Arabidopsis Research Roundup: August 27th

The Arabdopsis Research Roundup broadens its remit this week. As well as including three original research papers, which look at casparian strip formation, light and hormone signaling, we also highlight an important viewpoint article that aims to set standards for synthetic biology parts. In addition we include a meeting report from a plant synthetic biology summer school and interviews with plant scientists at the JIC, Caroline Dean and Anne Osbourn.

Kamiya T, Borghi M, Wang P, Danku JM, Kalmbach L, Hosmani PS, Naseer S, Fujiwara T, Geldner N, Salt DE (2015) The MYB36 transcription factor orchestrates Casparian strip formation Proc Natl Acad Sci USA http://dx.doi.org/10.1073/pnas.1507691112 Open Access

GARNet Advisory Board Chairman David Salt (Aberdeen) leads this international collaboration that looks at the (relatively) poorly understood Casparian strip (CS), a lignin-based filter that lies in root endodermal cells. Formation of the CS is initiated by Casparian strip domain proteins (CASPs) that recruit other proteins, which begin the process of lignin deposition. In this study the authors look upstream this process and identify the transcription factor MYB36 that directly regulates expression of CASPs and is essential for CS formation. Ectopic expression of MYB36 in root cortical tissues is sufficient to stimulate expression of CASP1-GFP and subsequent deposit a CS-like structure in the cell wall of cortex cells. These results have implications for the design of future experiments that aim to control how nutrients are taken up by the plant as even though myb36 mutants have a ‘root-defect’, they also have changes to their leaf ionome.

Sadanandom A, Ádám É, Orosa B, Viczián A, Klose C, Zhang C, Josse EM, Kozma-Bognár L, Nagy F (2015) SUMOylation of phytochrome-B negatively regulates light-induced signaling in Arabidopsis thaliana Proc Natl Acad Sci USA http://dx.doi.org/10.1073/pnas.1415260112 Open Access

Ari Sadanandom (Durham) and Ferenc Nagy (Edinburgh) are the leaders of this study that investigates the precise function of the PhyB photoreceptor protein. PhyB interacts with a wide range of downstream signaling partners including the PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors. The small ubiquitin-like modifier (SUMO) peptide is conjugated to larger proteins to bring about a variety of signaling outcomes. In this case the authors find that SUMO is preferentially attached to the C-term of PhyB under red light conditions, a relationship that occurs in a diurnal pattern. SUMOylation of PhyB prevents interaction with PIF5 whilst the OVERLY TOLERANT TO SALT 1 (OTS1) protein likely de-SUMOlyates PhyB in vivo. Altered levels of PhyB SUMOylation cause distinct light-responsive phenotypes and as such this paper adds another level of regulation to the already complex known network that controls light signaling.

Schuster C, Gaillochet C, Lohmann JU (2015) Arabidopsis HECATE genes function in phytohormone control during gynoecium development Development. http://dx.doi.org/10.1242/dev.120444 Open Access

Christopher Schuster who is now a postdoc based at the Sainsbury lab in Cambridge is the lead author on this investigation into the role of the HECATE (HEC) family of bHLH transcription factors on fruit development in Arabidopsis. During this process HEC proteins are involved in the response to both the phytohormones auxin and cytokinin, the authors proposing that HEC1 plays an essential role in Arabidopsis gynoecium formation.

Patron N et al (2015) Standards for plant synthetic biology: a common syntax for exchange of DNA parts New Phytologist http://dx.doi.org/10.1111/nph.13532 Open Access

Carmichael RE, Boyce A, Matthewman C Patron N (2015) An introduction to synthetic biology in plant systems New Phytologist http://dx.doi.org/10.1111/nph.13433 Open Access

Although not strictly based on Arabdopsis work, there are a couple of articles in New Phytologist that have broad relevance to plant scientists who are interested in plant synthetic biology. In the first of these Nicola Patron (The Sainsbury Laboratory) leads a wide consortium that aims to set parameters for the standardisation of parts in plant synthetic biology. It is hoped that as the principles of synbio are used more widley in the plant sciences that the proposals in this paper will serve as a useful guide to standidise part production. GARNet has recently written a blog post on this topic.
SynBioWorkshopPic
The associated meeting report looks at the use of plant synthetic biology in a teaching context with a synopsis of the ERASynBio summer school hosted by John Innes Centre. In this event, young researchers from a range of backgrounds were introduced to the power and potential of plant synthetic biology through a diverse course of lectures, practical session and group projects.

 

Vicente C (2015) An interview with Caroline Dean Development http://dx.doi.org/10.1242/dev.127548 Open Access

An interview with Anne Osbourn (2015) New Phytologist <a href="http://dx.doi acheter cialis.org/10.1111/nph.13616″ onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘http://dx.doi.org/10.1111/nph.13616’, ‘http://dx.doi.org/10.1111/nph.13616 ‘]);” target=”_blank”>http://dx.doi.org/10.1111/nph.13616 Open Access

These are interviews with eminent female plant molecular biologists who both work at the John Innes Centre. Caroline Dean’s lab focuses on the epigenetic mechanisms that regulate vernalisation whilst Anne Osbourn is interested in using synthetic biology approaches to engineer metabolic pathways for the production of novel compounds.

Plant synthetic biology takes centre stage

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Published on: October 27, 2014

On Monday and Tuesday last week I was at the Marriott Heathrow for the Global Engage Synthetic Biology Congress. Plant synthetic biology had a dedicated track, and while this meant I regretted missing some talks in the other sessions, it did enable me to be suitably impressed at the quality of plant synthetic biology research, mostly coming from the UK and Europe, and its exciting range of applications.

Plant synthetic biology at Global Engage

A highlight for me was Matias Zurbriggen’s excellent presentation on using plant signalling pathways to remotely control mammalian cells. His objective is to understand plant pathways by reconstructing them in other systems, and via research on phytochromes he has developed a tool to remotely control gene expression in mammalian cells (1) and a light-controlled switch for plant cells (2).

Birger Lindberg Møller gave an interesting and accessible talk about plant synthetic biology for high value product (HVP) synthesis. Whatever your level of expertise, if you’re interested in this area I recommend you watch this earlier version of his talk.

Continuing the HVP theme were Brian King, Vincent Martin and plenary speaker Jules Beekwilder. They all aim to make HVPs using simple chassis instead of relatively energy-intensive, and often inefficient, plants. (more…)

Plant synthetic biology in Europe

Categories: GARNet, synthetic biology
Comments: 1 Comment
Published on: May 20, 2014

Helsinki

On 8-9 May I attended a meeting hosted by PlantEngine to discuss the idea of a synthetic biology repository in Europe. The presentations were varied and interesting, and hopefully the other delegates enjoyed mine (PDF) too,

The meeting was at VTT in Espoo, a city very close to Helsinki. The local host Heiko Rischer gave a brief introduction to VTT, which is a Finnish institute but has bases all over the world. VTT is very separate from the university system, and although fundamental research gets done there it has a big commercial focus and strong links to Finnish industry. For example, VTT developed Arctic cloudberry stem cell technology for cosmetics with the R&D team from Finnish skincare company Lumene Oy.

PlantEngine itself was introduced by lead PI Heribert Warczecha. It is a European network focused on enhancing capacity in plant metabolic engineering by activities like defining target pathways, disseminate new technologies, and setting standards. There are currently over 70 labs in 23 EU countries in the network. They run training schools and workshops, and fund short-term scientific missions – check it out if you’re looking for funding for a short research trip to another lab.

One of PlantEngine’s aims is to explore synthetic biology for engineering plant products, which is the reason for the meeting I attended. (more…)

Golden Gate cloning: Tips and resources

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Published on: May 14, 2014

goldengate

Last week I was in Helsinki for a plant synthetic biology meeting, and I learned a lot about existing European synbio tools, resources and research. There’s a short Storify of Tweets from the meeting here, and I’ll do a round-up post very soon. But today I’m highlighting a tool presented at the workshop, which was also presented at our SynBio workshop last year and at PlantSci 2014 but still hasn’t really featured on this blog (rather remiss of me, I know).

The Golden Gate cloning and related MoClo systems were presented (PDF) by one of its inventors, Sylvestre Marillonnet, at our synbio workshop last year. Sylvestre has worked with Nicola Patron, Head of Synthetic Biology at The Sainsbury Laboratory, to make a MoClo toolkit and set of parts available on Addgene. The toolkit includes 39 parts encoding promoters and 5′ untranslated regions; antigenic tags; sub-cellular localisation signals; reporter genes; selectable marker genes; terminators; 3′ untranslated regions; a suppressor of silencing; and two linkers.

Unfortunately the paper describing the toolkit is behind a paywall, but I’ve been tipped off as to where to find all the practical information you need:

1. The supplementary data is accessible to anyone, and it is very informative. SD 2 and 4 list modules in the toolkit and parts kit respectively.

2. Nicola’s website, Synbio@TSL, has pages on how Golden Gate cloning works, making modules, and an assembly protocol.

3. Nicola presented the toolkit at PlantSci 2014 in May and her poster gives a good overview of the paper’s content: GG_Plant_Kit_Poster

Nicola has generated many other parts, which are listed on her website. Some of them can be obtained from Addgene, while others have to be requested from her lab. Synbio@TSL also has a nice introduction to synthetic biology, synthetic biology news, links to online resources and synbio centres, and guides to the major genome editing and DNA assembly techniques.

GoldenBraid is another modular cloning technique which has its own web resources and toolkit available. There’s a guest post coming up soon about that one though so no spoilers here!

The Golden Gate Toolkit is published in: Engler C, Youles M, Grüetzner R, Ehnert T-M, Werner S, Jones JDG, Patron N, Marillonnet S. (2014) A Golden Gate Modular Cloning Toolbox for Plants. ACS Synthetic Biology DOI: 10.1021/sb4001504

The MoClo system is published in: Weber E, Engler C, Gruetzner R, Werner S, Marillonnet S (2011) A Modular Cloning System for Standardized Assembly of Multigene Constructs. PLoS ONE 6(2): e16765. doi:10.1371/journal.pone.0016765

The GoldenBraid system was most recently published as: Sarrion-Perdigones A, Vazquez-Vilar M, Palací J, Castelijns B, Forment J, Ziarsolo P, Blanca J, Granell A, Orzaez D. (2013) GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology. Plant Physiol. 2013 162: 1618-1631. doi:10.1104/pp.113.217661

Image credit: Nicola Patron

Report launch: Developing Plant Synthetic Biology in the UK

Categories: GARNet, synthetic biology
Comments: No Comments
Published on: March 31, 2014

plant synthetic biology

 

We’ve been working on the meeting report from last year’s An Introduction to Plant Synthetic Biology workshop for months, so we’re delighted that GARNet Chair Professor Jim Murray is going to launch it tomorrow during his talk at PlantSci 2014!

You’ll be able to download the report, Developing Plant Synthetic Biology in the UK: Opportunities and Recommendations tomorrow on the GARNet website, or if you’re at the conference come and see Jim, Lisa or Charis to get a printed version.

To keep up with all the news from PlantSci 2014, follow #PlantSci2014

Opportunities in plant science, via social media

Categories: Arabidopsis, Workshops
Comments: No Comments
Published on: March 5, 2014

I don’t usually put this kind of thing on the blog – it’s prime mailing list fodder. But I was writing a round-up post and this section got more than long enough for its own post!

If you’re on our ArabUK mailing list, you’ve probably noticed a flurry of activity this week. There are a lot of post-doc and other job opportunities out there at the moment – Oxford Brookes, Warwick, Birmingham and East Malling research are all recruiting. Further afield, I’ve spotted Arabidopsis post-doc vacancies in Wageningen and Alabama.

There are also two  fully funded workshops open to applications from early career researchers at the moment. Erik Murchie is co-organising a workshop in Thailand (Thailand!) and is looking for post-docs who work on abiotic stress physiology and genetics. Successful applicants will work with rice researchers from Thailand at a 4-day workshop, with the aim of improving understanding of oxidative stress in rice. Apply by 1 May.

Secondly, this synthetic biology summer school in Berlin looks like a great opportunity for PhD students and post-docs working on, or are on the periphery of, synthetic biology. It sounds like an interesting 5 days discussing how to ‘evaluate new techno-scientific areas’ and ‘analyse the societal dimensions of synthetic biology’. As an aside, if you get selected I highly recommend the Alternative Tour of Berlin – it might even give you some ideas for the workshop! This one is a tight deadline, applications close on 10 March.

All of these, including the job at Warwick, for which the advertiser is across the corridor from me, crossed my path on Twitter. If you’re looking for a job or training opportunities and/or want to keep up with news from the community, Twitter is definitely a good place to start. Just follow the right people – try the GARNet accounts (obviously! Me, Lisa, Ruth) and also Mary Williams, Anne Osterrieder, BSPP and UKPSF. Anne even has lists of categorised tweets, a great place to find relevant Twitter users.

You can just use Twitter for harvesting information. You don’t even have to fill out your profile, though you do need a username. But it can be a valuable tool for networking and the ‘branding’ that careers advisors sometimes talk about. Anne has a great paper in Plant Methods about how to use social media as a plant scientist. I use it to share plant science and occasional sci-fi links I come across that I think others will find interesting – if I read an article or paper, attend a good talk, or see a plant science job opportunity or conference.

Photosynthesis for fresh water

Comments: 6 Comments
Published on: February 10, 2014

Annegret Honsbein is a post-doc in Anna Amtmann‘s lab at the University of Glasgow. As she explains in this guest post, she is working on an EPSRC project that hopes to harness the power of photosynthesis to desalinate sea water. 

Water covers more than 70% of Earth’s surface but less than 2% of it is available as freshwater. Many of the driest regions of our planet are close to the sea but irrigating fields with seawater – even if diluted – leads to build-up of salt in the soil to levels toxic to all common food crops. Current desalination technologies, such as membrane-based reverse osmosis, are successfully used in large-scale desalination plants, but they are expensive and energy inefficient.

desalinationOur multi-disciplinary EPSRC-funded project takes a synthetic biology approach to the development of an innovative desalination technology based on biological processes. We are a team of biologists and engineers from the Universities of Glasgow, Sheffield, Newcastle, Robert Gordon University at Aberdeen and Imperial College London, led by Dr. Anna Amtmann from Glasgow University.

Our idea is solar energy-fuelled desalination – with a twist. Instead of using solar panels we intend to let photosynthetic microorganisms desalinate the sea water. Cyanobacteria are ideal candidates, and we are currently working with two strains that are naturally able to adapt to a wide range of salt concentrations from fresh to sea water.

In principle, salt is toxic to all living cells, which is why most living systems have developed means to actively export sodium. In some cyanobacteria species that grow to very high densities, this ability means they actually form a low-salt reservoir within their saline environment.

We intend to use this low-salt reservoir as ion exchanger to extract the salt from the surrounding seawater. We aim to engineer cyanobacteria so we can switch off the endogenous salt export mechanism towards the end of their growth cycle, and activate a synthetic intracellular sodium accumulation unit. This synthetic unit will be assembled from membrane transport proteins evolved by different organisms to import sodium and chloride ions.

Our team’s engineers are developing techniques to manipulate the surface properties of the cyanobacteria and effectively separate the ‘salty’ cells from the desalinated water before they die, preventing release of the accumulated salt back into the ‘fresh’ water.

The final stage of the project will be to build a model version of the actual plant that could house our photosynthesis-driven bio-desalination process.

This work is published in: Jaime M. Amezaga, Anna Amtmann, Catherine A. Biggs, Tom Bond, Catherine J. Gandy, Annegret Honsbein, Esther Karunakaran, Linda Lawton, Mary Ann Madsen, Konstantinos Minas and Michael R. Templeton (2014) Biodesalination: A Case Study for Applications of Photosynthetic Bacteria in Water Treatment. Plant Physiology 164: 1661-1676; doi: http:/​/​dx.​doi.​org/​10.​1104/​pp.​113.​233973.

Image c/o Annegret Honsbein.

Biology by design

Categories: synthetic biology
Comments: No Comments
Published on: July 11, 2013

 

At the moment I’m reading a lot about synthetic biology (GARNet report and paper to come in the next few months) and it’s all technical stuff – genome assembly, online resources, transformation methodologies. Synthetic biology is the application of engineering principles to biology, so it’s natural that the technical challenges and ingenious solutions take centre stage.

But engineering isn’t all about building things that work. It’s also about the way things look. How much do synthetic biologists consider the aesthetics of their product? Do they need to?

In May, Daisy Ginsberg gave a talk at Warwick and argued strongly that aesthetics are a crucial part of synthetic biology. She is an artist and designer who works with scientists, including iGEM teams, to develop design principles in scientific research.

I think the idea of bringing art and science together to create beautiful, functional plant products is exciting in itself, and certainly another perspective to consider when planning a plant synthetic biology project. But a great aesthetic experience will also be very important when it comes to marketing and selling synthetic biology products, which is the ultimate goal for synthetic biology investors, and many scientists too.

Have a look at Synthetic Aesthetics, a joint project including scientists and artists run by the University of Edinburgh and Stanford University, in you are interested in aesthetics and design in synthetic biology. This recent article by Daisy on the ‘pre-future’ of synthetic biology is worth a read too.

The next time I blog it will be from Plant Biology 2013 – if you’re going, I hope to see you there!

Image credit: ‘Growth Assembly‘ by Alexandra Daisy Ginsberg and Sascha Pohflepp, illustration by Sion Ap Tomos.

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