Draft genome sequence of Streptomyces sp. strain SS, which produces a series of uridyl peptide antibiotic sansanmycins

Rescrutiny of the sansanmycin biosynthetic gene cluster leads to the discovery of a novel sansanmycin analogue with more potency against Mycobacterium tuberculosis

A novel sansanmycin analogue, sansanmycin Q (1), was identified by genome mining from the fermentation broth of Streptomyces sp. SS (CPCC 200442). In comparison with other sansanmycin compounds, sansanmycin Q has an extra glycine residue at the N-terminus of the pseudopeptide backbone. The additional glycine was proved to be assembled to sansanmycin A by SsaB, a tRNA-dependent aminoacyltransferase, based on the results of rescrutiny of sansanmycin biosynthetic gene cluster, and then overexpression and knockout of ssaB in the wild-type strain. The structure of sansanmycin Q was assigned by interpretation of NMR and mass spectral data. The results of the bioassay disclosed that sansanmycin Q exhibited more potency against Mycobacterium tuberculosis H₃₇Rv and a rifampicin- and isoniazid-resistant strain than sansanmycin A.

Exploiting Substrate Diversity of NRPS Led to the Generation of New Sansanmycin Analogs

Further exploration of substrate diversity of the sansanmycin biosynthetic pathway using available halogen- and methyl-phenylalanines led to the generation of diverse sansanmycin derivatives, either at the single C- or N-terminus alone or at both C- and N-termini. The structures of all of these derivatives were determined by MS/MS spectra, and amongst them, the structures of [2-Cl-Phe]-sansanmycin H (1) and [2-Cl-Phe]-sansanmycin A (2) were further identified by NMR. Both the C-terminal derivative 1 and the N-terminal derivative 2 were assayed for their antibacterial activities, and compound 1 exhibited moderate activity against P. aeruginosa and ΔtolC mutant E. coli.

NRPS substrate promiscuity leads to more potent antitubercular sansanmycin analogues

Sansanmycins, members of the uridyl peptide antibiotics, are assembled by nonribosomal peptide synthetases (NRPSs), the substrate promiscuity of which results in the diversity of products. Further exploration of the NRPSs' substrate promiscuity by reinvestigating sansanmycin producer strain led to the isolation and structural elucidation of eight new uridyl peptides, sansanmycins H-O (1-8). Among them, sansanmycin L, containing a 6-OH-bicyclic residue and Phe3 first found at the position AA3, exhibited activity against M. tuberculosis H37Rv with an MIC value of 2 μg/mL, 8-fold more potent than that of the major compound, sansanmycin A (MIC = 16 μg/mL).

MbtH homology codes to identify gifted microbes for genome mining

Advances in DNA sequencing technologies have made it possible to sequence large numbers of microbial genomes rapidly and inexpensively. In recent years, genome sequencing initiatives have demonstrated that actinomycetes with large genomes generally have the genetic potential to produce many secondary metabolites, most of which remain cryptic. Since the numbers of new and novel pathways vary considerably among actinomycetes, and the correct assembly of secondary metabolite pathways containing type I polyketide synthase or nonribosomal peptide synthetase (NRPS) genes is costly and time consuming, it would be advantageous to have simple genetic predictors for the number and potential novelty of secondary metabolite pathways in targeted microorganisms. For secondary metabolite pathways that utilize NRPS mechanisms, the small chaperone-like proteins related to MbtH encoded by Mycobacterium tuberculosis offer unique probes or beacons to identify gifted microbes encoding large numbers of diverse NRPS pathways because of their unique function(s) and small size. The small size of the mbtH-homolog genes makes surveying large numbers of genomes straight-forward with less than ten-fold sequencing coverage. Multiple MbtH orthologs and paralogs have been coupled to generate a 24-mer multiprobe to assign numerical codes to individual MbtH homologs by BLASTp analysis. This multiprobe can be used to identify gifted microbes encoding new and novel secondary metabolites for further focused exploration by extensive DNA sequencing, pathway assembly and annotation, and expression studies in homologous or heterologous hosts.

SsaA, a member of a novel class of transcriptional regulators, controls sansanmycin production in Streptomyces sp. strain SS through a feedback mechanism

Sansanmycins, produced by Streptomyces sp. strain SS, are uridyl peptide antibiotics with activities against Pseudomonas aeruginosa and multidrug-resistant Mycobacterium tuberculosis. In this work, the biosynthetic gene cluster of sansanmycins, comprised of 25 open reading frames (ORFs) showing considerable amino acid sequence identity to those of the pacidamycin and napsamycin gene cluster, was identified. SsaA, the archetype of a novel class of transcriptional regulators, was characterized in the sansanmycin gene cluster, with an N-terminal fork head-associated (FHA) domain and a C-terminal LuxR-type helix-turn-helix (HTH) motif. The disruption of ssaA abolished sansanmycin production, as well as the expression of the structural genes for sansanmycin biosynthesis, indicating that SsaA is a pivotal activator for sansanmycin biosynthesis. SsaA was proved to directly bind several putative promoter regions of biosynthetic genes, and comparison of sequences of the binding sites allowed the identification of a consensus SsaA binding sequence, GTMCTGACAN₂TGTCAGKAC. The DNA binding activity of SsaA was inhibited by sansanmycins A and H in a concentration-dependent manner. Furthermore, sansanmycins A and H were found to directly interact with SsaA. These results indicated that SsaA strictly controls the production of sansanmycins at the transcriptional level in a feedback regulatory mechanism by sensing the accumulation of the end products. As the first characterized regulator of uridyl peptide antibiotic biosynthesis, the understanding of this autoregulatory process involved in sansanmycin biosynthesis will likely provide an effective strategy for rational improvements in the yields of these uridyl peptide antibiotics.