Unveiling the structural diversity of non-ribosomal peptide synthetases in the Lactobacillaceae family through in silico approaches

Non-ribosomal peptide synthetases (NRPSs) are multi-modular enzymatic complexes that produce secondary metabolites with various structural variations and biological activities. They form the cornerstone of microbial chemical ecology, positioning them as a promising source of new bioactive compounds for industrial and pharmaceutical applications. NRPS systems are well-characterized across many bacterial phyla, particularly within Actinobacteria and Pseudomonas, where they play a crucial role in synthesizing diverse secondary metabolites that possess therapeutic value. Despite ongoing taxonomic reclassification and their growing significance in probiotics and industrial biotechnology, little is known about the presence, diversity, and structural organization of NRPSs within the Lactobacillaceae family. The Lactobacillus genus has recently undergone taxonomic revisions, expanding to 31 genera that include 363 species within the Lactobacillaceae family. This knowledge gap limits our understanding of the secondary metabolic potential of this functionally and phylogenetically diverse group of bacteria. The presence of NRPS was identified in 26 out of 31 genera, and further computational analysis and evolutionary distribution revealed conserved structural features, including amino acid adenylation domains, AMP-binding domains, and PCP domains consistent with the conventional NRPS framework found in other bacterial species. Glycine and isoleucine were identified as the most conserved amino acids; the motifs TSGTTG, FCGEEL, and RLPIG were found to be evolutionarily conserved across bacterial kingdoms. This study also predicts the substrate specificity code of the adenylation domains (NRPS codons) and specific substrates for various species of this family. Our research demonstrates the structural complexity and diversity of NRPS systems by revealing previously unknown biosynthetic capabilities within the Lactobacillaceae family. Along with advancing our knowledge of their secondary metabolic repertoire, this study lays the groundwork for future functional validation and synthetic biology-driven biotechnological potential exploitation.