21st Jan 2015

Lots of new and interesting papers to catch up on from the New Year break this week. Fans of proteomics will be happy as we have three proteomics papers from Edinburgh, Cambridge and Birmingham! The John Innes Centre and University of Warwick also have an update for us on how histone dynamics affect transcription; Norwich and Sainsbury Lab Cambridge-based researchers tell us more about ELF3; Rothamsted scientists reveal roles for CER2-LIKE proteins; and Donna Bond and Professor Sir David Baulcombe reveal how virus-induced gene silencing can be used to study transposable elements.


  • Krahmer J, Hindle MM, Martin SF, Le Bihan T and Millar AJ. Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana. Methods in Enzymology, 26 December 2014. DOI: 10.1016/bs.mie.2014.10.022.

This useful review from former GARNet PI Andrew Millar and team discusses methods used in phosphoproteomics – the study of post-translational protein phosphorylations.   


  • Rosa S, Ntoukakis V, Ohmido N, Pendle A, Abranches R and Shaw P. Cell differentiation and development in Arabidopsis are associated with changes in histone dynamics at the single cell level. The Plant Cell, 30 December 2014. DOI: 10.1105/tpc.114.133793. [Open Access]

In this really interesting Plant Cell paper, researchers including those from the John Innes Centre and the University of Warwick, provide evidence to suggest that stem cells have relatively mobile histones, whereas as cells differentiate, the histones become acetylated and thus more and more ‘fixed’ to the chromatin. This helps to explain how stem cells have the propensity to generate cells with different gene expression profiles, and why differentiated cells of a given type all express genes in a coordinated manner.


  • Box MS, Huang E, Domijan M, et al. ELF3 controls thermoresponsive growth in Arabidopsis. Current Biology, 30 December 2014. DOI: 10.1016/j.cub.2014.10.076.

Published just a little too late for Christmas (!), this paper comes from a collaboration between mostly Norwich Research Park-based scientists and those at the The Sainsbury Lab in Cambridge. The paper explores the role and function of the transcriptional regulator ELF3 (EARLY FLOWERING3). This gene encodes a protein that rapidly and reversibly binds to transcriptional targets in a temperature-dependent mechanism, thus regulating cell elongation in response to changes in ambient temperature.


  • Marondedze C, Wong A, Groen A, Serrano N, Jankovic B, Lilley K, Gehring C and Thomas L. Exploring the Arabidopsis proteome: influence of protein solubilization buffers on proteome coverage. International Journal of Molecular Science, 31 December 2014. DOI: 10.3390/ijms16010857. [Open Access]

Led by a Saudi Arabian team but involving the work of Arnoud Groen and Kathryn Lilley from the University of Cambridge, here’s another paper on the subject of methods in proteomics. In this work, using Arabidopsis thaliana as a model, the group assesses how variations in techniques and detergents used as the solubilisation buffer can affect the results of a proteomic study.



  • Roitinger E, Hofer M, Köcher T, Pichler P, Novatchkova M, Yang J, Schlögelhofer and Mechtler K. Quantitative phosphoproteomics of the ATM and ATR dependent DNA damage response in Arabidopsis thaliana. Molecular & Cellular Proteomics, 5 January 2015. DOI: 10.1074/mcp.M114.040352. [Open Access]

More proteomics! Jianhua Yang from the University of Birmingham is an author on this Austrian-led paper, in which a novel mass spec-based phosphoproteomics approach to study DNA damage repair in Arabidopsis thaliana is described. The approach allowed identification of nearly 11,000 proteins and 15,500 unique phosphopeptides, of which 134 ATM/ATR-dependent phosphopeptides were up-regulated, and 38 were down-regulated. Both known and novel targets of ATM/ATR were found.


  • Bond DM and Baulcombe DC. Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the USA, 5 January 2015. DOI: 10.1073/pnas.1413053112. [Open Access]

This PNAS offering is from Donna Bond and David Baulcombe from the University of Cambridge. Investigating the mechanisms by which RNA-directed DNA methylation (RdDM) is achieved to silence transposable elements, the authors wondered whether DNA methylation can be induced de novo at naïve sites, or whether it can only re-establish epigenetic silencing of active transposable elements. Using virus-induced epigenetic silencing (VIGS)-RdDM, it is demonstrated that epigenetic silencing can be achieved in a genetic mutant plant, mediated via virus-derived small RNAs. This has great potential for use as a tool in gene silencing studies.



  • Haslam T, Haslam RP, Thoraval D, et al. CER2-LIKE proteins have unique biochemical and physiological functions in very-long-chain fatty acid elongation. Plant Physiology, 14 January 2015. DOI: 10.1104/pp.114.253195. [Open Access]

This article, which involved the work of Richard Haslam, Frédéric Beaudoin and Johnathan Napier from Rothamsted Research, explores the functionality of the enzyme CER2 and its homologues; required for the elongation of fatty acids with chains longer than 28 carbons. Three CER2-LIKE proteins are shown to have unique effects on the substrate specificity of the same condensing enzyme (required to catalyse the first step of the fatty acid elongation process), and furthermore are important in cuticle formation and pollen coat function.