The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles

Abstract

BackgroundRibosomally synthesized and post-translationally modified peptides (RiPPs) are a burgeoning class of natural products with diverse activity that share a similar origin and common features in their biosynthetic pathways. The precursor peptides of these natural products are ribosomally produced, upon which a combination of modification enzymes installs diverse functional groups. This genetically encoded peptide-based strategy allows for rapid diversification of these natural products by mutation in the precursor genes merged with unique combinations of modification enzymes. Thiazole/oxazole-modified microcins (TOMMs) are a class of RiPPs defined by the presence of heterocycles derived from cysteine, serine, and threonine residues in the precursor peptide. TOMMs encompass a number of different families, including but not limited to the linear azol(in)e-containing peptides (streptolysin S, microcin B17, and plantazolicin), cyanobactins, thiopeptides, and bottromycins. Although many TOMMs have been explored, the increased availability of genome sequences has illuminated several unexplored TOMM producers.MethodsAll YcaO domain-containing proteins (D protein) and the surrounding genomic regions were were obtained from the European Molecular Biology Laboratory (EMBL) and the European Bioinformatics Institute (EBI). MultiGeneBlast was used to group gene clusters contain a D protein. A number of techniques were used to identify TOMM biosynthetic gene clusters from the D protein containing gene clusters. Precursor peptides from these gene clusters were also identified. Both sequence similarity and phylogenetic analysis were used to classify the 20 diverse TOMM clusters identified.ResultsGiven the remarkable structural and functional diversity displayed by known TOMMs, a comprehensive bioinformatic study to catalog and classify the entire RiPP class was undertaken. Here we report the bioinformatic characterization of nearly 1,500 TOMM gene clusters from genomes in the European Molecular Biology Laboratory (EMBL) and the European Bioinformatics Institute (EBI) sequence repository. Genome mining suggests a complex diversification of modification enzymes and precursor peptides to create more than 20 distinct families of TOMMs, nine of which have not heretofore been described. Many of the identified TOMM families have an abundance of diverse precursor peptide sequences as well as unfamiliar combinations of modification enzymes, signifying a potential wealth of novel natural products on known and unknown biosynthetic scaffolds. Phylogenetic analysis suggests a widespread distribution of TOMMs across multiple phyla; however, producers of similar TOMMs are generally found in the same phylum with few exceptions.ConclusionsThe comprehensive genome mining study described herein has uncovered a myriad of unique TOMM biosynthetic clusters and provides an atlas to guide future discovery efforts. These biosynthetic gene clusters are predicted to produce diverse final products, and the identification of additional combinations of...

Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining

“…Likewise, Cox et al (30) used YcaO proteins to identify thiazole/oxazole-modified macrocycles (TOMMs), a superfamily encompassing members of linear azol(in)e-containing peptides, cyanobactins, thiopeptides, and bottromycins, and identified nearly 1,500 clusters; however, their method required extensive manual annotation. Whereas automated methods for RiPP genome mining exist, these are often limited to a subset of RiPP families.…”

Chalkophores

“…While originally annotated as two open reading frames in the Ms. trichosporium OB3b operon (45), mbnB is a single gene in other Mbn operons, and the pseudogene observed in the published Ms. trichosporium OB3b genome is not present in all lineages of that strain (71). Although RiPPs containing amino acid–derived heterocycles such as thiazol(in)es and (methyl)oxazol(in)es are common, particularly in the TOMM family (84, 85), no precedents for enzymatic oxazolone biosynthesis have been found. The sole characterized oxazolone-containing natural product family, jadomycins, receives these modifications as part of the nonenzymatic incorporation of amino acids (86).…”

In Vitro Biosynthesis and Substrate Tolerance of the Plantazolicin Family of Natural Products

“…Within this broad space, the ribosomally synthesized and post-translationally modified peptide (RiPP) natural products comprise a class garnering increased attention (2). Plantazolicin (PZN) is an anti- B. anthracis RiPP produced by Bacillus velezensis (formerly Bacillus amyloliquefaciens ) FZB42 (3–6) and a member of a subclass of RiPPs termed the linear azol(in)e-containing peptides (LAPs) (7, 8). LAPs, thiopeptides, and azol(in)e-containing cyanobactins can also collectively be referred to as thiazole/oxazole-modified microcins (TOMMs) (2).…”

“…In addition to the PZN biosynthetic gene cluster (BGC) found in B. velezensis , homologous gene clusters have been identified in a number of other bacterial strains (Figure 1b, Supplementary Figure 1) (8), although only Bacillus pumilus has been demonstrated to produce PZN (4). The putative precursor peptides associated with these BGCs exhibit a highly conserved core region, which would result in similar groupings of contiguous heterocycles if indeed post-translationally modified like PZN (Figure 1c, Supplementary Figure 1).…”