Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis

Abstract

Significant developments and improvements in basic and clinical research notwithstanding, infectious diseases still claim at least 13 million lives annually. Classical research approaches have deciphered many molecular mechanisms underlying infection. Today it is increasingly recognized that multiple molecular mechanisms cooperate to constitute a complex system that is used by a given pathogen to interfere with the biochemical processes of the host. Therefore, systems-level approaches now complement the standard molecular biology techniques to investigate pathogens and their interactions with the human host. Here we review omic studies in Mycobacterium tuberculosis, the causative agent of tuberculosis, with a particular focus on proteomic methods and their application to the bacilli. Likewise, the discussed methods are directly portable to other bacterial pathogens.

Comprehensive Analysis and Comparison on the Codon Usage Pattern of Whole Mycobacterium tuberculosis Coding Genome from Different Area

“…Proteins in Mycobacterium tuberculosis could be analyzed via many methods, mass spectrometry, codon usage, and so on [ 25 , 26 ]. Codon usage is linked to nucleic acids and proteins, especially the GC content.…”

Proteomics of Mycobacterium Infection: Moving towards a Better Understanding of Pathogen-Driven Immunomodulation

“…These robust methodologies are increasingly applied to study host–pathogen interactions and to elucidate the proteome of the pathogen itself, of infected cells and of subcellular compartments. In the case of Mtb infection, protein profiling of different mycobacterial strains as well as of clinical, drug-resistant isolates increased tremendously our knowledge about their proteome ( 16 , 17 ), while MS methods also helped to identify biomarkers of Mtb-infected patients ( 18 ). Many previous MS studies on host infection were carried out with non-pathogenic mycobacteria strains or were performed with beads coated with single mycobacterial virulence factors, while data on virulent Mtb strains were scarce.…”

Importance of protein Ser/Thr/Tyr phosphorylation for bacterial pathogenesis

“…Another general theme of bacterial phosphoproteomes is that they, similar to the eukaryal ones, are dominated by pSer sites, followed by pThr and, to a lesser extent, pTyr modifications. One exception is M. tuberculosis where pThr sites are more frequently reported [149][150][151]. However, pTyr sites are likely underrepresented in phosphoproteomic datasets obtained with metal affinity chromatography as their relatively low abundance compared to pSer and pThr sites can result in their disproportional enrichment.…”