The genetic proteome: Using genetics to inform the proteome of mycobacterial pathogens

Abstract

Mycobacterial pathogens pose a sustained threat to human health. There is a critical need for new diagnostics, therapeutics, and vaccines targeting both tuberculous and nontuberculous mycobacterial species. Understanding the basic mechanisms used by diverse mycobacterial species to cause disease will facilitate efforts to design new approaches toward detection, treatment, and prevention of mycobacterial disease. Molecular, genetic, and biochemical approaches have been widely employed to define fundamental aspects of mycobacterial physiology and virulence. The recent expansion of genetic tools in mycobacteria has further increased the accessibility of forward genetic approaches. Proteomics has also emerged as a powerful approach to further our understanding of diverse mycobacterial species. Detection of large numbers of proteins and their modifications from complex mixtures of mycobacterial proteins is now routine, with efforts of quantification of these datasets becoming more robust. In this review, we discuss the “genetic proteome,” how the power of genetics, molecular biology, and biochemistry informs and amplifies the quality of subsequent analytical approaches and maximizes the potential of hypothesis-driven mycobacterial research. Published proteomics datasets can be used for hypothesis generation and effective post hoc supplementation to experimental data. Overall, we highlight how the integration of proteomics, genetic, molecular, and biochemical approaches can be employed successfully to define fundamental aspects of mycobacterial pathobiology.

Proteo-genetic analysis reveals clear hierarchy of ESX-1 secretion in Mycobacterium marinum

“…We used a proteo-genetic approach (i.e., using genetics to inform the proteome) to define the specific contribution of each known ESX-1 substrate to protein secretion in M. marinum ( 48 ). We generated 12 M. marinum strains with unmarked deletions of individual ESX-1 substrate genes and the 12 corresponding complementation strains.…”

Chemical Proteomics Strategies for Analyzing Protein Lipidation Reveal the Bacterial O-Mycoloylome

“…Although mycobacteria lack strict orthologs of Cg Cmt1, they possess multiple structurally similar mycoloyltransferases with relatively high substrate tolerance that should be explored for protein O -mycoloylation activity. The tools reported herein will facilitate efforts to discover and characterize O -mycoloylated proteins in additional organisms and, along with other emerging strategies for studying cell envelope proteins in the Corynebacterineae , , are expected to contribute to an improved understanding of the mycomembrane proteome. Our tools may also be useful for comparing and contrasting the scope and functional roles of O -mycoloylation and N -acyl- S -diacyl-glycerylation, the latter of which generates lipoproteins that associate with the cell envelope in corynebacteria and mycobacteria. , …”

The loss of the PDIM/PGL virulence lipids causes differential secretion of ESX-1 substrates inMycobacterium marinum

“…It is unclear whether PDIM is required for ESX-1 protein secretion across the MOM (3) or for ESX-1 substrate function within the phagosome (4). Our study uses a proteogenetic approach (55) to quantify how PDIM and PGL influence protein secretion from Mycobacterium marinum . Our studies provide an explanation for the ESX-1 phenotypes in the absence of PDIM, suggesting a broader role of PDIM and PGL outer lipids in translocating mycobacterial proteins across the MOM.…”