GARNet Research Roundup: June 12th 2019

In another big edition of the GARNet Research Roundup we cover many different areas of research that utilise a varied group of experimental organisms!

The first paper from the Feng lab at the John Innes Centre performs an assessment of the factors influencing heterochromatin activity in sperm companion cells. Second is work from the JIC and Cardiff University that looks at the role of an auxin minima during fruit valve margin differentiation.

The next two papers have authors from Edinburgh. Firstly the McCormick lab has developed a stereo-based 3D imaging system for plants while Steven Spoel is a co-author on a study that looks at the pathogen responsive gene NPR1.

Coming from across the M8 is a paper from the Christie lab in Glasgow that looks into using phototropin genes as potential targets for crop improvement.

The next paper is from Oxford Brookes University where they visualise the movement of protein nanodomain clusters within the plasma membrane. Elsewhere in Oxford is a paper from the van der Hoorn group that characterises the effect of a novel triazine herbicide.

Two papers from the University of Durham also identify and characterise the role of novel herbicides, in this case on the activity of inositol phosphorylceramide synthases.

The final five papers feature research that each use different experimental organisms. Firstly a paper from the Earlham Institute uses delayed fluorescence to investigate the circadian clock in wheat and OSR. Second is a paper from Warwick that assesses the role of nodulation during nitrogen uptake in Medicago. The next paper features the Yant lab at University of Nottingham looks at growth of two species of Arabidopsis in challenging environments.

The penultimate paper includes authors from the University of Oxford and provides a detailed analysis of the factors controlling leaf shape in Cardamine and Arabidopsis thaliana. The final paper uses the imaging facility at the Hounsfield facility in Nottingham to image the roots of date palms.


He S, Vickers M, Zhang J, Feng X (2019) Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. Elife. doi: 10.7554/eLife.42530

Open Access

Lead author on his paper is Shengbo He from Xiaoqi Feng’s lab at the John Innes Centre. This work looks at activation of Transposable elements (TEs) in the sperm companion cell of Arabidopsis. This is catalyzed by the DEMETER-catalyzed DNA demethylation in regions depleted of histone H1, demonstrating a key role for H1 in determining heterochromatin activity.

https://elifesciences.org/articles/42530

Li XR, Vroomans RMA, Fox S, Grieneisen VA, Østergaard L, Marée AFM (2019) Systems Biology Approach Pinpoints Minimum Requirements for Auxin Distribution during Fruit Opening. Mol Plant. doi: 10.1016/j.molp.2019.05.003

Open Access

Xin-Ran Li and Renske Vroomans are co-lead authors on this work from the Ostergaard, Grieneisen and Maree labs from the John Innes Centre and (now) Cardiff University.They look at the role of an auxin minima in the control of valve margin differentiation in Arabidopsis fruit. They used a cycle of experimental-modeling to develop a model that predicts the maturation of the auxin minimum to ensure timely fruit opening and seed dispersal.


Bernotas G, Scorza LCT, Hansen MF, Hales IJ, Halliday KJ, Smith LN, Smith ML, McCormick AJ (2019) A photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth. Gigascience. doi: 10.1093/gigascience/giz056

Open Access

Gytis Bernotas from UWE and Livia Scorza from the McCormick lab at the University of Edinburgh lead this work that is the result of a 2+ year collaboration with the Melvyn Smith and others at the Computer Machine Vision (CMV) facility at UWE. The authors have developed hardware and software (including a deep neural network) to automate the 3D imaging and segmentation of rosettes and individual leaves using a photometric stereo approach.

https://academic.oup.com/gigascience/article/8/5/giz056/5498634

Chen J, Mohan R, Zhang Y, Li M, Chen H, Palmer IA, Chang M, Qi G, Spoel SH, Mengiste T, Wang D, Liu F, Fu ZQ (2019) NPR1 promotes its own and target gene expression in plant defense by recruiting CDK8. Plant Physiol. doi: 10.1104/pp.19.00124

GARNet chairman Steven Spoel is a co-author on this US-led study with Jian Chen as lead author. The paper investigates the interacting partners of NPR1 (NONEXPRESSER OF PR GENES 1), which is a master regulator of salicyclic signaling and therefore an important regulation of plant defense response.


Hart JE, Sullivan S, Hermanowicz P, Petersen J, Diaz-Ramos LA, Hoey DJ, Łabuz J, Christie JM (2019) Engineering the phototropin photocycle improves photoreceptor performance and plant biomass production. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1902915116

Open Access

Jaynee Hart is first author on this research from Christie lab at the University of Glasgow in which they target the phototropin blue light receptor as a candidate for crop improvement. They showed plants that engineered to have a slow-photocycling version of PHOT1 or PHOT2 had increased biomass under low light conditions, due to their increased sensitivity to low light.


McKenna JF, Rolfe DJ, Webb SED, Tolmie AF, Botchway SW, Martin-Fernandez ML, Hawes C, Runions J (2019) The cell wall regulates dynamics and size of plasma-membrane nanodomains in Arabidopsis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1819077116

Open Access

Joe McKenna from Oxford Brookes University leads this work that takes advantage of their superb imaging facilities to assess the dynamic regulation of specific protein clusters in the Arabidopsis plasma membrane. They show that the cytoskeleton (both actin and microtubule) and the cell wall play roles in the control of intra-PM moment of the pathogen receptor FLS2 and the auxin transporter PIN3.

https://www.pnas.org/content/early/2019/06/07/1819077116

Morimoto K, Cole KS, Kourelis J, Witt CH, Brown D, Krahn D, Stegmann M, Kaschani F, Kaiser M, Burton J, Mohammed S, Yamaguchi-Shinozaki K, Weerapana E, van der Hoorn RAL (2019) Triazine probes targeting ascorbate peroxidases in plants. Plant Physiol. doi: 10.1104/pp.19.00481

Open Access

Kyoko Morimoto is first author on this UK-German-Japanese collaboration led from the lab of GARNet committee member Renier van der Hoorn. They characterise the herbicidal effect of the small 1,3,5-triazine KSC-3 on ascorbate peroxidases (APXs) across a range of plant species.


Pinneh EC, Stoppel R, Knight H, Knight MR, Steel PG, Denny PW (2019) Expression levels of inositol phosphorylceramide synthase modulate plant responses to biotic and abiotic stress in Arabidopsis thaliana. PLoS One. doi: 10.1371/journal.pone.0217087

Open Access

Pinneh EC, Mina JG, Stark MJR, Lindell SD, Luemmen P, Knight MR, Steel PG, Denny PW (2019) The identification of small molecule inhibitors of the plant inositol phosphorylceramide synthase which demonstrate herbicidal activity. Sci Rep. doi: 10.1038/s41598-019-44544-1

Open Access

Elizabeth Pinneh leads these two papers from the Denny lab in Durham. In the first paper they use RNAseq data and analysis of overexpression transgenic lines to define the role of inositol phosphorylceramide synthase (IPCS) during abiotic and biotic stress responses.

Secondly they screened a panel of 11000 compounds for their activity against the AtIPCS2 in a yeast two-hybrid assay. Successful hits from the screen were confirmed with in vitro enzyme assays and in planta against Arabidopsis.


Rees H, Duncan S, Gould P, Wells R, Greenwood M, Brabbs T, Hall A (2019) A high-throughput delayed fluorescence method reveals underlying differences in the control of circadian rhythms in Triticum aestivum and Brassica napus. Plant Methods. doi: 10.1186/s13007-019-0436-6

Open Access

Hannah Rees from Anthony Hall’s lab at the Earlham Institute leads this methods paper that introduces the use of delayed fluorescence to investigate the circadian rhythms in wheat and oil seed rape.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0436-6

Lagunas B, Achom M, Bonyadi-Pour R, Pardal AJ, Richmond BL, Sergaki C, Vázquez S, Schäfer P, Ott S, Hammond J, Gifford ML (2019) Regulation of Resource Partitioning Coordinates Nitrogen and Rhizobia Responses and Autoregulation of Nodulation in Medicago truncatula. Mol Plant. doi: 10.1016/j.molp.2019.03.014

Open Access

Beatriz Lagunas is lead author on this paper from the University of Warwick that investigates the role of nodulation in actual nitrogen uptake by the roots of Medicago truncatula. They use integrated molecular and phenotypic analysis to determine that the respond to nitrogen flux are processed on a whole plant level through multiple developmental processes.

https://www.cell.com/molecular-plant/fulltext/S1674-2052(19)30127-3?

Preite V, Sailer C, Syllwasschy L, Bray S, Ahmadi H, Krämer U, Yant L (2019) Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils Philos Trans R Soc Lond B Biol Sci. doi: 10.1098/rstb.2018.0243

Open Access

Veronica Preite is first author on this UK-German collaboration led by Ute Kraemer and Levi Yant in Nottingham. They performed whole genome resequenced of 64 individuals of two Arabidopsis species that grow on calamine metalliferous sites (which have toxic levels of the zinc and cadmium). They revealed a modest amount of gene and network convergence in plants that have colonised these challenging environments.


Kierzkowski D, Runions A, Vuolo F, Strauss S, Lymbouridou R, Routier-Kierzkowska AL, Wilson-Sánchez D, Jenke H, Galinha C, Mosca G, Zhang Z, Canales C, Dello Ioio R, Huijser P, Smith RS, Tsiantis M (2019) A Growth-Based Framework for Leaf Shape Development and Diversity. doi: 10.1016/j.cell.2019.05.011

Open Access

Claudia Canales and Carla Galinha from Oxford are co-authors on this German-led study from Miltos Tsiantis’ lab that performs a detailed dissection of the growth parameters that control differences in leaf-shape in Cardamine and Arabidopsis. They show critical roles for the SHOOTMERISTEMLESS and REDUCED COMPLEXITY homeobox proteins to define differences in shape determination.


Xiao T, Raygoza AA, Pérez JC, Kirschner G, Deng Y, Atkinson B, Sturrock C, Lube V, Wang JY, Lubineau G, Al-Babili S, Ramírez LAC, Bennett MJ, Blilou I (2019) Emergent Protective Organogenesis in Date Palms: A Morpho-devo-dynamic Adaptive Strategy During Early Development. Plant Cell. doi: 10.1105/tpc.19.00008

Open Access

Members of the Hounsfield CT Imaging Facility 
at the University of Nottingham are co-authors on this paper that is led by Tingting Xiao from KAUST in Saudi Arabia. The paper takes a detailed look at root morphology in Date Palm.

GARNet Research Roundup: April 29th 2019

This edition of the GARNet research roundup features fundamental plant science research conducted in a range of experimental organisms. Firstly Liam Dolan’s lab in Oxford looks at the function of bHLHs proteins in cell differentiation across land plant evolution. Secondly Anthony Hall’s group at the Earlham Institute have identified a novel RecQ helicase involved in work exclusively conducted in wheat. Thirdly researchers from Nottingham work with Arabidopsis to characterise an EXPANSIN protein essential for lateral root development.

The fourth paper is the first of two that look at germination and uses a new model, Aethionema arabicum, to study the role of light in seed dormancy. This work includes research from Royal Holloway. The second ‘dormancy’ paper is from Peter Eastmond’s lab at Rothamsted and further characterises the DOG1 gene in Arabidopsis. The penultimate paper includes co-authors from Warwick and Leeds and introduces a novel chemical inhibitor of auxin transport. The final paper from researchers in Birmingham introduces the 3DCellAtlas Meristem, a powerful tool for cellular annotation of the shoot apical meristem.


Bonnot C, Hetherington AJ, Champion C, Breuninger H, Kelly S, Dolan L (2019) Neofunctionalisation of basic helix loop helix proteins occurred when embryophytes colonised the land. New Phytol. doi: 10.1111/nph.15829 https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15829

Clemence Bonnot is lead author on this study from Liam Dolan’s lab at the University of Oxford in which the authors assess the role of ROOT HAIR DEFECTIVE SIX-LIKE (RSL) genes during evolution of plant development. They look at the function of a member of this bHLH transcription factor family called CbbHLHVIII identified in the charophyceaen alga Chara braunii. This gene is expressed at specific morphologically important regions in the algae and cannot rescue the function of related RSL genes in Marchantia or Arabidopsis. This suggests that the function of RSL proteins in cell differentiation has evolved by neofunctionalisation through land plant lineages.


Gardiner LJ, Wingen LU, Bailey P, Joynson R, Brabbs T, Wright J, Higgins JD, Hall N, Griffiths S, Clavijo BJ, Hall A (2019) Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency. Genome Biol. 20(1):69. doi: 10.1186/s13059-019-1675-6 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1675-6

Open Access

Laura Gardiner and Anthony Hall lead this work that was conducted at the Earlham Institute and uses a bespoke set of bioinformatic tools that allow fundamental questions to be asked in hexaploid wheat. They looked at crossover and gene conversion frequencies in 13 recombinant inbred mapping populations and were able to identity an important QTL and confirm functionality for a novel RecQ helicase gene. This gene does not exist in Arabidopsis and therefore this discovery-motivated research needed to be conducted in wheat. They hope that this identification will provide future opportunities to tackle the challenge of linkage drag when attempting to develop new crops varieties.


Ramakrishna P, Ruiz Duarte P, Rance GA, Schubert M, Vordermaier V, Vu LD, Murphy E, Vilches Barro A, Swarup K, Moirangthem K, Jørgensen B, van de Cotte B, Goh T, Lin Z, Voβ U, Beeckman T, Bennett MJ, Gevaert K, Maizel A, De Smet I (2019) EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation. Proc Natl Acad Sci U S A. 2019 Apr 3. pii: 201820882. doi: 10.1073/pnas.1820882116 https://www.pnas.org/content/early/2019/04/02/1820882116.long

Open Access

This pan-European study is led by Priya Ramakrishna at the University of Nottingham and includes co-authors from the UK, Belgium, Germany and Denmark. The authors look at the lateral root development and characterise the function of the EXPANSIN A1 protein. This protein influences the physical changes in the cell wall that are needed to enable the asymmetry cell divisions that define the location of a new lateral root. Plants lacking EXPA1 function do not properly form lateral roots and are unable to correctly respond to an inductive auxin signal. This clearly demonstrates an important requirement for the activity of genes that transmit cell signals into the physical relationships that exist between cells.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0413-0

Mérai Z, Graeber K, Wilhelmsson P, Ullrich KK, Arshad W, Grosche C, Tarkowská D, Turečková V, Strnad M, Rensing SA, Leubner-Metzger G, Scheid OM (2019) Aethionema arabicum: a novel model plant to study the light control of seed germination. J Exp Bot. pii: erz146. doi: 10.1093/jxb/erz146

https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erz146/5428144

Open Access

This paper includes authors from the UK, Germany, Austria and the Czech Republic including Kai Graeber and Gerhard Leubner-Metzger at Royal Holloway. They introduce the Brassica Aethionema arabicum as a new model to investigate the mechanism of germination inhibition by light as they have identified accessions that are either light-sensitive or light-neutral. In contrast germination in Arabidopsis is stimulated by light. Transcriptome analysis of Aethionema arabicum accessions reveal expression changes in key hormone-regulated genes. Overall they show that largely the same module of molecular components are involved in control of of seed dormancy irrespective of the effect of light on germination. Therefore any phenotypic changes likely result from changes in the activity organisms-specific of these genes.

https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erz146/5428144

Bryant FM, Hughes D, Hassani-Pak K, Eastmond PJ (2019) Basic LEUCINE ZIPPER TRANSCRIPTION FACTOR 67 transactivates DELAY OF GERMINATION 1 to establish primary seed dormancy in Arabidopsis. Plant Cell. pii: tpc.00892.2018. doi: 10.1105/tpc.18.00892 http://www.plantcell.org/content/early/2019/04/08/tpc.18.00892.long

Open Access

http://www.plantcell.org/content/early/2019/04/08/tpc.18.00892.long

Fiona Bryant is lead author on this research from Rothamsted Research that investigates the factors that control expression of the DOG1 gene, which is a key regulator of seed dormancy. They show that LEUCINE ZIPPER TRANSCRIPTION FACTOR67 (bZIP67) regulates DOG1 expression and have uncovered a mechanism that describes the temperature-dependent regulation of DOG1 expression. Finally they identity a molecular change that explains known allelic difference in DOG1 function, which informs different levels of dormancy in different accessions.


Oochi A, Hajny J, Fukui K, Nakao Y, Gallei M, Quareshy M, Takahashi K, Kinoshita T, Harborough SR, Kepinski S, Kasahara H, Napier RM, Friml J, Hayashi KI (2019) Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiol. 2019 Apr 1. pii: pp.00201.2019. doi: 10.1104/pp.19.00201 http://www.plantphysiol.org/content/early/2019/04/01/pp.19.00201.long

Open Access

http://www.plantphysiol.org/content/early/2019/04/01/pp.19.00201.long

This Japanese-led study includes co-authors from the Universities of Warwick and Leeds and describes the identification of a novel positive chemical modulator of auxin cellular efflux. This aptly named PInStatic Acid (PISA) prevents PIN protein internalization yet does not impact the SCFTIR1/AFB signaling cascade. Therefore the authors hope that PISA will be a useful tool for unpicking the cellular mechanisms that control auxin transport.


Montenegro-Johnson T, Strauss S, Jackson MDB, Walker L, Smith RS, Bassel GW. (2019) 3D Cell Atlas Meristem: a tool for the global cellular annotation of shoot apical meristems. Plant Methods. 15:33. doi: 10.1186/s13007-019-0413-0

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0413-0

Open Access

Thomas Montenegro-Johnson, Soeren Strauss, Matthew Jackson and Liam Walker lead this methods paper that was prepared following research that took place at the University of Birmingham and the Max Planck Institute for Plant Breeding Research in Cologne. They describe the 3DCellAtlas Meristem, a tool allows the complete cellular annotation of cells within a shoot apical meristem (SAM), which they have successfully tested in both Arabidopsis and tomato. The authors state that ‘this provides a rapid and robust means to perform comprehensive cellular annotation of SAMs and digital single cell analyses, including cell geometry and gene expression’.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0413-0

GARNet Research Roundup: April 11th 2019

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

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

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

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


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

Open Access

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


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

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

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

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

Open Access

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


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

Open Access

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


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

Open Access

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


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

Open Access

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


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

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

GARNet Research Roundup: March 21st 2019

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

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

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

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


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

Open Access

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

doi: 10.1016/j.cub.2019.01.057

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

Open Access

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


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

Open Access

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


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

Open Access

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


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

Open Access

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


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

Open Access

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


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

Open Access

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

GARNet Research Roundup: 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 21st 2018

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

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

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

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

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


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

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

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

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

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


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

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


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

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

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

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


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

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


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

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

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


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


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

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

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


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

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


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

Open Access with link: rdcu.be/bdLjy

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


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

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

GARNet Research Roundup: December 7th 2018

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

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

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


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

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

Open Access

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


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

Open Access

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


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

Open Access

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


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

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


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

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

Open Access

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


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

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


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

Open Access

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


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

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

Open Access

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


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

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

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

GARNet Research Roundup: November 22nd 2018

This GARNet Research Roundup begins with two studies from the University of Sheffield. First is research from Jurriaan Ton’s lab that looks at the interaction between CO2 concentration, the soil microbiome and plant growth. The second paper from Matt Davey and Peter Quick looks at the effect of cold acclimation on freezing tolerance in Arabidpsis lyrata.

The third study includes authors from Dundee and Durham and also looks at an impact of altered CO2 concentrations, in this case on nitrogen assimilation.

The next paper looks at the role of a GA signaling module on endosperm expansion during seed germination and includes authors from Nottingham and Birmingham.

The fifth paper includes Richard Morris at the JIC as a co-author and looks at the relationship between calcium signaling and changes in cellular pH. The penultimate study features co-authors from Warwick and Exeter in work that looks at the role of 3′-O-β-D-ribofuranosyladenosine during plant immunity. Finally is a paper that includes Steve Long from Lancaster and characterises the rubisco-chaperone BSD2.


Williams A, Pétriacq P, Beerling DJ, Cotton TEA, Ton J (2018) Impacts of Atmospheric CO(2) and Soil Nutritional Value on Plant Responses to Rhizosphere Colonization by Soil Bacteria. Front Plant Sci. doi: 10.3389/fpls.2018.01493

https://www.frontiersin.org/articles/10.3389/fpls.2018.01493/full

Open Access

Alex Williams is the lead author of this paper and works with Jurriaan Ton at the University of Sheffield. The impact of the soil rhizosphere on plant growth is emerging as an important growth determinant. In this paper the authors assess the role of altered [CO2] and soil carbon (C) and nitrogen (N) concentration in the colonisation of Arabidopsis roots by two different bacteria. Firstly they showed that altered [CO2] did not change the growth dynamics of the saprophytic bacteria Pseudomonas putida KT2440 and was independent of soil C or N. In contrast growth of the rhizobacterial strain Pseudomonas simiae WCS417 was sensitive to both changing [CO2] and soil composition. These results show the importance of the interaction between atmospheric CO2 and soil nutritional status during plant interactions with soil bacteria.


Davey MP, Palmer BG, Armitage E, Vergeer P, Kunin WE, Woodward FI, Quick WP (2018) Natural variation in tolerance to sub-zero temperatures among populations of Arabidopsis lyrata ssp. petraea. BMC Plant Biol. doi: 10.1186/s12870-018-1513-0

Open Access

Matthew Davey, now working in Cambridge, collaborated with Peter Quick at the University of Sheffield on this research that looks at the tolerance of Arabidopsis lyrata to freezing. They showed that populations from locations with colder winter climates were better able to survive subzero temperatures, particular when they have been acclimated at near zero for longer periods. This demonstrates that the adaptation of plants to cold temperatures allows them to better survive freezing, although surprisingly this effect is lessened when this acclimation period does not occur.


Andrews M, Condron LM, Kemp PD, Topping JF, Lindsey K, Hodge S, Raven JA (2018) Effects of elevated atmospheric [CO2] on nitrogen (N) assimilation and growth of C3 vascular plants will be similar regardless of N-form assimilated. J Exp Bot. doi: 10.1093/jxb/ery371

This UK-New Zealand collaboration is led by Mitchell Andrews and looks at the effect of elevated [CO2] on the nitrogen (N) assimilation when the plant is exposed to a variety of different N-sources. They show that in C3 plants the overall N assimilated will be the same whether the plant is under ammonium (NH4+) nutrition or under nitrate (NO3-) nutrition. These results are contrary to previous results that suggest elevated [CO2] reduces plant growth under NO3- nutrition.


Sánchez-Montesino R, Bouza-Morcillo L, Marquez J, Ghita M, Duran-Nebreda S, Gómez L, Holdsworth MJ, Bassel G, Oñate-Sánchez L (2018) A regulatory module controlling GA-mediated endosperm cell expansion is critical for seed germination in Arabidopsis. Mol Plant. doi: 10.1016/j.molp.2018.10.009 

https://www.sciencedirect.com/science/article/pii/S1674205218303356

Open Access

This Spanish-led project includes authors from the Universites of Nottingham and Birmingham. They look at the influence of a GA signalling module on endosperm cell separation, which is essential for Arabidopsis seed germination. They show the NAC transcription factors NAC25 and NAC1L control expression of the EXPANSION2 gene and that the GA signalling component RGL2 has a controlling influence by repressing this activity.


Behera S, Xu Z, Luoni L, Bonza C, Doccula FG, DeMichelis MI, Morris RJ, Schwarzländer M, Costa A (2018) Cellular Ca2+ signals generate defined pH signatures in plants. Plant Cell. doi: 10.1105/tpc.18.00655

Open Access

Richard Morris (John Innes Centre) is a co-author on this Italian-led study that investigates the role of Calcium ions in cell signalling. They use a set of genetically-encoded fluorescent sensors to visualise a link between Ca2+ signaling and changes in pH. If this link is maintained across all cell types it might represent an extra layer of complexity and control of cellular signal transduction.


Drenichev MS, Bennett M, Novikov RA, Mansfield J, Smirnoff N, Grant M, Mikhailov S (2018) A role for 3′-O-β-D-ribofuranosyladenosine in altering plant immunity. Phytochemistry. doi: 10.1016/j.phytochem.2018.10.016

https://www.sciencedirect.com/science/article/pii/S0031942218301997?via%3Dihub

This Russian-led study includes UK-based researchers Mark Bennett, Murray Grant, Nick Smirnoff and John Mansfield as co-authors. They show that the natural disaccharide nucleoside, 3′-O-β-D-ribofuranosyladenosine accumulated in plants infected with the bacterial pathogen P. syringae. Perhaps surprisingly the application of this nucleoside to the plant doesn’t effect bacterial multiplication, indicating that adds a significant metabolic burden to plants already battling new infections.


Conlan B, Birch R, Kelso C, Holland S, De Souza AP, Long SP, Beck JL, Whitney SM (2018) BSD2 is a Rubisco specific assembly chaperone, forms intermediary hetero-oligomeric complexes and is non-limiting to growth in tobacco. Plant Cell Environ. doi: 10.1111/pce.13473

Steve Long is a Professor at Lancaster Environment Centre and is a co-author on this Australia-led study that characterizes the role of the Rubisco chaperone BSD2 during Rubisco biogenesis. These results suggest this is the sole role of BSD2 and its activity is non-limiting to tobacco growth.

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