GARNet Research Roundup: Jan 11th 2019

The inaugural GARNet Research Roundup of 2019 firstly includes a paper from the University of Sheffield that has identified new pericentromeric epigenetic loci that affect the pathogen response. Secondly is a collaboration between researchers in Birmingham, Nottingham and Oxford that has identified a new mode of regulation of the VRN2 protein. Next are two papers from Jonathan Jones’ lab at The Sainsbury Laboratory in Norwich that firstly provides a toolkit for gene editing in Arabidopsis and secondly characterise the role of the NRG1 gene in the defense response. The penultimate paper is from Paul Devlin’s lab at RHUL and investigates the role of the circadian clock in the control of leaf overtopping whilst the final paper is a meeting report from a recent GARNet workshop on gene editing.


Furci L, Jain R, Stassen J, Berkowitz O, Whelan J, Roquis D, Baillet V, Colot V, Johannes F, Ton J (2019) Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis. Elife. doi: 10.7554/eLife.40655.

Open Access

Leonardo Furci and Ritushree Jain are the lead authors on this study conducted at the University of Sheffield. The authors used a population of epigenetic recombinant inbred lines (epiRILs) to screen for resistance to the oomycete pathogen Hyaloperonospora arabidopsidis. These lines each share genetic information but have varied epigenetic changes. This analysis enabled the identification of plants with hypomethylated pericentromeric regions that were primed to better respond to the presence of this pathogen. The authors discuss the mechanism through which this might affect the defence response albeit without altering other aspects of plant growth.

https://elifesciences.org/articles/40655

Gibbs DJ, Tedds HM, Labandera AM, Bailey M, White MD, Hartman S, Sprigg C, Mogg SL, Osborne R, Dambire C, Boeckx T, Paling Z, Voesenek LACJ, Flashman E, Holdsworth MJ (2018) Oxygen-dependent proteolysis regulates the stability of angiosperm polycomb repressive complex 2 subunit VERNALIZATION 2. Nat Commun. doi: 10.1038/s41467-018-07875-7

Open Access

This collaboration between the Universities of Birmingham, Nottingham, Oxford and colleagues in Utrecht is led by Daniel Gibbs. They demonstrate that the amount of VRN2 protein, which is a member of the Polycomb Repressive Complex2, is controlled by the N-end rule pathway and that this regulation responses to both cold and hypoxia stress. Whilst the VRN2 gene is expressed throughout the plant, the N-end rule degradation pathway ensures that the protein is restricted to meristematic regions until the plant senses the appropriate abiotic stress. Classically VRN2 has been linked to the regulation of flowering time by altering gene expression at the FLC locus so this study introduces new complexity into this process through the involvement of the N-end rule pathway. More information on this linkage will undoubtedly follow over the coming years.

Daniel kindly discusses this paper on the GARNet YouTube channel.


Castel B, Tomlinson L, Locci F, Yang Y, Jones JDG (2019) Optimization of T-DNA architecture for Cas9-mediated mutagenesis in Arabidopsis. PLoS One. doi: 10.1371/journal.pone.0204778

Open Access

Baptiste Castel is lead author of this work conducted at the Sainsbury Laboratory, Norwich in Jonathan Jones’ group. They have conducted a detailed analysis of the factors that contribute to successful gene editing by CRISPR-Cas9, specifically in Arabidopsis. This includes assessing the efficacy of different promotor sequences, guideRNAs, versions of Cas9 enzyme and associated regulatory sequences in the editing of a specific locus. Given that researchers are finding that different plants have different requirements when it comes to successful gene editing, this type of analysis will be invaluable for anyone who plans to conduct a gene editing experiment in Arabidopsis.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0204778

Castel B, Ngou PM, Cevik V, Redkar A, Kim DS, Yang Y, Ding P, Jones JDG (2018) Diverse NLR immune receptors activate defence via the RPW8-NLR NRG1. New Phytol. doi: 10.1111/nph.15659

In this second paper led by Baptiste Castel, they used the techniques outlined in the paper above to generate a set of CRISPR mutants deficient in NRG1, which is a RPW8-NLR resistance (R) gene. These nrg1 mutants have compromised signalling in all tested downstream TIR-NLR resistance genes. In addition the authors demonstrate that this signalling is needed for resistance to oomycete but not bacterial infection. Therefore this study reveals some significant details regarding the components of the disease response that are influenced by the activity of NRG1.


Woodley Of Menie MA, Pawlik P, Webb MT, Bruce KD, Devlin PF (2018) Circadian leaf movements facilitate overtopping of neighbors. Prog Biophys Mol Biol. doi: 10.1016/j.pbiomolbio.2018.12.012

This work is led by Michael Woodley Of Menie from Paul Devlin’s lab at Royal Holloway College and investigates the role of circadian leaf movements during shade avoidance and overtopping. Arabidopsis plants were grow in a grid system that meant leaves would interact with their neighbours and the authors show that plants with a normal circadian rhythm gained an advantage over those adapted to a longer period in which they were grown. This overtopping was additive to the advantage gained through shade avoidance and overall this paper shows that maintainance of clock-aligned leaf movements are beneficial to growth.


Parry G, Harrison CJ (2019) GARNet gene editing workshop. New Phytol. doi: 10.1111/nph.15573

Open Access

GARNet advisory committee member Jill Harrison and GARNet coordinator Geraint Parry are authors on this meeting report resulting from a GARNet organised workshop on gene editing that took place in March 2018 at the University of Bristol. Coincidentally part of the paper discusses the work that was presented at the meeting by Baptiste Castel, which is published in the paper described above.

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

GARNet Research Roundup: November 1st 2018

This week’s GARNet research roundup again features papers on a variety of topics. First is work from the University of Leeds that investigates the physical properties of callose:cellulose hydrogels and the implication for cell wall formation. Second is work from the University of York that assesses the role of the HSP90.2 protein in control of the circadian clock. The third paper features GARNet committee member Sarah McKim and looks at the genetic control of petal number whilst the next paper from the Universities of Warwick and Glasgow includes a proteomic analysis of different types of secretory vesicles.

The next two papers look at different aspects of hormone signaling. Firstly Alistair Hetherington from the University of Bristol is a co-author on a study that looks at the role of the BIG protein whilst Simon Turner’s lab in Manchester investigates the role of ABA in xylem fibre formation.

The penultimate paper includes Lindsey Turnbull from the University of Oxford and looks at the stability of epialleles across 5 generations of selection. Finally is a paper that includes researchers from TSL in Norwich who have contributed to a phosphoproteomic screen to identify phosphorylated amino acids that influence the defence response.


Abou-Saleh R, Hernandez-Gomez M, Amsbury S, Paniagua C, Bourdon M, Miyashima S, Helariutta Y, Fuller M, Budtova T, Connell SD, Ries ME, Benitez-Alfonso Y (2018) Interactions between callose and cellulose revealed through the analysis of biopolymer mixtures. Nature Communications DOI: 10.1038/s41467-018-06820-y

https://www.nature.com/articles/s41467-018-06820-y

Open Access
Radwa Abou-Saleh is lead author on this work from Yoselin Benitez-Alfonso’s lab at the University of Leeds. (1,3)-β-glucans such as callose play an important role in plant development yet their physical properties are largely unknown. This study analyses a set of callose:cellulose hydrogel mixtures as a proxy for different cell wall conditions. They show that callose:cellulose hydrogels are more elastic than those composed of only cellulose, providing evidence that the interactions between cellulose and callose are important for the structural features of cell walls.


Davis AM, Ronald J, Ma Z, Wilkinson AJ, Philippou K, Shindo T, Queitsch C, Davis SJ (2018) HSP90 Contributes To Entrainment of the Arabidopsis Circadian Clock via the Morning Loop. Genetics. doi: 10.1534/genetics.118.301586

http://www.genetics.org/content/early/2018/10/18/genetics.118.301586.long

Open Access
Amanda Davies is the first author on this study from Seth Davies’ lab at the University of York in which they assess the role of the molecular chaperone HSP90.2 on function of the circadian clock. The show hsp90.2-3 mutant plants have a lengthened circadian period with a specific defect in the morning. This data allows the authors to better understand the pathway through which HSP90.2 functions to entrain the circadian clock.


Monniaux M, Pieper B, McKim SM, Routier-Kierzkowska AL, Kierzkowski D, Smith RS, Hay A. The role of APETALA1 in petal number robustness. Elife. doi: 10.7554/eLife.39399

https://elifesciences.org/articles/39399

Open Access
GARNet committee member Sarah McKim is a co-author on this paper, that is led by Marie Monniaux, which includes research from her time at the University of Oxford. This work from the Hay lab in Cologne compares petal number in Arabidopsis thaliana, in which the number is invariant, and Cardamine hirsute, in which it varies. They show that petal number robustness can be attributed to the activity of the APETALA1 (AP1) floral regulator and that AP1 masks the activity of several genes in Arabidopsis but not in Cardamine.


Waghmare S, Lileikyte E, Karnik RA, Goodman JK, Blatt MR, Jones AME (2018) SNAREs SYNTAXIN OF PLANTS 121 (SYP121) and SYP122 mediate the secretion of distinct cargo subsets . Plant Physiol. doi: 10.1104/pp.18.00832

http://www.plantphysiol.org/content/early/2018/10/23/pp.18.00832.long

Open Access

This collaboration between the Universities of Glasgow and Warwick is led by Sakharam Waghmare, who works with Mike Blatt in Glasgow. This study uses proteomic approaches to characterise the secretory cargos within vesicles decorated with either of the SNARE proteins SYNTAXIN OF PLANTS 121 (SYP121) or SYP122. Genetic analysis suggests that SYP121 and SYP122 have redundant functions but this new research is able to identify cargo proteins that are either contained within both types of vesicle or that are specific to one or the other.


Zhang RX, Ge S, He J, Li S, Hao Y, Du H, Liu Z, Cheng R, Feng YQ, Xiong L, Li C, Hetherington AM, Liang YK (2018) BIG regulates stomatal immunity and jasmonate production in Arabidopsis. New Phytol. doi: 10.1111/nph.15568

Alistair Hetherington is a co-author on this China-based study led by Ruo‐Xi Zhang from Wuhan. This work adds to some recent interest in the BIG protein; in this study showing that it is involved in the interaction between JA and ethylene signaling during stress responses. In a complex set of interactions they show that the BIG protein differently alters opposing arms of the JA signaling pathway providing additional evidence that this protein is a key regulator of plant hormone signaling, albeit by a set of as yet unknown mechanisms.


Campbell L, Etchells JP, Cooper M, Kumar M, Turner SR. An essential role for Abscisic acid in the regulation of xylem fibre differentiation. Development. doi: 10.1242/dev.161992

This work from Simon Turner’s lab at the University of Manchester is led by Liam Campbell and identifies a novel role for ABA in the formation of xylem fibres during secondary thickening of the Arabidopsis hypocotyl. The action of ABA doesn’t alter the xylem:phloem ratio but rather the activity focuses on the formation of fibres within the already defined xylem tissue.


Schmid MW, Heichinger C, Coman Schmid D, Guthörl D, Gagliardini V, Bruggmann R, Aluri S, Aquino C, Schmid B, Turnbull LA, Grossniklaus U (2018) Contribution of epigenetic variation to adaptation in Arabidopsis. Nat Commun. doi: 10.1038/s41467-018-06932-5

https://www.nature.com/articles/s41467-018-06932-5

Open Access
Lindsey Turnbull (University of Oxford) is a co-author on this paper from Ueli Grossniklaus’ group in Zurich. Marc Schmid is lead author of the study that investigates the inheritance of Arabidopsis epialleles over 5 generations during conditions of simulated selection. The authors show that variations in methylation state are subject to selection and do indeed contribute to adaptive responses


Kadota Y, Liebrand TWH, Goto Y, Sklenar J, Derbyshire P, Menke FLH, Torres MA, Molina A, Zipfel C, Coaker G, Shirasu K (2018) Quantitative phosphoproteomic analysis reveals common regulatory mechanisms between effector- and PAMP-triggered immunity in plants. New Phytol. doi: 10.1111/nph.15523

Members of Cyril Zipfel’s group at The Sainsbury lab in Norwich are co-authors on this paper led by Yasuhiro Kadota from the RIKEN in Yokohama. They use a phosphoproteomic screen to identify a set of newly identified phosphorylation sites on membrane-associated proteins involved in effector-triggered immunity (ETI). Some of these phosphosites overlap with those known to be important for pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI), indicating a convergence of signaling control of both these pathways to certain key residues.

GARNet Research Roundup: October 10th 2018

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Published on: October 10, 2018

This edition of the GARNet research roundup begins with a paper from Jose Gutierrez-Marcos’ lab in Warwick that investigates the functional significance of inherited epigenetics marks in clonally propagated plants. Second is work from Sara Simonini and Lars Ostergaard (John Innes Centre) that defines a domain in the ETTIN protein important for the auxin response. Next is work from SLCU from Siobhan Braybrook and Henrik Jonsson that experimentally defines and models the role of cell wall composition in anisotropic hypocotyl growth. The fourth paper is from Jonathan Jones’ lab (TSL, Norwich) that adds to our understanding of the activity of the RRS1-R-RPS4 NLR immune complex.

The final three papers are each from the University of Edinburgh and look at different aspects of the relationship between light quality and the circadian clock. First is a paper from Karen Halliday’s lab that investigates the role of PHYA; next Andrew Millar is a co-author on a manuscript that looks at control of FT expression during seasonally realistic conditions. Finally Ference Nagy and Mirela Domijan (University of Liverpool) co-author a paper that assesses the role of HY5 in the response to blue-light.


Wibowo A, Becker C, Durr J, Price J, Spaepen S, Hilton S, Putra H, Papareddy R, Saintain Q, Harvey S, Bending GD, Schulze-Lefert P, Weigel D, Gutierrez-Marcos J (2018) Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation. Proc Natl Acad Sci U S A doi: 10.1073/pnas.1805371115

http://www.pnas.org/content/early/2018/09/06/1805371115.long

Open Access
Anjar Wibowo and Claude Becker are first authors on this UK-German collaboration from the labs of Jose Gutierrez-Marcos (University of Warwick) and Detlef Weigel (Max Planck Institutem, Tübingen). In this work they clonally propagate Arabidopsis and show that organ-specific epigenetic marks are maintained across generations. Interestingly these changes are then maintained through multiple rounds of sexual reproduction. These epigenetic marks provide heritable molecular and physiological phenotypes that can alter the response to pathogens, allowing progeny to maintain a beneficial epigenome that was generated in their parents.


Simonini S, Mas PJ, Mas CMVS, Østergaard L, Hart DJ (2018) Auxin sensing is a property of an unstructured domain in the Auxin Response Factor ETTIN of Arabidopsis thaliana. Sci Rep. doi: 10.1038/s41598-018-31634-9

https://www.nature.com/articles/s41598-018-31634-9

Open Access

This UK-France collaboration is led by Sara Simonini from the John Innes Centre and continues the Ostergaard lab’s work on the role of the auxin response factor ETTIN in the auxin response. In this paper they analyse the C-terminal ETT specific domain (ES domain) across plant lineages, showing that it does not directly bind auxin but could functional response to a dose response of auxin in a Y2H assay. Understanding more about this ES domain will increase our understanding of auxin sensing by ETTIN and more broadly about auxin-dependent gene regulation.


Bou Daher F, Chen Y, Bozorg B, Clough J, Jönsson H, Braybrook SA. Anisotropic growth is achieved through the additive mechanical effect of material anisotropy and elastic asymmetry. Elife.  doi: 10.7554/eLife.38161

https://elifesciences.org/articles/38161

Open Access

Firas Bou Daher is the first author on work from Siobhan Braybrook’s lab conducted both in the Sainsbury Lab Cambridge University and at its new home in California. In this work they look at anisotropic growth in the Arabidopsis hypocotyl and the relationship between cellulose orientation and pectin deposition in the control of this process. They provide experimental evidence that growth parameters are influenced by pectin biochemistry in processes that begin immediately after germination.


Ma Y, Guo H, Hu L, Martinez PP, Moschou PN, Cevik V, Ding P, Duxbury Z, Sarris PF, Jones JDG (2018) Distinct modes of derepression of an Arabidopsis immune receptor complex by two different bacterial effectors. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1811858115

Yan Ma and Hailong Guo are lead authors on this study from Jonathan Jones’ lab at The Sainsbury Lab, Norwich. They perform a detailed examination of the RRS1-R-RPS4 NLR protein complex, which is necessary to respond to at the bacterial effectors, AvrRps4 and PopP2. Deletion of a WRKY transcription factor domain in the RRS1-R protein causes constitutive activation of the defense response, indicating that this domain maintains the complex in an inactive state in the absence of pathogens. Indeed AvrRps4 does interact with this WRKY domain but interestingly PopP2 activation requires interaction with a longer C-terminal extension of RRS1-R. This demonstrates that although these bacterial effectors are recognised by the same complex the interactions occurs in a subtly but functionally distinct ways.


Seaton DD, Toledo-Ortiz G, Ganpudi A, Kubota A, Imaizumi T, Halliday KJ (2018) Dawn and photoperiod sensing by phytochrome A. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1803398115

Open Access

This research from Karen Halliday’s lab in Edinburgh is led by Daniel Seaton and provided a detailed assessment of the role of phytochrome A (phyA) in photoperiod sensing, which is defined as the relationship between the circadian clock and external light signals. They show that PHYA activity, controlled by the transcription factors, PIF4 and PIF5, is a key regulator of morning activity, particularly in short photoperiods. PHYA protein accumulates during the night and responds to light by promoting a burst of gene expression that prepares the plant for the upcoming daylight and places this light receptor as a key detector of dawn.


Song YH, Kubota A, Kwon MS, Covington MF, Lee N, Taagen ER, Laboy Cintrón D, Hwang DY, Akiyama R, Hodge SK, Huang H, Nguyen NH, Nusinow DA, Millar AJ, Shimizu KK, Imaizumi T (2018) Molecular basis of flowering under natural long-day conditions in Arabidopsis. Nat Plants. doi: 10.1038/s41477-018-0253-3

Andrew Millar is a co-author on this US-led paper that investigates the circadian regulation of the Arabidopsis florigen gene FLOWERING LOCUS T (FT) within an annual context, showing that during the spring FT shows a morning peak is absent in their usual lab experiments. By adjusting growth-room conditions to mimic natural seasonal variations they show that phytochrome A and EARLY FLOWERING 3 regulate morning FT expression by stabilizing the CONSTANS protein. This manuscript highlights the importance of providing seasonal-specific conditions in order to understand field-relevant regulation of plant growth.


Hajdu A, Dobos O, Domijan M, Bálint B, Nagy I, Nagy F, Kozma-Bognár L. ELONGATED HYPOCOTYL 5 mediates blue light signalling to the Arabidopsis circadian clock (2018) Plant J. doi: 10.1111/tpj.14106

Ferenc Nagy (University of Edinburgh) is a co-author on this Hungarian-led study that looks the effect of light quality on the function of the key signaling hub transcription factor ELONGATED HYPOCOTYL 5 (HY5). They show that hy5 mutants show shorter period rhythms in blue but not in red light or darkness. Even though the pattern and level of HY5 alters its binding to downstream promotor elements, subsequent gene expression is only altered in a few genes. In collaboration with Mirela Domijan (University of Liverpool) https://www.liverpool.ac.uk/mathematical-sciences/staff/mirela-domijan/ they model this response to suggest that clock feedback mechanisms mask HY5-induced changes. Ultimately they show that HY5 is important in decoding the blue:red mix of white light and that it at least partially informs activity of the circadian oscillator.

Arabidopsis Research Roundup: February 12th

This weeks Arabidopsis Research Roundup begins with a study from SLCU that investigates the interaction between nitrate and cytokinin signaling in the shoot meristem. Next is research from Sheffield that studies changes to the macromolecular composition of the photosynthetic apparatus following the transition from dark to light. Third are three papers that include University of Edinburgh faculty members as co-authors; Gary Loake is involved in a global study on NO signaling, Karen Halliday is included on a study into the relationship between clock components and the PIF-mediated hypocotyl elongation and Naomi Nakayama contributes to the development of a model that explains PIN protein localisation. Cyril Zipfel (TSL) is a co-author on the fifth paper, which introduces a new signaling component in the defence response and whilst the penultimate paper includes Denis Murphy (University of South Wales) and investigates the effect of dioxins on seed development. The final paper documents research from Manchester and Nottingham that uses a cress endosperm as a model to test the elastic properties of thin biological membranes.


Landrein B, Formosa-Jordan P, Malivert A,, Schuster C, Melnyk CW,, Yang W, Turnbull C, Meyerowitz EM, Locke JCW,, Jönsson H (2018) Nitrate modulates stem cell dynamics in Arabidopsis shoot meristems through cytokinins. PNAS doi: 10.1073/pnas.1718670115.

Open Access

http://www.pnas.org/content/early/2018/01/22/1718670115

Henrik Jonsson and James Locke (SLCU) are corresponding authors on this investigation into the relationship between nitrate and cytokinin signalling in the Arabidopsis shoot meristem (SAM). They show that nitrate availability determines the size of the SAM, which is controlled by the transport of cytokinin precursors from the root to the shoot. A discussion about this paper with lead author Benoit Landrien and Professor Jonsson is available on the GARNet YouTube and iTunes channels.


Wood WHJ, MacGregor-Chatwin C, Barnett SFH, Mayneord GE, Huang X, Hobbs JK, Hunter CN, Johnson MP (2018) Dynamic thylakoid stacking regulates the balance between linear and cyclic photosynthetic electron transfer. Nature Plants. doi: 10.1038/s41477-017-0092-7

Open with this link

This research in this manuscript has come from the University of Sheffield with Matthew Johnson as the corresponding author. They have used atomic force microscopy (AFM) to investigate how the transition from dark to light affects the macromolecular architecture of the photosynthetic apparatus within the thylakoid membrane. This transition does not alter the antenna size of either photosystem yet increases the number of thylakoid grana. Overall these changes serve to regulate the balance between light harvesting, CO2 fixation and enabling the protection of PSII activity from the destructive effects of non-photochemical quenching.


Imran QM, Hussain A, Lee SU, Mun BG, Falak N, Loake GJ, Yun BW (2018) Transcriptome profile of NO-induced Arabidopsis transcription factor genes suggests their putative regulatory role in multiple biological processes. Sci Rep. doi: 10.1038/s41598-017-18850-5.

https://www.nature.com/articles/s41598-017-18850-5

Open Access

Gary Loake (University of Edinburgh) is a contributor to this Korean-led manuscript that has performed expression analysis on plants treated with S-nitrosocysteine (CySNO). They have identified many novel NO-responsive transcription factors and were able to confirm the role of three random TFs in this response following analysis of loss of function mutants. This paper provides new insights into the molecular components that contribute to NO signalling during plant defence and immunity.


Martín G, Rovira A, Veciana N, Soy J, Toledo-Ortiz G, Gommers CMM, Boix M, Henriques R, Minguet EG, Alabadí D, Halliday KJ, Leivar P, Monte E Circadian Waves of Transcriptional Repression Shape PIF-Regulated Photoperiod-Responsive Growth in Arabidopsis. Curr Biol. doi: 10.1016/j.cub.2017.12.021

Karen Halliday (University of Ediburgh) is a co-author on this Spanish-led study that investigates how the expression of PHYTOCHROME-INTERACTING FACTORS (PIFs) genes is controlled. The activity of PIFs are responsible for determining the rate of hypocotyl elongation in different light conditions and this paper demonstrates that PSEUDO-RESPONSE REGULATORS PRR9/7/5 proteins act antagonistically to the PIFs by interacting at the promotor of the CDF5 transcription factor. This provides a mechanism to explain the circadian-controlled regulation of hypocotyl cell elongation.


Hernandez V, Barrio RA, Benítez M, Nakayama N, Romero-Arias JR, Villarreal Lujan C (2018) A physico-genetic module for the polarisation of auxin efflux carriers PIN-FORMED (PIN). Phys Biol. doi: 10.1088/1478-3975/aaac99

Naomi Nakayama (University of Edinburgh) is a co-author on this Mexican-led study that proposes a physico-genetic model that explains the localization of PIN auxin transporter proteins to the Arabidopsis plasma membrane. This model confirms experimental observations and allows the prediction that mechanical forces can predominate over molecular components.


www.cell.com/molecular-cell/fulltext/S1097-2765(17)30983-8

Wang J, Grubb LE, Wang J, Liang X, Li L, Gao C, Ma M, Feng F, Li M, Li L, Zhang X, Yu F, Xie Q, Chen S, Zipfel C, Monaghan J, Zhou JM (2018) A Regulatory Module Controlling Homeostasis of a Plant Immune Kinase. Mol Cell. doi: 10.1016/j.molcel.2017.12.026

This Chinese-led paper includes Cyril Zipfel (TSL) as a co-author and identifies the U-box proteins PUB25 and PUB26 as E3 ligases for the cytoplasmic kinase BIK1, which is a key rate limiting component of the plant defence response. This multi-protein regulatory module provides another level of complexity to our understanding of the molecular factors involved in plant immunity.


Hanano A, Almousally I, Shaban M, Murphy DJ (2018) Exposure of Arabidopsis Plants to Dioxin Results in a Wrinkled Seed Phenotype that is likely due to 20S Proteasomal Degradation of WRI1. J Exp Bot. doi: 10.1093/jxb/ery027

Denis Murphy (University of South Wales) is a co-author on this Syrian-led study that uses Arabidopsis seeds to test the negative effects of dioxins. Seeds treated with dioxins have a wrinked phenotype that corresponds to changes in the expression of genes related to lipid and carbohydrate metabolism. Overall this study reveals a novel set of genetic changes effects caused by dioxins that explain the profound effects on seed development.


S. P. Pearce, J. R. King, T. Steinbrecher, G. Leubner-Metzger, N. M. Everitt, M. J. Holdsworth (2018) Finite indentation of highly curved elastic shells Proceedings of the Royal Society A doi: 10.1098/rspa.2017.0482

Open Access

Plant scientist Mike Holdsworth (University of Nottingham) is a co-author on this paper that has used the endosperm from garden cress (Lepidium sativum) as the experimental model to define the elastic properties of a thin biological surface. Indentation experiments have been classically used to measure these properties and then develop mathematically models that explain their characteristics. These models rely on an assumed flat surface whereas in reality any surface will often be curved. By obtaining measurements from identations studies on the cress endosperm they are able to better refine the models that explain the properties of the membrane in this context.

Arabidopsis Research Roundup: January 23rd.

This weeks Arabidopsis Research Roundup begins with two papers from Royal Hollaway University of London that investigate the factors that control leaf development in the dark and the control of PIN1 phosphorylation. Third is a paper from Bristol that demonstrates the translation of research from Arabidopsis into coriander with regard the control of the response to UV light. Next is research from the John Innes Centre that characterises the role of DNA methylation during meiosis in the male lineage.

Christine Foyer (Leeds) leads the next paper that defines the relationship between cold treatment and strigolactone signalling. The penultimate paper is led by Richard Napier from the University of Warwick and determines the parameters that define the substrates of the AUX1 protein whilst the final paper includes Cyril Zipfel (TSL) as a co-author and uses systems biology approaches to characterise the interactions between leucine-rich repeat receptor kinases (LRR-RKs).


Mohammed B, Farahi Bilooei S, Doczi R, Grove E, Railo S, Palme K, Ditengou FA, Bögre L, Lopez-Juez E (2017) Converging energy and hormonal signalling control meristem activity, leaf initiation and growth Plant Phys doi: 10.1104/pp.17.01730

http://www.plantphysiol.org/content/early/2017/12/28/pp.17.01730.long

Open Access

Enrique Lopez-Juez (RHUL) leads this collaboration with German and Hungarian colleagues that investigates the fundamental question; ‘Why don’t leaves grow in the dark’. They show that this response is influenced by both auxin transport and the plants energy sensing mechanisms. Interestingly when energy is provided via external sucrose, leaves develop differently in the dark than they do in the light indicating that multiple signaling pathways differentially influence this phenotype.

Enrique discusses this paper on the GARNet YouTube page.


Dory M, Hatzimasoura E, Kállai BM, Nagy SK, Jäger K, Darula Z, Nádai TV, Mészáros T, López-Juez E, Barnabás B, Palme K,,, Bögre L, Ditengou FA,,, Dóczi R (2017) Coevolving MAPK and PID phosphosites indicate an ancient environmental control of PIN auxin transporters in land plants. FEBS Lett. doi: 10.1002/1873-3468.12929

Laszlo Bogre and Enrique Lopez-Juez (RHUL) are co-authors on this Hungarian-led study that has discovered 3 conserved putative MAPK sites within the auxin transport protein PIN1. Phosphorylation of two of these sites causes partial loss of PIN1 membrane localization and therefore opposes the effect of the PINOID kinase, whose activity promotes PIN1 membrane localisation.


https://www.nature.com/articles/s41598-017-18073-8

Fraser DP, Sharma A, Fletcher T, Budge S, Moncrieff C, Dodd AN, Franklin KA (2017) UV-B antagonises shade avoidance and increases levels of the flavonoid quercetin in coriander (Coriandrum sativum). Sci Rep. doi: 10.1038/s41598-017-18073-8 Open Access

Keara Franklin and Anthony Dodd (University of Bristol) lead this collaboration between academic researchers and those in the company Vitacress. They translate research from Arabidopsis into Coriander that looks at the effect of UV-B on stem elongation and the interaction with flavonoid signaling. This work shows that alterations to the UV-B regime during growth of potted herbs might reduce deleterious effects caused by neighbour proximity.


Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X (2017) Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nat Genet. doi: 10.1038/s41588-017-0008-5

Xiaoqi Feng (JIC) is the corresponding author on this collaboration with James Higgins from Leicester and they investigate the role of DNA methylation in the control of male meiosis. They demonstrate that RNA-directed DNA methylation (RdDM) in the male lineage regulates gene expression in meiocytes and results in the mis-splicing of the MPS1/PRD2 transcipt, which causes aberrant alterations in spindle formation.


Cooper JW, Hu Y, Beyyoudh L, Yildiz Dasgan H, Kunert K, Beveridge CA, Foyer CH (2018) Strigolactones positively regulate chilling tolerance in pea and in Arabidopsis. Plant Cell Environ. doi: 10.1111/pce.13147

Christine Foyer (Leeds) is the corresponding author on this collaboration with Australian, Turkish and South African colleagues that looks into the role strigolactones play during chilling tolerance in both Arabidopsis and pea plants. Plants that have been chilled during the night have reduced biomass, which was not observed in either pea or Arabidopsis strigolactone mutants. This demonstrates a clear role for this hormone in this response and provides a potential target for the manipulation of plant growth under environmental conditions.


Hoyerova K, Hosek P, Quareshy M, Li J, Klima P, Kubes M,, Yemm AA, Neve P, Tripathi A, Bennett MJ, Napier RM (2017) Auxin molecular field maps define AUX1 selectivity: many auxin herbicides are not substrates. New Phytol. doi: 10.1111/nph.14950

onlinelibrary.wiley.com/doi/10.1111/nph.14950/abstract

Together with Czech co-authors Richard Napier (Warwick University) leads this investigation into the mode of action of the AUX1 auxin influx carrier and its substrate preferences. This work made use of a novel auxin accumulation assay and associated mathematical modeling to describe the parameters that make difference auxins to be good candidates for the AUX1 transport. Interesting they find that many commonly used auxinicide herbicides are poor substrates for AUX1 and the relevance of this finding for herbicide management strategies.


https://www.nature.com/articles/nature25184

Smakowska-Luzan E et al (2018) An extracellular network of Arabidopsis leucine-rich repeat receptor kinases. Nature doi: 10.1038/nature25184

Cyril Zipfel (TSL) is a co-author on this US-European study that performs a systems-biology analysis on the possible interactions between extracellular domains of the leucine-rich repeat receptor kinases (LRR-RKs) gene family in Arabidopsis. Analysis of 40K potential interactions allows the generation of a LRR-based cell surface interaction network (CSI-LRR). This was used to discover previously uncharacterized interactions between LRR-RKs and to demonstrate that these interactions allow the translocation of extracellular signals in balanced and tightly regulated patterns.

Arabidopsis Research Roundup: January 10th 2018

This Arabidopsis Research Roundup covers the final papers of 2017 and the first of this new year. The initial paper is led by researchers in Bristol and characterises how the multifaceted BIG protein influences stomatal dynamics in response to altered CO2. Second is a manuscript from SLCU that for the first time in plants demonstrates nuclear sequestration of cell cycle regulated mRNAs.

Next is a paper from Rothamsted that describes a role for the hormone GA during floral development. David Salt (Nottingham) is then a co-author on a manuscript that has determined a role for the CTL protein in ion homeostasis.

Seth Davies from York is the lead author on the next study that investigates a link between metabolism and the circadian clock. The sixth paper looks at genes involved in the control of autophagy and features Patrick Gallois (Manchester) as a co-author.

There are three papers from researchers working on Norwich Research Park with Cyril Zipfel (TSL) involved in a study that looks at vacuolar trafficking of BR signaling components. Janneke Balk leads a study that characterises enzymes involved in biosynthesis of metal co-factors whilst the final NRP-based paper from Nick Pullen and Steven Penfield (John Innes Centre) describes the Leaf-GP open software for automated plant phenotyping.

The penultimate paper uses a set of PlantProbes (developed by Paul Knox at Leeds) to study pollen development whilst the final paper from Keith Lindsey (Durham) describes the application of a Bayesian statistical methodology to model the parameters that control a hormone signaling network.


He J, Zhang RX, Peng K, Tagliavia C, Li S, Xue S, Liu A, Hu H,, Zhang J, Hubbard KE,, Held K, McAinsh MR, Gray JE, Kudla J, Schroeder JI, Liang YK, Hetherington AM (2018) The BIG protein distinguishes the process of CO2 -induced stomatal closure from the inhibition of stomatal opening by CO2. New Phytol. doi: 10.1111/nph.14957 Open Access

Alistair Hetherington (University of Bristol) leads this UK-USA-China collaboration that has characterised a role for the mysterious BIG protein during stomatal closure in response to altered CO2 concentration. Interestingly BIG mutants do not show a defect in stomatal opening in response to altered CO2, allowing the dissection of this complex response through the activity of this protein. It remains to be determined exactly how the BIG protein influences this process.


Yang W, Wightman R, Meyerowitz EM (2017) Cell Cycle Control by Nuclear Sequestration of CDC20 and CDH1 mRNA in Plant Stem Cells. Mol Cell. doi: 10.1016/j.molcel.2017.11.008

Elliott Meyerowitz (SLCU) is the corresponding author of this research that provides the first characterisation in plants of nuclear sequestration of mRNAs from developmental important genes. The authors show that Arabidopsis anaphase-promoting complex/cyclosome (APC/C) coactivator genes CDC20 and CCS52B are confined to the nucleus in prophase, preventing translation of the cognate proteins until metaphase, which appears to protect cyclins from degradation at an inappropriate phase of the cell cycle


Plackett ARG, Powers SJ, Phillips AL, Wilson ZA, Hedden P, Thomas SG4 (2017) The early inflorescence of Arabidopsis thaliana demonstrates positional effects in floral organ growth and meristem patterning. Plant Reprod. doi: 10.1007/s00497-017-0320-3

This study is led from Rothamsted Research and includes Zoe Wilson from the University of Nottingham. They perform a systematic analysis of early floral organ initiation across the Arabidopsis inflorescence, discovering that both GA-dependent and independent stages are important for this process, albeit via the activity of presently unknown factors.


Gao YQ, Chen JG, Chen ZR An D, Lv QY, Han ML, Wang YL, Salt DE, Chao DY (2017) A new vesicle trafficking regulator CTL1 plays a crucial role in ion homeostasis. PLoS Biol. doi: 10.1371/journal.pbio.2002978

Open Access

David Salt (University of Nottingham) is a co-author on this Chinese-led investigation into the role of the vesicle trafficking regulator choline transporter (CTL) during the control of ionome homeostasis. Using ctl1 mutants they show that this function is required for the action of certain ion transporters as well as during plasmodesmata (PD) development. This study provides novel insights into the role of vesicular transport in the control of ion homeostasis and how the location of these ions might alter vesicle activity.


Sánchez-Villarreal A, Davis AM, Davis SJ (2017) AKIN10 Activity as a Cellular Link Between Metabolism and Circadian-Clock Entrainment in Arabidopsis thaliana.

Plant Signal Behav. doi: 10.1080/15592324.2017.1411448

Seth Davies (University of York) is the corresponding author on this study demonstrating that overexpression of the AKIN10 subunit of the SnRK1 complex results in increased period length of the circadian clock. The authors postulate about the possible links between metabolic rate and function of the clock, allowing them to present a model of action that features each of the central regulatory elements.


Havé M, Balliau T, Cottyn-Boitte B, Dérond E, Cueff G, Soulay F, Lornac A, Reichman P, Dissmeyer N, Avice JC, Gallois P, Rajjou L, Zivy M, Masclaux-Daubresse C (2017) Increase of proteasome and papain-like cysteine protease activities in autophagy mutants: backup compensatory effect or pro cell-death effect? J Exp Bot. doi: 10.1093/jxb/erx482

Open Access
This study is led by French researchers and includes Patrick Gallois (University of Manchester) as a co-author. The work focuses on the role of the ATG genes during autophagy, the key process that controls nutrient recycling during senescence. In atg5 mutants they show that different sets of proteases are misregulated, suggestive of a complex relationship between the enzymes involved in nutrient remobilization.


Liu Q, Vain T, Viotti C, Doyle SM, Tarkowská D, Novák O, Zipfel C, Sitbon F, Robert S, Hofius D (2017) Vacuole Integrity Maintained by DUF300 Proteins Is Required for Brassinosteroid Signaling Regulation. Mol Plant. doi: 10.1016/j.molp.2017.12.015

Cyril Zipfel (TSL) is a member of this Pan-European consortium that investigates the role of the vacuolar proteins, LAZARUS1 (LAZ1) and LAZ1 HOMOLOG1 (LAZ1H1) on the cellular cycling of BR-signaling components. Plants with mutations in laz1 and laz1h1 show increased BAK1 accumulation at the tonoplast as well as enhanced BRI1 trafficking and degradation. These DUF300 proteins appear to play a specific role in BR signalling as other vacuolar-associated proteins are not involved in this process.


Kruse I, Maclean A, Hill L, Balk J (2017) Genetic dissection of cyclic pyranopterin monophosphate biosynthesis in plant mitochondria. Biochem J. doi: 10.1042/BCJ20170559 Open Access

Janneke Balk (John Innes Centre) leads this study that has identified novel alleles in mitochondrial enzymes that are involved in the biosynthesis of metal cofactors. Analysis of these enzyme mutant reveals that they show deficiencies in the synthesis of cyclic pyranopterin monophosphate (cPMP), revealing fresh insights into the metabolic processes involving this key intermediate.


Zhou J, Applegate C, Alonso AD, Reynolds D, Orford S, Mackiewicz M, Griffiths S, Penfield S, Pullen N (2017) Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat. Plant Methods. doi: 10.1186/s13007-017-0266-3

Open Access

Nick Pullen and Steve Penfield (John Innes Centre) introduce this new software tool for the automated measurement of plant phenotypes. This Leaf-GP software is open access and has the sophistication to discriminate between different aspects of both Arabidopsis and greenhouse growth wheat.

This paper is back of a special issue of Plant Methods that is based on the use of Computer Vision in Plant Phenotyping.


Ndinyanka Fabrice T, Vogler H, Draeger C, Munglani G, Gupta S, Herger AG, Knox JP, Grossniklaus U, Ringli C (2017) LRX Proteins play a crucial role in pollen grain and pollen tube cell wall development. Plant Physiol. doi: 10.1104/pp.17.01374

Open Access

This Swiss-led study looks into the role of LRX proteins during cell wall formation and how they affect pollen germination and pollen tube formation. The authors took advantage of the molecular tools produced by Paul Knox (University of Leeds) as part of his Plant Probes project.


Vernon I, Liu J, Goldstein M, Rowe J, Topping J, Lindsey K (2017) Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions. BMC Syst Biol. doi: 10.1186/s12918-017-0484-3 Open Access

Keith Lindsey (University of Durham) leads this paper that applies a Bayesian statistical methodology to analyse a model of hormonal crosstalk in the Arabidopsis root. They show that this technique can provide new insight into the behavior of models and enables the identification of new interesting rate parameters.

Arabidopsis Research Roundup: September 6th

This largest ever Arabidopsis Research Roundup (ARR) includes 6 papers from Norwich Research Park (NRP), including three featuring Cyril Zipfel (TSL) as a co-author on papers that investigate different aspects of plant immune signaling. Elsewhere on the NRP site Veronica Grieneisen (JIC) is a co-author on a study that defines the root auxin maximum whilst Dale Sanders and Saskia Hogenhout lead a paper that defines a method for the analysis of calcium signaling. Finally Robert Sablowski’s group at the JIC investigates the role of the DELLA proteins during meristem development.

Elsewhere investigators from Kew Gardens and Bangor University have used nanopore sequencing for the facile characterisation of field populations of Arabidopsis. Similarly Seth Davies (University of York) is part of a collaboration that looks how alterations in the circadian clock might affect plant fitness.

Verena Kriechbaumer (Oxford Brookes) leads a phylogenetic study into the conservation of auxin biosynthesis genes whilst Hilary Rodgers (Cardiff University) is a co-author on a Chinese-led study that looks into role of cadmium on the Arabidopsis cell cycle.

This ARR is full of examples of UK researchers involved in global collaborations. This includes Cambridge researchers involved in a proteomic analysis of microsomes, Justin Goodrich from the University of Edinburgh as part of a US-led study that defines the regulation of the PRC2 complex and Katherine Denby (University of York) as a member of a consortium that has performed a network analysis of jasmonic acid signaling.

Finally are two studies in which the research takes place within a single institution. Malcolm Hawksford (Rothamsted Research) looks at the effect of wheat transcription factors in the response to the heavy metal zinc whilst Emily Larson and Mike Blatt (University of Glasgow) investigate the role of clathrin on plant vesicular transport.


D’Ambrosio JM, Couto D, Fabro G, Scuffi D, Lamattina L, Munnik T, Andersson MX, Alvarez ME, Zipfel C, Laxalt AM (2017) PLC2 Regulates MAMP-Triggered Immunity by Modulating ROS Production in Arabidopsis. Plant Physiol 10.1104/pp.17.00173

This Argentinian-led study includes Cyril Zipfel (TSL) as a co-author on this work that uses miRNA-mediated gene silencing to assess the role of the phosphoinositide-specific phospholipase C (PI-PLC) in plant immune signaling.


Imkampe J, Halter T, Huang S, Schulze S, Mazzotta S, Schmidt N, Manstretta R, Postel S, Wierzba M, Yang Y, vanDongen WM, Stahl M, Zipfel C, Goshe MB, Clouse S, de Vries SC, Tax F, Wang X, Kemmerling B (2017) The Arabidopsis Leucine-rich Repeat Receptor Kinase BIR3 Negatively Regulates BAK1 Receptor Complex Formation and Stabilizes BAK1. Plant Cell. 10.1105/tpc.17.00376

Cyril Zipfel (TSL) is a co-author on this global collaboration that further defines the role of the BAK1 receptor in hormone and immune signaling through its interaction with two LRR-RK proteins (BIR2 and BIR3).


Singh V, Perraki A, Kim SY, Shrivastava S, Lee JH, Zhao Y, Schwessinger B, Oh MH, Marshall-Colon A, Zipfel C, Huber SC (2017) Tyrosine-610 in the Receptor Kinase BAK1 Does Not Play a Major Role in Brassinosteroid Signaling or Innate Immunity. Front Plant Sci. 10.3389/fpls.2017.01273

Cyril Zipfel (TSL) is a co-author on this US-led manuscript that again looks into the role of the BRI1-ASSOCIATED KINASE1 (BAK1) on plant immune signaling. Importantly they show that the phosphorylation of tyrosine-610 is actually not necessary for this proteins role in brassinosteroid or immune signaling


Di Mambro R, De Ruvo M,,, Pacifici E, Salvi E, Sozzani R, Benfey PN,, Busch W, Novak O, Ljung K, Di Paola L, Marée AFM, Costantino P, Grieneisen VA, Sabatini S (2017) Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root. Proc Natl Acad Sci U S A 10.1073/pnas.1705833114

Veronica Grieneisen (JIC) is a co-corresponding author on this work with Sabrina Sabatini from the University of Rome. They define the auxin minimum, a newly characterised determinat of root patterning that delineates the separation of root division and the differentiation zones. This is defined by the interaction between cytokinin and auxin signaling cascades.

Veronica discusses this paper on the GARNet YouTube channel: https://www.youtube.com/watch?v=gYdL6eddOcA


Vincent TR, Canham J, Toyota M, Avramova M, Mugford ST, Gilroy S, Miller AJ, Hogenhout S, Sanders D (2017) Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor. J Vis Exp. 10.3791/56142

Dale Sanders and GARNet committee member Saskia Hogenhout (JIC) lead this study that describes an imaging technique that allows for the real time assessment of calcium dynamics using a fluorescently tagged sensor.


Serrano-Mislata A, Bencivenga S, Bush M, Schiessl K, Boden S, Sablowski R (2017) DELLA genes restrict inflorescence meristem function independently of plant height. Nature Plants. 10.1038/s41477-017-0003-y

Robert Sablowski (JIC) leads this paper that investigates the role of DELLA proteins in the control of cell cycle regulators and how this impacts meristem size in both barley and Arabidopsis. Read more about it on the John Innes Centre website.


Parker J, Helmstetter AJ, Devey D, Wilkinson T, Papadopulos AST (2017) Field-based species identification of closely-related plants using real-time nanopore sequencing. Sci Rep. 10.1038/s41598-017-08461-5 Open Access

This investigation led by researchers at Kew Gardens and at the Bangor University use Real Time Nanopore Sequencing (RTnS) that allows for rapid species identification in the field and that combining RTnS and laboratory-based high-throughput sequencing leads to a significant improvement in genome assembly.


Rubin MJ, Brock MT, Davis AM, German ZM, Knapp M, Welch SM, Harmer SL, Maloof JN7, Davis SJ, Weinig C (2017) Circadian rhythms vary over the growing season and correlate with fitness components. Mol Ecol. 10.1111/mec.14287 Open Access

Seth Davies (University of York) is a co-author on this US-led work that conducts a study of field-growth Arabidopsis to evaluate the contribution of the circadian clock toward survival and fecundity. They show that variation in clock function correlates with growth performance in a natural environment.


Poulet A, Kriechbaumer V (2017) Bioinformatics Analysis of Phylogeny and Transcription of TAA/YUC Auxin Biosynthetic Genes. Int J Mol Sci. 10.3390/ijms18081791 Open Access

The paper from Oxford Brookes University provides a phylogenetic analysis of TAA/TAR (tryptophan aminotransferase related) and YUCCA proteins that are involved in auxin biosynthesis. In addition they provide tissue and cell-specific information about the function of these proteins and that their function is conserved in lower plant species.


Cui W, Wang H, Song J, Cao X, Rogers HJ, Francis D, Jia C, Sun L, Hou M, Yang Y, Tai P, Liu W (2017) Cell cycle arrest mediated by Cd-induced DNA damage in Arabidopsis root tips. Ecotoxicol Environ Saf. 10.1016/j.ecoenv.2017.07.074 Open Access

Hilary Rodgers (Cardiff University) is a co-author on this Chinese-led study that looks into the effect of cadmium treatment on the regulation of the cell cycle and DNA damage repair. They show that different cadmium concentrations effect different phases of the cell cycle.


Alqurashi M, Thomas L, Gehring C, Marondedze C (2017) A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses. Proteomes. 10.3390/proteomes5030022 Open Access

This international collaboration includes members of the Cambridge Centre for Proteomics and conducts a quantitative analysis of the Arabidopsis microsomal proteome following treatment with hydrogen peroxide or ABA. Perhaps unsurprisingly a high number of proteins characterized as ‘responsing to stress’ were found upregulated following treatment with H2O2 or ABA.


Xiao J, Jin R, Yu X, Shen M, Wagner JD, Pai A, Song C, Zhuang M, Klasfeld S, He C, Santos AM, Helliwell C, Pruneda-Paz JL, Kay SA, Lin X, Cui S, Garcia MF, Clarenz O, Goodrich J, Zhang X, Austin RS,, Bonasio R, Wagner D (2017) Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nature Genet 10.1038/ng.3937

Justin Goodrich (University of Edinburgh) is a co-author on this US-led study that looks into the role of Polycomb response element (PREs) in directing the placement of the Polycomb repressive complex 2 (PRC2) via their interaction with a newly identified transcription factors. Justin has recently discussed a paper on a similar topic on the GARNet YouTube channel.


Hickman R, van Verk MC, Van Dijken AJH, Pereira Mendes M, Vroegop-Vos IA, Caarls L, Steenbergen M, Van Der Nagel I, Wesselink GJ, Jironkin A, Talbot A, Rhodes J, de Vries M, Schuurink RC, Denby K, Pieterse CMJ, Van Wees SCM (2017) Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network. The Plant Cell 10.1105/tpc.16.00958 Open Access

GARNet committee member Katherine Denby (University of York) is a member of this large consortium of researchers who have performed a network analysis on the dynamics of jasmonic acid signaling


Evens NP, Buchner P, Williams LE, Hawkesford MJ (2017) The role of ZIP transporters and group F bZIP transcription factors in the Zn-deficiency response of wheat (Triticum aestivum) Plant J. 10.1111/tpj.13655 Open Access

Malcolm Hawkesford (Rothamsted Research) leads this study that investigate a set of wheat bZIP transcription factors and ZIP transporters that are involved in the uptake and transport of zinc. As part of this work they use Arabidopsis to test the conserved function of these wheat proteins.


Larson ER, Van Zelm E, Roux C, Marion-Poll A, Blatt MR (2017) Clathrin Heavy Chain subunits coordinate endo- and exocytic traffic and affect stomatal movement. Plant Physiol. 10.1104/pp.17.00970 Open Access

Mike Blatt and Emily Larson (University of Glasgow) are the co-corresponding authors on this study that looks into the role of clathrin heavy chain on vesicular transport in Arabidopsis. They looked at clathrin mutants to show that the protein plays an unsurprisingly important role in both endo- and exocytosis.

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