26th May 2016

This weeks Arabidopsis Research Roundup includes six studies across a range of discplines. Firstly Alison Smith provides an excellent audio description of an investigation into the dynamics of night-time starch degradation.

Secondly three UK institutions (Durham, Exeter and Oxford Brookes) participate in a study of VAP27 membrane network proteins. Next a broad collaboration from CPIB in Nottingham then introduce a multi-scale model that helps describe Arabidopsis root development.

We also include two studies that involve collaborations with Korean researchers: Gary Loake is a contributor on a study that introduces plant RALF genes whilst Ian Henderson’s research group participates in a study into the function of the SWR1 complex in miRNA gene expression. Finally we highlight a new Plant Cell teaching tool put together by UK academics from Hull and Bristol.

Feike D, Seung D, Graf A, Bischof S, Ellick T, Coiro M, Soyk S, Eicke S, Mettler-Altmann T, Lu KJ, Trick M, Zeeman SC, Smith AM (2016) The starch granule-associated protein EARLY STARVATION1 (ESV1) is required for the control of starch degradation in Arabidopsis thaliana leaves Plant Cell Open Access

This UK and Swiss study is led by Alison Smith from the John Innes Centre and investigates starch degradation that occurs during nighttime. They developed a novel screen to identify an uncharacterized mutant called early starvation 1 (esv1) that more rapidly degraded starch so that it is exhausted earlier in the night. ESV1 and the related LESV1 proteins associated with starch granules within the chloroplast stroma. The authors propose that these proteins influence the organisation of the starch granule matrix, facilitating access for starch-degrading enzymes. In addition they also show that this function appears to be conserved throughout all starch-synthesizing organisms.

Professor Smith provides an audio description of this paper.

Wang P, Richardson C, Hawkins TJ, Sparkes I, Hawes C, Hussey PJ (2016) Plant VAP27 proteins: domain characterization, intracellular localization and role in plant development. New Phytol. 210(4):1311-1326

This cell biology-focused study is a collaboration between the Universities of Exeter, Durham and Oxford Brookes and investigates vesicle-associated membrane protein-associated proteins (VAPs), which form part of the network that links the plasma membrane and ER. The Arabidopsis genome contains 10 VAP homologues (VAP27-1 to -10) split into 3 clades. Members of clades I and II localise to both ER as well as to ER/PM contact sites (EPCSs) whilst clade II members are only found at the PM, all discovered through transient expression experiments in tobacco. Interestingly the localisation to the EPCSs is associated with the cytoskeleton but does not require the presence of that underlying structure. These proteins are expressed in most cell types and when their levels are altered, plants show pleiotropic phenotypes. Overall this study shows that VAP27 proteins are required for ER-cytoskeleton interactions that are critical for normal plant development.

Muraro D, Larrieu A, Lucas M, Chopard J, Byrne H, Godin C, King J (2016) A multi-scale model of the interplay between cell signalling and hormone transport in specifying the root meristem of Arabidopsis thaliana. J Theor Biol. S0022-5193(16)30070-4

This investigation was performed at CPIB in Nottingham in collaboration with the Virtual Plant Project in Montpellier and is led by John King. The authors have developed a multi-scale computational model that allows the study of signalling networks that occurs during Arabidopsis root growth. This model was experimentally tested to investigate how it is affected by hormonal changes during root growth. The model was able to identify two novel mutants that significantly alter root length through perturbations in meristem size. In general this study demonstrates the value of multi-scale modeling as part of the process of evaluating the function of the components that define the formation of the root meristem.

Sharma A, Hussain A, Mun BG, Imran QM, Falak N, Lee SU, Kim JY, Hong JK, Loake GJ, Ali A, Yun BW (2016) Comprehensive analysis of plant rapid alkalization factor (RALF) genes Plant Physiol Biochem. 106:82-90

This Korean-led study includes a contribution from Gary Loake from the University of Edinburgh and is the first comprehensive investigation of Rapid alkalization factor (RALF) proteins across plant species. These RALF proteins are thought to be important signalling molecules in plant defense and development. This study provides information on gene structure, subcellular locations, conserved motifs, protein structure, protein-ligand interactions and promoter analysis across Arabidopsis, rice, maize and soybean. The RALF genes are phylogenetically divided into 7 clades and their mRNA upregulation following nitrosative and oxidative stresses suggests that they are function in responding to changes in cellular redox status. Overall this manuscript provides a valuable resource to prime future research into the role of RALF genes.

Choi K, Kim J, Müller SY, Oh M, Underwood C, Henderson I, Lee I (2016) Regulation of microRNA-mediated developmental changes by the SWR1 chromatin remodeling complex in Arabidopsis thaliana. Plant Physiol.

GARNet committee member Ian Henderson (Cambridge) is a contributor on this study that is led by researchers in Seoul, South Korea. In the last ARR, Vinod Kumar described work that looked into the role of the SWR1 chromatin-remodeling complex and this study provides an insight into the role of this same SWR1 complex on microRNA (miRNA)-mediated transcriptional control. In SWR1 complex mutants (arp6, sef, and pie1), deep sequencing revealed that many miRNA types and their target mRNAs are misregulated in either direction. This further establishes the role of the SWR1 complex in the control of nucleosome occupancy, likely by mediating the exchange of H2A isoforms, for a range of genes involved in the fine-tuning of numerous developmental processes.

Hubbard, K, Dodd, A. (2016). Rhythms of Life: The Plant Circadian Clock. Teaching Tools in Plant Biology: Lecture Notes.

Katherine Hubbard and Anthony Dodd have produced a teaching resource focused on the Circadian Clock as part of the increasingly comprehensive Plant Cell Teaching Tools. Most academics are looking to save time and this resource will allow you to do this and provides excellent coverage of the topic.