Eirini Kaiserli talks GARNet

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Published on: May 8, 2018

Eirini Kaiserli talks to GARNet about a recent open access paper in PNAS entitled ‘ZINC-FINGER interactions mediate transcriptional regulation of hypocotyl growth in Arabidopsis‘.

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.

Ranjan Swarup talks to GARNet

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Published on: April 23, 2018

Ranjan Swarup (University of Nottingham) discusses a couple of recent papers published in Nature Communications that describe the relationship between phosphate and auxin signaling in the roots of Arabidopsis and rice plants.

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

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

GARNet Research Roundup: April 11th 2018

This weeks GARNet research roundup begins with a microscopy-based study led by Lorenzo Frigerio from the University of Warwick that investigates the origin of Protein Storage Vacuoles. The second paper from John Doonan at Aberystwyth University looks at how differential splicing of cyclin-dependent Kinase G1 effects the thermosensory response. Reiner van de Hoorn from Oxford leads the next paper that characterises the use of activity-based protein profiling (ABPP) to identify novel α-glycosidases in model and non-model plants. Simon McQueen-Mason from York is corresponding author of the next paper that identified a new QTL from Brachypodium that is involved in cell wall formation. The fifth paper is led by Anthony Dodd from Bristol and characterises the role of the SnRK1 complex in hypocotyl elongation whilst the penultimate manuscript from Julia Davies’s lab in Cambridge performs patch clamp analysis of dorn1 mutant plants. The final paper from Brendan Davies at the University of Leeds characterises the SMG kinase, a gene that is lacking from the Arabidopsis genome, in Physcomitrella patens.


http://www.plantphysiol.org/content/early/2018/03/19/pp.18.00010.long

Feeney M, Kittelmann M, Menassa R, Hawes C, Frigerio L. Protein storage vacuoles originate from remodelled pre-existing vacuoles in Arabidopsis thaliana (2018) Plant Physiol. 2018 Mar 19. pii: pp.00010.2018. doi: 10.1104/pp.18.00010 Open Access

This collaboration between the Universities of Warwick and Oxford Brookes is led by Lorenzo Frigerio and Chris Hawes. They have investigated the origin of seed Protein Storage Vacuoles (PSV) using a two-pronged approach using confocal and immunoelectron microscopy. They looked at embryo development as well as in leaf cells that have been reprogrammed for embryonic cell fate by overexpression of the LEAFY COTYLEDON2 TF. These studies indicate that PSVs are formed following the reprogramming of pre-existing embryonic vacuole (EV) rather than from de novo assembly.


https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.13914

Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan JH. The Cyclin Dependent Kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A (2018) Plant J. doi: 10.1111/tpj.13914 Open Access

John Doonan (Aberystwyth University) is the corresponding author on this UK-Austrian collaboration that presents the role of the cyclin-dependent Kinase G1 (CDKG1) in thermosensing in Arabidopsis. Ambient temperature change causes altered gene expression of the spliceosome component, ATU2AF65A. Interestingly the CDKG1 gene is differentially spliced and to produces two protein isoforms that are both needed to complement the expression of ATU2AF65A across a temperature range. This alternative splicing is dependent on CDKG2 and CYCLIN L1 and is a novel control mechanism in the temperature control response.


Husaini AM, Morimoto K, Chandrasekar B, Kelly S, Kaschani F, Palmero D, Jiang J, Kaiser M, Ahrazem O, Overkleeft HS, van der Hoorn RAL (2018) Multiplex fluorescent, activity-based protein profiling identifies active α-glycosidases and other hydrolases in plants. Plant Physiol. pii: pp.00250.2018. doi: 10.1104/pp.18.00250 Open Access

Renier Van de Hoorn (University of Oxford) leads this pan-european study that uses novel cyclophellitol aziridine probes that label α-glycosidase enzymes. They identified two novel α-glycosidases in Arabidopsis as well as using the technique in non-model saffron crocus. Finally they showed that this multiplex fluorescent labelling in combination with probes for serine hydrolases and cysteine proteases can be used to identify changes in hydrolase activity in response to pathogen infection.


Whitehead C, Ostos Garrido FJ, Reymond M, Simister R, Distelfeld A, Atienza SG, Piston F, Gomez LD, McQueen-Mason SJ (2018) A glycosyl transferase family 43 protein involved in xylan biosynthesis is associated with straw digestibility in Brachypodium distachyon. New Phytol. doi: 10.1111/nph.15089 Open Access

Simon McQueen-Mason (University of York) leads this study that use QTL mapping to identify a gene in Bracypodium that is involved in cell wall architecture, which might then be a target to develop plants with improved cellulose digestibility. This glycosyl transferase family (GT) 43 protein is an orthologue of Arabidopsis IRX14, which is involved in xylan biosynthesis. When RNAi was used to reduce expression of this gene the resulting plants showed increased digestibility, indicating that this BdGT43A will be a good target for future breeding plans.


Wang L, Wilkins KA, Davies JM (2018) Arabidopsis DORN1 extracellular ATP receptor; activation of plasma membrane K(+) -and Ca(2+) -permeable conductances New Phytol. 2018 Mar 25. doi: 10.1111/nph.15111. Open Access

This letter to New Phytologist from the lab of Julia Davis (University of Cambridge) outlines some experiments to determine whether the DORN1 plasma membrane receptor is responsible for transmitting a signal from extracellular ATP (eATP). They performed patch clamp analysis on isolated protoplasts and showed that DORN1 is involved in the activation of Ca+ and K+ pumps by eATP as, in contrast to wildtype, dorn1 mutant protoplast showed no voltage changes after incubation with eATP.


Simon NML, Sawkins E, Dodd AN. Involvement of the SnRK1 subunit KIN10 in sucrose-induced hypocotyl elongation (2018) Plant Signal Behav. 27:1-9. doi: 10.1080/15592324.2018.1457913.

Anthony Dodd (University of Bristol) is the corresponding author of this follow-on study from one that previously featured on the GARNet YouTube channel. This study measures sucrose-induced hypocotyl elongation in two T-DNA mutants of the SnRK1 subunit KIN10 gene. These mutants had altered responses to sucrose leading to the hypothesis that the SnRK1 complex suppresses hypocotyl elongation in the presence of external sugar.


Lloyd JPB, Lang D, Zimmer AD, Causier B, Reski R, Davies B (2018) The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens. Nucleic Acids Res. doi: 10.1093/nar/gky225 Open Access

Brendan Davis (University of Leeds) is the corresponding author on research that investigates the role of the SMG1 kinase during nonsense-mediated mRNA decay (NMD) in the moss Physcomitrella patens. This kinase plays a critical role in animals but as it is not present in Arabidopsis, its function is not well studied in plants. However moss smg mutants show expression changes in genes involved in a variety of processes indicating that NMD is a common control mechanism in moss. In addition these plants have increased susceptibility to DNA damage, which suggests that the SMG1 kinase is a key player in quality control mechanisms in plants.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky225/4955258

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: March 9th

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Published on: March 9, 2018

This Arabidopsis Research Roundup has five papers that includes two from the John Innes Centre and two from the University of Edinburgh. Firstly Kristen Bomblies’s group at the JIC have investigated the relationship between temperature and meiotic recombination rates. Secondly Veronica Grieneisen and Stan Maree have developed a mathematical model to characterise cell morphologies taken from a 2D image. Andrew Miller from Edinburgh is a co-corresponding author on a study that shows how the Arabidopsis proteome changes in different photoperiods. In the fourth paper Peter Doerner is a co-author on work that looks at the phosphate starvation response. Finally researchers from Bristol and Nottingham contribute to an investigation into a novel genetic component that controls auxin-induced root hair development.


Lloyd A, Morgan C, Franklin C, Bomblies K (2018) Plasticity of Meiotic Recombination Rates in Response to Temperature in Arabidopsis. Genetics. doi: 10.1534/genetics.117.300588

Open Access

Kristen Bomblies (John Innes Centre) leads this study that investigates the influence of temperature on meiotic recombination rate. They show that in Arabidopsis the number of crossovers positively correlates with increasing temperature. However the mechanistic explanation for the increase at higher temperatures remains opaque as, in contrast to findings from other plants, synaptonemal complex length negatively correlates with temperature.


Sánchez-Corrales YE, Hartley M, van Rooij J, Marée AFM, Grieneisen VA (2018) Morphometrics of complex cell shapes: Lobe Contribution Elliptic Fourier Analysis (LOCO-EFA). Development. doi: 10.1242/dev.15677

http://dev.biologists.org/content/early/2018/02/08/dev.156778.long

Open Access

Veronica Grieneisen and Stan Maree (John Innes Centre) lead this study that has developed the Lobe Contribution Elliptical Fourier Analysis (LOCO-EFA) method. This generates meaningful descriptors from a 2D image of cells that can then be linked to morphological features. This tool allows for the efficient phenotyping of cell morphologies that they demonstrate by analysing images of Arabidopsis leaf pavement cells. They extend this analysis to larger populations where they used LOCO-EFA to predict how cell shapes change when they move into a more crowded space.


Seaton DD, Graf A, Baerenfaller K, Stitt M, Millar AJ, Gruissem W (2018) Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism. Mol Syst Biol. doi: 10.15252/msb.20177962 Open Access

http://onlinelibrary.wiley.com/doi/10.15252/msb.20177962/abstract

Andrew Miller (University of Edinburgh) is the corresponding author on this collaboration with German and Swiss colleagues that compares the Arabidopsis proteome across four photoperiods. They shows coordinated changes across the proteome, most notably at longer photoperiods in the abundance of proteins involved in photosynthesis and metabolism. They show higher translation rates during the day that correspond with the increased RNA abundance that is a characteristic of circadian rhythms. This ‘translational coincidence’ describes the alignment of higher translation rates with high transcript levels and they assigned a mathematical model in an attempt to explain this phenomenon.


Hanchi M, Thibaud MC, Légeret B, Kuwata K, Pochon N, Beisson F, Cao A, Cuyas L, David P, Doerner P, Ferjani A, Lai F, Li-Beisson Y, Mutterer J, Philibert M, Raghothama KG, Rivasseau C, Secco D, Whelan J, Nussaume L, Javot H (2018) The phosphate fast-responsive genes PECP1 and PPsPase1 affect phosphocholine and phosphoethanolamine content. Plant Physiol. doi: 10.1104/pp.17.01246 Open Access

Peter Doerner (University of Edinburgh) is a co-author on this global study that characterises the phosphate starvation-mediated induction of the HAD-type phosphatases PPsPase1 (AT1G73010) and PECP1 (AT1G17710). They show that expression of these genes closely follows phosphate status but that their activity does not alter phospate content. The role of these proteins is to control phosphocholine and phosphoethanolamine content, which is a output of changing phosphate conditions. The authors conclude that expression of these genes can be an excellent molecular marker for the phosphate starvation response.


www.cell.com/current-biology/fulltext/S0960-9822(18)30083-6

Schoenaers S, Balcerowicz D, Breen G, Hill K, Zdanio M, Mouille G, Holman TJ, Oh J, Wilson MH, Nikonorova N, Vu LD, De Smet I, Swarup R, De Vos WH, Pintelon I, Adriaensen D, Grierson C, Bennett MJ, Vissenberg K (2018) The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth. Current Biology doi: 10.1016/j.cub.2018.01.050

This Belgian-led study includes contributions from Claire Greirson’s and Malcolm Bennett’s labs in Bristol and Nottingham respectively. They investigate the role of the ERULUS (ERU) protein, an auxin-induced receptor-like kinase, during the development of root hairs. ERU localises to the apical root hair plasma membrane and regulates cell wall composition by altering pectin dynamic. The authors conclude that ERU is a key regulator of auxin-mediated control of root hair development.

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.

Charles Melynk talks to GARNet

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Published on: March 1, 2018

Charles Melnyk discusses a new paper published in PNAS that describes the molecular events that occur during grafting. The paper is entitled ‘Transcriptome dynamics at Arabidopsis graft junctions reveal an intertissue recognition mechanism that activates vascular regeneration

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