This weeks Arabidopsis Roundup again includes a broad selection of research topics. Firstly researchers at SLCU are involved in work that describes Arabidopsis sepal development. Secondly Cyril Zipfel from TSL leads a study that adds a layer of complexity to our knowledge of cellular pathogen perception. Thirdly the group of Reiner van der Hoorn from Oxford introduces the use of a novel set of inhibitors that reveals differential activity of proteosomal subunits during bacterial infection. Finally Hugh Pritchard from Kew Gardens is a co-author on a lipidomic study of the seed dessication-stress response.
Meyer HM, Teles J, Formosa-Jordan P, Refahi Y, San-Bento R, Ingram G, Jönsson H, Locke JC, Roeder AH (2017) Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal. Elife.
James Locke and Henrik Jonsson (SLCU) are authors on this paper that is led by Adrienne Roeder at Cornell in the USA. The Roeder lab largely focused their research on development of the sepal. The SLCU researchers provided modeling support for this investigation into the critical role of the ATML1 gene in the differentiation of initially identical cells into giant or regular sized sepal cells. They show that there it is a threshold level of differential ATML1 expression that is key in determining cell fate. If this threshold is met during the G2 phase of the cell cycle the cells enter endoreduplication and become giant. If the threshold isn’t reached then the cells divide and remain at a ‘normal’ size. Ultimately they demonstrate a fluctuation-driven patterning mechanism that determines cell fate.
Stegmann M, Monaghan J, Smakowska-Luzan E, Rovenich H, Lehner A, Holton N, Belkhadir Y, Zipfel C (2017) The receptor kinase FER is a RALF-regulated scaffold controlling plant immune signaling Science
Cyril Zipfel (The Sainsbury Lab, Norwich) is the lead author of this study that builds upon his labs work into mechanisms of pathogen perception by cell-surface receptor kinases. In this latest work they show that the SITE-1 PROTEASE (ST1P) cleaves endogenous RAPID ALKALINIZATION FACTOR (RALF) propeptides to inhibit plant immunity, a response mediated via the receptor kinase FERONIA (FER). The FER protein is also involved in the formation of other immune complexes. The authors have discovered a mechanism by which FER reglates RALK signaling, indicating that they might have uncovered a more general mechanism for this key control point of immune signaling.
Misas-Villamil JC,, van der Burgh AM, Grosse-Holz F, Bach-Pages M, Kovács J,, Kaschani F, Schilasky S, Emon AE, Ruben M, Kaiser M, Overkleeft HS, van der Hoorn RA (2017) Subunit-selective proteasome activity profiling uncovers uncoupled proteasome subunit activities during bacterial infections. Plant Journal
Reiner van der Hoorn (University of Oxford) lead this cross-Europe collaboration that introduces a range of inhibitors and probes that can discriminate between catalytic subunits of the proteasome. These tools were studied in both Arabidopsis and Nicotiana benthamiana and the authors used the plant-microbe interactions to further validate their specificity. They show that proteasomal subunits have separate paralogs that are differentiatially incorperated into the larger complex depending on an interaction with pathogenic bacteria. Aliquots of these probes are available on request from firstname.lastname@example.org
The authors encourage their usage so as to increase the chance that they might become commercially available. More information from the Plant Chemetics lab.
Chen H, Yu X, Zhang X, Yang L, Huang X, Zhang J, Pritchard HW, Li W (2017) Phospholipase Dα1-mediated phosphatidic acid change is a key determinant of desiccation-induced viability loss in seeds. Plant Cell Environ.
Hugh Pritchard (Kew Gardens) is a co-author on this Chinese-led study that investigates the role of phosphatidic acid (PA) on seed viability. Higher levels of PA correlated with lower seed viability after a desiccation stress. Using Arabidopsis seeds they showed that the enzyme phospholipase D α1 (PLD α1) localises to the plasma membrane following desiccation, where it produces PA. When PLD α1 was suppressed, seed recovery following desiccation improved. The authors used comparative lipidomics to compare PA levels in eight plant species and from their Arabidopsis work, they propose a new model for the mechanism by which seed desiccation effects germination rates.
Todays Arabidopsis Research Roundup includes some excellent examples of UK labs engaged in collaborative work with researchers from around the globe. However first up is a study solely from the John Innes Centre, led by Vinod Kumar, that investigates the role of PIF4 during the thermosensory response. Secondly David Evans (Oxford Brookes University) is a co-author on a French-led study that has looked into the role of LINC complexes during interphase heterochromatin patterning. Thirdly is the description of the new PhenoTiki imaging tool that has come from the lab of Sotirios Tsaftaris in Edinburgh. Work from Paul Dupree (University of Cambridge) features in the ARR for the second consecutive week, this time with a study looking at the sugar composition of seed mucilage. The penultimate study is from the lab of Renier van der Hoorn (Oxford University) who investigates the role of Cys proteases during senescence and finally is a study from Seth Davis (University of York) that looks at the link between the circadian clock and the plants energy sensing mechanisms.
Gangappa SN, Berriri S, Kumar SV (2016) PIF4 Coordinates Thermosensory Growth and Immunity in Arabidopsis. Current Biology
Vinod Kumar (John Innes Centre) leads this study that looks at the role of the PHYTOCHROME INTERACTING FACTOR 4 (PIF4) transcription factor during the thermosensory response and its effect on plant architecture. They looked at the natural variation of PIF4, demonstrating the role of different varients on the balance between growth and immunity to pathogens. Pertubing PIF4-mediated effects result in temperature-resilient disease resistance. This study links with a paper highlighted in last weeks ARR from Kerry Franklin and co-authors that presented the role of UVR8 on the control of PIF4 heat responsive effects. These studies further confirm the important role of PIF4 in plant development in response to environmental change and biotic challenges.
Vinod discusses this paper and a related manuscript from next weeks ARR. Also available on the GARNet YouTube channel.
Poulet A, Duc C, Voisin M, Desset S, Tutois S, Vanrobays E, Benoit M, Evans DE, Probst AV, Tatout C (2017) The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants. J Cell Science.
This study is led by Christophe Tatout from Clermond-Ferrand and includes David Evans and Axel Poulet (Oxford Brookes University) as co-authors. The paper focuses on the role of the nuclear envelope-localised LInker of Nucleoskeleton and Cytoskeleton (LINC) complex on nuclear morphology and interphase chromatin localisation. This work is underpinned by the use of novel 3D imaging tools to define where in the nucleus the chromatin is localised in both wildtype and linc mutant plants. This allows the authors to show that the LINC complex is necessary for proper heterchromatin organisation at the nuclear periphery, which might have broad implications for gene expression and transcriptional silencing.
Minervini M, Giuffrida MV, Perata P, Tsaftaris SA (2017) Phenotiki: An open software and hardware platform for affordable and easy image-based phenotyping of rosette-shaped plants. Plant J. http://dx.doi.org/10.1111/tpj.13472
This manuscript describes the PhenoTiki tool that is designed for the automated phenotyping of Arabidopsis rosettes, work which is led by Sofortios Tsaftaris (University of Edinburgh). PhenoTiki describes both the imaging software and also cheap-to-use off-the-shelf hardware that allows for facile imaging at reduced costs. The proof-of-concept study in the paper shows a comprehensive analysis from a range of parameters in 24 Arabidopsis rosettes from different genotypes. This data is compared favourably to more expensive methods of automated phenotyping so the authors hope PhenoTiki can be adopted as a low-cost method for image analysis. Full details can be found at http://phenotiki.com.
Saez-Aguayo S, Rautengarten C, Temple H, Sanhueza D, Ejsmentewicz T, Sandoval-Ibañez O, Doñas-Cofré DA, Parra-Rojas JP, Ebert B, Lehner A, Mollet JC, Dupree P, Scheller HV, Heazlewood JL, Reyes FC, Orellana A (2016) UUAT1 Is a Golgi-Localized UDP-Uronic Acid Transporter that Modulates the Polysaccharide Composition of Arabidopsis Seed Mucilage. Plant Cell. http://dx.doi.org/10.1105/tpc.16.00465
Paul Dupree (University of Cambridge) is part of this global collaboration with colleagues from Australia, USA and Chile. The study investigates the intracellular movement of the plant cell polysaccharide pre-cursor UDP-glucuronic acid (UDP-GlcA). To identify genes involved in this process they cleverly screened mutants for alteration in seed mucilage, which has high level of other polysaccharides. This strategy identified UUAT1, which is a golgi-localised transporter of UDP-GlcA and UDP-galacturonic acid (UDP-GalA). Uuat1 mutants have altered sugar composition in both the seed coat mucilage and in other plant organs. These changes were also associated with an increase, by a currently unknown mechanism, of homogalacturonan methylation. Overall the authors show that UUAT1 is important for the correct distribution of cell wall polysaccahrides throughout growing embryo and will surely play important developmental roles in the function of the cell wall.
Pružinská A, Shindo T, Niessen S, Kaschani F, Tóth R, Millar AH, van der Hoorn RA (2017) Major Cys protease activities are not essential for senescence in individually darkened Arabidopsis leaves. BMC Plant Biol.
In this paper Renier van der Hoorn (University of Oxford) interacts with US, German and Australian colleagues to use the activity-based protein profiling (ABPP) technique to assess the activity of active enzymes during senescence. They show that in Arabidopsis leaves the expression of several Papain-like Cys Proteases (PLCPs) is elevated but the activity of many Vacuolar Processing Enzymes (VPEs) is decreased, even though their transcript level increases. The amount of senescence was assessed in plants with mutations in different members of these protease families and surprisingly did not find any difference when compared to wildtype plants. One exception was in plants containing a mutation in the AALP PLCP which showed a significant, albeit slight, descrease in the rate of senescence.
Shin J, Sánchez-Villarreal A,, Davis AM,, Du SX, Berendzen KW, Koncz C, Ding Z, Li C, Davis SJ (2017) The metabolic sensor AKIN10 modulates the Arabidopsis circadian clock in a light-dependent manner. Plant Cell Environ.
Seth Davies (University of York) leads this study that includes German, Mexican and Chinese collaborators and looks at the link between the circadian clock and plant metabolism. The energy sensing Snf1 (sucrose non-fermenting 1)-related kinase 1 (SnRK1) complex contains the catalytic AKIN10 protein, which plays an important role in clock function by controlling expression of the key evening element GIGANTEA (GI). This AKIN10 effect requires the clock regulator TIME FOR COFFEE (TIC) demonstrating an important role for the plants energy sensing mechanisms, via the AKIN10, in conditional control of clock gene expression.
This weeks Arabidopsis Research Roundup includes broad representation from Norwich Research Park with Caroline Dean, Enrico Coen and Cyril Zipfel each leading studies that focus respectively on the regulation of transcriptional state, auxin patterning that defines leaf shape or the molecular basis of the PAMP response.
Elsewhere Liam Dolan (Oxford) leads, and Malcolm Bennett (CPIB) is the principal UK contributor on studies that look into different aspects of the key molecular signals in either root hair or lateral root development.
Finally Richard Napier is a co-author on a study that better characterises the molecular basis of the well-used plant growth inhibitor MDCA.
Dame Caroline Dean and Martin Howard (JIC) lead this follow-on work from a paper highlighted in an ARR from the start of 2016. Here they use the FLOWERING LOCUS C (FLC) locus as a model to study the trans factors that control methylation state. They find a physical interaction between the H3K36 methyltransferase SDG8 (which promotes the active H3K36me3 mark) and the H3K27me3 demethylase ELF6 (which removes the silencing H3K27me3 mark). SDG8 also associated with RNA polymerase II and the PAF1 transcriptional regulatory complex. Therefore the authors suggest that the addition of active histone marks coincides with transcription at the locus whilst SDG8 and ELF6 exhibit co-dependent localisation to FLC chromatin. Therefore this interaction links activation and derepression and coordinates active transcription whilst preventing ectopic silencing.
Open Access Enrico Coen (JIC) is the corresponding author on this investigation that had generated models that predict locations of leaf outgrowth linked to auxin biosynthesis and transport. They use live imaging in wildtype and kanadi1kanadi2 mutants to show that the cellular polarity of the PIN1 auxin transporter is orientated so as to move auxin away from regions with high levels of biosynthesis. In turn, this moves auxin toward regions with high expression of AUX/LAX auxin importers. This data allows the generation of detailed models that describe the processes that control auxin-mediated tissue-patterning (and are impossible to describe in a single paragraph).
Couto D, Niebergall R, Liang X, Bücherl CA, Sklenar J, Macho AP, Ntoukakis V, Derbyshire P, Altenbach D, Maclean D, Robatzek S, Uhrig J, Menke F, Zhou JM, Zipfel C (2016) The Arabidopsis Protein Phosphatase PP2C38 Negatively Regulates the Central Immune Kinase BIK1 PLoS Pathog. http://dx.doi.org/10.1371/journal.ppat.1005811
Cyril Zipfel is the lead investigator on this study that links researchers at TSL with colleagues in China and Germany. The focus of this work is the cytoplasmic kinase BIK1, which is a target of several pattern recognition receptors (PRRs) that are involved in the defence response, and the novel protein phosphatase PP2C38, which acts as a negative regulator of BIK1. Under non-inductive conditions PP2C38 prevents BIK1 activity but following pathogen-associated molecular patterns (PAMP) perception, it is phosphorylated and dissociates from BIK1, allowing full activity. This study provides another layer of detail into the complex central immune response that allows plants to response to a vast array of pathogenic microorganisms.
Goh T, Toyokura K, Wells DM, Swarup K, Yamamoto M, Mimura T, Weijers D, Fukaki H, Laplaze L, Bennett MJ, Guyomarc’h S (2016) Quiescent center initiation in the Arabidopsis lateral root primordia is dependent on the SCARECROW transcription factor Development. http://dx.doi.org/10.1242/dev.135319
Malcolm Bennett and Darren Wells (CPIB) are authors on this international collaboration that links UK, Japanese, French and Dutch researchers. The essential role of the central organizer center (the quiescent center, QC) is well known in primary root meristem development but its role during lateral root (LR) formation remained unclear. LR formation is characterised by biphasic growth that involves early morphogenesis from the central stele and subsequent LR meristem formation. This study uses 3D imaging to demonstrate that LR QC cells originate from outer cell layers of early primordial, in a SCARECROW (SCR) dependent manner. Perturbing SCR function causes incorrect formation of the LR QC and prevents wildtype LR patterning. The manuscript also contains some excellent videos of growing LRs that are very informative. Kim CM, Dolan L (2016) ROOT HAIR DEFECTIVE SIX-LIKE Class I Genes Promote Root Hair Development in the Grass Brachypodium distachyon PLoS Genet.
This study comes from Liam Dolan’s lab at the University of Oxford and moves their research focus on root hair development from Arabidopsis into the grass Brachypodium distachyon. ROOT HAIR DEFECTIVE SIX-LIKE (RSL) class I basic helix loop helix genes are expressed in cells that develop root hair fate in Arabidopsis and this study indentifies 3 RSl1 genes in Brachypodium which, when ecoptically expressed, are sufficient for the development of root hairs in all cell files. The function of these RSL proteins is conserved as the Brachypodium versions are able to restore a wildtype phenotype to root hair-less Arabidopsis mutants. Even though root hair patterning is significantly different in Brachypodium and Arabidopsis, this study shows the role of the RSL genes is conserved.
Steenackers WJ, Cesarino I, Klíma P, Quareshy M, Vanholme R, Corneillie S, Kumpf RP, Van de Wouwer D, Ljung K, Goeminne G, Novak O, Zažímalová E, Napier RM, Boerjan WA, Vanholme B (2016) The allelochemical MDCA inhibits lignification and affects auxin homeostasis. Plant Physiology http://dx.doi.org/10.1104/pp.15.01972
Richard Napier (Warwick) is the UK PI on this pan-European study that investigates the molecular basis behind the physiological role of the compound phenylpropanoid 3,4-(methylenedioxy)cinnamic acid (MDCA), which inhibits the phenylpropanoid pathway, important in lignin formation. MDCA causes inhibition of primary root growth and increase proliferation of lateral roots, not through lignin perturbation but due to a disruption in auxin homeostasis. MS analysis demonstrates that MDCA causes overall changes in auxin biosynthesis, conjugation and catabolism, similar to changes observed in mutants involved in the phenylpropanoid pathways. These result link auxin and phenylpropanoid biosynthesis pathways and provide a new explanation for the well demonstrated phytotoxic properties of MDCA.
This weeks Arabidopsis Research Roundup includes six studies across a range of discplines. Firstly Alison Smith provides an excellent audio description of an investigation into the dynamics of night-time starch degradation.
Secondly three UK institutions (Durham, Exeter and Oxford Brookes) participate in a study of VAP27 membrane network proteins. Next a broad collaboration from CPIB in Nottingham then introduce a multi-scale model that helps describe Arabidopsis root development.
We also include two studies that involve collaborations with Korean researchers: Gary Loake is a contributor on a study that introduces plant RALF genes whilst Ian Henderson’s research group participates in a study into the function of the SWR1 complex in miRNA gene expression. Finally we highlight a new Plant Cell teaching tool put together by UK academics from Hull and Bristol.
Feike D, Seung D, Graf A, Bischof S, Ellick T, Coiro M, Soyk S, Eicke S, Mettler-Altmann T, Lu KJ, Trick M, Zeeman SC, Smith AM (2016) The starch granule-associated protein EARLY STARVATION1 (ESV1) is required for the control of starch degradation in Arabidopsis thaliana leaves Plant Cell
This UK and Swiss study is led by Alison Smith from the John Innes Centre and investigates starch degradation that occurs during nighttime. They developed a novel screen to identify an uncharacterized mutant called early starvation 1 (esv1) that more rapidly degraded starch so that it is exhausted earlier in the night. They found that ESV1 and the related LESV1 proteins associated with starch granules within the chloroplast stroma. The authors propose that these proteins influence the organisation of the starch granule matrix, facilitating access for starch-degrading enzymes. In addition they also show that this function appears to be conserved throughout all starch-synthesizing organisms.
Professor Smith provides an audio description of this paper:
Wang P, Richardson C, Hawkins TJ, Sparkes I, Hawes C, Hussey PJ (2016) Plant VAP27 proteins: domain characterization, intracellular localization and role in plant development. New Phytol. 210(4):1311-1326 http://dx.doi.org/10.1111/nph.13857
This cell biology-focused study is a collaboration between the Universities of Exeter, Durham and Oxford Brookes and investigates vesicle-associated membrane protein-associated proteins (VAPs), which form part of the network that links the plasma membrane and ER. The Arabidopsis genome contains 10 VAP homologues (VAP27-1 to -10) split into 3 clades. Members of clades I and II localise to both ER as well as to ER/PM contact sites (EPCSs) whilst clade II members are only found at the PM, all discovered through transient expression experiments in tobacco. Interestingly the localisation to the EPCSs is associated with the cytoskeleton but does not require the presence of that underlying structure. These proteins are expressed in most cell types and when their levels are altered, plants show pleiotropic phenotypes. Overall this study shows that VAP27 proteins are required for ER-cytoskeleton interactions that are critical for normal plant development.
Muraro D, Larrieu A, Lucas M, Chopard J, Byrne H, Godin C, King J (2016) A multi-scale model of the interplay between cell signalling and hormone transport in specifying the root meristem of Arabidopsis thaliana. J Theor Biol. S0022-5193(16)30070-4 http://dx.doi.org/10.1016/j.jtbi.2016.04.036
This investigation was performed at CPIB in Nottingham in collaboration with the Virtual Plant Project in Montpellier and is led by John King. The authors have developed a multi-scale computational model that allows the study of signalling networks that occurs during Arabidopsis root growth. This model was experimentally tested to investigate how it is affected by hormonal changes during root growth. The model was able to identify two novel mutants that significantly alter root length through perturbations in meristem size. In general this study demonstrates the value of multi-scale modeling as part of the process of evaluating the function of the components that define the formation of the root meristem.
Sharma A, Hussain A, Mun BG, Imran QM, Falak N, Lee SU, Kim JY, Hong JK, Loake GJ, Ali A, Yun BW (2016) Comprehensive analysis of plant rapid alkalization factor (RALF) genes Plant Physiol Biochem. 106:82-90
This Korean-led study includes a contribution from Gary Loake from the University of Edinburgh and is the first comprehensive investigation of Rapid alkalization factor (RALF) proteins across plant species. These RALF proteins are thought to be important signalling molecules in plant defense and development. This study provides information on gene structure, subcellular locations, conserved motifs, protein structure, protein-ligand interactions and promoter analysis across Arabidopsis, rice, maize and soybean. The RALF genes are phylogenetically divided into 7 clades and their mRNA upregulation following nitrosative and oxidative stresses suggests that they are function in responding to changes in cellular redox status. Overall this manuscript provides a valuable resource to prime future research into the role of RALF genes.
Choi K, Kim J, Müller SY, Oh M, Underwood C, Henderson I, Lee I (2016) Regulation of microRNA-mediated developmental changes by the SWR1 chromatin remodeling complex in Arabidopsis thaliana. Plant Physiol. http://dx.doi.org/10.1104/pp.16.00332
GARNet committee member Ian Henderson (Cambridge) is a contributor on this study that is led by researchers in Seoul, South Korea. In the last ARR, Vinod Kumar described work that looked into the role of the SWR1 chromatin-remodeling complex and this study provides an insight into the role of this same SWR1 complex on microRNA (miRNA)-mediated transcriptional control. In SWR1 complex mutants (arp6, sef, and pie1), deep sequencing revealed that many miRNA types and their target mRNAs are misregulated. This further establishes the role of the SWR1 complex in the control of nucleosome occupancy, likely by mediating the exchange of H2A isoforms, for a range of genes involved in the fine-tuning of numerous developmental processes.
Katherine Hubbard and Anthony Dodd have produced a teaching resource focused on the Circadian Clock as part of the increasingly comprehensive Plant Cell Teaching Tools. Most academics are looking to save time and this resource will allow them to do this and provides excellent coverage of the topic.
This weeks Arabidopsis Research Roundup includes two peer-reviewed papers and the release of a preprint. Vinod Kumar from the JIC provides an audio description of a study that investigates the role of the SWR1 complex in the defence response. Secondly Jessica Metcalf from Oxford is a contributor on a study that looks at population responses of Arabidopsis to simulated climate change. Finally John Brown (University of Dundee and the James Hutton Institute) is the corresponding authors on a preprint that introduces a new Arabidopsis transcriptome annotation.
Berriri S, Gangappa SN, Kumar SV (2016) SWR1 chromatin-remodelling complex subunits and H2A.Z have non-overlapping functions in immunity and gene regulation in Arabidopsis Molecular Plant http://dx.doi.org/10.1016/j.molp.2016.04.003Open Access
Vinod Kumar (John Innes Centre) is the corresponding author on this study that investigates the incorporation of the histone variant H2A.Z into Arabidopsis nucleosomes. This histone variant is important in the control of differential gene expression although its role in plant immunity is not well understood. H2A.Z is integrated into nucleosome by the SWR1 chromatin remodelling complex that contains a number of subunits namely PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 (PIE1), ACTIN-RELATED PROTEIN6 (ARP6), and SWR1 COMPLEX 6 (SWC6). Interestingly each subunit plays discrete roles in different pathogen response processes including basal resistance, enhanced resistance, effector-triggered immunity or in altered JA/ET-mediated immunity. Genome wide expression analysis reveals a role for PIE1 in the crosstalk between signalling processes and overall that SWR1c components might have distinct non-overlapping roles during gene regulation and expression.
Dr Kumar kindly provides a brief audio description of this paper:
Fournier-Level A, Perry EO, Wang JA, Braun PT, Migneault A, Cooper MD, Metcalf CJ, Schmitt J (2016) Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana PNAS http://dx.doi.org/10.1073/pnas.1517456113
Mathematician Jessica Metcalf (Oxford) is an author on this US-led study that uses Arabidopsis to investigate the effect of climate change on evolution of fitness. Over four seasons plants were grown under four climatic conditions (present day, overall increased temp, winter-warming and poleward-migration temp) and 12 traits were measured as a proxy for fitness evolution. The data was used to simulate evolutionary trajectories over a 50-100 year period. The authors found that each climatic condition resulted in different outcomes where populations with fewer founding genotypes or less initial diversity adapted less well to altered conditions. This suggests that successful adaptation to climate change is linked to the diversity within a given population prior to the change occurring.
Zhang R, Calixto C, Marquez Y, Venhuizen P, Tzioutziou N, Guo W, Spensley M, Frey N, Hirt H, James A, Nimmo H, Barta A, Kalyna M, Brown J (2016) AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data. Preprint BioRxiv http://dx.doi.org/10.1101/051938Open Access
This preprint includes researchers from the Universities of Dundee (John Brown), Glasgow (Hugh Nimmo) and Vienna and the James Hutton Institute and introduces AtRTD2, a new transcriptome for Arabidopsis and AtRTD2-QUASI for expression analysis and quantification of alternatively spliced isoforms in RNA-seq data.
There are six articles in this weeks Arabidopsis Research Roundup that bridge a diverse range of topics. Firstly lead author Deirdre McLachlan provides an audio description of a study that investigates the role of triacylglycerol breakdown in stomatal signaling. Secondly is a study that assesses the role of a Rab GTPase in control of anisotropic cell growth. The third and fourth papers looks into the defence response, focused on either JA or nitric oxide signaling. Finally are two papers that look into the response of Arabidopsis seedlings to growth on either arsenic or cadmium.
McLachlan DH, Lan J, Geilfus CM, Dodd AN, Larson T, Baker A, Hõrak H, Kollist H, He Z, Graham I, Mickelbart MV, Hetherington AM The Breakdown of Stored Triacylglycerols Is Required during Light-Induced Stomatal Opening Current Biology http://dx.doi.org/10.1016/j.cub.2016.01.019Open Access
The control of stomatal opening is a key environmental response to changes in CO2 levels and water availability. This study, led by Alistair Hetherington (Bristol), demonstrates that triacylglycerols (TAGs), contained in lipid droplets (LD), are critical for light-induced stomatal opening. Following illumination, the number of LDs are reduced through the β-oxidation pathway, a response that requires blue-light receptors. The authors postulate that a reduction in ATP-availability due to delayed fatty acid breakdown contributed to the stomatal phenotype. The lack of available ATP was confirmed following analysis of the activity of a plasma membrane H+-ATPase. Overall the authors suggest that the light-induced breakdown of TAG contributes to an evolutionarily conserved signaling pathway that controls stomatal opening therefore playing a key role in environmental adaptation.
The lead author of this study, Deidre McLachlan kindly provides a brief audio description of this paper.
During our discussion Deidre mentioned some related work that links blue-light signaling and starch degradation during stomatal opening that was included in a recent ARR.
Kirchhelle C, Chow CM, Foucart C, Neto H, Stierhof YD, Kalde M, Walton C, Fricker M, Smith RS, Jérusalem A, Irani N, Moore I (2016) The Specification of Geometric Edges by a Plant Rab GTPase Is an Essential Cell-Patterning Principle During Organogenesis in Arabidopsis. Developmental Cell 36(4):386-400 http://dx.doi.org/10.1016/j.devcel.2016.01.020Open Access Ian Moore (Oxford) is the corresponding author on this UK-German collaboration that investigates the role of a Rab GTPase in pattern formation during organogenesis. It is known that the endomembrane system controls the asymmetric distribution of cargoes to different ‘geometric edges’ of a plant cell, establishing biochemically distinct domains that are important for anisotropic growth. This study identifies a new type of membrane vesicle that accumulates specifically along geometric edges and that contains the RAB-A5c protein which, when inhibited, distorts the geometry of cells in subsequently formed lateral organs (in this case, lateral roots). Interestingly this effect is independent of changes to general endomembrane trafficking. The precise mechanism of RAB-A5c activity is unknown but loss of its activity reduces cell wall stiffness at domain-specific locations, therefore perturbing cell growth in those directions. Therefore this study provides interesting insight into fundamental mechanisms that control the growth of cells in a developing organ.
Thatcher LF, Cevik V, Grant M, Zhai B, Jones JD, Manners JM, Kazan K (2016) Characterization of a JAZ7 activation-tagged Arabidopsis mutant with increased susceptibility to the fungal pathogen Fusarium oxysporum J Exp Bot. http://dx.doi.org/10.1093/jxb/erw040Open Access
Jonathan Jones (TSL) and Murray Grant (Exeter) are collaborators on this research that investigates the role of jasmonic acid signaling in plant resistance to the fungal pathogen Fusarium oxysporum. In this study they show that the JASMONATE ZIM-domain7 (JAZ7) gene is induced by Fusarium oxysporum and that the jaz7-1D mutant has increased suspectibility to infection. This genotype has constitutive JAZ7 expression and also demonstrates sensitivity to a bacterial pathogen. To cause alterations in gene expression, the JAZ7 protein interacts with a range of transcriptional activators and repressors. The authors postulate that in wildtype plants JAZ7 represses the JA-transcriptional network through its interaction with the co-repressor TOPLESS protein and that in the jaz7-1D plants this response network is hyper-activated leading to an inappropriately high response to pathogen attack.
Yun BW, Skelly MJ, Yin M, Yu M, Mun BG, Lee SU, Hussain A, Spoel SH, Loake GJ (2016) Nitric oxide and S-nitrosoglutathione function additively during plant immunity. New Phytol. http://dx.doi.org/10.1111/nph.13903
Gary Loake and GARNet Advisory board member Steven Spoel (Edinburgh) are the leaders of this UK-Korean collaboration that studies the role of Nitric Oxide (NO) in the plant defence response. NO often undergoes S-nitrosylation to produce S-nitrosothiol (SNO), which is important for its bioactivity. This reaction involves the S-nitrosoglutathione reductase 1 (GSNOR1) enzyme, which serves to turnover the NO donor, S-nitrosoglutathione (GSNO). In this study the authors investigate mutant plants that accumulate NO and some a reduction in the basal defence response due to a reduction in salicylic acid (SA) signaling. This response was not rescued by the overexpression of GSNOR1 even though this was able to reduce phenotypes resulting from SNO accumulation. Mutant plants that have increased NO accumulation but lower activity of GSNOR1, so therefore an increased ratio of NO:SNO, were more suspectible to growth of bacterial pathogens. The authors conclude that the relationship between NO and GSNO is critically for plant immunity and development.
Francois Maathuis (York) is the corresponding author of this study that investigates the role of the Arabidopsis aquaglyceroporin NIP7;1 in the uptake of different chemical forms of arsenic. Mutant nip7;1 plants improved the tolerance of arsenic by reducing uptake of the chemical. This is the first demonstration for the role of a NIP transporter in the response to arsenic and highlights the possibility of focussing on these proteins as a target for breeding or genetically-modifying tolerance to this toxic metal.
Wang H, He L, Song J, Cui W, Zhang Y, Jia C, Francis D, Rogers HJ, Sun L, Tai P, Hui X, Yang Y, Liu W (2016) Cadmium-induced genomic instability in Arabidopsis: Molecular toxicological biomarkers for early diagnosis of cadmium stress Chemosphere 150:258-265 http://dx.doi.org/10.1016/j.chemosphere.2016.02.042
Hilary Rodgers (Cardiff) is the sole UK representative on this Chinese study that has developed screening parameters to evaluate the growth of plants on cadmium. The study uses microsatellite instability (MSI) analysis, random-amplified polymorphic DNA (RAPD), and methylation-sensitive arbitrarily primed PCR (MSAP-PCR) to define a range of genomic alterations that occurred after growth of Arabidopsis plants across a range of concentrations of cadmium. They conclude that analysis of genomic methylation polymorphisms were the most sensitive biomarkers to diagnosis early cadmium stress in these plants and provide important insights for future biomonitoring strategies.
Just three papers in this weeks Arabidopsis Research Roundup and they each cover fundamental aspects of the hormone and environmental control of gene expression. First Keith Lindsey provides an audio description of work that aims to dissect the complex hormonal regulation of root growth while secondly, Nick Harberd is involved in a study that investigates the HY5 shoot-root signaling protein. Finally Ian Graham leads a study into factors that regulate seed dormancy.
Rowe JH, Topping JF, Liu J, Lindsey K (2016) Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin New Phytol. http://dx.doi.org/ 10.1111/nph.13882Open Access Keith Lindsey (Durham) is the corresponding author for this study that investigates the complex hormonal network that regulates the Arabidopsis root response to osmotic stress. The effect of ABA, cytokinin and ethylene on auxin transport are assessed through changes in the dynamics of PIN protein expression. Unsurprisingly they discover a wide range of effects transmitted via crosstalk between these four hormones and that these effects act in a tissue specific manner, as the expression of PIN1 (in the vascular tissue) and PIN2 (in the lateral root cap and epidermis) are altered in different ways. Ultimately the authors conclude that the classic ‘stress hormone’ ABA regulates the root response to drought together with auxin, ethylene and cytokinin in a complex signaling network.
Keith has kindly supplied a brief audio description of this work.
Chen X, Yao Q, Gao X, Jiang C, Harberd NP, Fu X (2016) Shoot-to-Root Mobile Transcription Factor HY5 Coordinates Plant Carbon and Nitrogen Acquisitionhttp://dx.doi.org/10.1016/j.cub.2015.12.066
GARNet committee member Nick Harberd (Oxford) is the UK representative on this Chinese-led study that investigates the mode of action of the mobile transcription factor ELONGATED HYPOCOTYL5 (HY5). It has been long known that HY5, a bZIP TF, regulates growth responses to light and in this study the authors demonstrate that HY5 controls light-regulated root growth and nitrate uptake. Remarkably, HY5 from the shoot can activate root-derived HY5, in turn switching on the nitrate transporter NRT2.1. This response involves a mechanism that senses carbon:nitrogen balance across different light conditions, thus placing HY5 as a key regulator in the whole-plant response to changing environmental conditions.
Dave A, Vaistij FE, Gilday AD, Penfield SD, Graham IA (2016) Regulation of Arabidopsis thaliana seed dormancy and germination by 12-oxo-phytodienoic acid Journal of Experimental Botany http://dx.doi.org/10.1093/jxb/erw028Open Access
This paper results from a collaboration between the labs of Ian Graham (CNAP, York) and Steve Penfield (John Innes Centre) and features an investigation into factors that regulate seed germination. Previously it was known that oxylipin 12-oxo-phytodienoic acid (OPDA) acts together with ABA to regulate germination but this study elucidates that OPDA specifically acts via the ABI5 and RGL2 hormone-regulated proteins. Furthermore the OPDA-ABA signal also acts via another dormancy promoting factor, MOTHER-OF-FT-AND-TFL1 (MFT). Therefore maintenance of dormancy in Arabidopsis seedlings is regulated by ABA and MFT promoting the accumulation of OPDA, highlighting this as a critical control point in this complex process.
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.1518369112Open 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.
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.
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