Correlation of proteomic and transcriptomic profiles of Staphylococcus aureus during the post-exponential phase of growth

J Microbiol Methods. 2005 Feb;60(2):247-57. doi: 10.1016/j.mimet.2004.09.017.


A combined proteomic and transcriptomic analysis of Staphylococcus aureus strain N315 was performed to study a sequenced strain at the system level. Total protein and membrane protein extracts were prepared and analyzed using various proteomic workflows including: 2-DE, SDS-PAGE combined with microcapillary LC-MALDI-MS/MS, and multidimensional liquid chromatography. The presence of a protein was then correlated with its respective transcript level from S. aureus cells grown under the same conditions. Gene-expression data revealed that 97% of the 2'596 ORFs were detected during the post-exponential phase. At the protein level, 23% of these ORFs (591 proteins) were identified. Correlation of the two datasets revealed that 42% of the identified proteins (248 proteins) were amongst the top 25% of genes with highest mRNA signal intensities, and 69% of the identified proteins (406 proteins) were amongst the top 50% with the highest mRNA signal intensities. The fact that the remaining 31% of proteins were not strongly expressed at the RNA level indicates either that some low-abundance proteins were identified or that some transcripts or proteins showed extended half-lives. The most abundant classes identified with the combined proteomic and transcriptomic approach involved energy production, translational activities and nucleotide transport, reflecting an active metabolism. The simultaneous large-scale analysis of transcriptomes and proteomes enables a global and holistic view of the S. aureus biology, allowing the parallel study of multiple active events in an organism.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / biosynthesis*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / isolation & purification
  • Chromatography, Liquid
  • Computational Biology
  • Electrophoresis, Gel, Two-Dimensional
  • Electrophoresis, Polyacrylamide Gel
  • Gene Expression Regulation, Developmental
  • Nucleic Acid Hybridization
  • Oligonucleotide Array Sequence Analysis
  • Proteomics / methods*
  • RNA, Messenger / genetics
  • RNA, Messenger / isolation & purification
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Staphylococcus aureus / genetics*
  • Staphylococcus aureus / growth & development
  • Staphylococcus aureus / metabolism*
  • Transcription, Genetic / genetics
  • Transcription, Genetic / physiology


  • Bacterial Proteins
  • RNA, Messenger