|dc.description.abstract||Tuberculosis is a serious threat that claims 2 million lives annually.
Mycobacterium tuberculosis is the causative agent of tuberculosis. The fast-growing
bacteria Mycobacterium smegmatis is a model mycobacterial system, a non-pathogenic
soil bacterium that nonetheless shares many features with the pathogenic M. tuberculosis.
Multidimensional chromatography coupled with shotgun style tandem mass spectrometry
was used to detect and identify 2,550 distinct proteins from M. smegmatis with an
estimated 5% false positive identification rate, many predicted genes were annotated
using experimental results and protein expression levels were estimated from the shotgun
First, in 25 exponential and stationary phase experiments, we observed numerous
proteins involved in energy production, protein translation, and lipid biosynthesis. Protein
expression levels were estimated from the number of observations of each protein,
allowing measurement of differential expression of complete operons, and the
comparison of the stationary and exponential phase proteomes. Expression levels are
correlated with proteins' codon biases and mRNA expression levels.
Secondly, we measured changes in the proteome of Mycobacterium smegmatis in
response to three anti-tuberculosis drugs isoniazid (INH), ethambutol (EMB) and 5-
chloro-pyrazinamide (5-Cl-PZA). Protein expression levels were calculated from the
number of identified peptides for each protein. Translation, energy production, and
protein export are all down-regulated in the three drug treatments. By contrast, systems
related to drugs’ targets, including lipid, amino acid, nucleotide metabolism and
transport, show specific protein expression changes associated with each drug treatment.
We use these changes to infer likely targets for PZA.
Thirdly, computational methods were used to predict protein-protein interactions
and protein functions in a metabolic pathway in M. tuberculosis. Protein functional links
were built and specific functions were characterized for the pathway and its parallel
pathways in M. tuberculosis and other organisms.
Finally, multidimensional chromatography coupled with shotgun style tandem
mass spectrometry has been applied in the analysis of nuclear proteins from mammalian
cells. Nuclear proteins were identified from mouse T lymphoma cells. Nuclear matrixassociated
proteins were identified from human preliminary T cells during the transition
from quiescent state to proliferating state. These proteins are involved in the function of
DNA replication, RNA transcription, splicing, etc.||