Research

Ecological genetics

Understanding the function of organisms in their natural environment is the goal of many biologists. For organisms that are the size of birds progress can be made by observation alone, but in the absence of readily observable phenotypes microbiologists have taken to detecting changes in patterns of gene expression.  Genes expressed in one environment, but not in another are likely to encode traits relevant to the former environment, but not the latter.  Understanding the biological significance of these traits, their contribution to ecological performance and the regulatory networks that control their expression is central to our interests.

The bacterium that is (and has been) the focus of much of this research is Pseudomonas fluorescens SBW25. It is a plant colonizing bacterium that was originally isolated from the phyllosphere of a sugar beet plant, but it is equally at home in the rhizosphere. In fact it has a remarkable ability to colonize pretty much any part of a plant: 10 cells applied to a non-sterile (clay coated) sugar beet seed placed in non-sterile soil manages to multilpy to ~10^8 cells within 1 week.

In order to understand the mechanistic basis of SBW25's ecological performance a promoter trapping strategy known as IVET was devised and applied (the acronym stands for in vivo expression technology and was coined by Mike Mahan and colleagues (see Science 1993 259, 6860)). This strategy -- initially based on pantothenate auxotrophy (panB), but later (and more powerfully) based on diaminopimelate and lysine auxotrophy (dapB) -- has led to the identification of genes displaying elevated levels of expression in the plant environment (see Rainey 1999 Env Microbiol 1, 243 and Gal et al 2003 Mol Ecol 12, 3109). 

A good deal of work by a number of people over the last 10 years has provided much insight into the biological function and ecological significance of some of these plant / rhizoshere / phyllosphere-specific genes (see papers listed under 'ecological genetics' in publications). Indeed, for several of these loci we have gained some quite considerable insight, but it has been a slog. A particular challenge has been dealing with potentially interesting genes (for example the set that encodes an atypical type three secretion system) for which we have had little by way of concrete laboratory phenotype to get our teeth into. This is of course the downside -- or at least the highly challenging side -- of any attempt to understand the function of traits expressed in the wild: by definition, these traits are silent in the lab. A very staunch example of the effort required to make progress when phenotypes are subtle is in Jackson et al (2005) J Bacteriol 187, 8477; Zhang et al (2004) Microbiol 150, 2889 provides a further example.

More recently we (largely Steve Giddens, Rob Jackson and Christina Moon: see PNAS 104, 18247) described a genetic approach involving suppressor analyses for which we coined the term SPyVET (it is an extension of the IVET approach) that allows direct insight into phenotypes and regulatory networks that operate to control the expression of various traits expressed in the environment where the organism naturally resides. This has already allowed a good deal more progress than had previously been possible. Examples from on-going work include the cellulose-encoding wss operon and its regulatory ties with flagella mediated motility (with Rob Jackson) and the genes involved in copper homeostasis, pyoverdine production, histidine uptake and utilization and regulatory co-ordination of cellular carbon and nitrogen metabolism ((see Xue-Xian Zhang and the genetics of hut).

In addition to our IVET-dependent approach to ecological genetics we have long wanted to understand one particular locus to the extent that we could duplicate the efforts of Tony Dean and Dan Dyhuizen who examined the ecological significance of allelic variants in the lac operon. We are now in such a position with regard to our understanding of the histidine uptake and utilization locus. Hao Chang has begun to document and unravel some quite remarkable polymorphism (particularly in transporters) at the population level and this stands to develop into a significant area of our investigations.

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