Arabidopsis Research Roundup: May 5th

There are a bumper crop of papers in this edition of the Arabidopsis Research Roundup. First from the University of Manchester is a paper that identifies a protein involved in plant programmed cell death. Secondly are two papers from the University of Bristol that highlight the role of viruses in the reflectivity of plant leaves and an assessment of the growth parameters of Arabidopsis on different soil-types. Thirdly are three papers from University of Edinburgh that either use CRISPR-Cas technology to develop virus-research plants, investigate the relationship between photoperiod and metabolism or present a method for assessment of protein S-nitrosylation. Fourthly is a paper that includes a contribution from the University of Leeds that investigates the evolutionary and functional relationship of the WOX gene family. Finally is a study that highlights the role of the AUGMIN complex during microtubule activity that includes a contribution from the University of Leicester.

In addition, although not involving Arabidopsis, we should mention an exciting study from Gerben van Ooijen (Edinburgh) that has discovered a conserved circadian mechanism based on magnesium rhythms that is linked to energy expenditure.

Ge Y, Cai YM, Bonneau L, Rotari V, Danon A, McKenzie EA, McLellan H, Mach L, Gallois P (2016) Inhibition of cathepsin B by caspase-3 inhibitors blocks programmed cell death in Arabidopsis. Cell Death Differ. http://dx.doi.org/10.1038/cdd.2016.34 Open Access

The corresponding author of this paper is Patrick Gallois from the University of Manchester and includes contributions from Hazel McLellan in Dundee almongside Chinese and Austrian collaborators. This study investigates the role of caspase proteins on control of programmed cell death in plants. This research area has been hindered by the apparent lack of plant caspase orthologues despite pharmacological evidence that proteins with caspase activity are active in plants. The authors use a labeled caspase-3 inhibitor to identify the Arabidopsis Cathepsin B3 (AtCathB3) protein as having caspase activity, which was verified using recombinant proteins during in vitro enzyme assays. AtCathepsinB1,2,3 triple mutant plants demonstrate a reduction in PCD induced by different stresses and explains why caspase inhibitors are effective tools for studying PCD in plants. The core Cathepsin B protein is evolutionarily conserved suggesting that an ancestral pathway exists that controls PCD, the details of which require further study.

Maxwell DJ, Partridge JC, Roberts NW, Boonham N, Foster GD (2016) The Effects of Plant Virus Infection on Polarization Reflection from Leaves. PLoS One. 11(4):e0152836 http://dx.doi.org/ 10.1371/journal.pone.0152836 Open Access

Gary Foster’s research group at the University of Bristol collaborate with others at the University of York and in Australia for this study that investigates how plant viruses may modify gene expression to benefit their own transmission. They show that Potato virus Y and Cucumber mosaic virus (CMW), which both are transmitted by aphids, significantly reduce the amount of polarised light that is reflected from abaxial leaf surfaces of tobacco plants particularly when compared to the effects caused by non-insect vectored viruses. However this effect was not shown in Arabidopsis leaves infected by a variety of differently transmitted viruses. Interestingly ECERIFERUM6 (CER6) transcripts accumulate to higher levels following infection with insect vectored viruses and as this gene is involved in cuticle wax synthesis the authors suggest that induced changes in cuticle composition might be key in understanding how viruses encourage predation by their insect vectors. Finally the authors discuss the overall adaptive significance of these results.

Drake T, Keating M, Summers R, Yochikawa A, Pitman T, Dodd AN (2016) The Cultivation of Arabidopsis for Experimental Research Using Commercially Available Peat-Based and Peat-Free Growing Media. PLoS One. 11(4):e0153625 http://dx.doi.org/ 10.1371/journal.pone.0153625 Open AccessPeatPic

GARNet committee member Anthony Dodd, also from the University of Bristol, leads this study into the growth of Arabidopsis on peat-free media, which was motivated by the unsustainable use of peat-based composts. They found that biomass accumulation and seed yield were reduced on peat-free media and that some types of this media was more suspectible to fungal contamination. Overall vegetative phenotypic parameters were similar between plants grown on peat-based or peat-free media, indicating that this type of media will be appropriate for future analysis. However the seed yield was usually reduced, indicating that experiments looking at post-phase change phenotypes might not be as comparable between plants growth on media with different amount of peat.

Pyott DE, Sheehan E, Molnar A (2016) Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants Mol Plant Pathol. http://dx.doi.org/10.1111/mpp.12417

Attila Molnar (Edinburgh) is the corresponding author on this study that uses the transformative technology CRISPR/Cas9 to engineer Arabidopsis plants that are resistant to potyvirus infection. This is achieved by targeting the genes encoding the translation initiation factor eIF(iso)4E that had been previously identified as being critical for viral establishment. Importantly they subsequently selected transgene-free plants that have no phenotypic changes when compared to wildtype growth under standard conditions. As the potyvirus Turnip Mosaic Virus is an important pathogen for vegetable crops this is potentially an extremely powerful technique for generating virus-resistance food crops.

Flis A, Sulpice R, Seaton DD, Ivakov AA, Liput M, Abel C, Millar AJ, Stitt M (2016) Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis Plant Cell Environ. http://dx.doi.org/10.1111/pce.12754

This German–led study aims to connect the expression of photoperiod-length responsive circadian clock-regulated genes with those involved in metabolic processes such as starch degradation and includes a contribution from Professor Andrew Miller from the Edinburgh SynthSys Centre. The authors assess global gene expression by transcript profiling at photoperiods ranging from 4-18 hours and found that changes in transcript abundance at dawn throughout these photoperiods were as large as changes seen in individual experiments when comparing dawn and dusk. These complex interactions revealed coordinated regulation of key metabolic processes and begins to demonstrate how metabolism is linked to photoperiod.

Homem RA, Le Bihan T, Yu M, Loake GJ (2016) Identification of S-Nitrosothiols by the Sequential Cysteine Blocking Technique Methods Mol Biol. 1424:163-74. http://dx.doi.org/10.1007/978-1-4939-3600-7_14

This paper from the lab of Gary Loake (Edinburgh) describes the methods they use to investigate the role of protein S-nitrosylation in the immune responses of Arabidopsis. These are based on a modification of the biotin-switch technique, which they term sequential cysteine blocking.

Dolzblasz A, Nardmann J, Clerici E, Causier B, van der Graaff E, Chen J, Davies B, Werr W, Laux T (2016) Stem cell regulation by Arabidopsis WOX genes Mol Plant. S1674-2052(16)30029-6 http://dx.doi.org/10.1016/j.molp.2016.04.007

This German-led study includes work from the lab of Brendan Davies at the University of Leeds and investigates the role of the WUSCHEL-RELATED HOMEOBOX (WOX) transcription factor gene family during stem cell development and maintenance. Most members of the WUS-clade can largely substitute for WUSCHEL activity in the shoot meristem, which is absolutely dependent on a conserved WUS-box motif that is critical for the interaction with TOPLESS co-repressors. In contrast to the WUS clade, the WOX13 and WOX9 clades cannot substitute for WUS activity. The indicates that WOX control of shoot and floral meristem relies on certain currently not-fully-understood attributes of the WUS-clade of proteins.

Oh SA, Jeon J, Park HJ, Grini PE, Twell D, Park SK (2016) Analysis of gemini pollen 3 mutant suggests a broad function of AUGMIN in microtubule organization during sexual reproduction in Arabidopsis Plant J. http://dx.doi.org/10.1111/tpj.13192

David Twell (Leicester) is an author on his Korean-led study that reports on the identification of the new gem3 mutant, which displays defects in gametophytic development. Mutant plants exhibits disrupted cell division during male meiosis, at pollen mitosis I and throughout female gametogenesis. Gem3 is a hypomorphic allele of the AUGMIN subunit 6 gene, which is a component of Augmin complex responsible for microtubule (MT) nucleation in acentrosomal cells. In the gem3 mutant, the authors show that MT arrays are incorrectly distributed, likely causing the gametophyte-specific phenotypes and demonstrating a broad role for the augmin complex during sexual reproduction in flowering plants

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: August 21st.

There are a wide array of topics included in this weeks Arabidopsis Research Roundup, ranging from studies on stomatal density, thylakoid transport, metabolic flux analysis, mutant detection and root development. We feature unlinked studies from three researchers from the University of Oxford Plant Science (Paul Jarvis, Lee Sweetlove and Nick Harberd), whilst the papers from Julie Gray and Brian Forde share the broad theme that investigates different mechanisms that might be used to improve nitrogen uptake, either by modifying the expression of a single gene involved in root development or by altering stomatal density.

Hepworth C, Doheny-Adams T, Hunt L, Cameron DD, Gray JE (2015) Manipulating stomatal density enhances drought tolerance without deleterious effect on nutrient uptake New Phytol. http://dx.doi.org/10.1111/nph.13598

Julie Gray (University of Sheffield) is an expert on both stomatal biology and on the potential for manipulating stomatal density to improve crop production. In this study drought tolerance and soil water retention were measured in four Arabidopsis mutants with defects in epidermal patterning and stomatal density. Nutrient uptake was measured by mass flow of 15N. Plants with less stomata had reduced transpiration and were drought-tolerant yet interestingly showed little reduction in shoot N concentrations, especially when water availability is restricted. In contrast, plants with extra stomata could take up more N except when access to water was reduced. Therefore the authors show that by altering stomatal density they can generate plants that are drought resistance yet maintain nutrient uptake or generate plants with enhancing nutrient uptake is conditions with plentiful water.

Trösch R, Töpel M, Flores-Pérez Ú, Jarvis P (2015) Genetic and Physical Interaction Studies Reveal Functional Similarities between ALB3 and ALB4 in Arabidopsis. Plant Physiol. http://dx.doi.org/10.1104/pp.15.00376

This German, Swedish and UK collaboration is led by Paul Jarvis at the University of Oxford and broadly investigates thylakoid protein targeting. The ALB3 complex has previously been shown to target light harvesting complex proteins (LHCP) to the thylakoid. A related Arabidopsis protein, ALB4, had been proposed to interact not the LHCPs but rather with the ATP synthase complex. However this study shows that ALB3 and ALB4 have some overlapping roles in addition to their specific functions and that they can engage with a similar set of interactor proteins to bring their substrates to the thylakoid membrane.

Cheung CY, Ratcliffe RG, Sweetlove LJ (2015) A method of accounting for enzyme costs in flux balance analysis reveals alternative pathways and metabolite stores in an illuminated Arabidopsis leaf Plant Physiol. http://dx.doi.org/10.1104/pp.15.00880

Lee Sweetlove (Oxford University) leads this study that looks at the Flux Balance Analysis (FBA) of plant metabolism across several metabolic pathways by attaching ‘flux weighting factors’ to allow for the variable intrinsic cost of supporting each flux. This model has been applied to the Arabidopsis leaf exposed to different light regimes to explore the flexibility of the network in meeting its metabolic requirements. The authors discover interesting trade-offs between use of different carbon storage forms and in the variable consumption of ATP and NADPH by different metabolic pathways.

Belfield EJ, Brown C, Gan X, Jiang C, Baban D, Mithani A, Mott R, Ragoussis J, Harberd NP (2014) Microarray-based optimization to detect genomic deletion mutations Genom Data Dec;2:53-54 http://dx.doi.org/10.1016/j.gdata.2014.04.005

GARNet Advisory Board member Nick Harberd (Oxford University) leads this short communication that highlights the development of a tool for detection of genomic deletion mutants in Arabidopsis. Using a NimbleGen whole genome custom tiling array they successfully identify five mutants with deletion ranging from 4bp to 5kb and therefore introduce a powerful tool for analysing this type of genetic lesion in Arabidopsis and other plant species with well-constructed genomes.

Yu C, Liu Y, Zhang A, Su S, Yan A, Huang L, Ali I, Liu Y, Forde BG, Gan Y (2015) MADS-box Transcription Factor OsMADS25 Regulates Root Development through Affection of Nitrate Accumulation in Rice PLoS One http://dx.doi.org/10.1371/journal.pone.0135196

Brian Forde (Lancaster University) is the UK lead on this Chinese collaboration that focuses on nitrate accumulation and how it regulates root development in rice. This occurs via a MADS-box transcription factor OsMADS25 that, when overexpressed in Arabidopsis, promotes primary and lateral root development. Altered expression of this gene also affects root development in transgenic rice and includes significant changes in nitrate accumulation. Therefore this gene might prove to be an important target for future attempts to improve plant growth in regions with altered nitrate concentrations.

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