Arabidopsis Research Roundup: August 14th

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Published on: August 14, 2017

This weeks UK Arabidopsis Research Roundup includes a study from the lab of GARNet Chairman Steven Spoel that describes their work on the control of ROS signaling. The other two papers looks at different aspects of photosynthetic control. Firstly Giles Johnson (University of Manchester) investigates the proteomic changes that occur during dynamic acclimation. Finally Alex Webb’s lab (University of Cambridge) investigate how the products of photosynthesis feed into ethylene-dependent control of the circadian clock.

Kneeshaw S, Keyani R, Delorme-Hinoux V, Imrie L, Loake GJ, Le Bihan T, Reichheld JP, Spoel SH (2017) Nucleoredoxin guards against oxidative stress by protecting antioxidant enzymes.

PNAS Open Access

GARNet Chairman Steven Spoel (University of Edinburgh) leads this Franco-UK collaboration that investigated the role of the pathogen-induced oxidoreductase Nucleoredoxin 1 (NRX1) during the response to oxidative stress. They show that NRX1 targets a range of enzymes that are responsible for scavenging damaging cellular H2O2 and subsequently protect these enzymes from damage. This unexpected regulatory mechanism demonstrates a key role for NRX1 in protecting plants from the oxidative stress, which is an important component of the plants defence response.

Steven discussed this paper below. This audio is also on GARNet YouTube and iTunes channels.

Miller MAE, O’Cualain R, Selley J, Knight D, Karim MF, Hubbard SJ, Johnson GN (2017) Dynamic Acclimation to High Light in Arabidopsis thaliana Involves Widespread Reengineering of the Leaf Proteome Front Plant Sci. Open Access

Giles Johnson leads this collaborations between two departments from the University of Manchester that has looked at changes to the leaf proteome that occur under differing light conditions. Transferring leaves from low to high light conditions causes a process called dynamic acclimation, which is perturbed in gpt2 mutants. Proteomic analysis of wildtype and gpt2 leaves reveals that a similar number of proteins are changed during dynamic acclimation but the identify of these is altered, with a reduced abundance of proteins involved in photosynthesis. Interestingly gpt2 showed an increase in the number of proteins involved in the stress response.

In 2016 Giles talked to GARNet about a different paper that looks at cold acclimation in Arabidopsis.

Haydon MJ, Mielczarek O, Frank A, Román Á, Webb AA (2017) Sucrose and ethylene signaling interact to modulate the circadian clock. Plant Physiol. Open Access

Alex Webb (University of Cambridge) collaborates with Mike Laydon (previously at York, now at the University of Melbourne) on this study that links photosynthesis with circadian and hormone signalling. Previous work showed that GIGANTEA (GI) is necessary to maintain sucrose-dependent circadian oscillations in the dark. This extension of that work demonstrates that sucrose stabilises GI by altering the activity of the ZEITLUPE (ZTL) F-box protein, which is surprisingly dependent on the key ethylene signalling intermediate CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1). Over recent times the role of ethylene on control of the circadian clock has been overlooked but this study shows that the hormone can shorten the circadian period through the activity of sucrose and GI. This study integrates another signal into our understanding of the exquisite regulatory relationships that control clock function.

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Steven Spoel talks to GARNet

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Published on: August 10, 2017

Steven Spoel (University of Edinburgh and current GARNet chairman) talks to GARNet about a recent paper in PNAS entitled ‘Nucleoredoxin guards against oxidative stress by protecting antioxidant enzymes‘. Read more about Steven’s lab here.

Meeting Report: ICAR2017 in St Louis.

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Published on: August 4, 2017

Thanks to Janina Tamborski from The Sainsbury Lab in Norwich for providing this excellent meeting report!

The most exciting (and to some the scariest) part of a large scientific conference such as the International Conference on Arabidopsis Research (ICAR) is finding the right opportunity to talk to leading scientists. Sometimes it is all about thinking on your feet, as was the case for me when my colleague knocked my drink out of my hand, resulting in a soda fountain that splashed all bystanders. Luckily one of them was Wolfgang Busch, who I had been meaning to talk to after his exciting seminar but previously lacked an opportunity to approach. After I apologised, we had a very productive discussion, proving that you can make lemonade when life gives you lemons (or a lemonade fountain).

The 28th ICAR 2017 was held at the Hyatt and Donald Danforth Plant Science Center in St. Louis. With four keynote speakers, nine plenary, nine concurrent and two poster sessions, as well as six community organised workshops, it brought together many of the best scientists in Arabidopsis research. In addition to the five-day scientific program, there were also two career workshops for early career scientists that featured panellists from both academia and industry. The mixers afterwards offered career ideas and the opportunity to further expand ones’ professional network.

Image from @huotbethany

The four keynote speakers represented the wide range of topics pursued in Arabidopsis research: Sabeeha Merchant talked about a day in the life of Chlamydomonas, Mary Lou Guerinot about ionomics and gene discovery, Keiko Torii shared her latest breakthroughs in synthetic biology and Sheng Yang He wanted to achieve understanding of the disease-climate-microbiome triangle. Keiko Torii (Washington University) amazed the audience with her interdisciplinary approaches that arose from her close collaboration with researchers at the Institute of Transformative Bio-Molecules at Nagoya University. By engineering the auxin receptor TIR1 and creating a synthetic auxin ligand, she was able to show that the acid growth response is mediated by the TIR1 pathway. This is a prime example of how synthetic biology approaches can help us find answers to questions that have proven poorly tractable in genetics. Together with her screen of chemicals that influence stomatal patterning, her research promises to yield exciting results for us to watch out for in the future.

Of particular interest to me were the great talks on how Arabidopsis interacts with and manipulates its environment. Paul Schulze-Lefert’s (MPI Cologne) work focussed on the microbiome of Arabidopsis and in particular on the endophyte C. tofildiae and its ability to promote growth and reproductive success of Arabidopsis under phosphate-limiting conditions. A successful interaction requires the host to have a functioning phosphate starvation response system and the ability to suppress its innate immunity. Cara Haney (The University of British Columbia) identified 93 genes and 63 operons in P. fluorescens that are required for survival on Col-0. She furthermore compared bacterial strains that trigger Induced Systemic Resistance (ISR) or Induced Systemic Susceptibility (ISS) that are 98% identical in their 16S RNA. Her lab identified a gene cluster that differs in ISS strains and she proposed that the production of spermidine through polyamine synthases is responsible for ISS.

Niko Geldner (University of Lausanne) showed advances in understanding transport in the root and how the mutually exclusive localisation of lignin and suberin creates an active zone of uptake. Research from his group demonstrated that patchy transporter expression in roots correlates with the position of passage cells, forming a funnel-like pattern of cells to enable nutrient uptake in mature roots. Ute Kraemer (Ruhr University Bochum) unveiled how Arabidopsis thalianas’ relative A. halleri, who can thrive on metalliferous soils, prevents cadmium accumulation and poisoning of the seeds. This cadmium tolerance is associated with a sequence polymorphism in HMA2 that leads to an early stop codon and renders the protein non-functional. Gregory Vert uncovered how the metal transporter IRT1 controls its own stability through recruitment of CIPK23 after excess metal conditions. CIPK23 consequently phosphorylates the E3 ligase IDF1 that mediates IRT1s K63 ubiquitination and leads to its endocytosis and degradation in the vacuole.

I particularly enjoyed the session “Novel Approaches”, which showcased exciting tools from hormone biosensors (Alexander Jones, SLCU) to two-photon excitation microscopy (Minako Ueda, Nagoya University) and genome editing techniques (Dan Voytas, Minnesota Center of Genome Engineering). As a cell biologist, I could not help but be amazed by the images shown by Minako Ueda that showed cytoskeleton dynamics in the zygote in astonishing detail thanks to the high resolution achieved through two-photon excitation imaging.

Image from @huotbethany

The meeting was rounded off by the last keynote speaker Sheng Yang He (Michigan State University) who managed to convey complex immune resistance and susceptibility concepts in an accessible manner. He discussed his recent publication that showed that bacterial effectors promote pathogenicity by transforming the air-filled apoplast into an aqueous environment for bacteria to flourish. His elegant approach to engineer the common host target COI1 to break the evolutionary dilemma of salicylic acid signalling was a case-study in the success of rational design in synthetic biology.

The 29th ICAR2018 will be held from the 25-29 June in Turku, Finland. I am excited to see how Arabidopsis continues to evolve. I hope to see the changes made at ICAR2017 continue, including the shift in hormone research from auxin-dominated to a focus on other hormones, in particular the brassinosteroids. Synthetic biology approaches were emerging in all disciplines and ranged from novel biosensors to receptor engineering. For the first time there was also an exciting session on translational biology that I would like to see again next year. I cannot wait to see what the conference in Turku next year has to offer.

Arabidopsis Research Roundup: August 1st

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Published on: August 1, 2017

This weeks Arabidopsis Research Roundup has a tools-focus as it includes three papers that highlight new tools that are available to the plant science community. Silke Robatzek (TSL) leads research that has developed software for analysis of subcellular fluorescent markers whilst in a broadly similar area Mark Fricker (University of Oxford) is part of an international collaboration that characterises a tool that allows for analysis of intracellular ATP concentrations. Thirdly Phillip White (JHI) leads a consortium that has developed computer-assisted software to aid automated phenotyping. In the fourth paper Silke Robatzek again features as co-corresponding author with Richard Morris (JIC) in a study that mixes plant biology and computational analysis to model stomatal dynamics. Finally Christine Raines (University of Essex) leads research that has overexpressed a member of the photosynthetic apparatus that surprisingly results in plants with larger biomass and seed yield.

Faulkner C, Zhou J, Evrard A, Bourdais G, MacLean D, Häweker H, Eckes P, Robatzek S (2017) An automated quantitative image analysis tool for the identification of microtubule patterns in plants. Traffic. http:/​/​dx.​doi.​org/10.1111/tra.12505 Open Access

This research from The Sainsbury lab, Norwich and John Innes Centre includes Silke Robatzek as corresponding author as well as new faculty member Christine Faulkner as lead author. This paper documents the development of CellArchitect, which is an image analysis tool to track the movement of subcellular microtubule markers obtained using con-focal microscopy. They validated CellArchifect by treating with a variety of chemicals that alter microtubule dynamics. In addition they show that this software can be used to track actin or ER markers and as such should have broad utility for cell biology researchers particularly those that are undertaking often laborious chemical biology screens.

De Col V,, Fuchs P, Nietzel T, Elsässer M, Voon CP, Candeo A, Seeliger I, Fricker MD, Grefen C, Møller IM, Bassi A, Lim BL,, Zancani M, Meyer AJ,, Costa A, Wagner S, Schwarzländer M (2017) ATP sensing in living plant cells reveals tissue gradients and stress dynamics of energy physiology. Elife. http:/​/​dx.​doi.​org/10.7554/eLife.26770 Open Access

Mark Fricker (University of Oxford) is part of this international collaboration that have used a novel technique for visualizing ATP levels using a fluorescent biosensor in vitro, within isolated mitochondria and within intact seedlings. They demonstrate differing ATP concentrations within tissues, highlighting root hair cells. Induced hypoxia shows that there is significant plasticity in the cellular ATP concentrations and that these can be successful monitored using the biosensor tool.

Dupuy LX, Wright G, Thompson JA, Taylor A, Dekeyser S, White CP, Thomas WTB, Nightingale M, Hammond JP, Graham NS, Thomas CL, Broadley MR, White PJ (2017) Accelerating root system phenotyping of seedlings through a computer-assisted processing pipeline. Plant Methods.

http:/​/​dx.​doi.​org/10.1186/s13007-017-0207-1 Open Access

Phillip White (James Hutton Institute) and collaborators at the University of Nottingham have developed this computer-assisted pipeline designed to facilitate the phenotyping of plant roots. This can be scaled up for plants of different sizes and thus has broad utility. This software rapidly extracts root traits from image data, a process that can be a bottleneck in the screening process. This software complements parallel attempts that have developed automated platforms for sample preparation and handling.

Woolfenden HC, Bourdais G, Kopischke M, Miedes E, Molina A, Robatzek S, Morris RJ (2017) A computational approach for inferring the cell wall properties that govern guard cell dynamics. Plant J. http:/​/​dx.​doi.​org/10.1111/tpj.13640 Open Access

Richard Morris (John Innes Centre) and Silke Robatzek (The Sainsbury lab, Norwich) are the corresponding authors on this study in which they collaborate with Spanish colleagues. They investigate how different attributes of guard cell walls are responsible for the opening and closing of stomata. By considering the cell wall as a composite of a pectin rich matrix embedded within cellulose microfibrils they predict the movements that are responsible for stomatal dynamics. They validate their predictions using Arabidopsis mutants and they to show that stomatal opening/closing is brought about by a mix of hoop reinforcement and strain-stiffening resulting in anisotrophic growth.

Simkin AJ, McAusland L, Lawson T, Raines CA (2017) Over-expression of the RieskeFeS protein increases electron transport rates and biomass yield. Plant Physiol.

http:/​/​dx.​doi.​org/10.1104/pp.17.00622 Open Access

GARNet committee member Christine Raines (University of Essex) leads this study in which they have generated plants that overexpress the Rieske FeS protein (PetC), which is a component of the cytochrome b6f (cyt b6f) complex. These plants show equivalent increases in both proteins within the cytochrome b6f complex and more surprisingly within members of PSI and PSII. The mechanisms that explain these changes are currently unknown but these plants offer an exciting tool in order to study multiple aspects of photosynthetic biology. Perhaps more importantly these plants show increased biomass and seed yield indicating that manipulation of these proteins in crop plants might be important for developing higher yielding varieties.

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