Combining microbial functional metagenomics and Caenorhabditis elegans genetics to uncover and characterise novel bioactive compounds

Abstract

Marine bacteria produce a wide array of biologically active metabolites involved in defence strategies and pathogenesis against a range of metazoans target organisms. In return bacteriovorous metazoans, including nematodes, have developed sophisticated strategies to neutralise or avoid such bioactives. The overall objective of this study was to investigate the antagonistic activities of bacteria-eukaryote interactions.

The first aim of this thesis was to develop a novel functional (meta) genomic screen for the identification of inhibitors that target the nematode Caenorhabditis elegans. Environmental DNA from marine habitats was expressed in Escherichia coli and the resulting functional (meta) genomic libraries were screened by selective grazing of the nematode C. elegans, in a simple, rapid, high-throughput manner.

Next, this project aimed at characterizing antagonistic activities that target C. elegans and study their toxic effect in the nematode. Genetic and microscopic analysis uncovered known and novel bioactive compounds including the small molecules tambjamine and violacein, which appear to facilitate bacterial colonisation and induce apoptosis in the nematode. An array of genes and gene products involved in antinematode activities was also identified including a gene encoding for a novel protein involved in a fast killing activity.

Finally, this study investigated the sophisticated strategies that the nematode mounts to neutralize or avoid bacterial toxic compounds. The role of both C. elegans behavioural and immune system strategies in mediating the nematode defence in response to toxic bacterial compounds were investigated. In the nematode, a complex behavioural strategy known as aversive learning is employed to avoid violacein toxicity. When noxious violacein cannot be avoided, the toxic compound appears to activate the insulin-like signaling cascade, an evolutionary conserved innate immunity pathway.

In summary, this work combines functional (meta) genomics and C. elegans genetics to identify bioactive compounds from marine bacteria and uncover animal defence strategies in response to bacterial secondary metabolites.