Genome mining for ribosomally synthesized natural products

Abstract

In recent years, the number of known peptide natural products that are synthesized via the ribosomal pathway has rapidly grown. Taking advantage of sequence homology among genes encoding precursor peptides or biosynthetic proteins, in silico mining of genomes combined with molecular biology approaches has guided the discovery of a large number of new ribosomal natural products, including lantipeptides, cyanobactins, linear thiazole/oxazole-containing peptides, microviridins, lasso peptides, amatoxins, cyclotides, and conopeptides. In this review, we describe the strategies used for the identification of these ribosomally synthesized and posttranslationally modified peptides (RiPPs) and the structures of newly identified compounds. The increasing number of chemical entities and their remarkable structural and functional diversity may lead to novel pharmaceutical applications.

Figure 1. Lantipeptides recently discovered by genome mining

The two-component lantibiotics haloduracin from B. halodurans C-125 and lichenicidin from B. licheniformis ATCC 14580, DSM13, and VK21 were discovered after genome mining for LanM lanthionine synthetases. Venezuelin, a lantipeptide predicted from he genome sequence of S. venezuelae ATCC 10712, was produced in vitro after reconstitution of a novel LanL lanthionine synthetase. Prochlorosin 1.7 is one of 29 lantipeptides produced by Prochlorococcus MIT9313. BsaA2 was discovered after genome sequence analysis of several S. aureus strains. Dha: dehydroalanine, Dhb: dehydrobutyrine, Abu: α-aminobutyric acid. For the thioether crosslinks, residues derived from Ser/Thr are shown in red and residues originating from Cys are shown in blue.

Figure 2. Cyanobactins and thiopeptides discovered by genome mining approaches

Patellamide B produced by P. didemmni was discovered by sequencing of metagenomic samples. Trichamide was isolated from Trichodesmium sp. and microcyclamide 7806A and 7806B from M. aeurignosa PCC7806 were found after identification of orthologue patellamide biosynthetic gene clusters. Anacyclamide A10 was isolated after PCR detection of its biosynthetic gene cluster in Anabaena sp90. The thiopeptide thiocillin IV was discovered in the culture supernatant of B. cereus ATCC 14579 after identification of its biosynthetic gene cluster through genome analysis.

Figure 3. Ribosomal peptides discovered by genome mining containing lactones and lactams or C-terminal siderophores

The microviridin L biosynthetic gene cluster was detected in the genome of M. aeruginosa NIES843 after PCR screening and genomic DNA library construction. The capistruin gene cluster was identified in B. thailandensis E624 following orthologue neighborhood analysis of the gene cluster of the related peptide microcin J25 from E. coli. The siderophore-microcins MccM, MccH47, and MccG492 were discovered after genome sequence analysis of different Enterobacteriaceae.