Reprint of "Identification of staphylococcal species based on variations in protein sequences (mass spectrometry) and DNA sequence (sodA microarray)"

Mol Cell Probes. Apr-Jun 2014;28(2-3):73-82. doi: 10.1016/j.mcp.2014.01.003. Epub 2014 Jan 29.

Abstract

This report is among the first using sequence variation in newly discovered protein markers for staphylococcal (or indeed any other bacterial) speciation. Variation, at the DNA sequence level, in the sodA gene (commonly used for staphylococcal speciation) provided excellent correlation. Relatedness among strains was also assessed using protein profiling using microcapillary electrophoresis and pulsed field electrophoresis. A total of 64 strains were analyzed including reference strains representing the 11 staphylococcal species most commonly isolated from man (Staphylococcus aureus and 10 coagulase negative species [CoNS]). Matrix assisted time of flight ionization/ionization mass spectrometry (MALDI TOF MS) and liquid chromatography-electrospray ionization tandem mass spectrometry (LC ESI MS/MS) were used for peptide analysis of proteins isolated from gel bands. Comparison of experimental spectra of unknowns versus spectra of peptides derived from reference strains allowed bacterial identification after MALDI TOF MS analysis. After LC-MS/MS analysis of gel bands bacterial speciation was performed by comparing experimental spectra versus virtual spectra using the software X!Tandem. Finally LC-MS/MS was performed on whole proteomes and data analysis also employing X!tandem. Aconitate hydratase and oxoglutarate dehydrogenase served as marker proteins on focused analysis after gel separation. Alternatively on full proteomics analysis elongation factor Tu generally provided the highest confidence in staphylococcal speciation.

Keywords: Liquid chromatography-tandem mass spectrometry; Mass spectrometry; Peptide sequence; Soda microarray.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Corrected and Republished Article

MeSH terms

  • Aconitate Hydratase / chemistry
  • Aconitate Hydratase / genetics
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics*
  • Chromatography, Liquid
  • DNA, Bacterial / analysis
  • DNA, Bacterial / chemistry
  • Evolution, Molecular
  • Genetic Markers
  • Genetic Variation
  • Humans
  • Ketoglutarate Dehydrogenase Complex / chemistry
  • Ketoglutarate Dehydrogenase Complex / genetics
  • Male
  • Mass Spectrometry / methods
  • Molecular Typing / methods*
  • Oligonucleotide Array Sequence Analysis
  • Peptides / analysis
  • Peptides / chemistry
  • Phylogeny
  • Proteomics
  • RNA, Ribosomal, 16S / genetics
  • Software
  • Staphylococcus / classification*
  • Staphylococcus / genetics
  • Superoxide Dismutase / chemistry
  • Superoxide Dismutase / genetics*

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • Genetic Markers
  • Peptides
  • RNA, Ribosomal, 16S
  • SodA protein, Bacteria
  • Superoxide Dismutase
  • Ketoglutarate Dehydrogenase Complex
  • Aconitate Hydratase