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.
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