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.

Passing the threshold gives a Giant output!

Categories: Cambridge University
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Published on: February 23, 2017

A recent Arabidopsis Research Roundup included a paper from Adrienne Roeder’s lab in Cornell that includes James Locke and Henrik Jonsson from SLCU. The research focuses on the Arabidopsis sepal, which has been the central theme of the Roeder lab since it was set up a few years ago. On a personal level I recall seeing a talk on this topic maybe 10 years ago and it’s always struck me as a fantastically simplistic system that can be used to answer some fundamental questions about the processes that control cell patterning.

This latest paper is focused on the important question of how adjacent cells are set on different development paths, using the giant sepal cells as an excellent model system. This type of cell type specificity is thought to develop following mild stochastic fluctuations in gene expression that lead into feedback loops that accentuate these initial differences. However this has not yet been visualized in vivo until this new manuscript in Elife

The sepal is the outermost organ of the Arabidopsis flower and its correct shape relies on the formation of giant epidermal cells that can grow up to 20% of the entire organ length. These are necessary for the correct function of the organ (to facilitate flower opening) and they form in approximately equal numbers to non-giant cells. Prior to this paper the mechanism of this patterning remained opaque as giant cells can form either adjacent to or apart from each other. The ATML1 transcription factor plays an important role in general Arabidopsis epidermal patterning and has been shown to be required for the generation of giant sepal cells. Importantly the increased size of these giant cells is facilitated by rounds of endoreduplication that can result in 64C nuclei.


ATML1 is expressed in all sepal cells yet only a subset of these will become giant. By using ATML1-overexpression lines together with a simple genetic analysis, the authors show that gene dosage of the ATML1 gene determines the number of giant cells that form (constitutive ATML1 expression have all giant cells). The mechanism by which this dosage results in a mixed cell fate was unclear until they found (using a line containing a fluorescent ATML1-Citrine protein) that ATML1 expression fluctuated far more in the sepal cells than did other genes expressed in the same tissue.

The authors used some fantastic live imaging to show that there are high levels of ATML1 expression in cells destined for giant fate. Although this was not an absolute relationship (as some smaller cells also showed high ATML1 expression), they mathematically demonstrate that obtaining a high threshold of ATML1 correlated about 70% of the time with uptake of giant cell fate.

Finer detail was added to this picture when it became clear that obtaining this threshold at a particular phase of the cell cycle was much more strongly correlated with giant-cell fate. If this threshold is obtained when DNA content was 4C (occurring after DNA replication in G2 phase of the cell cycle) then in 80% of the time the cell became giant. As the authors state ‘a cell is competent to respond to high levels of ATML1 mainly during G2 to induce giant cell formation’.


Finally the authors used plants with a mutation in the LGO gene (LOSS OF GIANT CELLS FROM ORGANS), which have sepals with no giant cells, to determine whether there was feedback control of ATML1 once giant cell fate had been determined. The lgo mutant is epistatic to atml1 and consistent with this observation they show that ATML1 fluctuates normally in the lgo mutant but that this signal does not lead to endoreduplication and giant cell formation. Therefore there is no feedback loop that features endoreduplication and ATML1; rather there is a linear mechanism in which ATML1 fluctuations set in motion endoreduplication, which then continues independent of those ongoing fluctuations.

 

This data was then used to develop a model that could precisely predict the location of giant cell formation based on this information about rapid yet relatively small fluctuations in ATML1 levels.
  Overall this study is an outstanding example of using technological advances in live imaging in a simple experimental system to help develop an understanding of a complex regulatory system. It remains to be seen whether this type of threshold-fluctuation model is important for patterning in other tissues. However this case is an scientific tour of force, demonstrating what is possible when technical advances are put together with careful measurements and inspired experimental planning!

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 Roundup: January 11th

The first Arabidopsis Research Roundup of 2017 includes a wide range of studies that use our favourite model organism.

Firstly Kerry Franklin (University of Bristol) is the corresponding author on a paper that describes the complex interaction between the responses to sunlight and heat. Secondly Paul Dupree (University of Cambridge) leads a study that defines the important structural relationship between xylan and cellulose. Thirdly members of Gos Micklem’s group in Cambridge are part of the Araport team that present their ThaleMine tool.

Richard Napier (University of Warwick) is a co-author on the fourth paper that introduces a new chemical tool for study of the auxin response. The penultimate paper includes Matthew Terry (University of Southampton) on a paper that investigates the role of a Fe-S-containing protein cluster in chlorophyll biosynthesis and finally there is a methods paper from Stefanie Rosa in Caroline Dean’s lab at the John Innes Centre that describes the use of FISH to detect single molecules of RNA.


Hayes S, Sharma A, Fraser DP, Trevisan M, Cragg-Barber CK, Tavridou E, Fankhauser C, Jenkins GI, Franklin KA (2016) UV-B Perceived by the UVR8 Photoreceptor Inhibits Plant Thermomorphogenesis. Current Biology http:/​/​dx.​doi.​org/10.1016/j.cub.2016.11.004

Open Access

This collaboration between the research groups of Kerry Franklin (University of Bristol) and Gareth Jenkins (University of Glasgow) looks at how the perception of UV-B light inhibits the morphological changes that occur in response to increased temperatures (thermomorphogenesis). This response includes induced hypocotyl elongation, which is mediated via PIF4 and various players in the auxin response. Interestingly the authors show that UV-B light perceived by UVR8 attenautes this response by preventing PIF4 abundance and by stabilising the the bHLH protein LONG HYPOCOTYL IN FAR RED (HFR1) protein. These results suggest that there exists a precise mechanism for fine-tuning the growth responses that occur in sunlight that would usually include both increased temperature and UV-B irradiation.
UVB_pic


Simmons TJ, Mortimer JC, Bernardinelli OD, Pöppler AC, Brown SP, deAzevedo ER, Dupree R, Dupree P (2016) Folding of xylan onto cellulose fibrils in plant cell walls revealed by solid-state NMR. Nat Commun.

http:/​/​dx.​doi.​org/10.1038/ncomms13902 Open Access
In this paper Paul Dupree (University Cambridge) collaborates both with colleagues in Spain and with his father Ray, who is a physicist at the University of Warwick. They use NMR to perform a structural analysis of xylan, which is the most prevalent non-cellulosic polysaccharide in the cell wall matrix and binds to cellulose microfibrils. Whereas in solution xylan forms a threefold helical screw, it flattens into a twofold helical screw ribbon to closely bind to cellulose when in the cell wall. They used the cellulose-deficient Arabidopsis irx3 mutant to show that the xylan two-fold screw confirmation breaks down when it cannot bind cellulose. The authors state that this finding has important implications in our understanding of the formation of the cell wall and perhaps more importantly how it might be broken down during attempts to maximise economic usages of plant biomass.

A local Cambridge newspaper reported that this finding could ‘pave the way for wooden skyscrapers’
XylanPic


Krishnakumar V, Contrino S, Cheng CY, Belyaeva I, Ferlanti ES, Miller JR, Vaughn MW, Micklem G, Town CD, Chan AP (2016) ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery. Plant Cell Physiol http:/​/​dx.​doi.​org/10.1093/pcp/pcw200 Open Access

This paper is presented by the Araport team, which is based in the USA but includes representatives from Gos Micklem’s lab in University of Cambridge. They outline the functionality of the ThaleMine data warehouse which is an important component of the tools included on Araport (https://www.araport.org/). ThaleMine collects a wide variety of data from public datasets and presents it in a easy-to-interrogate form, facilitating the experiments of both lab-based researchers or bioinformaticians. This tool is build upon the InterMine software framework, which has been widely adopted across other model organisms.

Chris Town and Sergio Contrino provided a hands-on workshop describing the tools on Araport in last year GARNet2016 meeting and their workshop materials can be downloaded here.


Steenackers WJ, Klíma P, Quareshy M, Cesarino I, Kumpf RP, Corneillie S, Araújo P, Viaene T, Goeminne G, Nowack MK, Ljung K, Friml J, Blakeslee JJ, Novák O, Zažímalová E, Napier RM, Boerjan WA, Vanholme B (2016) cis-cinnamic acid is a novel, natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiol. http:/​/​dx.​doi.​org/pp.00943.2016 Open Access
cCApic
This pan-european collaboration includes members of Richard Napier’s lab at the University of Warwick. They outline the activity of a novel inhibitor of auxin efflux transport called cis-cinnamic acid (c-CA). When c-CA is applied to growth media plants appears to exhibit an auxin-response phenotype yet these experiments show that c-CA is neither an auxin or anti-auxin and in fact blocks local auxin efflux, thus causing buildup of cellular auxin. This effect does not occur with t-CA showing specificity for c-CA and it does not affect long distance auxin transport, which occurs through the phloem. Therefore this paper presents a new pharamolgical tool for the study of in planta auxin transport and homeostasis.


Hu X, Page MT, Sumida A, Tanaka A, Terry MJ, Tanaka R (2016) The iron-sulfur cluster biosynthesis protein SUFB is required for chlorophyll synthesis, but not phytochrome signaling. Plant J.

http:/​/​dx.​doi.​org/10.1111/tpj.13455

Matthew Terry and Mike Page (University of Southampton) are co-authors on this Japanese-led study that investigates the function of the SUFB subunit of the SUFBCD iron-sulfur cluster. These Fe-S protein clusters play roles in many metabolic processes and the SUFB mutant hmc1 exhibits a defect in chlorophyll biosynthesis due to an accumulation of Mg-containing biosynthetic intermediates. In addition both SUFC- and SUFD-deficient RNAi lines accumulated the same Mg intermediate indicating that the SUFBCD cluster is responsible for this step necessary for chlorophyll production.


Duncan S, Olsson TS, Hartley M, Dean C, Rosa S (2016) A method for detecting single mRNA molecules in Arabidopsis thaliana. Plant Methods. http:/​/​dx.​doi.​org/10.1186/s13007-016-0114-x

Open Access
This paper from is lead by Stefanie Rosa in Caroline Dean’s lab at the John Innes Centre describes a novel method for imaging single molecules of RNA by smFISH. They analyse the localisation of both nascent and mature mRNAs, allowing for analysis of the location of RNA processing and translation.<
RosaPic

Arabidopsis Research Roundup: December 29th

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Published on: December 28, 2016

The final Research Roundup of 2016 includes two papers that take different strategies toward the ultimate aim of crop improvement and use Arabidopsis as a tool for their initial discoveries. Firstly Christine Raines (University of Essex) uses a transgenic approach to upregulate enzymes of the calvin cycle while researchers from Rothamstead and Oxford use a chemical intervention strategy. Both of these strategies are successful in increasing yield.

Second are a set of back-to-back papers featuring Xiaoqi Feng (JIC) that investigate DNA methylation patterns in both male and female gametes.

Finally Henrik Jonsson (SLCU) leads a paper that precisely defines the parameters that are important in determining the relationship between cell size, location and cytokinesis.

 

Simkin AJ, Lopez-Calcagno PE, Davey PA, Headland LR, Lawson T, Timm S, Bauwe H, Raines CA (2016) Simultaneous stimulation of the SBPase, FBP aldolase and the photorespiratory GDC-H protein increases CO2 assimilation, vegetative biomass and seed yield in Arabidopsis. Plant Biotechnol J http://dx.doi.org/10.1111/pbi.12676

Open Access
Raines
GARNet Committee Member Christine Raines leads this UK-German study that alters the amounts of three calvin cycle enzymes and assesses the subsequent change in photosynthetic rate in Arabidopsis plants. These enzymes sedoheptulose 1,7-bisphosphatase (SBPase), fructose 1,6-bisphophate aldolase (FBPA) and the glycine decarboxylase H-protein (GDC-H) were overexpressed either individually or together and each plant shows an increase in the quantum efficiency of photosystem II. This results in improved CO2 fixation and a concomitant increase in leaf area and biomass. Overall the authors have shown that this transgenic gene stacking approach can have potential for improving plant productivity.


Griffiths CA, Sagar R, Geng Y, Primavesi LF, Patel MK, Passarelli MK, Gilmore IS, Steven RT, Bunch J,, Paul MJ, Davis BG (2016) Chemical intervention in plant sugar signalling increases yield and resilience. Nature

http://dx.doi.org/10.1038/nature20591

This study is a collaboration between Rothamstead Research and the University of Oxford and has been featured in a recent Nature podcast. This paper outlines a chemical intervention strategy to improve crop productivity and includes some fundamental work performed in Arabidopsis. They used a ”signaling-precursor concept” to design and synthesise a plant permeable version of Trehalose-6-phosphate (T6P), which could readily be uptaken and activated by sunlight in planta. Addition of T6P to wheat increases grain yield whilst when applied to leaf tissue it improves recovery from drought stress. This is an exciting test case to show the potential of chemical intervention yet the authors are rightly cautious when considering the general use of the compound given the variability of field conditions.
Nature


Hsieh PH, He S,, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X (2016) Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. PNAS http://dx.doi.org/10.1073/pnas.1619074114

Xiaoqi Feng (John Innes Centre) is the corresponding author on this study that investigates the transgenerational maintenance of methylation through the male germline. They undertook the challenging purification of Arabidopsis pollen sperm and vegetative cells from both wildtype plants and plants that contains mutations within different DNA methytransferases. They show that background methylation is equivalent in sperm, vegetative and somatic cells but that specific CG methylation is higher in pollen sperm and vegetative cells than in somatic cells. The authors suggest that this allows more accurate inheritance of methylation patterns across successive generations.


Park K, Kim MY, Vickers M, Park JS, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S (2016) DNA demethylation is initiated in the central cells of Arabidopsis and rice. PNAS http://dx.doi.org/10.1073/pnas.1619047114

In this second of back-to-back papers, Xiaoqi Feng is a co-author on an international study that looks into the role of the DEMETER DNA demethylase on the control of gene expression in the endosperm. This tissue results from the fusion of a male pollen sperm cell and the female central cell and is associated with significant demethylation. This study documents the first genome-wide analysis of DNA methylation in the female central cell in Arabidopsis. They show that DNA demethylation requires DEMETER function but that it is likely not associated with the downregulation of the MET1 methytransferase. Therefore the authors suggest that characteristic endospermal DNA demethylation occurs through locus-specific activity.


Willis L,, Refahi Y, Wightman R, Landrein B, Teles J, Huang KC,, Meyerowitz EM,,, Jönsson H (2016) Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche. PNAS http://dx.doi.org/10.1073/pnas.1616768113

Henrik Jonsson (Sainsbury Lab Cambridge) is the corresponding author on this UK-US collaboration that uses a 4D imaging pipeline to track the growth of epidermal cells in the Arabidopsis shoot apical meristem (SAM). They suggest that neither cell size or cell age are determinants for progression to cytokinesis, which is also independent of cell contact topologies and the cell position within the SAM. However they find that a more complex mix of parameters determine the constraints on determination of cell size. Following cell division they also show that a smaller daughter cell will grow at a faster rather than its larger sister, a finding that the authors suggest challenges present models of growth regulation.Jonsson

Arabidopsis Research Roundup: August 26th

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Published on: August 26, 2016

This weeks Arabidopsis Research Roundup includes three papers across a wide range of topics. Firstly is a widely-reported study, described here with an audio description by Nik Cunniffe and Sanjie Ziang, of the evolutionary relationship between viral infection, pollinator attraction, plant fertility and miRNA-regulated gene expression. Secondly, Gordon Simpson is a co-author on a paper that has elucidated the crystal structure of the FPA proteins and finally Gareth Jenkins leads an investigation into the relationship between UV light, the UVR8 protein and histone modifications.

Groen SC, Jiang S, Murphy AM, Cunniffe NJ, Westwood JH, Davey MP, Bruce TJ, Caulfield JC, Furzer OJ, Reed A, Robinson SI, Miller E, Davis CN, Pickett JA, Whitney HM, Glover BJ, Carr JP (2016) Virus Infection of Plants Alters Pollinator Preference: A Payback for Susceptible Hosts? PLoS Pathog. 12(8):e1005790

http:/​/​dx.​doi.​org/10.1371/journal.ppat.1005790

Open Access
BumbleBee
This pan-UK collaboration is led by John Carr, Beverly Glover and Nik Cunniffe at the University of Cambridge and has received wide attention in the general press. Nik Cunniffe also kindly provides an audio description of this work that looked into the effect of viral infection on the attraction of pollinators. The authors used GC-MS to look at the volatiles produced in virally infected Arabidopsis and tomato plants, showing that infection can alter the foraging behavior of bumblebees. Mutational analysis of both cucumber mosaic virus (CMV) and Arabidopsis showed that the microRNA pathway is involved in regulating the emission of these pollinator-perceivable volatiles. When virus-infected tomato plants were not pollinated there was a clear reduction in seed yield, indicating that the plant requires the volatile production following viral infection to attract pollinators, leading to reproductive success. Importantly the authors model the possible trade-off between viral infection and reproductive success in the wild, which might oppose the strong selective pressure for the establishment of disease-resistance genes. The authors speculate that this is a co-beneficial relationship for both virus and plant.

Nick Cunniffe and Sanjie Jiang kindly provide an audio description of this work.


 

Zhang Y, Rataj K, Simpson GG, Tong L (2016) Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA PLoS One 11(8):e0160694

http:/​/​dx.​doi.​org/10.1371/journal.pone.0160694

Open Access

Gordon Simpson (University of Dundee) in a co-author on this US-led study that has elucidated the crystal structure of the SPOC domain of the FPA floral regulator protein. FPA contains a N-terminal RNA recognition motif and a C-terminal SPEN paralog and ortholog C-terminal (SPOC) domain. This SPOC domain is highly conserved throughout plant species and this crystal structure is an important development in our understanding of the regulation of RNA 3’-end formation and how much the plant SPOC domains compare with an equivalent from metazoans.

 

Velanis CN, Herzyk P, Jenkins GI (2016) Regulation of transcription by the Arabidopsis UVR8 photoreceptor involves a specific histone modification Plant Mol Biol.

http:/​/​dx.​doi.​org/10.1007/s11103-016-0522-3

Open Access

Gareth Jenkins (Glasgow) leads this study that continues his groups work on the Arabidopsis UVR8 photoreceptor. They show that UV-B exposure increases histone lysine acetylation on UVR8-regulated genes in a UVR8 dependent manner. In fact all of the histone enrichments throughout the genome following UV-B required UVR8 activity. However the authors could find no direct interaction between UVR8 and the known enzymes involved in light-mediated histone modification indicating that UVR8 either interacts with a novel set of proteins or the UVR8 effect is mediated via a currently unknown signaling intermediate.
UVRpic

Arabidopsis Research Roundup: July 19th

There are six papers in this weeks Arabidopsis Research Roundup. Two of these include research on the stomatal patterning gene TMM. Firstly a White Rose consortium investigates the ancestral basis of stomatal patterning, whilst a Glasgow-based study investigates the relationship between patterning and the dynamics of guard cell opening. The GARNet committee is represented by work from Cardiff that looks at the relationship between seed size and shoot branching and also from Cambridge in research that studies meiotic recombination in genomic regions important for pathogen defense. Finally are two studies that look into aspects of root and shoot patterning and include co-authors from CPIB in Nottingham or the John Innes Centre.

Caine R, Chater CC, Kamisugi Y, Cuming AC, Beerling DJ, Gray JE, Fleming AJ (2016) An ancestral stomatal patterning module revealed in the non-vascular land plant Physcomitrella patens Development

http://dx.doi.org/10.1242/dev.135038 Open Access

This study is a collaboration between labs in Sheffield and Leeds, led by Andrew Fleming (Sheffield). They investigate the role that the signalling module comprised of Epidermal Patterning Factors (EPFs), ERECTA and TMM play during the evolution of stomatal patterning. This module is known to play an important role in Arabidopsis and in this study the authors show that the moss Physcomitrella patens contains homologs of each of the genes and that they perform the same function. When P.paten versions of these genes are transferred to equivalent Arabidopsis mutants they show conserved function demonstrating that this module is an example of an ancestral patterning system.

Andrew Fleming provides a brief audio description of this manuscript:

Papanatsiou M, Amtmann A, Blatt MR (2016) Stomatal spacing facilitates guard cell ion transport independent of the epidermal solute reservoir. Plant Physiol. http://dx.doi.org/10.1104/pp.16.00850 Open Access

Mike Blatt and Anna Amtmann (University of Glasgow) are the co-supervisors for this study into the relationshop between ion transport in stomatal guard cells and their physical positioning within a leaf. They used a genetic approach to assess the effect of stomatal clustering, showing that too many mouths (tmm) mutant plants have reduced stomatal movements associated with alterations in K+ channel gating and coincident with a surprising reduction in the level of K+ ions in guard cells. These results underline the importance of stomatal spacing in this process but do not provide a full explanation into the alteration in K+ ion dynamics.

Sornay E, Dewitte W, Murray JAH (2016) Seed size plasticity in response to embryonic lethality conferred by ectopic CYCD activation is dependent on plant architecture Plant Signaling and Behaviour e1192741

http://dx.doi.org/10.1080/15592324.2016.1192741 Open Access

From http://dx.doi.org/10.1080/15592324.2016.1192741
From http://dx.doi.org/10.1080/15592324.2016.1192741

This research comes from the lab of GARNet PI Jim Murray (Cardiff) and investigates cell proliferation and growth within a developing seed. They previously have shown that targeting of D-type cyclin CYCD7;1 to the central cell and early endosperm can trigger nuclear divisions and ovule abortion, which leads to a smaller number of larger seed. In this study they show that development of larger seed in transgenic plants is influenced by the architecture of the mother, as plants with increased side branches, caused by pruning of the main stem, do not generate this phenotype. This is indicative of a close relationship between the amount of resources allocated to different parts of the plant and that a transgenic effect was altered by a different plant morphology. This should provide an important insight into future work that aims to define the effect of any particular transgenic alteration.

Choi K, Reinhard C, Serra H, Ziolkowski PA,, Underwood CJ,, Zhao X, Hardcastle TJ, Yelina NE, Griffin C, Jackson M, Mézard C, McVean G, Copenhaver GP,, Henderson IR (2016) Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes. PLoS Genet. 12(7):e1006179.

http://dx.doi.org/10.1371/journal.pgen.1006179 Open Access

GARNet advisory board member Ian Henderson (Cambridge) is the corresponding author of this study that involves contributions from the UK, US, Poland and France. They investigate genomic regions that show increased meiotic recombination, which is predicted to occur coincident with genes involved in pathogen defence given their requirement to adapt to new external challenges. This study focuses on NBS-LRR domain proteins that tend to physically cluster in the Arabidopsis genome. Interesting they discovered both hot and coldspots for meiotic recombination that associate with NBS-LRR clusters, the later often correlating with structural heterozygosity. In a more detailed dissection of 1000 crossovers in the RESISTANCE TO ALBUGO CANDIDA1 (RAC1) R hotspot, they discovered higher recombination frequencies associating with known sequence motifs important for the pathogen response, which were influenced by ecotype-specific factors. Ultimately the authors note that there is a complex relationship between regions of meiotic recombination, structural heterozygosity and the evolutionary pressures that occurs with host-pathogen relationships.

Orman-Ligeza B, Parizot B, de Rycke R, Fernandez A, Himschoot E, Van Breusegem F, Bennett MJ, Périlleux C, Beeckman T, Draye X (2016) RBOH-mediated ROS production facilitates lateral root emergence in Arabidopsis. Development http://dx.doi.org/10.1242/dev.136465 Open Access

From http://dx.doi.org/10.1242/dev.136465
From http://dx.doi.org/10.1242/dev.136465

 Malcolm Bennett (CPIB) is the sole UK-based co-author on this study led by Belgian collaborators and investigates the role of reactive oxygen species (ROS) in auxin-regulated lateral root (LR) formation. They show that ROS can reactivate LR primordia and pre-branch sites, resulting in increased LR numbers. This occurs in both wildtype and in auxin mutants that have reduced numbers due to changes in auxin-mediated cell wall remodeling. ROS is deposited in the apoplast of emerging LR cells in a pattern that is coincident with the expression of the RESPIRATORY BURST OXIDASE HOMOLOGS (RBOH) genes. Concomitantly the altered expression of RBOH was shown to affect the development and emergence of LRs. This adds a further level of complexity to the current understanding of the signaling factors that converge to facilitate LR growth.

 

Shi B,, Zhang C, Tian C, Wang J,, Wang Q,, Xu T,, Xu Y, Ohno C, Sablowski R, Heisler MG, Theres K, Wang Y, Jiao Y (2016) Two-Step Regulation of a Meristematic Cell Population Acting in Shoot Branching in Arabidopsis. PLoS Genet. http://dx.doi.org/10.1371/journal.pgen.1006168 Open Access

This Chinese-led study includes Robert Sablowski (JIC) as a co-author and studies the factors that influence the development of axillary meristems. They use innovative live imaging to show that SHOOT MERISTEMLESS (STM) is continuously expressed and that this dependent on a leaf axil auxin minimum. Once STM expression is lost then the axil is unable to form a meristem even if STM is switched back later in development, indicating that cells undergo an irreversible developmental commitment. The expression domain of STM is under cell-type specific control of REVOLUTA (REV) DNA binding. Overall this study demonstrates that meristematic competence and initiation is dependent on differing levels of the key regulator STM.

From http://dx.doi.org/10.1371/journal.pgen.1006168
From http://dx.doi.org/10.1371/journal.pgen.1006168

Arabidopsis Research Roundup: June 9th

This edition of the Arabidopsis Research Roundup pleasingly includes four Open Access articles. Firstly Jose Gutierrez-Marcos leads an investigation into stress-induced memory, secondly Richard Morris is the corresponding author on a study that has developed a new model that explains waves of calcium signalling that response to environmental stresses. Thirdly is a UK-US collaboration that defines the factors that control carotenoid accumulation in seeds. Finally Chris Hawes leads a study that characterises the novel localisation of a subset of auxin biosynthetic enzymes.

Wibowo A, Becker C, Marconi G, Durr J, Price J, Hagmann J, Papareddy R, Putra H, Kageyama J, Becker J, Weigel D, Gutierrez-Marcos J (2016) Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity Elife http://dx.doi.org/10.7554/eLife.13546 Open AccessStress_Model

Jose Gutierrez-Marcos is the corresponding author on this pan-European study that adds to our increasing knowledge about the role of generational memory in the response to stress. Distinct regions of the Arabidopsis genome are susceptible to fluctuations in the level of DNA methylation in response to hyperosmotic stress, a condition that persists into a following generation. This effect is transmitted through the female lineage and the authors investigate this effect in more detail by focussing on a single epigenetically targeted locus. By designing experiments that ran over a series of generations they show that a plants ‘short term memory’ is reliant on the DNA methylation machinery and is able to transmit a distinct developmental response to immediate offspring.

Evans MJ, Choi WG, Gilroy S, Morris RJ (2016) A ROS-assisted Calcium Wave Dependent on AtRBOHD and TPC1 Propagates the Systemic Response to Salt Stress in Arabidopsis Roots. Plant Physiol.

http:/​/​dx.​doi.​org/​10.​1104/​pp.​16.​00215 Open Access

Richard Morris (JIC) leads this US-UK collaboration that investigates the downstream mechanisms that occur after the waves of ROS and Ca2+ signalling that respond to environmental stresses. The authors show that the current model for propagation of this wave, which relies upon a diffusive wave Ca2+ signalling, is unable to explain the speed of transmission of the wave. The authors develop a new model that adds a ROS-signalling component to explain the velocity of the Ca2+ wave and experimentally verify that their model could represent the in vivo situation. In addition they show that the effectiveness of this ROS-release signalling module is dependent on the activity of the vacuolar ion channel TPC1 and the NADPH Oxidase AtRBOHD.
CaWavePic
Gonzalez-Jorge S, Mehrshahi P, Magallanes-Lundback M, Lipka AE, Angelovici R, Gore MA, DellaPenna D (2016) ZEAXANTHIN EPOXIDASE activity potentiates carotenoid degradation in maturing Arabidopsis seed. Plant Physiol.

http:/​/​dx.​doi.​org/​10.​1104/​pp.​16.​00604 Open Access

The lead author of this US-led study is Sabrina Gonzalez-Jorge who is currently a post-doc in GARNet committee member Ian Henderson’s lab in Cambridge. This study elucidates nine loci that are involved in carotenoid homeostasis in Arabidopsis seeds and shows that plants lacking the ZEAXANTHIN EPOXIDASE (ZEP) protein have a six-fold reduction in total seed carotenoids. Natural variation within the ZEP gene is able to account for the fine-tuning of seed carotenoid content and acts upstream of two previously characterised CAROTENOID CLEAVAGE DIOXYGENASE enzymes. Importantly, and somewhat surprisingly, four of the nine Arabidopsis loci are thought to have conserved function in determining the composition of carotenoids in maize kernels. This demonstrates that studying this phenomonen in Arabidopsis is highly relevant for study of the same process in economically important crops.

Kriechbaumer V, Botchway SW, Hawes C (2016) Localization and interactions between Arabidopsis auxin biosynthetic enzymes in the TAA/YUC-dependent pathway J Exp Bot.

http://dx.doi.org/10.1093/jxb/erw195 Open Access

Chris Hawes (Oxford Brookes) leads this study that localised a subset of enzymes involved in auxin biosynthesis to the endoplasmic reticulum. In addition certain of these enzymes appear to physically interact. This localisation is confirmed by showing ER microsomal fractions are able to undertake auxin biosynthesis. The auxin signalling pathway is complex and well characterised yet this finding adds another layer of regulation that might influence the dynamics of auxin activity.

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