Arabidopsis Research Roundup: April 20th

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Published on: April 20, 2017

This Easter basket of papers again features a selection across many topics of research involving Arabidopsis work. Firstly is a paper led from Dundee that introduces a novel Arabidopsis genome assembly that takes into account alternatively spliced transcripts. Secondly is a paper that identifies a role for an auxin influx carrier in nodule formation in Medicago. Thirdly is a novel characterization of two enzymes involved in SA biosynthesis whilst the fourth paper identifies a novel signaling component that acts during innate immunity to nematodes. Finally is a study that demonstrates a use for microfluidics in the generation of in vitro plant membrane bilayers.

Zhang R, Calixto CP, Marquez Y, Venhuizen P, Tzioutziou NA, Guo W,, Spensley M, Entizne JC, Lewandowska D, Ten Have S, Frei Dit Frey N, Hirt H, James AB, Nimmo HG, Barta A, Kalyna M, Brown JW (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Res. https://doi.org/10.1093/nar/gkx267

Open Access

This work is led by John Brown (James Hutton Institute, University of Dundee) in collaboration with colleagues from Glasgow, Vienna and Paris and Toronto. They have looked at the wide array of transcript isoforms that are produced in the Arabidopsis transcriptome. For analysis of these isoforms these researchers have generated a novel pipeline that effectively discriminates between isoforms and results in a Reference Transcript Dataset for Arabidopsis (AtRTD2) that contains over 80K non-redundant transcripts from approximately 35K genes. The testing of AtRTD2 showed that it can outperform other transcriptomes in RNAseq analysis. In addition to their specific Arabidopsis work they provide a methodology for the design of similar workflows for use in other species. The AtRTD2 is currently being integrated with the new Araport11 genome assembly.

The differences between the RTD2 and Araport11 assemblies are presented in the GARNish Vol25 newsletter


Roy S, Robson FC, Lilley JL, Liu C, Cheng X, Wen J, Bone C, Walker S, Sun J, Cousins D, Bennett MJ, Downie JA, Swarup R, Oldroyd GE, Murray JD (2017) MtLAX2, a functional homologue of the auxin importer AtAUX1, is required for nodule organogenesis. Plant Physiology

http:/​/​dx.​doi.​org/10.1104/pp.16.01473 Open Access

Researchers from the JIC and Nottingham lead this study that looks at the role of the auxin influx carrier LAX2 in nodule organogenesis in Medicago. In Arabidopsis there are no reported specific roles for LAX2 but in Medicago they show that MtLAX2 is necessary for nodule formation alongside other auxin-mediated root growth responses. This provides insights into a developmental-specific role for this protein during plant evolution.


Macaulay KM, Heath GA, Ciulli A, Murphy AM, Abell C, Carr JP, Smith AG (2017) The biochemical properties of the two Arabidopsis thaliana isochorismate synthases. Biochem J. http:/​/​dx.​doi.​org/10.1042/BCJ20161069 Open Access

Alison Smith (Cambridge) is the lead author of this study that characterises two isochorismate synthase (ICS) enzymes that are involved in salicylic acid biosynthesis. Expression of AtICS1 is induced by pathogens whilst AtICS2 is constitutive expressed, mostly in vascular tissues. This work shows that both proteins are enzymatically active yet have a narrow window of activity.


Mendy B, Wang’ombe MW, Radakovic ZS, Holbein J, Ilyas M, Chopra D, Holton N, Zipfel C, Grundler FM, Siddique S (2017) Arabidopsis leucine-rich repeat receptor-like kinase NILR1 is required for induction of innate immunity to parasitic nematodes. PLoS Pathog.

http:/​/​dx.​doi.​org/10.1371/journal.ppat.1006284 Open Access

Cyril Zipfel (Sainsbury lab, Norwich) is a co-author on this study that investigates the role of the leucine-rich repeat receptor-like kinase NILR1 in the innate immune response. The novelty of this work comes in the fact that this is the first characterised immune receptor that responds to parasitic nematodes and therefore might provide a new target for pathogen control strategies in crop plants.


Barlow NE, Smpokou E, Friddin MS, Macey R, Gould IR, Turnbull C1, Flemming AJ, Brooks NJ, Ces O, Barter LM (2017) Engineering plant membranes using droplet interface bilayers. Biomicrofluidics. http:/​/​dx.​doi.​org/10.1063/1.4979045 Open Access

This fascinating study from resarchers at Imperial College describes the use of a microfluidic system to generate in vitro plant membrane bilayers. Droplet interface bilayers (DIBs) from Arabidopsis, tobacco and oat have been replicated by varying the amount of membrane components. In future this system could be used in experiments that study membrane translocation or in novel chemical biology screens.

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