Phylogenomic analysis of the diversity of graspetides and proteins involved in their biosynthesis

• DOI: 10.1186/s13062-022-00320-2
• Publication Date: 2022-03-21T18:03:53Z
• Authors: Kira S. Makarova; Brittney Blackburne; Yuri I. Wolf; Anastasia Nikolskaya; Svetlana Karamycheva; Marlene Espinoza; Clifton E. Barry; Carole A. Bewley; Eugene V. Koonin
• Keywords: Gene cluster; ENCODE

Abstract Background Bacteria and archaea produce an enormous diversity of modified peptides that are involved in various forms inter-microbial conflicts or communication. A vast class such Ribosomally synthesized, Postranslationally Peptides (RiPPs), a major group RiPPs graspetides, so named after ATP-grasp ligases catalyze the formation lactam lactone linkages these peptides. The multiple proteins encoded respective Biosynthetic Gene Clusters (BGCs) their evolution have not been studied full detail. In this work, we attempt comprehensive analysis graspetide-encoding BGCs report variety novel graspetide groups as well ancillary implicated biosynthesis expression. Results We compiled comprehensive, manually curated set graspetides includes 174 families including 115 new with distinct patterns amino acids macrocyclization further modification, roughly tripling known diversity. derived signature motifs for leader regions precursors could be used to facilitate prediction. Graspetide biosynthetic gene clusters specific were identified bacterial divisions previously encode RiPPs, particular, parasitic symbiotic bacteria Candidate phyla radiation. Bacteroides -specific (BGC) include remarkable same loci which predicted by ligase. details recently characterized chryseoviridin showed duplication horizonal exchange both contribute diversification during evolution. Conclusions demonstrate unsuspected sequences, even those associated closely related enzymes. Several unnoticed identified. results work substantially expand can harnessed advance approaches identification.