title: Genome mining for radical SAM protein determinants reveals multiple sactibiotic-like gene clusters.
abstract: Thuricin CD is a two-component bacteriocin produced by Bacillus thuringiensis that kills a wide range of clinically significant Clostridium difficile. This bacteriocin has recently been characterized and consists of two distinct peptides, Trnβ and Trnα, which both possess 3 intrapeptide sulphur to α-carbon bridges and act synergistically. Indeed, thuricin CD and subtilosin A are the only antimicrobials known to possess these unusual structures and are known as the sactibiotics (sulplur to alpha carbon-containing antibiotics). Analysis of the thuricin CD-associated gene cluster revealed the presence of genes encoding two highly unusual SAM proteins (TrnC and TrnD) which are proposed to be responsible for these unusual post-translational modifications. On the basis of the frequently high conservation among enzymes responsible for the post-translational modification of specific antimicrobials, we performed an in silico screen for novel thuricin CD-like gene clusters using the TrnC and TrnD radical SAM proteins as driver sequences to perform an initial homology search against the complete non-redundant database. Fifteen novel thuricin CD-like gene clusters were identified, based on the presence of TrnC and TrnD homologues in the context of neighbouring genes encoding potential bacteriocin structural peptides. Moreover, metagenomic analysis revealed that TrnC or TrnD homologs are present in a variety of metagenomic environments, suggesting a widespread distribution of thuricin-like operons in a variety of environments. In-silico analysis of radical SAM proteins is sufficient to identify novel putative sactibiotic clusters.
authors.affiliation: Microbiology Department, University College Cork, Cork, Ireland.
authors.forename: Kiera
authors.initials: K
authors.lastname: Murphy
authors.forename: Orla
authors.initials: O
authors.lastname: O'Sullivan
authors.forename: Mary C
authors.initials: MC
authors.lastname: Rea
authors.forename: Paul D
authors.initials: PD
authors.lastname: Cotter
authors.forename: R Paul
authors.initials: RP
authors.lastname: Ross
authors.forename: Colin
authors.initials: C
authors.lastname: Hill
mesh_terms: D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics*; D001430:Bacteriocins / Q000235:genetics; D003013:Clostridium / Q000235:genetics; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D057225:Data Mining; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D012436:S-Adenosylmethionine / Q000378:metabolism*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D001430:Bacteriocins; C059740:thuricin; D012436:S-Adenosylmethionine