Weeding the Gems

Some interesting and diverse papers in the Arabidopsis Research Round-up this week – check out these offerings from the University of Warwick, University College London, John Innes Centre, University of Cambridge and University of Leicester.

• Szakonyi D, Van Landeghem S, Baerenfaller K, Baeyens L, Blomme J, Casanova-Saez R, De Bodt S, Esteve-Bruna D, Fiorani F, Gonzalez N, et al. The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining.Current Plant Biology, 7 February 2015. DOI: 10.1016/j.cpb.2014.12.002. [Open Access]

This Current Plant Biology paper was authored by a multi-national collaboration including Vicky Buchanan-Wollaston from the University of Warwick. It describes the development of KnownLeaf – a database connecting Arabidopsis leaf growth and development genotype to phenotype data mined from scientific literature. In addition, the network LeafNet has also been developed to graphically represent leaf phenotype relations in a molecular context.

• Schwarte S, Wegner F, Havenstein K, Groth D, Steup M and Tiedemann R. Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana. Plant Molecular Biology, 8 February 2015. DOI: 10.1007/s11103-015-0293-2.

This largely German team (though Fanny Wegner is also affiliated to University College London) is exploring genetic diversity in starch-related genes. Twenty-six different Arabidopsis accessions were sequenced, and sequence data on a further 80 accessions were accessed from public database, to determine differences in transcript levels of 25 genes. Diversity was found to vary greatly between accessions, with starch synthases and phosphorylases showing the highest levels of nucleotide diversity, and pyrophosphatases and branching enzymes being the most highly conserved.

• Shimotohno A, Sotta N, Sato T, De Ruvo M, Maree AFM, Grieneisen VA and Fujiwara T. Mathematical modelling and experimental validation of spatial distribution of boron in the root of Arabidopsis thaliana identify high boron accumulation in the tip and predict a distinct root tip uptake function.Plant & Cell Physiology, 9 February 2015. DOI: 10.1093/pcp/pcv016.

Scientists from the John Innes Centre worked with Italian and Japanese colleagues to produce this offering from Plant & Cell Physiology, in which mathematical modelling is used to predict boron distribution in the Arabidopsis root tip. The model predicted that the concentration of soluble boron would be higher in a region around the quiescent centre; this was then validated experimentally by determining root boron distribution via laser ablation-inductivity-coupled plasma mass spectrometry.

• Mateos JL, Madrigal P, Tsuda K, Rawat V, Richter R, Romera-Branchat M, Fornara F, Schneeberger K, Krajewski P and Coupland G. Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis. Genome Biology, 11 February 2015. DOI: 10.1186/s13059-015-0597-1. [Open Access]

Working with plant scientists from around the world, this study of the combined and individual effects of transcription factors related to the initiation of flowering in Arabidopsis also included Pedro Madrigal, who is affiliated to the Wellcome Trust Sanger Institute and the University of Cambridge. Looking at the MADS-box transcription factors FLC and SVP, which form a complex, it was found that there is substantial flexibility in the ways these proteins work together, accounting for variation and robustness in the regulation of plant flowering.

• Huang Z, Ölçer-Footitt H, Footitt S and Finch-Savage WE. Seed dormancy is a dynamic state: variable responses to pre-and post-shedding environmental signals in seeds of contrasting Arabidopsis ecotypes. Seed Science Research, 12 February 2015. DOI: 10.1017/S096025851500001X.

Led by Bill Finch-Savage, this team from the University of Warwick looked at how environmental signals during seed development affected the mother plant in a winter and summer ecotype of Arabidopsis thaliana. Results presented show that environmental signals both pre- and post-shedding determine the depth of physiological dormancy and therefore the germination response to the ambient environment.

• Schoft VK, Chumak N, Bindics J, Slusarz L, Twell D, Kohler C and Tamaru H. SYBR Green-activated sorting of Arabidopsis pollen nuclei based on different DNA/RNA content. Plant Reproduction, 13 February 2015. DOI: 10.1007/s00497-015-0258-2.

With colleagues from Austria, Switzerland and Sweden, David Twell from the University of Leicester was involved in the preparation of this manuscript, which describes a novel method to separate SYBR Green-stained plant sperm cells using fluorescence-activated cell sorting (FACS). This method will be of great help to anyone studying germ cell genetics and epigenetic reprogramming during sexual reproduction, and should be applicable to crop plants too.

Here’s your Arabidopsis Research Round-up for this week! Today we have plenty of Scottish delights, including papers from the University of Aberdeen, Dundee,Glasgow, Edinburgh and the James Hutton Institute. There is also new work from researchers at the University of Durham, Nottingham, Leeds and Oxford.

• Pokhilko A, Bou-Torrent J, Pulido P, Rodrígues-Concepción M and Ebenhöh O. Mathematical modelling of the diurnal regulation of the MEP pathway in Arabidopsis. New Phytologist, 16 January 2015. DOI: 10.1111/nph.13258.

Alexandra Pokhilko and Oliver Ebenhöh are two members of the University of Aberdeen’s Institute for Complex Systems and Mathematical Biology. Both contributed to this New Phytologist paper, in which they describe a mathematical model of the diurnal regulation of the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway. Data show that flux through the MEP pathway is accelerated in light conditions. It is also shown that pathway products regulate the abundance and activity of DXS (the first enzyme in the pathway, 1-deoxy-d-xylulose 5-phosphate synthase), which alters flux under varying conditions.

• McCormick AJ and Kruger NJ. Lack of fructose 2,6-bisphosphate compromises photosynthesis and growth in Arabidopsis in fluctuating environments. The Plant Journal, 20 January 2015. DOI: 10.1111/tpj.12765.

Here, Alistair McCormick from SynthSys at the University of Edinburgh and Nick Kruger from the University of Oxford describe their research on understanding the physiological role of the signal metabolite fructose 2,6-bisphosphate (Fru-2,6-P₂). Plants from three independent T-DNA mutant lines deficient in 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (F2KP) grow normally in constant environments, but have reduced growth and seed yield in fluctuating light and/or temperatures. McCormick and Kruger suggest that Fru-2,6-P₂ is involved in the modulation of photoassimilate partitioning, and that this is an important determinant of growth and fitness in natural environments.

• Calixto CPG, Waugh R and Brown JWS. Evolutionary relationships among barley and Arabidopsis core circadian clock and clock-associated genes.Journal of Molecular Evolution, 22 January 2015. DOI: 10.1007/s00239-015-9665-0.

Presented by scientists from the James Hutton Institute and the University of Dundee, this paper provides a comprehensive analysis of circadian clock and clock-associated genes in Arabidopsis thaliana, barley, and eight other plant species. It is proposed that the common ancestor of Arabidopsis and barley had two-thirds of the key clock components identified in Arabidopsis prior to the divergence of monocot and dicot groups.

• Verma V, Sivaraman J, Srivastava AK, Sadanandom A and Kumar PP. Destabilization of interaction between cytokinin signalling intermediates AHP1 and ARR4 modulates Arabidopsis development. New Phytologist, 30 January 2015. DOI: 10.1111/nph.13297.

Working with Singaporean colleagues, this New Phytologist paper involved the work of Ari Sadanandom from the University of Durham. The group describe their research on the previously poorly understood relationship between histidine phosphotransfer proteins (e.g. AHP1) and response regulator proteins (e.g. ARR4 ).

• Wilson MH, Holman TJ, Sørensen I, et al. Multi-omics analysis identifies genes mediating the extension of cell walls in the Arabidopsis thaliana root elongation zone. Frontiers in Cell & Developmental Biology, 2 February 2015. DOI: 10.3389/fcell.2015.00010. [Open Access]

Scientists from the University of Leeds and the University of Nottingham (including former GARNet committee member Malcolm Bennett) here describe a multi-omics approach to understanding the regulation of cell wall extension in Arabidopsis roots.

• Preuten T, Blackwood L, Christie JM and Fankhauser C. Lipid anchoring of Arabidopsis phototropin 1 to assess the functional significance of receptor internalization: should I stay or should I go? New Phytologist, 3 February 2015. DOI: 10.1111/nph.13299.

John Christie and student Lisa Blackwood from the University of Glasgow were involved in another New Phytologist paper, led by a Swiss team from Lausanne. The group is attempting to work out why, when irradiated, a fraction of the plasma membrane-associated phototropin 1 (phot1) blue light receptor is internalized into the cytoplasm. Transgenic plants expressing a lipidated version of phot1 permanently anchored to the plasma membrane were used to assess the effect of internalisation on receptor turnover, phototropism and other phot1-mediated effects, however, data suggest that internalisation is not linked to receptor turnover or desensitisation.