GARNet Research Roundup: October 19th 2018

This edition of the GARNet research roundup includes six papers that look at different areas of plant biology. Firstly is a Belgian-led study with co-authors from Nottingham that introduces adaptive Xerobranching, a cereal-root response that can be mimicked in Arabidopsis by modulating ABA signaling. Second is study from Juriaan Ton’s lab in Sheffield that investigates the extent of DNA methylation during transgenerational acquired disease resistance. Third is paper from the John Innes Centre that places the DET1/COP1-PIF4 signaling module as a key determinant of the plants decision to allocate resources toward growth or defence.

The fourth paper is from Siobhan Braybrook’s (now ex-) lab at SLCU and provides an extensive dataset of the shape of leaf pavement cells across plant lineages. The penultimate paper is from a group at the University of Birmingham investigating the role of TOPII in the removal of damaging chromosome interlocks that occur during meiosis. The final paper returns to the ABA signalling with a study from Rothamsted Research that looks at the impact of the N-end rule on the different growth responses that occur during seed germination.


https://www.cell.com/current-biology/pdfExtended/S0960-9822(18)31004-2

Orman-Ligeza B, Morris EC, Parizot B, Lavigne T, Babé A, Ligeza A, Klein S, Sturrock C, Xuan W, Novák O, Ljung K, Fernandez MA, Rodriguez PL, Dodd IC, De Smet I, Chaumont F, Batoko H, Périlleux C, Lynch JP, Bennett MJ, Beeckman T, Draye X (2018) The Xerobranching Response Represses Lateral Root Formation When Roots Are Not in Contact with Water. Current Biology. doi: 10.1016/j.cub.2018.07.074

Open Access

Emily Morris and Beata Orman-Ligeza are co-authors on this Belgian-led study that includes authors from the Universities of Nottingham and Lancaster. They introduce a new adaptive response termed xerobranching that defines the repression of root branching when a root tip is not in contact with wet soil. This response occurs in cereal roots but can be mimicked in Arabidopsis by treatment with ABA as the authors show that the response is dependent on the PYR/PYL/RCAR-dependent signaling pathway. This response allows roots to respond to the realistically varied microclimate encountered through the soil and offers another excellent example of how using both cereals and Arabidopsis can provide answers that would not be possible from a single experimental system.


Stassen JHM, López A, Jain R, Pascual-Pardo D, Luna E, Smith LM, Ton J (2018) The relationship between transgenerational acquired resistance and global DNA methylation in Arabidopsis. Sci Rep. doi: 10.1038/s41598-018-32448-5

https://www.nature.com/articles/s41598-018-32448-5

Open Access

Joost Stassen and Ana Lopez are the lead authors of this study from Juriaan Ton’s lab in Sheffield that continues their work on mechanisms that explain transgenerational acquired resistance (TAR). TAR occurs in the progeny of heavily diseased plants and in this study they investigate the extent of DNA methylation in generations following exposure to pathogens. They find that the extent of TAR-induced methylation was in direct proportion to the number of previous generations that had been exposed to disease. The majority of this methylation was in the CG context in gene bodies and clearly shows that methylation is an important component of molecular changes that occur during TAR.


Gangappa SN, Kumar SV (2018) DET1 and COP1 Modulate the Coordination of Growth and Immunity in Response to Key Seasonal Signals in Arabidopsis. Cell Rep. doi: 10.1016/j.celrep.2018.08.096

https://www.cell.com/cell-reports/fulltext/S2211-1247(18)31415-3

Open Access

Sreeramaiah Gangappa performed this work with Vinod Kumar at the John Innes Centre in which they investigate the molecular pathways that regulate the environmental signals that feed into the balance decision between growth and defense responses. They show that De-Etiolated 1 (DET1) and Constitutive Photomorphogenic 1 (COP1) negatively regulate immunity during favourable growth conditions and that this response is coordinated through the PIF4 transcription factor. These findings lead the authors to conclude that the DET1/COP1-PIF4 module is a key determinant of the different growth requirements that are necessary to response to either environment and disease.


Vőfély RV, Gallagher J, Pisano GD, Bartlett M, Braybrook SA (2018) Of puzzles and pavements: a quantitative exploration of leaf epidermal cell shape. New Phytol. doi: 10.1111/nph.15461

Open Access

https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15461

Work from Siobhan Braybrook’s lab features in the Research Roundup for the second consecutive edition, this time led by Roza Vofely at the Sainsbury Lab Cambridge University (SLCU). In this study they have investigated the shape of leaf epidermal pavement cells from a remarkable 278 plant taxa in order to ascertain whether certain lineages are characterized by different cell shapes and whether the presence of an undulating cell wall is common, as in both maize and Arabidopsis. Interestingly they found that these primary examples were the exception as strongly undulating cell walls were unusual. They found that different lineages were characterised by similar levels of undulation and the authors conclude that this study sets a quantitative benchmark on which future experiments can be based that aim to understand the underlying factors that control pavement cell shape.


Martinez-Garcia M, Schubert V, Osman K, Darbyshire A, Sanchez-Moran E, Franklin FCH (2018) TOPII and chromosome movement help remove interlocks between entangled chromosomes during meiosis. J Cell Biol. doi: 10.1083/jcb.201803019

Open Access
Marina Martinez‐Garcia is the lead author on this work conducted during her time working with Eugenio Sanchez-Moran and Chris Franklin at the University of Birmingham. Normal meiosis requires a lack of structural interlocks between entangled chromosomes that can result from inevitable collisions in an area so packed with nucleic acid. In this paper the authors confirm a previously developed hypothesis that topoisomerase II (TOPII) is needed to remove interlocks. However it is not the only determinant of the number of interlocks as in Arabidopsis mutants in which chromosome movement is reduced, interlocks occur irrespective of the presence of TOPII.


Zhang H, Gannon L, Jones PD, Rundle CA, Hassall KL, Gibbs DJ, Holdsworth MJ, Theodoulou FL (2018) Genetic interactions between ABA signalling and the Arg/N-end rule pathway during Arabidopsis seedling establishment. Sci Rep. doi: 10.1038/s41598-018-33630-5

https://www.nature.com/articles/s41598-018-33630-5

Open Access

Hongtao Zhang is the lead author of this work from the lab of Freddie Theodoulou at Rothamsted Research that investigates the role of the PROTEOLYSIS6 (PRT6) N-recognin E3 ligase in the ABA response. PRT6 regulated degradation of Group VII of the Ethylene Response Factor superfamily (ERFVIIs) controls both sugar sensitivity and oil body breakdown in germinating Arabidopsis seedlings. They found that the former but not the latter response was enhanced by ABA signaling components when the ERFVIIs were stabilised. The authors conclude that during seed germination the N-end rule controls multiple layers of regulation, both in an ABA dependent and independent manner

GARNet Research Roundup: October 10th 2018

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Published on: October 10, 2018

This edition of the GARNet research roundup begins with a paper from Jose Gutierrez-Marcos’ lab in Warwick that investigates the functional significance of inherited epigenetics marks in clonally propagated plants. Second is work from Sara Simonini and Lars Ostergaard (John Innes Centre) that defines a domain in the ETTIN protein important for the auxin response. Next is work from SLCU from Siobhan Braybrook and Henrik Jonsson that experimentally defines and models the role of cell wall composition in anisotropic hypocotyl growth. The fourth paper is from Jonathan Jones’ lab (TSL, Norwich) that adds to our understanding of the activity of the RRS1-R-RPS4 NLR immune complex.

The final three papers are each from the University of Edinburgh and look at different aspects of the relationship between light quality and the circadian clock. First is a paper from Karen Halliday’s lab that investigates the role of PHYA; next Andrew Millar is a co-author on a manuscript that looks at control of FT expression during seasonally realistic conditions. Finally Ference Nagy and Mirela Domijan (University of Liverpool) co-author a paper that assesses the role of HY5 in the response to blue-light.


Wibowo A, Becker C, Durr J, Price J, Spaepen S, Hilton S, Putra H, Papareddy R, Saintain Q, Harvey S, Bending GD, Schulze-Lefert P, Weigel D, Gutierrez-Marcos J (2018) Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation. Proc Natl Acad Sci U S A doi: 10.1073/pnas.1805371115

http://www.pnas.org/content/early/2018/09/06/1805371115.long

Open Access
Anjar Wibowo and Claude Becker are first authors on this UK-German collaboration from the labs of Jose Gutierrez-Marcos (University of Warwick) and Detlef Weigel (Max Planck Institutem, Tübingen). In this work they clonally propagate Arabidopsis and show that organ-specific epigenetic marks are maintained across generations. Interestingly these changes are then maintained through multiple rounds of sexual reproduction. These epigenetic marks provide heritable molecular and physiological phenotypes that can alter the response to pathogens, allowing progeny to maintain a beneficial epigenome that was generated in their parents.


Simonini S, Mas PJ, Mas CMVS, Østergaard L, Hart DJ (2018) Auxin sensing is a property of an unstructured domain in the Auxin Response Factor ETTIN of Arabidopsis thaliana. Sci Rep. doi: 10.1038/s41598-018-31634-9

https://www.nature.com/articles/s41598-018-31634-9

Open Access

This UK-France collaboration is led by Sara Simonini from the John Innes Centre and continues the Ostergaard lab’s work on the role of the auxin response factor ETTIN in the auxin response. In this paper they analyse the C-terminal ETT specific domain (ES domain) across plant lineages, showing that it does not directly bind auxin but could functional response to a dose response of auxin in a Y2H assay. Understanding more about this ES domain will increase our understanding of auxin sensing by ETTIN and more broadly about auxin-dependent gene regulation.


Bou Daher F, Chen Y, Bozorg B, Clough J, Jönsson H, Braybrook SA. Anisotropic growth is achieved through the additive mechanical effect of material anisotropy and elastic asymmetry. Elife.  doi: 10.7554/eLife.38161

https://elifesciences.org/articles/38161

Open Access

Firas Bou Daher is the first author on work from Siobhan Braybrook’s lab conducted both in the Sainsbury Lab Cambridge University and at its new home in California. In this work they look at anisotropic growth in the Arabidopsis hypocotyl and the relationship between cellulose orientation and pectin deposition in the control of this process. They provide experimental evidence that growth parameters are influenced by pectin biochemistry in processes that begin immediately after germination.


Ma Y, Guo H, Hu L, Martinez PP, Moschou PN, Cevik V, Ding P, Duxbury Z, Sarris PF, Jones JDG (2018) Distinct modes of derepression of an Arabidopsis immune receptor complex by two different bacterial effectors. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1811858115

Yan Ma and Hailong Guo are lead authors on this study from Jonathan Jones’ lab at The Sainsbury Lab, Norwich. They perform a detailed examination of the RRS1-R-RPS4 NLR protein complex, which is necessary to respond to at the bacterial effectors, AvrRps4 and PopP2. Deletion of a WRKY transcription factor domain in the RRS1-R protein causes constitutive activation of the defense response, indicating that this domain maintains the complex in an inactive state in the absence of pathogens. Indeed AvrRps4 does interact with this WRKY domain but interestingly PopP2 activation requires interaction with a longer C-terminal extension of RRS1-R. This demonstrates that although these bacterial effectors are recognised by the same complex the interactions occurs in a subtly but functionally distinct ways.


Seaton DD, Toledo-Ortiz G, Ganpudi A, Kubota A, Imaizumi T, Halliday KJ (2018) Dawn and photoperiod sensing by phytochrome A. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1803398115

Open Access

This research from Karen Halliday’s lab in Edinburgh is led by Daniel Seaton and provided a detailed assessment of the role of phytochrome A (phyA) in photoperiod sensing, which is defined as the relationship between the circadian clock and external light signals. They show that PHYA activity, controlled by the transcription factors, PIF4 and PIF5, is a key regulator of morning activity, particularly in short photoperiods. PHYA protein accumulates during the night and responds to light by promoting a burst of gene expression that prepares the plant for the upcoming daylight and places this light receptor as a key detector of dawn.


Song YH, Kubota A, Kwon MS, Covington MF, Lee N, Taagen ER, Laboy Cintrón D, Hwang DY, Akiyama R, Hodge SK, Huang H, Nguyen NH, Nusinow DA, Millar AJ, Shimizu KK, Imaizumi T (2018) Molecular basis of flowering under natural long-day conditions in Arabidopsis. Nat Plants. doi: 10.1038/s41477-018-0253-3

Andrew Millar is a co-author on this US-led paper that investigates the circadian regulation of the Arabidopsis florigen gene FLOWERING LOCUS T (FT) within an annual context, showing that during the spring FT shows a morning peak is absent in their usual lab experiments. By adjusting growth-room conditions to mimic natural seasonal variations they show that phytochrome A and EARLY FLOWERING 3 regulate morning FT expression by stabilizing the CONSTANS protein. This manuscript highlights the importance of providing seasonal-specific conditions in order to understand field-relevant regulation of plant growth.


Hajdu A, Dobos O, Domijan M, Bálint B, Nagy I, Nagy F, Kozma-Bognár L. ELONGATED HYPOCOTYL 5 mediates blue light signalling to the Arabidopsis circadian clock (2018) Plant J. doi: 10.1111/tpj.14106

Ferenc Nagy (University of Edinburgh) is a co-author on this Hungarian-led study that looks the effect of light quality on the function of the key signaling hub transcription factor ELONGATED HYPOCOTYL 5 (HY5). They show that hy5 mutants show shorter period rhythms in blue but not in red light or darkness. Even though the pattern and level of HY5 alters its binding to downstream promotor elements, subsequent gene expression is only altered in a few genes. In collaboration with Mirela Domijan (University of Liverpool) https://www.liverpool.ac.uk/mathematical-sciences/staff/mirela-domijan/ they model this response to suggest that clock feedback mechanisms mask HY5-induced changes. Ultimately they show that HY5 is important in decoding the blue:red mix of white light and that it at least partially informs activity of the circadian oscillator.

High Value Chemicals from Plants Annual Meeting 2018

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Published on: October 3, 2018
Naomi Nakayama discusses plant cell factories

The final annual meeting in Phase I of the BBSRC-funded HVCfP NIBB network was held on October 1st in the delightful Royal College of Physicians, close to Regents Park in London. This single day meeting was a byte-size mix of invited talks and those provided by researchers who had received Proof of Concept (PoC) or Business Interaction Voucher (BIV) funding from the network.

From a GARNet perspective it was gratifying to hear presentations that included preliminary work conducted in Arabidopsis, demonstrating the importance of model organisms in the development of ideas that can lead to industrial biotechnology projects. Naomi Nakayama from the University of Edinburgh described her labs work aimed at optimising use of Arabidopsis cell cultures as well as in developing plant stem cells as ‘single cell factories’. Secondly Peter Eastmond from Rothamsted Research described the initial characterisation of the Sugar Dependent1 hydrolase enzyme that they are now developing as a potential industrial biocatalyst.


Paul Fraser from RHUL and Mike Roberts from Lancaster University introduced very different research projects that both use tomato plants. Long-term establishment of RIL lines have allowed the Fraser lab to identify tomato plants with increased levels of B-carotene in the fruit. This project has similarity to other attempts at vitamin A biofortification yet takes advantage of many years expertise working specifically with this plant. These B-carotene fortified lines are now ready for the field and should be particularly important in regions with high food insecurity and vitamin A deficiency.

Mike Roberts has a nascent industrial collaboration with greenhouse tomato producer APS Salads. Their soil-free growth of tomatoes generates a large amount of waste biomass, which is currently used for a variety of applications that rely on downstream anaerobic decomposition. It is known that mechanical disruption of plant tissue causes the release of protective defence chemicals so the Roberts lab have used HVCfP BIV funding to investigate whether macerated tomato waste has protective anti-pathogen properties. The initial characterisation of liquid fractions taken from the waste pipeline have given promising protective effects indicating that the mechanical disruption of the tissue generates an as-yet-unknown defense-promoting compound.

Michael Marsden discusses co-products, not plant waste.

On a related note, Michael Marsden provided an invited talk and asked delegates to re-think the idea of ‘plant waste’. His company AB Connect labels waste as ‘co-products’ and it was extremely informative to learn about all the possible uses of crop co-products across a range of industries. However there certainly remains additional potential in this area as technologies continue to develop for degradation of cellulosic material and improvement of manufacturing pipelines.


Sweet smelling success story of Oxford BioTrans.

Jason King from Oxford Biotrans provided the opening invited talk that was a real success story of activities that have taken place since he last presented at the 2015 annual HVCfP meeting. Their main product is the grapefruit flavour nootkatone that they produce from oranges using patented P450 enzymes. This industrial project was recently highlighted as a success story by the BBSRC. Oxford BioTrans are now investigating options for producing a range of other products using their set of novel P450s. Pleasingly Jason King reported that they have not had significant difficulties in obtaining funding for this project both from national funding bodies and local angel investors.


The afternoon invited speakers provided a different perspective on some wider issues surrounding the research environment. Kelly Vere is working with the Science Council on the establishment of the Technicians Committment, which is an initiative to provide recognition for the vital yet often underappreciated support provided by technical staff in higher education. Over 50 universities have signed up to the charter and many are taking steps to provide this extra support.


Alison Prendiville (University of the Arts London) and Sebastian Fuller (St George’s, University of London) described their involvement with the EU-funded Pharma-Factory project. This involves the input of numerous stakeholders associated with the use of the products generated by plant-based biofactories. These include potential patients, clinicians, regulators and researchers. They described how they are using the process of co-design to create partnerships that take into account stakeholder priorities in order to facilitate new methods of knowledge exchange. Intuitively it seems that this type of project might be challenging for bench scientists to fully appreciate so it will be interesting to observe where this project leads and to learn about their conclusions.


Due to the obvious links between the GARNet community and the type of PoC/BIV projects funded by the HVCfP network, the GARNet coordinator has attended and participated in a number of HVCfP events over the past four years. Although this annual meeting only highlighted a small set of supported projects it seems clear that the HVCfP network has succeeded in bringing together academics and industrial partners as well as supporting research in its early stages.

The decision regarding Phase II of the NIBBs will be announced over the next month so hopefully this plant-based network will gain follow-on funding to continue the progress they have made during Phase I.

Andrew Millar talks Open Data at GARNet2018

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Published on: October 2, 2018

Andrew Millar (University of Edinburgh) speaks at the GARNet2018 conference about ‘Being more Open by being more Productive’

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