Arabidopsis Research Roundup: January 29th

This weeks Arabidopsis Research Roundup features a paper from David Baulcombe and Joe Ecker that further deciphers mechanisms of RNA silencing and is kindly discussed by postdoc Mat Lewsey in a short audio description. Elsewhere there are three studies that include researchers from CPIB in Nottingham. Leah Band contributes to a study that links environment sensing, cell death and auxin signaling whilst Ive De Smet leads a study that finds new proteins involved in cell division. Malcolm Bennett and John King take a modeling approach to describe auxin signaling via the GH3 protein family. Finally Frank Menke leads a study that provides more detail into Pattern Recognition Receptor (PRR) mediated immune signaling and then Jim Dunwell participates in a paper that describes a new method of analyzing GWAS data.

Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker JR (2016) Mobile small RNAs regulate genome-wide DNA methylation. Proc Natl Acad Sci U S A. http://dx.doi.org/10.1073/pnas.1515072113 Open Access

Over the past few years RNA-mediated silencing has emerged a key mechanism for the control of gene expression. This study is a collaboration between the lab of Sir David Balcombe (Cambridge) and Joe Ecker at the SALK institute in California. Mat Lewsey, who is a British postdoc working with Professor Ecker, kindly provided a short audio description of the paper.

These groups have previously shown that sRNAs are highly mobile throughout the plant. This study shows that thousands of loci expressed in roots are dependent on mobile sRNAs generated from the shoot. They unpick the genetic basis of this response showing that it is largely dependent on the DOMAINS REARRANGED METHYLTRANSFERASES 1/2 (DRM1/DRM2) but not CHROMOMETHYLASE (CMT)2/3 DNA methyltransferases. They also show that mobile sRNAs are resposible for the silencing of TEs that are found in gene-rich regions, although this is not a physiologically important response in Arabidopsis, which contains a relatively small amount of transposon tissue. Interestingly they a show that sRNAs generated from different Arabidopsis ecotypes are able to move across graft junctions and can cause methylation in usually unmethylated regions.

PNASpicXuan W, Band LR, Kumpf RP, Van Damme D, Parizot B, De Rop G, Opdenacker D, Möller BK, Skorzinski N, Njo MF, De Rybel B, Audenaert D, Nowack MK, Vanneste S, Beeckman T (2016) Cyclic programmed cell death stimulates hormone signaling and root development in Arabidopsis. Science . 351(6271):384-7 http://dx.doi.org/10.1126/science.aad2776

This study is led by Tom Beeckman from Gent University and features Leah Band from CPIB in Nottingham. They reveal an exciting relationship between cell death in root cap cells and hormone signaling. The root cap is a protective tissue that overlies the Arabidopsis root tip and might be considered as an ‘inactive’ tissue. However this study shows that an auxin signal released from root cap cells sets the spacing of lateral organs along the root. As root cap cells move up the root they undergo programmed cell death, which in turn releases a pulse of auxin and establishes a pattern of lateral root formation. The authors suggest that this relationship might integrate external soil conditions so that lateral roots will develop to optimise uptake of water and nutrients. It is well known that an auxin signal simulates lateral root formation but this study provides an explanation as to the genesis of this signal and its integration with external environmental factors.

Yue K, Sandal P, Williams EL, Murphy E, Stes E, Nikonorova N, Ramakrishna P, Czyzewicz N, Montero-Morales L, Kumpf R, Lin Z, van de Cotte B, Iqbal M, Van Bel M, Van De Slijke E, Meyer MR, Gadeyne A, Zipfel C, De Jaeger G, Van Montagu M, Van Damme D, Gevaert K, Rao AG, Beeckman T, De Smet I (2016) PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root. Proc Natl Acad Sci U S A. http://dx.doi.org/10.1073/pnas.1525122113

This broad collaboration between US-UK and Belgian researchers is led by Tom Beeckman and Ive De Smet, who works at CPIB in Nottingham. In addition it includes a contribution from Cyril Zipfel at TSL. This study aimed to identify proteins that interact with the plasma membrane-localized receptor kinase ARABIDOPSIS CRINKLY 4 (ACR4), which plays a role in the control of cell division in the Arabidopsis root. They find that PROTEIN PHOSPHATASE 2A-3 (PP2A-3), a catalytic subunit of PP2A holoenzymes interacts with ACR4 and has a previous uncharacterised role in control of formative cell divisions. The authors show that the biochemical network that links ACR4 and PP2A-3 is regulated by phosphorylation.

Mellor N, Bennett MJ, King JR (2016) GH3-Mediated Auxin Conjugation Can Result in Either Transient or Oscillatory Transcriptional Auxin Responses. Bull Math Biol. http://dx.doi.org/10.1007/s11538-015-0137-x

This paper led by Professor Malcolm Bennett and John King from CPIB is an example of the growing number of multi-disciplinary interactions between biologists and mathematicians. Here a model is developed that interrogates auxin signaling and homeostasis through the GH3 gene family. This includes a parameter that considers auxin transport via the LAX3 influx protein, which, together with the activity of GH3 proteins can facilitate a positive feedback loop that allows cells to response to excess auxin.

Mithoe SC, Ludwig C, Pel MJ, Cucinotta M, Casartelli A, Mbengue M, Sklenar J, Derbyshire P, Robatzek S, Pieterse CM, Aebersold R, Menke FL (2016) Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase. EMBO Rep. http://dx.doi.org/10.15252/embr.201540806 Open Access

Frank Menke (TSL, Norwich) is the leader on this collaboration between UK, Dutch and Swiss researchers that investigates innate immunity signaling mediated via Pattern Recognition Receptors (PRRs). Tight control of this signalling is very important to prevent spurious activation of the immune response. These authors find that the differentially phosphorylated MKKK7 can interact with the FLS2 protein, which is key in the perception of bacterial flagellin. In turn MKKK7 attenuates the signalling of a downstream MAPK that contributes to defence-related gene expression. Therefore the show that the FLS2-MKKK7 signaling module is critical for control of innate immunity.

Wang SB, Feng JY, Ren WL, Huang B, Zhou L, Wen YJ, Zhang J, Dunwell JM, Xu S, Zhang YM (2016) Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology. Sci Rep. http://dx.doi.org/10.1038/srep19444 Open Access

Professor Jim Dunwell (Reading) is a UK contributor to this largely Chinese publication that introduces a new method to analysis GWAS-style data. They propose an analysis based on random-SNP-effect MLM (RMLM) and a multi-locus RMLM (MRMLM) and using stimulations show that their new method can be powerful than conventional types of analysis. To test the method they analysed flowering time traits in Arabidopsis and detected more genes that were involved in the process.

For those interested in different-types of GWAS analysis, Professor David Salt introduced another new method during a recent ARR.

Arabidopsis Research Roundup: January 8th

For the inaugural Arabidopsis Research Roundup of 2016 we feature the final publications of UK researchers from 2015. Martin Howard kindly provides an audio description of a paper that looks at a fundamental aspect of transcriptional regulation, through the lense of the FLC gene, whilst his co-author Caroline Dean on that paper is an author on another manuscript that investigates RNA stability in the same FLC locus. Katja Graumann leads a paper that looks into gene expression at the periphery of the nucleus whilst Ian Colbeck looks at the effect of silver nanoparticles on plant growth. Ari Sadanandom is the UK lead of a study that investigates of SUMOylation and Ian Fricker looks at the role of a cytochrome P450 on the defence response. Finally Liam Dolan is involved in a comparative analysis of the genes involved in tip growth in the cells of plants and moss.

Wu Z, Ietswaart R, Liu F, Yang H, Howard M, Dean C (2015) Quantitative regulation of FLC via coordinated transcriptional initiation and elongation. Proc Natl Acad Sci U S A. http://dx.doi.org/10.1073/pnas.1518369112 Open Access

Martin Howard and Caroline Dean lead this study that comes out of the John Innes Centre and is the result of the same collaboration that featured in an ARR earlier in 2015. In this study they investigate the mechanisms that control the quantitative regulation of gene expression by focusing on the complex regulation of the FLOWERING LOCUS C (FLC). FLC expression is controlled by a chromatin silencing mechanism involving alternative polyadenylation of antisense transcripts. However they surprisingly show that the amount of RNA Polymerase II occupancy at FLC does not coincide very well with levels of FLC transcription. They used modeling to predict that there is a tight coordination between transcriptional initiation and elongation, which was validated by detailed measurements of the levels of FLC intronic RNA. Variation within initiation and elongation rates were significantly different and was coincident with changes in H3K36me3 and H3K4me2 levels in the FLC gene. The authors propose that chromatin state can influence transcriptional initiation and elongation rates and may be a general mechanism for quantitative gene regulation in a chromatin context.

Martin Howard kindly provides an audio description of this paper and wider aspects of transcriptional regulation.

Wu Z, Zhu D, Lin X, Miao J, Gu L, Deng X, Yang Q, Sun K, Zhu D, Cao X, Tsuge T, Dean C, Aoyama T, Gu H, Qu LJ (2015) RNA-binding proteins At RZ-1B and At RZ-1C play a critical role in regulation of pre-mRNA splicing and gene expression during Arabidopsis development Plant Cell http://dx.doi.org/10.1105/tpc.15.00949

This study investigates a set of previously mysterious RNA-binding proteins and is led by Chinese researchers with a UK contribution from Caroline Dean (JIC). They look at two Arabidopsis proteins, AtRZ-1B and At RZ-1C that have RNA-binding domains and are localised to the mysterious nuclear speckles. In addition these proteins physically interact with a range of serine/arginine-rich (SR) proteins and disrupting this binding causes a range of growth phenotypes that are similar to that observed in At rz-1b/At rz-1c double mutants. These include delayed seed germination, reduced stature, and serrated leaves and on the cellular level this is accompanied by defective splicing and global changes in gene expression. Interestingly AtRz-1C directly effects the expression of the floral repressor FLC, which links this work with other research in the Dean lab. Overall this highlights the important role of At RZ-1B/1C in RNA splicing and the link to many developmental phenotypes.

Smith S, Galinha C, Desset S, Tolmie F, Evans D, Tatout C, Graumann K (2015) Marker gene tethering by nucleoporins affects gene expression in plants. Nucleus. http://dx.doi.org/10.1080/19491034.2015.1126028

Expression of Seh1-LacI-YFP at the nuclear periphery. From http://dx.doi.org/10.1080/19491034.2015.1126028
Expression of Seh1-LacI-YFP at the nuclear periphery. From http://dx.doi.org/10.1080/19491034.2015.1126028

Katja Graumann and David Evans (Oxford Brookes) are the lead academics on this collaboration with the lab of Christophe Tatout from Clermont Ferrand in France. They are attempting to answer a long standing question in the field of the biology of the nucleus; whether genes that are located close to nuclear pore complexes have increased gene expression. They used the Lac Operator/ Lac Repressor (LacI-LacO) system to assess changes in gene expression when a loci is tethered to the NPC by attaching the LacI domain to the nucleoporins Seh1 or NUP50a. The Seh1 clones localised to the nuclear periphery and showed higher RNA and protein expression of Luc. When this interaction at the periphery was distributed, the higher levels of expression were abolished. The authors therefore show that association with the nuclear periphery is important for the regulation of gene expression.

Sosan A, Svistunenko D, Straltsova D, Tsiurkina K, Smolich I, Lawson T, Subramaniam S, Golovko V, Anderson D, Sokolik A, Colbeck I, Demidchik V (2015) Engineered silver nanoparticles are sensed at the plasma membrane and dramatically modify physiology of Arabidopsis thaliana plants. Plant Journal http://dx.doi.org/10.1111/tpj.13105

Ian Colbeck (Essex) is the UK lead on this study that involves a collaboration between researchers in New Zealand, Belarus and Russia and focuses on the effect of silver nanoparticles (Ag NPs) on the growth of Arabidopsis seedlings. This type of nanoparticle is used for many difference applications so worries exist about the safety of their use. This study looks at the effect of Ag NPs on Arabidopsis root elongation and leaf expansion, both of which were inhibited at over [300mg/l] Ag NPs. In addition there were reductions of photosynthetic efficiency and accumulation of silver in plant tissues. They also showed that these particles altered the influx and efflux of metal ions whilst, although they were unable to catalyse hydroxyl radical generation, they did directly oxidise the major plant antioxidant, L-ascorbic acid. Overall the authors show that silver nanoparticles induce classical stress signalling responses but also illicit specific detrimental effects at the plasma membrane. At the whole plant level this study provides a worrying example for the role of Ag NPs on whole plant growth, even though the concentrations used in food preparation might be lower.

Crozet P, Margalha L, Butowt R, Fernandes N, Elias A, Orosa B, Tomanov K, Teige M, Bachmair A, Sadanandom A, Baena-González E (2015) SUMOylation represses SnRK1 signaling in Arabidopsis. Plant Journal http://dx.doi.org/10.1111/tpj.13096

This pan-European study features researchers from Portugal, Austria and the UK’s Durham University, led by Ari Sadanandom. They investigate the role of the SnRK1 protein kinase, which is a key enzyme for modulating the plant stress response. This paper adds detail to the cellular mechanisms that regulate SnRK1 and they show that SnRK1 is SUMOylated by the SIZ1 E3 SUMO ligase. SnRK1 is ubiquitinated and degraded in a SIZ1-dependent manner that is lacking in siz1 mutants. Interestingly only active SnRK1 is degraded as the inactive SnRK1 protein is stable but can be easily degraded upon SUMOylation. Finally they show that SnRK1 is involved in a negative feedback loop wherein it controls its own SUMOylation and degradation that, in wildtype cells, prevents a potentially detrimental stress response.

Fuchs R, Kopischke M, Klapprodt C, Hause G, Meyer AJ, Schwarzländer M, Fricker MD, Lipka V (2015) Immobilized subpopulations of leaf epidermal mitochondria mediate PEN2-dependent pathogen entry control in Arabidopsis. Plant Cell http://dx.doi.org/10.1105/tpc.15.00887

Mark Fricker (Oxford) is the UK research lead on this study that investigates the role of the atypical myrosinase PEN2 in the response to pathogen attack. PEN2 is targeted to both peroxisomes and mitochondria and can also form homo-oligomer complexes. PEN2 localised to mitochondria are immobilized following fungal invasion and this accompanies mitochondrial arrest. The substrate for PEN2 is produced by the cytochrome P450 monooxygenase CYP81F2, which is localized to the ER and moves toward immobilized mitochondria. The critical function of PEN2 in that organelle was confirmed by the result that showed exclusive mitochondria targeting could rescue pen2 mutant phenotypes. The authors show by live-cell imaging that arrested mitochondria in domains of plant-microbe interaction exhibit a pathogen-induced redox imbalance that may lead to production of intracellular signals.

Ortiz-Ramírez C, Hernandez-Coronado M, Thamm A, Catarino B, Wang M, Dolan L, Feijó JA, Becker JD (2015) A transcriptome atlas of Physcomitrella patens provides insights into the evolution and development of land plants. Mol Plant. http://dx.doi.org/10.1016/j.molp.2015.12.002

Liam Dolan (Oxford) is an author on this study that is led from Portugal and is an investigation of the transcriptome of the model moss Physcomitrella patens throughout its life cycle. They also compare transcriptomes from P.patens and Arabidopsis, allowing the authors to identify transcription factors that are expressed in tip growing cells. Interestingly they identified differences in expression patterns that might account for the differences between tip growth in moss and the Arabidopsis root hairs, an area that is the expertise of the Dolan lab.

Arabidopsis Research Roundup: December 18th

The final Arabidopsis Research Roundup of 2015 contains a bumper crop of papers that again highlights the diversity of research occuring in UK plant science. Justin Goodrich from the University of Edinburgh kindly provides an audio description of work that identifies a novel role for a member of a transposon gene family. Elsewhere are studies about a specific aspect of the biochemistry of crytochromes as well as confirmation of a role for DNA gyrases in Arabidopsis. Paul Dupree (Cambridge) leads a study into the mechanism of ascorbic acid production while Heather Knight is the UK representative in a study about cell wall composition. We also present an investigation into the mechanism and subsequent expression changes that occur following infection with different isolates of the Turnip Mosaic Potyvirus. Finally are two short studies from Ive de Smet (Nottingham) and Matt Jones (Essex).

Liang SC, Hartwig B, Perera P, Mora-García S, de Leau E, Thornton H, de Alves FL, Rapsilber J, Yang S, James GV, Schneeberger K, Finnegan EJ, Turck F, Goodrich J (2015) Kicking against the PRCs – A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2. PLoS Genet. 11 e1005660. http://dx.doi.org/10.1371/journal.pgen.1005660 Open Access

Justin Goodrich (Edinburgh) is the lead of this collaborative study between UK, German and Australian researchers that investigates the role of the evolutionarily conserved Polycomb group (PcG) and trithorax group (trxG) genes during plant development. These homeotic genes influence gene expression by causing epigenetic chromatin changes, usually in the form of histone methylation. Previously the ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN1 (ALP1) gene was found to act as a genetic suppressor the Arabidopsis PcG gene, LIKE HETEROCHROMATIN PROTEIN1 (LHP1). In this study ALP1 is shown to genetically interact with members of these two gene families and its activity is necessary for the activation of several floral homeotic genes. Surprisingly the ALP1 gene is shown to encode for a transposase of the PIF/Harbinger class, which is conserved throughout land plants. The authors suspect that the transposase activity has been lost in the angiosperm lineage, where the gene obtained a novel function. Interestingly ALP1 can interact with the core PrC complex, which most notably participates in H3K27me3 methylation and therefore appears to act, along with other proteins such as EMBRYONIC FLOWER 1 (EMF1), as a plant-specific accessory component that controls histone modification. The authors speculate that this novel function might have arisen as a “means for the cognate transposon to evade host surveillance or for the host to exploit features of the transposition machinery beneficial for epigenetic regulation of gene activity”. Over the coming years it will be interesting to discover if other transposon-encoded genes share novel functions and this study represents an important lesson for researchers not to ignore transposon sequences as ‘junk’ DNA that they might feel can clutter up their analysis!

Justin Goodrich kindly provides an audio summary of this paper:

van Wilderen LJ, Silkstone G, Mason M, van Thor JJ, Wilson MT (2015) Kinetic studies on the oxidation of semiquinone and hydroquinone forms of Arabidopsis cryptochrome by molecular oxygen FEBS Open Bio. 5:885-892 http://dx.doi.org/10.1016/j.fob.2015.10.007 Open Access

This study is a collaborative effort between researchers from Imperial College and the University of Essex, led by emeritus biochemistry Professor Michael Wilson and is an in vitro analysis of the oxidation of the Arabidopsis cryptochrome (CRY) photoreceptor in the presence and absence of an external electron donor. They show that a more complex model than previously thought is required to explain the mechanism by which the CRY-associated flavin molecule is oxidised. The authors propose that the final steps in this reaction require cooperative interaction between partners in a CRY homodimer or between separate CRY molecules.

Evans-Roberts KM, Mitchenall LA, Wall MK, Leroux J, Mylne JS, Maxwell A (2015) DNA Gyrase is the Target for the Quinolone Drug Ciprofloxacin in Arabidopsis thaliana. J Biol Chem. http://dx.doi.org/10.1074/jbc.M115.689554 Open Access

Antony Maxwell from the Biological Chemistry department from the John Innes Centre is the UK academic lead on this UK-Australian study. This group has previously shown that Arabidopsis contains three proteins thought to function as DNA Gyrases (AtGYRA, ATGYRB1, ATGYRB2) although they could not provide direct evidence that are were involved in DNA supercoiling. This study moves the work on by identifying mutant plants that are resistant to the drug ciprofloxacin and contain a point mutation in AtGYRA. Furthermore ATGYRA heterologously expressed in insect cells has supercoiling activity. Therefore the authors unequivocally show that plants encode an organellar-targeted DNA gyrase that, like bacterial gyrases, is a  target for ciprofloxacin. This work has important consequences for our understanding of plant physiology and in the future development of novel herbicides.

Sawake S, Tajima N, Mortimer JC, Lao J, Ishikawa T, Yu X, Yamanashi Y, Yoshimi Y, Kawai-Yamada M, Dupree P, Tsumuraya Y, Kotake T (2015) KONJAC1 and 2 Are Key Factors for GDP-Mannose Generation and Affect l-Ascorbic Acid and Glucomannan Biosynthesis in Arabidopsis The Plant Cell http://dx.doi.org/10.1105/tpc.15.00379

Paul Dupree (Cambridge) is the British lead on the UK-Japanese collaboration that investigates the role of the GDP-mannose pyrophosphorylase (GMPP), VITAMIN C DEFECTIVE1 (VTC1) enzyme in catalysis of the rate-limiting step in the production of ascorbic acid (AsA). They identify two novel pyrophosphorylase-like proteins, KONJAC1 (KJC1) and KJC2 that stimulate VTC1. Mutant analysis showed that these proteins are necessary for normal growth that coincides with control of AsA production via stimulating GMPP activity. Yeast 2 Hybrid  analysis is indicative of a direct interactin between KJC and VTC1 proteins. In future, it will be interesting to investigate the role of these proteins in plants that are more relevant to human consumption of AsA.

Sorek N, Szemenyei H, Sorek H, Landers A, Knight H, Bauer S, Wemmer DE, Somerville CR (2015) Identification of MEDIATOR16 as the Arabidopsis COBRA suppressor MONGOOSE1. PNAS http://dx.doi.org/10.1073/pnas.1521675112

Heather Knight (Durham) is the sole UK representative on this manuscript that is led by the lab of Chris Somerville from the University of California. In this work the authors identified suppressors of the Arabidopsis cobra mutant, which have defects in cellulose formation. The appropriately named mongoose (mon1) mutant partially restored cellulose levels and also restored the esterification ratio of pectin to wild-type levels. MON1 was cloned to the MEDIATOR16 (MED16)/ SENSITIVE TO FREEZING6 (SFR6) locus and single mon1 mutants are resistant to cellulose biosynthesis inhibitors. Concomitantly, transcriptome analysis demonstrated that a set of ‘cell wall’ genes are misregulated in mon1/med16/sfr6, including two encoding pectin methylesterase inhibitors. Overall the authors suggest that cellulose biosynthesis is closely linked to esterification levels of pectin and offer a number of possible explanations for this functional relationship.

Sánchez F, Manrique P, Mansilla C, Lunello P, Wang X, Rodrigo G, López-González S, Jenner C, González-Melendi P, Elena SF, Walsh J, Ponz F (2015) Viral Strain-Specific Differential Alterations in Arabidopsis Developmental Patterns Mol Plant Microbe Interact. http://dx.doi.org/10.1094/MPMI-05-15-0111-R

The UK contributor to this Spanish-led study is Carol Jenner, who at the time was a research fellow at the University of Warwick. This study highlights the morphological changes that occur in Arabidopsis plants infected by different isolates of Turnip mosaic virus (TuMW). The UK1 and JPN1 versions of TuMW were shown to have highest levels of sequence divergence in the P3 cistron and following the generation and use of viral chimeras, it is this region that was identified as the major viral determinant of plant developmental changes. However when the P3 gene was constitutively expressed in Arabidopsis it did not cause any development effects, which highlights the importance of performing infection studies in a whole-plant context. Latterly the authors performed transcriptomic and interactomic analysis, showing that infection with the most severe UK1 strain primarily causes changes, perhaps unsurprisingly, in genes involved in transport and in the stress response.

Czyzewicz N, De Smet I (2015) The Arabidopsis thaliana CLAVATA3/EMBRYO-SURROUNDING REGION 26 (CLE26) peptide is able to alter root architecture of Solanum lycopersicum and Brassica napus. Plant Signal Behav http://dx.doi.org/10.1080/15592324.2015.1118598

This work was performed in the lab of Ive De Smet, who is a BBSRC research fellow at the University of Nottingham. In this short communication they show that overexpression of the Arabidopsis AtCLE26 peptide is able to induce architectural change in the agriculturally important crops, Brassica napus and Solanum lycopersicum. Having previously shown that AtCLE26 is similarly active in Arabidopsis, Brachypodium and Triticum, these experiments further demonstrate that small peptide signaling plays an important role in root development across plant lineages.

Litthauer S1, Battle MW1, Jones MA (2015) Phototropins do not alter accumulation of evening-phased circadian transcripts under blue light. Plant Signal Behav. http://dx.doi.org/10.1080/15592324.2015.1126029

Matt Jones (Essex) leads this accompanying study to the more substantial project previously published in Plant Journal. This manuscript reports that phototropin photoreceptors are not involved in the nuclear accumulation of evening-phased circadian transcripts. In addition they show that even in phototropin mutants, the rhythms of nuclear clock transcript accumulation are maintained under fluctuating light regimes.

Great British Success in ERA-CAPS

The ERA-CAPS funding call was a major EU initiative that was focused on plant sciences. Recently the second set of successfully funded projects were announced, even though the funding levels have not been confirmed. Amongst these twelve successful bids, eight feature UK plant scientists (including four from the JIC). These successful projects are highlighted below:
logo-era-caps
Project Name: DesignStarch, Designing starch: harnessing carbohydrate polymer synthesis in plants

The UK representative Rob Field is a biochemist based at the John Innes Centre. The objective of this project is to ‘gain a profound understanding of the regulation and control of the biophysical and biochemical processes involved in the formation of the complex polymeric structure that is the starch granule’, which will involve in vitro analysis of the enzymology of starch formation with the ultimate aim of transferring their findings back into plants.

EfectaWheat: An Effector- and Genomics-Assisted Pipeline for Necrotrophic Pathogen Resistance Breeding in Wheat

James Cockram (NIAB) is the project leader on this grant that proposes to investigate the economically important wheat leaf spot group (LSG) of necrotrophic pathogens. The project will use a range of techniques such as high-density genotyping, pathogen re-sequencing and advanced virulence diagnosis to deliver a genomics- and effector-based pipeline for the genetic dissection of LSG host-pathogen interactions across Europe.

EVOREPRO: Evolution of Sexual Reproduction in Plants

Both David Twell (Leicester) and Jose Gutierrez-Marcos (Warwick) are included in this seven-group consortium that aims to investigate the origin of the mechanisms that predate double fertilization in plants. The project will take a comparative gene expression-based approach to investigate gametogenesis across Marchantia, Physcomitrella, Amborella, Arabidopsis and a range of crop species. The expected findings will allow the identification of specific mechanisms that are targeted by environmental stresses during sexual reproduction in crops and will assist in the selection of stress-resistant cultivars.

INTREPID: Investigating Triticeae Epigenomes for Domestication

GARNet advisory board member Anthony Hall (Liverpool) leads this group which includes long time collaborator Mike Bevan (JIC). This project will look at variations in the epigenome across eight diverse wheat lines with the aim of determined how epigenetic marks are re-set and stabilized during the formation of new wheat hybrids and how they might influence gene expression.

MAQBAT: Mechanistic Analysis of Quantitative Disease Resistance in Brassicas by Associative Transcriptomics

John Innes Centre scientist Chris Ridout leads this six PI consortium that will look at pathogen resistance in Brassica napus, where diseases are a major limiting factor in growth success. Almost 200 lines of B.napus will be screened against a range of specific and general pathogens in the aim of discovering important disease resistance loci. One proposed aspect of the work will look at the role of glucosinolates in both disease resistace and seed quality. The project also includes UK B.napus expert Bruce Fitt (Hertfordshore).

PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

Karen Halliday (Edinburgh) leads this three-PI group that will investigate the link between phytochrome signaling and resource allocation in both Arabidopsis and B.rapa. One aim of the project will be to build models that predict the dual action of phytochrome and photosynthesis on resource management and biomass production.

RegulaTomE: Regulating Tomato quality through Expression

Cathie Martin (JIB) leads this largest successful consortium of 8 labs that aim to link transcriptional regulation of metabolic pathways with tomato quality. Loci contributing to abiotic stress tolerance will also be identified toward the combined goals of obtaining more nutritious, stable and sustainable crops. The project will lead to regulatory gene identification (an important advance in terms of fundamental understanding), and provide new tools for metabolic engineering of fruit quality.

SOURSI: Simultaneous manipulation of source and sink metabolism for improved crop yield

Lee Sweetlove (Oxford) leads this group that aims to understand the linkages between source and sink tissues in the assimilation of carbon and nitrogen. The project claims to implement a metabolic engineering strategy of unprecedented scale in plants exploiting the new technique of biolistic combinatorial co-transformation.

Plant research goes EPIC

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Comments: 2 Comments
Published on: October 25, 2013
A DNA molecule that is methylated on both strands on the center cytosine. DNA methylation plays an important role for epigenetic gene regulation in development

Early last week I attended the EPIC (Epigenomics of Plants International Consortium) one day symposium on Mapping the Epigenomes of Plants and Animals at the John Innes Centre. Epigenomics is an exciting branch of biology, with active, cutting-edge research ongoing in plants, animals and microbes alike.

The EPIC Planning Committee aim to crack and control the ‘second code’ of biology (they overview the field and their plans in a 2012 open access Plant Cell paper). A major step toward this ambitious goal is the CoGe Epigenomics Browser, a web-based comparative genomics system that provides access to 20,000 genomes from 15,000 organisms, and users can take advantage of over 30 tools for the analysis, comparison, and visualisation of genomic data from the scale of whole genomes to individual nucleotides. The creators of CoGe, Eric Lyons and Brian Gregory, have worked with iPlant to build a secure and versatile user-data management system, and like iPlant CoGe has a Wiki with extensive tutorials and support pages.

The biggest session at the Symposium was on DNA methylation. Gavin Kelsey, Mary Gehring and Rob Martienssen, who is speaking at GARNet 2014, spoke about the mechanisms of parental imprinting and their impact, which can continue for generations – and I have to say, at this point I wondered how many lab conflicts and frustration-inducing experimental problems are caused by our current lack of understanding about epigenomic effects!

Julie Ahringer and Doris Wagner spoke about their research digging down into the physical properties of epigenomic features and the mechanisms of chromatin regulation. Oliver Stegle and Claude Becker are both working on understanding how genome, transcriptome, epigenome and environment interact to produce a phenotype. Xiaofeng Cao is applying this approach to controlling agricultural traits in rice.

There were a few non-plant science speakers, including Eric Miska who presented his research on piRNAs, which he has shown are vital for maintaining fertility over generations and are also involved in sperm production. Interestingly Blake Meyers has identified phasiRNAs in maize, small RNAs that are involved in sperm production and he suggested they may have convergently evolved to fulfil a similar role as piRNAs.

Image credit: Christoph Boch via Wikimedia Commons. “Details: The picture shows the crystal structure of a short DNA helix with sequence “accgcCGgcgcc”, which is methylated on both strands at the center cytosine.”

 

Pollen epigenetics

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Published on: October 11, 2012

Biology learned in school and as a first year undergraduate is easily forgotten if it is not relevant to your current research. Today’s highlighted article required me to refresh my memory of plant germ line development, so I included my basic research here.

Highlighted article: Joseph P. Calarco, Filipe Borges, Mark T.A. Donoghue, Frédéric Van Ex, Pauline E. Jullien, Telma Lopes, Rui Gardner, Frédéric Berger, José A. Feijó, Jörg D. Becker and Robert A. Martienssen (2012) Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA. Cell 151:194-205.

Germline biosynthesis: A pollen mother cell undergoes meiosis to make haploid microspores, which unevenly split into a larger vegetative cell and a small generative cell. The generative cell splits symmetrically into two – these are the plant ‘sperm’ cells. Each pollen grain contains two sperm cells, which are surrounded by a vegetative cell. The vegetative nucleus contains completely decondensed heterochromatin, but DNA in generative nuclei is tightly condensed.

The female gametophyte develops from a megaspore mother cell. Both the megaspore mother cell and pollen mother cell are specified from somatic cells in developing flowers.

GFP staining in the two sperm nuclei and vegetative nucleus in the vegetative cell.

Bisulphite sequencing is a DNA sequencing method which determines methylation pattern by treating DNA with sodium bisulphite before sequencing it using a conventional DNA sequencing method. Bisulphite induces the conversion of unmethylated cytosines to uracil, but this is not a perfect technique so unmethylated DNA may be recorded as methylated. Additionally, bisulphite treatment can cause DNA degradation. Sequencing the DNA of interest multiple times, in the case of Calarco et al., anywhere from 7 to 17 times, improves reliability of the method. There is a brief overview of DNA methylation in this post. (more…)

Summary for non-specialists: Science paper on epigenetics

Comments: 1 Comment
Published on: June 21, 2012

One of the things I wanted to do on this blog was to highlight recent plant science journal articles, and when I found back-to-back papers on Arabidopsis research in Science I thought they would be a good place to start.

But when I started to read, I realised the obvious – my cell wall biochemistry background will be no help at all when trying to understand other areas of plant science research. But I still want to highlight high-impact articles like this on the blog, so I decided to have a Summary for non-specialists series. Please feel free to comment if I’ve got something horribly wrong, and of course if anyone would like to provide a Summary by a Specialist that would be great!

Highlighted article

Qian et al., June 2012. A Histone Acetyltransferase Regulates Active DNA Demethylation in Arabidopsis. Science 336: 1445-1447

Prior to this research, little was known about the regulation of DNA methylation, or how DNA and histone modifications were related. Here, Qian et al. define a process in which histone modification is an essential part of DNA methylation. This research opens the door to deeper understanding of the regulation and mechanism of DNA modification, and possible manipulation of epigenetic mechanisms.

(more…)

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