Whole-genome sequencing of mutants with increased resistance against the two-peptide bacteriocin plantaricin JK reveals a putative receptor and potential docking site

Abstract

By whole-genome sequencing of resistant mutants, a putative receptor for plantaricin JK, a two-peptide bacteriocin produced by some Lactobacillus plantarum strains, was identified in Lactobacillus plantarum NCFB 965 and Weissella viridescens NCFB 1655. The receptors of the two species had 66% identical amino acid sequences and belong to the amino acid-polyamine-organocation (APC) transporter protein family. The resistant mutants contained point mutations in the protein-encoding gene resulting in either premature stop codons, leading to truncated versions of the protein, or single amino acid substitutions. The secondary structure of the W. viridescens protein was predicted to contain 12 transmembrane (TM) helices, a core structure shared by most members of the APC protein family. The single amino acid substitutions that resulted in resistant strains were located in a confined region of the protein that consists of TM helix 10, which is predicted to be part of an inner membrane pore, and an extracellular loop between TM helix 11 and 12. By use of template-based modeling a 3D structure model of the protein was obtained, which visualizes this mutational hotspot region and further strengthen the hypothesis that it represents a docking site for plantaricin JK.

Fig 1. A consensus sequence illustrating the conserved residues in the regions of interest in the membrane protein.

The consensus sequence using WebLogo (weblogo.berkeley.edu) was generated through a search with protein-BLAST using the APC family protein from W. viridescens NCFB 1655 as a template. The alignments reveal a highly conserved region spanning almost the entire TM helix 10 and to a lesser extent the loop between TM helix 11 and 12. The predicted TM helices 10–12 (from left to right) are indicated below as purple bars.

Fig 2. Side view of the I-TASSER-predicted structure of the APC family protein of W. viridescens NCFB 1655.

The mutated amino acids are highlighted in red. The TM helix 10 is colored in light orange, TM helix 11 in cyan and TM helix 12 in marine blue. The structure is based on a known crystal structure from another APC superfamily member [31].

Fig 3. Top view of the I-TASSER-predicted structure of the APC family protein of W. viridescens NCFB 1655.

The predicted structure illustrates that TM helix 10 is part of a membrane pore and that the loop between TM helix 11 and 12 are close to TM helix 10 in space. See Fig 2 for color-codes.