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Int. J. Mol. Sci. 2018, 19(9), 2650; https://doi.org/10.3390/ijms19092650

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

1
Biotechnology, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
2
Department of Biology, Lund University, SE-221 00 Lund, Sweden
*
Author to whom correspondence should be addressed.
Received: 10 July 2018 / Revised: 23 August 2018 / Accepted: 4 September 2018 / Published: 6 September 2018
(This article belongs to the Section Molecular Biophysics)
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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. View Full-Text
Keywords: antimicrobial; antiSMASH; bacteriocins; BAGEL; firmicutes; Geobacillus; lanthipeptides; lantibiotics; lantipeptides; Z-geobacillin antimicrobial; antiSMASH; bacteriocins; BAGEL; firmicutes; Geobacillus; lanthipeptides; lantibiotics; lantipeptides; Z-geobacillin
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Alkhalili, R.N.; Canbäck, B. 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. Int. J. Mol. Sci. 2018, 19, 2650.

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