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

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

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

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) 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.

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