Discovery of 16-demethylrifamycins by Removing Predominant Polyketide Biosynthetic Pathway in Micromonospora sp. TP-A0468.

A number of strategies have been developed to mine novel natural products based on biosynthetic gene clusters and there has been dozens of successful cases facilitated by the development of genomic sequencing. During our study on biosynthesis of the antitumor polyketide kosinostatin (KST), we found that the genome of Micromonospora sp. TP-A0468, the producer of KST, contains other potential polyketide gene clusters, with no encoded products detected. Deletion of kst cluster led to abolishment of KST and the enrichment of several new compounds which were isolated and characterized as 16-demethylrifamycins (3-6). Transcriptional analysis demonstrated that the expression of the essential genes related to the biosynthesis of 3-6 was in comparable level in wild type and kst cluster deletion strain. This indicates that the accumulation of these compounds was due to the redirection of metabolic flux rather than transcriptional activation. Genetic disruption, chemical complementation and bioinformatic analysis revealed that the production of 3-6 was accomplished by crosstalk between two distantly placed polyketide gene clusters pks3 and M-rif. This finding not only enriches the analogue pool and biosynthetic diversity of rifamycins, but also provides an auxiliary strategy for natural product discovery through genome mining in polyketide-producing microorganisms. Importance Natural products are essential in the development of novel clinically-used drugs. Discovering new natural products and modifying known compounds are still the two main ways to generate new 37 candidates. Here, we have discovered several rifamycins with varied skeleton by redirecting the metabolic flux from the predominant polyketide biosynthetic pathway to the rifamycin pathway in the marine actinomycetes species Micromonospora sp. TP-A0468. Rifamycins are indispensable chemotherapeutics in the treatment of various diseases such as tuberculosis, leprosy and AIDS-related mycobacterial infections. This work exemplifies a useful method for the discovery of cryptic natural products in genome-sequenced microbes. Moreover, the 16-demethylrifamycins and their genetically manipulable producer provides a new opportunity in the construction of novel rifamycin derivates to aid in the defense against the ever-growing drug-resistance of Mycobacterium tuberculosis. [ABSTRACT FROM AUTHOR]