11th Sep 2015

After a slow couple of weeks the Arabidopsis Research Roundup returns with some publications in high profile journals. None more so than the widely reported study from the University of York that highlights Arabidopsis plants which are able to grow on TNT-contaminated soils. Three other broadly cell biology-based studies from the JIC, Cardiff and Nottingham look at cell wall composition, vascular patterning and polyadenylation respectively. Finally a study from the James Hutton Institute presents an improved tool for identification of DNA-binding proteins in plants.

Johnston EJ, Rylott EL, Beynon E, Lorenz A, Chechik V, Bruce NC (2015) Monodehydroascorbate reductase mediates TNT toxicity in plants Science. 349 1072-1075

The most highly reported manuscript of this week comes from Neil Bruce’s group at the University of York. This publication in Science discusses the use of plants in the removal of historic pollution from TNT-based explosions. TNT phytotoxicity results from the creation of a reactive oxygen species in the mitochondria, a reaction catalyzed by monodehydroascorbate reductase6 (MDHAR6). The authors show that an Arabidopsis mdhar6 mutant is tolerance to TNT with no significant reduction in biomass. This discovery may very well contribute toward the remediation of contaminated sites with plants. This paper has been also reported widely in the general media including at Wired or Reuters.

Seguela-Arnaud M, Smith C, Uribe MC, May S, Fischl H, McKenzie N, Bevan MW (2015) The Mediator complex subunits MED25/PFT1 and MED8 are required for transcriptional responses to changes in cell wall arabinose composition and glucose treatment in Arabidopsis thaliana. BMC Plant Biol. 5;15(1):215

Mike Bevan at the JIC leads this work, which also includes GARNet board member Sean May that investigates the control of cell wall deposition. The Arabidopsis hsr8-1 mutant has an arabinose deficiency that prevents correct hypocotyl elongation due to a cell wall defect. This mutant is rescued by mutations in the Mediator transcription complex indicating that they have some specificity for genes involved in cell wall composition. This suppression alters gene expression is several glucose-induced genes, including cell wall enzymes and those involved in flavonoid and glucosinolate biosynthetic pathways.

Randall RS, Miyashima S, Blomster T, Zhang J, Elo A, Karlberg A, Immanen J, Nieminen K, Lee JY, Kakimoto T, Blajecka K, Melnyk CW, Alcasabas A, Forzani C, Matsumoto-Kitano M, Mähönen AP, Bhalerao R, Dewitte W, Helariutta Y, Murray JA

AINTEGUMENTA and the D-type cyclin CYCD3;1 regulate root secondary growth and respond to cytokinins Biol Open. bio.013128.

The aim of this multi-national collaboration led by GARNet PI Jim Murray (Cardiff)  and Yrjo Helariutta (SLCU) was to reset some established dogma which held that the AINTEGUMENTA (ANT) was epistatic to the D-type cycling CYCD3;1 in the control of vascular patterning. However this study shows that in the vascular cambium of Arabidipsis roots both genes respond to cytokinin and are required for proper root thickening. In addition this mechanism is maintained in the roots of poplar, suggesting a common regulatory mechanism.

Kappel C, Trost G, Czesnick H, Ramming A, Kolbe B, Vi SL, Bispo C, Becker JD, de Moor C, Lenhard M (2015) Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana PLoS Genet.11(8):e1005474

Corneila De Moor is a lecturer in the RNA biology group at the University of Nottingham, School of Pharmacy. However she is involved with this German-led study that looks at nuclear poly(A) polymerase (PAPS) in Arabidopsis. The three PAPS in Arabidopsis are functional specialised and this study investigates the transcriptional profile of altered poly(A) lengths to show that the PAPS1 protein is preferentially involved in ribosome biogenesis and redox homeostasis. This suggests that expression levels are strongly linked to poly(A) tail length and that relative activities of the PAPS isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.

Motion GB, Howden AJ, Huitema E, Jones S (2015) DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool Nucleic Acids Res.

Edgar Huitema is the plant science lead on this collaboration with computer scientists at the James Hutton Institute that introduces a new genome analysis tool that aims to functional annotate protein products. The focus of the study is on DNA-binding proteins and this new support vector machine model more accurately predicts this type of protein than generic versions. The model was developed in Arabidopsis but when turned to the tomato genome it annotated 36 currently uncharacterised proteins. This model is publically available and the authors hope that it will be used in combination with existing tools to increase annotation levels of DNA-binding proteins