Arabidopsis Research Roundup

Categories: Arabidopsis, GARNet, Global, UKPSF
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Published on: May 14, 2015

Your UK Arabidopsis Research Round-up this week contains studies that aim to define a network of lateral root formation, elucidate modes of calcium signaling, determine mechanisms of epigenetic memory and also the influence of exon-edge evolution in determining the extent of selective pressure.

Liu J, Whalley HJ, Knight MR. Combining modelling and experimental approaches to explain how calcium signatures are decoded by calmodulin-binding transcription activators (CAMTAs) to produce specific gene expression responses. New Phytologist. 2015 Apr 27. doi: 10.1111/nph.13428.

Marc Knight’s group at the University of Durham have attempted to decode the complex mechanism by which calcium controls changes in gene expression. They have developed an experimentally parameterized model that reveals calcium signals are amplified by the binding of calmodulin and calmodulin-binding transcription activators (CAMTAs). Interestingly, the model suggests that gene expression change in response to a calcium signature is defined by the previous history of that signal.

Lavenus J, Goh T, Guyomarc’h S, Hill K, Lucas M, Voß U, Kenobi K, Wilson MH, Farcot E, Hagen G, Guilfoyle TJ, Fukaki H, Laplaze L, Bennett MJ. Inference of the Arabidopsis Lateral Root Gene Regulatory Network Suggests a Bifurcation Mechanism That Defines Primordia Flanking and Central Zones. Plant Cell. 2015 May 5. pii: tpc.114.132993.

The biology of lateral root (LR) formation has been well researched over the past decade although a full robust regulatory network that controls this process has remained elusive. CPIB at the University of Nottingham, together with European collaborators have used a series of transcriptomic datasets to develop a time-delay correlation algorithm (TDCor) to infer the gene expression network (GRN) controlling LR initiation. The GRNs associated with AUXIN RESPONSE FACTOR7 and ARF5 predict a mutual inhibition and a patterning mechanism that controls flanking and central zone specification of LR primordia.

Berry S, Hartley M, Olsson TS, Dean C, Howard M Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance. Elife. 2015 May 8;4. doi: 10.7554/eLife.07205.

Epigenetic ‘memory’ allows plant cells to retain a memory of past environmental or development events. One key regulator of this process is the Polycomb Repressive Complex2 (PRC2). Histone proteins that are modified by the PRC2 can be inherited through cell division. The groups of Mark Howard and Caroline Dean at the JIC investigated whether this inheritance directs long term memory in a cis or trans manner. Two copies of the Arabidopsis FLC gene, which is a target for PRC2, were monitored in the same plant. Interestingly they reveal that one FLC copy could be silenced but the other remained active, providing evidence that epigenetic memory, at least of FLC, is stored in trans but not in cis.

Bush SJ, Kover PX, Urrutia AO. Lineage-specific sequence evolution and exon edge conservation partially explain the relationship of evolutionary rate and expression level in A. thaliana. Mol Ecol. 2015 Apr 30. doi: 10.1111/mec.13221.

Alongside genetic changes in response to phenotypic adaptation, the elements of a genes DNA structure can also affect evolutionary rates. In Arabidopsis the ‘edge’ of exons, which flank introns and contain splice enhancers are known to have a higher degree of evolutionary conservation compared to coding regions. Dr Arazi Urrutia and collaborators from the University of Bath assessed selective pressure (measured by dN/dS) and showed that exon edge conservation partially explains the relationship between rates of protein evolution and expression level. Without any consideration of exon-edge conservation can potentially increase the number of genes designated as being under adaptive selection. Therefore the authors conclude that exon-edge conversation should be an important consideration when assessing overall dN/dS ratios.

Arabidopsis Research Round-up

Just one new paper to share with you this week!


  • Binkert M, Kozma-Bognar L, Terecskei K, de Veylder L, Nagy F and Ulm R. UV-B-responsive association of the Arabidopsis bZIP transcription factor ELONGATED HYPOCOTYL5 with target genes, including its own promoter. The Plant Cell, 28 October 2014. DOI: 10.1105/tpc.114.130716. [Open Access]

Though he has a joint appointment at the Hungarian Academy of Sciences, Ferenc Nagy is also SULSA Chair of Cell Biology at the University of Edinburgh. Working with Swiss, Hungarian and Belgian colleagues, this paper describes research to understand the transcription factors regulating plants’ protective responses to UV-B. It is shown that, in Arabidopsis, binding of the bZIP transcription factor ELONGATED HYPOCOTYL5 (HY5) to the promoters of UV-B-responsive genes is enhanced by UV-B independently of the UV-B photoreceptor UV RESISTANCE LOCUS8 (UVR8).

Arabidopsis Research Round-up

Apologies there hasn’t been an Arabidopsis Research Round-up for a few weeks, I’ve been on annual leave getting married! Here’s a catch up of the newest Arabidopsis research papers from the UK community over the last month, including one from a GARNet committee member, and one from a former GARNet PI.


  • Schatlowski N, Wolff P, Santos-González J, Schoft V, Siretskiy A, Scott R, Tamaru H and Köhler C. Hypomethylated pollen bypasses the interploidy hybridization barrier in Arabidopsis. The Plant Cell, 1 September 2014. DOI: 10.1105/tpc.114.130120.

Rod Scott from the University of Bath was involved on this Plant Cell paper. With Swedish, Austrian and Swiss colleagues, it was identified that, through the suppression of expressed imprinted genes, hypomethylation can occur in pollen that alters the epigenetic control of the ‘interploidy hybridization barrier’. Based on these findings, the researchers here present a novel method for the generation of viable triploid Arabidopsis plants, which could have significant impact for plant breeding.


  • Chew YH, Wenden B, Flis A, et alMultiscale digital Arabidopsis predicts individual organ and whole-organism growth. Proceedings of the National Academy of Sciences of the United States of America, 2 September 2014. DOI: 10.1073/pnas.1410238111. [Open Access]

You can tell former GARNet PI Andrew Millar from the University of Edinburgh led this paper – it’s all about linking the Arabidopsis research community! Quantitative modeling is undeniably an important tool in modern predictive biology, but understanding plants at a molecular level doesn’t necessarily help us to ‘bridge the genotype to phenotype gap’ and predict how molecular changes affect the whole organism, or vice versa. Linking together several models across multiple scales, Millar and colleagues here present a validated multiscale model of Arabidopsis rosette growth, enabling prediction of how genetic regulation and biochemical dynamics may affect organ and whole-plant growth.


  • Chao D-Y, Baraniecka P, Danku J, Koprivova A, Lahner B, Luo H, Yakubova E, Dilkes BP, Kopriva S and Salt DE. Variation in sulfur and selenium accumulation is controlled by naturally occurring isoforms of the key sulfur assimilation enzyme APR2 across the Arabidopsis thaliana species range. Plant Physiology, 18 September 2014. DOI: 10.1104/pp.114.247825. [Open Access]

GARNet committee member and ‘Mr Ionomics’ David Salt, from the University of Aberdeen, was the lead on this new paper in Plant Physiology, working with colleagues from the John Innes Centre, Purdue, Cologne and Shanghai. This study used linkage mapping in synthetic F2 populations to investigate the natural variation in total leaf sulphur and selenium levels across a wide range of Arabidopsis thaliana accessions. Though the significance is not yet understood, it was found that the catalytic capacity of APR2, an enzyme important in allowing the accumulation of sulphur and selenium in leaves, varied by four orders of magnitude.


  • Fujikura U, Elsaesser L, Breuninger H, Sanchez-Rodriguez C, Ivakov A, Laux T, Findlay K, Persson S and Lenhard M. Atkinesin-13A modulates cell wall synthesis and cell expansion in Arabidopsis thaliana via the THESEUS1 pathway. PLOS Genetics, 18 September 2014. DOI: 10.1104/pp.114.247825. [Open Access]

For plants to grow they need to not only proliferate their cells, but expand the size of the cells too. Since plant cells are encased in a rigid cell wall, the cell wall structure must be temporarily loosened to allow expansion and the deposition of additional cell wall materials. Working with a German-led team and colleagues in Australia, Kim Findlay from the John Innes Centre contributed to this paper, which discusses the roles of AtKINESIN-13-A and its homologue AtKINESIN-13B in limiting cell expansion and size in Arabidopsis thaliana.


  • Johansson H, Jones HJ, Foreman J, Hemsted JR, Stewart K, Grima R and Halliday KJ. Arabidopsis cell expansion is controlled by a photothermal switch.Nature Communications, 26 September 2014. DOI: 10.1038/ncomms5848. [Open Access]

A second appearance in today’s Round-up for the University of Edinburgh’s Karen Halliday, and another paper discussing cell expansion. This time, this Nature Communications paper explores the finding that phytochrome B-controlled growth in the Arabidopsis hypocotyl is strictly regulated by temperature: a shift in temperature induces a dramatic reversal of response from inhibition to promotion of hypocotyl elongation by light.

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