GARNet Research Roundup: August 16th 2019

This holiday-time edition of the GARNet research roundup begins with two papers that include the late Ian Moore from the University of Oxford as a co-author. The first looks at the role of RAB-A5c in the control of cellular growth anisotropy whilst the second characterises the Transport Protein Particle II (TRAPPII) complex.

The third paper is a UK-wide collaboration that assesses the role of UVA signaling on stomatal development. Next is a paper from Cambridge and the JIC that has identified the TAF4b protein as a novel regulator of meiotic crossovers.

The fifth paper is from the University of York and characterizes a role for cis-12-oxo-phytodienoic acid (OPDA) during seed germination.

The next three papers feature scientists from the University of Leeds in research that investigates 1, a peroxisomal ABC transporter; 2, the role of LRR-RLKs in plasmodesmata development and 3, the cell wall characteristics of banana and mango fruit.

The ninth paper is from the University of Edinburgh and investigates the role of S-nitrosylation in the control of SUMO conjugation.

The next two papers include Steve Penfield at the JIC as a corresponding author; the first looks at the role of endosperm-expressed transcriptional factors during seed dormancy and the second, in collaboration with researchers at the University of Warwick, identifies novel QTLs involved in seed dormancy.

The penultimate study is from Lancaster and presents a surprising outcome resulting from the overexpression of the wheat CA1Pase gene. The final paper includes Alison Tidy and Zoe Wilson from University of Nottingham as co-authors on a study that looks at male fertility in Arabidopsis.


Kirchhelle C, Garcia-Gonzalez D, Irani NG, Jérusalem A, Moore I (2019) Two mechanisms regulate directional cell growth in Arabidopsis lateral roots. Elife. pii: e47988. doi: 10.7554/eLife.47988

Open Access

Charlotte Kirchhelle leads this work that was conducted in the lab of the late Ian Moore at the University of Oxford. She investigates the role of the plant-specific small GTPase RAB-A5c during growth anisotropy in lateral roots, which involves coordinated orientations of cellulose microfibrils (CMFs) and by cortical microtubules (CMTs). They identify RAB-A5c dependent and independent mechanisms to control cellular growth anisotropy in this growing tissue.

From https://elifesciences.org/articles/47988

Kalde M, Elliott L, Ravikumar R, Rybak K, Altmann M, Klaeger S, Wiese C, Abele M, Al B, Kalbfuß N, Qi X, Steiner A, Meng C, Zheng H, Kuster B, Falter-Braun P, Ludwig C, Moore I, Assaad FF (2019) Interactions between Transport Protein Particle (TRAPP) complexes and Rab GTPases in Arabidopsis. Plant J. doi: 10.1111/tpj.14442

This German-led study includes Monika Kalde from the University of Oxford as first author as well Ian Moore as co-author. They characterize the components and function of the Transport Protein Particle II (TRAPPII) complex. TRAPPII plays multiple roles in intra-cellular transport and this study identified 13 subunits, including several that were previously uncharacterised.


Isner JC, Olteanu VA, Hetherington AJ, Coupel-Ledru A, Sun P, Pridgeon AJ, Jones GS, Oates M, Williams TA, Maathuis FJM, Kift R, Webb AR, Gough J, Franklin KA, Hetherington AM (2019). Short- and Long-Term Effects of UVA on Arabidopsis Are Mediated by a Novel cGMP Phosphodiesterase. Curr Biol.29(15):2580-2585.e4. doi: 10.1016/j.cub.2019.06.071

Open Access

Jean-Charles Isner is the first author on this collaboration between labs in Bristol, York, Oxford and Cambridge. They show that UVA radiation (which represents 95% of the UV radiation reaching earth) inhibits stomatal opening through a process that involves a reduction in the cytosolic level of cGMP. The AtCN-PDE1 gene (a cGMP-activated phosphodiesterase) is needed to decrease cGMP levels in Arabidopsis. This response is present across the tree of life except in metazoans. They show AtCN-PDE1 is needed for the UVA response and that prolonged UVA exposure causes increased growth yet reduced water use efficiency.


Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR (2019) Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis. Curr Biol. pii: S0960-9822(19)30844-9. doi: 10.1016/j.cub.2019.06.084

Open Access

This work from Ian Henderson’s lab in Cambridge and Xiaoqi Feng’s lab at the JIC is led by Emma Lawrence and isolates a novel modifier of meiotic crossover frequency, TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. They show TAF4b expression is enriched in meiocytes, compared to the more general expression of its paralog TAF4. Ultimately they reveal TAF4b drives a novel mode of meiotic recombination control through its activity as a general transcription factor.


Barros-Galvão T, Dave A, Cole A, Harvey D, Langer S, Larson TR, Vaistij FE, Graham IA (2019) cis-12-oxo-phytodienoic acid represses Arabidopsis thaliana seed germination in shade light conditions. J Exp Bot. pii: erz337. doi: 10.1093/jxb/erz337

Open Access

Thiago Barros-Galvão is first author on this study from Ian Graham’s lab at the University of York. They investigate how the jasmonic acid pre-cursor cis-12-oxo-phytodienoic acid (OPDA) contributes to control of seed germination, particularly under shade conditions. OPDA acts through the activity of the transcription factor MOTHER-OF-FT-AND-TFL1 (MFT).

From https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erz337/5536641

Carrier DJ, van Roermund CWT, Schaedler TA, Rong HL, IJlst L, Wanders RJA, Baldwin SA, Waterham HR, Theodoulou FL, Baker A (2019) Mutagenesis separates ATPase and thioesterase activities of the peroxisomal ABC transporter, Comatose. Sci Rep. 9(1):10502. doi: 10.1038/s41598-019-46685-9

Open Access

Alison Baker at the University of Leeds is the corresponding author of this UK, Dutch collaboration that includes David Carrier as first author. They characterise the peroxisomal ABC transporter, Comatose (CTS) through mutagenesis of key residues responsible for the proteins intrinsic acyl-CoA thioesterase (ACOT) activity. Ultimately they show that ACOT activity depends of endogenous ATPase activity but that these activities could be functional separated by mutagenesis of key residues.


Grison M, Kirk P, Brault M, Wu XN, Schulze WX, Benitez-Alfonso Y, Immel F, Bayer EMF (2019). Plasma membrane-associated receptor like kinases relocalize to plasmodesmata in response to osmotic stress. Plant Physiol. pii: pp.00473.2019. doi: 10.1104/pp.19.00473

Open Access

GARNet advisory committee member Yoselin Benitez-Alfonso and members of her research group are co-authors on the next two studies. This work is led by Magali Grison in Emmanuelle Bayer’s lab in Bordeaux. They show that the PM-localised Leucine-Rich-Repeat Receptor-Like-Kinases (LRR-RLKs), QSK1 and IMK2 relocate and cluster to the plasmodesmata under osmotic stress conditions. Through a variety of assays that focuses on QSK1 the authors show that reorganisation of RLKs can be important for the regulation of callose deposition at plasmodesmata and under osmotic stress this can have a functional effect on lateral root development.


Rongkaumpan G, Amsbury S, Andablo-Reyes E, Linford H, Connell S, Knox JP, Sarkar A, Benitez-Alfonso Y, Orfila C (2019) Cell Wall Polymer Composition and Spatial Distribution in Ripe Banana and Mango Fruit: Implications for Cell Adhesion and Texture Perception. Front Plant Sci. 10:858. doi: 10.3389/fpls.2019.00858

Open Access

Ganittha Rongkaumpan is first author on this interdisciplinary collaborative research from multiple departments at the University of Leeds. They characterise the composition of the cell wall in two fruits, banana and mango, which soften during ripening. The authors compared structural information, obtained using Atomic Force Microscopy and biochemical analysis, with data from rheology and tribology assays to understand why these fruits feel different in the mouth during ingestion.


Skelly MJ, Malik SI, Le Bihan T, Bo Y, Jiang J, Spoel SH, Loake GJ (2019) A role for S-nitrosylation of the SUMO-conjugating enzyme SCE1 in plant immunity Proc Natl Acad Sci U S A. pii: 201900052. doi: 10.1073/pnas.1900052116

Michael Skelly from the University of Edinburgh is the lead author of this study from the labs of Gary Loake and GARNet chairman Steven Spoel. They investigate the mechanism through which nitric oxide signaling after pathogen recognition stimulates inhibitory S-nitrosylation of the Arabidopsis SUMO E2 enzyme, SCE1. S-nitrosylation occurs on the evolutionary conserved Cys139 of SCE1 and they investigate the wider significant of this residue in the control of immune responses across eukaryotes.


MacGregor DR, Zhang N, Iwasaki M, Chen M, Dave A, Lopez-Molina L, Penfield S (2019) ICE1 and ZOU determine the depth of primary seed dormancy in Arabidopsis independently of their role in endosperm development. Plant J. 98(2):277-290. doi: 10.1111/tpj.14211

Open Access

Dana MacGregor (now at Rothamsted Research) leads this work from the lab of Steve Penfield at the JIC that investigates the extent of control on depth of primary dormancy that is mediated by the endosperm-expressed transcription factors ZHOUPI (ZOU) and INDUCER OF CBF EXPRESSION1 (ICE1). These effects are additive and independent of their role in endosperm development since the dormancy defect in ice1 and zou mutants can be ameliorated without altering seed morphology. They show that ICE1 acts primarily through control of ABA INSENSITIVE 3 (ABI3).


Footitt S, Walley PG, Lynn JR, Hambidge AJ, Penfield S, Finch-Savage WE (2019) Trait analysis reveals DOG1 determines initial depth of seed dormancy, but not changes during dormancy cycling that result in seedling emergence timing. New Phytol. doi: 10.1111/nph.16081

This research is a collaboration between the John Innes Centre and the Universities Liverpool and Warwick, from which Steven Footitt is first author. They used two Arabidopsis ecotypes that have differences in the timing of seedling emergence to identify new QTLs involved in depth of seed dormancy and Seedling Emergence Timing (SET). They revealed that DOG1 is important for determining depth of dormancy. In addition they identified three new SET QTLs, which are each physically close to DOG1, that play a role in the control of SET in the field.


Lobo AKM, Orr D, Gutierrez MO, Andralojc J, Sparks C, Parry MAJ, Carmo-Silva E (2019) Overexpression of ca1pase decreases Rubisco abundance and grain yield in wheat. Plant Physiol. pii: pp.00693.2019. doi: 10.1104/pp.19.00693

Open Access

This research from Lancaster Environmental Centre and their Brazilian collaborators is led by Ana Karla Lobo and demonstrates that overexpression of 2-carboxy-D-arabinitol-1-phosphate phosphatase (CA1Pase) in wheat causes a reduction in above ground biomass and compromises wheat grain yields. As CA1Pase is involved in removing inhibitors of Rubisco activity this result is contrary to the anticipated outcome. This suggests that Rubisco inhibitors might actually protect enzyme activity, thus maintaining the number of active sites that the enzyme is able to support.


Zhao SQ, Li WC, Zhang Y, Tidy AC, Wilson ZA (2019) Knockdown of Arabidopsis ROOT UVB SENSITIVE4 Disrupts Anther Dehiscence by Suppressing Secondary Thickening in the Endothecium. Plant Cell Physiol. doi: 10.1093/pcp/pcz127

Shu-Qing Zhao is the lead author on this China-UK collaboration that includes Alison Tidy and Zoe Wilson from the University of Nottingham. They show that using an artificial microRNA to reduce levels of the RUS4 gene in Arabidopsis causes a decline in male fertility. They perform a detailed analysis of the RUS4 expression module and how it impacts fertility.

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: August 10th 2018

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Published on: August 10, 2018

There are three papers in this week’s GARNet research roundup. The first paper is led by Jill Harrison’s lab in Bristol and she also provides an audio description of this work that has characterised a role for CLAVATA genes in the transition from 2D to 3D plant growth. The second paper from Ian Graham’s lab in York introduces the role of the MOTHER-OF-FT-AND-TFL1 gene during seed germination whilst the final paper includes co-authors from SLCU and Nottingham and has identified the RALF34 protein as a novel ligand that influences cell wall growth.


Whitewoods CD, Cammarata J, Nemec Venza Z, Sang S, Crook AD, Aoyama T, Wang XY, Waller M, Kamisugi Y, Cuming AC, Szövényi P, Nimchuk ZL, Roeder AHK, Scanlon MJ, Harrison CJ (2018) CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants. Curr Biol. doi: 10.1016/j.cub.2018.05.068

https://linkinghub.elsevier.com/retrieve/pii/S0960982218307048

Open Access

Chris Whitewoods and Joe Cammarata are co-first authors in this UK-US-Japan collaboration that is led by GARNet committee member Jill Harrison from the University of Bristol. They have investigated the expression and function of CLAVATA genes during moss development with particular focus on the transition from 2D to 3D growth, showing that these genes are essential for gametophyte development. By showing the presence or absence of CLAVATA genes in different lower plant species they demonstrate that they are important for the transition between different modes of growth.

Jill talks about this work on the GARNet YouTube channel and podcast.


Vaistij FE, Barros-Galvão T, Cole AF, Gilday AD, He Z, Li Y, Harvey D, Larson TR, Graham IA (2018) MOTHER-OF-FT-AND-TFL1 represses seed germination under far-red light by modulating phytohormone responses in Arabidopsis thaliana. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1806460115

www.pnas.org/content/early/2018/07/25/1806460115

Open Access

Fabian Vaistij is the first author on this paper from the lab of Ian Graham at the University of York that investigates the role of the MOTHER-OF-FT-AND-TFL1 (MFT) in the control of seed germination in Arabidopsis. They show that MFT is upregulated by far red light via the previously characterised PIF1/SOM/ABI5/DELLA pathway whilst repressed by red light through the action of the SPATULA (SPT) transcription factor. The activity of MFT alters levels of ABA and GA that ultimately delay germination in conditions with higher levels of FR light.


Gonneau M, Desprez T, Martin M, Doblas VG, Bacete L, Miart F, Sormani R, Hématy K, Renou J, Landrein B, Murphy E, Van De Cotte B, Vernhettes S, De Smet I, Höfte H (2018) Receptor Kinase THESEUS1 Is a Rapid Alkalinization Factor 34 Receptor in Arabidopsis. Curr Biol. doi: 10.1016/j.cub.2018.05.075
This French-led study that has Martine Gonneau and Thierry Desprez as co-lead authors includes Benoit Landrien (SLCU, Cambridge) and Evan Murphy (University of Nottingham) as co-authors. This research adds further detail to a signaling network that coordinates cell wall growth following different stimuli. They show that the rapid peptide alkalinization factor 34 (RALF34) is the ligand for the previously characterized THESEUS1 receptor kinase and that the activity of this signaling module is dependent on FERONIA, which is another RALF receptor.

https://www.cell.com/current-biology/abstract/S0960-9822(18)30711-5#%20

GARNet Research Roundup: June 4th

This weeks GARNet Research Roundup begins with a paper from researchers at the University of Dundee, James Hutton Institute, Durham University and the University of Glasgow that characterises a functional role for alternative splicing during the cold response. Second is a paper from Newcastle University that investigates the role of the OXI1 kinase during aphid predation. Third is a paper that includes University of Bristol co-authors that looks at strigolactone signaling in moss whilst the fourth paper from researchers at Leeds and QMUL studies the role of ascorbate during photosynthesis. The final paper from Warwick and York uses gene expression data from pathogen-infected plants to generate a model for predicting a strategy for synthetic engineering of the defence response.


Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo H, Zhang R, Brown JWS (2018) Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome. Plant Cell doi: 10.1105/tpc.18.00177.

www.plantcell.org/content/early/2018/05/15/tpc.18.00177.long

Open Access

Cristiane Calixto and Wenbin Guo work with John Brown at University of Dundee and the James Hutton Institute and in this large-scale biology paper they characterise the role of alternative splicing (AS) during a stress response. RNAseq was performed on plants exposed to cold stress and they showed that hundreds of genes undergo AS just a few hours after temperature decrease and that this response is sensitive to small changes. The authors propose that AS is a mechanism to fine-tune changes in thermo-plasticity of gene expression and in addition they investigate the activity of the novel splicing factor U2B”-LIKE.

Christiane will discuss this research at the upcoming GARNet2018 meeting held at the University of York in September 2018.


Shoala T, Edwards MG, Knight MR, Gatehouse AMR. OXI1 kinase plays a key role in resistance of Arabidopsis towards aphids (Myzus persicae) (2018) Transgenic Res. doi: 10.1007/s11248-018-0078-x.

Open Access

This work is led by Tahsin Shoala in the lab of Angharad Gatehouse at Newcastle University and demonstrates a novel role for MAPK cascades in resistance to aphid predation. They investigate mutants in OXI1 kinase, a gene that activates MAPK signaling and demonstrate a reduction in the aphid population build-up. Furthermore they show that the effect of OXI works through a mechanism that involves callose deposition, demonstrated as oxi1 mutants lack the upregulation of a set of β-1,3-glucanase genes following predation.


Lopez-Obando M, de Villiers R, Hoffmann B, Ma L, de Saint Germain A, Kossmann J, Coudert Y, Harrison CJ, Rameau C, Hills P, Bonhomme S (2018) Physcomitrella patens MAX2 characterization suggests an ancient role for this F-box protein in photomorphogenesis rather than strigolactone signalling. New Phytol. doi: 10.1111/nph.15214

GARNet committee member Jill Harrison is a co-author on this paper that is led by Mauricio Lopez‐Obando working at Université Paris-Saclay. In Physcomitrella patens development they investigate the role of the moss ortholog of the Arabidopsis strigolactone signaling mutant MAX2. Previous work had shown that moss does response to SL signaing but they find that although Ppmax2 mutants showed defects in early development and photomorphogenesis they do not show changes in the SL response. Fascinatingly this indicates that the molecular components that control SL signaling have diverged in vascular plants and seemingly co-opted a role for MAX2 that was previously not required in mosses.


https://academic.oup.com/jxb/article/69/11/2823/4991886

Plumb W, Townsend AJ, Rasool B, Alomrani S, Razak N, Karpinska B, Ruban AV, Foyer CH. Ascorbate-mediated regulation of growth, photoprotection and photoinhibition in Arabidopsis thaliana (2018) J Exp Bot. doi: 10.1093/jxb/ery170

William Plumb (Leeds) and Alexandra Townsend (QMUL) are the lead authors on this study that investigates the importance of ascorbate during photosynthesis. In this work they analysed the growth of ascorbate synthesis mutants that are smaller and have less biomass than wildtype plants. However these plants have normal levels of non-photoinhibiton, allowing the authors to conclude that ascorbate is needed for growth but not photoprotection.


Foo M, Gherman I, Zhang P, Bates DG, Denby K (2018) A Framework for Engineering Stress Resilient Plants using Genetic Feedback Control and Regulatory Network Rewiring. ACS Synth Biol. doi: 10.1021/acssynbio.8b00037
Mathias Foo and Iulia Gherman (University of Warwick) are lead authors on work that analyses gene expression data taken from Botrytis cinerea-infected Arabidopsis. They have identified a network of genes involved in the defence response. They validate their model against previously obtained time series data and then perturb the model in two differences ways, focused on the transcription factor CHE. This analysis demonstrates the potential of combining feedback control theory with synthetic engineering in order to generate plants that are resistant to biotic stress.

https://pubs.acs.org/doi/10.1021/acssynbio.8b00037

GARNet Research Roundup: April 11th 2018

This weeks GARNet research roundup begins with a microscopy-based study led by Lorenzo Frigerio from the University of Warwick that investigates the origin of Protein Storage Vacuoles. The second paper from John Doonan at Aberystwyth University looks at how differential splicing of cyclin-dependent Kinase G1 effects the thermosensory response. Reiner van de Hoorn from Oxford leads the next paper that characterises the use of activity-based protein profiling (ABPP) to identify novel α-glycosidases in model and non-model plants. Simon McQueen-Mason from York is corresponding author of the next paper that identified a new QTL from Brachypodium that is involved in cell wall formation. The fifth paper is led by Anthony Dodd from Bristol and characterises the role of the SnRK1 complex in hypocotyl elongation whilst the penultimate manuscript from Julia Davies’s lab in Cambridge performs patch clamp analysis of dorn1 mutant plants. The final paper from Brendan Davies at the University of Leeds characterises the SMG kinase, a gene that is lacking from the Arabidopsis genome, in Physcomitrella patens.


http://www.plantphysiol.org/content/early/2018/03/19/pp.18.00010.long

Feeney M, Kittelmann M, Menassa R, Hawes C, Frigerio L. Protein storage vacuoles originate from remodelled pre-existing vacuoles in Arabidopsis thaliana (2018) Plant Physiol. 2018 Mar 19. pii: pp.00010.2018. doi: 10.1104/pp.18.00010 Open Access

This collaboration between the Universities of Warwick and Oxford Brookes is led by Lorenzo Frigerio and Chris Hawes. They have investigated the origin of seed Protein Storage Vacuoles (PSV) using a two-pronged approach using confocal and immunoelectron microscopy. They looked at embryo development as well as in leaf cells that have been reprogrammed for embryonic cell fate by overexpression of the LEAFY COTYLEDON2 TF. These studies indicate that PSVs are formed following the reprogramming of pre-existing embryonic vacuole (EV) rather than from de novo assembly.


https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.13914

Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan JH. The Cyclin Dependent Kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A (2018) Plant J. doi: 10.1111/tpj.13914 Open Access

John Doonan (Aberystwyth University) is the corresponding author on this UK-Austrian collaboration that presents the role of the cyclin-dependent Kinase G1 (CDKG1) in thermosensing in Arabidopsis. Ambient temperature change causes altered gene expression of the spliceosome component, ATU2AF65A. Interestingly the CDKG1 gene is differentially spliced and to produces two protein isoforms that are both needed to complement the expression of ATU2AF65A across a temperature range. This alternative splicing is dependent on CDKG2 and CYCLIN L1 and is a novel control mechanism in the temperature control response.


Husaini AM, Morimoto K, Chandrasekar B, Kelly S, Kaschani F, Palmero D, Jiang J, Kaiser M, Ahrazem O, Overkleeft HS, van der Hoorn RAL (2018) Multiplex fluorescent, activity-based protein profiling identifies active α-glycosidases and other hydrolases in plants. Plant Physiol. pii: pp.00250.2018. doi: 10.1104/pp.18.00250 Open Access

Renier Van de Hoorn (University of Oxford) leads this pan-european study that uses novel cyclophellitol aziridine probes that label α-glycosidase enzymes. They identified two novel α-glycosidases in Arabidopsis as well as using the technique in non-model saffron crocus. Finally they showed that this multiplex fluorescent labelling in combination with probes for serine hydrolases and cysteine proteases can be used to identify changes in hydrolase activity in response to pathogen infection.


Whitehead C, Ostos Garrido FJ, Reymond M, Simister R, Distelfeld A, Atienza SG, Piston F, Gomez LD, McQueen-Mason SJ (2018) A glycosyl transferase family 43 protein involved in xylan biosynthesis is associated with straw digestibility in Brachypodium distachyon. New Phytol. doi: 10.1111/nph.15089 Open Access

Simon McQueen-Mason (University of York) leads this study that use QTL mapping to identify a gene in Bracypodium that is involved in cell wall architecture, which might then be a target to develop plants with improved cellulose digestibility. This glycosyl transferase family (GT) 43 protein is an orthologue of Arabidopsis IRX14, which is involved in xylan biosynthesis. When RNAi was used to reduce expression of this gene the resulting plants showed increased digestibility, indicating that this BdGT43A will be a good target for future breeding plans.


Wang L, Wilkins KA, Davies JM (2018) Arabidopsis DORN1 extracellular ATP receptor; activation of plasma membrane K(+) -and Ca(2+) -permeable conductances New Phytol. 2018 Mar 25. doi: 10.1111/nph.15111. Open Access

This letter to New Phytologist from the lab of Julia Davis (University of Cambridge) outlines some experiments to determine whether the DORN1 plasma membrane receptor is responsible for transmitting a signal from extracellular ATP (eATP). They performed patch clamp analysis on isolated protoplasts and showed that DORN1 is involved in the activation of Ca+ and K+ pumps by eATP as, in contrast to wildtype, dorn1 mutant protoplast showed no voltage changes after incubation with eATP.


Simon NML, Sawkins E, Dodd AN. Involvement of the SnRK1 subunit KIN10 in sucrose-induced hypocotyl elongation (2018) Plant Signal Behav. 27:1-9. doi: 10.1080/15592324.2018.1457913.

Anthony Dodd (University of Bristol) is the corresponding author of this follow-on study from one that previously featured on the GARNet YouTube channel. This study measures sucrose-induced hypocotyl elongation in two T-DNA mutants of the SnRK1 subunit KIN10 gene. These mutants had altered responses to sucrose leading to the hypothesis that the SnRK1 complex suppresses hypocotyl elongation in the presence of external sugar.


Lloyd JPB, Lang D, Zimmer AD, Causier B, Reski R, Davies B (2018) The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens. Nucleic Acids Res. doi: 10.1093/nar/gky225 Open Access

Brendan Davis (University of Leeds) is the corresponding author on research that investigates the role of the SMG1 kinase during nonsense-mediated mRNA decay (NMD) in the moss Physcomitrella patens. This kinase plays a critical role in animals but as it is not present in Arabidopsis, its function is not well studied in plants. However moss smg mutants show expression changes in genes involved in a variety of processes indicating that NMD is a common control mechanism in moss. In addition these plants have increased susceptibility to DNA damage, which suggests that the SMG1 kinase is a key player in quality control mechanisms in plants.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky225/4955258

Arabidopsis Research Roundup: March 9th

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Published on: March 9, 2018

This Arabidopsis Research Roundup has five papers that includes two from the John Innes Centre and two from the University of Edinburgh. Firstly Kristen Bomblies’s group at the JIC have investigated the relationship between temperature and meiotic recombination rates. Secondly Veronica Grieneisen and Stan Maree have developed a mathematical model to characterise cell morphologies taken from a 2D image. Andrew Miller from Edinburgh is a co-corresponding author on a study that shows how the Arabidopsis proteome changes in different photoperiods. In the fourth paper Peter Doerner is a co-author on work that looks at the phosphate starvation response. Finally researchers from Bristol and Nottingham contribute to an investigation into a novel genetic component that controls auxin-induced root hair development.


Lloyd A, Morgan C, Franklin C, Bomblies K (2018) Plasticity of Meiotic Recombination Rates in Response to Temperature in Arabidopsis. Genetics. doi: 10.1534/genetics.117.300588

Open Access

Kristen Bomblies (John Innes Centre) leads this study that investigates the influence of temperature on meiotic recombination rate. They show that in Arabidopsis the number of crossovers positively correlates with increasing temperature. However the mechanistic explanation for the increase at higher temperatures remains opaque as, in contrast to findings from other plants, synaptonemal complex length negatively correlates with temperature.


Sánchez-Corrales YE, Hartley M, van Rooij J, Marée AFM, Grieneisen VA (2018) Morphometrics of complex cell shapes: Lobe Contribution Elliptic Fourier Analysis (LOCO-EFA). Development. doi: 10.1242/dev.15677

http://dev.biologists.org/content/early/2018/02/08/dev.156778.long

Open Access

Veronica Grieneisen and Stan Maree (John Innes Centre) lead this study that has developed the Lobe Contribution Elliptical Fourier Analysis (LOCO-EFA) method. This generates meaningful descriptors from a 2D image of cells that can then be linked to morphological features. This tool allows for the efficient phenotyping of cell morphologies that they demonstrate by analysing images of Arabidopsis leaf pavement cells. They extend this analysis to larger populations where they used LOCO-EFA to predict how cell shapes change when they move into a more crowded space.


Seaton DD, Graf A, Baerenfaller K, Stitt M, Millar AJ, Gruissem W (2018) Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism. Mol Syst Biol. doi: 10.15252/msb.20177962 Open Access

http://onlinelibrary.wiley.com/doi/10.15252/msb.20177962/abstract

Andrew Miller (University of Edinburgh) is the corresponding author on this collaboration with German and Swiss colleagues that compares the Arabidopsis proteome across four photoperiods. They shows coordinated changes across the proteome, most notably at longer photoperiods in the abundance of proteins involved in photosynthesis and metabolism. They show higher translation rates during the day that correspond with the increased RNA abundance that is a characteristic of circadian rhythms. This ‘translational coincidence’ describes the alignment of higher translation rates with high transcript levels and they assigned a mathematical model in an attempt to explain this phenomenon.


Hanchi M, Thibaud MC, Légeret B, Kuwata K, Pochon N, Beisson F, Cao A, Cuyas L, David P, Doerner P, Ferjani A, Lai F, Li-Beisson Y, Mutterer J, Philibert M, Raghothama KG, Rivasseau C, Secco D, Whelan J, Nussaume L, Javot H (2018) The phosphate fast-responsive genes PECP1 and PPsPase1 affect phosphocholine and phosphoethanolamine content. Plant Physiol. doi: 10.1104/pp.17.01246 Open Access

Peter Doerner (University of Edinburgh) is a co-author on this global study that characterises the phosphate starvation-mediated induction of the HAD-type phosphatases PPsPase1 (AT1G73010) and PECP1 (AT1G17710). They show that expression of these genes closely follows phosphate status but that their activity does not alter phospate content. The role of these proteins is to control phosphocholine and phosphoethanolamine content, which is a output of changing phosphate conditions. The authors conclude that expression of these genes can be an excellent molecular marker for the phosphate starvation response.


www.cell.com/current-biology/fulltext/S0960-9822(18)30083-6

Schoenaers S, Balcerowicz D, Breen G, Hill K, Zdanio M, Mouille G, Holman TJ, Oh J, Wilson MH, Nikonorova N, Vu LD, De Smet I, Swarup R, De Vos WH, Pintelon I, Adriaensen D, Grierson C, Bennett MJ, Vissenberg K (2018) The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth. Current Biology doi: 10.1016/j.cub.2018.01.050

This Belgian-led study includes contributions from Claire Greirson’s and Malcolm Bennett’s labs in Bristol and Nottingham respectively. They investigate the role of the ERULUS (ERU) protein, an auxin-induced receptor-like kinase, during the development of root hairs. ERU localises to the apical root hair plasma membrane and regulates cell wall composition by altering pectin dynamic. The authors conclude that ERU is a key regulator of auxin-mediated control of root hair development.

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