S35: Exploiting Functional Metagenomics: New Genes From Across A Wide Thermal Landscape

Metagenomic gene discovery provides an effective approach for accessing genomes and genes from the ‘uncultured microbial majority’, and offers realistic opportunities for accessing new areas of ‘sequence space’, ‘function space’ and even ‘structure space’. In conjunction with large-insert fosmid vector systems, we have successfully identified a range of enzyme genes which show high levels of sequence novelty. The screening of thermophile metagenome expression libraries for the enzymes involved in the degradation of lignocellulosic substrates resulted in the identification of a range of cellulase and ‘hemicellulase’ genes. Many of these genes show low to moderate nucleotide homologies with published sequences. The expression and functional characterization of these gene products contributes to the long term objective of developing optimised enzyme cocktails for efficient saccharification of specific lignocellulosic feedstocks. Using the same libraries but with a complementation screening approach, we have successfully identified genes implicated in bacterial stress adaptation. A novel bacterial Water Hypersensitivity protein showed substantial in vivo and in vitro functional complementation, with dramatic enhancement of E. colisolute resistance and stabilisation of purified enzymes to freeze-thaw inactivation. We suggest that, while metagenomic gene discovery offers must wider scope than can be achieved by classical culture-dependent methods, it retains substantial limitations imposed by available technology.  Here we discuss the future developments (and requirements) of expression screening in order to more effectively gain access to full metagenomes.

The author gratefully acknowledges the University of Pretoria, the National Research Foundation of South Africa and the Technology Innovation Agency for financial support.