Genetic diversity of the streptococcal competence (com) gene locus

Abstract

The com operon of naturally transformable streptococcal species contains three genes, comC, comD, and comE, involved in the regulation of competence. The comC gene encodes a competence-stimulating peptide (CSP) thought to induce competence in the bacterial population at a critical extracellular concentration. The comD and comE genes are believed to encode the transmembrane histidine kinase and response regulator proteins, respectively, of a two-component regulator, with the comD-encoded protein being a receptor for CSP. Here we report on the genetic variability of comC and comD within Streptococcus pneumoniae isolates. Comparative analysis of sequence variations of comC and comD shows that, despite evidence for horizontal gene transfer at this locus and the lack of transformability of many S. pneumoniae strains in the laboratory, there is a clear correlation between the presence of a particular comC allele and the cognate comD allele. These findings effectively rule out the possibility that the presence of noncognate comC and comD alleles may be responsible for the inability to induce competence in many isolates and indicate the importance of a functional com pathway in these isolates. In addition, we describe a number of novel CSPs from disease-associated strains of S. mitis and S. oralis. The CSPs from these isolates are much more closely related to those from S. pneumoniae than to most CSPs previously reported from S. mitis and S. oralis, suggesting that these particular organisms may be a potential source of DNA in recombination events generating the mosaic structures commonly reported in genes of S. pneumoniae that are under strong selective pressure.

FIG. 1

Alignments of the predicted amino acid sequences of the nine distinct CSPs characterized in this study. Asterisks represent amino acids conserved across all sequences, while dots represent conservative amino acid substitutions. Gaps in the alignment are represented by dashes. The predicted cleavage point of the mature peptide from the leader sequence, based on homology with other double-glycine-type leader peptides, is indicated by an arrow. The CSP-2 and CSP-6 groups are subdivided by coding changes in the leader peptide. The species of origin was S. oralis (O), S. pneumoniae (P), or S. mitis (M). (A) Sequences of the six distinct CSPs obtained from S. pneumoniae isolates. (B) Sequences obtained from isolates characterized as S. mitis or S. oralis alongside the sequences of three S.mitis CSPs and two S. oralis CSPs characterized by Håvarstein et al. (10).

FIG. 2

UPGMA trees constructed with DNA sequence data from comC (A) and the 5′ 384 bp of comD (B) illustrating the complete congruence of CSP (comC) and receptor (comD) sequences. The numbers at internal branches represent the bootstrap confidence levels of particular branches estimated from 500 resamplings of the data set.

FIG. 2

UPGMA trees constructed with DNA sequence data from comC (A) and the 5′ 384 bp of comD (B) illustrating the complete congruence of CSP (comC) and receptor (comD) sequences. The numbers at internal branches represent the bootstrap confidence levels of particular branches estimated from 500 resamplings of the data set.

FIG. 3

UPGMA tree demonstrating the relationships between ComC (CSP) proteins characterized in this study (CSP-1 and CSP-9) and previously identified CSPs.

FIG. 4

Alignment of the predicted amino acid sequences of the ComD proteins from streptococcal strains in comparison to the published S. pneumoniae Rx ComD sequence (19). Only residues which differ from the Rx sequence are shown. Identical residues are shown by dots. The active-site histidine residue of ComD is indicated by a number sign, while the predicted stop codon is indicated by an asterisk.

FIG. 5

Distribution of polymorphic sites among the sequences of the com operons of S. pneumoniae Rx, Pn59, and Pn13. Numbering, shown above the sequence, begins at the comC start codon, with residues identical to those in strain Rx shown by dots and gaps in the sequence alignment shown by dashes.