UC San Diego

The production of secondary metabolites is a fundamental way that bacteria interact with their environments, yet little is known about the fitness benefits conferred by specific molecules or the dynamics influencing the distribution of biosynthetic gene clusters among bacterial lineages. This dissertation consists of six chapters that address these topics in an unusual class of secondary metabolites called hybrid isoprenoids (HIs). The first chapter introduces microbial chemical ecology and secondary metabolism, followed by four research-oriented chapters and a summary chapter. Chapter 2 presents a literature review of the distribution of HI production within the actinobacterial genus Streptomyces. Reports of HI production were phylogenetically very scattered, with the exception of a putative marine Streptomyces lineage called the 'MAR4' clade. Following from this, Chapter 3 presents an in-depth study of the phylogenetic diversity of the MAR4 clade. Sequence data from a variety of sources led to a considerable expansion of the MAR4 clade, and representative strains were shown to produce 1-4 classes of HI molecules, an ability that is unmatched elsewhere in the streptomycetes. Chapter 4 presents an analysis of 120 Streptomyces genomes, including 12 MAR4 strains, which provides strong support for the hypothesis that this clade is enriched in gene clusters for HI production. Phylogenetic analysis of a HI biosynthesis gene suggest that vertical inheritance, horizontal gene transfer, duplication followed by functional divergence, and gene rearrangements have all contributed to the striking number of HI gene clusters found in MAR4 genomes. The final research chapter addresses the fact that none of these molecules have an experimentally characterized natural function, which is a major obstacle to understanding the unusual distribution of HI gene clusters. Because many HIs resemble characterized electron shuttles, the hypothesis that they function in redox cycling was explored. A redox- active pigment that was upregulated in low-oxygen conditions was isolated from a MAR4 strain. This compound was identified as an intermediate in a HI gene cluster, which largely goes to completion in aerobic culture. This provides an unusual example of how a single biosynthetic cluster can be used to generate products with distinct properties depending on culture conditions