UC Berkeley

Streptomyces coelicolor is a soil-dwelling prokaryote representative of an order of Gram-positive filamentous bacteria designated Actinomycetales, the richest known bacterial source of bioactive natural products. These specialized / secondary metabolites (including macrolides, aminoglycosides, tetracyclines, cephalosporins and polyketides) often have potent anti-microbial activity and, hence, have been a staple of modern medicine. Genome sequencing has revealed that a given actinomycete genome encodes the potential biosynthetic capacity to produce from 10 to 30, or even more, distinct natural products. S. coelicolor is a model organism for studying actinomycete development, genetics, and specialized metabolism. However, in its natural environment, S. coelicolor must engage with a heterogenous and complex collection of other microorganisms, as well as with abiotic factors in soil. Therefore, in the research described in this dissertation, I explored the role of interspecies interactions in regulating the production of specialized metabolites by S. coelicolor. To obtain insight about how production of these compounds is induced, I exploited the fact that S. coelicolor produces two, readily visualized, red-colored antibiotics (actinorhodin and undecyl-prodigiosin), but only when placed in close contact to certain other bacterial genera. I used extensive analysis of gene expression (RNA-seq) during interspecies interactions and, thereby, identified involvement of conservon8 in controlling induction of the red-colored antibiotics. A conservon is an operon so named because it encodes a characteristic set of four proteins and the S. coelicolor genome encodes 13 such cassettes that are highly homologous to each other. I constructed single-gene deletions in conservon 8 and determined, using transcriptome analysis, that CvnA8 and CvnF8 seem to function together. On the basis of my data, combined with bioinformatic analysis, I propose that CvnA8 is a membrane-bound signaling protein and CvnF8, a GAF domain-containing protein (an element that typically binds ligands and allosterically regulates proteins), serves as a sensor for CvnA8. From the gene expression patterns of deletion mutants, I deduce that CvnC8 and CvnD8 likely function together and hypothesize that CvnC8 is a transcription factor that is negatively regulated by CvnD8, which resembles a small RAS-like GTPase. Similarly, I observed that a ∆cvnB8 mutation has an intermediate effect on red pigment production and genome wide expression patterns, suggesting that it may connect CvnA8/F8 and CvnC8/D8, perhaps through regulation of the CvnD8 GTPase. Finally, my expression data additionally demonstrate that these conservon 8 factors also control expression of the gene clusters for at least two other specialized metabolites aside from the two red pigments, including a cryptic cluster that is predicted to encode a lanthipeptide.