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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

Alkhalili, Rawana N. LU and Canbäck, Björn LU (2018) In International Journal of Molecular Sciences 19(9).
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... (More)

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.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Antimicrobial, AntiSMASH, Bacteriocins, BAGEL, Firmicutes, Geobacillus, Lanthipeptides, Lantibiotics, Lantipeptides, Z-geobacillin
in
International Journal of Molecular Sciences
volume
19
issue
9
publisher
MOLECULAR DIVERSITY PRESERVATION INT
external identifiers
  • scopus:85053080685
ISSN
1661-6596
DOI
10.3390/ijms19092650
language
English
LU publication?
yes
id
64865c51-e71c-4233-91ad-92d6a870dd1c
date added to LUP
2018-10-12 07:57:49
date last changed
2019-06-11 03:54:50
@article{64865c51-e71c-4233-91ad-92d6a870dd1c,
  abstract     = {<p>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.</p>},
  articleno    = {2650},
  author       = {Alkhalili, Rawana N. and Canbäck, Björn},
  issn         = {1661-6596},
  keyword      = {Antimicrobial,AntiSMASH,Bacteriocins,BAGEL,Firmicutes,Geobacillus,Lanthipeptides,Lantibiotics,Lantipeptides,Z-geobacillin},
  language     = {eng},
  month        = {09},
  number       = {9},
  publisher    = {MOLECULAR DIVERSITY PRESERVATION INT},
  series       = {International Journal of Molecular Sciences},
  title        = {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},
  url          = {http://dx.doi.org/10.3390/ijms19092650},
  volume       = {19},
  year         = {2018},
}