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A chemical proteomics approach to profiling the ATP-binding proteome of Mycobacterium tuberculosis.

Wolfe LM, Veeraraghavan U, Idicula-Thomas S, Schürer S, Wennerberg K, Reynolds R, Besra GS, Dobos KM - Mol. Cell Proteomics (2013)

Bottom Line: Protein families vital to the survival of the tubercle bacillus during hypoxia emerged from our studies.Specifically, along with members of the DosR regulon, several proteins involved in energy metabolism (Icl/Rv0468 and Mdh/Rv1240) and lipid biosynthesis (UmaA/Rv0469, DesA1/Rv0824c, and DesA2/Rv1094) were found to be differentially abundant in hypoxic versus normal growing cultures.These pathways represent a subset of proteins that may be relevant therapeutic targets for development of novel ATP-competitive antibiotics.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Colorado State University, Fort Collins, Colorado 80523, USA.

ABSTRACT
Tuberculosis, caused by Mycobacterium tuberculosis, remains one of the leading causes of death worldwide despite extensive research, directly observed therapy using multidrug regimens, and the widespread use of a vaccine. The majority of patients harbor the bacterium in a state of metabolic dormancy. New drugs with novel modes of action are needed to target essential metabolic pathways in M. tuberculosis; ATP-competitive enzyme inhibitors are one such class. Previous screening efforts for ATP-competitive enzyme inhibitors identified several classes of lead compounds that demonstrated potent anti-mycobacterial efficacy as well as tolerable levels of toxicity in cell culture. In this report, a probe-based chemoproteomic approach was used to selectively profile the M. tuberculosis ATP-binding proteome in normally growing and hypoxic M. tuberculosis. From these studies, 122 ATP-binding proteins were identified in either metabolic state, and roughly 60% of these are reported to be essential for survival in vitro. These data are available through ProteomeXchange with identifier PXD000141. Protein families vital to the survival of the tubercle bacillus during hypoxia emerged from our studies. Specifically, along with members of the DosR regulon, several proteins involved in energy metabolism (Icl/Rv0468 and Mdh/Rv1240) and lipid biosynthesis (UmaA/Rv0469, DesA1/Rv0824c, and DesA2/Rv1094) were found to be differentially abundant in hypoxic versus normal growing cultures. These pathways represent a subset of proteins that may be relevant therapeutic targets for development of novel ATP-competitive antibiotics.

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Distribution of predicted and experimentally derived ATP-binding proteins by functional category. A predicted list of ATP-binding proteins was generated from two resources and sorted by functional category. A comparison between the predicted and experimentally derived ATPome demonstrates a range of distribution among each functional category. Representing nearly 50% of the experimental ATPome were proteins within functional Category 7, Intermediary Metabolism, and functional Category 2, Lipid Metabolism. Conserved Hypotheticals (functional Category 10) were the third most represented group.
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Figure 2: Distribution of predicted and experimentally derived ATP-binding proteins by functional category. A predicted list of ATP-binding proteins was generated from two resources and sorted by functional category. A comparison between the predicted and experimentally derived ATPome demonstrates a range of distribution among each functional category. Representing nearly 50% of the experimental ATPome were proteins within functional Category 7, Intermediary Metabolism, and functional Category 2, Lipid Metabolism. Conserved Hypotheticals (functional Category 10) were the third most represented group.

Mentions: To further define the functional classes of proteins within the experimental ATPome dataset, a predictive list of potential ATP-binding proteins was generated by query of the search term ATP-binding in The Tuberculosis Database and was combined with a list of proteins from another web-based resource PATRIC (supplemental Table S7) (26, 27). By functional class, categorization of the predicted M. tuberculosis ATP-binding proteome revealed that proteins associated with Category 7 (Intermediary Metabolism) and Category 2 (Information Pathways) were equally represented at 20% and that Category 3 (Cell Wall and Processes) represented ∼30% of the predicted subset. When compared with the experimentally derived ATPome subset, 30% of the proteins belong to Category 7, whereas Category 1 (Lipid Metabolism) and Category 10 (Conserved Hypotheticals) represent a collective 33% of the enriched experimental ATPome (Fig. 2). Proteins involved in fatty acid and mycolic acid biosynthesis (Category 1) are of interest due to their key roles in the maintenance of the cell envelope architecture and the essentiality of their encoding genes (24). A complete list of labeled and unlabeled protein IDs and their corresponding functional categories is provided in supplemental Table S1.


A chemical proteomics approach to profiling the ATP-binding proteome of Mycobacterium tuberculosis.

Wolfe LM, Veeraraghavan U, Idicula-Thomas S, Schürer S, Wennerberg K, Reynolds R, Besra GS, Dobos KM - Mol. Cell Proteomics (2013)

Distribution of predicted and experimentally derived ATP-binding proteins by functional category. A predicted list of ATP-binding proteins was generated from two resources and sorted by functional category. A comparison between the predicted and experimentally derived ATPome demonstrates a range of distribution among each functional category. Representing nearly 50% of the experimental ATPome were proteins within functional Category 7, Intermediary Metabolism, and functional Category 2, Lipid Metabolism. Conserved Hypotheticals (functional Category 10) were the third most represented group.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3675820&req=5

Figure 2: Distribution of predicted and experimentally derived ATP-binding proteins by functional category. A predicted list of ATP-binding proteins was generated from two resources and sorted by functional category. A comparison between the predicted and experimentally derived ATPome demonstrates a range of distribution among each functional category. Representing nearly 50% of the experimental ATPome were proteins within functional Category 7, Intermediary Metabolism, and functional Category 2, Lipid Metabolism. Conserved Hypotheticals (functional Category 10) were the third most represented group.
Mentions: To further define the functional classes of proteins within the experimental ATPome dataset, a predictive list of potential ATP-binding proteins was generated by query of the search term ATP-binding in The Tuberculosis Database and was combined with a list of proteins from another web-based resource PATRIC (supplemental Table S7) (26, 27). By functional class, categorization of the predicted M. tuberculosis ATP-binding proteome revealed that proteins associated with Category 7 (Intermediary Metabolism) and Category 2 (Information Pathways) were equally represented at 20% and that Category 3 (Cell Wall and Processes) represented ∼30% of the predicted subset. When compared with the experimentally derived ATPome subset, 30% of the proteins belong to Category 7, whereas Category 1 (Lipid Metabolism) and Category 10 (Conserved Hypotheticals) represent a collective 33% of the enriched experimental ATPome (Fig. 2). Proteins involved in fatty acid and mycolic acid biosynthesis (Category 1) are of interest due to their key roles in the maintenance of the cell envelope architecture and the essentiality of their encoding genes (24). A complete list of labeled and unlabeled protein IDs and their corresponding functional categories is provided in supplemental Table S1.

Bottom Line: Protein families vital to the survival of the tubercle bacillus during hypoxia emerged from our studies.Specifically, along with members of the DosR regulon, several proteins involved in energy metabolism (Icl/Rv0468 and Mdh/Rv1240) and lipid biosynthesis (UmaA/Rv0469, DesA1/Rv0824c, and DesA2/Rv1094) were found to be differentially abundant in hypoxic versus normal growing cultures.These pathways represent a subset of proteins that may be relevant therapeutic targets for development of novel ATP-competitive antibiotics.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Colorado State University, Fort Collins, Colorado 80523, USA.

ABSTRACT
Tuberculosis, caused by Mycobacterium tuberculosis, remains one of the leading causes of death worldwide despite extensive research, directly observed therapy using multidrug regimens, and the widespread use of a vaccine. The majority of patients harbor the bacterium in a state of metabolic dormancy. New drugs with novel modes of action are needed to target essential metabolic pathways in M. tuberculosis; ATP-competitive enzyme inhibitors are one such class. Previous screening efforts for ATP-competitive enzyme inhibitors identified several classes of lead compounds that demonstrated potent anti-mycobacterial efficacy as well as tolerable levels of toxicity in cell culture. In this report, a probe-based chemoproteomic approach was used to selectively profile the M. tuberculosis ATP-binding proteome in normally growing and hypoxic M. tuberculosis. From these studies, 122 ATP-binding proteins were identified in either metabolic state, and roughly 60% of these are reported to be essential for survival in vitro. These data are available through ProteomeXchange with identifier PXD000141. Protein families vital to the survival of the tubercle bacillus during hypoxia emerged from our studies. Specifically, along with members of the DosR regulon, several proteins involved in energy metabolism (Icl/Rv0468 and Mdh/Rv1240) and lipid biosynthesis (UmaA/Rv0469, DesA1/Rv0824c, and DesA2/Rv1094) were found to be differentially abundant in hypoxic versus normal growing cultures. These pathways represent a subset of proteins that may be relevant therapeutic targets for development of novel ATP-competitive antibiotics.

Show MeSH
Related in: MedlinePlus