Tuberculosis (TB), caused by infection with Mycobacterium tuberculosis, remains a major cause of human morbidity and mortality, particularly in the developing world. Chronic M. tuberculosis infection requires long- term interactions between the bacterium and host immune system, and tissue macrophages play key roles in the outcome of infection. Although technologies to monitor global changes in host gene expression have catalyzed our understanding of the important roles for TLR activation and interferon during TB infection, modulation of transcription represents only one of many cellular responses to bacterial infection. Post- translational modification of proteins, such as ubiquitylation, phosphorylation, and acetylation play a role in regulating virtually every cellular process. How these signaling events lead to observed changes in metabolic pathways, autophagy, and vesicular trafficking during bacterial infection remain unknown. Furthermore, how these processes may be manipulated by pathogens is crucial for understanding the pathogenic strategies of microorganisms. This proposal seeks to use powerful new proteomic technologies to globally quantify changes in ubiquitylation in order to identify novel functional macrophage responses to M. tuberculosis infection. Our preliminary experiments utilizing this approach have uncovered profound changes in host protein ubiquitylation in response to intracellular pathogens. These studies have provided the first glimpse into a vast unknown of post-translational modifications during innate immune responses. Our hypothesis is that these changes play fundamental roles in shaping the subsequent innate responses to infection by controlling autophagy, metabolism, protein degradation, and signaling, and may be manipulated by pathogens for their own benefit. Our preliminary genetic work indicates that novel pathways are controlled by ubiquitylation during infection and are capable of restricting M. tuberculosis growth in macrophages, further validating the power of this approach to uncover new biology. Ultimately, our long-term goal is to harness these powerful immune mechanisms for therapeutic purposes.

Public Health Relevance

This proposal seeks to identify novel macrophage pathways that function to limit M. tuberculosis infection by capitalizing on a powerful new proteomic platform that enables unparalleled discovery of regulated ubiquitylation events. Our preliminary findings indicate that profound, previously unrecognized, cellular changes occur at the post-transcriptional level at the very earliest stages of infection. Ultimately, our long-term goal is t harness these powerful immune mechanisms to design host-directed therapies that will synergize with traditional antibiotics to eradicate TB.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
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Special Emphasis Panel (ZRG1-IDM-R (02))
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Lacourciere, Karen A
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University of California San Francisco
Schools of Medicine
San Francisco
United States
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Mitchell, Gabriel; Cheng, Mandy I; Chen, Chen et al. (2018) Listeria monocytogenes triggers noncanonical autophagy upon phagocytosis, but avoids subsequent growth-restricting xenophagy. Proc Natl Acad Sci U S A 115:E210-E217
Penn, Bennett H; Netter, Zoe; Johnson, Jeffrey R et al. (2018) An Mtb-Human Protein-Protein Interaction Map Identifies a Switch between Host Antiviral and Antibacterial Responses. Mol Cell 71:637-648.e5
Chen, Si-Han; Jang, Gwendolyn M; Hüttenhain, Ruth et al. (2018) CRL4AMBRA1 targets Elongin C for ubiquitination and degradation to modulate CRL5 signaling. EMBO J 37:
Patrick, Kristin L; Wojcechowskyj, Jason A; Bell, Samantha L et al. (2018) Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection. Cell Syst 7:323-338.e6
Du, Dan; Roguev, Assen; Gordon, David E et al. (2017) Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods 14:577-580
Lobingier, Braden T; Hüttenhain, Ruth; Eichel, Kelsie et al. (2017) An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. Cell 169:350-360.e12