Identification of Putative Novel Class-I Lanthipeptides in Firmicutes: A Combinatorial In Silico Analysis Approach Performed on Genome Sequenced Bacteria and a Close Inspection of Z-Geobacillin Lanthipeptide Biosynthesis Gene Cluster of the Thermophilic Geobacillus sp. Strain ZGt-1

Abstract

Lanthipeptides are ribosomally synthesized and post-translationally modified polycyclic peptides. Lanthipeptides that have antimicrobial activity are known as lantibiotics. Accordingly, the discovery of novel lantibiotics constitutes a possible solution for the problem of antibiotic resistance. We utilized the publicly available genome sequences and the bioinformatic tools tailored for the detection of lanthipeptides. We designed our strategy for screening of 252 firmicute genomes and detecting class-I lanthipeptide-coding gene clusters. The designed strategy resulted in identifying 69 class-I lanthipeptide sequences, of which more than 10% were putative novel. The identified putative novel lanthipeptides have not been annotated on the original or the RefSeq genomes, or have been annotated merely as coding for hypothetical proteins. Additionally, we identified bacterial strains that have not been previously recognized as lanthipeptide-producers. Moreover, we suggest corrections for certain firmicute genome annotations, and recommend lanthipeptide records for enriching the bacteriocin genome mining tool (BAGEL) databases. Furthermore, we propose Z-geobacillin, a putative class-I lanthipeptide coded on the genome of the thermophilic strain Geobacillus sp. ZGt-1. We provide lists of putative novel lanthipeptide sequences and of the previously unrecognized lanthipeptide-producing bacterial strains, so they can be prioritized for experimental investigation. Our results are expected to benefit researchers interested in the in vitro production of lanthipeptides.

Antimicrobial Activity of a Synthetic Bacteriocin Found in the Genome of Lactobacillus Casei on the Microbiota of Antioquian Soft Cheese (Quesito Antioqueño)

“…Singh and cols (26), using the bioinformatic tool BAGEL 3, classified fifty-two putative bacteriocins across 20 LAB species, that have not been previously reported as bacteriocins producers, and class II was the most predominant. Similarly, Alkhalili and cols (27) analyzed 252 genomes and identified seven putative novel class-I lanthipeptides using BAGEL 3. Oliveira and cols (28) predicted in silico (using BAGEL 3) a putative bacteriocin produced by L. rhamnosus L156.4, and they confirmed the bacteriocin inhibition growth of several bacteria in vitro, including gram-positive human and foodborne bacterial pathogens.…”

In Silico Analysis of Pacific Oyster (Crassostrea gigas) Transcriptome over Developmental Stages Reveals Candidate Genes for Larval Settlement

“…Sequence selection criteria (genomic expression rate, specificity of organs or certain stages of development, functional annotations) are defined according to the biological questions raised. Meta-analyses based on the exploration of published genomes are becoming increasingly common [18,19,20]. For example, in C. gigas , a recent study focusing on adult photosensitivity used this method to identify genes involved in this process [21].…”

Aminovinyl Cysteine Containing Peptides: A Unique Motif That Imparts Key Biological Activity

“… Structures of Avi(Me)Cys-containing class I lanthipeptides; clausin ( 6 ), 21 gallidermin ( 7 ), 19 mutacin-1140 ( 8 ), 53 epidermin ( 9 ), 20 BsaA2 ( 10 ), 37 and microbisporicins A1 and A2 ( 11 ). 18 Pink = Avi(Me)Cys.…”