Weeding the Gems

It’s all about the Institutes in today’s UK Arabidopsis Research Round-up! New work this week comes from the John Innes Centre, the Sainsbury Laboratory, Rothamsted Research – and theEuropean Bioinformatics Institute, part of the European Molecular Biology Laboratory (EMBL-EBI) based in Cambridge, makes an appearance too.

• Wirthmueller L, Roth C, Fabro G, et al. Probing formation of cargo/importin-a transport complexes in plant cells using a pathogen effector. The Plant Journal, 17 November 2014. DOI: 10.1111/tpj.12691.

With collaborators in Germany, researchers from the John Innes Centre and the Sainsbury Laboratory in Norwich deduce that complexes between the adapter proteins importin-a, and the cargo proteins they recruit for active nuclear transport, are formed dependent upon cargo specificity, variation at the importin-a nuclear localisation sequence-binding sites, and tissue-specific expression levels of importin-a.

• Hsiao A-S, Haslam RP, Michaelson LV, Liao P, Chen Q-F, Sooriyaarachchi S, Mowbray SL, Napier JA, Tanner JA and Chye M-L. Arabidopsis cytosolic acyl-CoA-binding proteins ACBP4, ACBP5 and ACBP6 have overlapping but distinct roles in seed development. Bioscience Reports, 21 November 2014. DOI: 10.1042/BSR20140139.

This Bioscience Report included a number of researchers from Rothamsted Research, and explores the previously poorly understood roles of three cytosolic acyl-CoA-bding proteins (ACBPs). Microarray data revealed that all three are expressed in seeds, but further analysis in transgenic Arabidopsis revealed overlapping, but differing physiological effects on seeds.

• Cubillos FA, Stegle O, Grondin C, Canut M, Tisné S, Gy I and Loudet O. Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis. The Plant Cell, 26 November 2014. DOI: 10.1105/tpc.114.130310.

Led by a French team, this study also involved Oliver Stegle from EMBL-EBI in Cambridge. Using drought stress as an example of environmental variation, the aim here was to produce a detailed map of the ways in which cis- and trans-acting factors affect gene expression and responses to environmental conditions in Arabidopsis thaliana.

There are some really interesting new papers for you this week. We have two different protein interaction studies, one on microtubules involving scientists from Durham, and one on meiotic chromosome movement from Oxford Brookes and Birmingham. There’s also a report on ‘FANS’, a new technique used to study Arabidopsis embryos from Nottingham researchers, a US–UK collaborative project to develop Araport – a new online resource for plant scientists, and an exciting new rapid report from theJohn Innes Centre. Enjoy!

• Galva C, Kirik V, Lindeboom JJ, Kaloriti D, Rancour DM, Hussey PJ, Bednarek SY, Ehrhardt DW and Sedbrook JC. The microtubule plus-end tracking proteins SPR1 and EB1b interact to maintain polar cell elongation and directional organ growth in Arabidopsis. The Plant Cell, 18 November 2014.DOI: 10.1105/tpc.114.131482.

Researchers from the University of Durham were collaborators on this paper, which describes efforts to understand the interactions between the microtubule plus-end tracking proteins (+TIPS) EB1b and SPR1. Data suggest that SPR1 and EB1b have complex interactions as they load onto microtubule plus ends and direct polar cell expansion and organ growth in response to directional cues.

• Slane D, Kong J, Berendzen KW, et al. Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. Development, 19 November 2014. DOI: 10.1242/dev.116459.

Ive De Smet from the University of Nottingham worked with a German–Belgian team to put together this ‘Techniques and Resources’ paper in Development journal. Here, the team describes the use of fluorescence-activated nuclear sorting (FANS) to conduct cell type-specific transcriptome analysis in the early Arabidopsis embryo.

• Krishnakumar V, Hanlon MR, Contrino S, et al. Araport: the Arabidopsis Information Portal. Nucleic Acids Research, 20 November 2014. DOI: 10.1093/nar/gku1200.

This paper, involving scientists from the University of Cambridge, describes the Arabidopsis Information Portal (AIP, or Araport), a new online resource for plant biologists. At its core, it is the home for the Arabidopsis thaliana genome sequence and associated annotation, but it does much more than this. Users can access data curated from a variety of sources – including TAIR, GO, BAR, EBI, UniProt, PubMed and EPIC CoGe – as well as make use of feature-rich web applications to search, download, data-mine and genome-browse to their hearts content.

Araport also posts news, jobs and information relevant to the global Arabidopsis community – in fact, GARNet regularly posts information, including this Round-Up!https://www.araport.org/community/news.

• Varas J, Graumann K, Osman K, Pradillo M, Evans DE, Santos JL and Armstrong SJ. Absence of SUN1 and SUN2 proteins in Arabidopsis thaliana leads to a delay in meiotic progression and defects in synapsis and recombination. The Plant Journal, 21 November 2014. DOI: 10.1111/tpj.12730.

In eukaryotes, Sad1/UNC-84 (SUN)-domain proteins are part of a complex responsible for forming attachments between the chromosome telomeres and the components of the cytoplasm, which help the chromosomes to move appropriately during meiosis. This paper, involving scientists from Oxford Brookes University and the University of Birmingham, describes the discovery of homologous proteins – AtSUN1 and AtSUN2 – in Arabidopsis thaliana.

• Nützmann H-W and Osbourn A. Regulation of metabolic gene clusters in Arabidopsis thaliana. New Phytologist, 21 November 2014. DOI: 10.1111/nph.13189.

This rapid report comes from Hans-Wilhelm Nützmann and Anne Osbourn from the John Innes Centre. Comparing gene expression in chromatin mutants, they find that ARP6 and H2A.Z are involved in the regulatory process required for the normal expression of metabolic gene clusters in Arabidopsis. Specifically, these proteins are implicated in localized chromatin modifications that allow contiguous genes to be expressed in a coordinated way. This is a major finding that could open up new opportunities for the discovery and manipulation of specific metabolic pathways in plants!

Here’s your weekly round-up of the latest Arabidopsis research from the UK, this week including a mixed bag of studies from the Universities of Edinburgh, Oxford,Worcester, Warwick and Nottingham.

• Shi YZ, Zhu XF, Miller JG, Gregson T, Zheng SJ and Fry SC. Distinct catalytic capacities of two aluminium-repressed Arabidopsis thaliana xyloglucan endotransglucosylase/hydrolases, XTH15 and XTH31, heterologously produced in Pichia. Phytochemistry, 27 October 2014. DOI: 10.1016/j.phytochem.2014.09.020.

Janice Miller and Stephen Fry from the University of Edinburgh (with former lab member Tim Gregson now at the Lancaster Environment Centre) worked with Chinese collaborators on this study to further understand the roles of the xyloglucan endotransglucosylase/hydrolases (XTHs). They looked at two very different XTHs – XTH15 and XTH31 – to analyse their modes of action compared to the rest of this enzyme family.

• Berns MC, Nordström K, Cremer F, Tóth R, Hartke M, Simon S, Klasen JR, Bürstel I and Coupland G. Evening expression of Arabidopsis GIGANTEA is controlled by combinatorial interactions among evolutionarily conserved regulatory motifs. The Plant Cell, 27 October 2014. DOI: 10.1105/tpc.114.129437.

Though a former member of the Coupland lab at the Max Planck Institute for Plant Breeding Research, which led this study, Réka Tóth is now on staff at the University of Oxford. This paper explores the role of Arabidopsis GIGANTEA in its contributions to photoperiodic flowering, circadian clock control and photoreceptor signaling; in particular its transcription, which is regulated by light and the circadian clock. Three evolutionarily contrained motifs (CRMs) are identified within the GIGANTEA promoter which, combined with EVENING ELEMENTs and ABA RESPONSE ELEMENT LIKE motifs, contribute to diurnal transcription patterns.

• Andersson MX, Nilsson AK, Johansson ON, et al. Involvement of the electrophilic isothiocyanate sulforaphane in Arabidopsis local defense responses.Plant Physiology, 3 November 2014. DOI: 10.1104/pp.114.251892.

Working with Swedish and American partners, Gülin Boztas and Mahmut Tör from the University of Worcester were also collaborators on this paper. While the hypersenstive response of plants to pathogen effector molecules has long been documented, this research provides new detail on the nature of that response; specifically that sulforaphane – a compound triggering programmed cell death – is released by Arabidopsis thaliana when infected by Hyaloperonospora arabidopsidis.

• Piquerez SJ, Harvey SE, Beynon JL and Ntoukakis V. Improving crop disease resistance: lessons from research on Arabidopsis and tomato. Frontiers in Plant Science, 10 November 2014. DOI: 10.3389/fpls.2014.00671. [Open Access]

GARNet PI Jim Beynon is co-corresponding author for this helpful review. In it, Jim and colleagues from the University of Warwick describes how the use of Arabidopsis and tomato as model organisms for plant research have contributed knowledge and understanding of plant defense mechanisms, and how these have been and will continue to be applied to modern crop improvement programmes.

• Mellor N, Péret B, Porco S, Sairanen I, Ljung K, Bennett M and King J. Modelling of Arabidopsis LAX3 expression suggests auxin homeostasis. Journal of Theoretical Biology, 13 November 2014. DOI: 10.1016/j.jtbi.2014.11.003.

Former GARNet committee member Malcolm Bennett, together with colleagues from Nottingham, France and Sweden, present this paper in Journal of Theoretical Biology. They describe their development of a single-cell model of the auxin influx carrier LAX3 (which is mediated by the ARF7/19 IAA14 signalling module) to demonstrate that hysteresis and bistability may explain the experimentally observed ‘all-or-nothing’ LAX3 spatial expression pattern in cortical Arabidopsis root cells containing a gradient of auxin concentrations.