Determination and comparison of the Francisella tularensis subsp.novicida U112 proteome to other bacterial proteomes.
The proteins expressed by Francisella tularensis subsp. novicida U112 grown to midexponential phase were surveyed by nanoLC-tandem mass spectrometry (LC-MS/MS). To improve annotation of the genome and develop a technology to provide high-throughput analysis of the Francisella proteome in multiple conditions, we sought to establish a fast and simple analysis that would reduce as much as possible the false discovery rate. Our survey detected expression of 63.0% of the predicted proteome from the stable condition of growth in rich medium available at (www.francisella.org). On the basis of detection of essential proteins, we estimated coverage to be approximately 80% of the actual expressed proteome. This suggests that no less than 70% of the proteins could be expressed in this condition. This analysis revealed two previously unidentified protein coding open reading frames and validated 50% of the proteins annotated as hypothetical. On the basis of results of the screen to detect essential proteins, not all proteins expressed provide a measurable contribution to F.t. novicida growth in this condition. Comparison of this protein profile with other profiles previously published suggested that the genome size and number of genes involved in regulation have little effect on the number of proteins expressed in a given stable condition.
Rohmer
Laurence
L
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. lrohmer@u.washington.edu
Guina
Tina
T
Chen
Jinzhi
J
Gallis
Byron
B
Taylor
Greg K
GK
Shaffer
Scott A
SA
Miller
Samuel I
SI
Brittnacher
Mitchell J
MJ
Goodlett
David R
DR
D001426:Bacterial Proteins / Q000032:analysis* / Q000235:genetics; D002458:Cell Fractionation; D002853:Chromatography, Liquid / Q000295:instrumentation / Q000379:methods*; D005604:Francisella tularensis / Q000737:chemistry* / Q000235:genetics; D013058:Mass Spectrometry / Q000295:instrumentation / Q000379:methods*; D016366:Open Reading Frames; D010455:Peptides / Q000032:analysis / Q000235:genetics; D020543:Proteome; D015203:Reproducibility of Results
D001426:Bacterial Proteins; D010455:Peptides; D020543:Proteome