Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias

摘要: The fast-growing bacterium Mycobacterium smegmatis is a model mycobacterial system, nonpathogenic soil that nonetheless shares many features with the pathogenic tuberculosis, causative agent of tuberculosis. study M. expected to shed light on mechanisms growth and complex lipid metabolism, provides tractable system for antimycobacterial drug development. Although genome sequence not yet completed, we used multidimensional chromatography tandem mass spectrometry, in combination partially completed sequence, detect identify total 901 distinct proteins from over course 25 conditions, providing experimental annotation predicted genes an ∼5% false-positive identification rate. We observed numerous involved energy production (9.8% expressed proteins), protein translation (8.7%), biosynthesis (5.4%); 33% are unknown function. Protein expression levels were estimated number observations each protein, allowing measurement differential complete operons, comparison stationary exponential phase proteomes. Expression correlated proteins' codon biases mRNA levels, as measured by adaptation indices, principle component analysis frequencies, DNA microarray data. This observation consistent notions either (1) prokaryotic largely preset choice, or (2) choice optimized consistency average regardless mechanism regulating expression.