Revealing the first uridyl peptide antibiotic biosynthetic gene cluster and probing pacidamycin biosynthesis

Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces

Streptomyces are a large and valuable resource of bioactive and complex secondary metabolites, many of which have important clinical applications. With the advances in high throughput genome sequencing methods, various in silico genome mining strategies have been developed and applied to the mapping of the Streptomyces genome. These studies have revealed that Streptomyces possess an even more significant number of uncharacterized silent secondary metabolite biosynthetic gene clusters (smBGCs) than previously estimated. Linking smBGCs to their encoded products has played a critical role in the discovery of novel secondary metabolites, as well as, knowledge-based engineering of smBGCs to produce altered products. In this mini review, we discuss recent progress in Streptomyces genome sequencing and the application of genome mining approaches to identify and characterize smBGCs. Furthermore, we discuss several challenges that need to be overcome to accelerate the genome mining process and ultimately support the discovery of novel bioactive compounds.

High-level pacidamycin resistance in Pseudomonas aeruginosa is mediated by an opp oligopeptide permease encoded by the opp-fabI operon

Pacidamycins (or uridyl peptide antibiotics) possess selective in vivo activity against Pseudomonas aeruginosa. An important limitation for the therapeutic use of pacidamycins with P. aeruginosa is the high frequency (10(-6) to 10(-7)) at which resistant mutants emerge. To elucidate the mechanism(s) of this resistance, pacidamycin-resistant P. aeruginosa mutants were isolated. Two types of mutants were obtained. Type 1, or high-level resistance mutants with a pacidamycin MIC of 512 μg/ml, were more abundant, with a frequency of~2 × 10(-6), and did not show cross-resistance with other antibiotics. Type 2, low-level resistance mutants, were isolated with a frequency of ~10(-8) and had a pacidamycin MIC of 64 μg/ml (the MIC for the wild-type strain was 4 to 16 μg/ml). These mutants were cross-resistant to levofloxacin, tetracycline, and erythromycin and were shown to overexpress either the MexAB-OprM or MexCD-OprJ multidrug resistance efflux pumps. High-level resistant mutants were isolated by transposon mutagenesis and one insertion was localized to oppB, one of two periplasmic binding protein components of an oligopeptide transport system which is encoded by the opp-fabI operon. The Opp system is required for uptake of pacidamycin across the inner membrane, since various opp, but not fabI, mutants were resistant to high levels of pacidamycin. Both of the two putative Opp periplasmic binding proteins, OppA and OppB, were required for pacidamycin uptake. Although both impaired uptake into and efflux from the cell can cause pacidamycin resistance in P. aeruginosa, our data suggest that impaired uptake is the primary reason for the high-frequency and high-level pacidamycin resistance.