Correlation of proteomic and transcriptomic profiles of Staphylococcus aureus during the post-exponential phase of growth.
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.
Scherl
Alexander
A
Biomedical Proteomics Research Group, Geneva University Hospitals, Geneva, Switzerland.
François
Patrice
P
Bento
Manuela
M
Deshusses
Jacques M
JM
Charbonnier
Yvan
Y
Converset
Véronique
V
Huyghe
Antoine
A
Walter
Nadia
N
Hoogland
Christine
C
Appel
Ron D
RD
Sanchez
Jean-Charles
JC
Zimmermann-Ivol
Catherine G
CG
Corthals
Garry L
GL
Hochstrasser
Denis F
DF
Schrenzel
Jacques
J
D001426:Bacterial Proteins / Q000096:biosynthesis* / Q000235:genetics / Q000302:isolation & purification; D002853:Chromatography, Liquid; D019295:Computational Biology; D015180:Electrophoresis, Gel, Two-Dimensional; D004591:Electrophoresis, Polyacrylamide Gel; D018507:Gene Expression Regulation, Developmental; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D040901:Proteomics / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics / Q000302:isolation & purification; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013211:Staphylococcus aureus / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D014158:Transcription, Genetic / Q000235:genetics / Q000502:physiology
D001426:Bacterial Proteins; D012333:RNA, Messenger