GARNet Research Roundup: June 4th

This weeks GARNet Research Roundup begins with a paper from researchers at the University of Dundee, James Hutton Institute, Durham University and the University of Glasgow that characterises a functional role for alternative splicing during the cold response. Second is a paper from Newcastle University that investigates the role of the OXI1 kinase during aphid predation. Third is a paper that includes University of Bristol co-authors that looks at strigolactone signaling in moss whilst the fourth paper from researchers at Leeds and QMUL studies the role of ascorbate during photosynthesis. The final paper from Warwick and York uses gene expression data from pathogen-infected plants to generate a model for predicting a strategy for synthetic engineering of the defence response.


Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo H, Zhang R, Brown JWS (2018) Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome. Plant Cell doi: 10.1105/tpc.18.00177.

www.plantcell.org/content/early/2018/05/15/tpc.18.00177.long

Open Access

Cristiane Calixto and Wenbin Guo work with John Brown at University of Dundee and the James Hutton Institute and in this large-scale biology paper they characterise the role of alternative splicing (AS) during a stress response. RNAseq was performed on plants exposed to cold stress and they showed that hundreds of genes undergo AS just a few hours after temperature decrease and that this response is sensitive to small changes. The authors propose that AS is a mechanism to fine-tune changes in thermo-plasticity of gene expression and in addition they investigate the activity of the novel splicing factor U2B”-LIKE.

Christiane will discuss this research at the upcoming GARNet2018 meeting held at the University of York in September 2018.


Shoala T, Edwards MG, Knight MR, Gatehouse AMR. OXI1 kinase plays a key role in resistance of Arabidopsis towards aphids (Myzus persicae) (2018) Transgenic Res. doi: 10.1007/s11248-018-0078-x.

Open Access

This work is led by Tahsin Shoala in the lab of Angharad Gatehouse at Newcastle University and demonstrates a novel role for MAPK cascades in resistance to aphid predation. They investigate mutants in OXI1 kinase, a gene that activates MAPK signaling and demonstrate a reduction in the aphid population build-up. Furthermore they show that the effect of OXI works through a mechanism that involves callose deposition, demonstrated as oxi1 mutants lack the upregulation of a set of β-1,3-glucanase genes following predation.


Lopez-Obando M, de Villiers R, Hoffmann B, Ma L, de Saint Germain A, Kossmann J, Coudert Y, Harrison CJ, Rameau C, Hills P, Bonhomme S (2018) Physcomitrella patens MAX2 characterization suggests an ancient role for this F-box protein in photomorphogenesis rather than strigolactone signalling. New Phytol. doi: 10.1111/nph.15214

GARNet committee member Jill Harrison is a co-author on this paper that is led by Mauricio Lopez‐Obando working at Université Paris-Saclay. In Physcomitrella patens development they investigate the role of the moss ortholog of the Arabidopsis strigolactone signaling mutant MAX2. Previous work had shown that moss does response to SL signaing but they find that although Ppmax2 mutants showed defects in early development and photomorphogenesis they do not show changes in the SL response. Fascinatingly this indicates that the molecular components that control SL signaling have diverged in vascular plants and seemingly co-opted a role for MAX2 that was previously not required in mosses.


https://academic.oup.com/jxb/article/69/11/2823/4991886

Plumb W, Townsend AJ, Rasool B, Alomrani S, Razak N, Karpinska B, Ruban AV, Foyer CH. Ascorbate-mediated regulation of growth, photoprotection and photoinhibition in Arabidopsis thaliana (2018) J Exp Bot. doi: 10.1093/jxb/ery170

William Plumb (Leeds) and Alexandra Townsend (QMUL) are the lead authors on this study that investigates the importance of ascorbate during photosynthesis. In this work they analysed the growth of ascorbate synthesis mutants that are smaller and have less biomass than wildtype plants. However these plants have normal levels of non-photoinhibiton, allowing the authors to conclude that ascorbate is needed for growth but not photoprotection.


Foo M, Gherman I, Zhang P, Bates DG, Denby K (2018) A Framework for Engineering Stress Resilient Plants using Genetic Feedback Control and Regulatory Network Rewiring. ACS Synth Biol. doi: 10.1021/acssynbio.8b00037
Mathias Foo and Iulia Gherman (University of Warwick) are lead authors on work that analyses gene expression data taken from Botrytis cinerea-infected Arabidopsis. They have identified a network of genes involved in the defence response. They validate their model against previously obtained time series data and then perturb the model in two differences ways, focused on the transcription factor CHE. This analysis demonstrates the potential of combining feedback control theory with synthetic engineering in order to generate plants that are resistant to biotic stress.

https://pubs.acs.org/doi/10.1021/acssynbio.8b00037

GARNet Research Roundup: May 17th

This weeks GARNet research roundup includes six excellent papers investigating many aspects of Arabidopsis cell biology. Firstly Eirini Kaiserli from Glasgow introduces a novel regulator of blue-light signaling. Second is a paper that analyses the circadian clock with single cell resolution and is led by James Locke (SLCU) and Anthony Hall (Earlham Institute). The next two papers investigate different aspects of hormone signaling, with Keith Lindsey’s group at Durham looking at the relationshop between the HYDRA protein and the auxin response whilst Ottoline Leysers group in Cambridge looks at the link between auxin and cytokinin during shoot growth. The fifth paper from Phillip Mullineaux (University of Essex) provides a genome-wide analysis into the role of HEAT SHOCK TRANSCRIPTION FACTORA1b protein. The final paper from the lab of Piers Hemsley (James Hutton Institute, University of Dundee) should be of interest to many plant molecular biologists as they assess the functional significance of different epitope tags.


Perrella G, Davidson MLH, O’Donnell L, Nastase AM, Herzyk P, Breton G, Pruneda-Paz JL, Kay SA, Chory J, Kaiserli E (2018) ZINC-FINGER interactions mediate transcriptional regulation of hypocotyl growth in Arabidopsis. Proc Natl Acad Sci U S A.. pii: 201718099. doi: 10.1073/pnas.1718099115

Open Access

Eirini Kaiserli (University of Glasgow) leads this study that identifies the ZINC-FINGER HOMEODOMAIN 10 (ZFHD10) as a novel regulator of light signaling. ZFHD10 physically interacts with TANDEM ZINC-FINGER PLUS3 (TZP) and these proteins coassociate at promotors that are blue-light regulated. These results reveal of novel mechanism of action for the key multiple signal integrator TZP in the light regulated growth of Arabidopsis hypocotyls.

Eirini discusses this paper on the GARNet YouTube channel.


Gould PD, Domijan M, Greenwood M, Tokuda IT, Rees H, Kozma-Bognar L, Hall AJ, Locke JC (2018). Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression. Elife. 26;7. pii: e31700. doi: 10.7554/eLife.31700 Open Access

https://elifesciences.org/articles/31700

This paper is led by James Locke (SLCU) and Anthony Hall (Earlham) and investigates the circadian clock at single cell resolution. They use Arabidopsis plants grown in constant environmental conditions to show two desynchronised yet robust single cell oscillations that move both up and down the root. Their results indicate that the clock shows cell-to-cell coupling and they they modeled this relationship to recapitulate the observed waves of activity. Overall their results are suggestive of multiple coordination points for the Arabidopsis clock, which is different from the mammalian system of regulation.


http://dev.biologists.org/content/145/10/dev160572

Short E, Leighton M, Imriz G, Liu D, Cope-Selby N, Hetherington F, Smertenko A, Hussey PJ, Topping JF, Lindsey K (2018) Epidermal expression of a sterol biosynthesis gene regulates root growth by a non-cell autonomous mechanism in Arabidopsis. Development . pii: dev.160572. doi: 10.1242/dev.160572 Open Access

This collaboration between the research groups of Keith Lindsey and Patrick Hussey at the University of Durham investigates the role of the HYDRA1 (HYD1) sterol Δ8-Δ7 isomerase in epidermal patterning. This tissue shows highest HYD1 expression and hyd mutants have major root patterning defects. Tissue-specific expression of HYD1 indicates that it is involved with some type of non-cell autonomous signaling. Analysis of PIN1 and PIN2 protein expression suggests that auxin might be this functional signal


http://www.plantphysiol.org/content/early/2018/05/01/pp.17.01691.long

Waldie T, Leyser O (2018) Cytokinin targets auxin transport to promote shoot branching. Plant Physiol. 2018 May 1. pii: pp.01691.2017. doi: 10.1104/pp.17.01691.Open Access

This study from the lab of Ottoline Leyser (SLCU) investigates the integration between the plant hormones cytokinin and auxin. They investigate the role of cytokinin in shoot branching through analysis of Arabidopsis Response Regulators (ARRs) mutants. They show arr mutant phenotypes correlate with changes in stem auxin transport mediated by the PIN3, PIN4 and PIN7 efflux carriers, the expression of each respond to cytokinin signaling. Overall this study identifies a novel alternative pathway by which cytokinin impacts bud outgrowth through alterations in auxin transport.


Albihlal WS, Irabonosi O, Blein T, Persad R, Chernukhin I, Crespi M, Bechtold U, Mullineaux PM (2018) Arabidopsis Heat Shock Transcription FactorA1b regulates multiple developmental genes under benign and stress conditions. J Exp Bot. doi: 10.1093/jxb/ery142 Open Access

Phillip Mullineaux (University of Essex) leads this collaboration with French colleagues in a study that investigates the genome-wide targets of the HEAT SHOCK TRANSCRIPTION FACTORA1b (HSFA1b) protein. Under non-stress ad heat-stress conditions they showed that 1000s of genes are differentially expressed with a smaller proportion of genes showing different levels of direct interaction. The indirect targets of HSFA1b are regulated through a network of 27 transcription factors and they also provide evidence for the role of hundreds of natural antisense non-coding RNA in the regulation of HSFA1b targets. Overall they show that HSFA1b is a key regulator of environmental cues to regulate both developmental genes and those involved in stress tolerance.


Hurst CH, Turnbull D, Myles SM, Leslie K, Keinath NF, Hemsley PA (2018) Variable effects of C-terminal tags on FLS2 function – not all epitope tags are created equal. Plant Physiol. doi: 10.1104/pp.17.01700 Open Access

This study from the Hemsley lab (James Hutton Institute, University of Dundee) is a cautionary tale on the use and interpretation of results obtained from experiments with commonly-used epitope tags. They assessed the activity of plants containing transgenic FLS2 proteins, which is a receptor-like kinase (RLKs) involved in the defence response. They show that various FLS2 C-terminal epitope fusions reveal highly variable and unpredictable outputs, indicating that the presence of different tags significantly alters protein function. This finding might require a reassessment of many experiments that rely on interpreting the function of epitope-tagged proteins and has significant for many if not all plant molecular biologists.

GARNet Research Roundup: March 29th

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Published on: March 29, 2018

This edition of the GARNet research roundup begins with an analysis of the CELLULOSE SYNTHASE COMPLEX led by Simon Turner in Manchester. Next are two papers from Ian Henderson at Cambridge who, in collaboration with Rob Martienssen in the USA, has investigated the epigenetic factors that control meiotic recombination. Next are two papers led by Hugh Nimmo (Glasgow) who is researching alternative splicing of the LATE ELONGATED HYPOCOTYL transcript. Marc Vendrell and Karl Oparka at the University of Edinburgh are co-authors in the next paper that investigates the binding specificity of the AtSUC2 protein. The seventh paper includes David Salt (Nottingham) as a co-author in an investigation in the plants response to zinc. The final three papers are methods papers on gravitropism, ChIP-Seq and calcium sensing from Nottingham University, SLCU and the John Innes Centre respectively.


Kumar M, Mishra L, Carr P, Pilling M, Gardner P, Mansfield SD, Turner SR (2018) Exploiting CELLULOSE SYNTHASE (CESA) class-specificity to probe cellulose microfibril biosynthesis. Plant Physiol. doi: 10.1104/pp.18.00263 Open Access

Simon Turner (University of Manchester) leads this study that investigates the subunit specificity of the CELLULOSE SYNTHASE COMPLEX, which is composed of many CESA components. Mutant cesa plants were used to probe the specificity of these subunits. Overall the authors found that CESA classes have similar roles in determining cellulose microfibril structure but that the rates of cellulose synthesis might be altered in a subunit-specific manner.


Choi K,, Zhao X, Tock AJ, Lambing C, Underwood CJ,, Hardcastle TJ, Serra H, Kim J, Cho HS, Kim J, Ziolkowski PA, Yelina NE, Hwang I, Martienssen RA, Henderson IR (2018) Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. Genome Res. doi: 10.1101/gr.225599.117
The research groups of Ian Henderson (University of Cambridge) and Rob Martienssen (CSHL) co-lead back-to-back papers that investigate the factors that influence meiotic recombination frequencies. The Henderson led-paper focuses on the position of the SPO11 topoisomerase and the epigenetic factors, such as H3K4me3 and DNA methylation that reside in those areas. They discovered some surprising relationships between SPO11 binding and different transposon classes.


Underwood CJ, Choi K, Lambing C, Zhao X, Serra H, Borges F, Simorowski J, Ernst E, Jacob Y, Henderson IR, Martienssen RA (2018) Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation. Genome Res. doi: 10.1101/gr.227116.117

Open Access

The Martienssen–led paper focuses on epigenetic marks, such as H3K9me2 and non-CG DNA methylation that reside at pericentromeric regions. By altering the distribution of these marks, the amount of pericentrometric recombination can be changed and that the number of double stranded breaks increase in H3K9me2/non-CG mutants.


James AB, Sullivan S, Nimmo HG (2018) Global spatial analysis of Arabidopsis natural variants implicates 5’UTR splicing of LATE ELONGATED HYPOCOTYL in responses to temperature. Plant Cell Environment. doi: 10.1111/pce.13188

James AB, Calixto CPG, Tzioutziou NA, Guo W, Zhang R, Simpson CG, Jiang W, Nimmo GA, Brown JWS, Nimmo HG (2018) How does temperature affect splicing events? Isoform switching of splicing factors regulates splicing of LATE ELONGATED HYPOCOTYL (LHY). Plant Cell Environ. doi: 10.1111/pce.13193

The first of these back-to-back papers is led by Hugh Nimmo (Glasgow) in a study that characterises a set of 5’UTRs in the LATE ELONGATED HYPOCOTYL (LHY) gene and how they change in response to temperature. This is linked to a correlation of how these LHY haplotypes are global distributed.

The second paper is an extension of this study and includes Hugh Nimmo (Glasgow) and John Brown (JHI, Dundee) as co-corresponding authors. They that show RNA-binding splicing factors (SFs) are necessary for temperature-induced changes in the LHY transcript. LHY might be considered a molecular thermostat whose splicing can response to changes as little as 2°C.


De Moliner F, Knox K, Reinders A, Ward J, McLaughlin P, Oparka K, Vendrell M (2018) Probing binding specificity of the sucrose transporter AtSUC2 with fluorescent coumarin glucosides. J Exp Bot. doi: 10.1093/jxb/ery075 Open Access

Marc Vendrell and Karl Oparka (University of Edinburgh) are the corresponding authors on this bioimaging study that probes the specificity of the AtSUC2 phloem sucrose transporter. They use structural varieties in coumarin glucosides to precisely define the binding characteristics of AtSUC2.


Chen ZR, Kuang L, Gao YQ, Wang YL, Salt DE, Chao DY (2018) AtHMA4 Drives Natural Variation in Leaf Zn Concentration of Arabidopsis thaliana. Front Plant Sci. doi: 10.3389/fpls.2018.00270

Open Access

David Salt (University of Nottingham) is a co-author on this Chinese study that characterises the role of the Heavy Metal-ATPase 4 (HMA4) in the respond to zinc.


Muller L, Bennett MJ, French A, Wells DM, Swarup R (2018) Root Gravitropism: Quantification, Challenges, and Solutions. Methods Mol Biol. doi: 10.1007/978-1-4939-7747-5_8

Ranjan Swarup (University of Nottingham) leads this methods paper that describes techniques for the automated measurement of root gravitropic responses.


Cortijo S, Charoensawan V, Roudier F, Wigge PA (2018) Chromatin Immunoprecipitation Sequencing (ChIP-Seq) for Transcription Factors and Chromatin Factors in Arabidopsis thaliana Roots: From Material Collection to Data Analysis. Methods Mol Biol. doi: 10.1007/978-1-4939-7747-5_18

Phillip Wigge (SLCU) leads this methods paper that outlines the technical details for the now common and important technique of ChIP-Seq from Arabidopsis roots.


Kelner A, Leitão N, Chabaud M, Charpentier M, de Carvalho-Niebel F (2018) Dual Color Sensors for Simultaneous Analysis of Calcium Signal Dynamics in the Nuclear and Cytoplasmic Compartments of Plant Cells. Front Plant Sci. doi: 10.3389/fpls.2018.00245 Open Access

Miriam Charpentier (John Innes Centre) is a co-author on this work that uses fluorescent protein-based Ca2+ sensors, the GECOs, to successfully monitor the calcium response to a range of biotic and abiotic elicitors. These GECO-based sensors represent an exciting new tool for the study of calcium dynamics.

Arabidopsis Research Roundup: Nov 24th

The week’s UK Arabidopsis research roundup includes seven papers from groups who work on a range of topics.

Firstly Antony Dodd (Bristol) investigates the role of sugar signaling during hypocotyl elongation and provides an audio description of this groups work. Secondly Mike Holdsworth (Nottingham) leads a paper that demonstrates the importance of the N-rule pathway in the response to abiotic stresses. Thirdly are a set of papers that have developed models on three different topics. Mike Blatt’s group at Glasgow University has a cross-scale model that is applied to stomatal opening whilst Stan Maree and Veronica Griensien (JIC) use modeling to predict how the topology of pavement cells is determined. Finally Arabidopsis is used as an example that fits a model that investigates how critical mutation rate (CMR) changes with population size. In the sixth paper Lorraine Williams and colleagues (University of Southampton) investigate the function of a rice transport protein involved in manganese tolerance by expressing it in Arabidopsis. The final paper from Jerzy Paszkowski (SLCU) outlines a novel screening strategy for retrotransposons and the identification of an ecotype specific element.


Simon NM, Kusakina J, Fernández-López Á, Chembath A, Belbin FE, Dodd AN (2017) The energy-signalling hub SnRK1 is important for sucrose-induced hypocotyl elongation. Plant Physiol. doi: 10.1104/pp.17.01395

Open Access

This UK-wide collaboration is led by Anthony Dodd at the University of Bristol and has looked at the factors that control hypocotyl elongation in response to sugar signalling. This response is integrated through the sugar-signalling hub, SnRK1 and is regulated by trehalose-6-phosphate (Tre6P). They also integrate hormone signalling and the influence of diurnal rhythms into the control of this process, importantly showing that the ubiquitous sugar regulator hexokinase is not involved in this process.

Antony kindly provides an audio description of this research that can be found on YouTube or on the GARNet iTunes channel. Please subscribe!


Vicente J, Mendiondo GM, Movahedi M, Peirats-Llobet M, Juan YT, Shen YY, Dambire C, Smart K, Rodriguez PL, Charng YY, Gray JE, Holdsworth MJ (2017) The Cys-Arg/N-End Rule Pathway Is a General Sensor of Abiotic Stress in Flowering Plants. Current Biology doi: 10.1016/j.cub.2017.09.006

Open Access

Mike Holdsworth (University of Nottingham) is the corresponding author of this collaboration with colleagues from Sheffield, Spain and Taiwan that investigates how the N-rule degradation pathway acts a sensor of general abiotic stress in both Arabidopsis and Barley. These responses are integrated through degradation of the group VII Ethylene Response Factor transcription factors (ERFVIIs) family via direct and indirect pathways. In addition they link ERFVII activity with chromatin-remodeling ATPase BRAHMA providing evidence for a single mechanism that links the responses to a number of environmental signals.


Wang Y, Hills A, Vialet-Chabrand SR, Papanatsiou M, Griffiths H, Rogers S, Lawson T, Lew V, Blatt MR (2017) Unexpected Connections between Humidity and Ion Transport Discovered using a Model to Bridge Guard Cell-to-Leaf Scales. Plant Cell. doi: 10.1105/tpc.17.00694

Open Access

Mike Blatt (University of Glasgow) leads this collaboration with researchers at the Universities of Cambridge and Essex. They have developed the OnGuard2 quantitative systems platform that integrates numerous parameters that control guard cell dynamics across many scales including at molecular, cellular, tissue and canopy levels. They experimentally demonstrate that OnGuard2 faithfully reproduces the kinetics of real stomatal movement and therefore that this modeling is able to bridge the micro-macro divide.


Carter R, Sánchez-Corrales YE, Hartley M, Grieneisen VA, Marée AFM (2017) Pavement cells and the topology puzzle. Development. doi: 10.1242/dev.157073

Stan Maree and Veronica Griensien (John Innes Centre) lead this study that has looked at the patterning of 50000 Arabidopsis pavement cells to understand the topological signatures that exist in this population. They have developed a heuristic cellular division rule to produce a model that can reproduce their observations by predicting how these cells divide. They confirmed their model by tracking 800 mitotic events, allowing them to conclude that distinct topology is not a direct consequence of the jigsaw-like shape of the cells, but rather owes itself to life-history-driven process, with limited impact from cell surface mechanics.


Aston E, Channon A, Belavkin RV, Gifford DR, Krašovec R, Knight CG (2017) Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover. Sci Rep. doi: 10.1038/s41598-017-14628-x

Open Access

In this study a team of computational biologists from Keele, Middlesex and Manchester have used Arabidopsis as an exemplar to understand how critical mutation rate (CMR) provides insights into the shift between survival-of-the-fittest and survival of individuals with greater mutational robustness. They have produced a simulation for these parameters that predicts outcomes for a range of biological organisms, showing that CMR decreases with reduced population size. They suggest that the model can be used to understand the conservation strategies exhibited in populations that are approaching extinction.


Farthing EC, Menguer PK, Fett JP, Williams LE (2017) OsMTP11 is localised at the Golgi and contributes to Mn tolerance. Sci Rep. doi: 10.1038/s41598-017-15324-6
Lorraine Williams (University of Southampton) and her colleagues have identified a transporter protein from rice, OsMTP11 that is involved in mangenase tolerance. They show that heterologous expression of this protein is able to rescue the manganese sensitive phenotype of Arabidopsis mtp11-3 knockouts. They show that OsMTP11 localises to the Golgi and have also conducted site directed mutagenesis to identify key residues that are important for the function of this protein.


Griffiths J, Catoni M, Iwasaki M, Paszkowski J (2017) Sequence-independent identification of active LTR retrotransposons in Arabidopsis. Mol Plant. doi: 10.1016/j.molp.2017.10.012

Open Access

Jerzy Paszkowski (SLCU) leads this single-figure short manuscript that has characterised the population of retrotransposons in Arabidopsis. They develop a novel cost-effective screening strategy that allows them to identify sequences found on extrachromosomal DNA (ecDNA), which includes a retroelement found in Lansberg erecta but not in the reference genome ecotype Col-0.

Arabidopsis Research Roundup: October 5th

After a brief hiatus the UK Arabidopsis Research Roundup returns with eight papers that focus on different aspects of Arabidopsis cell biology.

Firstly GARNet PI Jim Murray leads a study that performs a genome-wide analysis of sub-nucleosomal particles whilst Phil Wigge’s lab at SLCU conducts a more focused study on G-box regulatory sequences.

Thirdly Veronica Grieneisen (JIC) and co-workers have modelled the process of boron transport in the root, revealing exciting insights into how traffic jams might form.

Fourthly is a large scale biology paper led by Miriam Gifford (University of Warwick) that looks at the temporal and spatial expression patterns that control lateral root development.

Next Alexander Ruban (QMUL) investigates how low-light acclimated plants respond to high light.

The sixth and seventh studies are led by Alison Baker (Leeds) or Bill Davies (Lancaster) and look at phosphate or hormone signaling respectively.

Finally Gareth Jenkins (University of Glasgow) compares the UV-B signaling module in lower plants with that in Arabidopsis.


Pass DA, Sornay E, Marchbank A, Crawford MR, Paszkiewicz K, Kent NA, Murray JAH (2017) Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PLoS Genet. doi: 10.1371/journal.pgen.1006988

Open Access

GARNet PI Jim Murray is the corresponding author on this study that performs a whole-genome scan of sub-nucleosomal particles (subNSPs) that have been identified using differential micrococcal nuclease (MNase) digestion. They link the position of subNSPs with RNAseq data taken from plants grown in different light conditions. They show that this new technique is able to discriminate regulatory regions that have been obscured by previous experimental procedures and therefore represents a very useful experimental method.


Ezer D, Shepherd SJ, Brestovitsky A, Dickinson P, Cortijo S, Charoensawan V, Box MS, Biswas S, Jaeger K, Wigge PA (2017) The G-box transcriptional regulatory code in Arabidopsis. Plant Physiol. 10.1104/pp.17.01086

Open Access

Phil Wigge (SLCU) is the corresponding author of this study that investigates the sequence elements that are linked to the conserved G-box regulatory motifs. They identify a set of bZIP and bHLH transcription factors that predict the expression of genes downstream of perfect G-boxes. In addition they have developed a website that provide visualisations of the G-box regulatory network (araboxcis.org).


Sotta N, Duncan S, Tanaka M, Takafumi S, Marée AF, Fujiwara T, Grieneisen VA (2017) Rapid transporter regulation prevents substrate flow traffic jams in boron transport. Elife. doi: 10.7554/eLife.27038

Open Access

Veronica Grieneisen (JIC) is the lead author on this detailed analysis of the regulatory circuits that are established during boron uptake in Arabidopsis roots. They used mathematical modelling to show that during boron uptake, swift regulation of transport activity is needed to prevent toxic accumulation of the metal. This system has analogy to the way in which traffic jams of nutrient flow might form and has relevance for regulatory systems outside of plant science. https://www.sciencedaily.com/releases/2017/09/170905104358.htm


Walker L, Boddington C, Jenkins D, Wang Y, Grønlund JT, Hulsmans J, Kumar S, Patel D, Moore JD, Carter A, Samavedam S, Bomono G, Hersh DS, Coruzzi GM, Burroughs NJ, Gifford ML (2017) Root architecture shaping by the environment is orchestrated by dynamic gene expression in space and time. Plant Cell. doi: 10.1105/tpc.16.00961

Open Access

Miriam Gifford (University of Warwick) leads this broad consortium that has taken a systems biology approach to better define the environmental factors that control dynamic root architecture. They track transcriptional responses during lateral root development in remarkable detail, looking at individual transcripts. They confirm the idea that the activity of a gene is not simply a function of its amino acid sequence but rather the temporal and spatial regulation of its expression.


Tian Y, Sacharz J, Ware MA, Zhang H, Ruban AV (2017) Effects of periodic photoinhibitory light exposure on physiology and productivity of Arabidopsis plants grown under low light. J Exp Bot. doi: 10.1093/jxb/erx213. Open Access

Alexander Ruban (QMUL) is the corresponding author on this collaboration with Chinese colleagues that examined the effect of high-light stress on low-light acclimated Arabidopsis plants. Initially these plants showed significant photo-inhibition but that they recovered rapidly and after 2 weeks of treatment there was no change in photosynthetic yield. In addition high light acclimated plants showed accelerated reproductive phase change that coincided with higher seed yield.


Qi W, Manfield IW, Muench SP, Baker A (2017) AtSPX1 affects the AtPHR1 -DNA binding equilibrium by binding monomeric AtPHR1 in solution. Biochem J. doi: 10.1042/BCJ20170522 Open Access

Alison Baker (University of Leeds) leads this research that focusses on the binding of the Phosphate Starvation Response 1 (PHR1) transcription factor to regulatory P1BS DNA sequences. They show a tandem P1BS sequence is bound more strongly than a single P1BS site. Ultimately they demonstrate tight regulation of phosphate signaling both by the concentration of phosphate as well as the activity of the interacting SPX protein.


Li X, Chen L, Forde BG, Davies WJ (2017) The Biphasic Root Growth Response to Abscisic Acid in Arabidopsis Involves Interaction with Ethylene and Auxin Signalling Pathways. Front Plant Sci. doi: 10.3389/fpls.2017.01493 Open Access

Bill Davies and Brian Forde (Lancaster University) lead this work that investigates the effect on ethylene and auxin on the biphasic response to ABA during root elongation. They used a range of hormone signalling mutants to show that the response to high ABA is via both ethylene and auzin signalling. In contrast the response to low ABA does not require ethylene signalling.


Soriano G, Cloix C, Heilmann M, Núñez-Olivera E, Martínez-Abaigar J, Jenkins GI (2017) Evolutionary conservation of structure and function of the UVR8 photoreceptor from the liverwort Marchantia polymorpha and the moss Physcomitrella patens. New Phytol. doi: 10.1111/nph.14767

Gareth Jenkins (University of Glasgow) is the corresponding author of this work that looks at the role of the UVR8 UV-B receptor in lower plants. They expressed the versions of UVR8 from a moss or a liverwort in Arabidopsis and showed that although there appears to be differences in the regulation of this protein, the mechanism of UV-B signaling is evolutionarily conserved

Arabidopsis Research Roundup: September 6th

This largest ever Arabidopsis Research Roundup (ARR) includes 6 papers from Norwich Research Park (NRP), including three featuring Cyril Zipfel (TSL) as a co-author on papers that investigate different aspects of plant immune signaling. Elsewhere on the NRP site Veronica Grieneisen (JIC) is a co-author on a study that defines the root auxin maximum whilst Dale Sanders and Saskia Hogenhout lead a paper that defines a method for the analysis of calcium signaling. Finally Robert Sablowski’s group at the JIC investigates the role of the DELLA proteins during meristem development.

Elsewhere investigators from Kew Gardens and Bangor University have used nanopore sequencing for the facile characterisation of field populations of Arabidopsis. Similarly Seth Davies (University of York) is part of a collaboration that looks how alterations in the circadian clock might affect plant fitness.

Verena Kriechbaumer (Oxford Brookes) leads a phylogenetic study into the conservation of auxin biosynthesis genes whilst Hilary Rodgers (Cardiff University) is a co-author on a Chinese-led study that looks into role of cadmium on the Arabidopsis cell cycle.

This ARR is full of examples of UK researchers involved in global collaborations. This includes Cambridge researchers involved in a proteomic analysis of microsomes, Justin Goodrich from the University of Edinburgh as part of a US-led study that defines the regulation of the PRC2 complex and Katherine Denby (University of York) as a member of a consortium that has performed a network analysis of jasmonic acid signaling.

Finally are two studies in which the research takes place within a single institution. Malcolm Hawksford (Rothamsted Research) looks at the effect of wheat transcription factors in the response to the heavy metal zinc whilst Emily Larson and Mike Blatt (University of Glasgow) investigate the role of clathrin on plant vesicular transport.


D’Ambrosio JM, Couto D, Fabro G, Scuffi D, Lamattina L, Munnik T, Andersson MX, Alvarez ME, Zipfel C, Laxalt AM (2017) PLC2 Regulates MAMP-Triggered Immunity by Modulating ROS Production in Arabidopsis. Plant Physiol 10.1104/pp.17.00173

This Argentinian-led study includes Cyril Zipfel (TSL) as a co-author on this work that uses miRNA-mediated gene silencing to assess the role of the phosphoinositide-specific phospholipase C (PI-PLC) in plant immune signaling.


Imkampe J, Halter T, Huang S, Schulze S, Mazzotta S, Schmidt N, Manstretta R, Postel S, Wierzba M, Yang Y, vanDongen WM, Stahl M, Zipfel C, Goshe MB, Clouse S, de Vries SC, Tax F, Wang X, Kemmerling B (2017) The Arabidopsis Leucine-rich Repeat Receptor Kinase BIR3 Negatively Regulates BAK1 Receptor Complex Formation and Stabilizes BAK1. Plant Cell. 10.1105/tpc.17.00376

Cyril Zipfel (TSL) is a co-author on this global collaboration that further defines the role of the BAK1 receptor in hormone and immune signaling through its interaction with two LRR-RK proteins (BIR2 and BIR3).


Singh V, Perraki A, Kim SY, Shrivastava S, Lee JH, Zhao Y, Schwessinger B, Oh MH, Marshall-Colon A, Zipfel C, Huber SC (2017) Tyrosine-610 in the Receptor Kinase BAK1 Does Not Play a Major Role in Brassinosteroid Signaling or Innate Immunity. Front Plant Sci. 10.3389/fpls.2017.01273

Cyril Zipfel (TSL) is a co-author on this US-led manuscript that again looks into the role of the BRI1-ASSOCIATED KINASE1 (BAK1) on plant immune signaling. Importantly they show that the phosphorylation of tyrosine-610 is actually not necessary for this proteins role in brassinosteroid or immune signaling


Di Mambro R, De Ruvo M,,, Pacifici E, Salvi E, Sozzani R, Benfey PN,, Busch W, Novak O, Ljung K, Di Paola L, Marée AFM, Costantino P, Grieneisen VA, Sabatini S (2017) Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root. Proc Natl Acad Sci U S A 10.1073/pnas.1705833114

Veronica Grieneisen (JIC) is a co-corresponding author on this work with Sabrina Sabatini from the University of Rome. They define the auxin minimum, a newly characterised determinat of root patterning that delineates the separation of root division and the differentiation zones. This is defined by the interaction between cytokinin and auxin signaling cascades.

Veronica discusses this paper on the GARNet YouTube channel: https://www.youtube.com/watch?v=gYdL6eddOcA


Vincent TR, Canham J, Toyota M, Avramova M, Mugford ST, Gilroy S, Miller AJ, Hogenhout S, Sanders D (2017) Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor. J Vis Exp. 10.3791/56142

Dale Sanders and GARNet committee member Saskia Hogenhout (JIC) lead this study that describes an imaging technique that allows for the real time assessment of calcium dynamics using a fluorescently tagged sensor.


Serrano-Mislata A, Bencivenga S, Bush M, Schiessl K, Boden S, Sablowski R (2017) DELLA genes restrict inflorescence meristem function independently of plant height. Nature Plants. 10.1038/s41477-017-0003-y

Robert Sablowski (JIC) leads this paper that investigates the role of DELLA proteins in the control of cell cycle regulators and how this impacts meristem size in both barley and Arabidopsis. Read more about it on the John Innes Centre website.


Parker J, Helmstetter AJ, Devey D, Wilkinson T, Papadopulos AST (2017) Field-based species identification of closely-related plants using real-time nanopore sequencing. Sci Rep. 10.1038/s41598-017-08461-5 Open Access

This investigation led by researchers at Kew Gardens and at the Bangor University use Real Time Nanopore Sequencing (RTnS) that allows for rapid species identification in the field and that combining RTnS and laboratory-based high-throughput sequencing leads to a significant improvement in genome assembly.


Rubin MJ, Brock MT, Davis AM, German ZM, Knapp M, Welch SM, Harmer SL, Maloof JN7, Davis SJ, Weinig C (2017) Circadian rhythms vary over the growing season and correlate with fitness components. Mol Ecol. 10.1111/mec.14287 Open Access

Seth Davies (University of York) is a co-author on this US-led work that conducts a study of field-growth Arabidopsis to evaluate the contribution of the circadian clock toward survival and fecundity. They show that variation in clock function correlates with growth performance in a natural environment.


Poulet A, Kriechbaumer V (2017) Bioinformatics Analysis of Phylogeny and Transcription of TAA/YUC Auxin Biosynthetic Genes. Int J Mol Sci. 10.3390/ijms18081791 Open Access

The paper from Oxford Brookes University provides a phylogenetic analysis of TAA/TAR (tryptophan aminotransferase related) and YUCCA proteins that are involved in auxin biosynthesis. In addition they provide tissue and cell-specific information about the function of these proteins and that their function is conserved in lower plant species.


Cui W, Wang H, Song J, Cao X, Rogers HJ, Francis D, Jia C, Sun L, Hou M, Yang Y, Tai P, Liu W (2017) Cell cycle arrest mediated by Cd-induced DNA damage in Arabidopsis root tips. Ecotoxicol Environ Saf. 10.1016/j.ecoenv.2017.07.074 Open Access

Hilary Rodgers (Cardiff University) is a co-author on this Chinese-led study that looks into the effect of cadmium treatment on the regulation of the cell cycle and DNA damage repair. They show that different cadmium concentrations effect different phases of the cell cycle.


Alqurashi M, Thomas L, Gehring C, Marondedze C (2017) A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses. Proteomes. 10.3390/proteomes5030022 Open Access

This international collaboration includes members of the Cambridge Centre for Proteomics and conducts a quantitative analysis of the Arabidopsis microsomal proteome following treatment with hydrogen peroxide or ABA. Perhaps unsurprisingly a high number of proteins characterized as ‘responsing to stress’ were found upregulated following treatment with H2O2 or ABA.


Xiao J, Jin R, Yu X, Shen M, Wagner JD, Pai A, Song C, Zhuang M, Klasfeld S, He C, Santos AM, Helliwell C, Pruneda-Paz JL, Kay SA, Lin X, Cui S, Garcia MF, Clarenz O, Goodrich J, Zhang X, Austin RS,, Bonasio R, Wagner D (2017) Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nature Genet 10.1038/ng.3937

Justin Goodrich (University of Edinburgh) is a co-author on this US-led study that looks into the role of Polycomb response element (PREs) in directing the placement of the Polycomb repressive complex 2 (PRC2) via their interaction with a newly identified transcription factors. Justin has recently discussed a paper on a similar topic on the GARNet YouTube channel.


Hickman R, van Verk MC, Van Dijken AJH, Pereira Mendes M, Vroegop-Vos IA, Caarls L, Steenbergen M, Van Der Nagel I, Wesselink GJ, Jironkin A, Talbot A, Rhodes J, de Vries M, Schuurink RC, Denby K, Pieterse CMJ, Van Wees SCM (2017) Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network. The Plant Cell 10.1105/tpc.16.00958 Open Access

GARNet committee member Katherine Denby (University of York) is a member of this large consortium of researchers who have performed a network analysis on the dynamics of jasmonic acid signaling


Evens NP, Buchner P, Williams LE, Hawkesford MJ (2017) The role of ZIP transporters and group F bZIP transcription factors in the Zn-deficiency response of wheat (Triticum aestivum) Plant J. 10.1111/tpj.13655 Open Access

Malcolm Hawkesford (Rothamsted Research) leads this study that investigate a set of wheat bZIP transcription factors and ZIP transporters that are involved in the uptake and transport of zinc. As part of this work they use Arabidopsis to test the conserved function of these wheat proteins.


Larson ER, Van Zelm E, Roux C, Marion-Poll A, Blatt MR (2017) Clathrin Heavy Chain subunits coordinate endo- and exocytic traffic and affect stomatal movement. Plant Physiol. 10.1104/pp.17.00970 Open Access

Mike Blatt and Emily Larson (University of Glasgow) are the co-corresponding authors on this study that looks into the role of clathrin heavy chain on vesicular transport in Arabidopsis. They looked at clathrin mutants to show that the protein plays an unsurprisingly important role in both endo- and exocytosis.

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 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

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