Arabidopsis Research Round-up

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Published on: November 26, 2014

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!


  • 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!

Arabidopsis Research Round-Up

Categories: Arabidopsis, Global, Round-up
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Published on: November 20, 2014

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.

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

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Published on: October 30, 2014

It’s all about Norwich Research Park this week as Jonathan Jones, Dan MacLean (The Sainsbury Laboratory) and Caroline Dean (John Innes Centre) take the lead on this week’s papers. As a bonus, they’re all open access!


  • Sohn KH, Segonzac C, Rallapalli G, Sarris PF, Woo JY, Williams SJ, Newman TE, Paek KH, Kobe B and Jones JDG. The nuclear immune receptor RPS4 is required for RRS1SLH1-dependent constitutive defense activation in Arabidopsis thaliana. PLOS Genetics, 23 October 2014. DOI: 10.1371/journal.pgen.1004655. [Open Access]

While it is known that plant nucleotide-binding leucine-rich repeat (NB-LRR) disease resistance proteins recognise specific ‘avirulent’ pathogen effectors and activate immune responses, the mechanisms by which they do this are not well understood. This article challenges previous hypotheses and advances our understanding of how immune receptors activate defense in Arabidopsis.


  • Younsi R and MacLean D. Using 2k + 2 bubble searches to find single nucleotide polymorphisms in k-mer graphs. Bioinformatics, 24 October 2014.DOI: 10.1093/bioinformatics/btu706. [Open Access]

In this Bioinformatics paper, Younsi and MacLean from The Sainsbury Laboratory describe how they used sequence data from 16 Arabidopsis thaliana ecotypes to test and validate an algorithm capable of accurately detecting single nucleotide polymorphisms from de Bruijn graphs.


  • Csorba T, Questa JI, Sun Q and Dean C. Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization.Proceedings of the National Academy of Sciences of the USA, 27 October 2014. DOI: 10.1073/pnas.1419030111. [Open Access]

In previous work, Caroline Dean and colleagues from the John Innes Centre showed that expression of FLOWERING LOCUS C (FLC) is regulated epigenetically by modifications to the histones: accumulation of H3K36me6 causes FLC to be expressed, thus applying a ‘brake’ to flowering, while accumulation of H2K27me3 removes the brake. However, this is not the whole story, and now the Dean lab has identified another component of the mechanism – antisense non-coding RNA transcripts calledCOOLAIR.

You can read more about this story in this press release: Plants require COOLAIR to flower in spring.

Arabidopsis Research Round-up

There are three new and exciting Arabidopsis papers from the UK research community this week. The University of Bath makes two appearances, once with a Genetics paper, and once in collaboration with the University of Oxford in Genome Research. Representing Norwich this week, Jonathan Jones heads up a Sainsbury Lab/John Innes Centre collaboration to investigate simultaneous changes in gene expression between Arabidopsis and a pathogen.


  • Gnan S, Priest A and Kover PX. The genetic basis of natural variation in seed size and seed number and their trade-off using Arabidopsis thalianaMAGIC lines. Genetics, 13 October 2014. DOI: 10.1534/genetics.114.170746.

This team from the University of Bath explored the natural variation in genes affecting seed size and seed number in Arabidopsis. Both seed size and seed number were found to be affected by non-overlapping QTLs, therefore suggesting these two traits can evolve independently of each other. Trade-off between these two traits in terms of fecundity and yield is dependent upon life history traits.


  • Jiang C, Mithani A, Belfield EJ, Mott R, Hurst LD and Harberd NP. Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations. Genome Research, 14 October 2014. DOI: 10.1101/gr.177659.114. [Open Access]

GARNet committee member Nick Harberd led on this Genome Research paper, along with co-corresponding author Caifu Jiang from China, and colleagues from theUniversity of Bath and Pakistan. In animal cells, repeated or prolonged presentation of a stressor often leads to increased mutations, which can increase the risk of cancer. Being sessile, plants do not get cancer in the same way that humans do, but do they acquire more mutations? Does stress – here the example of high soil salinity is used – drive the evolution of plants through increased phenotypic diversity? Yes, it seems so.


  • Asai S, Rallapalli G, Piquerez SJM, Caillaud M-C, Furzer OJ, Ishaque N, Wirthmueller L, Fabro G, Shirasu K and Jones JDG. Expression profiling during Arabidopsis/downy mildew interaction reveals a highly expressed effector that attenuates responses to salicylic acid. PLOS Pathogens, 16 October 2014. DOI: 10.1371/journal.ppat.1004443. [Open Access]

Led by Jonathan Jones, scientists from The Sainsbury Laboratory in Norwich worked with Lennart Wirthmueller from the John Innes Centre, and two Japanese collaborators, to produce this PLOS Genetics paper. Though gene expression patterns have been studied independently in the pathogen Hyaloperenospora arabidopsidis, and in its host Arabidopsis thaliana, they have not been compared simultaneously. Using a high-throughput cDNA tag sequencing method, this paper describes simultaneous changes in gene expression profiles in both host and pathogen.

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: October 16, 2014

Two new UK Arabidopsis papers for your reading pleasure this week: a Plant, Cell & Environment paper involving researchers from Hull and York, and a New Phytologistpaper proposing a new model of flowering time in annual plants, which involved Oxbridge scientists.


  • Atkinson LJ, Sherlock DJ and Atkin OK. Source of nitrogen associated with recovery of relative growth rate in Arabidopsis thaliana acclimated to sustained cold treatment. Plant, Cell & Environment, 8 October 2014. DOI: 10.1111/pce.12460.

Lindsay Atkinson from the University of Hull’s Geography Department worked with York biology research technician David Sherlock and an Australian plant scientist on this paper in Plant, Cell & Environment. The team looked at whether plants acclimated to the cold were able to recover their previous relative growth rate, and if so, whether soil N status played a part in the plant’s efficiency of doing this. It was found that both increased N use efficiency and increase in nitrogen content per se play a role in the recovery of carbon metabolism in the cold.


  • Guilbaud CSE, Dalchau N, Purves DW and Turnbull LA. Is ‘peak N’ key to understanding the timing of flowering is annual plants? New Phytologist, 8 October 2014. DOI: 10.1111/nph.13095. [Open Access]

A previously prevailing theory suggests that flowering time in annual plants has evolved over evolutionary time to maximize fitness over a particular season length. However, in this paper a team from OxfordCambridge and Zurich propose a new model whereby flowering time is instead underpinned by peak uptake of nitrogen. Using mathematical models, and comparing against data collected from Arabidopsis thaliana, the researchers predict that flowers will never emerge after ‘peak N time’, and suggest further correlations between flowering time, vegetative growth rates and response to increased N availability.

Also spotted: acknowledgements for behind-the-scenes contributions from GARNet committee members Antony Dodd (Bristol) and Nick Harberd (Oxford).

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: October 9, 2014

It’s a strong week for the institutes this week with appearances in the Round-up from Rothamsted ResearchThe Sainsbury Laboratory and the John Innes CentreThe Sainsbury Laboratory at the University of Cambridge also gets a mention, as does the University of Glasgow also gets a mention with Emily Larson’s contribution to a newPlant Method.


  • Hsiao A-S, Haslam RP, Michaelson LV, Liao P, Napier JA and Chye M-L. Gene expression in plant lipid metabolism in Arabidopsis seedlings. PLOS One, 29 September 2014. DOI: 10.1371/journal.pone.0107372. [Open Access]

This paper was a collaborative effort between scientists from Hong Kong, and Richard HaslamLouise Michaelson and Johnathan Napier from Rothamsted Research. Using quantitative, real-time PCR analysis, the researchers investigated whether target genes associated with acyl-lipid transfer, b-oxidation and triacylglycerol synthesis and hydrolysis were under diurnal control in early seedling growth. A number of differentially expressed genes between two and five-day old seedlings suggest that yes, lipid metabolism in Arabidopsis seedling development is under diurnal control.


  • Paganelli L, Caillaud M-C, Quentin M, Damiani I, Givetto B, Lecomte P, Karpov PA, Abad P, Chabouté M-E and Favery B. Three BUB1 and BUBR1/MAD3-related spindle assembly checkpoint proteins are required for accurate mitosis in Arabidopsis. New Phytologist, 29 September 2014. DOI: 10.1111/nph.13073.

Marie-Cecile Caillaud, affiliated to The Sainsbury Laboratory and the John Innes Centre, contributed to this New Phytologist paper investigating protein interactions during plant mitosis. Though the spindle assembly checkpoint (SAC) has been studied extensively in metazoans and yeast, little is known about the roles of microtubule-associated proteins in plants. This research demonstrates the key roles that the Arabidopsis SAC proteins BRK1, BUBR/MAD3 and their associates play in ensuring chromosomes do not segregate before they have properly formed kinetochore attachments.


  • Lee S, Lee H-J, Jung J-H and Park C-M. The Arabidopsis thaliana RNA-binding protein FCA regulates thermotolerance by modulating the detoxification of reactive oxygen species. New Phytologist, 30 September 2014. DOI: 10.1111/nph.13079.

Working with Korean colleagues, Jae-Hoon Jung from The Sainsbury Laboratory at Cambridge University contributed to this paper in which the role of the RNA-binding protein FCA is discussed in terms of heat stress. The researchers found that transgenic plants over-expressing the FCA gene were resistant to heat stress, while FCAdefective mutants were sensitive to it. It is proposed that FCA induces thermotolerance by triggering antioxidant accumulations under heat stress conditions.


  • Larson ER, Tierney ML, Tinaz B and Domozych DS. Using monoclonal antibodies to label living root hairs: a novel tool for studying cell wall microarchitecture and dynamics in Arabidopsis. Plant Methods, 2 October 2014. DOI: 10.1186/1746-4811-10-30. [Open Access]

Calling all root biologists! Here’s a new Plant Method for live cell labeling of roots with monoclonal antibodies that bind to specific cell wall polymers. Developed by researchers from the US and also involving Emily Larson from the University of Glasgow, the protocol allows for direct visualization of cell wall dynamics throughout development in stable transgenic plant lines.


  • Yang L, Zhao X, Paul M, Zhu H, Zu Y and Tang Z. Exogenous trehalose largely alleviates ionic unbalance, ROS burst and PCD occurrence induced by high salinity in Arabidopsis seedlings. Frontiers in Plant Science, 03 October 2014. DOI: 10.3389/fpls.2014.00570. [Open Access]

This Chinese-led paper also involved Matthew Paul from Rothamsted Research, who provided data analysis and helped to prepare the manuscript. Here, the scientists demonstrate the ability of trehalose to improve Arabidopsis’ resistance to salt stress by regulating the redox state of the plant, as well as programmed cell death and distribution of ions.

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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