Characterization of the ‘pristinamycin supercluster’ of Streptomyces pristinaespiralis

Abstract

SummaryPristinamycin, produced by Streptomyces pristinaespiralis Pr11, is a streptogramin antibiotic consisting of two chemically unrelated compounds, pristinamycin I and pristinamycin II. The semi‐synthetic derivatives of these compounds are used in human medicine as therapeutic agents against methicillin‐resistant Staphylococcus aureus strains. Only the partial sequence of the pristinamycin biosynthetic gene cluster has been previously reported. To complete the sequence, overlapping cosmids were isolated from a S. pristinaespiralis Pr11 gene library and sequenced. The boundaries of the cluster were deduced, limiting the cluster size to approximately 210 kb. In the central region of the cluster, previously unknown pristinamycin biosynthetic genes were identified. Combining the current and previously identified sequence information, we propose that all essential pristinamycin biosynthetic genes are included in the 210 kb region. A pristinamycin biosynthetic pathway was established. Furthermore, the pristinamycin gene cluster was found to be interspersed by a cryptic secondary metabolite cluster, which probably codes for a glycosylated aromatic polyketide. Gene inactivation experiments revealed that this cluster has no influence on pristinamycin production. Overall, this work provides new insights into pristinamycin biosynthesis and the unique genetic organization of the pristinamycin gene region, which is the largest antibiotic ‘supercluster’ known so far.

Identification and Characterization of the Pyridomycin Biosynthetic Gene Cluster of Streptomyces pyridomyceticus NRRL B-2517

“…A predicted PCP gene (pyrU orthologue; SSDG_07480; Table 1) was found in the S. pristinaespiralis ATCC 25486 genome sequence, outside the pristinamycin biosynthetic gene cluster (45). We thus predict that the separate PCP may participate in the biosynthesis of pristinamycin I and other streptogramin B compounds.…”

“…The search for a carrier protein identified PyrU, a small 84-aa protein that has not been observed in the streptogramin B antibiotics biosynthesis (14,45). Although it shows low homology with known PCPs or aryl carrier proteins (ArCPs), it features the conserved LGXXS motif for phosphopantetheinylation (supplemental Fig.…”

“…Similar gene pairs of unknown functions (snaO (67% aa identity) and snaN (58% aa identity), and virN (65% aa identity) and virM (58% aa identity)) occur in the pristinamycin II (45) and in the virginamycin M biosynthesis gene clusters (14). Genes Involved in Regulation and Self-resistance-Pyr3, a putative membrane protein, could be involved in a transport system for pyridomycin export and self-resistance.…”

Toward Systems Metabolic Engineering of Streptomycetes for Secondary Metabolites Production

“…[77] A more recent example of using a combinatorial metabolic engineering approach has been presented for the production of streptogramin-like antibiotic pristinamycin, which consists of two chemically unrelated compounds PI and PII. [78] As the native host S. pristinaespiralis suffers from low yields, additional copies of the two BGCs responsible for the production of PI and PII were introduced in addition to the deletion of repressors. [74,75] .…”

PapR6, a Putative Atypical Response Regulator, Functions as a Pathway-Specific Activator of Pristinamycin II Biosynthesis in Streptomyces pristinaespiralis

“…The gene cluster responsible for the biosynthesis of PI and PII has been well characterized for S. pristinaespiralis (3)(4)(5)(6)(7)(8)(9); all essential PI/PII biosynthetic genes are proposed to be included in a 210-kb "supercluster," in which the pristinamycin gene cluster is interspersed with a cryptic type II polyketide biosynthetic gene cluster (10). Interestingly, there are seven regulatory genes in the pristinamycin biosynthetic gene cluster, including papR1 to papR6 and spbR, which infers a complicated regulatory mechanism for pristinamycin production.…”