Identification and functional analysis of genome mutations in a fluoride-resistant Streptococcus mutans strain

PLoS One. 2015 Apr 9;10(4):e0122630. doi: 10.1371/journal.pone.0122630. eCollection 2015.

Abstract

It is known that fluoride-resistant microorganisms are different from fluoride-sensitive ones in growth, adherence and metabolic activity. It was hypothesized that these phenotypic differences were due to stable genotypic changes in the fluoride-resistant strains. However, until now, no studies have reported these genotypic changes. The aim of this study is to identify such changes in a fluoride-resistant Streptococcus mutans strain (C180-2FR) using whole-genome shotgun (WGS) sequencing and to examine the potential function of the identified mutations by comparing gene expression between the fluoride-sensitive (C180-2) and C180-2FR strains. We performed 50 bp paired-end Illumina shotgun sequencing for both strains. Through extensive bioinformatic analysis, we were able to identify 8 single nucleotide polymorphisms (SNPs) in the genome of C180-2FR, which were further confirmed by Sanger sequencing. Expression of the genes containing or in proximity to the SNPs in C180-2 and C180-2FR was then quantified by real-time PCR. A gene cluster containing genes coding for fluoride antiporters was up-regulated 10-fold in C180-2FR when compared to that in C180-2, independent of growth phase. Two SNPs are located in this gene cluster, one in its promoter region and the other in its protein-coding region. In addition, one gene, which codes for a putative glycerol uptake facilitator protein, was found to be down-regulated by 60% in C180-2FR at an early growth phase. The promoter region of this gene contained a SNP. No difference in expression was found for the other SNP-containing genes. In summary, using WGS sequencing, we were able to uncover genetic changes in the genome of a fluoride-resistant strain. These findings can provide new insights into the mechanism of microbial fluoride resistance.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Biological Transport
  • Carrier Proteins / genetics*
  • Carrier Proteins / metabolism
  • Dental Caries / microbiology
  • Drug Resistance, Bacterial / genetics*
  • Fluorides / pharmacology
  • Genome, Bacterial*
  • Genotype
  • Glycerol / metabolism
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Hydrogen-Ion Concentration
  • Molecular Sequence Data
  • Multigene Family
  • Mutation*
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Promoter Regions, Genetic
  • Streptococcus mutans / drug effects
  • Streptococcus mutans / genetics*
  • Streptococcus mutans / metabolism

Substances

  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Carrier Proteins
  • Glycerol
  • Fluorides

Grant support

This research was supported by the National Natural Science Foundation of China (No. 81371135) and "Twelfth Five-Year" National Science and Technology Support Project (20911BAZ03171). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.