Expanded Natural Product Diversity Revealed by Analysis of Lanthipeptide-Like Gene Clusters in Actinobacteria

Abstract

Lanthionine-containing peptides (lanthipeptides) are a rapidly growing family of polycyclic peptide natural products belonging to the large class of ribosomally synthesized and posttranslationally modified peptides (RiPPs). Lanthipeptides are widely distributed in taxonomically distant species, and their currently known biosynthetic systems and biological activities are diverse. Building on the recent natural product gene cluster family (GCF) project, we report here large-scale analysis of lanthipeptidelike biosynthetic gene clusters from Actinobacteria. Our analysis suggests that lanthipeptide biosynthetic pathways, and by extrapolation the natural products themselves, are much more diverse than currently appreciated and contain many different posttranslational modifications. Furthermore, lanthionine synthetases are much more diverse in sequence and domain topology than currently characterized systems, and they are used by the biosynthetic machineries for natural products other than lanthipeptides. The gene cluster families described here significantly expand the chemical diversity and biosynthetic repertoire of lanthionine-related natural products. Biosynthesis of these novel natural products likely involves unusual and unprecedented biochemistries, as illustrated by several examples discussed in this study. In addition, class IV lanthipeptide gene clusters are shown not to be silent, setting the stage to investigate their biological activities. Lanthipeptides are a rapidly growing family of polycyclic peptides characterized by the presence of the thioether crosslinked amino acids lanthionine and methyllanthionine (1-5). These compounds are widely distributed in taxonomically distant species and display very diverse biological activities, ranging from antimicrobial to antiallodynic (5-7). Antibacterial lanthipeptides, such as the commercially used food preservative nisin, are termed lantibiotics (8). Lanthipeptides are generated from a ribosomally synthesized linear precursor peptide (generically termed LanA) and therefore belong to the large class of natural products that are ribosomally synthesized and posttranslationally modified peptides (RiPPs) (9). The precursor peptide LanA consists of a C-terminal core peptide where all posttranslational modifications take place and an N-terminal leader peptide that is important for posttranslational modifications and that is subsequently removed by proteolysis (10, 11). The installation of the (methyl)lanthionine thioether bridges is achieved by the initial dehydration of Ser and Thr residues in the precursor peptides, followed by stereoselective intramolecular Michael-type addition of Cys thiols to the newly formed dehydroamino acids (Fig. 1A).Four classes of biosynthetic enzymes are known to catalyze lanthionine formation (2, 12) (Fig. 1B). Class I lanthionine synthetases consist of a dehydratase and a cyclase that are generically termed LanB and LanC, respectively (8). Class II enzymes are generically named LanMs, which are single polypeptides containing an N-termi...

Structure and tRNA Specificity of MibB, a Lantibiotic Dehydratase from Actinobacteria Involved in NAI-107 Biosynthesis

“…Recent genome mining efforts have identified Actinobacteria as a vast reservoir of previously uncharacterized lanthipeptides (Zhang et al, 2015). The recent characterization of a new family of class I lantibiotics from Actinobacteria exemplify the opportunities for discovery of novel compounds in this phylum (Maffioli et al, 2015).…”

“…The acquired knowledge regarding the tRNA specificity of MibB allowed the development of an expression system in Escherichia coli suitable for the heterologous production of NAI-107 analogs. This methodology provides an alternative route for the study and characterization of class I lantibiotics produced by Actinobacteria, a phylum that has recently emerged with a vast potential for producing previously uncharacterized lantibiotics (Li and O'Sullivan, 2012, Maffioli et al, 2015, Zhang et al, 2015). …”

New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products

“…This promise is exemplified by the discovery of the gene clusters responsible for the biosynthesis of streptide and thioviridamide, both carrying unique PTMs defining new RiPP subfamilies (Izawa et al, 2013, Schramma et al, 2015). In addition, genome mining of >800 Actinobacteria genomes revealed unusual open reading frames associated with lanthipeptide biosynthetic gene clusters, suggesting this RiPP subfamily to contain additional currently uncharacterized PTMs (Zhang et al, 2015). …”

Quinovosamycins: new tunicamycin-type antibiotics in which the α, β-1″,11′-linked N-acetylglucosamine residue is replaced by N-acetylquinovosamine

“…2,3 Hence, genomic-enhanced discovery has led to the identification of phosphonate-based anti-metabolites and to the occurrence of uncommon biosynthetic pathways for nonribosomal peptides and polyketides. [4][5][6] Tunicamycins (TUNs) are a heterologous family of nucleoside antibiotics that target the early stages of biosynthesis for bacterial peptidoglycan and eukaryotic N-glycoproteins. [7][8][9] The mode of action is known, with the TUN-Mg 2+ complex established as a transition state analog for several hexosamine-1-phosphate:prenol phosphate translocases.…”