Bioinformatic prospecting and phylogenetic analysis reveals 94 undescribed circular bacteriocins and key motifs

Ben Vezina,Andrew T Smith,Bernd H A Rehm

doi:10.1186/s12866-020-01772-0

Abstract

BackgroundCircular bacteriocins are antimicrobial peptides produced by bacteria with a N and C termini ligation. They have desirable properties such as activity at low concentrations along with thermal, pH and proteolytic resistance. There are twenty experimentally confirmed circular bacteriocins as part of bacteriocin gene clusters, with transport, membrane and immunity proteins. Traditionally, novel antimicrobials are found by testing large numbers of isolates against indicator strains, with no promise of corresponding novel sequence.ResultsThrough bioprospecting publicly available sequence databases, we identified ninety-nine circular bacteriocins across a variety of bacteria bringing the total to 119. They were grouped into two families within class I modified bacteriocins (i and ii) and further divided into subfamilies based on similarity to experimentally confirmed circular bacteriocins. Within subfamilies, sequences overwhelmingly shared similar characteristics such as sequence length, presence of a polybasic region, conserved locations of aromatic residues, C and N termini, gene clusters similarity, translational coupling and hydrophobicity profiles. At least ninety were predicted to be putatively functional based on gene clusters. Furthermore, bacteriocins identified from Enterococcus, Staphylococcus and Streptococcus species may have activity against clinically relevant strains, due to the presence of putative immunity genes required for expression in a toxin-antitoxin system. Some strains such as Paenibacillus larvae subsp. pulvifaciens SAG 10367 contained multiple circular bacteriocin gene clusters from different subfamilies, while some strains such as Bacillus cereus BCE-01 contained clusters with multiple circular bacteriocin structural genes.ConclusionsSequence analysis provided rapid insight into identification of novel, putative circular bacteriocins, as well as conserved genes likely essential for circularisation. This represents an expanded library of putative antimicrobial proteins which are potentially active against human, plant and animal pathogens.

Highlights

Circular bacteriocins are antimicrobial peptides produced by bacteria with a N and C termini ligation
By removing them from database mining identification of distantly-related putative circular bacteriocins was based on functional antimicrobial protein sequence, rather than irrelevant signal sequence
A small number of these sequences have been previously described by bioinformatic approaches [28], other sequences identified in this work were either incorrectly annotated in publicly available databases or not annotated at all

Summary

Introduction

Circular bacteriocins are antimicrobial peptides produced by bacteria with a N and C termini ligation. They have desirable properties such as activity at low concentrations along with thermal, pH and proteolytic resistance. It means they can be genetically engineered and targeted towards specific organisms [14, 15]. Due to these characteristics, there is considerable scope for use in anti-spoilage and food-safety applications. Class I circular bacteriocins are short sequences (58–70 amino acids in length), four (five in the case of AS-48 and BacA) helical segments that enclose a tightly packed hydrophobic core, a saposin fold, no cysteine pairs, and all (except butyrivibriocin AR10) contain a polybasic region involved in binding to target cell membranes [11, 30, 34, 35]

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