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.

GARNet Research Roundup: May 29th 2020

This bumper GARNet Research Roundup begins with two sets of papers in related areas. First are three papers that investigate the biology of plasmodesmatata. These include work from the Faulkner lab at the JIC, the Band lab at Nottingham and a broad European collaboration that includes co-authors from Durham, Cambridge and St Andrews.

The second set of two papers features work on different species of Kalanchoë, which is a key model for the study of CAM. This research is from the Hartwell lab in Liverpool and the Borland lab in Newcastle.

The fifth paper is from RHUL and looks at the relationship between nucleus and chloroplast signaling. The sixth paper is from QMUL and introduces research suggesting that a rethink is needed in our understanding of the relationship between chloroplast movement and photoprotection.

The next paper is from the University of the West of England and looks at the effect of ionising radiation on multiple generation of Arabidopsis growth whilst the eighth paper investigates the relationship between starch degradation and stomatal movements in guard cells and includes co-authors from Essex and Glasgow.

The next two papers include research undertaken in Cambridge; firstly looking at the integration of signalling between karrikin and strigolactone signaling in rice and secondly identifying a novel mRNA thermoswitch that controls thermomorphogenesis.

The next paper is a pan-European project led from Nottingham that has characterised the role of the CEP5 peptide during regulation of osmostic stress, drought and auxin signaling.

The twelveth paper is from the University of Warwick and also looks at the auxin response, this time during senescence. The next paper as well includes co-authors from Warwick in a study that investigates the global regulatory role for the histone acetyltransferase GCN5.

The penultimate paper includes co-authors from Norwich Research Park looks at the evolution of immune NLR signaling between closely related species. The final paper includes Patrick Hussey from Durham as a co-author in a Spanish study that identifies an uncharacterized compartment of the plant vacuolar trafficking pathway.


Cheval C, Samwald S, Johnston MG, de Keijzer J, Breakspear A, Liu X, Bellandi A, Kadota Y, Zipfel C, Faulkner C (2020) Chitin perception in plasmodesmata characterizes submembrane immune-signaling specificity in plants. Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9621-9629. doi: 10.1073/pnas.1907799117 Open Access

Cecilia Cheval, Sebastian Samwald and Matthew Johnston are co-first authors on this work from the Faulkner lab at the John Innes Centre. They looked at a plasmodesmata-localised plasma membrane microdomain, which hosts specific receptors and responses. They showed that immune chitin signalling requires the plasmodesmal PM localised LYM2 and LYK4 proteins. Overall this demonstrates that distinct membrane domains can integrate common signals to produce a localized response.

https://www.pnas.org/content/117/17/9621.long

Brault ML, Petit JD, Immel F, Nicolas WJ, Glavier M, Brocard L, Gaston A, Fouché M, Hawkins TJ, Crowet JM, Grison MS, Germain V, Rocher M, Kraner M, Alva V, Claverol S, Paterlini A, Helariutta Y, Deleu M, Lins L, Tilsner J, Bayer EM (2020) Multiple C2 domains and transmembrane region proteins (MCTPs) tether membranes at plasmodesmata. EMBO Rep. 2019 Aug;20(8):e47182. doi: 10.15252/embr.201847182 Open Access

Marie Brault works with Emmualle Bayer is first author on this French-led pan-European study that includes co-authors from Durham, Cambridge and St Andrews. They investigate the plasmodesmal plasma membrane and show that Multiple C2 domains and transmembrane region proteins (MCTP) are needed to tether ER-PM linkages at this location. They show Atmctp3/Atmctp4 loss of function double mutants have plant developmental defects demonstrating that MCTPs also play a significant role in cell-to-cell signalling.

https://www.embopress.org/doi/full/10.15252/embr.201847182#.XSRrrlB2xG0.twitter

Mellor NL, Voß U, Janes G, Bennett MJ, Wells DM, Band LR (2020) Auxin fluxes through plasmodesmata modify root-tip auxin distribution. Development. doi: 10.1242/dev.181669 Open Access

Nathan Mellor leads this research from the University of Nottingham that has developed a model to explain auxin movement around the Arabidopsis root tip. They propose that carrier mediated movement is not sufficient foir this and that there must be a symplastic route via plasmodesmata. This introduces plasmodesmata as playing a key role in hormone signaling.

https://dev.biologists.org/content/147/6/dev181669

GARNet committee member Yoselin Benitez-Alfonso discusses her labs work on plasmodesmata in the first #GARNetPresents webinar


Boxall SF, Kadu N, Dever LV, Kneřová J, Waller JL, Gould PJD, Hartwell J (2020) Kalanchoë PPC1 Is Essential for Crassulacean Acid Metabolism and the Regulation of Core Circadian Clock and Guard Cell Signaling Genes. Plant Cell. doi: 10.1105/tpc.19.00481

Susie Boxall leads this study from the Hartwell lab at the University of Liverpool in which they investigate the role of the phosphoenolpyruvate carboxylase gene in the CAM-plant Kalanchoë laxiflora. They use RNA interference to silence the PPC1 gene and show that these transgenic plants have defects in guard cell signaling and regulation of the circadian clock. These findings provide direct evidence that the regulatory patterns of key guard cell signaling genes are linked with the characteristic inverse pattern of stomatal opening and closing during CAM.

http://www.plantcell.org/content/32/4/1136.long

Abraham PE, Hurtado Castano N, Cowan-Turner D, Barnes J, Poudel S, Hettich R, Flütsch S, Santelia D, Borland AM (2020) Peeling back the layers of Crassulacean acid metabolism: functional differentiation between Kalanchoë fedtschenkoi epidermis and mesophyll proteomes. Plant J. doi: 10.1111/tpj.14757 Open Access

Paul Abraham is first author on this work from the Borland lab at the University of Newcastle. They are working with the CAM species Kalanchoë fedtschenkoi and here perform a large-scale proteomics analysis of the epidermis and mesophyll cell layers. This reveals that different proteins and biological processes are enriched in each layer, showing how plants adapt to hot and dry environments by modifying leaf physiology for improved plant sustainability.


Loudya N, Okunola T, He J, Jarvis P, López-Juez E (2020) Retrograde signalling in a virescent mutant triggers an anterograde delay of chloroplast biogenesis that requires GUN1 and is essential for survival Philos Trans R Soc Lond B Biol Sci. 2020;375(1801):20190400. doi:10.1098/rstb.2019.0400 Open Access

Naresh Loudya from Royal Hollaway University of London is first author on this work that investigates the relationship between nucleus and chloroplast gene expression in the control of chloroplast biogenesis. They analyse the cue8 mutant that shows differential changes in the activity of plastid-encoded and nucleus-encoded polymerases.

Naresh discussed this paper on the GARNet Community podcast.


Wilson S, Ruban AV (2020) Rethinking the influence of chloroplast movements on non-photochemical quenching and photoprotection. Plant Physiol. 2020 May 13. pii: pp.00549.2020. doi: 10.1104/pp.20.00549 Open Access

Sam Wilson is first author on this work from the Ruban lab at the Queen Mary University of London. In this study they have assessed the relationship between blue light induced chloroplast relocation and high-light tolerance. Their data argues against the existence of a chloroplast movement-dependent component of the non-photochemical quenching (NPQ) respose. Therefore the authors suggest that thinking on the influence of chloroplast movements on photoprotection should be reevaluated.


Caplin NM, Halliday A, Willey NJ (2020) Developmental, Morphological and Physiological Traits in Plants Exposed for Five Generations to Chronic Low-Level Ionising Radiation. Front Plant Sci. doi: 10.3389/fpls.2020.00389 Open Access

Nicol Caplin is first author on this research from the University of the West of England that looked at the effects of ionising radiation (IR) on seven generations of Arabidopsis growth. They found that although chronic exposure to IR caused some individual trait changes, these are not carried across generations at the population level but still call for more research in this area to be sure of the current regulations provided by the International Commission for Radiological Protection (ICRP).

https://www.frontiersin.org/articles/10.3389/fpls.2020.00389/full

Flütsch S, Wang Y, Takemiya A, Vialet-Chabrand SR, Klejchova M, Nigro A, Hills A, Lawson T, Blatt MR, Santelia D (2020) Guard Cell Starch Degradation Yields Glucose for Rapid Stomatal Opening in Arabidopsis. Plant Cell. doi: 10.1105/tpc.18.00802

This Swiss-led study has Sabrina Flütsch as first author and co-authors from Essex and Glasgow. They looked at the integration of starch degradation in guard cells with the kinetics of stomatal reopening. The timing of rapid stomatal unopening was unchanged in starch degrading mutants but there were alterations in slower responses, most likely due to alterations in the composition of guard cell starch metabolites.


Choi J, Lee T, Cho J, Servante EK, Pucker B, Summers W, Bowden S, Rahimi M, An K, An G, Bouwmeester HJ, Wallington EJ, Oldroyd G, Paszkowski U (2020) The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice. Nat Commun. doi: 10.1038/s41467-020-16021-1 Open Access

This research is led from the Paszkowski lab at the University of Cambridge by Jeongmin Choi. They have found that the rice ortholog of Arabidopsis Suppressor of MAX2-1 plays a novel role to link the pre-symbiotic perception of arbuscular mycorrhizal fungi with karrikin and strigolactone signaling. This response functions through a modification of the D14L signalling pathway.


Chung BYW, Balcerowicz M, Di Antonio M, Jaeger KE, Geng F, Franaszek K, Marriott P, Brierley I, Firth AE, Wigge PA (2020) An RNA thermoswitch regulates daytime growth in Arabidopsis. Nat Plants. doi: 10.1038/s41477-020-0633-3

This Wigge lab-led collaboration includes Betty Chung as first author and investigate the role of the PIF7 messenger RNA as a thermoswitch that activates the thermomorphogenesis pathway. This is controlled by the formation of an RNA hairpin within the mRNA and they show that this mechanism is conserved so controls translation of other mRNAs, enabling the plant to respond and adapt rapidly to high temperatures.


Smith S, Zhu S, Joos L, Roberts I, Nikonorova N, Vu LD, Stes E, Cho H, Larrieu A, Xuan W, Goodall B, van de Cotte B, Waite JM, Rigal A, R Harborough SR, Persiau G, Vanneste S, Kirschner GK, Vandermarliere E, Martens L, Stahl Y, Audenaert D, Friml J, Felix G, Simon R, Bennett M, Bishopp A, De Jaeger G, Ljung K, Kepinski S, Robert S, Nemhauser J, Hwang I, Gevaert K, Beeckman T, De Smet I (2020) The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis. Mol Cell Proteomics. 2020 May 13. pii: mcp.RA119.001826. doi: 10.1074/mcp.RA119.001826 Open Access

Stephanie Smith at the University of Nottingham is first author on this collaboration between researchers in 8 different countries. They use quantitative proteomics to assess the role of the CEP8 peptide in the response to osmotic and drought stress and in the control of auxin signaling.


Gören-Sağlam N, Harrison E, Breeze E, Öz G, Buchanan-Wollaston V (2020) Analysis of the impact of indole-3-acetic acid (IAA) on gene expression during leaf senescence in Arabidopsis thaliana. Physiol Mol Biol Plants. doi: 10.1007/s12298-019-00752-7

Nihal Gören-Sağlam is first author on this study from the University of Warwick in which they investigate the role of externally applied auxin on senescence in Arabidopsis thaliana. They show that PSII activity, as a determinant of chlorophyll fluorescence, declined after auxin treatment and that this response changed across different leaves.


Kim S, Piquerez SJM, Ramirez-Prado JS, Mastorakis E, Veluchamy A, Latrasse D, Manza-Mianza D, Brik-Chaouche R, Huang Y, Rodriguez-Granados NY, Concia L, Blein T, Citerne S, Bendahmane A, Bergounioux C, Crespi M, Mahfouz MM, Raynaud C, Hirt H, Ntoukakis V, Benhamed M (2020) GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5′ and 3′ ends of its target genes. Nucleic Acids Res. doi: 10.1093/nar/gkaa369 Open Access

This French-led study includes Soonkap Kim as first author and co-authors from the University of Warwick. They analysed the role of the histone acetyltransferase GCN5 in global control of gene expression. They used several methodologies (ATAC-seq, ChIP-seq and RNA-seq) to assess the effect of GCN5 loss-of-function on the expression and epigenetic regulation of its target genes.


Baggs E, Monroe JG, Thanki AS, O’Grady R, Schudoma C, Haerty W, Krasileva KV (2020) Convergent Loss of an EDS1/PAD4 Signaling Pathway in Several Plant Lineages Reveals Co-evolved Components of Plant Immunity and Drought Response. Plant Cell. doi: 10.1105/tpc.19.00903 Open Access

This research is led by Erin Baggs in the Krasileva lab at the University of California Berkeley and includes co-authors from Norwich Research Park. They assessed the variation in nucleotide-binding leucine-rich repeat receptors (NLRs) involved in plant immunity, focusing on closely related species that have different NLR compositions. Loss of NLRs corresponds to other changes in downstream immune signaling complexes. This excellent extensive multi-omic analysis provides evolutionary evidence for the rewiring of immunity in some plant lineages.

http://www.plantcell.org/content/early/2020/05/14/tpc.19.00903.long

Delgadillo MO, Ruano G, Zouhar J, Sauer M, Shen J, Lazarova A, Sanmartín M, Lai LTF, Deng C, Wang P, Hussey PJ, Sánchez-Serrano JJ, Jiang L, Rojo E (2020) MTV proteins unveil ER- and microtubule-associated compartments in the plant vacuolar trafficking pathway. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1919820117

María Otilia Delgadillo is first author on this Spanish-led study that includes Patrick Hussey from Durham as a co-author. The study identifies 13 components of the vacuolar trafficking machinery through a genetic screen for mutants that abnormally secrete the synthetic vacuolar cargo VAC2. Eight of these components localize at the interface between the trans-Golgi network (TGN) and the multivesicular bodies (MVBs), which excitingly reveals a previously uncharacterized compartment of the plant vacuolar trafficking pathway.

https://www.pnas.org/content/117/20/10623

GARNet Research Roundup: May 7th 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.


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

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.


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: 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.

https://www.nature.com/articles/s41467-020-14995-6

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.

https://academic.oup.com/gigascience/article/9/3/giaa012/5780255

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 Research Roundup: February 18th 2020

This weeks GARNet Research Roundup begins with two studies that characterize the role of proteins that are involved in the control of meiotic recombination. The first study is from the Henderson lab at the University of Cambridge and investigates the role of the REC8 protein whilst the second is from John Doonan’s group at Aberystwyth University and investigates the role of the cyclin-dependent kinase CDKG.

The third paper is from the same research group in Aberystwyth and investigates how alternative splicing can impact the function of the FLOWERING LOCUS M gene.

The next papers is a cross-UK collaboration led from Rothamsted Research and the John Innes Centre that identifies an important QTL associated with the generation of high-fibre wheat. The fifth paper is from the JIC and reveals how the immune resistance gene MLO plays a role in a plants association with beneficial microbial symbiotes.

The sixth paper is from the Gibbs lab at the University of Birmingham and further characterizes the function of the VRN2 component of the polycomb repressive complex 2.

Nick Harberd from Oxford is a corresponding author of the next paper, which identifies a new gene that could be used to improve nitrogen-use efficiency in rice.

The eighth paper is a proteomic-based study from the University of Cambridge that identifies novel stress-induced components of the Arabidopsis spliceosome.

The penultimate paper is from Jonathan Jones’ lab at the Sainsbury lab, Norwich in which they characterize a new transgenic line useful for studying the plant immune response.

The final paper includes Liam Dolan from Oxford as a co-author in a study that characterizes a novel ATPase from the algae Chara australis.


Lambing C, Tock AJ, Topp SD, Choi K, Kuo PC, Zhao X, Osman K, Higgins J, Franklin FCH, Henderson IR (2020) Interacting genomic landscapes of REC8-cohesin, chromatin and meiotic recombination in Arabidopsis thaliana. Plant Cell. doi: 10.1105/tpc.19.00866
Open Access

This study is led by Chris Lambing from Ian Henderson’s group at the University of Cambridge and includes collaborators from Leicester and Birmingham. They use ChIP-seq to identify the genomic regions associated with the REC8 protein, showing that it interacts with regions with multiple distinct chromatin states. This interaction plays a key role in controlling the formation of double strands breaks and is required to organize meiotic chromosome architecture and interhomolog recombination.


Nibau C, Lloyd AH, Dadarou D, Betekhtin A, Tsilimigka F, Phillips DW, Doonan JH (2020) CDKG1 Is Required for Meiotic and Somatic Recombination Intermediate Processing in Arabidopsis. Plant Cell. doi: 10.1105/tpc.19.00942 Open Access

Candida Nibau from Aberystwyth University leads this research that reveals a critical role for the cyclin-dependent kinase G1 (CDKG) in the control of recombination, both during meiosis and within somatic cells. The authors discover that this role occurs early in the process through the stabilization of recombination intermediates.


Nibau C, Gallemí M, Dadarou D, Doonan JH, Cavallari N (2020) Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2. Front Plant Sci. doi: 10.3389/fpls.2019.01680 Open Access

Candida Nibau is first author on this collaboration between researchers in the UK (Aberystwyth University) and Vienna, Austria. They assess the factors that control the contribution of two splicing variants of the FLOWERING LOCUS M gene on flowering time across a temperature range. They find that this process is controlled by the activity of the cyclin-dependent kinase G2 (CDKG2) and its cognate cyclin, CYCLIN L1 (CYCL1).

https://www.frontiersin.org/articles/10.3389/fpls.2019.01680/full

Lovegrove A, Wingen LU, Plummer A, Wood A, Passmore D, Kosik O, Freeman J, Mitchell RAC, Hassall K, Ulker M, Tremmel-Bede K, Rakszegi M, Bedő Z, Perretant MR, Charmet G, Pont C, Salse J, Waite ML, Orford S, Burridge A, Pellny TK, Shewry PR, Griffiths S (2020) Identification of a major QTL and associated molecular marker for high arabinoxylan fibre in white wheat flour. PLoS One. doi: 10.1371/journal.pone.0227826
Open Access

Alison Lovegrove at Rothamsted Research is the first author on this cross-UK research that has gained significant interest from the main–stream media. Through analysis of a Chinese wheat variety with high dietary fibre due to the high amounts of cell wall polysaccharide arabinoxylan the authors identified a QTL that is responsible for this phenotype. Understanding this QTL will allow use of both marker-assisted breeding and new breeding technologies to aid in the generation of high yield, high fibre varieties.


Jacott CN, Charpentier M, Murray JD, Ridout CJ (2020) Mildew Locus O facilitates colonization by arbuscular mycorrhizal fungi in angiosperms. New Phytol. doi: 10.1111/nph.16465

Catherine Jacott is first author on this study from the JIC that investigates the role of the known barley resistance gene Mildew Resistance Locus O (MLO) during arbuscular mycorrhizal interactions in wheat, barley and Medicago. They show that MLO is important for this beneficial symbiotic association and that the role of MLO has been appropriated during infection with pathogenic powdery mildew.


Labandera AM, Tedds HM, Bailey M, Sprigg C, Etherington RD, Akintewe O, Kalleechurn G, Holdsworth MJ, Gibbs DJ (2020) The PRT6 N-degron pathway restricts VERNALIZATION 2 to endogenous hypoxic niches to modulate plant development. New Phytol. doi: 10.1111/nph.16477

Anne-Marie Labandera is first author on this work from Dan Gibbs’ lab in Birmingham. They show that ubiquitin-mediated proteolysis of the VERNALIZATION2 (VRN2) protein via the oxygen-dependent PRT6 N-degron pathway is important for many areas of plant development. This regulation of VRN2 has different developmental outcomes depending on whether it occurs in or out of meristematic tissues.


Wu K, Wang S, Song W, Zhang J, Wang Y, Liu Q, Yu J, Ye Y, Li S, Chen J, Zhao Y, Wang J, Wu X, Wang M, Zhang Y, Liu B, Wu Y, Harberd NP, Fu X (2020) Enhanced sustainable green revolution yield via nitrogen-responsive chromatin modulation in rice. Science. doi: 10.1126/science.aaz2046

Kun Wu is first author on this Chinese-led investigation that also includes Nick Harberd from Oxford University as a corresponding author. Working in rice they link genomic-wide chromatin changes with expression of the NGR5 (NITROGEN-MEDIATED TILLER GROWTH RESPONSE 5) transcription factor during nitrogen-induced growth. Overexpression of NGR5 can uncouple nitrogen-sensing from tiller production and therefore provide a novel tool to possibly enhance agricultural production in low nitrogen conditions.

https://science.sciencemag.org/content/367/6478/eaaz2046.long

Marondedze C, Thomas L, Lilley KS, Gehring C (2020) Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components. Front Mol Biosci. doi: 10.3389/fmolb.2019.00163 Open Access

Claudius Marondedze is the first author on this collaboration between the University of Cambridge and KAUST in Saudi Arabia. They perform label-free mRNA interactome-capture to identify RNA interacting proteins that are induced after drought stress. This reveals over 40 novel spliceosome-interacting proteins but also 32 proteins that associate with stress granules, which are indicative of transcriptional arrest. This provides new insights into how plant stress responses might be altered by the activity of spliceosome components.


Ngou BPM, Ahn HK, Ding P, Redkar A, Brown H, Ma Y, Youles M, Tomlinson L, Jones JDG (2020) Estradiol-inducible AvrRps4 expression reveals distinct properties of TIR-NLR-mediated effector-triggered immunity. J Exp Bot. doi: 10.1093/jxb/erz571

This research from Jonathan Jones’ group at the Sainsbury Lab, Norwich is led by Bruno Pok Man Ngou. They have developed a transgenic line that enables the transient in planta expression of AvrRps4, which is a potent bacterial immune effector. This stimulates the RRS1/RPS4-dependent immune response and provides insights into certain mechanisms of this pathway without exposing the plants to pathogens.


Zhang S, Habets M, Breuninger H, Dolan L, Offringa R, van Duijn B (2020) Evolutionary and Functional Analysis of a Chara Plasma Membrane H(+)-ATPase. Front Plant Sci. doi: 10.3389/fpls.2019.01707 Open Access

Liam Dolan from the University of Oxford is a co-author on this Dutch-led research that includes Sutun Zhang as first author. They characterize a plasma membrane localised ATPase from the algae Chara australis and perform complementation studies in both yeast and Arabidopsis. These studies allow the authors to propose that the mode of regulation of this algal ATPase is likely different from that of known yeast and land plant PM H+-ATPases.

GARNet Research Roundup: February 7th 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.


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.


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.


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

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.


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.


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.


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.


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.

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