GARNet Research Roundup: April 27th

This weeks GARNet research roundup features four papers that include Malcolm Bennett (University of Nottingham) as an author. The first three are linked manuscripts that investigate the role of auxin on root hair development that is controlled by varying phosphate levels. Ranjan Swarup provides an audio summary of two of these papers on the GARNet YouTube and podcast feeds.

The fourth paper from Nottingham is a collaboration with GARNet PI Jim Murray (Cardiff University) that characterises the STM gene network and its influence on meristem development.

The fifth paper from the lab of Paul Dupree in Cambridge characterises the stem transcriptome whilst the next paper from Iain Johnston and George Bassel (University of Birmingham) identifies a bet-hedging network that influences seed germination. The final paper features Seth Davies (University of York) as a co-author and investigates the impact of changes in circadian rhythms on short architecture.


Researchers at the University of Nottingham are involved in three back-to-back papers that add a mechanistic framework to the relationship between phosphate and auxin signaling in root hairs.

Bhosale R, Giri J, Pandey BK, Giehl RFH, Hartmann A, Traini R, Truskina J, Leftley N, Hanlon M, Swarup K, Rashed A, Voß U, Alonso J, Stepanova A, Yun J, Ljung K, Brown KM, Lynch JP, Dolan L, Vernoux T, Bishopp A, Wells D, von Wirén N, Bennett MJ, Swarup R (2018) A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate. Nat Commun. 9(1):1409. doi: 10.1038/s41467-018-03851-3

https://www.nature.com/articles/s41467-018-03851-3

Open Access

The first paper is led by Ranjan Swarup and defines components of auxin biosynthetic, transport and signaling pathways that are involved in the change root hair development in response to different phosphate concentrations in Arabidopsis. Ranjan discusses this paper on YouTube.

Giri J, Bhosale R, Huang G, Pandey BK, Parker H, Zappala S, Yang J, Dievart A, Bureau C, Ljung K, Price A, Rose T, Larrieu A, Mairhofer S, Sturrock CJ, White P, Dupuy L, Hawkesford M, Perin C, Liang W, Peret B, Hodgman CT, Lynch J, Wissuwa M, Zhang D, Pridmore T, Mooney SJ, Guiderdoni E, Swarup R, Bennett MJ (2018). Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate. Nat Commun. 9(1):1408. doi: 10.1038/s41467-018-03850-4

https://www.nature.com/articles/s41467-018-03850-4

Open Access

This paper led by Malcolm Bennett uses a rice model to investigate the relationship between auxin and root hair elongation in response to low concentrations of phosphate. They show rice aux1 mutants have significant changes in root architecture.

Dindas J, Scherzer S, Roelfsema MRG, von Meyer K, Müller HM, Al-Rasheid KAS, Palme K, Dietrich P, Becker D, Bennett MJ, Hedrich R (2018) AUX1-mediated root hair auxin influx governs SCF(TIR1/AFB)-type Ca(2+) signaling. Nat Commun. 9(1):1174. doi: 10.1038/s41467-018-03582-5

Open Access

The third paper includes Malcolm Bennett as a co-author and investigates how the auxin transport and signaling pathways stimulate calcium signaling during root hair elongation.


Scofield S, Murison A, Jones A, Fozard J, Aida M, Band LR, Bennett M, Murray JAH (2018) Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network. Development pii: dev.157081. doi: 10.1242/dev.157081

http://dev.biologists.org/content/early/2018/04/12/dev.157081.long

Open Access
GARNet PI Jim Murray is the corresponding author on this manuscript that is led by Dr Simon Scofield and includes collaborators from the University of Nottingham. They have explored the gene regulatory network that is regulated by the key meristem identity gene SHOOT MERISTEMLESS (STM). This network includes an over-representation of transcription factor families, each of which have distinct roles in meristem development. They use in planta experimentation and in silico modeling to investigate the relationship between STM and CUC1 in more detail. Overall this study confirms that STM is a central regulator of shoot meristem function.


Faria-Blanc N, Mortimer JC, Dupree P (2018) A Transcriptomic Analysis of Xylan Mutants Does Not Support the Existence of a Secondary Cell Wall Integrity System in Arabidopsis. Front Plant Sci. 9:384. doi: 10.3389/fpls.2018.00384

Open Access

Paul Dupree (University of Cambridge) is the corresponding author of this study that uses a range of Arabidopsis cell wall mutants to investigate the stem transcriptome. In plants with defects in xylan synthesis the authors found surprisingly few transcriptional changes. This indicates that once plants have committed to a terminal secondary cell wall program there is little need for transcriptional changes even after cell wall damage.


Johnston IG, Bassel GW (2018) Identification of a bet-hedging network motif generating noise in hormone concentrations and germination propensity in Arabidopsis. J R Soc Interface. 15(141). pii: 20180042. doi: 10.1098/rsif.2018.0042.

Open Access
Iain Johnston (University of Birmingham) leads this study that has identified a bet-hedging network that links hormone signaling during Arabidopsis germination. This type of network allows plants to more easily adapt to varying environmental conditions but can preclude maximum growth. In this system the network is based upon the regulation of ABA synthesis, activity and degradation, which is maintained at a constant mean level even though it exhibits significant noise. They investigate the parameters that might be tweaked to reduce variation in germination rate and therefore might be targets for modification in order to maximise responses under particular environmental conditions.

George Bassel who is a co-author on this paper will be speaking at the GARNet2018 Meeting in York in September.

http://rsif.royalsocietypublishing.org/content/15/141/20180042.long

Rubin MJ, Brock MT, Baker RL, Wilcox S, Anderson K, Davis SJ, Weinig C (2018) Circadian rhythms are associated with shoot architecture in natural settings. New Phytol. doi: 10.1111/nph.15162.

Seth Davies (University of York) is a co-author on this study that assesses the effect of circadian rhythms on aerial phenotypes that lead to fruit production in field grown Arabidopsis. This was assessed over two growing seasons and they show that variation in clock function significantly impacts shoot architecture.

Arabidopsis Research Roundup: March 2nd.

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Published on: March 2, 2018

The first two papers in this weeks Arabidopsis Research Roundup investigate different aspects of the plants response to temperature fluctuations. Firstly Lars Ostergaard (JIC) looks at the influence of temperature in the control of fruit dehiscence whilst Phil Wigge (SLCU) investigates crosstalk between chloroplast and nuclear signaling.

The third paper from Ian Henderson (University of Cambridge) studies the genetic elements that control rates of meiotic recombination. The next paper from the University of Leeds looks at the potential of using MET1 in the induction of novel epi-alleles whilst the penultimate paper includes the GARNet PI Jim Murray (Cardiff University) as a co-author and defines the role of CYCD7;1 in guard cell formation.

The final paper focusses on an enzyme involved in chlorophyll biosynthesis and includes Guy Hanke (QMUL) as a co-author.


https://linkinghub.elsevier.com/retrieve/pii/S1674-2052(18)30023-6

Li XR, Deb J, Kumar SV, Østergaard L (2018) Temperature Modulates Tissue-Specification Program to Control Fruit Dehiscence in Brassicaceae. Molecular Plant doi: 10.1016/j.molp.2018.01.003 Open Access

Lars Ostergaard (John Innes Centre) is the corresponding author that continues his groups work on the function of the INDEHISCENT protein, on this occasion looking at its involvement in the link between temperature and fruit dehiscence. They show that fruit valve margin development is accelerated at higher temperatures, facilitated by the activity of IND. This activity is associated with the changes in the induction dynamics of the known thermosensory histone H2A.Z and demonstrate a molecular framework for the response to changing temperature during fruit ripening.


http://www.cell.com/cell-reports/references/S2211-1247(18)30103-7

Dickinson PJ, Kumar M, Martinho C, Yoo SJ, Lan H, Artavanis G, Charoensawan V, Schöttler MA, Bock R, Jaeger KE, Wigge PA (2018) Chloroplast Signaling Gates Thermotolerance in Arabidopsis. Cell Rep. doi: 10.1016/j.celrep.2018.01.054 Open Access

Phil Wigge (SLCU) is the corresponding author on this study of the link between light-induced chloroplast signaling and thermotolerance. A forward genetic screen allowed the authors to identify two genes that demonstrated a key role for chloroplast signaling in controlling the activity of heat shock factors (HSFs), which enable the plant to cope with temperature variations. Subsequently they show that altering the binding activities of the HSFA1a protein can mimic heat shock response independent of any changes in temperature.


Serra H, Lambing C, Griffin CH, Topp SD, Nageswaran DC, Underwood CJ, Ziolkowski PA, Séguéla-Arnaud M, Fernandes JB,, Mercier R, Henderson IR (2018) Massive crossover elevation via combination of HEI10 and recq4a recq4b during Arabidopsis meiosis. PNAS doi: 10.1073/pnas.1713071115

Ian Henderson (University of Cambridge) is the corresponding author on this collaboration with French colleagues in a study that investigates the factors that control recombination frequency in meiosis. During normal meiotic recombination the majority of double stranded breaks will not form crossovers (over 90%) so to increase this frequency they altered the active dosage of genetic elements that are either pro-crossover or anti-crossover control. This strategy results in a massive increase in crossovers and provides a genetic framework for increasing recombination, a strategy that can be critically important for increasing variation during crop breeding.


Brocklehurst S, Watson M, Carr IM, Out S, Heidmann I, Meyer P (2018) Induction of epigenetic variation in Arabidopsis by over-expression of DNA METHYLTRANSFERASE1 (MET1). PLoS One. doi: 10.1371/journal.pone.0192170 Open Access

This study from the University of Leeds is led by Peter Meyer and investigates how overexpression of the METHYLTRANSFERASE1 (MET1) gene might generate novel epi-alleles that result in altered gene expression. This strategy indeed generated novel epi-alleles that increased expression at loci encoding TEs, non-coding RNAs and protein coding genes. Importantly any altered expression can be transmitted to the next generation, independent of the presence of a MET1 expressing transgene. However the long term stability of these epi-alleles differs in an loci-specific manner.


Weimer AK, Matos JL, Sharma N, Patell F, Murray JAH, Dewitte W, Bergmann DC (2018) Lineage and stage-specific expressed CYCD7;1 coordinates the single symmetric division that creates stomatal guard cells. Development. doi: 10.1242/dev.160671

GARNet PI Jim Murray and Walter DeWitte (Cardiff University) are co-authors on this US-led study that adds complexity to our understanding of the molecular players that control guard cell specification. The authors show that the D-type cyclin CYCD7;1 is expressed during a short time window prior to the symmetry division that forms two guard cells. This activity is controlled by cell-type specific transcription factors acting in the appropriate time period.

http://dev.biologists.org/content/early/2018/02/14/dev.160671.long

Herbst J, Girke A, Hajirezaei MR, Hanke G, Grimm B (2018) Potential Roles of YCF54 and Ferredoxin-NADPH Reductase for Magnesium Protoporphyrin Monomethylester Cyclase. Plant J. doi: 10.1111/tpj.13869

Guy Hanke (QMUL) is a co-author on this German-led study that investigates an enzyme reactions that occur during chlorophyll biosynthesis. Specifically they showed that plants lacking the LCAA/YCF54 subunit of the enzyme MgProto monomethylester (MgProtoME) cyclase causes accumulation of MgProtoME and destabilization of the entire cyclase enzyme. This disrupts chlorophyll synthesis and negatively effects photosynthetic activity.

Daniel Pass talks to GARNet

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Published on: October 16, 2017

Daniel Pass (Cardiff University) discusses his recent paper published in PLoS Genetics entitled ‘Genome-wide chromatin mapping with size resolution reveals a dynamic sub- nucleosomal landscape in Arabidopsis’. Dan highlights his Github page where the code for the novel graphics in this paper are held.

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006988

https://github.com/ChromatinCardiff/DanielPassProcessingPipelines

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.

Arabdopsis Research Roundup: May 11th

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Published on: May 11, 2017

This weeks Arabidopsis Research Roundup is lead by two papers that characterise the relationship between cell size and growth in different Arabidopsis tissues. Firstly the lab of GARNet PI Jim Murray look at how the cell cycle influences cell size progression in the SAM whilst George Bassel’s group from Birmingham investigate cell growth within a developing embryo. Thirdly is a paper from the University of Essex that further defines the role of the CP12 protein in control of photosynthesis. Next is a paper from researchers from the University of Warwick who lead a fascinating piece of rocket science that identifies differences in the vernalisation requirement across Brassica species whilst in the fifth paper, researchers from Lancaster identify environmentally defined QTLs that determine the plant response to glutamate. Finally is a paper that highlights a new software tool that has the self-explanatory title of the ‘UEA small RNA Workbench’ and is applicable for use with plant-derived datasets.

R Jones A, Forero-Vargas M, Withers SP, Smith RS, Traas J, Dewitte W, Murray JAH (2017) Cell-size dependent progression of the cell cycle creates homeostasis and flexibility of plant cell size. Nat Commun http:/​/​dx.​doi.​org/10.1038/ncomms15060

Open Access

This study comes from the lab of current GARNet PI Jim Murray at the Cardiff University. Lead author Angharad Jones kindly provides an audio description of the paper for the GARNet YouTube channel. This  investigation looks at the factors that control the interaction between cell size and cell growth in a developing shoot meristem. They show that the dynamic regulation of this relationship is linked to the activity of two cyclin dependent kinases (CDKs) and that cell size is key in controlling the transition from G1>S and from G2>M phases of the cell cycle. Importantly this work uses precise imaging to track the progression of individual cell lineages and is therefore able to suggest that cell size is an emergent and not a directly determined property.


Souza NM, Topham AT, Bassel GW (2017) Quantitative analysis of the 3D cell shape changes driving soybean germination. J Exp Bot. http:/​/​dx.​doi.​org/10.1093/jxb/erx048

Open Access

George Bassel (University of Birmingham) leads this paper that uses information gained from the study of patterns of cell expansion in Arabidopsis embryos to investigate a similar process in soybean. Indeed as in Arabidopsis they show that there is preferential early cell expansion closest to the soybean radicle and that starting cell size corresponds to different growth rates. In addition they show that the growing hypocotyl has complex regulation and that differential ansiotrophy growth drives forward the process of germination. Ultimately they show that this occurs equivalently in both model and crop species.


Elena López-Calcagno P, Omar Abuzaid A, Lawson T, Anne Raines C (2017) Arabidopsis CP12 mutants have reduced levels of phosphoribulokinase and impaired function of the Calvin-Benson cycle. J Exp Bot http:/​/​dx.​doi.​org/10.1093/jxb/erx084 Open Access
This study from the photosynthesis group at the University of Essex is led by Tracey Lawson and GARNet committee member Christine Raines. They investigate the role of the CP12 multigene family that has three members in Arabidopsis. These are redox-sensitive proteins that facilitate the formation of a complex between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) during the Calvin-Benson cycle. They show that plants with reduced levels of CP12-1 or CP12-2 have lower photosynthetic capacity and subsequently exhibit slower growth. The cell biological explanation for this alteration appears to focus on the PRK protein, which is present at lower levels in plants with reduced CP12-1 or CP12-2. Therefore the authors find that CP12-1 and CP12-2 are the key members of this gene family and they likely show functional redundancy in the tight control of photosynthesis.


Taylor JL, Massiah A, Kennedy S, Hong Y, Jackson SD (2017) FLC expression is down-regulated by cold treatment in Diplotaxis tenuifolia (wild rocket), but flowering time is unaffected. J Plant Physiol.

http:/​/​dx.​doi.​org/10.1016/j.jplph.2017.03.015 Open Access
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Steve Jackson (University of Warwick) leads this work that also features Chinese collaborators and investigates the role of FLOWERING LOCUS C (FLC) in the popular peppery salad plant Rocket (Diplotaxis tenuifolia) that, as a Brassica, is a somewhat closely related to Arabdopsis. The authors studied the vernalisation requirement in this plant so isolated its version of FLC, which was shown to functional compliment an Arabidopsis flc null mutant. However they showed that even though cold treatment reduced levels of DtFLC this did not alter the bolting time of the plant. This somewhat surprising result demonstrates that the link between FLC and flowering time is uncoupled in this species and that other mechanisms may take precedence, a situation different to that observed in Arabidopsis and other Brassicas.


Walch-Liu P, Meyer RC, Altmann T, Forde BG (2017) QTL analysis of the developmental response to L-glutamate in Arabidopsis roots and its genotype-by-environment interactions. J Exp Bot.

http:/​/​dx.​doi.​org/10.1093/jxb/erx132 Open Access Researchers from the groups of Brian Forde (Lancaster University) and Thomas Altmann (Leibniz Institute) collaborate in this research that identifies three novel QTLs (GluS1-3) that are involved in the response of Arabdopsis roots to external L-glutamate. When this experiment was extended they discovered that different environmental factors play a significant role in the control of this trait. The GluS1 locus is located on Chr3 yet is epistatically controlled by loci on Chr1 and Chr5 in response to temperatures. Overall this study demonstrates that the response to glutamate is controlled by multiple environmentally sensitive loci that vary between Arabidopsis ecotypes


Mohorianu I, Stocks MB, Applegate CS, Folkes L, Moulton V (2017) The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis. Methods Mol Biol.

http:/​/​dx.​doi.​org/10.1007/978-1-4939-6866-4_14

This manuscript from the University of East Anglia describes a set of software tools for the analysis of small RNAs. They used an Arabidopsis dataset to demonstrate the utility of the UEA small RNA Workbench, which can be found here: http://srna-workbench.cmp.uea.ac.uk/

Arabidopsis Research Roundup: July 19th

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

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

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

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

Andrew Fleming provides a brief audio description of this manuscript:

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

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

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

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

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

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

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

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

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

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

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

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

 

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

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

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

Arabidopsis Research Roundup: April 14th

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

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

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

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

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

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

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

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

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

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

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