Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface

• Published in: mBio 2018-03, Vol.9 (2)
• Main Authors: Carette, Xavier, Platig, John, Young, David C, Helmel, Michaela, Young, Albert T, Wang, Zhe, Potluri, Lakshmi-Prasad, Moody, Cameron Stuver, Zeng, Jumei, Prisic, Sladjana, Paulson, Joseph N, Muntel, Jan, Madduri, Ashoka V R, Velarde, Jorge, Mayfield, Jacob A, Locher, Christopher, Wang, Tiansheng, Quackenbush, John, Rhee, Kyu Y, Moody, D Branch, Steen, Hanno, Husson, Robert N
• Format: Article
• Language: English
• Subjects: Adenosine Triphosphate - metabolism; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Gene Expression Regulation, Bacterial - genetics; Gene Expression Regulation, Bacterial - physiology; Mycobacterium tuberculosis - genetics; Mycobacterium tuberculosis - metabolism; Phosphorylation - genetics; Phosphorylation - physiology; Protein Serine-Threonine Kinases - genetics; Protein Serine-Threonine Kinases - metabolism; Signal Transduction - genetics; Signal Transduction - physiology
• ISSN: 2161-2129; 2150-7511
• DOI: 10.1128/mBio.02333-17

Tuberculosis is the leading killer among infectious diseases worldwide. Increasing multidrug resistance has prompted new approaches for tuberculosis drug development, including targeted inhibition of virulence determinants and of signaling cascades that control many downstream pathways. We used a multisystem approach to determine the effects of a potent small-molecule inhibitor of the essential Ser/Thr protein kinases PknA and PknB. We observed differential levels of phosphorylation of many proteins and extensive changes in levels of gene expression, protein abundance, cell wall lipids, and intracellular metabolites. The patterns of these changes indicate regulation by PknA and PknB of several pathways required for cell growth, including ATP synthesis, DNA synthesis, and translation. These data also highlight effects on pathways for remodeling of the mycobacterial cell envelope via control of peptidoglycan turnover, lipid content, a SigE-mediated envelope stress response, transmembrane transport systems, and protein secretion systems. Integrated analysis of phosphoproteins, transcripts, proteins, and lipids identified an unexpected pathway whereby threonine phosphorylation of the essential response regulator MtrA decreases its DNA binding activity. Inhibition of this phosphorylation is linked to decreased expression of genes for peptidoglycan turnover, and of genes for mycolyl transferases, with concomitant changes in mycolates and glycolipids in the cell envelope. These findings reveal novel roles for PknA and PknB in regulating multiple essential cell functions and confirm that these kinases are potentially valuable targets for new antituberculosis drugs. In addition, the data from these linked multisystems provide a valuable resource for future targeted investigations into the pathways regulated by these kinases in the cell. Tuberculosis is the leading killer among infectious diseases worldwide. Increasing drug resistance threatens efforts to control this epidemic; thus, new antitubercular drugs are urgently needed. We performed an integrated, multisystem analysis of responses to inhibition of its two essential serine/threonine protein kinases. These kinases allow the bacterium to adapt to its environment by phosphorylating cellular proteins in response to extracellular signals. We identified differentially phosphorylated proteins, downstream changes in levels of specific mRNA and protein abundance, and alterations in the metabolite and lipid content of