A systems biology approach to study the phagosomal proteome modulated by mycobacterial infections

Systems biology and proteomics have recently contributed significantly to the insight into the biogenesis and immunity-related functions of the phagosome. To gain insight into the modulation of the phagosomal proteome by the wild-type Mycobacterium tuberculosis H37Rv reference strain, an attenuated mutant of the H37Rv strain, and the BCG Pasteur vaccine strain, we employed the nano-liquid chromatography/LTQ-FTMS based proteomics approach and a systems biology approach to analyze the bacillus-containing phagosomes purified from the bone-marrow-derived BMA3.A3 macrophages infected with the three different mycobacterial strains. We identified 322 proteins at a false-discovery rate of 2%. These proteins were quantified with a label-free proteomics method. All but one of these proteins is mouse proteins. The gene ontology analysis of these mouse proteins suggests that lysosomal proteins represented <3% of the detected proteins, supporting the observation that these mycobacterial strains inhibit or limit the phagosome maturation process. The results also indicate that the endoplasmic reticulum (ER) proteins do not constitute a major part of the phagosome proteome, supporting the phagosome maturation model of the role of ER in phagosome biogenesis. This phagosome maturation model is in contrast to the phagocytosis model which predicts that half of the phagosome membrane is derived from ER. This pilot study demonstrates that a combination of proteomics, multivariate analysis, and systems biology promises to bring forward new insights into the mycobacterial pathogenesis and the interconnected phagosome biology.