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GARNet Research Roundup: December 7th 2018

Categories: Aberystwyth University, Global, John Innes Centre, Lancaster University, Nottingham University, Rothamsted Research, Sainsbury Lab, SLCU, University of Birmingham, University of Bristol, University of Sheffield

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Published on: December 7, 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: July 16th

by Geraint

Categories: Aberystwyth University, Durham University, Exeter University, Global, John Innes Centre, New Phytologist, Nottingham University, Oxford Brookes University, Oxford University, Uncategorized, University of Oxford, University of Southampton

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Published on: July 16, 2018

This week’s GARNet research roundup begins with a set of papers looking at aspects of the plant defence response with a focus on the cell wall. Firstly work from Mike Deeks’ lab in Exeter assesses the role of FORMIN4 during pre-invasion cell wall apposition. Secondly Sara Pose and Paul Knox (Leeds) are involved with a study looking at how altered cell wall lignin composition alters the defense response. Finally Joe McKenna and Cyril Zipfel are co-authors on a Norwegian-led study that looks at the influence of plant cell wall integrity maintenance in immune signalling.

Relatedly is a study from the Devoto lab at RHUL looks at the role of the defence hormone methyl jasmonate in Arabidopsis cell culture.

Next are two papers that research different aspects of the plant ER. Verena Kriechbaumer (Oxford Brookes) looks at plant ER-localised Lunapark proteins whilst a study from the University of Warwick provides a preliminary structural analysis of the RTNLB13 reticulon protein.

The seventh and eight papers are involved with the plant response to different growth conditions. Research from University of Nottingham looks at the response of the cortical cell layer of the root meristem to low phosphate conditions whilst work from University of Southampton investigates the relationship between nitrate and copper signaling.

The next paper is from Emily Flashman’s lab at the University of Oxford and looks at the role of plant cysteine oxidases as oxygen sensors whilst the tenth paper features John Doonan (Aberystwyth University) as a co-author and investigates how a histone acetyltransferase affects trichome development.

Finally is a paper from Pierre Baudal and Kirsten Bomblies (John Innes Centre) that uses Arabidopsis arenosa as a model to investigate the emergence of novel flowering time alleles in populations that have colonised along railway corridors.

Sassmann S, Rodrigues C, Milne SW, Nenninger A, Allwood E, Littlejohn GR, Talbot NJ, Soeller C, Davies B, Hussey PJ, Deeks MJ (2018) An Immune-Responsive Cytoskeletal-Plasma Membrane Feedback Loop in Plants. Curr Biol. doi: 10.1016/j.cub.2018.05.014

https://www.sciencedirect.com/science/article/pii/S096098221830616X?via%3Dihub

Open Access

Stefan Sassmann is the lead author of this paper from Mike Deeks’s lab in Exeter. They investigate the role of the membrane-integrated FORMIN4 protein in the process of cell wall apposition, which occurs as part of the plant immune response and is dependent on actin dynamics. FORMIN4 is stably localised apart from the active traffic of the endomembrane system and removing its function compromises the defense response, presumably by altering actin distribution at sites of cell wall apposition. This work demonstrates that FORMIN4 acts as a key component of the pre-invasion defense response.

Gallego-Giraldo L, Posé S, Pattathil S, Peralta AG, Hahn MG, Ayre BG, Sunuwar J, Hernandez J, Patel M, Shah J, Rao X, Knox JP, Dixon RA (2018) Elicitors and defense gene induction in plants with altered lignin compositions. New Phytol. doi: 10.1111/nph.15258

Open Access

Sara Pose and Paul Knox (University of Leeds) are co-authors on this US-led study that investigates how lignin composition can influence the defence response. Plants with the same lignin content but changed lignin compositions show altered expression in genes involved with different arms of the defense response. This indicates that cell wall lignin composition plays a significant role in the plants ability to response to different sources of pathogen attack.

Engelsdorf T, Gigli-Bisceglia N, Veerabagu M, McKenna JF, Vaahtera L, Augstein F, Van der Does D, Zipfel C, Hamann T (2018) The plant cell wall integrity maintenance and immune signaling systems cooperate to control stress responses in Arabidopsis thaliana. Sci Signal. doi: 10.1126/scisignal.aao3070

Joe McKenna (Imperial College, now Oxford Brookes University) and Cyril Zipfel (The Sainsbury Laboratory, Norwich) are co-authors on this Norwegian-led study that looks at the plant cell wall integrity maintenance mechanism and how it responses to the challenges of growth, development and environmental stresses. They identified a set of receptor-like kinases that are key for the responses elicted by cell wall damage (CWD). Conversely they showed that the components of the pattern-triggered immunity (PTI) signaling pathway repress responses to CWD. This study provides insights into how cell wall responses interact with downstream gene expression changes following pathogen challenge.

Bömer M, O’Brien JA, Pérez-Salamó I, Krasauskas J, Finch P, Briones A, Daudi A, Souda P, Tsui TL, Whitelegge JP, Paul Bolwell G, Devoto A (2018) COI1-dependent jasmonate signalling affects growth, metabolite production and cell wall protein composition in Arabidopsis. Ann Bot. doi: 10.1093/aob/mcy109

Open Access

Moritz Bömer works with Alessandra Devoto at Royal Holloway University of London and leads this research that looks at the effect of MeJA treatment on growth and gene expression in Arabidopsis cell culture. They demonstrate that both MeJA treatment or COI1 overexpression causes changes in the abundance of proteins involved in cell wall loosening as well as altered levels of primary metabolites alanine, serine and succinic acid. This work demonstrates a close link between hormone signaling, the defence response and the metabolic profile of Arabidopsis cells.

Dr Devoto and her academic colleagues at RHUL are profiled in the latest GARNish newsletter available for download from the GARNet website.

Kriechbaumer V, Breeze E, Pain C, Tolmie F, Frigerio L, Hawes C (2018) Arabidopsis Lunapark proteins are involved in ER cisternae formation. New Phytol. doi: 10.1111/nph.15228

https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15228

Open Access

Verena Kriechbaumer from Oxford Brookes University leads this research that investigates the in planta function of novel ER network-shaping proteins called Lunaparks (LNP). They show that these proteins localise to the entire ER network in Arabidopsis. They use confocal microscopy to show that altering the level of LNP gene expression changes ER morphology, possibly by regulating the formation of ER cisternae.

Chow M, Sklepari M, Frigerio L, Dixon AM (2018) Bacterial expression, purification and biophysical characterization of the smallest plant reticulon isoform, RTNLB13 Protein Expr Purif. doi: 10.1016/j.pep.2018.06.015

Open Access

Michael Chow worked with Lorenzo Frigerio and Ann Dixon at the University of Warwick to provide a preliminary structure and topology analysis of the plant RTNLB13 reticulon protein. This ER-associated integral membrane protein was expressed in bacteria and then a variety of analysis techniques were used to suggest that RTNLB13 has a high level of self-association and protein-membrane interactions.

Janes G, von Wangenheim D, Cowling S, Kerr I, Band L, French AP, Bishopp A (2018) Cellular Patterning of Arabidopsis Roots Under Low Phosphate Conditions Front Plant Sci. doi: 10.3389/fpls.2018.00735

https://www.frontiersin.org/articles/10.3389/fpls.2018.00735/full

Open Access

George Janes works with Anthony Bishopp at the University of Nottingham and leads this study that looks at root meristem development under low phosphate conditions. They show that in phosphate-limiting conditions the cortex layer of the root meristem contains almost double the number of cells, which results in a greater number of root hair-forming epidermal cells. As this change can occur within 24hrs the rapidity of the response represents a significant adaptation to a changing root environment.

Hippler FWR, Mattos-Jr D, Boaretto RM, Williams LE (2018) Copper excess reduces nitrate uptake by Arabidopsis roots with specific effects on gene expression J Plant Physiol. doi: 10.1016/j.jplph.2018.06.005

https://www.sciencedirect.com/science/article/pii/S0176161718302888

Open Access

Franz Hippler (University of Southampton) leads this UK-Brazil collaboration showing that growth of Arabidopsis plants in excess copper conditions causes a downregulation in nitrate uptake. This is due to both direct and indirect changes on the gene expression of nitrate transporters as well as a reduction in transcript level of the plasma membrane proton pump, AHA2. This effect was altered when copper levels were reduced demonstrating that copper toxicity acts at the level of nitrate transport and homeostasis.

White MD, Kamps JJAG, East S, Taylor Kearney LJ, Flashman E (2018) The Plant Cysteine Oxidases from Arabidopsis thaliana are kinetically tailored to act as oxygen sensors J Biol Chem.

doi: 10.1074/jbc.RA118.003496

Open Access

Mark White is the lead author on this work from the lab of Emily Flashman at the University of Oxford in which they look at the role of plant cysteine oxidases (PCOs) as oxygen sensors. They assessed the kinetics of each of AtPCO1 to AtPCO5 proteins and show that the most catalytically competent isoform is AtPCO4, in terms of both responding to O2, and oxidizing hypoxic responsive proteins. This work validates an O2-sensing role for the PCOs and provides evidence for functional differences between members of this enzyme family.

Kotak J, Saisana M, Gegas V, Pechlivani N, Kaldis A, Papoutsoglou P, Makris A, Burns J, Kendig AL, Sheikh M, Kuschner CE, Whitney G, Caiola H, Doonan JH, Vlachonasios KE, McCain ER, Hark AT (2018) The histone acetyltransferase GCN5 and the transcriptional coactivator ADA2b affect leaf development and trichome morphogenesis in Arabidopsis. Planta. doi: 10.1007/s00425-018-2923-9 Open Access

John Doonan (Aberystwyth University) is a co-author on this manuscript led by Jenna Kotak and Amy Herd in the USA. They investigate plants that have mutations in the histone acetyltransferase GCN5 and associated transcriptional coactivator ADA2b. These genes have been previously demonstrated as being involved in endoreduplication and trichome branching. They show that these mutants have alterations in the number and patterning of trichome-branches and that ADA2b and GCN5 are required to couple nuclear content with cell growth and morphogenesis.

Baduel P, Hunter B, Yeola S, Bomblies K. Genetic basis and evolution of rapid cycling in railway populations of tetraploid Arabidopsis arenosa (2018) PLoS Genet.

doi: 10.1371/journal.pgen.1007510 Open Access

Pierre Baduel and Kirsten Bomblies (John Innes Centre) lead this work that was conducted prior to Kirsten’s move to Norwich. In this study they follow the colonization of populations of Arabidopsis arenosa along mountain railway corridors. They demonstrate that selective pressure has occurred on novel alleles of flowering time genes and discuss the implications for ruderal communities linked to railways as allele conduits linked to local adaptations.

Arabidopsis Research Roundup: December 18th

by Geraint

Categories: Aberystwyth University, Global, John Innes Centre, Kew Gardens, Nottingham University, Oxford University, SLCU, University of Oxford

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Published on: December 18, 2017

This festive Arabidopsis Research Roundup begins with a commentary article from a global consortium of plant scientists who propose a framework of future training for researchers who will take advantage of the experimental tools available in Arabidopsis. Secondly is study from Caroline Dean (JIC) that defines the role of the LHP1 protein in epigenetic control of gene expression. Thirdly John Doonan (Aberystwyth) is a co-author of work that defines an important component of mitotic spindle formation. Next is a study led by Zinnia Gonzalez-Carranza in Nottingham that offers further insights into the function of the HWS gene. The fifth study comes from the lab of Alexander Ruban (QMUL), further investigating the importance of NPQ in photosynthetic control. The sixth paper from the Van Ooijen lab (Edinburgh) characterises the role of sumoylation in the control of CCA1 activity. The penultimate paper from the Harberd lab in Oxford defines the importance of DNA mismatch repair on genome sequence integrity whilst the final paper characterises the next phase in the long story of Arabidopsis ALF4 function and includes Charles Melynk (SLCU) as a co-author.

Friesner J et al (2017) The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiol. doi: 10.1104/pp.17.01490. Open Access

The current GARNet PI Jim Murray and past GARNet coordinator Ruth Bastow are authors in this international consortium that suggests future directions for the global Arabidopsis community. This consortium is led by Joanna Friesner and concludes that it is critical that the next generation of plant scientists receive appropriate training in bioinformatics and quantitative biology so as to take advantage of the remarkable array of datasets that are now available to Arabidopsis researchers.

Berry S, Rosa S, Howard M, Bühler M, Dean C (2017) Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression Genes Dev. doi: 10.1101/gad.305227.117 Open Access

Caroline Dean (John Innes Centre) leads this study that investigates the role of the polycomb associated protein LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) in the regulation of the repressive histone mark H3K27me3. They demonstrate that the intrinsically disordered hinge region of LHP1 is responsible for RNA-binding and that disruption of this region prevents the formation of sub-nuclei foci, provides a potential link to wider epigenetic regulation.

Lee YJ, Hiwatashi Y, Hotta T, Xie T, Doonan JH, Liu B (2017) The Mitotic Function of Augmin Is Dependent on Its Microtubule-Associated Protein Subunit EDE1 in Arabidopsis thaliana. Current Biol. doi: 10.1016/j.cub.2017.11.030

Open Access

John Doonan and colleagues at Aberystwyth University are co-authors on this study regarding the role of the Microtubule-Associated Protein Subunit EDE1, which is a member of the Augmin complex, during mitosis. EDE1 specifically localised with the augmin complex during spindle formation, a role that cannot be replaced by the homologous protein AUG8. This work reveals that specificity of the augmin complex can be determined by interaction with subunits that only contribute to complex function during particular phases of the cell cycle.

Zhang X, Jayaweera D, Peters JL, Szecsi J, Bendahmane M, Roberts JA, González-Carranza ZH (2017) The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT is a new player in the microRNA pathway. PLoS One. doi: 10.1371/journal.pone.0189788 Open Access

Zinnia Gonzalez-Carranza (Nottingham) is the corresponding author on this study that follows on from work published earlier in 2017 regarding the role of the HAWAIIAN SKIRT gene is plant development. In this latest work they identify mutations in the previously characterized Exportin-5 HASTY gene as suppressors of the hws mutant phenotype. Further investigation shows that HWS genetically interacts with other genes involved in miRNA pathway indicates that HWS somehow interacts with biogenesis, accumulation or function of these small RNAs.

Townsend AJ1, Ware MA1, Ruban AV (2017) Dynamic interplay between photodamage and photoprotection in photosystem II. Plant Cell Environ doi: 10.1111/pce.13107

In this paper Alexander Ruban (QMUL) is the corresponding author on work that expands his groups contribution to the understanding of the role non-photochemical quenching (NPQ) plays during photoinhibition. In this work they compare the activity of NPQ versus endogenous photosystemI repair mechanisms in the maintenance of photosynthetic activity during photoinhibitory conditions. Overall they conclude that NPQ is a more important mechanism for photoprotection under short periods of illumination.

Hansen LL, Imrie L, Le Bihan T, van den Burg HA, van Ooijen G (2017) Sumoylation of the Plant Clock Transcription Factor CCA1 Suppresses DNA Binding. J Biol Rhythms doi: 10.1177/0748730417737695 Open Access

This paper from the Van Ooijen lab accompanies one that was featured in last weeks ARR and extends their finding that sumoylation plays an important role in control of the circadian clock. In this paper they show that the CCA1 clock protein is sumoylated and that perturbing this modification alters the binding of CCA1 to a target promotor, even though it’s localization or stability were unaffected. Using an in vitro system they show that sumoylation is a direct determinant of CCA1 binding to its target promotor suggesting that this PTM fine tunes the activity of this key circadian control element.

Belfield EJ, Ding ZJ, Jamieson FJC, Visscher AM, Zheng SJ, Mithani A, Harberd NP (2017) DNA mismatch repair preferentially protects genes from mutation. Genome Res. doi: 10.1101/gr.219303.116

Past GARNet Advisory board member Nick Harberd (Oxford) leads this multi-generational study on the effect of DNA mismatch repair (MMR) on maintenance of an entire genome. They perform whole genome sequencing across five generations of Arabidopsis plants with a mutation in the MMR pathway and show that particular types of nucleotide error are more prevelant amongst the total 9000 mutations that accumulate. Interestingly they show that single nucleotide variants are more likely to accumulate in genic regions, indicating that protein coding areas of the genome are preferentially protected from damage.

Bagchi R, Melnyk CW, Christ G, Winkler M,, Kirchsteiner K, Salehin M, Mergner J, Niemeyer M, Schwechheimer C, Calderón Villalobos LIA, Estelle M (2017) The Arabidopsis ALF4 protein is a regulator of SCF E3 ligases. EMBO J. doi: 10.15252/embj.201797159

During his time as a research fellow at the Sainsbury lab in Cambridge. Charles Melynk contributed to this research that is a throwback to the early day of Arabidopsis mutant analysis. The alf4 was first described as a possible auxin mutant in 1995 and this work brings this study full circle by characterising the ALF4 protein as a novel regulator of SCF complexes, which are known to be involved in auxin and GA signaling. ALF4 specifically functions by interacting with the SCF-core component RBX1. Future work will determine whether this effect is specific to SCFs involved in hormone signaling or whether it is a more general effect.

Arabidopsis Research Roundup: July 11th

by Geraint

Categories: Aberdeen University, Aberystwyth University, Arabidopsis, Audio, GARNet, Global, James Hutton Institute, John Innes Centre, Uncategorized, University of Manchester

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Published on: July 11, 2016

After a conference break the Arabidopsis Research Roundup returns with an outstanding selection of papers from UK (and mostly Scotland-based) researchers. Firstly Levi Yant provides an audio description of work that has identified important loci for adaption to harsh environments. Secondly John Doonan leads a multi-national group investigating the role of eiF4A phosphorylation within proliferating cells. Next two Scottish-based studies both investigate aspects of light signalling on different scales: a Glasgow-based consortium dissects the UVR8 signaling module while the role of phytochrome on global carbon allocation is studied by Karen Halliday’s group in Edinburgh. The final paper also involves significant Scottish involvement with Piers Hemsley at Dundee together with Simon Turner at Manchester investigating the role of s-acylation in the activity of the cellulose synthase complex.

Arnold BJ, Lahner B, DaCosta JM, Weisman CM, Hollister JD, Salt DE, Bomblies K, Yant L (2016) Borrowed alleles and convergence in serpentine adaptation. PNAS http://dx.doi.org/10.1073/pnas.1600405113 Open Access

New investigator at the John Innes Centre, Levi Yant, is the corresponding author on this study that also includes contributions from the labs of Kristen Bomblies and current GARNet Chairman David Salt. This investigation uses GWAS techniques to identify loci in Arabidopsis Arenosa that are important for growth on serpentine barrens, which are characterised by drought, mineral paucity and high levels of heavy metals. They showed that polygenic multi-trait genomic locations are important for serpentine adaptation. The authors reassessed previous independent datasets and showed that 11 loci have been identified across these studies and are therefore good candidates as drivers of convergent evolution. This study provides evidence that certain A.arenosa alleles have been introgressed from A.lyrata and that these may facilitate adaptation to a multi-hazard environment.

Levi kindly provides a short audio description of this work, that also touches on ionomics and data reuse!

Bush MS, Pierrat O, Nibau C, Mikitova V, Zheng T, Corke FM, Vlachonasios K, Mayberry LK, Browning KS, Doonan JH (2016) eIF4A RNA Helicase Associates with Cyclin-Dependent Protein Kinase A in Proliferating Cells and is Modulated by Phosphorylation Plant Physiol. http://dx.doi.org/10.1104/pp.16.00435 Open Access

Growth of phospho-null or phospho-mimetic mutants of eif4a1

John Doonan (Aberystwyth) is the leader of this wide collaboration of UK, US, Czech, Greek and Chinese researchers that investigate the interaction of the eIF4A RNA helicase with cyclin-dependent protein kinase A (CDKA). This interaction only occurs in proliferating cells where CDKA acts by phosphorylating specific amino acids on eIF4A. Throughout in vivo and in vitro experiments using phospho-null and phosphor-mimetic version of eIF4A, the authors show that phosphorylation acts to downregulate eIF4A activity, subsequently altering the efficacy of translation.

Heilmann M, Velanis CN, Cloix C, Smith BO, Christie JM, Jenkins GI (2016) Dimer/monomer status and in vivo function of salt-bridge mutants of the plant UV-B photoreceptor UVR8. Plant J http://dx.doi.org/10.1111/tpj.13260 Open Access

This exclusively University of Glasgow study is led by John Christie and Gareth Jenkins. Dimeric UVR8 is a UV photoreceptor that after UV-B interaction dissociates into monomers, which interact with COP1 to begin signal transduction. The UVR8 dimer develops through the formation of salt-bridges between individual UVR8 proteins. In this study the details of the dimerization are dissected, showing that several salt-bridge amino acids are necessary for the multiple functions of both the UVR8 dimer and monomer. Interestingly the authors show that UVR8 with conservative mutations of Asp96 and Asp107 to Asn96 and Asn107 are unable to form dimers yet retain wildtype responses to UV-B. This shows that monomeric UVR8 has the ability to normally initiate a signal transduction pathway and complicates our understanding of the in vivo role of the UVR8 dimer.

Phy mutants have reduced biomass. Taken from: http://www.pnas.org/content/113/27/7667.abstract

Yang D, Seaton DD, Krahmer J, Halliday KJ (2016) Photoreceptor effects on plant biomass, resource allocation, and metabolic state. PNAS 113(27):7667-72 http://dx.doi.org/10.1073/pnas.1601309113

Karen Halliday (Edinburgh) is the corresponding author on this investigation into the broader impact of Arabidopsis phytochromes on carbon allocation and biomass production. Even though phytochrome mutants have reduced CO2 uptake they overaccumulate resources into sucrose and starch and show altered day:night growth rates. Overall this leads to reduced growth coincident with reduced expression of CELLULOSE SYNTHASE-LIKE genes. The authors demonstrate that phytochromes play a significant role in the control of biomass allocation and that they additionally differentially respond to external stresses. Evolutionarily this indicates that modification of phytochrome expression might be an important mechanism for responding to changing environments.

Kumar M, Wightman R, Atanassov I, Gupta A, Hurst CH, Hemsley PA, Turner S (2016) S-Acylation of the cellulose synthase complex is essential for its plasma membrane localization. Science. 353(6295):166-9 http://dx.doi.org/10.1126/science.aaf4009

Simon Turner (Manchester) and Piers Hemsley (James Hutton Institute, University of Dundee) lead this research which amalgamates the work from their individual labs and assesses the role of S-acylation on the activity of cellulose synthase complex (CSC). They show that core subunits of the CSC, cellulose synthase A (CESA) proteins, require s-acylation for their localisation to the plasma membrane, which is necessary for their in vivo activity. The authors estimate that a CSC might contain over 100 S-acyl groups, which could significantly alter its hydrophobicity and its interactions within the membrane environment.

CES localisation: Taken from http://science.sciencemag.org/content/353/6295/166.full.pdf+html

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Arabidopsis Research Roundup: Oct 28th

by Geraint

Categories: Aberystwyth University, Arabidopsis, Cambridge University, Durham University, GARNet, John Innes Centre, University of Manchester, University of Oxford

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Published on: October 28, 2015

This latest Arabidopsis Research Roundup is rather GARNet-focused as members of the current Advisory Board lead three of the featured papers. Firstly we present a study into mechanisms that control meiotic recombination, which also includes a short audio-description from the lead author Dr Ian Henderson. Secondly we introduce a paper that identifies the function of a novel gene in the control of male fertility and thirdly, a study of a translation control-factor that is involved in regulation of cell size and ovule development. In addition we introduce some highly collaborative work that looks into the role of SUMO proteases in SA signaling. Finally there is a methods paper that presents a new protocol for measurement of cellulose content in Arabidopsis stems.

Yelina N, Lambing C, Hardcastle T, Zhao X, Santos B, Henderson I (2015) DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis Genes & Dev. 29: 2183-2202 http://dx.doi.org/10.1101/gad.270876.115

GARNet advisory board member Ian Henderson leads this study that assesses how methylation state influences the chromosomal regions that undergo meiotic recombination. It was previously known that highly-methylated regions, such as centromeres, do not often undergo recombination. This work naturally extends that knowledge by using RNA-directed DNA methylation to show that methylation of local euchromatic regions also have reduced recombination levels. Equally they show that global reductions in CG methylation, such as in met1 mutants, cause wide-scale alterations in recombination remodeling. Use of recombination mutants shows that these changes are due to the redistribution of interfering crossovers. Overall they confirm that DNA methylation is critical in establishing domains of meiotic recombination.

In this short audio file, Dr Henderson explains the main features of this paper.

Visscher AM, Belfield EJ, Vlad D, Irani N, Moore I, Harberd NP (2015) Overexpressing the Multiple-Stress Responsive Gene At1g74450 Reduces Plant Height and Male Fertility in Arabidopsis thaliana. PLoS One.;10(10):e0140368. http://dx.doi.org/10.1371/journal.pone.0140368

Ian Moore and Nick Harberd (Oxford), who is also on the GARNet Advisory Board, present this investigation of five unknown genes that had been previously identified from global expression studies as playing a role in multiple stress-responses. These are somewhat unimaginatively identified by their ‘At’ numbers and even though they are each responsive to multiple stresses, mutants with a T-DNA insertion in any of these genes have no change in phenotype compared to wildtype plants. In contrast, overexpression of At1g74450, but no other of the tested genes, resulted in stunted growth and reduced male fertility. As the stress-response is often manifested by alterations in male gametophyte development, this work introduces the function of a gene that may provide an important link between multiple environmental factors, fertility and plant growth. In future the authors hope to provide further insight into the function of At1g74450.

Bush M, Crowe N, Zheng T, Doonan J (2015) The RNA helicase, eIF4A-1, is required for ovule development and cell size homeostasis in Arabidopsis Plant J. http://dx.doi.org/10.1111/tpj.13062

John Doonan, another GARNet board member, leads this collaborative work between Aberystwyth and Norwich. They investigate the function of the RNA helicase/ATPase eIF4A-1 that is involved in the initiation of mRNA translation. Arabidopsis contains two isoforms of this genes and the knockdown eif4a-1 mutant displays a range of altered phenotypes that includes a reduction in the amount of mitotic cells in the root meristem. This change skews the relationship between cell size and cell cycle progression. Concomitantly several cell cycle-regulated genes have reduced expression in this mutant. Each of the eIF4A isoforms plays an important role in plant fertility as although single eif4a-1 mutants display some defects in ovule development, double eif4a1eif4a2 mutants cannot be isolated.

Bailey M, Srivastava A, Conti L, Nelis S, Zhang C, Florance H, Love A, Milner J, Napier R, Grant M, Sadanandom A (2015) Stability of small ubiquitin-like modifier (SUMO) proteases OVERLY TOLERANT TO SALT1 and -2 modulates salicylic acid signalling and SUMO1/2 conjugation in Arabidopsis thaliana J Exp Bot. http://dx.doi.org/10.1093/jxb/erv468

This study of the SUMO proteases OVERLY TOLERANT TO SALT1 and -2 (OTS) is a real pan-UK collaboration that features researchers from six institutions, led by Ari Sadanandom at Durham. The OTS proteins have been previously linked to salicylic acid (SA) signaling and this manuscript shows that in addition to containing higher level of SA, ots1ots2 double mutants are more resistant to virulent Pseudomonas syringae. This is in part linked to an upregulation of the SA biosynthetic gene ICS1. In wildtype plants SA promotes degradation of OTS1/2, which indicates that these proteins are involved in a positive feedback loop that ensures a higher SA response, which increases the efficacy of certain defence responses. However de novo synthesis of OTS1/2 will be antagonistic to SA biosynthesis and provides a brake to prevent the over-accumulation of SA-responses.

Kumar M, Turner S (2015) Protocol: a medium-throughput method for determination of cellulose content from single stem pieces of Arabidopsis thaliana Plant Methods. 11:46. http://dx.doi.org/10.1186/s13007-015-0090-6

Simon Turner (Manchester) is the lead author of this paper that presents a new method for determining cellulose content from Arabidopsis stems. This protocol is an adaptation of a previous method and uses aspiration rather than centrifugation for recovery of liquids throughout the procedure. This increases the throughout of the method and improves its potential usage as a screening protocol to identify mutants with altered cell wall composition.

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Weeding the Gems

GARNet Research Roundup: December 7th 2018

GARNet Research Roundup: July 16th

Arabidopsis Research Roundup: December 18th

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Arabidopsis Research Roundup: Oct 28th