Arabidopsis Research Roundup: December 8th.

This weeks Research Roundup begins with two papers from the University of Edinburgh on very different topics of Arabidopsis research. Firstly Alistair McCormick and Sofirtios Tsaftaris introduce a new low-cost phenotyping platform whilst Gerben Ooijen’s group has analysed the role of SUMOylation in the control of the circadian clock. The next three papers each involve wide UK collaborations and either look at plant nutrient composition (Nottingham, Dundee, York), the role of N-end rule pathway in the control of seed storage mobilisation (Rothamsted, Nottingham, Oxford, Birmingham, Cambridge) or the development of a new tool for the study of phloem sieve elements (Leeds, Rothamsted, Cambridge, Newcastle). The penultimate paper from Daniel Zilbermann (JIC) highlights the global mechanisms of methyltransferase function in Arabidopsis and mice whilst the final paper from Alexandre Ruban (QMUL) and co-authors continues his groups work to unpick the specifics of NPQ.


Dobrescu A, Scorza LCT, Tsaftaris SA, McCormick AJ (2017) A “Do-It-Yourself” phenotyping system: measuring growth and morphology throughout the diel cycle in rosette shaped plants. Plant Methods. doi: 10.1186/s13007-017-0247-6

Open Access

University of Edinburgh colleagues Alistair McCormick and Sofirtios Tsaftaris lead this work that presents a low cost phenotyping system for the analysis of the growth rate and phenotypic characteristics of Arabidopsis thaliana rosettes. The software that they have developed allows the accurate segmentation of multiple rosettes within a single image and overall offers a straightforward solution for automated phenotyping across a range of growth environments.


Hansen LL, van den Burg HA, van Ooijen G (2017) Sumoylation Contributes to Timekeeping and Temperature Compensation of the Plant Circadian Clock. J Biol Rhythms. doi: 10.1177/0748730417737633

Gerben van Ooijen (University of Edinburgh) is the corresponding author of this work that has identified SUMOylation as a novel mechanism of regulating circadian clock genes in Arabidopsis. Plants with defects in sumoylation have altered circadian periods that exhibit incorrect temperature compensation. Overall these results indicate that sumoylation importantly buffers clock function in response to changing temperatures.


Alcock TD, Havlickova L, He Z, Bancroft I, White PJ, Broadley MR, Graham NS (2017) Identification of Candidate Genes for Calcium and Magnesium Accumulation in Brassica napus L. by Association Genetics. Front Plant Sci. doi: 10.3389/fpls.2017.01968

Open Access

Neil Graham and Martin Broadley (University of Nottingham) are the corresponding authors of this study that has taken advantage of the Brassica napus Associative Transcriptomes RIPR diversity panel developed by Ian Bancroft’s lab in York. Novel loci involved with an altered response to calcium and magnesium were identified in B.napus before mineral composition was analysed in Arabidopsis mutants defective in orthologous genes. The analysed plants exhibited alteration in mineral composition, meaning that the associated Brassica loci might be targets for future breeding strategies aimed at improving plant nutrient compositions.


Zhang H, Gannon L, Hassall KL, Deery MJ, Gibbs DJ, Holdsworth MJ, van der Hoorn RAL, Lilley KS, Theodoulou FL (2017) N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway. New Phytol. doi: 10.1111/nph.14909

Freddie Theodoulou (Rothamsted Research) is the corresponding author of this research that involved a collaboration with colleagues in Cambridge, Birmingham, Nottingham and Oxford. They have performed a proteomic analysis on etiolated seedlings to identify those proteins designated for degradation by the N-end rule pathway. They analysed prt6 mutant plants that lack the function of the E3 ligase PROTEOLYSIS6 (PRT6) and discovered that N-terminal peptides from 45 protein groups were upregulated in this mutant, corresponding to the equivalent downregulation of several known N-end rule proteases. Overall the authors show that PRT6 plays an important role in the regulation of seed storage mobilisation in young seedlings and is therefore a possible future target to manipulate the plant responses to adverse environmental conditions. Dr Kirsty Hassall, a statistician at Rothamsted, is an author on this paper and in the latest edition of the GARNish newsletter explains how she interacts with plant scientists during her work.


Torode TA, O’Neill RE, Marcus SE, Cornuault V, Pose-Albacete S, Lauder RP, Kracun SK, Gro Rydahl M, Andersen MCF, Willats WGT, Braybrook SA, Townsend BJ, Clausen MH, Knox JP (2017) Branched pectic galactan in phloem-sieve-element cell walls: implications for cell mechanics. Plant Physiol. doi: 10.1104/pp.17.01568 Open Access

Paul Knox (University of Leeds) is the corresponding author of this study that includes contributions from researchers at SLCU, Newcastle and Rothamsted. This work is based around the development of a monoclonal antibody, LM26 that is able to recognize a β-1,6-galactosyl substitution of β-1,4-galactan. LM26 has allowed the identification of this unusual branched galactan that is specific to phloem elements and the authors hope that it can be a useful tool in future studies on the biology of phloem elements


Lyons DB, Zilberman D (2017) DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. Elife. doi: 10.7554/eLife.30674 Open Access

Daniel Zilberman has recently moved to the John Innes Centre and is the lead author of this work that was conducted when he was working in US. This research is a cross-kingdom analysis showing that nucleosome-free DNA is the preferred target for methyltransferases in both Arabidopsis and mice, and that nucleosomes appear to be a barrier to the function of these enzymes. Furthermore they demonstrate that linker-specific methylation that is usually absent in Arabidopsis can be introduced by removal of histone H1. This shows that flowering plants still possess this ability despite its loss, during the evolution of H1, over a billion years ago.


Tutkus M, Chmeliov J, Rutkauskas D, Ruban AV, Valkunas L (2017) Influence of the Carotenoid Composition on the Conformational Dynamics of Photosynthetic Light-Harvesting Complexes. J Phys Chem Lett. doi: 10.1021/acs.jpclett.7b02634

Alexandre Ruban (QMUL) is a co-author on this study that investigates the role that carotenoid composition plays in the control of Non-photochemical quenching (NPQ), a mechanism that protects the photosynthetic apparatus from light-damage. Arabidopsis mutants with differing carotenoid compositions were analysed for the dynamics of the conformation switches that occur during NPQ. Interestingly they show that LHCII has robust function  that is resistant to different carotenoid concentrations.

Arabidopsis Research Roundup: August 14th

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Published on: August 14, 2017

This weeks UK Arabidopsis Research Roundup includes a study from the lab of GARNet Chairman Steven Spoel that describes their work on the control of ROS signaling. The other two papers looks at different aspects of photosynthetic control. Firstly Giles Johnson (University of Manchester) investigates the proteomic changes that occur during dynamic acclimation. Finally Alex Webb’s lab (University of Cambridge) investigate how the products of photosynthesis feed into ethylene-dependent control of the circadian clock.


Kneeshaw S, Keyani R, Delorme-Hinoux V, Imrie L, Loake GJ, Le Bihan T, Reichheld JP, Spoel SH (2017) Nucleoredoxin guards against oxidative stress by protecting antioxidant enzymes.

PNAS https://doi.org/10.1073/pnas.1703344114 Open Access

GARNet Chairman Steven Spoel (University of Edinburgh) leads this Franco-UK collaboration that investigated the role of the pathogen-induced oxidoreductase Nucleoredoxin 1 (NRX1) during the response to oxidative stress. They show that NRX1 targets a range of enzymes that are responsible for scavenging damaging cellular H2O2 and subsequently protect these enzymes from damage. This unexpected regulatory mechanism demonstrates a key role for NRX1 in protecting plants from the oxidative stress, which is an important component of the plants defence response.

Steven discussed this paper below. This audio is also on GARNet YouTube and iTunes channels.


Miller MAE, O’Cualain R, Selley J, Knight D, Karim MF, Hubbard SJ, Johnson GN (2017) Dynamic Acclimation to High Light in Arabidopsis thaliana Involves Widespread Reengineering of the Leaf Proteome Front Plant Sci. https://doi.org/10.3389/fpls.2017.01239 Open Access

Giles Johnson leads this collaborations between two departments from the University of Manchester that has looked at changes to the leaf proteome that occur under differing light conditions. Transferring leaves from low to high light conditions causes a process called dynamic acclimation, which is perturbed in gpt2 mutants. Proteomic analysis of wildtype and gpt2 leaves reveals that a similar number of proteins are changed during dynamic acclimation but the identify of these is altered, with a reduced abundance of proteins involved in photosynthesis. Interestingly gpt2 showed an increase in the number of proteins involved in the stress response.

In 2016 Giles talked to GARNet about a different paper that looks at cold acclimation in Arabidopsis.


Haydon MJ, Mielczarek O, Frank A, Román Á, Webb AA (2017) Sucrose and ethylene signaling interact to modulate the circadian clock. Plant Physiol. https://doi.org/10.1104/pp.17.00592 Open Access

Alex Webb (University of Cambridge) collaborates with Mike Laydon (previously at York, now at the University of Melbourne) on this study that links photosynthesis with circadian and hormone signalling. Previous work showed that GIGANTEA (GI) is necessary to maintain sucrose-dependent circadian oscillations in the dark. This extension of that work demonstrates that sucrose stabilises GI by altering the activity of the ZEITLUPE (ZTL) F-box protein, which is surprisingly dependent on the key ethylene signalling intermediate CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1). Over recent times the role of ethylene on control of the circadian clock has been overlooked but this study shows that the hormone can shorten the circadian period through the activity of sucrose and GI. This study integrates another signal into our understanding of the exquisite regulatory relationships that control clock function.


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Arabidopsis Research Roundup: March 6th.

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Published on: March 6, 2017

This weeks Arabidopsis Research Roundup includes four papers that focus on different aspects of plant cell biology. Firstly Ian Henderson’s research group in Cambridge defines the role of a critical component that determines crossover frequency in plants and other eukaryotes. Secondly Karl Oparka (Edinburgh) leads a broad collaboration that defines the mechanism of unloading of solutes and macromolecules from the root phloem. Thirdly Keith Lindsey (Durham) has developed a model that describes how auxin patterns the Arabidopsis root. Finally Mike Blatt (Glasgow) is part of a group that uses Arabidopsis as a framework for the study of ABA-signaling during stomatal movement in ferns.


Ziolkowski PA, Underwood CJ, Lambing C, Martinez-Garcia M, Lawrence EJ, Ziolkowska L, Griffin C, Choi K, Franklin FC, Martienssen RA, Henderson IR (2017) Natural variation and dosage of the HEI10 meiotic E3 ligase control Arabidopsis crossover recombination. Genes Dev

http:/​/​dx.​doi.​org/10.1101/gad.295501.116

Open Access

GARNet committee member Ian Henderson (University of Cambridge) leads this work that features collaborators from the UK, US and Poland. They use an experimental technique that allows facile analysis of recombination rates alongside a study of Arabidopsis natural variation to isolate a QTL that is critical for maintaining the correct number of crossovers during meiosis. This HEI10 gene codes for an E3 ligase (the targets of which are currently unknown) whose copy number is a key component in the control of recombination rate. Hei10 mutants have less crossovers whilst plants with extra copies of HEI10 have an increased number, especially in sub-telomeric regions of the genome. HEI10 is a highly conserved protein, demonstrating its important role to ensure appropriate levels of recombination throughout the evolution of eukaryotes.

Ian kindly takes ten minutes to discuss this paper with GARNet on our YouTube Channel.


Ross-Elliott TJ, Jensen KH, Haaning KS, Wager BM, Knoblauch J, Howell AH, Mullendore DL, Monteith AG, Paultre D, Yan D, Otero-Perez S, Bourdon M, Sager R, Lee JY, Helariutta Y, Knoblauch M, Oparka KJ (2017) Phloem unloading in Arabidopsis roots is convective and regulated by the phloem-pole pericycle. Elife.

http:/​/​dx.​doi.​org/10.7554/eLife.24125

Open Access

Karl Oparka (University of Edinburgh) is the corresponding author of this study that includes researchers from the UK, US and Denmark. Movement of solutes and macromolecules through the plant phloem is key for the correct distribution of nutrients allowing for optimal growth. In this paper they discover that unloading of molecules from the phloem occurs via a set of specialized funnel plasmodesmata that link the phloem to adjacent pericycle cells. Remarkably they find that whereas solutes are constantly unloaded, larger proteins are released through these plasmodesmata in discrete pulses, which they describe as ‘batch unloading’. Overall this study provides evidence of a major role for the phloem-pericycle cells in the process of moving essential nutrients from the phloem into surrounding tissues.


Moore S, Liu J, Zhang X, Lindsey K (2017) A recovery principle provides insight into auxin pattern control in the Arabidopsis root. Sci Rep. http:/​/​dx.​doi.​org/10.1038/srep43004

Open Access

The work comes from the lab of Keith Lindsey (University of Durham) and developes a data-driven model that predicts the role of auxin patterning in the recovery of an Arabidopsis root following a perturbation of polar auxin transport. They demonstrate three main principles that define the role of auxin influx and efflux carriers in this process and also provide experimental validation for their predictions.


Cai S, Chen G, Wang Y, Huang Y, Marchant B, Wang Y, Yang Q, Dai F, Hills A, Franks PJ, Nevo E, Soltis D, Soltis P, Sessa E, Wolf PG, Xue D, Zhang G, Pogson BJ, Blatt MR, Chen ZH (2017)

Evolutionary Conservation of ABA Signaling for Stomatal Closure in Ferns Plant Physiol

http:/​/​dx.​doi.​org/10.1104/pp.16.01848

Open Access

Mike Blatt (University of Glasgow) is a co-author on this global study that looks into the evolution of ABA-signaling in the control of stomatal closure. Although this study is focused on this process in ferns they build their findings on the analysis of transcriptional networks from Arabidopsis. Ultimately they find that the evolution of ABA-controlled guard cells movements are important in the adaptation of ferns to a terrestrial environment.

Arabidopsis Research Roundup: January 17th

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

http:/​/​dx.​doi.​org/10.1016/j.cub.2016.11.012

Open Access
PIF4
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.

http:/​/​dx.​doi.​org/10.1242/jcs.194712

Open Access

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.
LINC


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

Open Access
PhenoTiki
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

Open Access
CysProtease
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.

http:/​/​dx.​doi.​org/10.1186/s12870-016-0955-5

Open Access

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.

<a href=”http://onlinelibrary.wiley.com/doi/10.1111/pce.12903/full” onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘http://onlinelibrary.wiley generic cialis express.com/doi/10.1111/pce.12903/full’, ‘http:/​/​dx.​doi.​org/10.1111/pce.12903’]);” target=”_blank”>http:/​/​dx.​doi.​org/10.1111/pce.12903

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.

Arabidopsis Research Report: May 26th

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

http://dx.doi.org/10.1105/tpc.16.00011 Open Access

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

From 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

http://dx.doi.org/10.1016/j.plaphy.2016.03.037

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.

Hubbard, K, Dodd, A. (2016). Rhythms of Life: The Plant Circadian Clock. Teaching Tools in Plant Biology: Lecture Notes. http://dx.doi.org/10.1105/tpc.116.tt0416

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.

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: April 14th

This week Arabidopsis Research Roundup contains two studies that originate at the University of Birmingham. Firstly George Bassel kindly provides an audio description of a study that looks at the processes regulating seed germination. Secondly Juliet Coates leads an investigation into the function of evolutionarily conserved ARABIDILLO proteins. Elsewhere is a University of Edinburgh study into the tissue-specificity of PhyA responses and lastly an investigation of the phytotoxic effects of Cerium nanoparticles.

Nieuwland J, Stamm P, Wen B, Randall RS, Murray JA, Bassel GW (2016) Re-induction of the cell cycle in the Arabidopsis post-embryonic root meristem is ABA-insensitive, GA-dependent and repressed by KRP6. Sci Rep. http://dx.doi.org/10.1038/srep23586 Open AccessRootTip

George Bassel (Birmingham), GARNet PI Jim Murray (Cardiff) and Jeroen Nieuwland (South Wales) are the leaders of this study that investigates the activation of the root meristem during germination, a process that requires de novo GA synthesis. Using hormone applications and genetic analysis the authors show that root meristem can begin elongation independent of germination, which is defined as occurring following both testa rupture and radicle protrusion. KRP6 is a cell cycle regulator and partially represses activation of the cell cycle by GA so krp6 mutants germinate more rapidly. Overall this study concludes that the cell cycle can uncouple the interactions of GA and ABA that act to conclude germination and promote root meristem elongation.

George Bassel kindly provides a short audio description of this paper.

Moody LA, Saidi Y, Gibbs DJ, Choudhary A, Holloway D, Vesty EF, Bansal KK, Bradshaw SJ, Coates JC (2016) An ancient and conserved function for Armadillo-related proteins in the control of spore and seed germination by abscisic acid. New Phytol. http://dx.doi.org/10.1111/nph.13938 Open Access

This study comes exclusively from the University of Birmingham and is led by Juliet Coates. This group investigates the role of Armadillo-related ARABIDILLO proteins on branching processes across plant species. In the moss Physcomitrella patens these proteins are linked to the action of the hormone ABA on spore germination, which converges with a role for the proteins in Arabidopsis seed germination. Importantly both P.patens and Selaginella moellendorffii ARABIDILLO proteins are able to substitute for native proteins in Arabidopsis, demonstrating their conserved function. The authors conclude that these proteins were co-opted into the regulation of both sporophytic and gametophytic processes early in plant evolution.

Kirchenbauer D, Viczián A, Ádám É, Hegedűs Z, Klose C, Leppert M, Hiltbrunner A, Kircher S, Schäfer E, Nagy F (2016) Characterization of photomorphogenic responses and signaling cascades controlled by phytochrome-A expressed in different tissues. New Phytologist . http://dx.doi.org/10.1111/nph.13941 Open Access

Ferenc Nagy (Edinburgh) is the corresponding author of this Hungaro-German study that focuses on how phytochrome responses are mediated in a tissue-specific manner. Considering that phyA is expressed throughout plant tissues it remained a mystery as to how the PhyA responses are able to control plant development. This study used tissue-specific promotors to drive PHYA production in a variety of tissues and discovered that expression in a limited number of tissues is able to regulate flowering time and root growth. In addition they find evidence for the intercellular movement of PhyA. The authors conclude that the PhyA response is partly controlled by a mix of tissue-specific expression and the regulation of key downstream factors in a tissue-autonomous cell activity.

Yang X, Pan H, Wang P, Zhao FJ (2016) Particle-specific toxicity and bioavailability of cerium oxide (CeO2) nanoparticles to Arabidopsis thaliana J Hazard Mater. http://dx.doi.org/10.1016/j.jhazmat.2016.03.054

GraphThis Sino-UK-Australian study is led by Fang-Jie Zhao at Rothamstead Research. They investigate the uptake and phytotoxicity of commonly used (in consumer products) cerium oxide nanoparticles (CeO2-NPs) into Arabidopsis. At high concentrations the NP component, but not the Ce ions, were shown to have toxic effects on plant growth. These CeO2-NPs were taken up and translocated to the shoot where they aggregate in needle-like particles. This movement was independent of the type or concentation of Ce. The authors suggest this represents important information for the environmental considerations linked to the use and disposal of this type of NPs.

Arabidopsis Research Roundup: March 4th 2016

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 (2016) The Breakdown of Stored Triacylglycerols Is Required during Light-Induced Stomatal Opening Current Biology http://dx.doi.org/10.1016/j.cub.2016.01.019 Open Access
Slide 1
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.2016.01.020 Open Access
Rab5C
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/erw040 Open 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.

Lindsay ER, Maathuis FJ (2016) Arabidopsis thaliana NIP7;1 is Involved in Tissue Arsenic Distribution and Tolerance in Response to Arsenate FEBS Lett. http://dx.doi.org/10.1002/1873-3468.12103

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.

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