Arabidopsis Research Roundup: July 20th

There is a bumper crop of publications in high quality journals in this weeks UK Arabidopsis Research Roundup, including manuscripts in PNAS, Nature Communications, PLoS Genetics , PloS One and Plant Physiology. Malcolm Bennett, Alex Webb and Anthony Hall lead a major collaborative effort that links the circadian clock with lateral root formation whilst Ottoline Leyser (SLCU) and Mike Bevan (JIC) participate in a similarly broad consortium in a study linking organ size and MAPK signaling. Liam Dolan’s group from Oxford looks at mechanisms of tip-growth across the plant kingdoms whilst elsewhere three members of faculty at the University of Birmingham are involved in two papers looking at the regulation of meiosis. Finally there are two US-led studies that include significant contributions from UK-based researchers, including Matthew Jones from the University of Essex.

 

Voß U, Wilson MH, Kenobi K, Gould PD, Robertson FC, Peer WA, Lucas M, Swarup K, Casimiro I, Holman TJ, Wells DM, Péret B, Goh T, Fukaki H, Hodgman TC, Laplaze L, Halliday KJ, Ljung K, Murphy AS, Hall AJ, Webb AA, Bennett MJ (2015) The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana Nature Communication 6:7641. http://dx.doi.org/10.1038/ncomms8641

Once again Malcolm Bennett (CPIB) leads a multi-Institute collaboration that includes Alex Webb (Cambridge) and current GARNet board member Anthony Hall (Liverpool). This is also an extremely international effect with groups from the UK, USA, Sweden, Japan, Spain and France. The science looks at lateral root stems cells and how the circadian clock is rephased during LR emergence. They show that the clock controls auxin levels and auxin-related genes. The conclusion is that the circadian clock acts to gate auxin signalling during LR development to facilitate organ emergence and adds to a growing portfolio of evidence that suggest the circadian clock might act in a cell autonomous manner. Anthony Hall, James Locke and Peter Gould currently have a grant that is looking at this phenomenon in Arabidopsis root cells.

 

Johnson KL, Ramm S, Kappel C, Ward S, Leyser O, Sakamoto T, Kurata T, Bevan MW, Lenhard M (2015) The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis PLoS One.10(7):e0131103. http://dx.doi.org/10.1371/journal.pone.0131103

Ottoline Leyser, Sally Ward (Sainsbury lab, Cambridge) and Mike Bevan (JIC) are the UK contributors to this joint UK-German-Japanese-Australian collaboration. This study follows a screen for plants with reduced organ size and introduces a novel allele of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5), named Tinkerbell (tink). This mutation reveals that IBR5 is a novel regulator of organ size by changing the growth rate in petals and leaves although this occurs independent of the previously characterised KLU pathway. The authors use microarray data to suggest an additional role for TINK/IBR5 during male gametophyte development. Ultimately they conclude that IBR5 might influence organ size through auxin and TCP growth regulatory pathways.

 

Tam TH, Catarino B, Dolan L (2015) Conserved regulatory mechanism controls the development of cells with rooting functions in land plants Proc Natl Acad Sci U S A. http://dx.doi.org/10.1073/pnas.1416324112

Liam Dolan’s lab at the University of Oxford is a world leader in the study of root hair development. Previously it has been shown the group XI basic helix-loop-helix (bHLH) transcription factor (LOTUS JAPONICUS ROOTHAIRLESS1-LIKE (LRL) regulates root hair growth in Arabidopsis, Lotus or rice. This study investigates the equivalent proteins in the moss Phycomitrella patens and show that they are involved in an auxin signaling pathway that promotes cell outgrowth albeit via a different set of signaling intermediates. Overall the authors show that a core auxin network that supports cellular ‘tip-growth’ exists throughout land plant lineages even though the specificity of this signaling has diverged over the course of the ~420million years that separates angiosperms and mosses.

 

Varas J, Sánchez-Morán E, Copenhaver GP, Santos JL, Pradillo M (2015) Analysis of the Relationships between DNA Double-Strand Breaks, Synaptonemal Complex and Crossovers Using the Atfas1-4 Mutant. PLoS Genet.11(7): e1005301. http://dx.doi.org/10.1371/journal.pgen.1005301

The work led by Monica Pradillo at the University of Madrid includes a contribution from Eugenio Sanchez-Moran from the University of Birmingham. This work focuses on the hetero-trimeric Chromatin Assembly Factor 1 (CAF-1), which is a histone chaperone that assembles acetylated histones H3/H4 onto newly synthesized DNA. In Arabidopsis the CAF1 complex is composed of the FAS1, FAS2 and MSI1 proteins. Atfas1 mutant plants are less fertility, have a higher number of double stranded breaks (DSB) and show a higher gene conversion frequency. The authors investigate how DSBs can influence meiotic recombination and synaptonemal complex (SC) formation by genetic analysis of Atfas1-containing double mutants. Ultimately their experiments provide new insights into the relationships between different recombinase proteins in Arabidopsis. Overall an increase in the number of DSBs does not translate to an increase in the number of crossovers (COs) but instead in a higher GC frequency. The authors provide different theories to explain this mechanism, including the possible existence of CO homeostasis in plants.

 

Lambing C, Osman K, Nuntasoontorn K, West A, Higgins JD, Copenhaver GP, Yang J, Armstrong SJ, Mechtler K, Roitinger E, Franklin FC (2015) Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers PLoS Genetics 11(7):e1005372 http://dx.doi.org/10.1371/journal.pgen.1005372

The University of Birmingham is the lead Instiution in this study that also investigates regulation of meiosis. The groups of Chris Franklin and Sue Armstrong collaborate with US and Austrian partners to study the organization of meiotic chromosomes during prophase I. Using structured illumination microscopy (SIM) they show that dynamic changes in chromosome axis is coincident with synaptonemal complex (SC) formation and depletion of the ASY1 protein, which requires the function of the PCH2 ATPase. Using a pch2 mutant the authors are able to tease apart different aspects of ‘crossover’ (CO) biology and that the pch2 defect occurs precisely during CO maturation, not during designation. In addition, CO distribution is also affected in some chromosome regions showing that failure to deplete ASY1 can result in downstream events that include disruption of CO patterning.

 

Jones MA, Hu W, Litthauer S, Lagarias JC, Harmer S (2015) A Constitutively Active Allele of Phytochrome B Maintains Circadian Robustness in the Absence of Light Plant Physiology. http://dx.doi.org/pp.00782.2015

Matthew Jones (University of Essex) is the primary author of this work that comes from a collaboration from his time in the lab of Stacey Harmer in UC Davis. Since 2012 Matthew has been a lecturer at the University of Essex where he continues with work of this nature. In this study they introduce a constitutively active allele of the PHYB photoreceptor that is able to phenoopy red-light input into the circadian clock. In these mutants the pace of the clock is insensitive to light-intensity and this response is dependant on its PHYB nuclear localisation. Finally they show that fine tuning of PHYB signalling requires PHYC and overall they conclude that nuclear phytocrome signalling is necessary for sustaining clock function under red light.

 

Chakravorty D, Gookin TE, Milner M, Yu Y, Assmann SM (2015) Extra-Large G proteins (XLGs) expand the repertoire of subunits in Arabidopsis heterotrimeric G protein signalling Plant Physiol. http://dx.doi.org/10.1104/pp.15.00251

Sally Assman from Penn State University leads this study that includes a contribution from Matthew Milner who now works at NIAB. The number of proposed G protein subunits is greatly reduced in diploid plant genomes yet this study shows that a family of Arabidopsis GPA-related proteins (XLG1-3) can increase the repertoire of potential G proteins interactions by interacting with beta and gamma subunits. The authors propose they have uncovered a new plant-specific paradigm in cell signaling.

Arabidopsis Research Round-up

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Published on: April 7, 2015

Your UK Arabidopsis Research Round-up this week includes a mixed bag of research, including a basic study that could help improve biofuel production, work on differential metabolism of sphingolipids in pollen, analysis of leaf movements of Arabidopsis plants grown in space, and more!

 

  • Lunn D, Ibbett R, Tucker GA and Lycett GW. Impact of altered cell wall composition on saccharification efficiency in stem tissue of Arabidopsis RABA GTPase-deficient knockout mutants. BioEnergy Research, 13 March 2015. DOI: 10.1007/s12155-015-9599-9. [Open Access]

In an effort to understand how plants can be manipulated for increased biofuel production, this team from the University of Nottingham is exploring a clade of Rab GTPase proteins called RABA. These proteins are involved in the control of trafficking to the cell wall, and their manipulation may help to overcome the cell wall’s inherent recalcitrance to digestion. The group first developed a saccharification process for Arabidopsis, then used this to demonstrate that rab4 mutant lines released more sugar, with or without pre-treatment, on saccharification.

 

  • Luttgeharm KD, Kimberlin AN, Cahoon RE, Cerny RL, Napier JA, Marckham JE and Cahoon EB. Sphingolipid metabolism is strikingly different between pollen and leaf in Arabidopsis as revealed by compositional and gene expression profiling. Phytochemistry, 17 March 2015. DOI: 10.1016/j.phytochem.2015.02.019.

It has been known for some time that sphingolipids are essential for make gametophytic development in Arabidopsis thaliana, but their composition and gene expression patterns have not been studied in pollen. This study, involving the work of Rothamsted’s Johnathan Napier, investigated pollen from wild type Col-0 and a long-chain base Δ4 desaturase mutant. Though we are as yet unsure why, the findings reveal that sphingolipid metabolism is very much different in Arabidopsis pollen compared to leaves.

 

  • Fisahn J, Klingele E and Barlow P. Lunar gravity affects leaf movement of Arabidopsis thaliana in the International Space Station. Planta, 21 March 2015. DOI: 10.1007/s00425-015-2280-x.

Peter Barlow from the University of Bristol is the last author on this study, which takes an interesting look at Arabidopsis plants in space! Using data collected on the International Space Station, Barlow – together with Joachim Fisahn from Germany and Emile Kingele from Switzerland – explored the relationship between oscillations of leaf movements and the lunisolar tide.

 

  • Grison MS, Brocard L, Fouillen L, et al. Specific membrane lipid composition is important for plasmodesmata function in Arabidopsis. The Plant Cell, 27 March 2015. DOI: 10.1105/tpc.114.135731.

Working with French and German collaborators, this paper involves the work of Yoselin Benitez-Alfonso from the University of Leeds. In order to understand more about the roles of the major constituents of the plasma membranes (PMs) of plasmodesmata (PD), the group isolated “native” PD membrane fractions and carried out comparative mass spectrometry analysis. They determined that lipids are laterally segregated along the PM at the PD cell-to-cell junction in Arabidopsis thaliana and that, compared to the bulk of the PM, PD membranes are enriched with sterols and sphingolipids with very long chain saturated fatty acids.

 

  • Massalski C, Bloch J, Zebisch M and Steinebrunner I. The biochemical properties of the Arabidopsis ecto-nucleoside triphosphate diphosphohydrolase AtAPY1 contradict a direct role in purinergic signalling. PLOS ONE, 30 March 2015. DOI: 10.1371/journal.pone.0115832. [Open Access]

Matthias Zebisch from the University of Oxford worked with German colleagues on this PLOS ONE paper, in which the previously assumed role of AtAPY1 is questioned. Previous work proposed that AtAPY1 was involved in growth and development, pollen germination and stress responses through a mechanism involving regulation of extracellular ATP signals. This work shows that ATP is not a substrate of AtAPY1, which is in fact more likely to function as a GDPase.

Arabidopsis Research Round-up

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Published on: February 23, 2015

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.

Arabidopsis Research Round-up

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Published on: February 9, 2015

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.

Arabidopsis Research Round-up

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Published on: January 21, 2015

Lots of new and interesting papers to catch up on from the New Year break this week. Fans of proteomics will be happy as we have three proteomics papers fromEdinburgh, Cambridge and Birmingham! The John Innes Centre and University of Warwick also have an update for us on how histone dynamics affect transcription;Norwich and Sainsbury Lab Cambridge-based researchers tell us more about ELF3; Rothamsted scientists reveal roles for CER2-LIKE proteins; and Donna Bond andProfessor Sir David Baulcombe reveal how virus-induced gene silencing can be used to study transposable elements.

 

  • Krahmer J, Hindle MM, Martin SF, Le Bihan T and Millar AJ. Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana. Methods in Enzymology, 26 December 2014. DOI: 10.1016/bs.mie.2014.10.022.

This useful review from former GARNet PI Andrew Millar and team discusses methods used in phosphoproteomics – the study of post-translational protein phosphorylations.

 

  • Rosa S, Ntoukakis V, Ohmido N, Pendle A, Abranches R and Shaw P. Cell differentiation and development in Arabidopsis are associated with changes in histone dynamics at the single cell level. The Plant Cell, 30 December 2014. DOI: 10.1105/tpc.114.133793. [Open Access]

In this really interesting Plant Cell paper, researchers including those from the John Innes Centre and the University of Warwick, provide evidence to suggest that stem cells have relatively mobile histones, whereas as cells differentiate, the histones become acetylated and thus more and more ‘fixed’ to the chromatin. This helps to explain how stem cells have the propensity to generate cells with different gene expression profiles, and why differentiated cells of a given type all express genes in a coordinated manner.

 

  • Box MS, Huang E, Domijan M, et al. ELF3 controls thermoresponsive growth in Arabidopsis. Current Biology, 30 December 2014. DOI: 10.1016/j.cub.2014.10.076.

Published just a little too late for Christmas (!), this paper comes from a collaboration between mostly Norwich Research Park-based scientists and those at the The Sainsbury Lab in Cambridge. The paper explores the role and function of the transcriptional regulator ELF3 (EARLY FLOWERING3). This gene encodes a protein that rapidly and reversibly binds to transcriptional targets in a temperature-dependent mechanism, thus regulating cell elongation in response to changes in ambient temperature.

 

  • Marondedze C, Wong A, Groen A, Serrano N, Jankovic B, Lilley K, Gehring C and Thomas L. Exploring the Arabidopsis proteome: influence of protein solubilization buffers on proteome coverage. International Journal of Molecular Science, 31 December 2014. DOI: 10.3390/ijms16010857. [Open Access]

Led by a Saudi Arabian team but involving the work of Arnoud Groen and Kathryn Lilley from the University of Cambridge, here’s another paper on the subject of methods in proteomics. In this work, using Arabidopsis thaliana as a model, the group assesses how variations in techniques and detergents used as the solubilisation buffer can affect the results of a proteomic study.

 

  • Roitinger E, Hofer M, Köcher T, Pichler P, Novatchkova M, Yang J, Schlögelhofer and Mechtler K. Quantitative phosphoproteomics of the ATM and ATR dependent DNA damage response in Arabidopsis thaliana. Molecular & Cellular Proteomics, 5 January 2015. DOI: 10.1074/mcp.M114.040352. [Open Access]

More proteomics! Jianhua Yang from the University of Birmingham is an author on this Austrian-led paper, in which a novel mass spec-based phosphoproteomics approach to study DNA damage repair in Arabidopsis thaliana is described. The approach allowed identification of nearly 11,000 proteins and 15,500 unique phosphopeptides, of which 134 ATM/ATR-dependent phosphopeptides were up-regulated, and 38 were down-regulated. Both known and novel targets of ATM/ATR were found.

 

  • Bond DM and Baulcombe DC. Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the USA, 5 January 2015. DOI: 10.1073/pnas.1413053112. [Open Access]

This PNAS offering is from Donna Bond and David Baulcombe from the University of Cambridge. Investigating the mechanisms by which RNA-directed DNA methylation (RdDM) is achieved to silence transposable elements, the authors wondered whether DNA methylation can be induced de novo at naïve sites, or whether it can only re-establish epigenetic silencing of active transposable elements. Using virus-induced epigenetic silencing (VIGS)-RdDM, it is demonstrated that epigenetic silencing can be achieved in a genetic mutant plant, mediated via virus-derived small RNAs. This has great potential for use as a tool in gene silencing studies.

 

  • Haslam T, Haslam RP, Thoraval D, et al. CER2-LIKE proteins have unique biochemical and physiological functions in very-long-chain fatty acid elongation. Plant Physiology, 14 January 2015. DOI: 10.1104/pp.114.253195. [Open Access]

This article, which involved the work of Richard Haslam, Frédéric Beaudoin and Johnathan Napier from Rothamsted Research, explores the functionality of the enzyme CER2 and its homologues; required for the elongation of fatty acids with chains longer than 28 carbons. Three CER2-LIKE proteins are shown to have unique effects on the substrate specificity of the same condensing enzyme (required to catalyse the first step of the fatty acid elongation process), and furthermore are important in cuticle formation and pollen coat function.

Arabidopsis Research Round-up

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Published on: January 14, 2015

Back after our Christmas/New Year break, here’s a catch-up of the some of the new Arabidopsis papers to be published before Christmas. Today’s round-up features new work by scientists from the Universities of York, Leicester, Cambridge, Edinburgh and Leeds, and from the institutes Rothamsted Research and the James Hutton Institute.

 

  • Delker C, Sonntag L, James GV, et al. The DET1-COP1-HY5 pathway constitutes a multipurpose signaling module regulating plant photomorphogenesis and thermomorphogenesis. Cell Reports, 18 December 2014. DOI: 10.1016/j.celrep.2014.11.043. [Open Access]

Though it has been known for some time that the transcription factor PHYTOCHROME INTERACTING FACTOR4 (PIF4) regulates the growth response of Arabidopsis thaliana to elevated ambient temperature by activating hormonal modules, it is not known how, exactly, temperature regulates PIF4 activity. Using a forward genetic approach, this group of German researchers – with the help of Seth J. Davis from the University of York – provide evidence to suggest that seedling growth in response to elevated temperature is transcriptionally regulated by the DE-ETIOLATED 1 (DET1)-CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1)-ELONGATED HYPOCOTYL 5 (HY5)-dependent photomorphogensis pathway.

 

  • Park GT, Frost JM, Park J-S, Kim TH, Lee JS, Oh SA, Twell D, Brooks JS, Fischer RL and Choi Y. Nucleoporin MOS7/Nup88 is required for mitosis in gametogenesis and seed development in Arabidopsis. Proceedings of the National Academy of Sciences of the USA, 8 December 2014. DOI: 10.1073/pnas.1421911112. [Open Access]

Working with Korean and American colleagues, David Twell from the University of Leicester was involved in this fascinating study of the mos7-5 mutant line of Arabidopsis thaliana. mos7-5  mutants experience ovule and pollen abortion in MOS7/mos7-5 heterozygous plants, and preglobular statge lethality in homozygous mos7-5 seeds. This study shoes that MOS7 is localized to the nuclear membrane but associated with the spindle apparatus during postmeiotic mitosis; in MOS7/mos7-5 heterozygotes, abortion is accompanied by a failure of spindle formation, cell fate specification and phragmoplast activity. These findings provide an important advance on current knowledge for plant scientists, but because the regulation of mitosis is highly conserved between plants and animals, it could be significant for animal researchers too.

 

  • Landrein B, Refahi Y, Besnard F, Hervieux N, Mirabet V, Boudaoud A, Vernoux T and Hamant O. Meristem size contributes to the robustness of phyllotaxis in Arabidopsis. Journal of Experimental Botany, 11 December 2014. DOI: 10.1093/jxb/eru482. [Open Access]

Led by a French team, this J Ex Bot paper included work by Yassin Refahi of the Sainsbury Laboratory at Cambridge. Using Arabidopsis, the group studied the relationship between day length, the size of the shoot apical meristem, and the robustness of phyllotactic patterns. Among several patterns identified was the overall finding that robustness of the phyllotactic pattern is not optimal in the wild type plant, suggesting that it is regulated by day length; a new example of the link between plant patterning and its environment.

 

  • Bielecka M, Watanabe M, Morcuende R, Scheible WR, Hawkesford MJ, Hesse H and Hoefgen R. Transcription and metabolome analysis of plant sulphate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulphur, nitrogen and phosphorus nutritional responses in Arabidopsis. Frontiers in Plant Science, 22 December 2014. DOI: 10.3389/fpls.2014.00805. [Open Access]

This Frontiers in Plant Science paper advances our basic understanding of the transcriptional effects of short-term sulphur starvation and re-supply in Arabidopsis thaliana; in turn this could have significance down the line for crop improvement. An international collaboration including Malcolm Hawkesford from Rothamsted Researchused a combination of transcriptomics and metabolomics analysis to not only identify the differential expression of 21 transcription factors in response to sulphur levels, but also to predict their downstream gene targets.

 

  • Hu X, Kong X, Wang C, et al. Proteasome-mediated degradation of FRIGIDA modulates flowering time in Arabidopsis during vernalization. The Plant Cell, 23 December 2014. DOI: 10.1105/tpc.114.132738.

Gary Loake from the University of Edinburgh was involved in this Plant Cell paper, in which the mostly Chinese team identify that FRIGIDA – a scaffold protein involved in the recruitment of chromatin modifiers that cause epigenetic changes to regulate flowering genes – is degraded in a proteasome-mediated mechanism. The proteolysis mechanism is induced by WRKY34 and is dependent upon CULLIN3A.

 

  • Taylor-Teeples M, Lin L, de Lucas M, et al. An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature, 24 December 2014. DOI: 10.1038/nature14099.

Led by the Brady lab at UC Davis, this Nature paper also involved the work of Cambridge-based theoretical biophysicist, Sebastian Ahnert. The paper presents a novel protein–DNA network model showing the interactions between Arabidopsis thaliana transcription factors and secondary cell wall metabolite genes. This model allowed the group to develop and validate new hypotheses about secondary cell wall gene regulation under abiotic stress.

 

  • Foyer CH, Verrall SR and Hancock RD. Systematic analysis of phloem-feeding insect-induced transcriptional reprogramming in Arabidopsis highlights common features and reveals distinct responses to specialist and generalist insects. Journal of Experimental Botany, 24 December 2014.DOI: 10.1093/jxb/eru491.

In terms of immunity, plants may respond very differently to phloem-feeding insects (PFIs) compared to chewing insects. Here, Christine Foyer from the University of Leeds, and Susan Verrall and Robert Hancock from the James Hutton Institute, provide a comprehensive transcriptomic analysis of Arabidopis thaliana when infested withMyzus persicae, Bemisa tabaci or Brevicoryne brassicae. Though an increase in transcripts associated with WRKY transcription factor genes is a common feature of PFI infestation, there is significant divergeance in secondary metabolism depending on the species of PFI. Nevertheless, this research suggests that plants recognize and respond to perturbations in the cell wall during PFI infestation.

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: December 10, 2014

Lots of new and interesting papers from the UK Arabidopsis research community this week! New papers have been published by scientists from Rothamsted Research and the Universities of Warwick, Leicester, Aberdeen and Manchester.

 

  • Brewer HC, Hawkins ND and Hammond-Kosack KE. Mutations in the Arabidopsis homoserine kinase gene DMR1 confer enhanced resistance toFusarium culmorum and F. graminearum. BMC Plant Biology, 29 November 2014. DOI: 10.1186/s12870-014-0317-0. [Open Access]

It was already known that mutations to the DMR1 gene affect Arabidopsis’ resistance to the biotrophic pathogens Hyaloperonospora arabidopsidis and Oidium neolycopersici. In this BMC Plant Biology paper, Nelly Brewer, Nathaniel Hawkins and Kim Hammond-Kosack from Rothamsted Research instead investigate the effects of these mutations on resistance to the ascomycete pathogens Fusarium culmorum and F. graminearum.

 

  • Footitt S, Müller K, Kermode AR and Finch-Savage WE. Seed dormancy cycling in Arabidopsis: Chromatin remodelling and regulation of DOG1 in response to seasonal environmental signals. The Plant Journal, 1 December 2014. DOI: 10.1111/tpj.12735.

Working with collaborators in Canada, Bill Finch-Savage and Steven Footitt from the University of Warwick’s Crop Centre present the findings of a study to investigate natural variation in the expression of genes involved in chromatin remodeling in two Arabidopsis ecotypes. Several key observations were made, including changes detected in the histone modifications H3K4me3 and H3K27me3 of the DOG1 gene during dormancy cycling, leading to the proposal that these histone marks serve as a thermal sensing mechanism during dormancy cycling in preparation for light repression of dormancy.

 

  • Hoedemaekers K, Derksen J, Hoogstrate SW, Wolters-Arts M, Oh S-A, Twell D, Mariani C and Rieu I. BURSTING POLLEN is required to organize the pollen germination plaque and pollen tube tip in Arabidopsis thaliana. New Phytologist, 1 December 2014. DOI: 10.1111/nph.13200.

David Twell from the University of Leicester was involved in this study with Dutch colleagues from Radboud University Nijmegen. The group explored the processes taking place during pollen hydration in Arabidopsis; the step in pollination before emergence of the pollen tube. Expression of the gene BURSTING POLLEN (BUP) was found to be essential for the correct organisation of a ‘germination plaque’ – an intine-like structure consisting of cellulose, callose and party de-esterified pectin – which provides passage for the emerging pollen tube.

 

  • Chao D-Y, Chen Y, Chen J, Shi S, Chen Z, Wang C, Danku JM, Zhao F-J and Salt DE. Genome-wide association mapping identified a new arsenate reductase enzyme critical for limiting arsenic accumulation in plants. PLOS Biology, 2 December 2014. DOI: 10.1371/journal.pbio.1002009. [Open Access]

In a collaboration with scientists based in China, Fang-Jie Zhao and Yi Chen (Rothamsted Research), and new GARNet Chair David Salt (University of Aberdeen) carried out genome-wide association mapping in Arabidopsis in order to learn more about natural variation in the genetic control of the reduction of arsenate to arsenite. Understanding the control of this chemical reaction, and the extent to which inorganic arsenic accumulates in crops such as rice, is key to reducing the carcinogenic risk to human health. Analysis revealed a new arsenate reductase enzyme, High Arsenic Content 1 (HAC1).

 

  • Dyson BC, Allwood JW, Feil R, Xu Y, Miller M, Bowsher CG, Goodacre R, Lunn JE and Johnson GN. Acclimation of metabolism to light in Arabidopsis thaliana – the glucose 6-phosphate/phosphate translocator GPT2 directs metabolic acclimation. Plant, Cell & Environment, 4 December 2014. DOI: 10.1111/pce.12495.

When transferred from low light conditions to high light conditions, mature plant leaves typically increase their photosynthetic capacity via expression of GPT2. In this study, researchers from Germany and the University of Manchester used wild type and GPT2 knockout plants to try and work out how and why this happens.

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: December 3, 2014

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.

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