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: November 22nd 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: October 17th 2019

This edition of the GARNet Research Roundup includes a superb selection of papers by scientists from across the UK. First is work from the Spoel lab in Edinburgh that characterizes the fine-tuning of NPR1 activity during the plant immune response. Second is work from SLCU and the University of Helsinki that is an extensive investigation into the molecular basis of cambial development. Next is research from Nottingham that looks at the importance of soil macro-structures during the growth of wheat roots.

Fourth are three papers that highlight the breadth of research occurring at the John Innes Centre. The first paper is from Enrico Coen’s lab that applies their expertise in computational modeling to leaf development in the carnivorous plant Utricularia gibba. Second is work from Saskia Hogenhout’s lab that looks at immunity to infection by Phytoplasma pathogens. Last is work from Lars Ostergaard’s lab that characterises the role of Auxin Binding promoter elements in floral development.

The seventh paper from Bristol and Glasgow looks at shade avoidance signaling via PIF5, COP1 and UVR8 whilst the eighth paper, which is from Rothamsted, demonstrates how metabolic engineering in Arabidopsis seeds can result in a high proportion of human milk fat substitute. The next paper is from the University of Durham and investigates how the composition of the Arabidopsis cell wall impacts freezing tolerance. The first author of this paper, Dr Paige Panter discusses the paper on the GARNet community podcast.

The tenth paper is from Julia Davies’s lab at the University of Cambridge and introduces an uncharacterised response to extracellular ATP signals in Arabidopsis roots. The next paper is from Mike Blatt’s group at University of Glasgow and characterises a new interaction between vesicular transport and ion channels. The penultimate entry includes co-authors from the JIC on a Chinese-led study that demonstrates improved seed vigour in wheat through overexpression of a NAC transcription factor. Finally are two methods papers taken from a special journal issue on ‘Plant Meiosis’.


Skelly MJ, Furniss JJ, Grey HL, Wong KW, Spoel SH (2019) Dynamic ubiquitination determines transcriptional activity of the plant immune coactivator NPR1. Elife. doi: 10.7554/eLife.47005
Open Access

Michael Skelly is lead author on this paper from the lab of current GARNet chair Steven Spoel. In it they investigate the mechanisms that fine-tune the function of NPR1, a key player in the plant immune response. Progressive ubiquitination of NPR1 by an E3 ligase causes both its interaction with target genes and its subsequent degradation by an E4 ligase. This latter occurrence is opposed by the deubiquitinase activity of UBP6/7, setting up a complex regulatory environment that allows the plant to rapidly response to pathogen attack.


Zhang J, Eswaran G, Alonso-Serra J, Kucukoglu M, Xiang J, Yang W, Elo A, Nieminen K, Damén T, Joung JG, Yun JY, Lee JH, Ragni L, Barbier de Reuille P, Ahnert SE, Lee JY, Mähönen AP, Helariutta Y (2019) Transcriptional regulatory framework for vascular cambium development in Arabidopsis roots. Nat Plants. doi: 10.1038/s41477-019-0522-9

This pan-European-Korean collaboration has Jing Zhang from the University of Helsinki and the Sainsbury Laboratory, University of Cambridge as first author. They use cambium cell-specific transcript profiling and follow-on network analysis to discover 62 new transcription factors involved in cambial development in Arabidopsis. This information was used to engineer plants with increased radial growth through ectopic cambial activity as well as to generate plants with no cambial activity. This understanding provides a platform for possible future improvements in production of woody biomass.


Atkinson JA, Hawkesford MJ, Whalley WR, Zhou H, Mooney SJ (2019) Soil strength influences wheat root interactions with soil macropores. Plant Cell Environ. doi: 10.1111/pce.13659
This work is led from the University of Nottingham by John Atkinson and Sacha Mooney. They use X-ray Computed Tomography to investigate a trait called trematotropism, which applies to the ability of deep rooting plants to search out macropores and avoid densely packed soil. They show root colonisation of macropores is an important adaptive trait and that strategies should be put in place to increase these structures within the natural soil environment.


Lee KJI, Bushell C, Koide Y, Fozard JA, Piao C, Yu M, Newman J, Whitewoods C, Avondo J, Kennaway R, Marée AFM, Cui M, Coen E (2019) Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism. PLoS Biol. doi: 10.1371/journal.pbio.3000427
Open Access

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000427

Karen Lee, Claire Bushell and Yohei Koide are co-first authors on this work led by Enrico Coen at the John Innes Centre and Minlong Cui at the Zhejiang Agriculture and Forestry University in China. This study uses 3D imaging, cellular and clonal analysis, combined with computational modelling to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. They identify growth ansiotrophies that result in the final leave shape that develops from an initial near-spherical form. These processes have some similarities to the polar growth seen in Arabidopsis leaves. Overall they show that ‘simple modulations of a common growth framework underlie the shaping of a diverse range of morphologies’.


Pecher P, Moro G, Canale MC, Capdevielle S, Singh A, MacLean A, Sugio A, Kuo CH, Lopes JRS, Hogenhout SA (2019) Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize. PLoS Pathog. doi: 10.1371/journal.ppat.1008035
Open Access

This work from Saskia Hogenhout’s lab at the John Innes Centre is led by Pascal Pecher and Gabriele Moro. They look at the effect of SAP11 effectors from Phytoplasma species that infect either Arabidopsis or maize. They demonstrate that although both related versions of SAP11 destabilise plant TCP transcription factors, their modes of action have significant differences. Please look out for Saskia discussing this paper on the GARNet Community podcast next week.


Kuhn A, Runciman B, Tasker-Brown W, Østergaard L 92019) Two Auxin Response Elements Fine-Tune PINOID Expression During Gynoecium Development in Arabidopsis thaliana. Biomolecules. doi: 10.3390/biom9100526
Open Access

Andre Kuhn is first author of this research from Lars Østergaard’s lab at the John Innes Centre. They functional characterise two Auxin-responsive Elements (AuxRE) within the promotor of the PINOID gene, which are bound by the ETITIN/ARF3 Auxin Response Factor. Alteration of this AuxRE causes phenotypic changes during flower development demonstrating that even with a complex regulatory environment, small changes to cis-elements can have significant developmental consequences.


Sharma A, Sharma B, Hayes S, Kerner K, Hoecker U, Jenkins GI, Franklin KA (2019) UVR8 disrupts stabilisation of PIF5 by COP1 to inhibit plant stem elongation in sunlight. Nat Commun. doi: 10.1038/s41467-019-12369-1
Open Access

Ashutosh Sharma is first author of this UK-Spanish-Germany collaboration led by Keara Franklin at University of Bristol. They have characterised the interaction between three significant molecular players that function during the shade avoidance response in Arabidopsis; PIF5, UVR8 and COP1. In shaded conditions, UVR8 indirectly promotes rapid degradation of PIF5 through their interactions with the E3 ubiquitin ligase COP1.


van Erp H, Bryant FM, Martin-Moreno J, Michaelson LV, Bhutada G, Eastmond PJ (2019) Engineering the stereoisomeric structure of seed oil to mimic human milk fat. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1907915116

Open Access

Harrie Van Arp and Peter Eastmond at Rothamsted Research lead this extremely translational study in which they have modified the metabolic pathway for triacylglycerol (TAG) biosynthesis. By modifying the location of one biosynthesis enzyme and removing the activity of another, the fats produced in these Arabidopsis seeds are enriched to contain TAGs that are similar to those found in human milk. They propose that this technology could be used to develop a source of plant-derived human milk fat substitute.


Panter PE, Kent O, Dale M, Smith SJ, Skipsey M, Thorlby G, Cummins I, Ramsay N, Begum RA, Sanhueza D, Fry SC, Knight MR, Knight H (2019) MUR1-mediated cell-wall fucosylation is required for freezing tolerance in Arabidopsis thaliana. New Phytol. doi: 10.1111/nph.16209

Paige Panter led this work as part of her PhD at the University of Durham in the lab of Heather Knight. They characterise the role of the MUR1 protein in the control of cell wall fucosylation and how this contributes to plant freezing tolerance. Paige discusses this paper and the long history of MUR1 on the GARNet Community podcast. Please check it out!


Wang L, Stacey G, Leblanc-Fournier N, Legué V, Moulia B, Davies JM (2019) Early Extracellular ATP Signaling in Arabidopsis Root Epidermis: A Multi-Conductance Process. Front Plant Sci. doi: 10.3389/fpls.2019.01064.

Open Access

The UK-French collaboration is led by Limin Wang from Julia Davies’s lab in Cambridge. They use patch clamp electrophysiology to identify previously uncharacterized channel conductances that respond to extracellular ATP across the root elongation zone epidermal plasma membrane.


Waghmare S, Lefoulon C, Zhang B, Lileikyte E, Donald NA, Blatt MR (2019) K+ channel-SEC11 binding exchange regulates SNARE assembly for secretory traffic. Plant Physiol. doi: 10.1104/pp.19.00919

Open Access

This work from Mike Blatt’s lab in Glasgow is led by Sakharam Waghmare. They look at the interaction between SNARE proteins, which are involved in vesicular fusion and K+ channels, which help control turgor pressure during cell expansion. Through combining analysis of protein-protein interactions and electrophysiological measurement they have found that this interaction requires the activity of the regulatory protein SEC11.


Li W, He X, Chen Y, Jing Y, Shen C, Yang J, Teng W, Zhao X, Hu W, Hu M, Li H, Miller AJ, Tong Y (2019) A wheat transcription factor positively sets seed vigour by regulating the grain nitrate signal. New Phytol. doi: 10.1111/nph.16234
Wenjing Li is first author of this Chinese study that includes Yi Chen and Anthony Miller from the John Innes Centre as co-authors. This research shows that seed vigour and nitrate accumulation in wheat is regulated by the TaNAC2 transcriptions factor through its control of the TaNRT2.5 nitrate transporter. The authors suggest that both genes could be used as potential future targets to increase grain yield and nitrogen use efficiency.


The Special Issue of Methods in Molecular Biology on Plant Meiosis includes papers from the University of Cambridge, led by Christophe Lambing and the James Hutton Institute, led by Benoit Darrier.

Lambing C, Choi K, Blackwell AR, Henderson IR (2019) Chromatin Immunoprecipitation of Meiotically Expressed Proteins from Arabidopsis thaliana Flowers. Methods Mol Biol. doi: 10.1007/978-1-4939-9818-0_16
Darrier B, Arrieta M, Mittmann SU, Sourdille P, Ramsay L, Waugh R, Colas I (2019) Following the Formation of Synaptonemal Complex Formation in Wheat and Barley by High-Resolution Microscopy. Methods Mol Biol. doi: 10.1007/978-1-4939-9818-0_15

GARNet Research Roundup: March 21st 2019

This edition of the GARNet research roundup begins with a study from the John Innes Centre that investigates the role of auxin in the control of fruit development in Capsella.

Auxin is also a central focus of the next paper that is from SLCU, in which the authors characterise the role of different types of auxin transport during shoot development. The third paper, also from Cambridge, identifies a new function for members of the DUF579 enzyme family. The final paper from Cambridge reports on an outstanding citizen science project that looks at how different temperature and light conditions influence the growth of spring onions.

The next paper is from the University of Glasgow and investigates the role of the SNARE protein complex during vesicle transport in Arabidopsis.

The final two papers include authors from the University of Nottingham. Firstly Anthony Bishopp leads research that defines determinants of vascular patterning across plant species. Finally Don Grierson is a co-author on work that has identified novel signaling components involved in the response to hypoxia in Persimmon and Arabidopsis.


Dong Y, Jantzen F, Stacey N, Łangowski Ł, Moubayidin L, Šimura J, Ljung K, Østergaard L (2019) Regulatory Diversification of INDEHISCENT in the Capsella Genus Directs Variation in Fruit Morphology. Curr Biol. doi: 10.1016/j.cub.2019.01.057

Open Access

This research from Lars Ostergaard’s lab in the John Innes Centre is led by Yang Dong. The work is primarily conducted in Capsella and investigates the role of the INDEHISCENT (IND) protein in this plant, which has fruits that are morphologically distinct from those in Arabidopsis. Expression of CrIND controls fruit shape by influencing auxin biosynthesis leading to auxin accumulation in specific maxima that are localised to the fruit valves.

doi: 10.1016/j.cub.2019.01.057

van Rongen M, Bennett T, Ticchiarelli F, Leyser O (2019) Connective auxin transport contributes to strigolactone-mediated shoot branching control independent of the transcription factor BRC1. PLoS Genet. doi: 10.1371/journal.pgen.1008023

Open Access

Martin Van Rongen is the lead author on this research performed under the supervision of Ottoline Leyser at the Sainsbury Lab, Cambridge University. They investigate the hormonal signals that underpin the remarkable plasticity of shoot patterning, focusing on a genetic analysis of connective auxin transport (CAT), which moves the hormone across the stem (in contrast to up-down polar transport). Using multiple pin mutant plants, they show CAT is important in the regulation of strigolactone-mediated shoot branching. However shoot branching controlled by the BRANCHED1 transcription factor is reliant on the ABCB19 auxin export protein and is not significantly influenced by the activity of PIN proteins. Martin van Rongen discusses this paper on the GARNet YouTube channel.


Temple, H, Mortimer, JC, Tryfona, T, et al (2019) Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis. Plant Direct. https://doi.org/10.1002/pld

Open Access

Henry Temple works with Paul Dupree at the University of Cambridge and leads this study that identifies a novel activity of two DUF579 enzymes in the methylation of glucuronic acid within highly glycosylated arabinogalactan proteins (AGPs). This differs from all other previously characterized DUF579 members that have been previously shown to methylate glucuronic acid within the cell wall component xylan.


Brestovitsky, A, Ezer, D (2019) A mass participatory experiment provides a rich temporal profile of temperature response in spring onions. Plant Direct. 2019; 3: 1– 11. https://doi.org/10.1002/pld3.126

Open Access

This citizen science project led by Anna Brestovitsky and Daphne Ezer was performed in collaboration with the BBC Terrific Scientific program. In this study primary school students from across the UK recorded the growth of spring onions over a two-week period, which was then cross-referenced with detailed hourly meteorological data. This allowed the authors to discern the effect of minute temperature and light changes on plant growth and perhaps more importantly demonstrated that even the youngest researchers, when involved a well-designed citizen science project, can yield very useful data.


Zhang B, Karnik RA, Alvim JC, Donald NA, Blatt MR (2019) Dual Sites for SEC11 on the SNARE SYP121 Implicate a Binding Exchange during Secretory Traffic. Plant Physiol. doi: 10.1104/pp.18.01315

Open Access

Ben Zhang and Rucha Karnik are first authors on this paper that continues Mike Blatt‘s lab’s study of SNARE proteins, which are involved in vesicle trafficking. This study defines a new amino acid motif within SNARE SYP121 that is needed for the binding of the SEC11 protein but is not involved in binding plasma membrane K+ channels. This motif is essential for assembly of the entire SNARE complex yet does not influence the interaction of SYP121 with the uptake of K+ ions.


Mellor N, Vaughan-Hirsch J, Kümpers BMC, Help-Rinta-Rahko H, Miyashima S, Mähönen AP, Campilho A, King JR, Bishopp A (2019) A core mechanism for specifying root vascular patterning can replicate the anatomical variation seen in diverse plant species. Development. doi: 10.1242/dev.172411

Open Access

Nathan Mellor is first author on this work led by the lab of Anthony Bishopp at the University of Nottingham. The primary accomplishment of this work is in the development of a mathematical model that is able to predict the role of auxin in the specification of vascular patterning during embryonic development. This model has been tested through experimental interrogation of both transgenic Arabidopsis plants and in a range of other species with different vascular development patterns. Importantly they show that a heterologous auxin input might not be as critical in vascular development when compared to growth patterns that arise from spatial constraints. The authors show that this model has broad relevance to define early vascular patterning across plant species.


Zhu QG, Gong Z, Huang J, Grierson D, Chen KS, Yin XR (2019) High-CO2/hypoxia-responsive transcription factors DkERF24 and DkWRKY1 interact and activate DkPDC2 promoter. Plant Physiol. doi: 10.1104/pp.18.01552

Open Access

Don Greirson is a co-author on this Chinese-led study that identifies a set of transcription factors from Persimmon ((Diospyros kaki). These TFs are involved in responses to high CO2 and the authors show that their Arabidopsis orthologs play a similar role. The authors introduce a new response module that may be important during this key environmental response.

GARNet Research Roundup: January 31st 2019

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Published on: January 31, 2019

This edition of the GARNet research roundup has an initial focus on the shoot apical meristem. Firstly a study from the University of Birmingham performs network analysis to define the connections that control the global organisation of this tissue.

Second is the first of a group of papers involving authors from the Sainsbury Lab, Cambridge University and the University of Cambridge. Henrik Jönsson and Henrik Ahl contribute to a study that refines our understanding about the role of auxin in leaf dorsoventral patterning. Next from SLCU are two papers published in collaboration with the University of Helsinki that identify a set of novel regulators of cambial development.

The final SLCU paper from James Locke’s group attempts to tackle the challenging topic of ‘noise’ in biological systems. The final paper from the University of Cambridge investigate factors involved in karrikin signaling.

The penultimate paper characterises the LINC complex in monocots and includes authors from Oxford Brookes University whilst the final paper is from the University of York and performs a structural analysis of a key enzyme involved in the potential phytoremediation of TNT.


Jackson MDB, Duran-Nebreda S, Kierzkowski D, Strauss S, Xu H, Landrein B, Hamant O, Smith RS, Johnston IG, Bassel GW (2019) Global Topological Order Emerges through Local Mechanical Control of Cell Divisions in the Arabidopsis Shoot Apical Meristem. Cell Syst. doi: 10.1016/j.cels.2018.12.009

Open Access

George Bassel is corresponding author of this paper led by Matthew Jackson at the University of Birmingham. They use live 3D imaging and computational analysis to identify a network of cellular connections in the shoot apical meristem. They show that locally generated cell division rules lead to emergence of global tissue organisation, which facilitates cellular communication. In addition they show that global cellular organization requires the activity of the KATANIN protein.


Bhatia N, Åhl H, Jönsson H, Heisler MG (2019) Quantitative analysis of auxin sensing in leaf primordia argues against proposed role in regulating leaf dorsoventrality. Elife. doi: 10.7554/eLife.39298

Open Access

Henrik Jönsson and Henrik Ahl at SLCU are co-authors on this study led by Neha Bhatia at the University of Sydney. They use data gained from analysis of the R2D2 auxin sensor to argue against the current hypothesis stating that asymmetric auxin distribution is necessary to define the dorso-ventral polarity of the Arabidopsis leaf. They repeat previous experiments using the DII auxin sensor and through additional analysis using an auxin insensitive version of the sensor (mDII), provide results that contrast to previously published data.

https://elifesciences.org/articles/39298

Miyashima S, Roszak P, Sevilem I, Toyokura K, Blob B, Heo JO, Mellor N, Help-Rinta-Rahko H, Otero S, Smet W, Boekschoten M, Hooiveld G, Hashimoto K, Smetana O, Siligato R, Wallner ES, Mähönen AP, Kondo Y, Melnyk CW, Greb T, Nakajima K, Sozzani R, Bishopp A, De Rybel B, Helariutta Y (2019). Mobile PEAR transcription factors integrate positional cues to prime cambial growth. Nature doi: 10.1038/s41586-018-0839-y

Smetana O, Mäkilä R, Lyu M, Amiryousefi A, Sánchez Rodríguez F, Wu MF, Solé-Gil A, Leal Gavarrón M, Siligato R, Miyashima S, Roszak P, Blomster T, Reed JW, Broholm S, Mähönen AP (2019). High levels of auxin signalling define the stem-cell organizer of the vascular cambium. Nature. doi: 10.1038/s41586-018-0837-0

These back-to-back manuscripts include Pawel Roszak from the SLCU as an author in both papers. The corresponding author for the first paper, which is a true global collaboration, is Yrjo Helariutta who holds research positions at both SLCU and the University of Helsinki. These papers introduce a new signalling module of transcriptional factors that control radial growth initiated in procambial cells. In root protophloem cells cytokinin induces the expression of a newly characterised set of PEAR transcription factors, which form a short-range concentration gradient and initiate radial growth. To maintain tight developmental control of this program PEAR protein activity is antagonised by HD-ZIP III proteins, whose expression domain is controlled by the activity of auxin and a set of mobile miRNAs. The identification of this signalling module increases our understanding about the factors that control the growth of woody tissues and therefore has enormous translational significance.


Cortijo S, Aydin Z, Ahnert S, Locke JC (2019) Widespread inter-individual gene expression variability in Arabidopsis thaliana Mol Syst Biol. doi: 10.15252/msb.20188591

Open Access

Sandra Cortijo is the lead author of this paper and works with James Locke at SLCU. They have attempted to address the fundamental question of noise within biological outputs through analysis of gene expression from a set of identical Arabidopsis plants grown in identical conditions. They identify hundreds of genes that show variable expression between these plants, with different gene sets changing throughout the diurnal cycle. They further define this variability by identifying gene length, the number of transcription factors regulating the genes and the chromatin environment as contributory factors to explain why this variation occurs.


Swarbreck SM, Guerringue Y, Matthus E, Jamieson FJC, Davies JM (2019) Impairment in karrikin but not strigolactone sensing enhances root skewing in Arabidopsis thaliana. Plant J. doi: 10.1111/tpj.14233

Stéphanie Swarbreck is the first author of this work from Julia Davies’ lab at the University of Cambridge. They show that perception of karrikins (smoke-derived butenolides) through the interaction of the KAI2 hydrolase and MAX2 F-box protein occurs independent of strigolactone-sensing mechanism of the MAX2-D14 hydrolase interaction. Karrikins cause a root skewing phenotype so the authors use this output to identify that previously characterised SMAX1 (SUPPRESSOR OF MAX2-1)/SMXL2 and SMXL6,7,8 (SUPPRESSOR OF MAX2-1-LIKE) proteins are targets of degradation by the KAI2/MAX2 complex. Overall they show that KAI2/MAX2 limits root skewing but is not involved in the role KAI2 plays in gravi- or mechano-sensing. These results are indicative of a set of KAI2 specific ligands that control root skewing yet candidate proteins for these roles remain to be identified.


Gumber HK, McKenna JF, Estrada AL, Tolmie AF, Graumann K, Bass HW (2019) Identification and characterization of genes encoding the nuclear envelope LINC complex in the monocot species Zea mays. J Cell Sci. doi: 10.1242/jcs.221390

This paper is led by Hank Bass and Hardeep Gumber from Florida State University and includes Joe McKenna, Andrea Tolmie and Katja Graumann at Oxford Brookes as co-authors. They use phylogenetic and microscopic analysis to identify and characterise components of the nuclear-envelope spanning LINC (Linker of Nucleoskeleton to Cytoskeleton) complex in Zea mays. They identify a set of monocot-specific members of the LINC complex, which will allow an increased understanding about the functional linkages between the cytoplasm, nuclear envelope, nucleoplasm and chromatin.

Hank Bass discusses this paper on the GARNet YouTube channel. Hank and Katja are members of the EU COST action entitled ‘Impact of Nuclear Domains On Gene Expression and Plant Traits (INDEPTH).


Tzafestas K, Ahmad L, Dani MP, Grogan G, Rylott EL, Bruce NC (2018) Structure-Guided Mechanisms Behind the Metabolism of 2,4,6-Trinitrotoluene by Glutathione Transferases U25 and U24 That Lead to Alternate Product Distribution Front Plant Sci. doi: 10.3389/fpls.2018.01846

Open Access

Kyriakos Tzafestas is the first author on this paper from the University of York led by Neil Bruce. They perform a structural analysis of the Arabidopsis tau class glutathione transferase, GSTU25, which is involved in the phytoremediation of 2,4,6-trinitrotoluene (TNT). This analysis identified of a key set of amino acids involved in a precise part of its enzymatic activity, which can in turn be transferred to the related, but enzymatically-inert GSTU24. These findings will aid in the development of increasingly efficient strategies for plant-based remediation of environmental TNT.

GARNet Research Roundup: December 21st 2018

This bumper Festive Edition of the GARNet Research Roundup begins with two papers that have Beatriz Orosa-Puente as lead author following her work on SUMOylation with Ari Sadanandom at Durham. These papers looks at the role of SUMOylation in either auxin-mediated hydropatterning or in the defence response. Malcolm Bennett at Nottingham is a co-author on both papers and provided an audio description of the auxin-focused paper on the GARNet YouTube channel.

The next three papers are from the University of Edinburgh, the first that defines the role of HECT ubiquitin ligases in the defence response, the second that conducts a proteomic analysis of the GIGANTEA-interactome and the third that introduces a set of new tools for inducible gene expression in Arabidopsis roots.

The sixth and seventh papers feature authors from the John Innes Centre. Martin Howard and Caroline Dean are corresponding authors on a multi-scale analysis of the factors that control FLC expression whilst Myriam Charpentier’s lab has contributed to an investigation about LINC complexes in Medicago.

David Salt and Levi Yant from Nottingham lead the next paper that provides an analysis of the genetic determinants of adaptation to different salt conditions.

The final three papers are from Cambridge. Firstly Ian Henderson is the corresponding author on work that looks at crossover rates in specific disease resistance loci. Second is work from the Paszkowski lab at SLCU that introduces a new method for the analysis of active retrotransposons in crop plants whilst finally James Locke, also at SLCU, uses the method of distributed delays to simplify the complexity of biological network models.


Orosa-Puente B, Leftley N, von Wangenheim D, Banda J, Srivastava AK, Hill K, Truskina J, Bhosale R, Morris E, Srivastava M, Kümpers B, Goh T, Fukaki H, Vermeer J, Vernoux T, Dinneny JR, French AP, Bishopp A, Sadanandom A , Bennett MJ (2018) Roots branch towarss water by post-translational modification of the transcription factor ARF7 Science DOI: 10.1126/science.aau3956

Orosa B, Yates G, Verma V, Srivastava AK, Srivastava M, Campanaro A, De Vega D, Fernandes A, Zhang C, Lee J, Bennett MJ, Sadanandom A (2018) SUMO conjugation to the pattern recognition receptor FLS2 triggers intracellular signalling in plant innate immunity. Nat Commun. doi: 10.1038/s41467-018-07696-8 Open Access

http://science.sciencemag.org/content/362/6421/1407

Beatriz Orosa-Puente is the lead author on two publications that have arisen from a collaboration between the labs of Ari Sadanandom at Durham and Malcolm Bennett at Nottingham. In the first paper Beatriz is co-first author with Nicola Leftley and Daniel von Wangenheim in research that links the auxin response, SUMOylation and the search for water. They reveal a novel mechanism for controlling the auxin response in which SUMOylation regulates the interaction between the ARF7 and IAA3 proteins. In turn this controls asymmetric expression of genes downstream of ARF7 and determines how different parts of the root response to the presence or absence of water.

The second paper continues with the Sadanandom lab’s focus on SUMOylation, in this case during control of the defence response. They show that SUMO is conjugated to the FLAGELLIN-SENSITIVE 2 (FLS2) receptor that senses bacterial flagellin. This releases downstream cytoplasmic effectors and enhances the immune response. The authors show that there is additional complexity to this system by also showing that flagellin induces degradation of the deSUMOylating enzyme Desi3a, thus allowing the plant to make a stronger immune response.


Furniss JJ, Grey H, Wang Z, Nomoto M, Jackson L, Tada Y, Spoel SH (2018) Proteasome-associated HECT-type ubiquitin ligase activity is required for plant immunity. PLoS Pathog. doi: 10.1371/journal.ppat.1007447 Open Access

James Furniss is the lead author on this paper from the lab of current GARNet Chairman Steven Spoel at the University of Edinburgh. They show that a family of HECT domain-containing ubiquitin protein ligases (UPLs) are involved in defence responses mediated by the hormone salicylic acid (SA). Upl3 mutants show reprogramming of the entire SA transcriptional response and they are unable to establish immunity against a hemi-biotrophic pathogen, demonstrating their key role in this important process.


https://febs.onlinelibrary.wiley.com/doi/abs/10.1002/1873-3468.13311

Krahmer J, Goralogia GS, Kubota A, Zardilis A, Johnson RS, Song YH, MacCoss MJ, LeBihan T, Halliday KJ, Imaizumi T, Millar AJ (2018) Time-resolved Interaction Proteomics of the GIGANTEA Protein Under Diurnal Cycles in Arabidopsis. FEBS Lett. doi: 10.1002/1873-3468.13311 Open Access

This paper is a collaboration between researchers in Edinburgh and Seattle for which Johanna Krahmer is lead author. They used a proteomic approach to identify proteins that interacted with a tagged-version of the key circadian regulator GIGANTEA. They successfully identified the novel transcription factor CYCLING DOF FACTOR (CDF)6. CDF6 was confirmed as interacting with GI and playing a role in the control of flowering. The time series of proteomic data produced in this study is available for use by any other interested researcher.

http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD006859


Machin FQ, Beckers M, Tian X, Fairnie A, Cheng T, Scheible WR, Doerner P (2018) Inducible reporter/driver lines for the Arabidopsis root with intrinsic reporting of activity state. Plant Journal. doi: 10.1111/tpj.14192

Frank Qasim Machin is the lead author on this Technical Advance from Peter Doerner’s lab at the University of Edinburgh. They have developed a Gateway-based system for tightly controlled inducible expression across all the major cell types of the Arabidopsis roots. They have fully characterised reference driver lines that can be adapted for specific experimental requirements and hope that this contributes towards enhancing reproducibility of qualitative and quantitative analyses.


https://www.sciencedirect.com/science/article/pii/S2405471218304368?via%3Dihub

Antoniou-Kourounioti RL, Hepworth J, Heckmann A, Duncan S, Qüesta J, Rosa S, Säll T, Holm S, Dean C, Howard M (2018) Temperature Sensing Is Distributed throughout the Regulatory Network that Controls FLC Epigenetic Silencing in Vernalization. Cell Syst. doi: 10.1016/j.cels.2018.10.011 Open Access

This work results from the successful collaboration between Caroline Dean and Martin Howard at the John Innes Centre and includes Rea Antoniou-Kourounioti and Jo Hepworth as co-first authors. They attempt to understand how the upregulation of VERNALIZATION INSENSITIVE3 (VIN3) and silencing of FLOWERING LOCUS C (FLC) is controlled during fluctuating temperatures over month-long time scales. They develop a mathematical model that integrates information from hour, day and month-long datasets to show that temperature is sensed across the entire regulatory network and not focussed on specific nodes. This allows a final effect to only be realised once all parts of the network have been appropriately changed. This model with matches new field data and therefore represents a predictive tool for the effects of climate change on plant growth.


Newman-Griffis AH, Del Cerro P, Charpentier M, Meier I (2018) Medicago LINC complexes function in nuclear morphology, nuclear movement, and root nodule symbiosis Plant Physiol. http://www.plantphysiol.org/content/early/2018/12/10/pp.18.01111 Open Access
Pablo del Cerro and Myriam Charpentier at the John Innes Centre are co-authors on this paper from Iris Meier’s lab at The Ohio State University. They identify and characterise the Linker of Nucleoskeleton and Cytoskeleton (LINC) family of nucleus-membrane-associated proteins. They show that, as in Arabidopsis, these proteins are required for nucleus movement in the root tip cells of Medicago truncatula and that they are an important contributor to nodulation. Both Iris and Myriam are members of the INDEPTH consortium that includes researchers who study this broad area of plant cell biology.


https://www.pnas.org/content/early/2018/12/11/1816964115.long

Busoms S, Paajanen P, Marburger S, Bray S, Huang XY, Poschenrieder C, Yant L, Salt DE (2018) Fluctuating selection on migrant adaptive sodium transporter alleles in  coastal Arabidopsis thaliana. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1816964115 Open Access

This UK-Sino-Spanish collaboration is led by David Salt and Levi Yant at the University of Nottingham. Silvia Busoms is the first author on the study that investigates the genetics of adaptive salt tolerance in a cohort of 77 individuals grown across a salinity gradient in a coastal region of Catalonia. By integrating their data with the 1135 genomes project they are able to trace the ancestry of these populations and define that growth in high salt conditions is associated with increased expression of the high-affinity K+ transporter (HKT1;1). This demonstrates that this gene plays a key role in the adaptation to salt stress.


Serra H, Choi K, Zhao X, Blackwell AR, Kim J, Henderson IR. Interhomolog polymorphism shapes meiotic crossover within the Arabidopsis RAC1 and RPP13 disease resistance genes (2018) PLoS Genet. doi: 10.1371/journal.pgen.1007843 Open Access

This UK-Korean collaboration is led by the Heidi Serra and Ian Henderson at the University of Cambridge. They mapped the meiotic crossover hotspots that are located within the RAC1 and RPP13 disease resistance genes in Arabidopsis. They assessed these locations in plants with altered recombination rates and surprisingly showed that these effects have little impact at the RAC1 loci. Therefore they show that chromosome location and local chromatin environment are important for regulation of crossover activity. Overall they demonstrate that interhomolog divergence is important in shaping recombination within plant disease resistance genes and crossover hotspots.


Cho J, Benoit M, Catoni M, Drost HG, Brestovitsky A, Oosterbeek M, Paszkowski J (2018) Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants. Nat Plants. doi: 10.1038/s41477-018-0320-9

Open Access with link: rdcu.be/bdLjy

For the second edition in succession, the GARNet research roundup features work from Jerzy Paszkowski’s lab at SLCU. In this case Jungnam Cho is lead author on work that has developed a new technique called ALE-seq (amplification of LTR of eclDNAs followed by sequencing) for analysis of transposon-rich genomes from crop plants. Through characterisation of extrachromosomal linear DNA (eclDNA), ALE-seq allows the identification of active transposons. The authors use this technique in both rice and tomato and successfully identify a set of developmentally regulated transposable elements. This paper includes details of a bioinformatic pipeline that is adapted for ALE-seq data analyses, the scripts for which are available on GitHub.


Tokuda IT, Akman OE, Locke JCW. Reducing the Complexity of Mathematical Models for the Plant Circadian Clock by Distributed Delays (2018) J Theor Biol. doi: 10.1016/j.jtbi.2018.12.014

This UK-Japanese study includes James Locke at SLCU as corresponding author. They address the challenge of integrating an increasing number of parameters into large biological network models. Their system of study is the Arabidopsis circadian clock and they use the method of distributed delays to simplify the complexity of existing models. They demonstrate this effect by updating a model that explains the regulation of the PRR9 and PRR7 genes by LHY. They use recent experimental data and revise the previous model to show that it is more accurately reproduces the LHY-induction experiments of core clock genes. As stated they show that overall use of distributed delays facilitates the optimisation and reformulation of genetic network models.

GARNet Research Roundup: December 7th 2018

The first four papers in this GARNet Research Roundup includes research from Norwich Research Park. Firstly members of Jonathan Jones’ lab have identified a new Avr gene from Hyaloperonospora arabidopsidis. Secondly Anne Osbourn’s lab characterises two novel arabinosyltransferases that are involved in the plant defence response. Thirdly Cathie Martin’s group is involved in a study that investigates the biosynthesis of the metabolite ubiquinone. Finally in research from NRP is from Silke Robatzek’s lab, where they use a novel quantitative imaging system to characterise stomatal mutants.

The next two papers arise from work at SLCU, firstly looking at the possible role of a novel transposon family during gene-shuffling and secondly a paper that investigates the structure of an important component of the strigolactone signaling pathway.

The seventh paper from Peter Eastmond’s lab at Rothamsted Research identifies a novel gene involved in seed oil composition. The penultimate paper is from Peter Unwin at the University of Leeds and assesses the cell wall composition of ‘giant’ root cells induced by nematode Meloidogyne spp. Finally is a methods paper that describes how microCT imaging can be used to measure different leaf parameters.


Asai S, Furzer O, Cavik V, Kim DS, Ishaque N, Goritschnig S, Staskawicz B, Shirasu K, Jones JDG (2018) A downy mildew effector evades recognition by polymorphism of expression and subcellular localization. Nature Communications doi: 10.1038/s41467-018-07469-3

https://www.nature.com/articles/s41467-018-07469-3

Open Access

Shuta Asai from Jonathan Jones’ lab at The Sainsbury Lab, Norwich is the lead-author on this study that looks at co-evolution of host and pathogen resistance genes. The relationship between Hyaloperonospora arabidopsidis (Hpa) and Arabidopsis is defined by the gene-for-gene model of host Resistance (R) genes and pathogen Avirulence (AVR) genes. In this study the authors identify the HaRxL103Emoy2 AVR gene that is recognised by the R gene RPP4 and how this resistance is broken by altered expression or cellular localization.


Louveau T, Orme A, Pfalzgraf H, Stephenson M, Melton RE, Saalbach G, Hemmings  AM, Leveau A, Rejzek M, Vickerstaff RJ, Langdon T, Field R, Osbourn AE (2018) Analysis of two new arabinosyltransferases belonging to the carbohydrate-active enzyme (CAZY) glycosyl transferase family 1 provides insights into disease resistance and sugar donor specificity. Plant Cell. doi: 10.1105/tpc.18.00641

Open Access

This research from the John Innes Centre, East Maling and Aberystwyth University is led by Thomas Louveau and Anne Osbourn and characterises two new arabinosyltransferases from oat and soybean. These enzymes are involved in the production of saponins that are involved in defence responses. These enzymes normally transfer arabinose to their substrates but through targeted mutations the authors modified one of them to instead transfer glucose. This study provides insights into the specifics of ‘sugar-donation’ and has identified potential novel targets for manipulating defence responses in two crop species.


Soubeyrand E, Johnson TS, Latimer S, Block A, Kim J, Colquhoun TA, Butelli E,  Martin C, Wilson MA, Basset G (2018) The Peroxidative Cleavage of Kaempferol Contributes to the Biosynthesis of the Benzenoid Moiety of Ubiquinone in Plants. Plant Cell. 2018 Nov 14. pii: tpc.00688.2018. doi: 10.1105/tpc.18.00688

Open Access

This US-led study includes members of Cathie Martin’s lab at the John Innes Centre as co-authors in which they investigate the flavonoid-biosynthesis pathway, in particular the land-plant-specific synthesis of ubiquinone. They used Arabidopsis and tomato mutants to dissect the ubiquinone biosynthesis pathway, revealing that the B-ring of the specalised metabolite kaempferol is incorporated into the primary metabolite ubiquinone.


Bourdais G, McLachlan DH, Rickett LM, Zhou J, Siwoszek A, Häweker H, Hartley M, Kuhn H, Morris RJ, MacLean D, Robatzek S (2018) The use of quantitative imaging to investigate regulators of membrane trafficking in Arabidopsis stomatal closure. Traffic. doi: 10.1111/tra.12625

This work from both Norwich Research Park and the University of Bristol is led by Gildas Bourdais and describes a high-throughput quantitative imaging, reverse genetic screen to characterize known stomatal mutants on the basis of their effect on the endomembrane system. This screen allowed them to precisely define the point in the signaling pathway at which each mutant was affected, providing a genetic framework for the control of stomatal closure. This image-based tool should be a valuable addition to future studies that aim to use quantitative image analysis.


https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky1196/5198529

Catoni M, Jonesman T, Cerruti E, Paszkowski J (2018) Mobilization of Pack-CACTA transposons in Arabidopsis suggests the mechanism of gene shuffling (2018) Nucleic Acids Res. doi: 10.1093/nar/gky1196

Open Access

This work was performed at SLCU in Jerzy Paszkowski’s lab by current University of Birmingham lecturer Marco Catoni and analyses the genomic impact of the mobilisation of Pack-TYPE transposons. They track the movement of these transposons over multiple generations, showing that they can insert into genic regions and that their subsequent incomplete excisions can cause deleterious effect on gene function. Over evolutionary time the action of this type of mobile element might therefore importantly influence gene shuffling.


Shabek N, Ticchiarelli F, Mao H, Hinds TR, Leyser O, Zheng N (2018) Structural plasticity of D3-D14 ubiquitin ligase in strigolactone signalling. Nature. doi: 10.1038/s41586-018-0743-5

Nitzan Shabek is the lead author on his US-led paper that includes Fabrizio Ticchiarelli and Ottoline Leyser from SLCU as co-authors. This paper reveals the structure of the interaction between the Arabidopsis α/β hydrolase D14 and the D3 F-box protein, which is important for multiple aspects of strigolactone signaling. They show that structural plasticity of the D3 C-terminal α-helix, which can switch between two different forms, enables the interaction between D14 and the D53 repressor protein. Providing insight into these specific interactions is key to increasing understanding of how the D14-D3 complex influences strigolactone signaling.


Menard GN, Bryant FM, Kelly AA, Craddock CP, Lavagi I, Hassani-Pak K, Kurup S, Eastmond PJ (2018) Natural variation in acyl editing is a determinant of seed storage oil composition. Sci Rep. doi: 10.1038/s41598-018-35136-6

Open Access

This work is led from Rothamsted Research with Guillaume Menard as first author and uses the Arabidopsis MAGIC population to identify novel genetic loci involved in seed oil composition. They identified multiple QTLs associated with the quantity of the major very long chain fatty acid species 11-eicosenoic acid (20:1), showing that the enzyme LYSOPHOSPHATIDYLCHOLINE ACYLTRANSFERASE 2 (LPCAT2), which is involved in the acyl-editing pathway, was the primary QTL. Subsequently they show LPCAT2 expression was key for varying seed 20:1 content and that natural variation in the capacity for acyl editing is an important determinant of oil content.


Bozbuga R, Lilley CJ, Knox JP, Urwin PE (2018) Host-specific signatures of the cell  wall changes induced by the plant parasitic nematode, Meloidogyne incognita (2018). Sci  Rep. doi: 10.1038/s41598-018-35529-7

https://www.nature.com/articles/s41598-018-35529-7

Open Access

Refik Bozbuga at the University of Leeds is first author on this study that investigates the cell wall composition of nutrient-supplying ‘giant cells’ that are induced in roots following infection with Meloidogyne spp nematodes. They analysed the cell walls of giant cells from three species (Arabidopsis, maize and aduki bean) as well as using a set of Arabidopsis mutants to characterise the possible cell wall components that might influence infection rates.


Mathers AW, Hepworth C, Baillie AL, Sloan J, Jones H, Lundgren M, Fleming AJ,  Mooney SJ, Sturrock CJ (2018) Investigating the microstructure of plant leaves in 3D with lab-based X-ray computed tomography. Plant Methods. doi:  10.1186/s13007-018-0367-7

Open Access
This paper from the Universities of Nottingham, Sheffield and Lancaster provides a methodology that uses a microCT image pipeline to measure leaf intercellular airspace and to provide quantitative data on descriptors of leaf cellular architecture. They measured 6 different plant species, showing that this 3D method generates an improved dataset when compared to traditional 2D methods of measurement.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-018-0367-7

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