Arabidopsis Research Roundup: July 3rd.

The Arabidopsis Research Roundup returns this week with selection of publications from institutions across the UK. Firstly George Bassel (Birmingham) leads a study that investigates the integration of inductive signals in the embryonic root. Secondly a group from the Oxford Brookes plant science group look into the literal linkages between the golgi apparatus and ER. Thirdly John Christie (Glasgow) and co-workers define a new variant of the phototropin receptor. Next Caroline Dean and Martin Howard (John Innes Centre) collaborate on work that defines the relationship between FLC, COOLAIR and cell size. The fifth paper is led by members of SLCU and investigates the regulatory influence of the Evening Complex of the circadian clock. The penultimate paper features work from Alison Smith’s group at the JIC that looks at dynamics of starch accumulation and degradation. Lastly is research from NIAB that defines the pathogeniticity of novel UK isolates of the fungal pathogen Verticillium longisporum.

Topham AT, Taylor RE, Yan D, Nambara E, Johnston IG, Bassel GW (2017) Temperature variability is integrated by a spatially embedded decision-making center to break dormancy in Arabidopsis seeds. PNAS


Open Access

George Bassel (University of Birmingham) leads this study that identifies a decision making centre in the embryonic root that is defined by the intimate interaction between the hormones abscisic acid (ABA) and gibberellin (GA). The activity of this ‘decision centre’ is linked to both hormone transport and changes in temperature, the overall output of which is the decision to promotes seed germination or to delay until more favourable environmental conditions.

George discusses this paper on the GARNet YouTube channel.

Osterrieder A, Sparkes IA, Botchway SW, Ward A, Ketelaar T, de Ruijter N, Hawes C (2017) Stacks off tracks: a role for the golgin AtCASP in plant endoplasmic reticulum-Golgi apparatus tethering. J Exp Bot. http:/​/​dx.​doi.​org/10.1093/jxb/erx167

Open Access

Anne Osterrieder and Chris Hawes (Oxford Brookes University) continue their work that looks at  the cellular dynamics of the golgi apparatus with this study that identifies the AtCASP protein as a important component that tethers the golgi to the ER. They use live-cell imaging to visualise golgi formation in cells that have different levels of AtCASP, allowing the authors to confirm that ER-golgi tethering is disrupted without the activity of this protein.

Petersen J, Inoue SI, Kelly SM, Sullivan S, Kinoshita T, Christie JM (2017) Functional Characterization of a Constitutively Active Kinase Variant of Arabidopsis Phototropin 1

J Biol Chem. http:/​/​dx.​doi.​org/10.1074/jbc.M117.799643

Open Access

John Christie (University of Glasgow) collaborates with Japanese colleagues to identify a novel variant of the phototropin receptor. Study of this variant allows a greater understanding regarding the mode of action of this protein under different light conditions, as controlled by phosphorylation.

Ietswaart R, Rosa S, Wu Z, Dean C, Howard M (2017) Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation. Cell Syst. http:/​/​dx.​doi.​org/10.1016/j.cels.2017.05.010

Open Access

Martin Howard and Caroline Dean (John Innes Centre) again collaborate on research that analyses the mode of regulation of FLC. They dissect RNA dynamics of FLC expression by single molecule in situ RNA fluorescence, showing that this is dependent on the presence of the antisense COOLAIR regulatory DNA. In the absence of COOLAIR they show FLC expression has a linear relationship with cell size but in the presence of the antisense transcript, FLC expression decreases with cell size. Overall they demonstrate FLC expression is tightly dependent on the presence of the antisense COOLAIR transcript.

Ezer D, Jung JH, Lan H, Biswas S, Gregoire L, Box MS, Charoensawan V,, Cortijo S, Lai X,, Stöckle D, Zubieta C, Jaeger KE, Wigge PA (2017) The evening complex coordinates environmental and endogenous signals in Arabidopsis. Nat Plants.


Free to view with this URL.

Phil Wigge and Katja Jaeger (SLCU) lead this study that investigates how the evening complex of the circadian clock coordinates the expression of numerous important growth regulators. This genome wide regulation is determined by temperature and concides with the binding of phytochrome B, which provides a cellularly mechanism of this level of environmental control.

Fernandez O, Ishihara H, George GM, Mengin V, Flis A, Sumner D, Arrivault S, Feil R, Lunn JE, Zeeman SC, Smith AM, Stitt M (2017) Foliar starch turnover occurs in long days and in falling light at the end of the day. Plant Physiol. http:/​/​dx.​doi.​org/10.1104/pp.17.00601

Open Access

On this paper Alison Smith (John Innes Centre) is a co-corresponding author together with Mark Stitt from the Max Planck Institute for Molecular Plant Physiology in Potsdam. They continue their work to investigate the dynamics of starch metabolism in Arabidopsis leaves. Broadly they show the rate of starch accumulation corresponds to the photosynthetic rate whilst degradation is linked to correct functioning of the circadian clock. They investigate this process in more detail by determining how the rate of starch degradation alters dependent on the time after dawn.

Depotter J, Rodriguez-Moreno L, Thomma BP, Wood T (2017) The emerging British Verticillium longisporum population consists of aggressive Brassica pathogens. Phytopathology http:/​/​dx.​doi.​org/10.1094/PHYTO-05-17-0184-R

Tom Wood (NIAB) is the corresponding author of this study that characterises four new UK isolates of the fungal pathogen Verticillium longisporum. The pathogenticity of V.longisporum was tested on Arabidopsis alongside three other Brassica crops. They demonstrate that the UK isolates were unusually aggressive yet this was not consistent across all Brassica cultivars with different fungal lineages showing different effects on oil seed rape, cabbage or cauliflower.

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


Open Access
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.


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.

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
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

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
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.


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=”” onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘http://onlinelibrary.wiley generic cialis’, ‘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: August 8th

This weeks Arabidopsis Roundup contains a wide breadth of UK research. Firstly the lab of Jurriaan Ton undertakes a global analysis into the role of methylation in the immune response. Jurriaan kindly provides a short audio description of this work. Secondly Dame Caroline Dean’s lab further add to our understanding of the vernalisation response in Arabidopsis. Thirdly is work from Rothamstead that evaluates the fatty acid composition of the seed aleurone while fourthly is a study from Durham and Oxford Brookes that introduces a novel regulator of autophagy. Finally is a study that adds clarity to the phenotypic effects resulting from ascorbic acid deficiency.

López Sánchez A, H M Stassen J, Furci L, Smith LM, Ton J (2016) The role of DNA (de)methylation in immune responsiveness of Arabidopsis Plant Journal Open Access

Jurriaan Ton is the corresponding for study from the University of Sheffield that looks into the role of reversible methylation on the Arabidopsis immune response. Methylation is a well known regulator of gene expression and in this research the authors attempt to interrogate its effect on the immune response. Hypo-methylated mutants are more resistant, whilst hyper-methylated mutants are more suspectible to the biotrophic pathogen Hyaloperonospora arabidopsidis (Hpa). Downstream gene expression changes in these methylation mutants focus at the level of cell-wall modification and salicylic acid (SA)-responses. Oppositely the hypo-methylated mutant nrpe1 is more suspective to the necrotrophic pathogen Plectosphaerella cucumerina whilst the hyper-methylated ros1 mutant is resistant to this organism. The Ton-lab has been involved in the discovery of the exciting phenomon of transgenerational acquired resistance, and both nrpe1 and ros1 fail to develop this response against Hpa. Global gene expression shows that either NRPE1 or ROS1 influence about 50% of the gene expression changes that occur following Hpa infection. Finally since less than 15% of genes with altered gene expression reside close to NRPE1 or ROS1, the authors are able to propose that much of this regulation is due to methylation effects that act in trans- throughout the genome.

Jurriaan kindly provides a comprehensive description of this work:

Qüesta JI, Song J, Geraldo N, An H, Dean C (2016) Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization Science. 353(6298):485-8


Dame Caroline Dean (John Innes Centre) is the lead author of this manuscript that builds upon the portfolio of work from her lab aimed at characterising the vernalization response. This work again uses the FLOWERING LOCUS C (FLC) gene as a model to study the factors that allow gene-silencing mediated by Polycomb silencing complexes. The authors find that a single intragenic point mutation prevents nucleation of the homeodomain-Polycomb repressive complex 2 (PHD-PRC2) to this region, a process that involves the transcriptional repressor VAL1. In the wildtype FLC locus the localisation of VAL1 promotes transcriptional silencing through histone deacylation through interaction with the conserved apoptosis- and splicing-associated protein (ASAP) complex. This study adds an additional layer of molecular complexity to the process of regulating the FLC locus and provides insight into the important role for primary sequence-specific targeting during gene silencing.

Bryant F, Munoz-Azcarate O, Kelly AA, Beaudoin F, Kurup S, Eastmond PJ (2016) Acyl carrier protein DESATURASE 2 and 3 are responsible for making omega-7 fatty acids in the aleurone Plant Physiology Open Access

Peter Eastmond (Rothamstead) leads this work that investigates the components that determine seed fatty acid content. Specifically Omega-7 monounsaturated fatty acids (ω-7s) are enriched in the aleurone of Arabidopsis seeds so this study used a Multiparent Advanced Generation Inter-Cross population to identify a QTL linked to ω-7 content that includes the ACYL-ACYL CARRIER PROTEIN DESATURASE1 (AAD1) and AAD3 genes. AAD family members possess both stearoyl- and palmitoyl-ACP Δ9 desaturase activity and aad3 mutants show a significant reduction in ω-7 content, which is common with mutants in other AAD family members. In addition the authors show that the FATTY ACID ELONGASE1 protein is required for accumulation of long-chain ω-7s in the aleurone. Overall this research provides new insight into the pathway that produces ω-7s in the aleurone, indicating that these genes might represent a target for future strategies to alter seed fatty acid content.

Wang P, Richardson C, Hawes C, Hussey PJ.(2016) Arabidopsis NAP1 Regulates the Formation of Autophagosomes Current Biology


This is collaborative effort between the labs of Patrick Hussey (Durham) and Chris Hawes (Oxford Brookes) investigates the role of the NAP1 protein, which is a member of the SCAR/WAVE complex, on the formation of autophagosomes. These organelles are induced by certain stress conditions and fewer are produced in nap1 mutants after starvation stress. This also corresponds to wildtype NAP1 localisation. Concomitantly nap1 mutants, as well as mutants of other members of SCAR/WAVE complex, are more suspectible to nitrogen starvation and is less tolerant to salt stress. The best characterised role of the SCAR/WAVE complex is during ARP2/3-mediated actin nucleation yet this study demonstrates an addition function as a regulatory of autophagy.

Lim B, Smirnoff N, Cobbett CS, Golz JF (2016) Ascorbate-Deficient vtc2 Mutants in Arabidopsis Do Not Exhibit Decreased Growth Front Plant Sci. 7:1025 Open Access

Nick Smirnoff (Exeter) is a co-author on the Australian-led research into Arabidopsis vtc mutants, which have a significant reduction in ascorbate-acid levels. Ascorbate is synthesized via the L-galactose pathway, the first enzyme of which is encoded by the paralogs VITAMIN C2 (VTC2) and VTC5. This study characterises the growth of a vtc2 T-DNA mutant that has a 30% reduction in ascorbate levels. Surprisingly this does not result in any signficant phenotypic and they suggest that a previously characterised growth reduction in other vtc2 mutant alleles is likely due to unknown genetic lesions.

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 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.
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. 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.

Arabidopsis Research Roundup: January 8th

For the inaugural Arabidopsis Research Roundup of 2016 we feature the final publications of UK researchers from 2015. Martin Howard kindly provides an audio description of a paper that looks at a fundamental aspect of transcriptional regulation, through the lense of the FLC gene, whilst his co-author Caroline Dean on that paper is an author on another manuscript that investigates RNA stability in the same FLC locus. Katja Graumann leads a paper that looks into gene expression at the periphery of the nucleus whilst Ian Colbeck looks at the effect of silver nanoparticles on plant growth. Ari Sadanandom is the UK lead of a study that investigates of SUMOylation and Ian Fricker looks at the role of a cytochrome P450 on the defence response. Finally Liam Dolan is involved in a comparative analysis of the genes involved in tip growth in the cells of plants and moss.

Wu Z, Ietswaart R, Liu F, Yang H, Howard M, Dean C (2015) Quantitative regulation of FLC via coordinated transcriptional initiation and elongation. Proc Natl Acad Sci U S A. Open Access

Martin Howard and Caroline Dean lead this study that comes out of the John Innes Centre and is the result of the same collaboration that featured in an ARR earlier in 2015. In this study they investigate the mechanisms that control the quantitative regulation of gene expression by focusing on the complex regulation of the FLOWERING LOCUS C (FLC). FLC expression is controlled by a chromatin silencing mechanism involving alternative polyadenylation of antisense transcripts. However they surprisingly show that the amount of RNA Polymerase II occupancy at FLC does not coincide very well with levels of FLC transcription. They used modeling to predict that there is a tight coordination between transcriptional initiation and elongation, which was validated by detailed measurements of the levels of FLC intronic RNA. Variation within initiation and elongation rates were significantly different and was coincident with changes in H3K36me3 and H3K4me2 levels in the FLC gene. The authors propose that chromatin state can influence transcriptional initiation and elongation rates and may be a general mechanism for quantitative gene regulation in a chromatin context.

Martin Howard kindly provides an audio description of this paper and wider aspects of transcriptional regulation.

Wu Z, Zhu D, Lin X, Miao J, Gu L, Deng X, Yang Q, Sun K, Zhu D, Cao X, Tsuge T, Dean C, Aoyama T, Gu H, Qu LJ (2015) RNA-binding proteins At RZ-1B and At RZ-1C play a critical role in regulation of pre-mRNA splicing and gene expression during Arabidopsis development Plant Cell

This study investigates a set of previously mysterious RNA-binding proteins and is led by Chinese researchers with a UK contribution from Caroline Dean (JIC). They look at two Arabidopsis proteins, AtRZ-1B and At RZ-1C that have RNA-binding domains and are localised to the mysterious nuclear speckles. In addition these proteins physically interact with a range of serine/arginine-rich (SR) proteins and disrupting this binding causes a range of growth phenotypes that are similar to that observed in At rz-1b/At rz-1c double mutants. These include delayed seed germination, reduced stature, and serrated leaves and on the cellular level this is accompanied by defective splicing and global changes in gene expression. Interestingly AtRz-1C directly effects the expression of the floral repressor FLC, which links this work with other research in the Dean lab. Overall this highlights the important role of At RZ-1B/1C in RNA splicing and the link to many developmental phenotypes.

Smith S, Galinha C, Desset S, Tolmie F, Evans D, Tatout C, Graumann K (2015) Marker gene tethering by nucleoporins affects gene expression in plants. Nucleus.

Expression of Seh1-LacI-YFP at the nuclear periphery. From
Expression of Seh1-LacI-YFP at the nuclear periphery. From

Katja Graumann and David Evans (Oxford Brookes) are the lead academics on this collaboration with the lab of Christophe Tatout from Clermont Ferrand in France. They are attempting to answer a long standing question in the field of the biology of the nucleus; whether genes that are located close to nuclear pore complexes have increased gene expression. They used the Lac Operator/ Lac Repressor (LacI-LacO) system to assess changes in gene expression when a loci is tethered to the NPC by attaching the LacI domain to the nucleoporins Seh1 or NUP50a. The Seh1 clones localised to the nuclear periphery and showed higher RNA and protein expression of Luc. When this interaction at the periphery was distributed, the higher levels of expression were abolished. The authors therefore show that association with the nuclear periphery is important for the regulation of gene expression.

Sosan A, Svistunenko D, Straltsova D, Tsiurkina K, Smolich I, Lawson T, Subramaniam S, Golovko V, Anderson D, Sokolik A, Colbeck I, Demidchik V (2015) Engineered silver nanoparticles are sensed at the plasma membrane and dramatically modify physiology of Arabidopsis thaliana plants. Plant Journal

Ian Colbeck (Essex) is the UK lead on this study that involves a collaboration between researchers in New Zealand, Belarus and Russia and focuses on the effect of silver nanoparticles (Ag NPs) on the growth of Arabidopsis seedlings. This type of nanoparticle is used for many difference applications so worries exist about the safety of their use. This study looks at the effect of Ag NPs on Arabidopsis root elongation and leaf expansion, both of which were inhibited at over [300mg/l] Ag NPs. In addition there were reductions of photosynthetic efficiency and accumulation of silver in plant tissues. They also showed that these particles altered the influx and efflux of metal ions whilst, although they were unable to catalyse hydroxyl radical generation, they did directly oxidise the major plant antioxidant, L-ascorbic acid. Overall the authors show that silver nanoparticles induce classical stress signalling responses but also illicit specific detrimental effects at the plasma membrane. At the whole plant level this study provides a worrying example for the role of Ag NPs on whole plant growth, even though the concentrations used in food preparation might be lower.

Crozet P, Margalha L, Butowt R, Fernandes N, Elias A, Orosa B, Tomanov K, Teige M, Bachmair A, Sadanandom A, Baena-González E (2015) SUMOylation represses SnRK1 signaling in Arabidopsis. Plant Journal

This pan-European study features researchers from Portugal, Austria and the UK’s Durham University, led by Ari Sadanandom. They investigate the role of the SnRK1 protein kinase, which is a key enzyme for modulating the plant stress response. This paper adds detail to the cellular mechanisms that regulate SnRK1 and they show that SnRK1 is SUMOylated by the SIZ1 E3 SUMO ligase. SnRK1 is ubiquitinated and degraded in a SIZ1-dependent manner that is lacking in siz1 mutants. Interestingly only active SnRK1 is degraded as the inactive SnRK1 protein is stable but can be easily degraded upon SUMOylation. Finally they show that SnRK1 is involved in a negative feedback loop wherein it controls its own SUMOylation and degradation that, in wildtype cells, prevents a potentially detrimental stress response.

Fuchs R, Kopischke M, Klapprodt C, Hause G, Meyer AJ, Schwarzländer M, Fricker MD, Lipka V (2015) Immobilized subpopulations of leaf epidermal mitochondria mediate PEN2-dependent pathogen entry control in Arabidopsis. Plant Cell

Mark Fricker (Oxford) is the UK research lead on this study that investigates the role of the atypical myrosinase PEN2 in the response to pathogen attack. PEN2 is targeted to both peroxisomes and mitochondria and can also form homo-oligomer complexes. PEN2 localised to mitochondria are immobilized following fungal invasion and this accompanies mitochondrial arrest. The substrate for PEN2 is produced by the cytochrome P450 monooxygenase CYP81F2, which is localized to the ER and moves toward immobilized mitochondria. The critical function of PEN2 in that organelle was confirmed by the result that showed exclusive mitochondria targeting could rescue pen2 mutant phenotypes. The authors show by live-cell imaging that arrested mitochondria in domains of plant-microbe interaction exhibit a pathogen-induced redox imbalance that may lead to production of intracellular signals.

Ortiz-Ramírez C, Hernandez-Coronado M, Thamm A, Catarino B, Wang M, Dolan L, Feijó JA, Becker JD (2015) A transcriptome atlas of Physcomitrella patens provides insights into the evolution and development of land plants. Mol Plant.

Liam Dolan (Oxford) is an author on this study that is led from Portugal and is an investigation of the transcriptome of the model moss Physcomitrella patens throughout its life cycle. They also compare transcriptomes from P.patens and Arabidopsis, allowing the authors to identify transcription factors that are expressed in tip growing cells. Interestingly they identified differences in expression patterns that might account for the differences between tip growth in moss and the Arabidopsis root hairs, an area that is the expertise of the Dolan lab.

Arabidopsis Research Roundup: November 5th

Academics from the John Innes Centre lead two of the papers featured in this week Arabidopsis Research Roundup. Firstly Veronica Grieneisen leads a study that combines modeling and experimental work to assess the factors that establish the root auxin maximum and secondly the structural biologist David Lawson heads up an investigation into the plastid-localised enzyme, DPE1. Seemingly a common theme in UK-Arabidopsis research focuses on the factors that control the dynamics of stomatal opening and this week Mike Blatt from Glasgow heads a team that investigates the role of potassium and nitric oxide in this process. Finally we present a paper that investigates proteins that interact within the ER.

El-Showk S, Help-Rinta-Rahko H, Blomster T, Siligato R, Marée AF, Mähönen AP, Grieneisen VA (2015) Parsimonious Model of Vascular Patterning Links Transverse Hormone Fluxes to Lateral Root Initiation: Auxin Leads the Way, while Cytokinin Levels Out PLoS Comput Biol. e1004450Picture Open Access

Veronica Grieneisen (JIC) is the UK-based leader of this work that was performed with her Finnish collaborators. They work on the modeling the processes that define the auxin maximum in the root meristem. This patterning is defined by the activity of the PIN-formed auxin efflux transport proteins and the AHP6 protein, an inhibitor of cytokinin signaling. The authors implement a parsimonious computational model of auxin transport that considers hormonal regulation of the auxin transporters within a spatial context, explicitly taking into account cell shape and polarity and the presence of cell walls. They initially find that variation in cytokinin signaling, mediated by diffusion of the hormone is insufficient for patterning but rather it is an auxin-dependent modification of the cytokinin signal that can define the auxin maximum. Although the role that the PIN proteins play in root vascular patterning is well established, the authors experimentally verify a role for the AUX/LAX auxin influx carrier family of proteins. They also show that polar PIN localisation generates a flux of auxin flow that ultimately causes its own accumulation in the pericycle cells that signal for lateral root initiation. Finally their model confirms the supposition that these pericycle cells compete for auxin accumulation, therefore ensuring that lateral roots develop in the correct localisation. The associated figure is from this paper.

O’Neill EC, Stevenson CE, Tantanarat K, Latousakis D, Donaldson MI, Rejzek M, Nepogodiev SA, Limpaseni T, Field RA, Lawson DM (2015) Structural Dissection of the Maltodextrin Disproportionation Cycle of the Arabidopsis Plastidial Enzyme DPE1. Journal of Biological Chemistry Open Access

This is another paper led by JIC researchers, this time in collaboration with Thai partners. This focuses on determining the structure of the Arabidopsis Plastidial Disproportionating Enzyme 1 (DPE1) that acts to convert two maltotriose molecules to a molecule of maltopentaose and a molecule of glucose, which, for different reasons, are both more functional useful molecules for the plant. They have used ligand soaking techniques to trap the DPE1 in a different set of conformational states and have found that it exists as a homodimer with a variety of interesting features. This includes a dynamic ‘gate’ loop that may play a role in substrate capture, subtle changes in which could alter the efficacy of the active site. The structural insights provided by this study allow the authors to confidently delineate the complete AtDPE1 disproportionation cycle

Chen ZH, Wang Y, Wang JW, Babla M, Zhao C, García-Mata C, Sani E, Differ C, Mak M, Hills A, Amtmann A, Blatt MR (2015) Nitrate reductase mutation alters potassium nutrition as well as nitric oxide-mediated control of guard cell ion channels in Arabidopsis New Phytol. Open Access

<a href="http://www.gla cialis vente en” onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘’, ‘Mike Blatt’]);” target=”_blank”>Mike Blatt (Glasgow) is the lead on this UK-Sino-Australino-Argentine collaboration that investigates the role of nitrate reductase enzyme in potassium flux in guard cells. This flux is necessary for a plants adaption to the environment and is controlled by the activity of ABA via the activity of H2O2 and Nitric Oxide (NO). The authors showed that multiple responses to ABA were impaired in nia1nia2 nitrate reductase mutants, which includes the K+ IN current in guard cells, required for stomatal closure. This response was rescued by exogenous NO and allowed the authors to demonstrate that there exists a complex interaction involving ABA, NO, potassium nutrition and nitrogen metabolism that is necessary to ensure correct stomatal responses.

Kriechbaumer V, Botchway SW, Slade SE, Knox K, Frigerio L, Oparka K, Hawes C (2015) Reticulomics: Protein-Protein Interaction Studies with Two Plasmodesmata-Localized Reticulon Family Proteins Identify Binding Partners Enriched at Plasmodesmata, Endoplasmic Reticulum, and the Plasma Membrane Plant Physiol. 169(3):1933-45

This proteomic analysis of endoplasmic reticulum components is a collaboration between the Central Laser Facility at Didcot, Warwick, Edinburgh and Oxford Brookes Universities, led by Professor Chris Hawes. Plant Reticulon proteins (RTNLB) specifically populate and tubulate the ER, mediated by their varied multi-meric interactions. In addition, certain RTNLB are also present in plasmodesmata (PD) and two of these proteins, RTNLB3 and RTNLB6 were GFP-tagged, Co-IPed and interacting proteins were analysed by MS. This identified a range of known PD-localised proteins, and these interactions were experimentally verified in tobacco cells using FRET-microscopy. The authors suggest that this data shows that RTNLB proteins may play important roles in linking the cortical ER to the plasma membrane. This paper is the ‘sister’ to another manuscript in Plant Physiology that was highlighted in a recent Arabidopsis Research Roundup.

Arabidopsis Research Roundup: August 12th

The UK Arabidopsis Research Roundup this week includes a couple of EVO-DEVO-type studies that compare processes within different organisms (Physcomitrella and Cardamine) to those occurring in Arabidopsis. These include the evolution of both hormone signaling and leaf development. Elsewhere a cell-biological focused study looks at the factors that control formation of plasmodesmata whilst another manuscript investigates the details of a plants mechanism to avoid photoinhibition.

Yasumura Y1, Pierik R2, Kelly S3, Sakuta M4, Voesenek LA5, Harberd NP (2015) An Ancestral Role for Constitutive Triple Response 1 (CTR1) Proteins in Both Ethylene and Abscisic Acid Signaling Plant Physiology

GARNet Advisory Board Member Nick Harberd leads this study that investigates the evolution of the CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1) protein, which has known to be involved in ethylene signalling for two decades. CTR1 is compared between mosses, lycophytes and angiosperms, showing that PpCTR1 from moss Physcomitrella patens has the same function and the Arabidopsis equivalent, indicating that this signaling pathway predates the land plant lineage. However PpCTR1 is also involved in ABA signaling, which is not the case with AtCTR1 and may be explained by the presence of an AtCTR1 homolog in angiosperms. The authors state that this work provides new insights into the molecular events that contributed to the adaptive evolution of regulatory mechanisms across plant species

Kirsten Knox, Pengwei Wang, Verena Kriechbaumer, Jens Tilsner, Lorenzo Frigerio, Imogen Sparkes, Chris Hawes, Karl Oparka (2015) Putting the Squeeze on Plasmodesmata: A Role for Reticulons in Primary Plasmodesmata Formation Plant Physiology

This study is led by Karl Oparka (Edinburgh) and Chris Hawes (Oxford Brookes) as well as including PIs from Exeter (Sparkes), Warwick (<a href="http://www2.warwick cialis professional 20” onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘’, ‘Frigerio’]);” target=”_blank”>Frigerio) and St Andrews (Tilsner). The manuscript investigates formation of plasmodesmata (PD), which are known to form from endoplasmic reticulum (ER) via an intermediant termed the desmotubule. Members of the Reticulon (RTNLB) family of ER-tubulating proteins are found in the PD proteome are are associated with developing PD following cell division. The authors use super-resolution imaging to show that RTNLB6 colocalises with desmotubules. The mobility of these RTNLB proteins was show, using FRAP, to vary dependent on their positioning within a developing cell plate. Mutant studies show that RTNLB proteins act as important regulators of the formation of PDs and the authors discuss the wider potential roles of these proteins in this process.

Ware MA, Giovagnetti V, Belgio E, Ruban AV (2015) PsbS protein modulates non-photochemical chlorophyll fluorescence quenching in membranes depleted of photosystems J Photochem Photobiol B

Alexander Ruban (QMUL) continues a fine run of recent publications with this study that investigates plants that express increased levels of the photosynthetic PsbS protein, in the context of a subsequent increase in levels of non-photochemical fluorescence quenching (NPQ). In these PsbS overexpressors, there is increased amplitude of the irreversible NPQ component, qI, which likely results from aggregation of the LHCII antenna complex. Use of freeze-fracture electron microscopy show that quenched thylakoids have 3x more aggregated LHCII particles compared to those that are dark-adapted. Overall, these results demonstrate the importance of this LHCII aggregation in the NPQ mechanism whilst showing that structure of the PSII supercomplex plays no role in formation in process of quenching.

Cartolano M, Pieper B, Lempe J, Tattersall A, Huijser P, Tresch A, Darrah PR, Hay A, Tsiantis M (2015) Heterochrony underpins natural variation in Cardamine hirsuta leaf form Proc Natl Acad Sci U S A. 2015 Aug 4.

The study is a continuation of many years of work led by Miltos Tsiantis (who maintains links with Oxford University), aimed at increasing the understanding of how different morphological patterns develop. They compare leaf patterning in Arabidopsis (which has a simple leaf) and in the related plant, Cardamine (that has a complex leaf). They have identified a novel QTL from Cardamine that shows that age-dependent progression of leaf form underlies variation in this trait within species. Interestingly the QTL mapped to a cis-acting region controlling expression of the floral regulator FLC. Genotypes expressing low levels of FLC show early flowering and accelerated changes in leaf form, including faster leaflet production. These findings link reproductive timing with leaf development and the authors speculate that this may help to optimize resource allocation to the next generation.

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