24th Sep 2013

Apologies that there was no Arabidopsis Research Round-up last week – we were really busy with our 4-day ‘Data Mining with iPlant’ workshop! However, it does mean that we have a bumper crop of UK Arabidopsis papers to share with you from the last couple of weeks, including research from the John Innes Centre, and the Universities of Cambridge, Oxford, Nottingham, York, Leeds and Manchester!


  • Marti M, Rosa S, Stancombe MA and Webb A. Cell- and stimulus-type-specific intracellular-free CA2+ signals in Arabidopsis thaliana. Plant Physiology, September 2013. DOI: 10.1104/pp.113.222901. [Open Access]

This paper, led by Alex Webb, Head of Cambridge University’s Circadian Signal Transduction group, stems from the group’s work on understanding how signal transduction pathways elicit characteristic responses to specific stimuli in different cell types. Here, using GAL4 transactivation of aequorin in enhancer trap lines of Arabidopsis thaliana, the authors tested the hypothesis that stimulus- and cell-specific responses to touch, cold and H2O2 can be encoded in the pattern of changes in intracellular-free ([Ca2+]i). 


  • Koprivova A, Giovannetti M, Baraniecka P, Lee B-R, Grondin C, Loudet O and Kopriva S. Natural variation in ATPS1 isoform of ATP sulfurylase contributes to control of sulfate levels in Arabidopsis. Plant Physiology, September 2013. DOI: 10.1104/pp.113.225748.

In previous work, this collaboration between the John Innes Centre, the Institut Jean-Pierre Bourgin in France, and Korean and Italian colleagues, revealed by quantitative trait loci (QTL) analysis that the regulation of sulphate content in Arabidopsis leaves was underlied by the APR2 isoform of adenosine 5’-phosphosulphate reductase. In this new paper, the authors show that a second QTL is underlied by the ATPS1 isoform of ATP sulphurylase. Therefore, sulphate content in Arabidopsis leaves is controlled by two genes involved in the sulphate assimilation pathway.


  • Czyzewicz N, Yue K, Beeckman T and De Smet I. Message in a bottle: small signaling peptide outputs during growth and development. Journal of Experimental Botany, 7 September 2013. DOI: 10.1093/jxb/ert283.

There are estimated to be over 1000 sequences in the Arabidopsis thaliana genome encoding small signalling peptides, yet only a few have been functionally characterised. This paper, which included authors from the University of Nottingham, provides a fascinating review of the molecular, biochemical and morphological effects that small signalling peptides potentially have in A. thaliana and other plant species.


  • Boutte Y, Jonsson K, McFarlane HE et al. ECHIDNA-mediated post-Golgi trafficking of auxin carrier for differential cell elongation. Proceedings of the National Academy of Sciences USA, 16 September 2013. DOI: 10.1073/pnas.1309057110.

This PNAS paper involved researchers from France, Canada, Austria and Sweden, as well as Ranjan Swarup from the University of Nottingham, and Errin Johnson, currently based at Oxford. After observing that the Arabidopsis mutant echidna (ech) exhibits defective cell elongation during apical hook development, it was deduced that ECH is required for the trans-Golgi network (TGN)-mediated trafficking of the auxin influx carrier AUX1, while not significantly affecting two other hook development proteins, LIKE-AUX1-3 or PIN-FORMED-3.


Daily and seasonal changes in temperature have a large effect on Arabidopsis growth and development, disease resistance pathways and the circadian clock, and yet even with such a wide range of normal ambient temperatures, temperature stress pathways are only activated in the most extreme conditions. This paper from the Sainsbury Laboratory’s Philip Wigge provides a review of research into the effects of temperature signals and developmental signalling.


  • Dodd AN, Dalchau N, Gardner MJ, Baek S-J and Webb AAR. The circadian clock has transient plasticity of period and is required for timing of nocturnal processes in Arabidopsis. New Phytologist, 17 September 2013. DOI: 10.1111/nph.12489.

GARNet committee member Antony Dodd, from the University of Bristol, and his co-authors Alex Webb, Seong-Jin Baek (University of Cambridge), Neil Dalchau (Microsoft Research, Cambridge), and Michael Gardner (Deakin University, Australia) collaborated on this New Phytologist paper, which explores how regulation of the Arabidopsis circadian clock affects the timing of cellular processes. By examining wild type and circadian period mutants under light : day cycles of varying lengths, it was found that Arabidopsis is able to best anticipate dawn, and the timing of nocturnal events, when the circadian period is resonant with that of the environment.


  • Lloyds JPB and Davies B. SMG1 is an ancient nonsense-mediated mRNA decay effector. The Plant Journal, September 2013. DOI: 10.1111/tpj.12329

In this offering from the University of Leeds, James Lloyd and Brendan Davies challenge the belief that SMG1, the core kinase involved in nonsense-mediated mRNA decay, is specific only to animals. Although not present in Arabidopsis thaliana or fungi, Lloyd and Davies present evidence that SMG1 is conserved in a range of eukaryotes, including all examined green plants with the exception of A. thaliana. Moreover, they conclude, the evolutionary loss of SMG1 occurred at an early stage in the fungal lineage, and more recently in A. thaliana.


  • Pantin F, Renaud J, Barbier F, et al. Developmental priming of stomatal sensitivity to abscisic acid by leaf microclimate. Current Biology, 12 September 2013. DOI: 10.1016/j.cub.2013.07.050.

While it has long been known that plant water loss and CO2 uptake are controlled via the stomata, and that the stomatal aperture is regulated via hormonal and environmental signals, it was not previously understood how stomatal sensitivity to the drought hormone abscisic acid (ABA) is acquired. In this Current Biology paper, the authors demonstrate that, in the rosette plant Arabidopsis, as young leaves in the centre of the rosette grow larger and therefore are exposed to an increasingly dry atmosphere, they acquire increased ABA sensitivity.


  • Xia T, Li N, Dumenil J, Li J, Kamenski A, Bevan MW, Gao F and Li Y. The ubiquitin receptor DA1 interacts with the E3 ubiquitin ligase DA2 to regulate seed and organ size in Arabidopsis. The Plant Cell, September 2013. DOI: 10.1105/tpc.113.115063.

Scientists from the John Innes Centre and the University of York worked alongside Chinese colleagues in this Nature Genetics paper, which builds on previous work investigating the genetic and molecular mechanisms of seed size regulation in Arabidopsis thaliana. Here, the researchers describe the findings that Arabidopsis plants with a DA2-1 mutation develop abnormally large seeds, while over-expression of this gene results in small seed size. The DA2 protein is shown to physically interact with DA1 (identified in the previous study) to regulate seed size.


  • Wightman R, Chomicki G, Kumar M, Carr P and Turner SR. SPIRAL2 determines plant microtubule organization by modulating microtubule severing. Current Biology, 19 September 2013. DOI: 10.1016/j.cub.2013.07.061.

Another Current Biology paper, this time involving the Turner lab at the University of Manchester. Turner and his team have identified that a protein called SPIRAL2 regulates the structure of the plant cell’s microtubule network, which in turn dictates the way in which cellulose is laid down in the cell wall, and ultimately affects the direction of cell elongation. You can read more about this study here.


  • Choi K, Zhao X, Kelly KA, et al. Arabidopsis meiotic crossover hot spots overlap with H2A.Z nucleosomes at gene promoters. Nature Genetics, 22 September 2013. DOI: 10.1038/ng.2766.

To investigate meiotic crossover hot spots in plants, scientists from the Universities of Cambridge, Oxford, Birmingham, Poznan and North Carolina used coalescent analysis of genetic variation in Arabidopsis thaliana. It was found that hot spots for crossing over were associated with active chromatin modifications, being asymmetric around promoters, and most frequent over CTT-repeat motifs and H2A.Z nucleosomes. It is proposed that ancestrally, gene chromatin designates hot spots within eukaryotic cells.