Matthew Parker, Kasia Knop and Anya Sherwood talk to the GARNet community podcast

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Published on: February 12, 2020

This research team from the Simpson lab at the James Hutton Institute, University of Dundee discuss a recent paper published in elife entitled ‘Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification.

Apologies for the poor sound quality of the transmission coming down the line from Dundee!

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: October 17th 2019

This edition of the GARNet Research Roundup includes a superb selection of papers by scientists from across the UK. First is work from the Spoel lab in Edinburgh that characterizes the fine-tuning of NPR1 activity during the plant immune response. Second is work from SLCU and the University of Helsinki that is an extensive investigation into the molecular basis of cambial development. Next is research from Nottingham that looks at the importance of soil macro-structures during the growth of wheat roots.

Fourth are three papers that highlight the breadth of research occurring at the John Innes Centre. The first paper is from Enrico Coen’s lab that applies their expertise in computational modeling to leaf development in the carnivorous plant Utricularia gibba. Second is work from Saskia Hogenhout’s lab that looks at immunity to infection by Phytoplasma pathogens. Last is work from Lars Ostergaard’s lab that characterises the role of Auxin Binding promoter elements in floral development.

The seventh paper from Bristol and Glasgow looks at shade avoidance signaling via PIF5, COP1 and UVR8 whilst the eighth paper, which is from Rothamsted, demonstrates how metabolic engineering in Arabidopsis seeds can result in a high proportion of human milk fat substitute. The next paper is from the University of Durham and investigates how the composition of the Arabidopsis cell wall impacts freezing tolerance. The first author of this paper, Dr Paige Panter discusses the paper on the GARNet community podcast.

The tenth paper is from Julia Davies’s lab at the University of Cambridge and introduces an uncharacterised response to extracellular ATP signals in Arabidopsis roots. The next paper is from Mike Blatt’s group at University of Glasgow and characterises a new interaction between vesicular transport and ion channels. The penultimate entry includes co-authors from the JIC on a Chinese-led study that demonstrates improved seed vigour in wheat through overexpression of a NAC transcription factor. Finally are two methods papers taken from a special journal issue on ‘Plant Meiosis’.


Skelly MJ, Furniss JJ, Grey HL, Wong KW, Spoel SH (2019) Dynamic ubiquitination determines transcriptional activity of the plant immune coactivator NPR1. Elife. doi: 10.7554/eLife.47005
Open Access

Michael Skelly is lead author on this paper from the lab of current GARNet chair Steven Spoel. In it they investigate the mechanisms that fine-tune the function of NPR1, a key player in the plant immune response. Progressive ubiquitination of NPR1 by an E3 ligase causes both its interaction with target genes and its subsequent degradation by an E4 ligase. This latter occurrence is opposed by the deubiquitinase activity of UBP6/7, setting up a complex regulatory environment that allows the plant to rapidly response to pathogen attack.


Zhang J, Eswaran G, Alonso-Serra J, Kucukoglu M, Xiang J, Yang W, Elo A, Nieminen K, Damén T, Joung JG, Yun JY, Lee JH, Ragni L, Barbier de Reuille P, Ahnert SE, Lee JY, Mähönen AP, Helariutta Y (2019) Transcriptional regulatory framework for vascular cambium development in Arabidopsis roots. Nat Plants. doi: 10.1038/s41477-019-0522-9

This pan-European-Korean collaboration has Jing Zhang from the University of Helsinki and the Sainsbury Laboratory, University of Cambridge as first author. They use cambium cell-specific transcript profiling and follow-on network analysis to discover 62 new transcription factors involved in cambial development in Arabidopsis. This information was used to engineer plants with increased radial growth through ectopic cambial activity as well as to generate plants with no cambial activity. This understanding provides a platform for possible future improvements in production of woody biomass.


Atkinson JA, Hawkesford MJ, Whalley WR, Zhou H, Mooney SJ (2019) Soil strength influences wheat root interactions with soil macropores. Plant Cell Environ. doi: 10.1111/pce.13659
This work is led from the University of Nottingham by John Atkinson and Sacha Mooney. They use X-ray Computed Tomography to investigate a trait called trematotropism, which applies to the ability of deep rooting plants to search out macropores and avoid densely packed soil. They show root colonisation of macropores is an important adaptive trait and that strategies should be put in place to increase these structures within the natural soil environment.


Lee KJI, Bushell C, Koide Y, Fozard JA, Piao C, Yu M, Newman J, Whitewoods C, Avondo J, Kennaway R, Marée AFM, Cui M, Coen E (2019) Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism. PLoS Biol. doi: 10.1371/journal.pbio.3000427
Open Access

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000427

Karen Lee, Claire Bushell and Yohei Koide are co-first authors on this work led by Enrico Coen at the John Innes Centre and Minlong Cui at the Zhejiang Agriculture and Forestry University in China. This study uses 3D imaging, cellular and clonal analysis, combined with computational modelling to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. They identify growth ansiotrophies that result in the final leave shape that develops from an initial near-spherical form. These processes have some similarities to the polar growth seen in Arabidopsis leaves. Overall they show that ‘simple modulations of a common growth framework underlie the shaping of a diverse range of morphologies’.


Pecher P, Moro G, Canale MC, Capdevielle S, Singh A, MacLean A, Sugio A, Kuo CH, Lopes JRS, Hogenhout SA (2019) Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize. PLoS Pathog. doi: 10.1371/journal.ppat.1008035
Open Access

This work from Saskia Hogenhout’s lab at the John Innes Centre is led by Pascal Pecher and Gabriele Moro. They look at the effect of SAP11 effectors from Phytoplasma species that infect either Arabidopsis or maize. They demonstrate that although both related versions of SAP11 destabilise plant TCP transcription factors, their modes of action have significant differences. Please look out for Saskia discussing this paper on the GARNet Community podcast next week.


Kuhn A, Runciman B, Tasker-Brown W, Østergaard L 92019) Two Auxin Response Elements Fine-Tune PINOID Expression During Gynoecium Development in Arabidopsis thaliana. Biomolecules. doi: 10.3390/biom9100526
Open Access

Andre Kuhn is first author of this research from Lars Østergaard’s lab at the John Innes Centre. They functional characterise two Auxin-responsive Elements (AuxRE) within the promotor of the PINOID gene, which are bound by the ETITIN/ARF3 Auxin Response Factor. Alteration of this AuxRE causes phenotypic changes during flower development demonstrating that even with a complex regulatory environment, small changes to cis-elements can have significant developmental consequences.


Sharma A, Sharma B, Hayes S, Kerner K, Hoecker U, Jenkins GI, Franklin KA (2019) UVR8 disrupts stabilisation of PIF5 by COP1 to inhibit plant stem elongation in sunlight. Nat Commun. doi: 10.1038/s41467-019-12369-1
Open Access

Ashutosh Sharma is first author of this UK-Spanish-Germany collaboration led by Keara Franklin at University of Bristol. They have characterised the interaction between three significant molecular players that function during the shade avoidance response in Arabidopsis; PIF5, UVR8 and COP1. In shaded conditions, UVR8 indirectly promotes rapid degradation of PIF5 through their interactions with the E3 ubiquitin ligase COP1.


van Erp H, Bryant FM, Martin-Moreno J, Michaelson LV, Bhutada G, Eastmond PJ (2019) Engineering the stereoisomeric structure of seed oil to mimic human milk fat. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1907915116

Open Access

Harrie Van Arp and Peter Eastmond at Rothamsted Research lead this extremely translational study in which they have modified the metabolic pathway for triacylglycerol (TAG) biosynthesis. By modifying the location of one biosynthesis enzyme and removing the activity of another, the fats produced in these Arabidopsis seeds are enriched to contain TAGs that are similar to those found in human milk. They propose that this technology could be used to develop a source of plant-derived human milk fat substitute.


Panter PE, Kent O, Dale M, Smith SJ, Skipsey M, Thorlby G, Cummins I, Ramsay N, Begum RA, Sanhueza D, Fry SC, Knight MR, Knight H (2019) MUR1-mediated cell-wall fucosylation is required for freezing tolerance in Arabidopsis thaliana. New Phytol. doi: 10.1111/nph.16209

Paige Panter led this work as part of her PhD at the University of Durham in the lab of Heather Knight. They characterise the role of the MUR1 protein in the control of cell wall fucosylation and how this contributes to plant freezing tolerance. Paige discusses this paper and the long history of MUR1 on the GARNet Community podcast. Please check it out!


Wang L, Stacey G, Leblanc-Fournier N, Legué V, Moulia B, Davies JM (2019) Early Extracellular ATP Signaling in Arabidopsis Root Epidermis: A Multi-Conductance Process. Front Plant Sci. doi: 10.3389/fpls.2019.01064.

Open Access

The UK-French collaboration is led by Limin Wang from Julia Davies’s lab in Cambridge. They use patch clamp electrophysiology to identify previously uncharacterized channel conductances that respond to extracellular ATP across the root elongation zone epidermal plasma membrane.


Waghmare S, Lefoulon C, Zhang B, Lileikyte E, Donald NA, Blatt MR (2019) K+ channel-SEC11 binding exchange regulates SNARE assembly for secretory traffic. Plant Physiol. doi: 10.1104/pp.19.00919

Open Access

This work from Mike Blatt’s lab in Glasgow is led by Sakharam Waghmare. They look at the interaction between SNARE proteins, which are involved in vesicular fusion and K+ channels, which help control turgor pressure during cell expansion. Through combining analysis of protein-protein interactions and electrophysiological measurement they have found that this interaction requires the activity of the regulatory protein SEC11.


Li W, He X, Chen Y, Jing Y, Shen C, Yang J, Teng W, Zhao X, Hu W, Hu M, Li H, Miller AJ, Tong Y (2019) A wheat transcription factor positively sets seed vigour by regulating the grain nitrate signal. New Phytol. doi: 10.1111/nph.16234
Wenjing Li is first author of this Chinese study that includes Yi Chen and Anthony Miller from the John Innes Centre as co-authors. This research shows that seed vigour and nitrate accumulation in wheat is regulated by the TaNAC2 transcriptions factor through its control of the TaNRT2.5 nitrate transporter. The authors suggest that both genes could be used as potential future targets to increase grain yield and nitrogen use efficiency.


The Special Issue of Methods in Molecular Biology on Plant Meiosis includes papers from the University of Cambridge, led by Christophe Lambing and the James Hutton Institute, led by Benoit Darrier.

Lambing C, Choi K, Blackwell AR, Henderson IR (2019) Chromatin Immunoprecipitation of Meiotically Expressed Proteins from Arabidopsis thaliana Flowers. Methods Mol Biol. doi: 10.1007/978-1-4939-9818-0_16
Darrier B, Arrieta M, Mittmann SU, Sourdille P, Ramsay L, Waugh R, Colas I (2019) Following the Formation of Synaptonemal Complex Formation in Wheat and Barley by High-Resolution Microscopy. Methods Mol Biol. doi: 10.1007/978-1-4939-9818-0_15

GARNet Research Roundup: September 24th 2019

Due to a significant delay this GARNet Research Roundup is a bumper overview of recent(ish) publications across discovery-led plant science, which have at least one contributor from a UK institution.

These can be (very) loosely separated into the following categories:

Circadian Clock: Greenwood et al, PloS Biology. Belbin et al, Nature Communications.

Environmental responses: Rodríguez-Celma et al, PNAS. Walker and Bennett, Nature Plants. Conn et al, PLoS Comput Biology. de Jong et al,PLoS Genetics. Molina-Contreras et al,The Plant Cell.

Defence signaling: Van de Weyer et al, Cell.Hurst et al, Scientific Reports. Xiao et al, Nature. Wong et al, PNAS.

Cell Biology: Miller et al, The Plant Cell. Coudert et al, Current Biology. Burgess et al,The Plant Cell. Harrington et al, BMC Plant Biology.

Metabolism: Jia et al, J Biol Chem. Perdomo et al, Biochem J. Gurrieri et al, Frontiers in Plant Science. Mucha et al, The Plant Cell. Atkinson et al, JXBot.

Cell Wall Composition: Wightman et al, Micron. Milhinhos et al, PNAS.

Signaling: Hartman et al, Nature Communications. Dittrich et al, Nature Plants. Villaécija-Aguilar et al, PLoS Genetics


Greenwood M, Domijan M, Gould PD, Hall AJW, Locke JCW (2019) Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana. PLoS Biol. 17(8):e3000407. doi: 10.1371/journal.pbio.300040 Open Access

Lead author is Mark Greenwood. UK contribution from The Sainsbury lab University of Cambridge, University of Liverpool and Earlham Institute. Using a mixture of experimental and modeling this paper shows that individual organs have circadian clocks that runs at different speeds.


Belbin FE, Hall GJ, Jackson AB, Schanschieff FE, Archibald G, Formstone C, Dodd AN (2019) Plant circadian rhythms regulate the effectiveness of a glyphosate-based herbicide. Nat Commun. 2019 Aug 16;10(1):3704. doi: 10.1038/s41467-019-11709-5 Open Access

Lead author is Fiona Belbin. UK contribution from University of Bristol and Syngenta Jealott’s Hill. Activity of the circadian clock determines that the plant response to the herbicide glyphosate is lessened at dusk, promoting the idea of agricultural chronotherapy. Fiona discusses this paper on the GARNet Community Podcast.


Rodríguez-Celma J, Connorton JM, Kruse I, Green RT, Franceschetti M, Chen YT, Cui Y, Ling HQ, Yeh KC, Balk J (2019) Arabidopsis BRUTUS-LIKE E3 ligases negatively regulate iron uptake by targeting transcription factor FIT for recycling. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1907971116 Open Access

Lead author is Jorge Rodríguez-Celma. UK contribution from John Innes Centre, University of East Anglia.The Arabidopsis E3 ubiquitin ligases, BRUTUS-LIKE1 (BTSL1) and BTSL2 target the FIT transcription factor for degradation, altering the plant response to harmful level of iron.


Walker CH, Bennett T (2019) A distributive ‘50% rule’ determines floral initiation rates in the Brassicaceae. Nat Plants. doi: 10.1038/s41477-019-0503-z
Lead author Catriona Walker. UK contribution from the University of Leeds. The authors introduce the 50%-rule that defines the relationshop between the total number of flowers the number of secondary inflorescences


Conn A, Chandrasekhar A, Rongen MV, Leyser O, Chory J, Navlakha S (2019) Network trade-offs and homeostasis in Arabidopsis shoot architectures. PLoS Comput Biol. doi: 10.1371/journal.pcbi.100732 Open Access

Lead author is Adam Conn. UK contribution from Sainsbury Laboratory, University of Cambridge. This study performed 3D scanning of 152 Arabidopsis shoot architectures to investigate how plants make trade-offs between competing objectives.


de Jong M, Tavares H, Pasam RK, Butler R, Ward S, George G, Melnyk CW, Challis R, Kover PX, Leyser O (2019) Natural variation in Arabidopsis shoot branching plasticity in response to nitrate supply affects fitness. PLoS Genet. doi: 10.1371/journal.pgen.1008366 Open Access

Lead author is Maaike de Jong. UK contribution from the Sainsbury Laboratory, University of Cambridge, the University of York and the University of Bath. This study looks at phenotypic plasticity of shoot branching in Arabidopsis diversity panels grown until different nitrate concentrations.


Molina-Contreras MJ, Paulišić S, Then C, Moreno-Romero J, Pastor-Andreu P, Morelli L, Roig-Villanova I, Jenkins H, Hallab A, Gan X, Gómez-Cadenas A, Tsiantis M, Rodriguez-Concepcion M, Martinez-Garcia JF (2019) Photoreceptor Activity Contributes to Contrasting Responses to Shade in Cardamine and Arabidopsis Seedlings. Plant Cell. doi: 10.1105/tpc.19.00275 Open Access

Lead author is Maria Jose Molina-Contreras. UK contribution from the University of Oxford. The authors looks at the response to different light conditions and how they contribute to phenotypic determination in Cardamine and Arabidopsis seedlings.


Van de Weyer AL, Monteiro F, Furzer OJ, Nishimura MT, Cevik V, Witek K, Jones JDG, Dangl JL, Weigel D, Bemm F (2019) A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. Cell. doi: 10.1016/j.cell.2019.07.038 Open Access

Lead author is Anna-Lena Van de Weyer. UK contribution from The Sainsbury Laboratory, Norwich. Using sequence enrichment and long-read sequencing the authors present the pan-NLRome constructed from 40 Arabidopsis accessions.


Hurst CH, Wright KM, Turnbull D, Leslie K, Jones S, Hemsley PA (2019) Juxta-membrane S-acylation of plant receptor-like kinases is likely fortuitous and does not necessarily impact upon function. Sci Rep. doi: 10.1038/s41598-019-49302-x Open Access

Lead author is Charlotte Hurst. UK contribution from the James Hutton Institute and the University of Dundee. They look at the functional role of post-translational modification S-acylation with a focus on the plant pathogen perceiving receptor-like kinase FLS2.


Xiao Y, Stegmann M, Han Z, DeFalco TA, Parys K, Xu L, Belkhadir Y, Zipfel C, Chai J (2019) Mechanisms of RALF peptide perception by a heterotypic receptor complex. Nature. doi: 10.1038/s41586-019-1409-7
Lead author is Yu Xiao. UK contribution from The Sainsbury Laboratory, Norwich. This study investigates how RAPID ALKALINIZATION FACTOR (RALF) peptides induce receptor complex formation to regulate immune signaling.


Wong JEMM, Nadzieja M, Madsen LH, Bücherl CA, Dam S, Sandal NN, Couto D, Derbyshire P, Uldum-Berentsen M, Schroeder S, Schwämmle V, Nogueira FCS, Asmussen MH, Thirup S, Radutoiu S, Blaise M, Andersen KR, Menke FLH, Zipfel C, Stougaard J (2019). A Lotus japonicus cytoplasmic kinase connects Nod factor perception by the NFR5 LysM receptor to nodulation. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1815425116
Open Access

Lead author is Jaslyn Wong. UK contribution from The Sainsbury Laboratory, University of East Anglia. This work was conducted in the legume Lotus and after a proteomic screen, the authors identified NFR5-interacting cytoplasmic kinase 4 that is involved in control of Nod factor perception.


Miller C, Wells R, McKenzie N, Trick M, Ball J, Fatihi A, Dubreucq B, Chardot T, Lepiniec L, Bevan MW (2019) Variation in expression of the HECT E3 ligase UPL3 modulates LEC2 levels, seed size and crop yield in Brassica napus. Plant Cell. doi: 10.1105/tpc.18.00577
Open Access

Lead author in Charlotte Miller. UK contribution from the John Innes Centre. Activity of the Brassica napus HECT E3 ligase gene BnaUPL3 controls seed weight per pod through degradation of LEC2, a master transcriptional regulator of seed maturation and reveals a potential target for crop improvement


Coudert Y, Novák O, Harrison CJ (2019) A KNOX-Cytokinin Regulatory Module Predates the Origin of Indeterminate Vascular Plants. Curr Biol. 2019 Aug 19;29(16):2743-2750.e5. doi: 10.1016/j.cub.2019.06.083

Lead author is Yoan Coudert. UK contribution from the University of Cambridge and University of Bristol. Class I KNOX gene activity is shown to be necessary for axis extension from an intercalary region of determinate moss shoots, in part through promotion of cytokinin biosynthesis.


Burgess SJ, Reyna-Llorens I, Stevenson SR, Singh P, Jaeger K, Hibberd JM (2019) Genome-wide transcription factor binding in leaves from C3 and C4 grasses Plant Cell.  doi: 10.1105/tpc.19.00078 Open Access

Lead author is Steven Burgess. UK contribution from University of Cambridge, The Sainsbury lab University of Cambridge, University of Leeds The authors use DNaseI-SEQ to assess the similarities and differences in transcription factor binding sites in the leaves across a set of four C3 and C4 grasses.


Harrington SA, Overend LE, Cobo N, Borrill P, Uauy C (2019) Conserved residues in the wheat (Triticum aestivum) NAM-A1 NAC domain are required for protein binding and when mutated lead to delayed peduncle and flag leaf senescence. BMC Plant Biol. doi: 10.1186/s12870-019-2022-
Lead author is Sophie Harrington. UK contributions from the John Innes Centre and University of Birmingham. The authors used a wheat TILLING resource to investigate mutrant allele with the NAC domain of the NAM-A1 transcription factor and their contribution to phenotypes in lab and field.


Jia Y, Burbidge CA, Sweetman C, Schutz E, Soole K, Jenkins C, Hancock RD, Bruning JB, Ford CM (2019) An aldo-keto reductase with 2-keto- L-gulonate reductase activity functions in L-tartaric acid biosynthesis from vitamin C in Vitis vinifera. J Biol Chem. doi: 10.1074/jbc.RA119.010196 Open Access

Lead author Yong Jia. UK contribution from the James Hutton Institute. This work conducted in grape reveals the mechanism by which an aldo-keto reductase functions in tartaric acid biosynthesis.


Perdomo JA, Degen GE, Worrall D, Carmo-Silva E (2019) Rubisco activation by wheat Rubisco activase isoform 2β is insensitive to inhibition by ADP. Biochem J. doi: 10.1042/BCJ2019011 Open Access

Lead author is Juan Alejandro Perdomo. UK contribution from Lancaster University. They show through analysis of site-directed mutations across three isoforms of wheat Rubisco activase that these isoforms have different sensitivities to ADP.


Gurrieri L, Distefano L, Pirone C, Horrer D, Seung D, Zaffagnini M, Rouhier N, Trost P, Santelia D, Sparla F (2019) The Thioredoxin-Regulated α-Amylase 3 of Arabidopsis thaliana Is a Target of S-Glutathionylation. Front Plant Sci. doi: 10.3389/fpls.2019.00993 Open Access

Lead author is Libero Gurrieri. UK contribution from John Innes Centre. The chloroplastic α-Amylases, AtAMY3 is post-translationally modified by S-glutathionylation in response to oxidative stress.


Mucha S, Heinzlmeir S, Kriechbaumer V, Strickland B, Kirchhelle C, Choudhary M, Kowalski N, Eichmann R, Hueckelhoven R, Grill E, Kuster B, Glawischnig E (2019) The formation of a camalexin-biosynthetic metabolon. Plant Cell. doi: 10.1105/tpc.19.00403 Open Access

Lead author is Stefanie Mucha. UK contribution from Oxford Brookes University and University of Warwick. The authors performed two independent untargeted co-immunoprecipitations to identify components involved in biosynthesis of the antifungal phytoalexin camalexin.


Atkinson N, Velanis CN, Wunder T, Clarke DJ, Mueller-Cajar O, McCormick AJ (2019) The pyrenoidal linker protein EPYC1 phase separates with hybrid Arabidopsis-Chlamydomonas Rubisco through interactions with the algal Rubisco small subunit. J Exp Bot. doi: 10.1093/jxb/erz275
Open Access

Lead author is Nicky Atkinson. UK contribution from the University of Edinburgh. This study uses Arabidopsis-Chlamydomonas to investigate the protein-protein interaction between Rubisco and essential pyrenoid component 1 (EPYC1).


Wightman R, Busse-Wicher M, Dupree P (2019) Correlative FLIM-confocal-Raman mapping applied to plant lignin composition and autofluorescence. Micron. doi: 10.1016/j.micron.2019.102733
Lead author Raymond Wightman. UK contribution from the Sainsbury Laboratory, University of Cambridge and the University of Cambridge. This study uses applies a novelmethod of correlative FLIM-confocal-Raman imaging to analyse lignin composition in Arabidopsis stems.


Milhinhos A, Vera-Sirera F, Blanco-Touriñán N, Mari-Carmona C, Carrió-Seguí À, Forment J, Champion C, Thamm A, Urbez C, Prescott H, Agustí J (2019) SOBIR1/EVR prevents precocious initiation of fiber differentiation during wood development through a mechanism involving BP and ERECTA. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1807863116
Lead author is Ana Milhinho. UK contribution from the University of Oxford. The authors used GWAS in Arabidopsis to identify the SOBIR1/EVR as an important regulator of the control of secondary growth in xylem fibers.


Hartman S, Liu Z, van Veen H, Vicente J, Reinen E, Martopawiro S, Zhang H, van Dongen N, Bosman F, Bassel GW, Visser EJW, Bailey-Serres J, Theodoulou FL, Hebelstrup KH, Gibbs DJ, Holdsworth MJ, Sasidharan R, Voesenek LACJ (2019) Ethylene-mediated nitric oxide depletion pre-adapts plants to hypoxia stress. Nat Commun. doi: 10.1038/s41467-019-12045-4 Open Access

Lead author is Sjon Hartman. UK contribution from the University of Nottingham, Rothamsted Research and the University of Birmingham. This multinational collaboration looks into the relationship of how ethylene mediated nitric-oxide signaling responds to environmental signals.


Dittrich M, Mueller HM, Bauer H, Peirats-Llobet M, Rodriguez PL, Geilfus CM, Carpentier SC, Al Rasheid KAS, Kollist H, Merilo E, Herrmann J, Müller T, Ache P, Hetherington AM, Hedrich R (2019) The role of Arabidopsis ABA receptors from the PYR/PYL/RCAR family in stomatal acclimation and closure signal integration. Nat Plants. doi: 10.1038/s41477-019-0490-0
Lead author Marcus Dittrich. UK contribution from the University of Bristol. This work looks at the role of ABA signaling in stomatal responses and that the multiple ABA receptors can be modulated differentially in a stimulus-specific manner.


Villaécija-Aguilar JA, Hamon-Josse M, Carbonnel S, Kretschmar A, Schmid C, Dawid C, Bennett T, Gutjahr C (2019). SMAX1/SMXL2 regulate root and root hair development downstream of KAI2-mediated signalling in Arabidopsis. PLoS Genet. doi: 10.1371/journal.pgen.1008327 Open Access

Lead author Jose Antonio Villaécija-Aguilar. UK contribution from the University of Leeds and The Sainsbury lab, University of Cambridge. This demonstrates that KAI2 signalling through SMAX1/SMXL2 , is an important new regulator of root hair and root development in Arabidopsis.

GARNet Research Roundup: July 5th 2019

This edition of the GARNet research roundup begins with a study from the University Leicester that investigates the rate of selection of genes expressed in Arabidopsis pollen.

The second and third papers focus on the function of members of the AP2 family of transcription factors. Sarah McKim’s lab in Dundee characterizes the role of APETALA2 during barley stem elongation whilst the other paper investigates the function of the Arabidopsis PUCHI gene and includes co-authors from the University of Nottingham.

The fourth paper is from Lars Ostergaard’s lab at the John Innes Centre and demonstrates the benefit of using models to understand developmental processes in crop plants. The next paper from the University of Glasgow investigates the plant response to low fluence rates of UV-B light.

The penultimate paper features authors from Oxford Brookes University and characterizes a novel LINC-KASH protein in maize whilst the final paper is from the University of Cambridge and investigates the novel function of two members of DUF579 family in methylation of glucuronic acid residues.


Harrison MC, Mallon EB, Twell D, Hammond RL (2019) Deleterious mutation accumulation in Arabidopsis thaliana pollen genes: a role for a recent relaxation of selection. Genome Biol Evol. doi: 10.1093/gbe/evz127

Open Access

This research from Hammond and Twell lab’s at the University of Leicester uses Arabidopsis to investigate the hypothesis that pollen genes evolve faster than sporophytic genes. This study is challenging to perform in Arabidopsis as for the past million years the plant has been self-compatible, which causes reduction in pollen competition, increased homozygosity and a dilution of masking in diploid expressed, sporophytic genes. This study has two main findings: firstly prior to becoming self-compatible pollen genes evolved faster than sporophytic genes. Secondly, since becoming self-compatible selection has relaxed causing higher polymorphism levels and a higher build-up of deleterious mutations.


Patil V, McDermott HI, McAllister T, Cummins M, Silva JC, Mollison E, Meikle R, Morris J, Hedley PE, Waugh R, Dockter C, Hansson M, McKim SM (2019) APETALA2 control of barley internode elongation. Development. doi: 10.1242/dev.170373

Open Access

Vrushali Patil leads his study from the lab of current GARNet committee member Sarah McKim at the James Hutton Institute in Dundee. They show that the APETALA2 (AP2) transcription factor is necessary for stem elongation in Barley. In addition they demonstrate that AP2 expression is controlled by the activity of the microRNA mi172 as well as jasmonate signaling.

https://dev.biologists.org/content/146/11/dev170373.long

Trinh DC, Lavenus J, Goh T, Boutté Y, Drogue Q, Vaissayre V, Tellier F, Lucas M, Voß U, Gantet P, Faure JD, Dussert S, Fukaki H, Bennett MJ, Laplaze L, Guyomarc’h S (2019) PUCHI regulates very long chain fatty acid biosynthesis during lateral root and callus formation. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1906300116

Julien Lavenus, Ute Voß and Malcolm Bennett from University of Nottingham are co-authors on this French-led study that investigates the mechanism by which the AP2 family transcription factor PUCHI controls lateral root development. By performing a transcriptional analysis of developing lateral root cells they show that genes involved in very long chain fatty acid (VLCFA) biosynthesis enzymes are induced in a PUCHI dependent manner. Concomitantly they show puchi-1 mutant roots have reduced VLCFA content when compared with wildtype roots. They conclude that PUCHI regulates VLCFA biosynthesis as part of a pathway controlling cell proliferation during lateral root formation.


Stephenson P, Stacey N, Brüser M, Pullen N, Ilyas M, O’Neill C, Wells R, Østergaard L (2019) The power of model-to-crop translation illustrated by reducing seed loss from pod shatter in oilseed rape. Plant Reprod. doi: 10.1007/s00497-019-00374-9

Open Access

Pauline Stephenson and Lars Østergaard at the John Innes Centre lead this study in which they demonstrate that lessons learnt from understanding the genes involved in fruit ripening in Arabidopsis lead to an ability to adjust the pod-opening process in oilseed rape. They have combined two mutant alleles, first characterized in Arabidopsis, to develop OSR plants that have significantly increased yield. In addition they present a new software tool for the analysis of pod shatter data in other crops plants.


O’Hara A, Headland LR, Díaz-Ramos LA, Morales LO, Strid Å, Jenkins GI (2019) Regulation of Arabidopsis gene expression by low fluence rate UV-B independently of UVR8 and stress signaling. Photochem Photobiol Sci. doi: 10.1039/c9pp00151d

Open Access

This UK-Swedish collaboration is led by Andrew O’Hara from the Jenkins lab in the University of Glasgow. They continue the lab focus on the UV-B receptor UVR8, in this case performing a transcriptomic analysis of wildtype and uvr8 mutants grown under low UV-B fluence rates. They analyse one differentially expressed gene in more detail, the transcription factor ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 13 (ANAC13), which was induced by UV-B but by the activity of any other photoreceptor.


Gumber HK, McKenna JF, Tolmie AF, Jalovec AM, Kartick AC, Graumann K, Bass HW (2019) MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation Nucleus. doi: 10.1080/19491034.2019.1629795

Open Access

Hardeep Gumber is first author on this US-led study that includes Joe KcKenna, Andrea Tolmie and Katja Graumann from Oxford Brookes as co-authors. They characterise the Maize LINC KASH AtSINE-like2 protein, MLKS2, whose targeting to the nuclear periphery requires its N-terminal armadillo repeats. Mutant mlks2 plants have pleiotropic plant phenotypes and on a nuclear level show defects in chromosome segregation and positioning. These findings support a model in which cytoplasmic actin is linked to chromatin through the LINC-KASH nuclear envelope network.

https://www.tandfonline.com/doi/full/10.1080/19491034.2019.1629795

Temple H, Mortimer JC, Tryfona T, Yu X, Lopez-Hernandez F, Sorieul M, Anders N, Dupree P (2019) Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis. Plant Direct. doi: 10.1002/pld3.117

Open Access

Henry Temple is first author on this work from the University of Cambridge that characterizes two members of the DUF579 family (AGM1 and AGM2). These proteins are required for 4-O-methylation of glucuronic acid within highly glycosylated arabinogalactan proteins (AGPs).


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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: March 7th 2019

This edition of the GARNet research roundup begins with a study into the genetic basis of fertility in barley led by Sarah McKim from Dundee. Second is a study from Oxford and Leicester that characterizes the proteolytic control of chloroplast import. The third paper from Levi Yant’s group at JIC and Nottingham that attempts to discover the influence of polyploidism on population genomic effects whilst the fourth paper from Juliet Coates’ lab in Birmingham uses the growth of Arabidopsis to assess the potential of algal biomass as a biofertiliser. The next two papers include co-authors from Oxford and Warwick respectively and investigate different factors that control seed viability in Arabidopsis and Brassica oleracea. The final paper includes Seth Davies from York as a co-author on a study that looks at control of the circadian clock in field-grown Arabidopsis.


Zwirek M, Waugh R, McKim SM (2019) Interaction between row-type genes in barley controls meristem determinacy and reveals novel routes to improved grain. New Phytol. doi: 10.1111/nph.15548

Open Access

Current GARNet committee members Sarah McKim is the leader of this study in which first author is Monica Zwirek. They investigate the mechanism through which the barley VRS genes contribute to spikelet fertility. They undercover the epistatic relationship between five VRS genes that explains how they contribute to controlling fertility of lateral spikelets. Importantly they demonstrate that various vrs mutant combinations improve fertility in a variety of ways, information that will be useful during the generation of new varieties of barley.

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15548

Ling Q, Broad W, Trösch R, Töpel M, Demiral Sert T, Lymperopoulos P, Baldwin A, Jarvis RP (2019) Ubiquitin-dependent chloroplast-associated protein degradation in plants. Science. doi: 10.1126/science.aav4467

Qihua Ling and William Broad are the first authors on this study from the Universities of Oxford and Leicester. They investigate the role of proteolysis in the functional control of chloroplast-envelope translocases, which are required for the transport of proteins from nucleus-encoded genes into the chloroplast. They identify two newly characterised proteins that function in the same pathway as the known ubiquitin E3 ligase SP1. These novel proteins, SP2 and CDC48, are both required for the movement of ubiquitinated proteins from the chloroplast outer envelope membrane (OEM) into the cytosol, where they are degraded by the proteolytic machinery. This process of chloroplast-associated protein degradation (CHLORAD) maintains tight control of the activity of OEM proteins and is essential for organelle function.

http://science.sciencemag.org/content/363/6429/eaav4467.long

Monnahan P, Kolář F, Baduel P, Sailer C, Koch J, Horvath R, Laenen B, Schmickl R, Paajanen P, Šrámková G, Bohutínská M, Arnold B, Weisman CM, Marhold K, Slotte T, Bomblies K, Yant L (2019) Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa. Nat Ecol Evol. doi: 10.1038/s41559-019-0807-4.

Patrick Monnahan at the John Innes Centre is first author on this study from the Yant lab that has recently moved to the University of Nottingham. In this collaboration with colleagues in the US, Austria, Sweden, the Czech Republic and Slovakia, they have performed large scale sequencing on 39 populations of Arabidopsis arenosa. These plants have differing levels of ploidy and they are attempting to understand how ploidy effects population genomics. They demonstrate that the ploidy effects are subtle but significant and that masking of deleterious mutations, faster substitution rates and interploidy introgression will likely impact the evolution of populations where polyploidy is common.


Ghaderiardakani F, Collas E, Damiano DK, Tagg K, Graham NS, Coates J (2019) Effects of green seaweed extract on Arabidopsis early development suggest roles for hormone signalling in plant responses to algal fertilisers. Sci Rep. doi: 10.1038/s41598-018-38093-2

Open Access

This work from the Coates lab at the University of Birmingham is led by Fatemeh Ghaderiardakani and looked into the potential of algal extracts as biofertiliser. They showed that at >0.1%, extracts taken from the common green seaweed Ulva intestinalis inhibit Arabidopsis seed germination and root elongation. At lower concentrations primary root elongation was promoted albeit with a complete loss of lateral root formation. Elemental analysis allows the authors to suggest that this effect was mediated via a novel mechanism involving aluminium. Overall the authors caution against the use of algal biofertilisers due to potential unforeseen negative effects on plant growth.


Viñegra de la Torre N, Kaschani F, Kaiser M, van der Hoorn RAL, Soppe WJJ, Misas Villamil JC (2019) Dynamic hydrolase labelling as a marker for seed quality in Arabidopsis seeds. Biochem J. doi: 10.1042/BCJ20180911.

GARNet Committee member Renier van der Hoorn is a co-author on this German-led study that investigates how the activity of seed-localised proteases can affect Arabidopsis seed germination. This study has clear real-world application regarding the storage of economically important seed stocks. They show that vacuolar processing enzymes (VPEs) become more active during aging whilst the activity of serine hydrolases declines alongside seed quality. This information has allowed the authors to develop protease-activity-based markers that will provide information about seed quality.


Schausberger C, Roach T, Stöggl WM, Arc E, Finch-Savage WE, Kranner I (2019) Abscisic acid-determined seed vigour differences do not influence redox regulation during ageing. Biochem J. doi: 10.1042/BCJ20180903

William Finch-Savage from the University of Warwick is a co-author on this Austrian-led study that looks at the effect of aging on the quality of Brassica oleracea seeds stored at two oxygen concentrations. Higher O2 causes a more rapid decrease in seed quality through aging yet in contrast aging did not alter the impact of the hormone ABA on seed viability. This study enables the authors to uncover two mechanisms that control seed quality that appear to act through different mechanisms.


Rubin MJ, Brock MT, Davis SJ, Weinig C (2019) QTL Underlying Circadian Clock Parameters Under Seasonally Variable Field Settings in Arabidopsis thaliana G3 (Bethesda). doi: 10.1534/g3.118.200770

Open Access

Seth Davies from the University of York is a co-author on this study led by Matthew Rubin from the University of Wyoming. They looked at the growth of Arabidopsis thaliana recombinant inbred lines grown in field conditions and found an extremely nuanced relationship regarding how QTLs that influence the circadian clock respond to environmental conditions. For example the authors showed that plant growth in June, July and September is controlled by different QTL architecture, demonstrating the complex regulation of the circadian clock in these field growth plants.

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Welcome , today is Monday, October 26, 2020