Weeding the Gems

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 fromEdinburgh, 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 andProfessor 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.

Back after our Christmas/New Year break, here’s a catch-up of the some of the new Arabidopsis papers to be published before Christmas. Today’s round-up features new work by scientists from the Universities of York, Leicester, Cambridge, Edinburgh and Leeds, and from the institutes Rothamsted Research and the James Hutton Institute.

• Delker C, Sonntag L, James GV, et al. The DET1-COP1-HY5 pathway constitutes a multipurpose signaling module regulating plant photomorphogenesis and thermomorphogenesis. Cell Reports, 18 December 2014. DOI: 10.1016/j.celrep.2014.11.043. [Open Access]

Though it has been known for some time that the transcription factor PHYTOCHROME INTERACTING FACTOR4 (PIF4) regulates the growth response of Arabidopsis thaliana to elevated ambient temperature by activating hormonal modules, it is not known how, exactly, temperature regulates PIF4 activity. Using a forward genetic approach, this group of German researchers – with the help of Seth J. Davis from the University of York – provide evidence to suggest that seedling growth in response to elevated temperature is transcriptionally regulated by the DE-ETIOLATED 1 (DET1)-CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1)-ELONGATED HYPOCOTYL 5 (HY5)-dependent photomorphogensis pathway.

• Park GT, Frost JM, Park J-S, Kim TH, Lee JS, Oh SA, Twell D, Brooks JS, Fischer RL and Choi Y. Nucleoporin MOS7/Nup88 is required for mitosis in gametogenesis and seed development in Arabidopsis. Proceedings of the National Academy of Sciences of the USA, 8 December 2014. DOI: 10.1073/pnas.1421911112. [Open Access]

Working with Korean and American colleagues, David Twell from the University of Leicester was involved in this fascinating study of the mos7-5 mutant line of Arabidopsis thaliana. mos7-5  mutants experience ovule and pollen abortion in MOS7/mos7-5 heterozygous plants, and preglobular statge lethality in homozygous mos7-5 seeds. This study shoes that MOS7 is localized to the nuclear membrane but associated with the spindle apparatus during postmeiotic mitosis; in MOS7/mos7-5 heterozygotes, abortion is accompanied by a failure of spindle formation, cell fate specification and phragmoplast activity. These findings provide an important advance on current knowledge for plant scientists, but because the regulation of mitosis is highly conserved between plants and animals, it could be significant for animal researchers too.

• Landrein B, Refahi Y, Besnard F, Hervieux N, Mirabet V, Boudaoud A, Vernoux T and Hamant O. Meristem size contributes to the robustness of phyllotaxis in Arabidopsis. Journal of Experimental Botany, 11 December 2014. DOI: 10.1093/jxb/eru482. [Open Access]

Led by a French team, this J Ex Bot paper included work by Yassin Refahi of the Sainsbury Laboratory at Cambridge. Using Arabidopsis, the group studied the relationship between day length, the size of the shoot apical meristem, and the robustness of phyllotactic patterns. Among several patterns identified was the overall finding that robustness of the phyllotactic pattern is not optimal in the wild type plant, suggesting that it is regulated by day length; a new example of the link between plant patterning and its environment.

• Bielecka M, Watanabe M, Morcuende R, Scheible WR, Hawkesford MJ, Hesse H and Hoefgen R. Transcription and metabolome analysis of plant sulphate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulphur, nitrogen and phosphorus nutritional responses in Arabidopsis. Frontiers in Plant Science, 22 December 2014. DOI: 10.3389/fpls.2014.00805. [Open Access]

This Frontiers in Plant Science paper advances our basic understanding of the transcriptional effects of short-term sulphur starvation and re-supply in Arabidopsis thaliana; in turn this could have significance down the line for crop improvement. An international collaboration including Malcolm Hawkesford from Rothamsted Researchused a combination of transcriptomics and metabolomics analysis to not only identify the differential expression of 21 transcription factors in response to sulphur levels, but also to predict their downstream gene targets.

• Hu X, Kong X, Wang C, et al. Proteasome-mediated degradation of FRIGIDA modulates flowering time in Arabidopsis during vernalization. The Plant Cell, 23 December 2014. DOI: 10.1105/tpc.114.132738.

Gary Loake from the University of Edinburgh was involved in this Plant Cell paper, in which the mostly Chinese team identify that FRIGIDA – a scaffold protein involved in the recruitment of chromatin modifiers that cause epigenetic changes to regulate flowering genes – is degraded in a proteasome-mediated mechanism. The proteolysis mechanism is induced by WRKY34 and is dependent upon CULLIN3A.

• Taylor-Teeples M, Lin L, de Lucas M, et al. An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature, 24 December 2014. DOI: 10.1038/nature14099.

Led by the Brady lab at UC Davis, this Nature paper also involved the work of Cambridge-based theoretical biophysicist, Sebastian Ahnert. The paper presents a novel protein–DNA network model showing the interactions between Arabidopsis thaliana transcription factors and secondary cell wall metabolite genes. This model allowed the group to develop and validate new hypotheses about secondary cell wall gene regulation under abiotic stress.

• Foyer CH, Verrall SR and Hancock RD. Systematic analysis of phloem-feeding insect-induced transcriptional reprogramming in Arabidopsis highlights common features and reveals distinct responses to specialist and generalist insects. Journal of Experimental Botany, 24 December 2014.DOI: 10.1093/jxb/eru491.

In terms of immunity, plants may respond very differently to phloem-feeding insects (PFIs) compared to chewing insects. Here, Christine Foyer from the University of Leeds, and Susan Verrall and Robert Hancock from the James Hutton Institute, provide a comprehensive transcriptomic analysis of Arabidopis thaliana when infested withMyzus persicae, Bemisa tabaci or Brevicoryne brassicae. Though an increase in transcripts associated with WRKY transcription factor genes is a common feature of PFI infestation, there is significant divergeance in secondary metabolism depending on the species of PFI. Nevertheless, this research suggests that plants recognize and respond to perturbations in the cell wall during PFI infestation.