25th Nov 2015

This weeks Arabidopsis Research Roundup contains four papers each with a different focus. Firstly is a large-scale investigation that attempts to define the transcriptional changes that occur in response to bacterial infection. Second is a study that investigates a newly proposed role for the chloroplast chaperone Hsp93. Thirdly is another piece of work that also involves University of Oxford researchers and investigates the genetic networks that control leaf morphology. Finally is an updated plant-specific protocol for the commonly used technique of Chromatin Immunoprecipitation.

Lewis LA, Polanski K, de Torres-Zabala M, Jayaraman S, Bowden L, Moore J, Penfold CA, Jenkins DJ, Hill C, Baxter L, Kulasekaran S, Truman W, Littlejohn G, Prusinska J, Mead A, Steinbrenner J, Hickman R, Rand D, Wild DL, Ott S, Buchanan-Wollaston V, Smirnoff N, Beynon J, Denby K, Grant M (2015) Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000 Plant Cell. Open Access

This ‘Large Scale Biology’ publication is a collaboration between the Universities of Exeter and Warwick, led by Murray Grant and current GARNet Advisory board member Katherine Denby. This study investigates the transcriptional changes that occur over a long time course in response to infection by the pathogen Pseudomonas syringae pv tomato DC3000. The authors aim to differentiate between the changes associated with endogenous microbial-associated molecular pattern (MAMP)-triggered immunity (MTI) and those orchestrated by pathogen effectors. The responses to pathogenic and non-pathogenic P.syringae were compared and using novel computational analysis, it was shown that the majority of gene expression changes that contribute to disease or defense responses occurred within 6hour post-infection, well before pathogen multiplication. Broadly it was found that chloroplast-associated genes are suppressed by a MAMP-triggered response, presumably to restrict nutrient availability. Ultimately this manuscript identified specific promotor elements that are involved in either the MTI response or utilised by the infecting bacteria.

Corresponding author Professor Murray Grant kindly takes ten minutes to discuss the finding of this paper and the community resource that it represents. He also discusses another paper involving the Jasmonate response that resulted from this dataset and was recently highlighted in the Research Roundup.

Flores-Pérez Ú1, Bédard J1, Tanabe N2, Lymperopoulos P2, Clarke AK3, Jarvis P (2015) Functional analysis of the Hsp93/ClpC chaperone at the chloroplast envelope Plant Physiology. Open Access

Paul Jarvis (Oxford) is the corresponding author on this study in which his lab collaborates with Swedish researchers to investigate the role of the Hsp93/ClpC chaperone protein in protein import into the chloroplast. This recently postulated role for this protein has not yet been experimental tested so they generated a hsp93[P-] mutant that lacked a functional ClpP-binding motif (PBM), which confers the already determined role for Hsp93 in proteolysis that occurs in the chloroplast stroma. The hsp93[P-] mutant localises to the chloroplast envelope and associates with TIC transport machinery but was unable to complement the phenotypes of a hsp93 null mutant. This showed that the PBM domain was essential for its function. Expression of the Hsp93[P-] mutant in the hsp93 null background did not improve protein import so the authors concluded that these results do not confirm this newly postulated role for the protein and they suggest that its functional role occurs immediately after its substrate had been transported into the chloroplast.

Rast-Somssich MI, Broholm S, Jenkins H, Canales C, Vlad D, Kwantes M, Bilsborough G, Dello Ioio R, Ewing RM, Laufs P, Huijser P, Ohno C, Heisler MG, Hay A, Tsiantis M (2015) Alternate wiring of a KNOXI genetic network underlies differences in leaf development of A. thaliana and C. hirsuta Genes Dev. 29(22):2391-404 Open Access

The study includes researchers from Oxford and Southampton Universities in collaboration with those from Italy, France and Germany in work that is led by Angela Hay and Miltos Tsiantis, who were both previously based in Oxford. This is familiar territory for this group as they compare leaf development between Arabidopsis, which has simple leaves, and the related , Cardamine hirsuta, which has dissected leaves. In this new work they transfer the SHOOTMERISTEMLESS (STM) and BREVIPEDICELLUS (BP) homeobox genes between the two species and investigate their ability to modify leaf form. In Cardamine, expression of BP is controlled by crosstalk between the microRNA164A (MIR164A)/ChCUP-SHAPED COTYLEDON (ChCUC) module and ChASYMMETRIC LEAVES1 (ChAS1) gene. However this regulatory network does not function in Arabidopsis and therefore leads to the establishment of differing regulatory networks that the authors propose are responsible for the alterations in organ geometry.

Posé D, Yant L (2016) DNA-Binding Factor Target Identification by Chromatin Immunoprecipitation (ChIP) in Plants Methods Mol Biol. 1363:25-35.

Levi Yant is a new member of faculty at the John Innes Centre and is the lead author on this paper that introduces an updated protocol for Chromatin Immunoprecipitation in Plants (ChIP). They have used this technique in his lab to identify target genes for a number of transcriptional regulators that are involved in Arabidopsis floral development.