Jonathan Budzik, MD

Asst Professor In Residence
Medicine
[email protected]
+1 415 476-7147

My research is focused on the innate immune mechanisms that control M. tuberculosis infection.  Autophagy is one mechanism that macrophages use to control microbial infection by targeting bacteria for degradation in the lysosome. Activation of autophagy is mediated by kinases that phosphorylate autophagy adaptors, which are proteins that direct cargo to the autophagy machinery.  By using global phosphoproteomics, we are studying the changes in autophagy adaptor phosphorylation levels during TB infection.  My ultimate hope is that a better understanding of the mechanism of autophagy targeting of TB will facilitate the development of host direct therapies for TB.

UCSF Center for Tuberculosis Initiatives:
TB RAMP Scholar | Class 2025

Publications: 

Author Correction: Autophagy restricts Mycobacterium tuberculosis during acute infection in mice.

Nature microbiology

Golovkine GR, Roberts AW, Morrison HM, Rivera-Lugo R, McCall RM, Nilsson H, Garelis NE, Repasy T, Cronce M, Budzik J, Van Dis E, Popov LM, Mitchell G, Zalpuri R, Jorgens D, Cox JS

History of tuberculosis disease is associated with genetic regulatory variation in Peruvians.

PLoS genetics

Nieto-Caballero VE, Reijneveld JF, Ruvalcaba A, Innocenzi G, Abeydeera N, Asgari S, Lopez K, Iwany SK, Luo Y, Nathan A, Fernandez-Salinas D, Chiñas M, Huang CC, Zhang Z, León SR, Calderon RI, Lecca L, Budzik JM, Murray M, Van Rhijn I, Raychaudhuri S, Moody DB, Suliman S, Gutierrez-Arcelus M

Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection.

PLoS pathogens

Zheng W, Chang IC, Limberis J, Budzik JM, Zha BS, Howard Z, Chen L, Ernst JD

Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection.

Research square

Zheng W, Chang IC, Limberis J, Budzik J, Zha BS, Howard Z, Chen L, Ernst J

Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during persistent infection.

bioRxiv : the preprint server for biology

Zheng W, Chang IC, Limberis J, Budzik JM, Zha BS, Howard Z, Ernst JD

Autophagy restricts Mycobacterium tuberculosis during acute infection in mice.

Nature microbiology

Golovkine GR, Roberts AW, Morrison HM, Rivera-Lugo R, McCall RM, Nilsson H, Garelis NE, Repasy T, Cronce M, Budzik J, Van Dis E, Popov LM, Mitchell G, Zalpuri R, Jorgens D, Cox JS

Ceragenins and Antimicrobial Peptides Kill Bacteria through Distinct Mechanisms.

mBio

Mitchell G, Silvis MR, Talkington KC, Budzik JM, Dodd CE, Paluba JM, Oki EA, Trotta KL, Licht DJ, Jimenez-Morales D, Chou S, Savage PB, Gross CA, Marletta MA, Cox JS

Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins.

Cell reports

Hiatt J, Cavero DA, McGregor MJ, Zheng W, Budzik JM, Roth TL, Haas KM, Wu D, Rathore U, Meyer-Franke A, Bouzidi MS, Shifrut E, Lee Y, Kumar VE, Dang EV, Gordon DE, Wojcechowskyj JA, Hultquist JF, Fontaine KA, Pillai SK, Cox JS, Ernst JD, Krogan NJ, Marson A

Antibiotic adverse reactions in adult cystic fibrosis patients.

The journal of allergy and clinical immunology. In practice

Anstey KM, Lee M, Dawson D, Jue V, Budzik JM, Yu M, Kleinhenz ME, Otani IM

Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages.

eLife

Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE, Repasy T, Roberts AW, Popov LM, Parry TJ, Pratt D, Ideker T, Krogan NJ, Cox JS

Pyrazinamide resistance, Mycobacterium tuberculosis lineage and treatment outcomes in San Francisco, California.

PloS one

Budzik JM, Jarlsberg LG, Higashi J, Grinsdale J, Hopewell PC, Kato-Maeda M, Nahid P

Isopeptide bonds of the major pilin protein BcpA influence pilus structure and bundle formation on the surface of Bacillus cereus.

Molecular microbiology

Hendrickx AP, Poor CB, Jureller JE, Budzik JM, He C, Schneewind O

Disseminated Nocardia farcinica: literature review and fatal outcome in an immunocompetent patient.

Surgical infections

Budzik JM, Hosseini M, Mackinnon AC, Taxy JB

Two capsular polysaccharides enable Bacillus cereus G9241 to cause anthrax-like disease.

Molecular microbiology

Oh SY, Budzik JM, Garufi G, Schneewind O

Architects at the bacterial surface - sortases and the assembly of pili with isopeptide bonds.

Nature reviews. Microbiology

Hendrickx AP, Budzik JM, Oh SY, Schneewind O

Intramolecular amide bonds stabilize pili on the surface of bacilli.

Proceedings of the National Academy of Sciences of the United States of America

Budzik JM, Poor CB, Faull KF, Whitelegge JP, He C, Schneewind O

Sortase D forms the covalent bond that links BcpB to the tip of Bacillus cereus pili.

The Journal of biological chemistry

Budzik JM, Oh SY, Schneewind O

Capsule anchoring in Bacillus anthracis occurs by a transpeptidation reaction that is inhibited by capsidin.

Molecular microbiology

Richter S, Anderson VJ, Garufi G, Lu L, Budzik JM, Joachimiak A, He C, Schneewind O, Missiakas D

Cell wall anchor structure of BcpA pili in Bacillus anthracis.

The Journal of biological chemistry

Budzik JM, Oh SY, Schneewind O

Sortases make pili from three ingredients.

Proceedings of the National Academy of Sciences of the United States of America

Oh SY, Budzik JM, Schneewind O

Amide bonds assemble pili on the surface of bacilli.

Proceedings of the National Academy of Sciences of the United States of America

Budzik JM, Marraffini LA, Souda P, Whitelegge JP, Faull KF, Schneewind O

Assembly of pili on the surface of Bacillus cereus vegetative cells.

Molecular microbiology

Budzik JM, Marraffini LA, Schneewind O

Pili prove pertinent to enterococcal endocarditis.

The Journal of clinical investigation

Budzik JM, Schneewind O

The role of bacterial biofilms in ocular infections.

DNA and cell biology

Zegans ME, Becker HI, Budzik J, O'Toole G