Ehrt Lab & Schnappinger Lab

Schnappinger Lab

Schnappinger Lab Research


A central goal of our lab is to facilitate the development of new medicines for the treatment and prevention of Tuberculosis (TB). TB is an infectious disease caused by the bacterium Mycobacterium tuberculosis (Mtb), a pathogen that is probably as old as the human species and still claims millions of lives each year.

We began our drug-discovery related work with developing a regulatory system that allows us to turn Mtb genes on and off, both in vitro and during infections (1,2). Since its publication in 2005, this system has been refined (3,4) and used by us and others to evaluate dozens of Mtb gene products as new targets for TB drug development (for a few recent examples see references 5-10). This work has been highlighted and commented on by others, for example in Nature Reviews Drug Discovery (11), PNAS (12), the NIAID blog (13), and the LA Times (14). In related work we apply partial gene silencing, resulting in conditional hypomorphs, to specifically sensitize Mtb to inhibitors of the protein of interest. We first used this principle to study Mtb’s thioredoxin reductase (15) and, more recently, helped to apply this approach to over 100 Mtb genes (16).

Drug development requires a broad spectrum of expertise and techniques. Our work in this area therefore includes close collaborations with the labs led by Courtney Aldrich (University of Minnesota), Clifton Barry III (NIH), Veronique Dartois (Center for Discovery and Innovation), Deborah Hung (Broad Institute), Sabine Ehrt (Weill Cornell), Valerie Mizrahi (University of Cape Town), Carl Nathan (Weill Cornell), Kyu Rhee (Weill Cornell), Jeremy Rock (Rockefeller University), Eric Rubin (Harvard University), Christopher Sassetti (University of Massachusetts) and several pharmaceutical companies that participate in the TB Drug Accelerator program (17).

Our biology-centric projects are frequently motivated by genes and pathways we initially studied due to their potential relevance for drug development. For example, we first got interested in biotin metabolism due to Mtb’s susceptibility to inhibition of biotin-dependent enzymes (18). We then determined the consequences of inhibiting different Mtb enzymes required for protein biotinylation in vitro and during infection (9, 19). In ongoing work, we are studying the transcriptomic responses to inhibition of biotin deprivation in Mtb and M. smegmatis, the mechanism of biotin-starvation induced cell death, the accessory factors required to convert dethiobiotin into biotin, biotin import, and the host defense mechanisms that cause killing of biotin auxotrophs in mice.

In more recent and currently unpublished work, we began to use our genetic tools to also help with the development of effective vaccines to prevent pulmonary TB in adults. Our specific goals are to (i) improve safety of the widely used vaccine M. bovis BCG to allow its use for alternative routes of vaccination in humans, and (ii) to construct conditionally replicating Mtb strains that are safe enough for human challenge studies. We pursue these goals in collaboration with Sabine Ehrt (Weill Cornell), JoAnne Flynn (University of Pittsburgh), Sarah Fortune (Harvard University), Eric Rubin (Harvard University) and Robert Seder (NIH). 



1.         Ehrt, S., et al. Controlling gene expression in mycobacteria with anhydrotetracycline and Tet repressor. Nucleic Acids Research 33, e21 (2005).
2.         Gandotra, S., Schnappinger, D., Monteleone, M., Hillen, W. & Ehrt, S. In vivo gene silencing identifies the Mycobacterium tuberculosis proteasome as essential for the bacteria to persist in mice. Nature Medicine 13, 1515-1520 (2007).
3.         Kim, J.H., et al. A genetic strategy to identify targets for the development of drugs that prevent bacterial persistence. Proceedings of the National Academy of Sciences of the United States of America 110, 19095-19100 (2013)
4.         Klotzsche, M., Ehrt, S. & Schnappinger, D. Improved tetracycline repressors for gene silencing in mycobacteria. Nucleic acids research 37, 1778-1788 (2009).
5.         Botella, L., Vaubourgeix, J., Livny, J. & Schnappinger, D. Depleting Mycobacterium tuberculosis of the transcription termination factor Rho causes pervasive transcription and rapid death. Nat Commun 8, 14731 (2017).
6.         Evans, J.C., et al. Validation of CoaBC as a Bactericidal Target in the Coenzyme A Pathway of Mycobacterium tuberculosis. ACS Infect Dis 2, 958-968 (2016).
7.    Lin, K., et al. Mycobacterium tuberculosis Thioredoxin Reductase Is Essential for Thiol Redox Homeostasis but Plays a Minor Role in Antioxidant Defense. PLoS pathogens 12, e1005675 (2016).
8.         Puckett, S., et al. Glyoxylate detoxification is an essential function of malate synthase required for carbon assimilation in Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America 114, E2225-E2232 (2017).
9.         Tiwari, D., et al. Targeting protein biotinylation enhances tuberculosis chemotherapy. Sci Transl Med 10(2018).
10.      Li, W., et al. Therapeutic Potential of the Mycobacterium tuberculosis Mycolic Acid Transporter, MmpL3. Antimicrob Agents Chemother 60, 5198-5207 (2016).
11.      Kahrstrom, C.T. Antibacterial drugs: Persisters come under fire. Nat Rev Drug Discov 13, 18-19 (2014).
15.      Lin, K., et al. Mycobacterium tuberculosis Thioredoxin Reductase Is Essential for Thiol Redox Homeostasis but Plays a Minor Role in Antioxidant Defense. PLoS Pathogens 12, e1005675 (2016).
18.      Duckworth, B.P., et al. Bisubstrate adenylation inhibitors of biotin protein ligase from Mycobacterium tuberculosis. Chemistry & biology 18, 1432-1441 (2011).
19.      Woong Park, S., et al. Evaluating the sensitivity of Mycobacterium tuberculosis to biotin deprivation using regulated gene expression. PLoS Pathogens 7, e1002264 (2011).