Chapter 25
Metabolomics of Mycobacterium tuberculosis
Kyle A. Planck and Kyu Rhee
Abstract
Enzymes fuel the biochemical activities of all cells. Their substrates and products thus represent a potential
window into the physiologic state of a cell. Metabolomics focuses on the global, or systems-level, study of
small molecules in a given biological system and has thus provided an experimental tool with which to study
cellular physiology, including the biochemistry within pathogenic microorganisms. While metabolomic
studies of Mycobacterium tuberculosis are still in their infancy, recent studies have begun to deliver unique
insights into the composition, organization, activity, and regulation of the bacterium’s physiologic network
not accessible by other approaches. Here, we outline practical methods for the culture, collection, and
analysis of metabolomic samples from M. tuberculosis that emphasize minimally perturbing sample
handling, broad and native metabolite recovery, and sensitive, biologically agnostic metabolite detection.
Key words Metabolomics, Tuberculosis, Enzymes, Metabolism
1 Introduction
1.1 Metabolomics in
Mycobacterium
tuberculosis
Prior to the advent of systems-level metabolomic technologies,
studies of cellular metabolism were largely limited to the use of
isolated enzyme preparations and/or genetically engineered
mutant strains. The significance of these investigations rested on
extrapolation to the native biochemical milieu of the cell in combination with the accuracy or completeness of their accompanying
bioinformatic annotations. Recently, more streamlined approaches,
such as the one described here, have allowed for more direct
measurements of the in situ biochemical function of a given enzyme
or physiologic state of cells in a given condition [1–4]. Metabolomic
studies have thus helped assign novel functions to previously
mis-annotated enzymes in M. tuberculosis [5, 6] and resolve the
level and direction of metabolic reactions within the bacterial cytosol [7–10]. Together, such studies have revealed previously unrecognized metabolic pathways and capabilities not readily encoded in
the bacterium’s genomic composition [5, 8, 11–18]. Metabolomics
has also impacted anti-infective development by helping to resolve
Tanya Parish and Anuradha Kumar (eds.), Mycobacteria Protocols, Methods in Molecular Biology, vol. 2314,
https://doi.org/10.1007/978-1-0716-1460-0_25, © Springer Science+Business Media, LLC, part of Springer Nature 2021
579
Metabolomics of Mycobacterium tuberculosis
Kyle A. Planck and Kyu Rhee
Abstract
Enzymes fuel the biochemical activities of all cells. Their substrates and products thus represent a potential
window into the physiologic state of a cell. Metabolomics focuses on the global, or systems-level, study of
small molecules in a given biological system and has thus provided an experimental tool with which to study
cellular physiology, including the biochemistry within pathogenic microorganisms. While metabolomic
studies of Mycobacterium tuberculosis are still in their infancy, recent studies have begun to deliver unique
insights into the composition, organization, activity, and regulation of the bacterium’s physiologic network
not accessible by other approaches. Here, we outline practical methods for the culture, collection, and
analysis of metabolomic samples from M. tuberculosis that emphasize minimally perturbing sample
handling, broad and native metabolite recovery, and sensitive, biologically agnostic metabolite detection.
Key words Metabolomics, Tuberculosis, Enzymes, Metabolism
1 Introduction
1.1 Metabolomics in
Mycobacterium
tuberculosis
Prior to the advent of systems-level metabolomic technologies,
studies of cellular metabolism were largely limited to the use of
isolated enzyme preparations and/or genetically engineered
mutant strains. The significance of these investigations rested on
extrapolation to the native biochemical milieu of the cell in combination with the accuracy or completeness of their accompanying
bioinformatic annotations. Recently, more streamlined approaches,
such as the one described here, have allowed for more direct
measurements of the in situ biochemical function of a given enzyme
or physiologic state of cells in a given condition [1–4]. Metabolomic
studies have thus helped assign novel functions to previously
mis-annotated enzymes in M. tuberculosis [5, 6] and resolve the
level and direction of metabolic reactions within the bacterial cytosol [7–10]. Together, such studies have revealed previously unrecognized metabolic pathways and capabilities not readily encoded in
the bacterium’s genomic composition [5, 8, 11–18]. Metabolomics
has also impacted anti-infective development by helping to resolve
Tanya Parish and Anuradha Kumar (eds.), Mycobacteria Protocols, Methods in Molecular Biology, vol. 2314,
https://doi.org/10.1007/978-1-0716-1460-0_25, © Springer Science+Business Media, LLC, part of Springer Nature 2021
579