Steven Spoel talks to GARNet

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Published on: October 30, 2019

Steven Spoel discusses a recent paper published in Elife entitled ‘ Dynamic ubiquitination determines transcriptional activity of the plant immune coactivator NPR1‘. This paper characterises the molecular fine-tuning that controls the transcriptional outputs and degradation of the NPR1 protein, which is a key player in the plant immune response. Thanks to Steven for the really interesting chat!

Saskia Hogenhout talks to GARNet

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Published on: October 23, 2019

Saskia Hogenhout from the John Innes Centre discusses her labs recent paper in PLOS Pathogens titled ‘Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize‘. We also briefly discuss her international collaborations working on Phytoplasma-Crop interactions.

Fascination of Plants 2019 Success Stories

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Published on: October 21, 2019

Thank you again for all your hard work towards making this year’s Fascination of Plants Day a big success! The Success Stories 2019 report (PDF) from International Fascination of Plants Day 2019 has now been published. The FoPD coordinator Carmel Edwards thanks everyone for sending stories and photos! This will be promoted again in December when there is a full set of videos additional document. Please pass it on!

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

Paige Panter talks to GARNet

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Published on: October 16, 2019

Dr Paige Panter talks to GARNet about her PhD research conducted at the University of Durham. This paper is published in New Phytologist and is titled ‘MUR1-mediated cell-wall fucosylation is required for freezing tolerance in Arabidopsis thaliana‘. Paige is currently working with Antony Dodd in Bristol and some moving to the John Innes Centre! Good work with the move and the new project!

Janneke Balk talks to GARNet

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Published on: October 9, 2019

Janneke Balk from the John Innes Centre discusses a recent paper from PNAS titled ‘Arabidopsis BRUTUS-LIKE E3 ligases negatively regulate iron uptake by targeting transcription factor FIT for recycling‘. Thanks for discussion and good luck on gaining the follow-on funding for this exciting work! 9/10/19

GARNet Workshop on ‘Advances in Plant Imaging’

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Published on: October 8, 2019

By Geraint Parry

https://garnetimaging19.weebly.com/

Download the Workshop Abstract Book.

            Over 60 delegates travelled to the University of Warwick for the GARNet workshop on ‘Advances in Plant Imaging’, which received kind support from the Society of Experimantal Biology. This meeting was led by Professor Murray Grant, who is currently a member of the GARNet Advisory Committee.

            The primary aim of this workshop was to introduce early career researchers to the techniques used by researchers who are at the cutting edge of different imaging systems. Throughout the workshop we aimed to engender an atmosphere of discussion and collaboration so to that end we included an early session of short talks so delegates could introduce their work prior to discussions over dinner and drinks. The official Poster session was scheduled after all of the talks had concluded so as to give all the speakers the opportunity to later discuss their work. This timing also allowed attendees to visit posters without the authors in attendance so that they could formulate their own questions to be asked later! Finally we encouraged attendees to use ‘post-its’ to note the techniques and/or initiatives that they would find most useful to aid their future research. These replies were collated and considered at a final wrap-up discussion session.

            These responses could be separated into two main categories; 1, Software and 2, Community; highlighting the need for training in new imaging and imaging analysis techniques and the integration of plant scientists with different communities, such as hardware developers or the experts in computer vision. This feedback was shared with the UKRI-BBSRC representative who attended the meeting and was incorporated into a recent GARNet grant proposal.


            The workshop began with a session on ‘High Resolution Microscopy for Plant Cell Biologythat included talks from Joe McKenna and Martin Goldberg from Oxford Brookes and Durham respectively. They talked about the opportunities available through use of Super Resolution Microscopy and Scanning Electron Microscopy. There was some excitment in the room as Martin supplied ‘old-style’ 3D glasses to view some of his excellent images of the nuclear envelope.

3D images from Martin Golderg, please put on your glasses!

            The bulk of the second day of the workshop was split into two sessions titled Imaging across scales and Imaging with Novel Genetically encoded Reporters. The eight speakers in these sessions had an even gender split and featured two PhD students, two postdocs and four PIs. In particular the PhD students, Anis Meschichi and Emily Morris gave fantastic talks that included some great images. Anis talked about the work from Stefanie Rosa’s lab on single molecule RNA FISH whilst Emily presented amazing whole-root images taken at the Hounsfield microCT facility at the University of Nottingham. Each speaker in these sessions should be credited for excellently presenting their own research as well as providing insights into the opportunities that exist to use different tools and technologies, such as live imaging with light sheet microscopy (Giovanni Sena) or use of novel calcium (Myriam Charpentier) or redox (Phil Mullineaux) responsive reporters.

Emily Morris presenting her research

            A post-workshop survey confirmed that attendees very much enjoyed the talks and the opportunities provided for discussion….. although the catering and arrangements at Warwick weren’t universally enjoyed! Something to learn for next time!

            Throughout the meeting GARNet got the clear message that there is a community-need for a workshop on general Image Analysis and we will look at organising something in this area early in 2020. Watch this space!

Mike Bevan talks to GARNet

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Published on: October 2, 2019

Mike Bevan from the John Innes Centre talks to GARNet about a paper published in The Plant Cell titled ‘Variation in expression of the HECT E3 ligase UPL3 modulates LEC2 levels, seed size and crop yield in Brassica napus‘. Thanks very much to Mike for the discussion. 2/10/19

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