Reveals the Presence of Macrofibrils and Their Formation Requires Normal Cellulose, Lignin and Xylan Biosynthesis. Front Plant Sci. doi: 10.3389/fpls.2019.01398
Open Access

Jan Lyczakowski from the Dupree lab at the University of Cambridge is first author on this study that has adapted low temperature scanning electron microscopy (cryo-SEM) to visualize the cell walls of both angiosperm and gymnosperms. They have used Arabidopsis mutants to reveal that cell wall macrofibrils at composed of cellulose, xylan, and lignin. They demonstrate that cryo-SEM is a useful tool for native nanoscale cell wall architectures.

Rasool B, Karpinska B, Pascual J, Kangasjärvi S, Foyer CH (2019) Catalase, glutathione and protein phosphatase 2A-dependent organellar redox signalling regulate aphid fecundity under moderate and high irradiance. Plant Cell Environ. doi: 10.1111/pce.13669
Brwa Rasool is first author on this collaboration between the Universities of Birmingham and Helsinki that looks at how aphids respond to redox changes in Arabidopsis thaliana grown under different light conditions. They also identified defence-related transcription factors differentially upregulated by aphid predation in different light conditions. Overall they show aphid fecundity is in part determined by the plants cellular redox signaling.

Őszi E, Papdi C, Mohammed B, Pettkó-Szandtner A, Vaskó-Leviczky T, Molnár E, Ampudia CG, Khan S, Lopez-Juez E, Horváth B, Bögre L, Magyar Z (2019) E2FB interacts with RETINOBLASTOMA RELATED and regulates cell proliferation during leaf development. Plant Physiol. doi: 10.1104/pp.19.00212
Erika Oszi is first author of this Hungarian-led research that includes co-authors from Royal Holloway University of London. This research looks at the interaction between the transcription factors E2FB and RETINOBLASTOMA-RELATED (RBR) and how this contributes to cell proliferation during organ development in Arabidopsis leaves. The relationship between these proteins changes throughout the stages of leaf development and is critical to determine final leaf cell number.

http://www.plantphysiol.org/content/early/2019/11/06/pp.19.00212.long

GARNet Research Roundup: July 5th 2019

by Geraint

Categories: Cambridge University, Glasgow University, Global, James Hutton Institute, John Innes Centre, Nottingham University, Oxford Brookes University, Uncategorized, University of Dundee, University of Leicester, University of Nottingham

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Published on: July 5, 2019

This edition of the GARNet research roundup begins with a study from the University Leicester that investigates the rate of selection of genes expressed in Arabidopsis pollen.

The second and third papers focus on the function of members of the AP2 family of transcription factors. Sarah McKim’s lab in Dundee characterizes the role of APETALA2 during barley stem elongation whilst the other paper investigates the function of the Arabidopsis PUCHI gene and includes co-authors from the University of Nottingham.

The fourth paper is from Lars Ostergaard’s lab at the John Innes Centre and demonstrates the benefit of using models to understand developmental processes in crop plants. The next paper from the University of Glasgow investigates the plant response to low fluence rates of UV-B light.

The penultimate paper features authors from Oxford Brookes University and characterizes a novel LINC-KASH protein in maize whilst the final paper is from the University of Cambridge and investigates the novel function of two members of DUF579 family in methylation of glucuronic acid residues.

Harrison MC, Mallon EB, Twell D, Hammond RL (2019) Deleterious mutation accumulation in Arabidopsis thaliana pollen genes: a role for a recent relaxation of selection. Genome Biol Evol. doi: 10.1093/gbe/evz127

Open Access

This research from Hammond and Twell lab’s at the University of Leicester uses Arabidopsis to investigate the hypothesis that pollen genes evolve faster than sporophytic genes. This study is challenging to perform in Arabidopsis as for the past million years the plant has been self-compatible, which causes reduction in pollen competition, increased homozygosity and a dilution of masking in diploid expressed, sporophytic genes. This study has two main findings: firstly prior to becoming self-compatible pollen genes evolved faster than sporophytic genes. Secondly, since becoming self-compatible selection has relaxed causing higher polymorphism levels and a higher build-up of deleterious mutations.

https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evz127/5519772

Patil V, McDermott HI, McAllister T, Cummins M, Silva JC, Mollison E, Meikle R, Morris J, Hedley PE, Waugh R, Dockter C, Hansson M, McKim SM (2019) APETALA2 control of barley internode elongation. Development. doi: 10.1242/dev.170373

Open Access

Vrushali Patil leads his study from the lab of current GARNet committee member Sarah McKim at the James Hutton Institute in Dundee. They show that the APETALA2 (AP2) transcription factor is necessary for stem elongation in Barley. In addition they demonstrate that AP2 expression is controlled by the activity of the microRNA mi172 as well as jasmonate signaling.

https://dev.biologists.org/content/146/11/dev170373.long

Trinh DC, Lavenus J, Goh T, Boutté Y, Drogue Q, Vaissayre V, Tellier F, Lucas M, Voß U, Gantet P, Faure JD, Dussert S, Fukaki H, Bennett MJ, Laplaze L, Guyomarc’h S (2019) PUCHI regulates very long chain fatty acid biosynthesis during lateral root and callus formation. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1906300116

Julien Lavenus, Ute Voß and Malcolm Bennett from University of Nottingham are co-authors on this French-led study that investigates the mechanism by which the AP2 family transcription factor PUCHI controls lateral root development. By performing a transcriptional analysis of developing lateral root cells they show that genes involved in very long chain fatty acid (VLCFA) biosynthesis enzymes are induced in a PUCHI dependent manner. Concomitantly they show puchi-1 mutant roots have reduced VLCFA content when compared with wildtype roots. They conclude that PUCHI regulates VLCFA biosynthesis as part of a pathway controlling cell proliferation during lateral root formation.

Stephenson P, Stacey N, Brüser M, Pullen N, Ilyas M, O’Neill C, Wells R, Østergaard L (2019) The power of model-to-crop translation illustrated by reducing seed loss from pod shatter in oilseed rape. Plant Reprod. doi: 10.1007/s00497-019-00374-9

Open Access

Pauline Stephenson and Lars Østergaard at the John Innes Centre lead this study in which they demonstrate that lessons learnt from understanding the genes involved in fruit ripening in Arabidopsis lead to an ability to adjust the pod-opening process in oilseed rape. They have combined two mutant alleles, first characterized in Arabidopsis, to develop OSR plants that have significantly increased yield. In addition they present a new software tool for the analysis of pod shatter data in other crops plants.

O’Hara A, Headland LR, Díaz-Ramos LA, Morales LO, Strid Å, Jenkins GI (2019) Regulation of Arabidopsis gene expression by low fluence rate UV-B independently of UVR8 and stress signaling. Photochem Photobiol Sci. doi: 10.1039/c9pp00151d

Open Access

This UK-Swedish collaboration is led by Andrew O’Hara from the Jenkins lab in the University of Glasgow. They continue the lab focus on the UV-B receptor UVR8, in this case performing a transcriptomic analysis of wildtype and uvr8 mutants grown under low UV-B fluence rates. They analyse one differentially expressed gene in more detail, the transcription factor ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 13 (ANAC13), which was induced by UV-B but by the activity of any other photoreceptor.

Gumber HK, McKenna JF, Tolmie AF, Jalovec AM, Kartick AC, Graumann K, Bass HW (2019) MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation Nucleus. doi: 10.1080/19491034.2019.1629795

Open Access

Hardeep Gumber is first author on this US-led study that includes Joe KcKenna, Andrea Tolmie and Katja Graumann from Oxford Brookes as co-authors. They characterise the Maize LINC KASH AtSINE-like2 protein, MLKS2, whose targeting to the nuclear periphery requires its N-terminal armadillo repeats. Mutant mlks2 plants have pleiotropic plant phenotypes and on a nuclear level show defects in chromosome segregation and positioning. These findings support a model in which cytoplasmic actin is linked to chromatin through the LINC-KASH nuclear envelope network.

https://www.tandfonline.com/doi/full/10.1080/19491034.2019.1629795

Temple H, Mortimer JC, Tryfona T, Yu X, Lopez-Hernandez F, Sorieul M, Anders N, Dupree P (2019) Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis. Plant Direct. doi: 10.1002/pld3.117

Open Access

Henry Temple is first author on this work from the University of Cambridge that characterizes two members of the DUF579 family (AGM1 and AGM2). These proteins are required for 4-O-methylation of glucuronic acid within highly glycosylated arabinogalactan proteins (AGPs).

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GARNet Research Roundup: April 11th 2019

by Geraint

Categories: Aberystwyth University, Glasgow University, Global, James Hutton Institute, Nottingham University, QMUL, RHUL, Uncategorized, University of Dundee

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Published on: April 11, 2019

This edition of the GARNet Research Roundup is led by two papers from John Christie’s lab at the University of Glasgow. First is a study that looks at the function of the NPH3 protein during phototropism whilst the second paper is a collaboration with Mike Blatt’s group and has used an synthetic biology approach to increase plant biomass by altering stomatal conductance.

Third is a paper from the University Dundee and James Hutton Institute that looks at the extent of alternative splicing of long non-coding RNAs in response to cold stress.

The fourth paper is from Royal Holloway and defines the role of a MAP kinase module during meristem development. The fifth paper is led by Charles Spillane in Galway and includes Mary O’Connell at the University of Nottingham as a co-author and investigates the selective pressures that are applied to parentally imprinted genes.

The penultimate paper is from Aberystwyth and uses microCT imaging to determine grain parameters in wheat and barley whilst the final paper is from Queens Mary University of London looks at nonphotochemical quenching in Berteroa incana.

Sullivan S, Kharshiing E, Laird J, Sakai T, Christie J (2019) De-etiolation Enhances Phototropism by Modulating NON-PHOTOTROPIC HYPOCOTYL 3 Phosphorylation Status. Plant Physiol. doi: 10.1104/pp.19.00206

Open Access

http://www.plantphysiol.org/content/early/2019/04/08/pp.19.00206.long

Stuart Sullivan is first author on this work from John Christie’s lab at the University of Glasgow in which they investigate the functional significance of dephosphorylation of the NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3) protein that occurs following activation of Phototropin receptor kinases. They show that plant greening (de-etiolation) enhances phototropic responses that are coincident with reduced NPH3 dephosphorylation and increased plasma membrane retention of the protein. They further investigate other genetic and environmental factors that impact NPH3 dephosphorylation, which allows young seedlings to maximise their establishment under changing light conditions.

Papanatsiou M, Petersen J, Henderson L, Wang Y, Christie JM, Blatt MR (2019) Optogenetic manipulation of stomatal kinetics improves carbon assimilation, water use, and growth. Science. doi: 10.1126/science.aaw0046

Maria Papanatsiou is lead author on this work from the University of Glasgow that occured in the labs of Mike Blatt and John Christie. They aimed to address a phenomonen that occurs during changing environmental conditions in which stomatal dynamics lag behind biochemical photosynthetic changes. This prevents plants from maximising their outputs due to inefficiencies in gas and water exchange. In this work they express a synthetic blue light-gated K+ channel BLINK1 in guard cells. This introduced a K+ conductance to these cells resulting in accelerated stomatal opening under light exposure and closing after irradiation. Ultimately they show that this significantly increases biomass without incurring a water use cost. This approach has clear potential for improving plant productivity under changing environmental conditions.

https://science.sciencemag.org/content/363/6434/1456.long

Calixto CPG, Tzioutziou NA, James AB, Hornyik C, Guo W, Zhang R, Nimmo HG, Brown JWS (2019) Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs. Front Plant Sci. doi: 10.3389/fpls.2019.00235

Open Access

Cristiane Calixto and John Brown from the University of Dundee and the James Hutton Institute lead this study into alternative splicing of lncRNAs in response to cold. This is a follow-up to their large scale scale study on the extent of alternative splicing in Arabidopsis. The authors identified 135 lncRNA genes with cold-dependent differential expression (DE) and/or differential alternative splicing (DAS), some of which were highly sensitive to small temperature changes. This system identified a set of lncRNAs that could be targets for future research aimed at understanding how plants respond to cold and freezing stresses.

Dóczi R, Hatzimasoura E, Farahi Bilooei S, Ahmad Z, Ditengou FA, López-Juez E, Palme K, Bögre L (2019) The MKK7-MPK6 MAP Kinase Module Is a Regulator of Meristem Quiescence or Active Growth in Arabidopsis. Front Plant Sci. doi: 10.3389/fpls.2019.00202

Open Access

https://www.frontiersin.org/articles/10.3389/fpls.2019.00202/full

Robert Doczi is the first author on this UK, Hungarian and German collaboration that is led from Royal Holloway University of London. They use genetic approaches to show that the MKK7-MPK6 MAP kinase module is a suppressor of meristem activity. They use mkk7 and mpk6 mutants as well as overexpression lines to demonstrate that perturbation of the MAPK signaling pathway alters both shoot and root meristem development and plays important roles in the control of plant developmental plasticity.

Tuteja R, McKeown PC, Ryan P, Morgan CC, Donoghue MTA, Downing T, O’Connell MJ, Spillane C (2019) Paternally expressed imprinted genes under positive Darwinian selection in Arabidopsis thaliana. Mol Biol Evol. doi: 10.1093/molbev/msz063

Open Access

Reetu Tuteja from the National University of Ireland at Galway is first author on this paper that includes Mary O’Connell from the University of Nottingham. The authors used Arabidopsis to look at 140 endosperm-expressed genes that are regulated by genomic imprinting and found that they were evolving more rapidly than expected. This investigation was extended across 34 other plant species and they found that paternally, but not maternally imprinted genes were under positive selection, indicating that imprinted genes of different parental origin were subject to different selective pressures. This data supports a model wherein positive selection effects paternally-expressed genes that are under continued conflict with maternal sporophyte tissues.

https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msz063/5380439

Hughes N, Oliveira HR, Fradgley N, Corke FMK, Cockram J, Doonan JH, Nibau C (2019) μCT trait analysis reveals morphometric differences between domesticated temperate small grain cereals and their wild relatives. Plant J doi: 10.1111/tpj.14312

Open Access

https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.14312

Nathan Hughes and Candida Nibau at the Aberystwyth University lead this work that uses microCT imaging alongside novel image analysis techniques and mathematical modeling to assess grain size and shape across accessions of wheat and barley. They find that grain depth is a major driver of shape change and that it is also an excellent predictor of ploidy levels. In addition they have developed a model that enables the prediction of the origin of a grain sample from measurements of its length, width and depth.

Wilson S, Ruban AV (2019) Enhanced NPQ affects long-term acclimation in the spring ephemeral Berteroa incana. Biochim Biophys Acta Bioenerg. doi: 10.1016/j.bbabio.2019.03.005

This study is led by Sam Wilson and Alexander Ruban at QMUL and investigates nonphotochemical quenching in the Arabidopsis-relative Berteroa incana. They show that light tolerance and ability to recover from light stress is greatly enhanced in Berteroa compared to Arabidopsis. This is due to faster synthesis of zeaxanthin and a larger xanthophyll cycle (XC) pool available for deepoxidation. This result gives B.incana a greater capacity for protective NPQ allowing enhanced light-harvesting capability when acclimated to a range of light conditions. The authors suggest this short-term protection prevents the need for the metabolic toll of making long-term acclimations.

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