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.

Arabidopsis Research Roundup: Oct 28th

This latest Arabidopsis Research Roundup is rather GARNet-focused as members of the current Advisory Board lead three of the featured papers. Firstly we present a study into mechanisms that control meiotic recombination, which also includes a short audio-description from the lead author Dr Ian Henderson. Secondly we introduce a paper that identifies the function of a novel gene in the control of male fertility and thirdly, a study of a translation control-factor that is involved in regulation of cell size and ovule development. In addition we introduce some highly collaborative work that looks into the role of SUMO proteases in SA signaling. Finally there is a methods paper that presents a new protocol for measurement of cellulose content in Arabidopsis stems.

Yelina N, Lambing C, Hardcastle T, Zhao X, Santos B, Henderson I (2015) DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis Genes & Dev. 29: 2183-2202 http://dx.doi.org/10.1101/gad.270876.115

GARNet advisory board member Ian Henderson leads this study that assesses how methylation state influences the chromosomal regions that undergo meiotic recombination. It was previously known that highly-methylated regions, such as centromeres, do not often undergo recombination. This work naturally extends that knowledge by using RNA-directed DNA methylation to show that methylation of local euchromatic regions also have reduced recombination levels. Equally they show that global reductions in CG methylation, such as in met1 mutants, cause wide-scale alterations in recombination remodeling. Use of recombination mutants shows that these changes are due to the redistribution of interfering crossovers. Overall they confirm that DNA methylation is critical in establishing domains of meiotic recombination.

In this short audio file, Dr Henderson explains the main features of this paper.

Visscher AM, Belfield EJ, Vlad D, Irani N, Moore I, Harberd NP (2015) Overexpressing the Multiple-Stress Responsive Gene At1g74450 Reduces Plant Height and Male Fertility in Arabidopsis thaliana. PLoS One.;10(10):e0140368. http://dx.doi.org/10.1371/journal.pone.0140368

Ian Moore and Nick Harberd (Oxford), who is also on the GARNet Advisory Board,  present this investigation of five unknown genes that had been previously identified from global expression studies as playing a role in multiple stress-responses. These are somewhat unimaginatively identified by their ‘At’ numbers and even though they are each responsive to multiple stresses, mutants with a T-DNA insertion in any of these genes have no change in phenotype compared to wildtype plants. In contrast, overexpression of At1g74450, but no other of the tested genes, resulted in stunted growth and reduced male fertility. As the stress-response is often manifested by alterations in male gametophyte development, this work introduces the function of a gene that may provide an important link between multiple environmental factors, fertility and plant growth. In future the authors hope to provide further insight into the function of At1g74450.

Bush M, Crowe N, Zheng T, Doonan J (2015) The RNA helicase, eIF4A-1, is required for ovule development and cell size homeostasis in Arabidopsis Plant J. http://dx.doi.org/10.1111/tpj.13062

John Doonan, another GARNet board member, leads this collaborative work between Aberystwyth and Norwich. They investigate the function of the RNA helicase/ATPase eIF4A-1 that is involved in the initiation of mRNA translation. Arabidopsis contains two isoforms of this genes and the knockdown eif4a-1 mutant displays a range of altered phenotypes that includes a reduction in the amount of mitotic cells in the root meristem. This change skews the relationship between cell size and cell cycle progression. Concomitantly several cell cycle-regulated genes have reduced expression in this mutant. Each of the eIF4A isoforms plays an important role in plant fertility as although single eif4a-1 mutants display some defects in ovule development, double eif4a1eif4a2 mutants cannot be isolated.

Bailey M, Srivastava A, Conti L, Nelis S, Zhang C, Florance H, Love A, Milner J, Napier R, Grant M, Sadanandom A (2015) Stability of small ubiquitin-like modifier (SUMO) proteases OVERLY TOLERANT TO SALT1 and -2 modulates salicylic acid signalling and SUMO1/2 conjugation in Arabidopsis thaliana J Exp Bot. http://dx.doi.org/10.1093/jxb/erv468

This study of the SUMO proteases OVERLY TOLERANT TO SALT1 and -2 (OTS) is a real pan-UK collaboration that features researchers from six institutions, led by Ari Sadanandom at Durham. The OTS proteins have been previously linked to salicylic acid (SA) signaling and this manuscript shows that in addition to containing higher level of SA, ots1ots2 double mutants are more resistant to virulent Pseudomonas syringae. This is in part linked to an upregulation of the SA biosynthetic gene ICS1. In wildtype plants SA promotes degradation of OTS1/2, which indicates that these proteins are involved in a positive feedback loop that ensures a higher SA response, which increases the efficacy of certain defence responses. However de novo synthesis of OTS1/2 will be antagonistic to SA biosynthesis and provides a brake to prevent the over-accumulation of SA-responses.

Kumar M, Turner S (2015) Protocol: a medium-throughput method for determination of cellulose content from single stem pieces of Arabidopsis thaliana Plant Methods. 11:46. http://dx.doi.org/10.1186/s13007-015-0090-6

Simon Turner (Manchester) is the lead author of this paper that presents a new method for determining cellulose content from Arabidopsis stems. This protocol is an adaptation of a previous method and uses aspiration rather than centrifugation for recovery of liquids throughout the procedure. This increases the throughout of the method and improves its potential usage as a screening protocol to identify mutants with altered cell wall composition.

Arabidopsis Research Roundup: August 27th

The Arabdopsis Research Roundup broadens its remit this week. As well as including three original research papers, which look at casparian strip formation, light and hormone signaling, we also highlight an important viewpoint article that aims to set standards for synthetic biology parts. In addition we include a meeting report from a plant synthetic biology summer school and interviews with plant scientists at the JIC, Caroline Dean and Anne Osbourn.

Kamiya T, Borghi M, Wang P, Danku JM, Kalmbach L, Hosmani PS, Naseer S, Fujiwara T, Geldner N, Salt DE (2015) The MYB36 transcription factor orchestrates Casparian strip formation Proc Natl Acad Sci USA http://dx.doi.org/10.1073/pnas.1507691112 Open Access

GARNet Advisory Board Chairman David Salt (Aberdeen) leads this international collaboration that looks at the (relatively) poorly understood Casparian strip (CS), a lignin-based filter that lies in root endodermal cells. Formation of the CS is initiated by Casparian strip domain proteins (CASPs) that recruit other proteins, which begin the process of lignin deposition. In this study the authors look upstream this process and identify the transcription factor MYB36 that directly regulates expression of CASPs and is essential for CS formation. Ectopic expression of MYB36 in root cortical tissues is sufficient to stimulate expression of CASP1-GFP and subsequent deposit a CS-like structure in the cell wall of cortex cells. These results have implications for the design of future experiments that aim to control how nutrients are taken up by the plant as even though myb36 mutants have a ‘root-defect’, they also have changes to their leaf ionome.

Sadanandom A, Ádám É, Orosa B, Viczián A, Klose C, Zhang C, Josse EM, Kozma-Bognár L, Nagy F (2015) SUMOylation of phytochrome-B negatively regulates light-induced signaling in Arabidopsis thaliana Proc Natl Acad Sci USA http://dx.doi.org/10.1073/pnas.1415260112 Open Access

Ari Sadanandom (Durham) and Ferenc Nagy (Edinburgh) are the leaders of this study that investigates the precise function of the PhyB photoreceptor protein. PhyB interacts with a wide range of downstream signaling partners including the PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors. The small ubiquitin-like modifier (SUMO) peptide is conjugated to larger proteins to bring about a variety of signaling outcomes. In this case the authors find that SUMO is preferentially attached to the C-term of PhyB under red light conditions, a relationship that occurs in a diurnal pattern. SUMOylation of PhyB prevents interaction with PIF5 whilst the OVERLY TOLERANT TO SALT 1 (OTS1) protein likely de-SUMOlyates PhyB in vivo. Altered levels of PhyB SUMOylation cause distinct light-responsive phenotypes and as such this paper adds another level of regulation to the already complex known network that controls light signaling.

Schuster C, Gaillochet C, Lohmann JU (2015) Arabidopsis HECATE genes function in phytohormone control during gynoecium development Development. http://dx.doi.org/10.1242/dev.120444 Open Access

Christopher Schuster who is now a postdoc based at the Sainsbury lab in Cambridge is the lead author on this investigation into the role of the HECATE (HEC) family of bHLH transcription factors on fruit development in Arabidopsis. During this process HEC proteins are involved in the response to both the phytohormones auxin and cytokinin, the authors proposing that HEC1 plays an essential role in Arabidopsis gynoecium formation.

Patron N et al (2015) Standards for plant synthetic biology: a common syntax for exchange of DNA parts New Phytologist http://dx.doi.org/10.1111/nph.13532 Open Access

Carmichael RE, Boyce A, Matthewman C Patron N (2015) An introduction to synthetic biology in plant systems New Phytologist http://dx.doi.org/10.1111/nph.13433 Open Access

Although not strictly based on Arabdopsis work, there are a couple of articles in New Phytologist that have broad relevance to plant scientists who are interested in plant synthetic biology. In the first of these Nicola Patron (The Sainsbury Laboratory) leads a wide consortium that aims to set parameters for the standardisation of parts in plant synthetic biology. It is hoped that as the principles of synbio are used more widley in the plant sciences that the proposals in this paper will serve as a useful guide to standidise part production. GARNet has recently written a blog post on this topic.
SynBioWorkshopPic
The associated meeting report looks at the use of plant synthetic biology in a teaching context with a synopsis of the ERASynBio summer school hosted by John Innes Centre. In this event, young researchers from a range of backgrounds were introduced to the power and potential of plant synthetic biology through a diverse course of lectures, practical session and group projects.

 

Vicente C (2015) An interview with Caroline Dean Development http://dx.doi.org/10.1242/dev.127548 Open Access

An interview with Anne Osbourn (2015) New Phytologist <a href="http://dx.doi acheter cialis.org/10.1111/nph.13616″ onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘http://dx.doi.org/10.1111/nph.13616’, ‘http://dx.doi.org/10.1111/nph.13616 ‘]);” target=”_blank”>http://dx.doi.org/10.1111/nph.13616 Open Access

These are interviews with eminent female plant molecular biologists who both work at the John Innes Centre. Caroline Dean’s lab focuses on the epigenetic mechanisms that regulate vernalisation whilst Anne Osbourn is interested in using synthetic biology approaches to engineer metabolic pathways for the production of novel compounds.

Arabidopsis Research Roundup: August 5th

This weeks Arabidopsis Research Roundup bucks the recent trend of featuring large consortium-led studies as it contains four studies each from a single UK Institution. Matthew Jones (Essex) looks at the link between photosynthesis, the circadian clock and blue-light signaling whilst Miriam Gifford (Warwick) uses cell sorting to more precisely define the plants response to an oomycete pathogen. Elsewhere Peter Eastmond (Rothamstead) looks at lipid metabolism and Keith Lindsey (Durham) leads a theorectical study on the effectiveness of methods for modelling hormone crosstalk in the root.

Litthauer S, Battle M, Lawson T, Jones MA (2015) Phototropins Maintain Robust Circadian Oscillation of PSII Operating Efficiency Under Blue Light Plant J. http://dx.doi.org/10.1111/tpj.12947

Matt Jones is a Leuverhulme Research Fellow at the University of Essex and this study is his first output as a group leader. It investigates the affect of the circadian clock on the operating efficiency of photosystem II (PSII). Previous this efficiency had been shown to be controlled by transcriptional feedback loops within the nucleus. However this study shows that in blue light it is maintained by phototropin receptors, which do not influence the nucleus. The novel imaging methodology used in this study highlight differences between the modulation of circadian outputs in distinct subcellular compartments.

Coker TL, Cevik V, Beynon JL, Gifford ML (2015) Spatial dissection of the Arabidopsis thaliana transcriptional response to downy mildew using Fluorescence Activated Cell Sorting Front Plant Sci. http://dx.doi.org/10.3389/fpls.2015.00527

Miriam Gifford leads this study from the University of Warwick that looks at the transcriptional response of Arabidopsis to downy mildew infection. The Gifford lab are experts in analysis of transcriptional data from microarrays. This study uses FACS-sorted cells infected with the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis in an attempt to focus-in on infected cells without the diluting effects of non-infected cells within the same tissue. Almost 300 transcripts were differentially expressed between haustoriated and non-haustoriated cells and this technique uncovered novel genes that had previously not been implicated in playing a role in this pathogen response.

Craddock CP, Adams N, Bryant FM, Kurup S, Eastmond PJ (2015) Regulation of endomembrane biogenesis in Arabidopsis by PHOSPATIDIC ACID HYDROLASE Plant Signal Behav. http://dx.doi.org/10.1080/15592324.2015.1065367

This study was wholly undertaken at Rothamsted Research led by Peter Eastmond. They investigate the coordination of lipid biosynthesis by focussing on the activity of two different enzymes, PHOSPHATIDIC ACID PHOSPHOHYDROLASE (PAH) and PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE (CCT). These enzymes participate in a feedback loop to control the biosynthesis of phosphaticylcholine (PC) and phosphatidic acid (PA), which is linked to biogenesis of the endoplasmic reticulum. This work offers a clue that PAH activity may require phosphorylation even though this data is not yet clear.

Simon Moore, Xiaoxian Zhang, Junli Liu & Keith Lindsey (2015) Some fundamental aspects of modelling auxin patterning in the context of auxin-ethylene-cytokinin crosstalk Plant Signalling and Behaviour http://dx.doi.org/10.1080/15592324.2015.1056424

In this manuscript Keith Lindsey and colleagues from Durham University use the paradigm of root-tip auxin-ethylene-cytokinin signaling to discuss the effectiveness of linking experimental data, reaction kinetics and spatiotemporal modelling to dissect hormonal crosstalk. The authors agree that the integration of kinetic equations with spatial root structure can produce powerful models for assessing the crosstalk of multiple hormone interactions in a spatiotemporal manner. Finally the authors come up with key recommendations to be considered when developing models for spatiotemporal hormonal crosstalk in the Arabidopsis root

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