UC Berkeley

Secondary metabolites, or natural products, are small molecules which frequently possess biological activities and are a critically important resource for the development of new pharmaceuticals, pigments, and agrochemicals. The need for new natural product sources has led to the genomics-driven identification of the anaerobes as a promising and relatively untapped reservoir of natural product diversity. Soil isolates such as the industrially significant solventogenic clostridia are obligate anaerobes which can ferment carbohydrates to produce acetone and butanol. These bacteria are an especially promising subset of the anaerobes for discovery of natural products. This work begins with a description of the limited repertoire of known natural products isolated from anaerobes, showcasing their chemical diversity and broad range of bioactivity. Then, we describe genome mining efforts in different solventogenic clostridia. In Clostridium saccharoperbutylacetonicum, we describe genome and transcriptome profiling of secondary metabolite biosynthetic gene clusters (BGCs) to enable in-depth characterization of a nonribosomal peptide synthetase conserved in other solventogenic clostridia. This led to the discovery of a novel compound, an N-acyl dipeptidyl alcohol. We further discuss the association of the biosynthetic gene with butanol tolerance, a phenotype with industrial significance. In Clostridium roseum, we describe methods for gene delivery to enable targeting of BGCs for knockout and characterization. The products of one BGC are reported, a novel family of unusual solvatochromic compounds named the clostyrylpyrones. The biosynthesis of these compounds is proposed. In a broader survey of secondary metabolism in clostridia, we describe efforts in a panel of ten species of clostridia to identify antimicrobial potential using a traditional disc-diffusion approach. We also describe, for two of the strains, implementation of a high-throughput media screening study to identify BGC-specific chemical inducers of secondary metabolism. Overall, this work expands the known chemical diversity of natural products derived from anaerobes, supports the value of targeting these bacteria for genome mining, and extends our understanding of secondary metabolism in solventogenic clostridia.