The wrong plant?

Many of us here at the John Innes Centre and the Sainsbury Laboratory use the model plant Arabidopsis thaliana for our research. Its small size, simple genome and rapid lifecycle make it an ideal model in many disciplines within plant science. From leaf development to interactions with pathogens, the wealth of resources available to Arabidopsis researchers makes it an invaluable system.

Arabidopsis_thaliana_inflorescencias

Arabidopsis – the perfect model or the wrong answer?

But James Lloyd, a PhD student at the University of Leeds, and his supervisor, Brendan Davies, have shown there to be a slight problem in using the plant.

The group is looking at nonsense-mediated mRNA decay (NMD) – a mechanism used by eukaryotes for regulating gene expression. In animals, this mechanism relies on a protein called SMG1. But this was thought to be an animal-specific pathway: the SMG1 gene had not been identified in fungi or in Arabidopsis.

It seems, however, that our favourite model is rather unusual in its lack of SMG1. The group managed to identify SMG1 in all the other plants that they looked at. Discussing the research, published in The Plant Journal, Davies said: “Everybody thought that this protein was only in animals. They thought that because, basically, most of the world studies one plant: Arabidopsis thaliana.”

A. thaliana appears to be a complete anomaly in this respect. The protein was even found in its close relative Arabidopsis lyrata, suggesting a loss of function as recently as 5-10 million years ago.

Arabidopsis thaliana, or thale cress, was first described by Johannes Thal in the 16th century. It was first proposed as a model organism for studying plant genetics by Friedrich Laibach in 1943, and has been an integral part of plant molecular genetics work since the late 1970s.

While he looks towards examining what alternatives Arabidopsis and fungi have found to SMG1, Davies is keen not to dishearten his fellow plant scientists: “It is still a fantastically useful model. We would not be anywhere close to where we are in understanding plant biology without it.” But he warns that the research highlights the importance of using a range of models when studying plant processes. “Evolution does strange and unpredictable things,” he said.

And, of course, a diversity of model species exists already within plant science research. From Medicago truncatula’s use as a model for root nodulation to the rise and rise of Brachypodium as a model cereal, research at the John Innes Centre certainly isn’t restricted to the humble thale cress!

The research paper can be found here: dx.doi.org/10.1111/tpj.12329

More information on Professor Davies’ lab homepage (http://www.plants.leeds.ac.uk/people/groups_dav.php) and the Arabidopsis Information Resource’s guide to the plant (http://www.arabidopsis.org/portals/education/aboutarabidopsis.jsp).

by Mabon Elis – a first year PhD student in the lab of Enrico Coen

Advertisements

Featured Scientist (II): Prof Kazuki Saito

We were fortunate to have Professor Kazuki Saito, the deputy director of the RIKEN Plant Science Center, and Group director of the Metabolomic Function research group, give a seminar on his work in plant metabolomics at the John Innes Centre. Professor Saito is a leading scientist in the area of metabolomics based functional genomics. The ‘-omics’ technologies are a dominant force in science. They developed as a result of the adaptation of high-throughput technologies to measuring biological samples, together with the ability to effectively store all the data accumulated. Metabolomics is the field of science which identifies all the metabolites (small molecules) within a cell, tissue or biological species, and thereby provides its chemical fingerprint. Functional genomics tries to take the wealth of sequence data, gene expression data (transcriptomics), and protein expression data (proteomics) of a biological sample that is available to understand gene and network function at a holistic level. By combining metabolomics and functional genomics, it is possible to see how changes in gene and protein levels may impact the chemical fingerprint of a biological sample. In doing so this can lead to the identification of novel genes that produce interesting metabolites, as well as an overarching appreciation of how metabolic networks are regulated.

During the student lunch we discussed developments in the field of plant secondary metabolism, where Prof Saito thought key breakthroughs would be in metabolomics, as well as the technological advances in this field. We were also able to discuss the opportunities for post-doctoral fellows in Japan, and Prof Saito emphasised the multi-cultural nature of the RIKEN institute.

Prof Kazuki Saito (image courtesy of http://www.metabolomicssociety.org)

Prof Kazuki Saito (image courtesy of www.metabolomicssociety.org)

 Can you give me 3 words that best describe your work

If you ask me the interest of my work, I would say ‘plant chemical diversity’

If you weren’t a scientist what would you be?

An archaeologist, which was my dream when I was a kid.

Where have you studied/countries you have lived in?

Japan and Belgium.

What was your route to project leader?

My route is one of the typical ways for a natural scientific scholar in Japan. After obtaining a Ph. D., I served as a research associate in two Universities (similar to post-doc level), trained in a foreign country (Belgium) as a visiting fellow (post-doc), I went back to a Japanese university as a faculty member, and then climbed positions, from lecturer, associate professor to full professor and group director.

Which part of your work are you most proud of?

I am proud that we could show, for the first time, the proof-of-concept for functional genomics by integration of transcriptomics and metabolomics in plants. In fact, a series of these papers (PNAS, 101, 10205 (2004), Plant J., 42, 218 (2005), JBC, 280, 25590 (2005), PNAS, 104, 6478 (2007)) are highly cited. In older days, the very first molecular cloning of cysteine synthase from plants (PNAS, 89, 8078 (1992)), which was actually the first molecular cloning of genes in sulfur metabolism, is one of my proudest works.

 What was your “big break” career-wise?

In 1987, I had a big chance to join the lab of Prof. Marc Van Montagu in Ghent, Belgium. Until that time, I had no experience of plant molecular biology at all and had only been experienced in biochemistry and bioorganic chemistry, spanning plants, microorganisms and animals. However, before choosing my stay away from a University in Japan for a year, I was fully convinced that I had to be involved in molecular biology of plant secondary metabolism, which had never been developed yet. Therefore, I was very much eager to join to Marc’s lab, and luckily though the connection of my supervisor I could finally join his group in Ghent (thanks Marc!). This was really a big break for my career. Since then I have been able pave the way for my own research, on which I am still working and will pursue in future as well.

 What’s the best advice you would give to an early career scientist

Have a dream – organize yourself – work hard – stay on target – enjoy yourself –keep the faith

by Richard Payne – a second year PhD student in the lab of Prof Sarah O’Connor