GARNet Research Roundup: March 13th 2020

This edition of the GARNet Research Roundup begins with research from Durham University that links environmental sensing, SUMOylation and BR signaling. The second paper is from the Baulcombe lab in Cambridge and investigates the epigenetic control of transposons. The third paper is from Aberystwyth University and introduces the DeepPod learning framework for the automated counting of Arabidopsis siliques.

The fourth paper includes co-authors from the University of Nottingham in research that conducts a comprehensive analysis of the Arabidopsis auxin receptor gene family. The next paper from the University of Bristol looks at different statistical methods to measure segregation distortion.

The sixth paper is a structural-biology study of an Arabidopsis histone methyltransferase and includes co-authors from King’s College London and the Crick Institute. The penultimate paper includes Brian Forde from Lancaster University as a co-author and analyses the ZmTMM1 transcription factor from maize. The final paper investigates the role of the WRKY6 transcription factor during seed development and includes Ian Bancroft as a co-author.


Srivastava M, Srivastava AK, Orosa-Puente B, Campanaro A, Zhang C, Sadanandom A (2020) SUMO Conjugation to BZR1 Enables Brassinosteroid Signaling to Integrate Environmental Cues to Shape Plant Growth. Curr Biol. doi: 10.1016/j.cub.2020.01.089 Open Access

Moumita Srivastava is first author on this study from Durham University that introduces SUMO regulation of brassinosteroid (BR) signalling through the BZR1 transcription factor. During salt stress Arabidopsis plants arrest growth by upregulating the SUMO protease ULP1a that in turn deSUMOylates BZR1 allowing for its destabilizing interaction with the BIN2 kinase. This study environmental sensing, SUMOylation and the BR response.


Wang Z, Baulcombe DC (2020) Transposon age and non-CG methylation. Nat Commun. doi: 10.1038/s41467-020-14995-6 Open Access

Zhengming Wang and David Baulcombe from the University of Cambridge are authors on this research that assesses the ordering of the mechanisms through which transposon-containing chromatin is silenced. They demonstrate that both RNA-directed DNA methylation (RdDM) and RNA-independent silencing through chromodomain DNA methyltransferases (CMTs) occurs to provide long-term control of transposons and concomitant alterations to the transcriptome.

https://www.nature.com/articles/s41467-020-14995-6

Hamidinekoo A, Garzón-Martínez GA, Ghahremani M, Corke FMK, Zwiggelaar R, Doonan JH, Lu C (2020) DeepPod: a convolutional neural network based quantification of fruit number in Arabidopsis. Gigascience doi: 10.1093/gigascience/giaa012 Open Access

This research from Aberystwyth University includes Azam Hamidinekoo as first author in which they have developed the DeepPod deep learning framework for the automated identification of Arabidopsis siliques from complex images. They used a training set of over 2400 images to develop prediction software that had comparable success with manual expert human counting. The project code is available on GitHub.

https://academic.oup.com/gigascience/article/9/3/giaa012/5780255

Prigge MJ, Platre M, Kadakia N, Zhang Y, Greenham K, Szutu W, Pandey BK, Bhosale RA, Bennett MJ, Busch W, Estelle M (2020) Genetic analysis of the Arabidopsis TIR1/AFB auxin receptors reveals both overlapping and specialized functions. Elife doi: 10.7554/eLife.54740 Open Access

Mike Prigge from UCSD in California leads this research that includes co-authors from the University of Nottingham. They analyse the phenotypes of all mutant combinations of the six-member TIR1/AFB family of auxin receptors, demonstrating significant functional overlap but that the presence of a functional TIR1 or AFB2 is needed to maintain growth throughout the life cycle. Interestingly they find that the mysterious AFB1 receptor appears to play a specalised role in processes dependent on more rapid auxin-mediated effects.


Coulton A, Przewieslik-Allen AM, Burridge AJ, Shaw DS, Edwards KJ, Barker GLA (2020) Segregation distortion: Utilizing simulated genotyping data to evaluate statistical methods. PLoS One. doi: 10.1371/journal.pone.0228951 Open Access

Alexander Coulton is the first author on this study from the University of Bristol that looks at different statistical tests that are used to confirm segregation distortion in high-density SNP data. In this data they find that the false discovery rate correction best fits the traditional p-value threshold of 0.05 and they perform empirical tests using mapping populations generated between different wheat varieties.


Dobrovolska O, Brilkov M, Madeleine N, Ødegård-Fougner Ø, Strømland Ø, Martin SR, De Marco V, Christodoulou E, Teigen K, Isaksson J, Underhaug J, Reuter N, Aalen RB, Aasland R, Halskau Ø (2020) The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection. FEBS J doi: 10.1111/febs.15256

This Norwegian-led study has Olena Dobrovolska as first author and co-authors from King’s College London and the Crick Institute. They have performed a structural analysis using NMR and molecular dynamics of the Arabidopsis Histone lysine methyltransferase ASHH2.


Liu Y, Jia Z, Li X, Wang Z, Chen F, Mi G, Forde B, Takahashi H, Yuan L (2020) Involvement of a truncated MADS-box transcription factor ZmTMM1 in root nitrate foraging. J Exp Bot. doi: 10.1093/jxb/eraa116

Ying Liu leads this Chinese study that includes Brian Forde from Lancaster as a co-author. They show that the maize ZmTMM1 transcription factor is able to rescue the nitrate foraging defect in Arabidopsis anr1agl21 double mutants, demonstrating a link between nitrate-induced transcriptional regulation in grasses and dicots.


Song G, Li X, Munir R, Khan AR, Azhar W, Yasin MU, Jiang Q, Bancroft I, Gan Y (2020) The WRKY6 transcription factor affects seed oil accumulation and alters fatty acid compositions in Arabidopsis thaliana. Physiol Plant. doi: 10.1111/ppl.13082

Ian Bancroft from the University of York is a co-author on this Chinese-led study in which Ge Song is first author. They discovered a high expression level of the WRKY6 transcription factor in developing seeds of Arabidopsis and that wrky6 mutants have larger seeds with altered fatty acid (FA) content and composition. The authors suggest that WRKY6 could be a target for the genetic improvement of FA content in the oil-seed crop of Brassica napus.

GARNet Research Roundup: February 18th 2020

This weeks GARNet Research Roundup begins with two studies that characterize the role of proteins that are involved in the control of meiotic recombination. The first study is from the Henderson lab at the University of Cambridge and investigates the role of the REC8 protein whilst the second is from John Doonan’s group at Aberystwyth University and investigates the role of the cyclin-dependent kinase CDKG.

The third paper is from the same research group in Aberystwyth and investigates how alternative splicing can impact the function of the FLOWERING LOCUS M gene.

The next papers is a cross-UK collaboration led from Rothamsted Research and the John Innes Centre that identifies an important QTL associated with the generation of high-fibre wheat. The fifth paper is from the JIC and reveals how the immune resistance gene MLO plays a role in a plants association with beneficial microbial symbiotes.

The sixth paper is from the Gibbs lab at the University of Birmingham and further characterizes the function of the VRN2 component of the polycomb repressive complex 2.

Nick Harberd from Oxford is a corresponding author of the next paper, which identifies a new gene that could be used to improve nitrogen-use efficiency in rice.

The eighth paper is a proteomic-based study from the University of Cambridge that identifies novel stress-induced components of the Arabidopsis spliceosome.

The penultimate paper is from Jonathan Jones’ lab at the Sainsbury lab, Norwich in which they characterize a new transgenic line useful for studying the plant immune response.

The final paper includes Liam Dolan from Oxford as a co-author in a study that characterizes a novel ATPase from the algae Chara australis.


Lambing C, Tock AJ, Topp SD, Choi K, Kuo PC, Zhao X, Osman K, Higgins J, Franklin FCH, Henderson IR (2020) Interacting genomic landscapes of REC8-cohesin, chromatin and meiotic recombination in Arabidopsis thaliana. Plant Cell. doi: 10.1105/tpc.19.00866
Open Access

This study is led by Chris Lambing from Ian Henderson’s group at the University of Cambridge and includes collaborators from Leicester and Birmingham. They use ChIP-seq to identify the genomic regions associated with the REC8 protein, showing that it interacts with regions with multiple distinct chromatin states. This interaction plays a key role in controlling the formation of double strands breaks and is required to organize meiotic chromosome architecture and interhomolog recombination.


Nibau C, Lloyd AH, Dadarou D, Betekhtin A, Tsilimigka F, Phillips DW, Doonan JH (2020) CDKG1 Is Required for Meiotic and Somatic Recombination Intermediate Processing in Arabidopsis. Plant Cell. doi: 10.1105/tpc.19.00942 Open Access

Candida Nibau from Aberystwyth University leads this research that reveals a critical role for the cyclin-dependent kinase G1 (CDKG) in the control of recombination, both during meiosis and within somatic cells. The authors discover that this role occurs early in the process through the stabilization of recombination intermediates.


Nibau C, Gallemí M, Dadarou D, Doonan JH, Cavallari N (2020) Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2. Front Plant Sci. doi: 10.3389/fpls.2019.01680 Open Access

Candida Nibau is first author on this collaboration between researchers in the UK (Aberystwyth University) and Vienna, Austria. They assess the factors that control the contribution of two splicing variants of the FLOWERING LOCUS M gene on flowering time across a temperature range. They find that this process is controlled by the activity of the cyclin-dependent kinase G2 (CDKG2) and its cognate cyclin, CYCLIN L1 (CYCL1).

https://www.frontiersin.org/articles/10.3389/fpls.2019.01680/full

Lovegrove A, Wingen LU, Plummer A, Wood A, Passmore D, Kosik O, Freeman J, Mitchell RAC, Hassall K, Ulker M, Tremmel-Bede K, Rakszegi M, Bedő Z, Perretant MR, Charmet G, Pont C, Salse J, Waite ML, Orford S, Burridge A, Pellny TK, Shewry PR, Griffiths S (2020) Identification of a major QTL and associated molecular marker for high arabinoxylan fibre in white wheat flour. PLoS One. doi: 10.1371/journal.pone.0227826
Open Access

Alison Lovegrove at Rothamsted Research is the first author on this cross-UK research that has gained significant interest from the main–stream media. Through analysis of a Chinese wheat variety with high dietary fibre due to the high amounts of cell wall polysaccharide arabinoxylan the authors identified a QTL that is responsible for this phenotype. Understanding this QTL will allow use of both marker-assisted breeding and new breeding technologies to aid in the generation of high yield, high fibre varieties.


Jacott CN, Charpentier M, Murray JD, Ridout CJ (2020) Mildew Locus O facilitates colonization by arbuscular mycorrhizal fungi in angiosperms. New Phytol. doi: 10.1111/nph.16465

Catherine Jacott is first author on this study from the JIC that investigates the role of the known barley resistance gene Mildew Resistance Locus O (MLO) during arbuscular mycorrhizal interactions in wheat, barley and Medicago. They show that MLO is important for this beneficial symbiotic association and that the role of MLO has been appropriated during infection with pathogenic powdery mildew.


Labandera AM, Tedds HM, Bailey M, Sprigg C, Etherington RD, Akintewe O, Kalleechurn G, Holdsworth MJ, Gibbs DJ (2020) The PRT6 N-degron pathway restricts VERNALIZATION 2 to endogenous hypoxic niches to modulate plant development. New Phytol. doi: 10.1111/nph.16477

Anne-Marie Labandera is first author on this work from Dan Gibbs’ lab in Birmingham. They show that ubiquitin-mediated proteolysis of the VERNALIZATION2 (VRN2) protein via the oxygen-dependent PRT6 N-degron pathway is important for many areas of plant development. This regulation of VRN2 has different developmental outcomes depending on whether it occurs in or out of meristematic tissues.


Wu K, Wang S, Song W, Zhang J, Wang Y, Liu Q, Yu J, Ye Y, Li S, Chen J, Zhao Y, Wang J, Wu X, Wang M, Zhang Y, Liu B, Wu Y, Harberd NP, Fu X (2020) Enhanced sustainable green revolution yield via nitrogen-responsive chromatin modulation in rice. Science. doi: 10.1126/science.aaz2046

Kun Wu is first author on this Chinese-led investigation that also includes Nick Harberd from Oxford University as a corresponding author. Working in rice they link genomic-wide chromatin changes with expression of the NGR5 (NITROGEN-MEDIATED TILLER GROWTH RESPONSE 5) transcription factor during nitrogen-induced growth. Overexpression of NGR5 can uncouple nitrogen-sensing from tiller production and therefore provide a novel tool to possibly enhance agricultural production in low nitrogen conditions.

https://science.sciencemag.org/content/367/6478/eaaz2046.long

Marondedze C, Thomas L, Lilley KS, Gehring C (2020) Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components. Front Mol Biosci. doi: 10.3389/fmolb.2019.00163 Open Access

Claudius Marondedze is the first author on this collaboration between the University of Cambridge and KAUST in Saudi Arabia. They perform label-free mRNA interactome-capture to identify RNA interacting proteins that are induced after drought stress. This reveals over 40 novel spliceosome-interacting proteins but also 32 proteins that associate with stress granules, which are indicative of transcriptional arrest. This provides new insights into how plant stress responses might be altered by the activity of spliceosome components.


Ngou BPM, Ahn HK, Ding P, Redkar A, Brown H, Ma Y, Youles M, Tomlinson L, Jones JDG (2020) Estradiol-inducible AvrRps4 expression reveals distinct properties of TIR-NLR-mediated effector-triggered immunity. J Exp Bot. doi: 10.1093/jxb/erz571

This research from Jonathan Jones’ group at the Sainsbury Lab, Norwich is led by Bruno Pok Man Ngou. They have developed a transgenic line that enables the transient in planta expression of AvrRps4, which is a potent bacterial immune effector. This stimulates the RRS1/RPS4-dependent immune response and provides insights into certain mechanisms of this pathway without exposing the plants to pathogens.


Zhang S, Habets M, Breuninger H, Dolan L, Offringa R, van Duijn B (2020) Evolutionary and Functional Analysis of a Chara Plasma Membrane H(+)-ATPase. Front Plant Sci. doi: 10.3389/fpls.2019.01707 Open Access

Liam Dolan from the University of Oxford is a co-author on this Dutch-led research that includes Sutun Zhang as first author. They characterize a plasma membrane localised ATPase from the algae Chara australis and perform complementation studies in both yeast and Arabidopsis. These studies allow the authors to propose that the mode of regulation of this algal ATPase is likely different from that of known yeast and land plant PM H+-ATPases.

GARNet Research Roundup: February 7th 2020

This latest edition of the GARNet Research Roundup begins with two studies that look at different aspects of lateral root formation and include members of Malcolm Bennett’s lab in Nottingham. The first investigates a critical role for hydropatterning in the control of lateral root initiation whilst the second looks at how cell death in overlying tissue layers plays an active role in the control of lateral root emergence.

The third paper is from the John Innes Centre and investigates the mechanism through which a small number of noncoding SNPs can alter chromatin dynamics at the FLC locus. The fourth paper is from Glasgow and assesses a link between auxin signaling and proteins involved in membrane trafficking.

The next paper is from Rothamsted Research and looks at how aerial differences in wheat cultivars can affect the root-associated microbiome. The sixth paper is from the James Hutton Institute and investigates the relationship between phosphate and zinc signaling during the growth of Brassica oleracea.

The final three papers focus on some aspect of plant mechanical strength. The first paper is from Aberystwyth and looks at the how mechanical stress impacts growth of Brachypodium. The next two papers are led from the US and Sweden respectively and include UK co-authors from Leeds, the JIC and York. The first looks at how lignin modifications illicits defence responses whilst the second begins to demonstrate how xyloglucan modifications alter secondary cell wall growth.


von Wangenheim D, Banda J, Schmitz A, Boland J, Bishopp A, Maizel A, Stelzer EHK, Bennett M (2020) Early developmental plasticity of lateral roots in response to asymmetric water availability. Nat Plants. doi: 10.1038/s41477-019-0580-z Open Access with link.

This brief communication is led by Daniel von Wangenheim, who worked with Malcolm Bennett and colleagues at the University of Nottingham. They use light sheet fluorescence microscopy to investigate how the local water environment controls the initiation of lateral root primordia. They show that this response is extremely plastic and that the initiation of pericycle cell files is linked to the external hydrological landscape. This study reveals a potential adaptive advantage when roots forage under heterogeneous soil conditions, which of course exists in all ‘real-world’ situations.

BotanyOne has written a nice blog about this paper and Daniel von Wangenheim has produced a superb explanatory video.


Escamez S, André D, Sztojka B, Bollhöner B, Hall H, Berthet B, Voß U, Lers A, Maizel A, Andersson M, Bennett M, Tuominen H (2020) Cell Death in Cells Overlying Lateral Root Primordia Facilitates Organ Growth in Arabidopsis. Curr Biol. doi: 10.1016/j.cub.2019.11.078 Open Access

Ute Voss and Malcolm Bennett from Nottingham are co-authors on this Finnish-led study in which Sacha Escamez is first author. They show that cell death occuring in advance of emerging lateral roots is an active developmental process rather than a passive effect of lateral root initiation. Plants with a cell-death-deficiency show delayed lateral root development, which is rescued through physical or genetic removal of outer cell files.


Qüesta JI, Antoniou-Kourounioti RL, Rosa S, Li P, Duncan S, Whittaker C, Howard M, Dean C (2020) Noncoding SNPs influence a distinct phase of Polycomb silencing to destabilize long-term epigenetic memory at Arabidopsis FLC. Genes Dev. doi: 10.1101/gad.333245.119 Open Access

This research from the John Innes Centre is led by Julia Qüesta and Rea Antoniou-Kourounioti. They show that four noncoding SNPs in the Lov-1 Arabidopsis accession are responsible for the reactivation of FLC after only a short cold treatment. They combine experimentation and modelling to also propose that the control of FLC reactivation is linked to the extent of DNA replication during the cold period.

Rea discusses this paper on the GARNet Community podcast. Look out for it on February 19th.


Xia L, Marquès-Bueno MM, Karnik RA (2020) Trafficking SNARE SYP132 Partakes in Auxin-associated Root Growth. Plant Physiol. doi: 10.1104/pp.19.01301 Open Access

This short communication is led by Lingfeng Xia in the Karnik lab at the University of Glasgow and looks at the role of auxin in the control of expression of the SNARE protein SYP132 during root growth and the gravitropic response. This linkage is indicative of an important role for membrane trafficking during the auxin response.


Kavamura VN, Robinson RJ, Hughes D, Clark I, Rossmann M, Melo IS, Hirsch PR, Mendes R, Mauchline TH (2020) Wheat dwarfing influences selection of the rhizosphere microbiome. Sci Rep. doi: 10.1038/s41598-020-58402-y
Open Access

Vanessa Kavamura is first author on this study led from Rothamsted Research that looks at how the aerial phenotypes of different wheat cultivars impacts root traits and the soil microbiome. Interestingly they show that taller wheat varieties are predicted to have a more connected bacterial network, which might lead to a more favourably rhizosphere for plant growth.


Pongrac P, Fischer S, Thompson JA, Wright G, White PJ (2020) Early Responses of Brassica oleracea Roots to Zinc Supply Under Sufficient and Sub-Optimal Phosphorus Supply. Front Plant Sci. doi: 10.3389/fpls.2019.01645 Open Access

Paula Pongrac is the first author on this study led from the James Hutton Institute in which they investigate how plants respond to their access to environmental phosphate and zinc. They assess gene expression of Brassica oleracea plants grown under different mineral conditions and reveal important relationships between the response to phosphorous and zinc that will inform future nutrient supply strategies and identification of novel germplasm.


Gladala-Kostarz A, Doonan JH, Bosch M (2020) Mechanical stimulation in Brachypodium distachyon: implications for fitness, productivity and cell wall properties. Plant Cell Environ. doi: 10.1111/pce.13724.

Agnieszka Gladala‐Kostarz who works with Maurice Bosch at Aberystwyth University is the first author on this research that looked at the effect of both wind- and mechanical- treatments on growth of two accessions of Brachypodium distachyon. They catalogue the physical changes that occur in this important base-line study that tracks the relevance of these environmental factors on the multiple growth traits.


Gallego-Giraldo L, Liu C, Pose-Albacete S, Pattathil S, Peralta AG, Young J, Westpheling J, Hahn MG, Rao X, Knox JP, De Meester B, Boerjan W, Dixon RA (2020) ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1) releases latent defense signals in stems with reduced lignin content. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1914422117 Open Access

Lina Gallego-Giraldo is the first author on the US-led paper that includes Paul Knox and Sara Pose-Albacete from the University of Leeds. In this work they look at the link between lignin modifications and the inappropriate initiation of plant defence responses. They show that cell wall pectin remodeling mediated by the ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1) protein releases defence elicitors and as such provides important information on the link between these processes.


Kushwah S, Banasiak A, Nishikubo N, Derba-Maceluch M, Majda M, Endo S, Kumar V, Gomez L, Gorzsás A, McQueen-Mason S, Braam J, Sundberg B, Mellerowicz EJ (2020) Arabidopsis XTH4 and XTH9 contribute to wood cell expansion and secondary wall formation. Plant Physiol. doi: 10.1104/pp.19.01529 Open Access

Sunita Kushwah leads this Swedish-study that has co-authors from the JIC and York. They investigate a novel role for the XTH4 and XTH9 xyloglucan endo-transglycosylase/ hydrolases during secondary growth in Arabidopsis. The activity of these enzymes has a significant effect on cell wall composition and in the control of wood formation

https://www.nottingham.ac.uk/biosciences/people/ute.voss

GARNet Research Roundup: Jan 24th 2020

The first GARNet Research Roundup of 2020 begins with a study from the University of Dundee at the James Hutton Institute in which they have adapted nanopore direct sequencing to analyse the Arabidopsis mRNA methylome. The second study is also from Dundee and is an analysis of alternative splicing in C4 sugarcane.

The next two papers look at the control of stomatal development. In the first, researchers from Bristol investigate the integration of temperature and light-induced signals whilst the second paper is from Sheffield and looks at the role, or lack thereof, of the HY5 protein. The fifth paper is also from Sheffield and looks at the role of the MALECTIN DOMAIN KINESIN 2 protein in dividing tissues.

The next two papers investigate the control of lateral root formation. Firstly researchers from Glasgow look at how potassium signaling integrates with both the mechanisms of RNA-directed DNA-methylation and the auxin response. The other paper looks at how auxin signaling integrates with the plasmodesmata development and includes co-authors from the University of Nottingham.

The eighth paper is led from Nottingham and looks at the role of the PROTEOLYSIS (PRT)1 during the plant immune response whilst the next paper, which is from the University of Cambridge, also looks at plant immunity, specifically at how the biosynthesis of phytic acid impacts this response.

The remaining four papers include UK-based co-authors from University of South Wales, Rothamsted and Cardiff, Durham, Oxford and Aberystwyth in international research teams led from Malaysian (the expression of Acyl-CoA-binding proteins in oil palm), China (the effect of silver nanoparticles on plant growth), Japan (convergent evolution of lateral organ formation) and Chile (the factors that influence grain filling in wheat) respectively.


Parker MT, Knop K, Sherwood AV, Schurch NJ, Mackinnon K, Gould PD, Hall AJ, Barton GJ, Simpson GG (2020) Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m(6)A modification. Elife. doi: 10.7554/eLife.49658 Open Access

Matt Parker, Kasia Knop, Anya Sherwood and Nicholas Schurch are co-first authors on this study from the University of Dundee at the James Hutton Institute in which they perform direct RNA sequencing using a nanopore sequencer. They used this technical advance to analyse the mRNA (m6A) methylome and reveal a contribution to the control of the circadian clock. Future use of this technique will undoubtedly allow for an improved annotation of the Arabidopsis genome (and others).

https://elifesciences.org/articles/49658

Dantas LLB, Calixto CPG, Dourado MM, Carneiro MS, Brown JWS, Hotta CT (2019) Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane. Front Plant Sci. doi: 10.3389/fpls.2019.01614 Open Access

This study is led from Brazil with Luiza Dantas as first author and includes co-authors from the University of Dundee at the James Hutton Institute. They investigate the level of alternative splicing (AS) in commercial sugarcane, which is an important C4 crop. Tissue samples were collected in winter and summer and this analysis reveals temperature- and organ-dependent differences in the levels of AS across a set of genes under circadian control.


Kostaki KI, Coupel-Ledru A, Bonnell VC, Gustavsson M, Sun P, Mclaughlin FJ, Fraser DP, McLachlan DH, Hetherington AM, Dodd AN, Franklin KA (2020). Guard cells integrate light and temperature signals to control stomatal aperture. Plant Physiol. doi: 10.1104/pp.19.01528 Open Access

Kalliopi-Ioanna Kostaki is first author on this study from the University of Bristol that begins to unpick the mechanisms that integrate light and temperature signals in the control of stomatal development. These signals converge on phototropin photoreceptors and multiple members of the 14-3-3 protein family. This work also reveals a currently uncharacterised pathway that controls temperature regulation of guard cell movement.


Zoulias N, Brown J, Rowe J, Casson SA (2020) HY5 is not integral to light mediated stomatal development in Arabidopsis. PLoS One. doi: 10.1371/journal.pone.0222480 Open Access

Nick Zoulias is first author on this study from the Casson lab at University of Sheffield. ELONGATED HYPOCOTYL 5 (HY5) is a key regulator of light-mediated development yet in this study the authors show that the HY5-signaling cascade does not play a role in stomatal development. This key finding shows that phytochrome and cryptochrome signaling in guard cells is transmitted via non-HY5 signaling components.


Galindo-Trigo S, Grand TM, Voigt CA, Smith LM (2020) A malectin domain kinesin functions in pollen and seed development in Arabidopsis. J Exp Bot doi: 10.1093/jxb/eraa023
This research from the Smith lab at the University of Sheffield is led by Sergio Galindo-Trigo. They show that MALECTIN DOMAIN KINESIN 2 (MDKIN2) is involved in pollen, embryo and endosperm development. Malectin domains bind polysaccharides and peptides when found extracellularly in receptor-like kinases so this might suggest that in dividing tissues MDKIN2 plays a role during the physical division of cells.


Shahzad Z, Eaglesfield R, Carr C, Amtmann A (2020) Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed. Nat Commun. doi: 10.1038/s41467-019-13927-3 Open Access

Zaigham Shahzad at the University of Glasgow is the first author in this study that looks at the relationship between potassium deficiency and lateral root formation. This effect is mediated via the impact of CLSY1, a key component of the RNA-directed DNA-methylation machinery, on the transcriptional repression of the AuxIAA protein IAA27. Interestingly this system appears to act as a backup to the auxin-dependent proteolysis pathway that is primarily responsible for the control of IAA27 activity.


Sager R, Wang X, Hill K, Yoo BC, Caplan J, Nedo A, Tran T, Bennett MJ, Lee JY (2020) Auxin-dependent control of a plasmodesmal regulator creates a negative feedback loop modulating lateral root emergence. Nat Commun. doi: 10.1038/s41467-019-14226-7.

This US study is led by Ross Sager and includes co-authors from the University of Nottingham. This research links the role of auxin in lateral root formation with plasmodesmata development through control of the plasmodesmal regulator PDLP5. They present a model wherein molecules required for lateral root emergence transit through plasmodesmata following an inductive auxin signal.


Till CJ, Vicente J, Zhang H, Oszvald M, Deery MJ, Pastor V, Lilley KS, Ray RV, Theodoulou FL, Holdsworth MJ (2019) The Arabidopsis thaliana N-recognin E3 ligase PROTEOLYSIS1 influences the immune response. Plant Direct. doi: 10.1002/pld3.194 Open Access

Christopher Till, Jorge Vicente and Hongtao Zhangis are co-first authors on this research led from the University of Nottingham and Rothamsted Research that involves use of quantitative proteomics to define the role of the N-recognin E3 ligase PROTEOLYSIS (PRT)1 during the plant immune response.


Poon JSY, Le Fevre RE, Carr JP, Hanke DE, Murphy AM (2019) Inositol hexakisphosphate biosynthesis underpins PAMP-triggered immunity to Pseudomonas syringae pv. tomato in Arabidopsis thaliana but is dispensable for establishment of systemic acquired resistance. Mol Plant Pathol. doi: 10.1111/mpp.12902
This research from the University of Cambridge is led by Jacquelyne Poon and Alex Murphy and looks at the role of the phytic acid (inositol hexakisphosphate, InsP6) biosynthesis in dividing tissues during the plant immune response. They characterize Arabidopsis plants with mutations in biosynthetic enzymes to show that there are multiple mechanisms of basal resistance that are dependent upon InsP6.


Amiruddin N, Chan PL, Azizi N, Morris PE, Chan KL, Ong PW, Rosli R, Masura SS, Murphy DJ, Sambanthamurthi R, Haslam RP, Chye ML, Harwood JL, Low EL (2019) Characterisation of Oil Palm Acyl-CoA-Binding Proteins and Correlation of their Gene Expression with Oil Synthesis. Plant Cell Physiol. doi: 10.1093/pcp/pcz237.
Nadzirah Amiruddin is lead author on this Malaysian-led research that includes collaborators from the University of South Wales, Rothamsted Research and Cardiff University. This paper looks at the expression of Acyl-CoA-binding proteins (ACBPs) in oil palm; providing important information about the role of this protein family during oil synthesis in the world’s most important oil crop.


Wang L, Sun J, Lin L, Fu Y, Alenius H, Lindsey K, Chen C (2019) Silver nanoparticles regulate Arabidopsis root growth by concentration-dependent modification of reactive oxygen species accumulation and cell division. Ecotoxicol Environ Saf. doi: 10.1016/j.ecoenv.2019.110072.

This Chinese-study is led by Likai Wang and includes Keith Lindsey from Durham University as a co-author. They look at the effect of silver nanoparticles (AgNPs) on growth of Arabidopsis. AgNPs are taken up by roots and have opposing effects at either 50 mg L-1 or 100mg mg L-1. This is an important preliminary study to understand how plant growth might be altered if AgNP’s are used as a delivery mechanism.


Naramoto S, Jones VAS, Trozzi N, Sato M, Toyooka K, Shimamura M, Ishida S, Nishitani K, Ishizaki K, Nishihama R, Kohchi T, Dolan L, Kyozuka J (2019) A conserved regulatory mechanism mediates the convergent evolution of plant shoot lateral organs. PLoS Biol. 2019 doi: 10.1371/journal.pbio.3000560 Open Access

This Japanese study is led by Satoshi Naramoto and Junko Kyozuka and includes co-authors from the University of Oxford. They performed a mutant screen in the liverwort Marchantia polymorpha to identify the LATERAL ORGAN SUPRESSOR 1 (MpLOS1) gene, which regulates meristem maintenance and lateral organ development. Remarkably they showed this gene is also functions in the control of lateral organ development in rice, therefore demonstrating convergent evolution across plant lineages in the control of lateral organs.


Del Pozo A, Méndez-Espinoza AM, Romero-Bravo S, Garriga M, Estrada F, Alcaíno M, Camargo-Rodriguez AV, Corke FMK, Doonan JH, Lobos GA (2020) Genotypic variations in leaf and whole-plant water use efficiencies are closely related in bread wheat genotypes under well-watered and water-limited conditions during grain filling. Sci Rep. doi: 10.1038/s41598-019-57116-0 Open Access

Alejandro del Pozo leads this Chilean study that includes co-authors from Aberystwyth and NIAB. This large-scale glasshouse experiment looked at the effect of water deficit on the growth of 14 bread wheat genotypes. Measurement of multiple parameters revealed that plants face limitations to the assimilation process during grain filling due to natural senesce and water stress.

GARNet Research Roundup: July 26th 2019

This summer-time-reading bumper edition of the GARNet Research Roundup begins with two papers from the University of Sheffield that each use advanced imaging techniques. Firstly Andrew Fleming’s group leads a study on the link between stomatal function and mesophyll space morphology. Second is a study from Matthew Johnson’s group that looks at the dynamic arrangement of thylakoid stacks.

Next are two papers that include Alison Smith from the JIC as a corresponding author. The first also includes Vasilios Andriotis from the University of Newcastle and looks at the role of the plastidial pentose phosphate pathway during post-germination growth. Second uses a gene-editing strategy to generate potatoes with altered starch morphologies.

The fifth paper also looks at starch; researchers from Cambridge and Norwich are involved in a study that characterises the role of the LIKE SEX4 1 protein in starch degradation.

The sixth paper is from Aberystwyth University and identifies a transcription factor that alters secondary cell wall composition in Brachypodium and maize. Next is research from the University of Bath that looks at the role of a protein S-acyl transferase during seed germination.

The eighth and ninth papers are led by Spanish research groups and include contributions from UK-based co-authors in Cambridge and Nottingham, working on photoperiod perception or phosphate signaling respectively.

The tenth paper features work from Cardiff University and looks at the role of heterologous expression of the Arabidopsis WEE1 protein. The Bancroft lab from the University of York leads the next paper that investigates glucosinolate signaling in Brassica napus.

The final three manuscripts are methods papers. The first from Edinburgh introduces a new NanoLUC reporter whilst the other two include techniques involved in the investigation of light-regulated growth processes.


Lundgren MR, Mathers A, Baillie AL, Dunn J, Wilson MJ, Hunt L, Pajor R, Fradera-Soler M, Rolfe S, Osborne CP, Sturrock CJ, Gray JE, Mooney SJ, Fleming AJ (2019) Mesophyll porosity is modulated by the presence of functional stomata. Nat Commun. doi: 10.1038/s41467-019-10826-5

Open Access

This UK-wide study is led from Andrew Fleming’s lab in Sheffield and includes Marjorie Lundgren as first author (now working in Lancaster). They use microCT imaging alongside more traditional measurements linked to analysis of gas exchange to show that mesophyll airspace formation is linked to stomatal function in both Arabidopsis and wheat. This allows the authors to propose that coordination of stomata and mesophyll airspace pattern underpins water use efficiency in crops.

https://www.nature.com/articles/s41467-019-10826-5

Wood WH, Barnett SFH, Flannery S, Hunter CN, Johnson MP (2019) Dynamic thylakoid stacking is regulated by LHCII phosphorylation but not its interaction with photosystem I. Plant Physiol. doi: 10.1104/pp.19.00503

Open Access

William Wood is the first author on this study from the University of Sheffield that uses 3D structured illumination microscopy (3D-SIM) to look at the dynamics of thylakoid stacking in both Arabidopsis and spinach. They show that the processes they observe are dependent on light harvesting complex II phosphorylation.

http://www.plantphysiol.org/content/early/2019/06/11/pp.19.00503.long

Andriotis VME, Smith AM (2019) The plastidial pentose phosphate pathway is essential for postglobular embryo development in Arabidopsis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1908556116

Open Access

Vasilios Andriotis (now at the University of Newcastle) is the lead author of this work performed in Alison Smith’s lab at the JIC. They look at the role of the plastidial oxidative pentose phosphate pathway (OPPP) during embryo development. This involved demonstrating that production of ribose-5-phosphate (R5P), which in turn leads to synthesis of purine nucleotides, is a critical function of the OPPP.


Tuncel A, Corbin KR, Ahn-Jarvis J, Harris S, Hawkins E, Smedley MA, Harwood W, Warren FJ, Patron NJ, Smith AM (2019) Cas9-mediated mutagenesis of potato starch-branching enzymes generates a range of tuber starch phenotypes. Plant Biotechnol J. doi: 10.1111/pbi.13137

Open Access

Alison Smith and Nicola Patron who work in Norwich Research Park are corresponding authors of this study that includes Aytug Tuncel as first author. They have used Cas9-mediated gene editing to generate potato plants that have a range of different tuber starch structures. This shows that gene-editing techniques allows the transgene-free alteration to generate potentially healthier crops.


Schreier TB, Umhang M, Lee SK, Lue WL, Shen Z, Silver D, Graf A, Müller A, Eicke S, Stadler M, Seung D, Bischof S, Briggs SP, Kötting O, Moorhead GB, Chen J, Zeeman SC (2019) LIKE SEX4 1 acts as a β-amylase-binding scaffold on starch granules during starch degradation. Plant Cell. doi: 10.1105/tpc.19.00089

Open Access

Tina Schreier from the University of Cambridge is the first author on this international study led from Switzerland that also includes Alexander Graf and David Seung from the JIC as co-authors. This study defines a precise role for the LIKE SEX FOUR 1 (LSF1) protein that binds starch and is required for normal starch degradation. Through a variety of experiments they show that the glucan binding, rather than phosphatase activity, is required for LSF1 function during starch degradation.


Bhatia R, Dalton S, Roberts LA, Moron-Garcia OM, Iacono R, Kosik O, Gallagher JA, Bosch M (2019) Modified expression of ZmMYB167 in Brachypodium distachyon and Zea mays leads to increased cell wall lignin and phenolic content. Sci Rep. doi: 10.1038/s41598-019-45225-9

Open Access

Rakesh Bhatia is the first author on this work from the lab of Maurice Bosch at Aberystwyth University. They overexpress the maize MYB transcription factor ZmMYB167 in both Brachypodium and maize. Both species show increased lignin content with Brachypodium but not maize showing a biomass deficit. This indicates that ZmMYB167 could be a useful molecular tool for the alteration of secondary cell wall biosynthesis.

https://www.nature.com/articles/s41598-019-45225-9

Li Y, Xu J, Li G, Wan S, Batistic O, Sun M, Zhang Y, Scott R, Qi B (2019) Protein S-acyl Transferase 15 is Involved in Seed Triacylglycerol Catabolism during Early Seedling Growth in Arabidopsis (2019) J Exp Bot. doi: 10.1093/jxb/erz282

First author on this UK-Chinese collaboration is Yaxiao Li who works with Baoxiu Qi at the University of Bath. The authors characterise the function of Arabidopsis Protein Acyl Transferase 15, AtPAT15. This protein is involved in essential β-oxidation of triacylglycerols during post-germination growth.


Ramos-Sánchez JM, Triozzi PM, Alique D, Geng F, Gao M, Jaeger KE, Wigge PA, Allona I, Perales M (2019) LHY2 Integrates Night-Length Information to Determine Timing of Poplar Photoperiodic Growth. Curr Biol. doi: 10.1016/j.cub.2019.06.003

Open Access

This Spanish-led study includes co-authors from the Sainsbury Laboratory in Cambridge and attempts to define the factors that control photoperiod perception in trees, using poplar as a model system. FLOWERING LOCUS T2 (FT2) has been previously shown to be involved in this process and this study builds on that work to show that night-length information is transmitted by the clock gene LATE ELONGATED HYPOCOTYL 2 (LHY2) and is able to control FT2 expression.

https://www.cell.com/current-biology/fulltext/S0960-9822(19)30696-7?

Silva-Navas J, Conesa CM, Saez A, Navarro-Neila S, Garcia-Mina JM, Zamarreño AM, Baigorri R, Swarup R, Del Pozo JC (2019) Role of cis-zeatin in root responses to phosphate starvation. New Phytol. doi: 10.1111/nph.16020

Ranjan Swarup from the University of Nottingham is a co-author on this Spanish-led study that has Javier Silva-Navas as first author. Through analysis of dark-grown seedlings they have identified a set of new genes involved in root phosphate signaling. In addition they provide evidence of a links between cytokinin and phosphate signaling through modulation of the cell cycle.


Siciliano I, Lentz Grønlund A, Ševčíková H, Spadafora ND, Rafiei G, Francis D, Herbert RJ, Bitonti MB, Rogers HJ, Lipavská H (2019) Expression of Arabidopsis WEE1 in tobacco induces unexpected morphological and developmental changes. Sci Rep. 2019 Jun 18;9(1):8695. doi: 10.1038/s41598-019-45015-3

Open Access

Ilario Siciliano leads this work that includes colleagues from Hilary Rogers’ lab at Cardiff University. The WEE1 protein regulates the cell cycle across eukaryote lineages. In this work they show that overexpression of AtWEE1 in tobacco causes precocious flowering and increased shoot morphogenesis of stem explants whilst in cell culture this WEE1 OX causes smaller cell sizes.


Kittipol V, He Z, Wang L, Doheny-Adams T, Langer S, Bancroft I (2019) Genetic architecture of glucosinolate variation in Brassica napus. J Plant Physiol. doi: 10.1016/j.jplph.2019.06.001

Open Access

This study from the Bancroft lab at the University of York is led by Varanya Kittipol. Through use of Associative Transcriptomics (AT) across a diversity panel of 288 Brassica napus genotypes they are able to identify a set of genes involved in synthesis of glucosinate hydrolysis products.


Urquiza-García U, Millar AJ (2019). Expanding the bioluminescent reporter toolkit for plant science with NanoLUC. Plant Methods. doi: 10.1186/s13007-019-0454-4

Open Access

This study from the University of Edinburgh introduces NanoLUC, a new more stable luciferase-based reporter for use by the plant community.

The final two papers are methods papers that focus on different aspects of light-regulated growth. These are from the University of Southampton and University of York.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0454-4

Terry MJ, Kacprzak SM (2019) A Simple Method for Quantification of Protochlorophyllide in Etiolated Arabidopsis Seedlings. Methods Mol Biol. doi: 10.1007/978-1-4939-9612-4_14

Oakenfull RJ, Ronald J, Davis SJ (2019) Measuring Phytochrome-Dependent Light Input to the Plant Circadian Clock. Methods Mol Biol. doi: 10.1007/978-1-4939-9612-4_15

GARNet Research Roundup: April 11th 2019

This edition of the GARNet Research Roundup is led by two papers from John Christie’s lab at the University of Glasgow. First is a study that looks at the function of the NPH3 protein during phototropism whilst the second paper is a collaboration with Mike Blatt’s group and has used an synthetic biology approach to increase plant biomass by altering stomatal conductance.

Third is a paper from the University Dundee and James Hutton Institute that looks at the extent of alternative splicing of long non-coding RNAs in response to cold stress.

The fourth paper is from Royal Holloway and defines the role of a MAP kinase module during meristem development. The fifth paper is led by Charles Spillane in Galway and includes Mary O’Connell at the University of Nottingham as a co-author and investigates the selective pressures that are applied to parentally imprinted genes.

The penultimate paper is from Aberystwyth and uses microCT imaging to determine grain parameters in wheat and barley whilst the final paper is from Queens Mary University of London looks at nonphotochemical quenching in Berteroa incana.


Sullivan S, Kharshiing E, Laird J, Sakai T, Christie J (2019) De-etiolation Enhances Phototropism by Modulating NON-PHOTOTROPIC HYPOCOTYL 3 Phosphorylation Status. Plant Physiol. doi: 10.1104/pp.19.00206

Open Access

Stuart Sullivan is first author on this work from John Christie’s lab at the University of Glasgow in which they investigate the functional significance of dephosphorylation of the NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3) protein that occurs following activation of Phototropin receptor kinases. They show that plant greening (de-etiolation) enhances phototropic responses that are coincident with reduced NPH3 dephosphorylation and increased plasma membrane retention of the protein. They further investigate other genetic and environmental factors that impact NPH3 dephosphorylation, which allows young seedlings to maximise their establishment under changing light conditions.


Papanatsiou M, Petersen J, Henderson L, Wang Y, Christie JM, Blatt MR (2019) Optogenetic manipulation of stomatal kinetics improves carbon assimilation, water use, and growth. Science. doi: 10.1126/science.aaw0046

Maria Papanatsiou is lead author on this work from the University of Glasgow that occured in the labs of Mike Blatt and John Christie. They aimed to address a phenomonen that occurs during changing environmental conditions in which stomatal dynamics lag behind biochemical photosynthetic changes. This prevents plants from maximising their outputs due to inefficiencies in gas and water exchange. In this work they express a synthetic blue light-gated K+ channel BLINK1 in guard cells. This introduced a K+ conductance to these cells resulting in accelerated stomatal opening under light exposure and closing after irradiation. Ultimately they show that this significantly increases biomass without incurring a water use cost. This approach has clear potential for improving plant productivity under changing environmental conditions.

https://science.sciencemag.org/content/363/6434/1456.long

Calixto CPG, Tzioutziou NA, James AB, Hornyik C, Guo W, Zhang R, Nimmo HG, Brown JWS (2019) Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs. Front Plant Sci. doi: 10.3389/fpls.2019.00235

Open Access

Cristiane Calixto and John Brown from the University of Dundee and the James Hutton Institute lead this study into alternative splicing of lncRNAs in response to cold. This is a follow-up to their large scale scale study on the extent of alternative splicing in Arabidopsis.  The authors identified 135 lncRNA genes with cold-dependent differential expression (DE) and/or differential alternative splicing (DAS), some of which were highly sensitive to small temperature changes. This system identified a set of lncRNAs that could be targets for future research aimed at understanding how plants respond to cold and freezing stresses.


Dóczi R, Hatzimasoura E, Farahi Bilooei S, Ahmad Z, Ditengou FA, López-Juez E, Palme K, Bögre L (2019) The MKK7-MPK6 MAP Kinase Module Is a Regulator of Meristem Quiescence or Active Growth in Arabidopsis. Front Plant Sci. doi: 10.3389/fpls.2019.00202

Open Access

Robert Doczi is the first author on this UK, Hungarian and German collaboration that is led from Royal Holloway University of London. They use genetic approaches to show that the MKK7-MPK6 MAP kinase module is a suppressor of meristem activity. They use mkk7 and mpk6 mutants as well as overexpression lines to demonstrate that perturbation of the MAPK signaling pathway alters both shoot and root meristem development and plays important roles in the control of plant developmental plasticity.


Tuteja R, McKeown PC, Ryan P, Morgan CC, Donoghue MTA, Downing T, O’Connell MJ, Spillane C (2019) Paternally expressed imprinted genes under positive Darwinian selection in Arabidopsis thaliana. Mol Biol Evol. doi: 10.1093/molbev/msz063

Open Access

Reetu Tuteja from the National University of Ireland at Galway is first author on this paper that includes Mary O’Connell from the University of Nottingham. The authors used Arabidopsis to look at 140 endosperm-expressed genes that are regulated by genomic imprinting and found that they were evolving more rapidly than expected. This investigation was extended across 34 other plant species and they found that paternally, but not maternally imprinted genes were under positive selection, indicating that imprinted genes of different parental origin were subject to different selective pressures. This data supports a model wherein positive selection effects paternally-expressed genes that are under continued conflict with maternal sporophyte tissues.


Hughes N, Oliveira HR, Fradgley N, Corke FMK, Cockram J, Doonan JH, Nibau C (2019) μCT trait analysis reveals morphometric differences between domesticated temperate small grain cereals and their wild relatives. Plant J doi: 10.1111/tpj.14312

Open Access

Nathan Hughes and Candida Nibau at the Aberystwyth University lead this work that uses microCT imaging alongside novel image analysis techniques and mathematical modeling to assess grain size and shape across accessions of wheat and barley. They find that grain depth is a major driver of shape change and that it is also an excellent predictor of ploidy levels. In addition they have developed a model that enables the prediction of the origin of a grain sample from measurements of its length, width and depth.


Wilson S, Ruban AV (2019) Enhanced NPQ affects long-term acclimation in the spring ephemeral Berteroa incana. Biochim Biophys Acta Bioenerg. doi: 10.1016/j.bbabio.2019.03.005

This study is led by Sam Wilson and Alexander Ruban at QMUL and investigates nonphotochemical quenching in the Arabidopsis-relative Berteroa incana. They show that light tolerance and ability to recover from light stress is greatly enhanced in Berteroa compared to Arabidopsis. This is due to faster synthesis of zeaxanthin and a larger xanthophyll cycle (XC) pool available for deepoxidation. This result gives B.incana a greater capacity for protective NPQ allowing enhanced light-harvesting capability when acclimated to a range of light conditions. The authors suggest this short-term protection prevents the need for the metabolic toll of making long-term acclimations.

GARNet Research Roundup: December 7th 2018

The first four papers in this GARNet Research Roundup includes research from Norwich Research Park. Firstly members of Jonathan Jones’ lab have identified a new Avr gene from Hyaloperonospora arabidopsidis. Secondly Anne Osbourn’s lab characterises two novel arabinosyltransferases that are involved in the plant defence response. Thirdly Cathie Martin’s group is involved in a study that investigates the biosynthesis of the metabolite ubiquinone. Finally in research from NRP is from Silke Robatzek’s lab, where they use a novel quantitative imaging system to characterise stomatal mutants.

The next two papers arise from work at SLCU, firstly looking at the possible role of a novel transposon family during gene-shuffling and secondly a paper that investigates the structure of an important component of the strigolactone signaling pathway.

The seventh paper from Peter Eastmond’s lab at Rothamsted Research identifies a novel gene involved in seed oil composition. The penultimate paper is from Peter Unwin at the University of Leeds and assesses the cell wall composition of ‘giant’ root cells induced by nematode Meloidogyne spp. Finally is a methods paper that describes how microCT imaging can be used to measure different leaf parameters.


Asai S, Furzer O, Cavik V, Kim DS, Ishaque N, Goritschnig S, Staskawicz B, Shirasu K, Jones JDG (2018) A downy mildew effector evades recognition by polymorphism of expression and subcellular localization. Nature Communications doi: 10.1038/s41467-018-07469-3

https://www.nature.com/articles/s41467-018-07469-3

Open Access

Shuta Asai from Jonathan Jones’ lab at The Sainsbury Lab, Norwich is the lead-author on this study that looks at co-evolution of host and pathogen resistance genes. The relationship between Hyaloperonospora arabidopsidis (Hpa) and Arabidopsis is defined by the gene-for-gene model of host Resistance (R) genes and pathogen Avirulence (AVR) genes. In this study the authors identify the HaRxL103Emoy2 AVR gene that is recognised by the R gene RPP4 and how this resistance is broken by altered expression or cellular localization.


Louveau T, Orme A, Pfalzgraf H, Stephenson M, Melton RE, Saalbach G, Hemmings  AM, Leveau A, Rejzek M, Vickerstaff RJ, Langdon T, Field R, Osbourn AE (2018) Analysis of two new arabinosyltransferases belonging to the carbohydrate-active enzyme (CAZY) glycosyl transferase family 1 provides insights into disease resistance and sugar donor specificity. Plant Cell. doi: 10.1105/tpc.18.00641

Open Access

This research from the John Innes Centre, East Maling and Aberystwyth University is led by Thomas Louveau and Anne Osbourn and characterises two new arabinosyltransferases from oat and soybean. These enzymes are involved in the production of saponins that are involved in defence responses. These enzymes normally transfer arabinose to their substrates but through targeted mutations the authors modified one of them to instead transfer glucose. This study provides insights into the specifics of ‘sugar-donation’ and has identified potential novel targets for manipulating defence responses in two crop species.


Soubeyrand E, Johnson TS, Latimer S, Block A, Kim J, Colquhoun TA, Butelli E,  Martin C, Wilson MA, Basset G (2018) The Peroxidative Cleavage of Kaempferol Contributes to the Biosynthesis of the Benzenoid Moiety of Ubiquinone in Plants. Plant Cell. 2018 Nov 14. pii: tpc.00688.2018. doi: 10.1105/tpc.18.00688

Open Access

This US-led study includes members of Cathie Martin’s lab at the John Innes Centre as co-authors in which they investigate the flavonoid-biosynthesis pathway, in particular the land-plant-specific synthesis of ubiquinone. They used Arabidopsis and tomato mutants to dissect the ubiquinone biosynthesis pathway, revealing that the B-ring of the specalised metabolite kaempferol is incorporated into the primary metabolite ubiquinone.


Bourdais G, McLachlan DH, Rickett LM, Zhou J, Siwoszek A, Häweker H, Hartley M, Kuhn H, Morris RJ, MacLean D, Robatzek S (2018) The use of quantitative imaging to investigate regulators of membrane trafficking in Arabidopsis stomatal closure. Traffic. doi: 10.1111/tra.12625

This work from both Norwich Research Park and the University of Bristol is led by Gildas Bourdais and describes a high-throughput quantitative imaging, reverse genetic screen to characterize known stomatal mutants on the basis of their effect on the endomembrane system. This screen allowed them to precisely define the point in the signaling pathway at which each mutant was affected, providing a genetic framework for the control of stomatal closure. This image-based tool should be a valuable addition to future studies that aim to use quantitative image analysis.


https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky1196/5198529

Catoni M, Jonesman T, Cerruti E, Paszkowski J (2018) Mobilization of Pack-CACTA transposons in Arabidopsis suggests the mechanism of gene shuffling (2018) Nucleic Acids Res. doi: 10.1093/nar/gky1196

Open Access

This work was performed at SLCU in Jerzy Paszkowski’s lab by current University of Birmingham lecturer Marco Catoni and analyses the genomic impact of the mobilisation of Pack-TYPE transposons. They track the movement of these transposons over multiple generations, showing that they can insert into genic regions and that their subsequent incomplete excisions can cause deleterious effect on gene function. Over evolutionary time the action of this type of mobile element might therefore importantly influence gene shuffling.


Shabek N, Ticchiarelli F, Mao H, Hinds TR, Leyser O, Zheng N (2018) Structural plasticity of D3-D14 ubiquitin ligase in strigolactone signalling. Nature. doi: 10.1038/s41586-018-0743-5

Nitzan Shabek is the lead author on his US-led paper that includes Fabrizio Ticchiarelli and Ottoline Leyser from SLCU as co-authors. This paper reveals the structure of the interaction between the Arabidopsis α/β hydrolase D14 and the D3 F-box protein, which is important for multiple aspects of strigolactone signaling. They show that structural plasticity of the D3 C-terminal α-helix, which can switch between two different forms, enables the interaction between D14 and the D53 repressor protein. Providing insight into these specific interactions is key to increasing understanding of how the D14-D3 complex influences strigolactone signaling.


Menard GN, Bryant FM, Kelly AA, Craddock CP, Lavagi I, Hassani-Pak K, Kurup S, Eastmond PJ (2018) Natural variation in acyl editing is a determinant of seed storage oil composition. Sci Rep. doi: 10.1038/s41598-018-35136-6

Open Access

This work is led from Rothamsted Research with Guillaume Menard as first author and uses the Arabidopsis MAGIC population to identify novel genetic loci involved in seed oil composition. They identified multiple QTLs associated with the quantity of the major very long chain fatty acid species 11-eicosenoic acid (20:1), showing that the enzyme LYSOPHOSPHATIDYLCHOLINE ACYLTRANSFERASE 2 (LPCAT2), which is involved in the acyl-editing pathway, was the primary QTL. Subsequently they show LPCAT2 expression was key for varying seed 20:1 content and that natural variation in the capacity for acyl editing is an important determinant of oil content.


Bozbuga R, Lilley CJ, Knox JP, Urwin PE (2018) Host-specific signatures of the cell  wall changes induced by the plant parasitic nematode, Meloidogyne incognita (2018). Sci  Rep. doi: 10.1038/s41598-018-35529-7

https://www.nature.com/articles/s41598-018-35529-7

Open Access

Refik Bozbuga at the University of Leeds is first author on this study that investigates the cell wall composition of nutrient-supplying ‘giant cells’ that are induced in roots following infection with Meloidogyne spp nematodes. They analysed the cell walls of giant cells from three species (Arabidopsis, maize and aduki bean) as well as using a set of Arabidopsis mutants to characterise the possible cell wall components that might influence infection rates.


Mathers AW, Hepworth C, Baillie AL, Sloan J, Jones H, Lundgren M, Fleming AJ,  Mooney SJ, Sturrock CJ (2018) Investigating the microstructure of plant leaves in 3D with lab-based X-ray computed tomography. Plant Methods. doi:  10.1186/s13007-018-0367-7

Open Access
This paper from the Universities of Nottingham, Sheffield and Lancaster provides a methodology that uses a microCT image pipeline to measure leaf intercellular airspace and to provide quantitative data on descriptors of leaf cellular architecture. They measured 6 different plant species, showing that this 3D method generates an improved dataset when compared to traditional 2D methods of measurement.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-018-0367-7

GARNet Research Roundup: July 16th

This week’s GARNet research roundup begins with a set of papers looking at aspects of the plant defence response with a focus on the cell wall. Firstly work from Mike Deeks’ lab in Exeter assesses the role of FORMIN4 during pre-invasion cell wall apposition. Secondly Sara Pose and Paul Knox (Leeds) are involved with a study looking at how altered cell wall lignin composition alters the defense response. Finally Joe McKenna and Cyril Zipfel are co-authors on a Norwegian-led study that looks at the influence of plant cell wall integrity maintenance in immune signalling.

Relatedly is a study from the Devoto lab at RHUL looks at the role of the defence hormone methyl jasmonate in Arabidopsis cell culture.

Next are two papers that research different aspects of the plant ER. Verena Kriechbaumer (Oxford Brookes) looks at plant ER-localised Lunapark proteins whilst a study from the University of Warwick provides a preliminary structural analysis of the RTNLB13 reticulon protein.

The seventh and eight papers are involved with the plant response to different growth conditions. Research from University of Nottingham looks at the response of the cortical cell layer of the root meristem to low phosphate conditions whilst work from University of Southampton investigates the relationship between nitrate and copper signaling.

The next paper is from Emily Flashman’s lab at the University of Oxford and looks at the role of plant cysteine oxidases as oxygen sensors whilst the tenth paper features John Doonan (Aberystwyth University) as a co-author and investigates how a histone acetyltransferase affects trichome development.

Finally is a paper from Pierre Baudal and Kirsten Bomblies (John Innes Centre) that uses Arabidopsis arenosa as a model to investigate the emergence of novel flowering time alleles in populations that have colonised along railway corridors.


Sassmann S, Rodrigues C, Milne SW, Nenninger A, Allwood E, Littlejohn GR, Talbot NJ, Soeller C, Davies B, Hussey PJ, Deeks MJ (2018) An Immune-Responsive Cytoskeletal-Plasma Membrane Feedback Loop in Plants. Curr Biol. doi: 10.1016/j.cub.2018.05.014

https://www.sciencedirect.com/science/article/pii/S096098221830616X?via%3Dihub

Open Access

Stefan Sassmann is the lead author of this paper from Mike Deeks’s lab in Exeter. They investigate the role of the membrane-integrated FORMIN4 protein in the process of cell wall apposition, which occurs as part of the plant immune response and is dependent on actin dynamics. FORMIN4 is stably localised apart from the active traffic of the endomembrane system and removing its function compromises the defense response, presumably by altering actin distribution at sites of cell wall apposition. This work demonstrates that FORMIN4 acts as a key component of the pre-invasion defense response.


Gallego-Giraldo L, Posé S, Pattathil S, Peralta AG, Hahn MG, Ayre BG, Sunuwar J, Hernandez J, Patel M, Shah J, Rao X, Knox JP, Dixon RA (2018) Elicitors and defense gene induction in plants with altered lignin compositions. New Phytol. doi: 10.1111/nph.15258

Open Access

Sara Pose and Paul Knox (University of Leeds) are co-authors on this US-led study that investigates how lignin composition can influence the defence response. Plants with the same lignin content but changed lignin compositions show altered expression in genes involved with different arms of the defense response. This indicates that cell wall lignin composition plays a significant role in the plants ability to response to different sources of pathogen attack.


Engelsdorf T, Gigli-Bisceglia N, Veerabagu M, McKenna JF, Vaahtera L, Augstein F, Van der Does D, Zipfel C, Hamann T (2018) The plant cell wall integrity maintenance and immune signaling systems cooperate to control stress responses in Arabidopsis thaliana. Sci Signal. doi: 10.1126/scisignal.aao3070

Joe McKenna (Imperial College, now Oxford Brookes University) and Cyril Zipfel (The Sainsbury Laboratory, Norwich) are co-authors on this Norwegian-led study that looks at the plant cell wall integrity maintenance mechanism and how it responses to the challenges of growth, development and environmental stresses. They identified a set of receptor-like kinases that are key for the responses elicted by cell wall damage (CWD). Conversely they showed that the components of the pattern-triggered immunity (PTI) signaling pathway repress responses to CWD. This study provides insights into how cell wall responses interact with downstream gene expression changes following pathogen challenge.


Bömer M, O’Brien JA, Pérez-Salamó I, Krasauskas J, Finch P, Briones A, Daudi A, Souda P, Tsui TL, Whitelegge JP, Paul Bolwell G, Devoto A (2018) COI1-dependent jasmonate signalling affects growth, metabolite production and cell wall protein composition in Arabidopsis. Ann Bot. doi: 10.1093/aob/mcy109

Open Access

Moritz Bömer works with Alessandra Devoto at Royal Holloway University of London and leads this research that looks at the effect of MeJA treatment on growth and gene expression in Arabidopsis cell culture. They demonstrate that both MeJA treatment or COI1 overexpression causes changes in the abundance of proteins involved in cell wall loosening as well as altered levels of primary metabolites alanine, serine and succinic acid. This work demonstrates a close link between hormone signaling, the defence response and the metabolic profile of Arabidopsis cells.

Dr Devoto and her academic colleagues at RHUL are profiled in the latest GARNish newsletter available for download from the GARNet website.


Kriechbaumer V, Breeze E, Pain C, Tolmie F, Frigerio L, Hawes C (2018) Arabidopsis Lunapark proteins are involved in ER cisternae formation. New Phytol. doi: 10.1111/nph.15228

https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15228

Open Access

Verena Kriechbaumer from Oxford Brookes University leads this research that investigates the in planta function of novel ER network-shaping proteins called Lunaparks (LNP). They show that these proteins localise to the entire ER network in Arabidopsis. They use confocal microscopy to show that altering the level of LNP gene expression changes ER morphology, possibly by regulating the formation of ER cisternae.


Chow M, Sklepari M, Frigerio L, Dixon AM (2018) Bacterial expression, purification and biophysical characterization of the smallest plant reticulon isoform, RTNLB13 Protein Expr Purif. doi: 10.1016/j.pep.2018.06.015

Open Access

Michael Chow worked with Lorenzo Frigerio and Ann Dixon at the University of Warwick to provide a preliminary structure and topology analysis of the plant RTNLB13 reticulon protein. This ER-associated integral membrane protein was expressed in bacteria and then a variety of analysis techniques were used to suggest that RTNLB13 has a high level of self-association and protein-membrane interactions.


Janes G, von Wangenheim D, Cowling S, Kerr I, Band L, French AP, Bishopp A (2018) Cellular Patterning of Arabidopsis Roots Under Low Phosphate Conditions Front Plant Sci. doi: 10.3389/fpls.2018.00735

https://www.frontiersin.org/articles/10.3389/fpls.2018.00735/full

Open Access

George Janes works with Anthony Bishopp at the University of Nottingham and leads this study that looks at root meristem development under low phosphate conditions. They show that in phosphate-limiting conditions the cortex layer of the root meristem contains almost double the number of cells, which results in a greater number of root hair-forming epidermal cells. As this change can occur within 24hrs the rapidity of the response represents a significant adaptation to a changing root environment.


Hippler FWR, Mattos-Jr D, Boaretto RM, Williams LE (2018) Copper excess reduces nitrate uptake by Arabidopsis roots with specific effects on gene expression J Plant Physiol. doi: 10.1016/j.jplph.2018.06.005

https://www.sciencedirect.com/science/article/pii/S0176161718302888

Open Access

Franz Hippler (University of Southampton) leads this UK-Brazil collaboration showing that growth of Arabidopsis plants in excess copper conditions causes a downregulation in nitrate uptake. This is due to both direct and indirect changes on the gene expression of nitrate transporters as well as a reduction in transcript level of the plasma membrane proton pump, AHA2. This effect was altered when copper levels were reduced demonstrating that copper toxicity acts at the level of nitrate transport and homeostasis.


White MD, Kamps JJAG, East S, Taylor Kearney LJ, Flashman E (2018) The Plant Cysteine Oxidases from Arabidopsis thaliana are kinetically tailored to act as oxygen sensors J Biol Chem.

doi: 10.1074/jbc.RA118.003496

Open Access

Mark White is the lead author on this work from the lab of Emily Flashman at the University of Oxford in which they look at the role of plant cysteine oxidases (PCOs) as oxygen sensors. They assessed the kinetics of each of AtPCO1 to AtPCO5 proteins and show that the most catalytically competent isoform is AtPCO4, in terms of both responding to O2, and oxidizing hypoxic responsive proteins. This work validates an O2-sensing role for the PCOs and provides evidence for functional differences between members of this enzyme family.


Kotak J, Saisana M, Gegas V, Pechlivani N, Kaldis A, Papoutsoglou P, Makris A, Burns J, Kendig AL, Sheikh M, Kuschner CE, Whitney G, Caiola H, Doonan JH, Vlachonasios KE, McCain ER, Hark AT (2018) The histone acetyltransferase GCN5 and the transcriptional coactivator ADA2b affect leaf development and trichome morphogenesis in Arabidopsis. Planta. doi: 10.1007/s00425-018-2923-9 Open Access

John Doonan (Aberystwyth University) is a co-author on this manuscript led by Jenna Kotak and Amy Herd in the USA. They investigate plants that have mutations in the histone acetyltransferase GCN5 and associated transcriptional coactivator ADA2b. These genes have been previously demonstrated as being involved in endoreduplication and trichome branching. They show that these mutants have alterations in the number and patterning of trichome-branches and that ADA2b and GCN5 are required to couple nuclear content with cell growth and morphogenesis.


Baduel P, Hunter B, Yeola S, Bomblies K. Genetic basis and evolution of rapid cycling in railway populations of tetraploid Arabidopsis arenosa (2018) PLoS Genet.

doi: 10.1371/journal.pgen.1007510 Open Access

Pierre Baduel and Kirsten Bomblies (John Innes Centre) lead this work that was conducted prior to Kirsten’s move to Norwich. In this study they follow the colonization of populations of Arabidopsis arenosa along mountain railway corridors. They demonstrate that selective pressure has occurred on novel alleles of flowering time genes and discuss the implications for ruderal communities linked to railways as allele conduits linked to local adaptations.

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