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Joseph Bondy-Denomy, PhD

Title(s)Assistant Professor, Microbiology and Immunology
SchoolSchool of Medicine
Phone415-514-1381
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    Collapse Biography 
    Collapse Education and Training
    University of Waterloo, Waterloo, ONBSc08/2008Biology, Microbiology
    University of Toronto, Toronto, ONPhD11/2014Molecular Genetics

    Collapse Overview 
    Collapse Overview
    In the Bondy-Denomy lab, we study CRISPR-Cas bacterial immune systems in an effort to understand their role in antagonizing viruses called bacteriophages. We are very interested in how CRISPR works and the ways that phages inhibit and evade CRISPR-Cas function.

    Collapse Research 
    Collapse Research Activities and Funding
    Uncovering the mechanism and role of a widespread anti-CRISPR-Cas9 protein
    NIH/NIGMS R01GM127489Apr 9, 2018 - Mar 31, 2023
    Role: Principal Investigator
    Discovering New Roles for CRISPR-Cas in Bacterial Pathogenesis
    NIH DP5OD021344Sep 25, 2015 - Aug 31, 2020
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications
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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Mahendra C, Christie KA, Osuna BA, Pinilla-Redondo R, Kleinstiver BP, Bondy-Denomy J. Author Correction: Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer. Nat Microbiol. 2020 Apr 23. PMID: 32327734.
      View in: PubMed
    2. Osuna BA, Karambelkar S, Mahendra C, Sarbach A, Johnson MC, Kilcher S, Bondy-Denomy J. Critical Anti-CRISPR Locus Repression by a Bi-functional Cas9 Inhibitor. Cell Host Microbe. 2020 Apr 21. PMID: 32325051.
      View in: PubMed
    3. Osuna BA, Karambelkar S, Mahendra C, Christie KA, Garcia B, Davidson AR, Kleinstiver BP, Kilcher S, Bondy-Denomy J. Listeria Phages Induce Cas9 Degradation to Protect Lysogenic Genomes. Cell Host Microbe. 2020 Apr 18. PMID: 32325050.
      View in: PubMed
    4. Mahendra C, Christie KA, Osuna BA, Pinilla-Redondo R, Kleinstiver BP, Bondy-Denomy J. Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer. Nat Microbiol. 2020 Apr; 5(4):620-629. PMID: 32218510.
      View in: PubMed
    5. Borges AL, Castro B, Govindarajan S, Solvik T, Escalante V, Bondy-Denomy J. Bacterial alginate regulators and phage homologs repress CRISPR-Cas immunity. Nat Microbiol. 2020 Mar 23. PMID: 32203410.
      View in: PubMed
    6. Marino ND, Pinilla-Redondo R, Csörgo B, Bondy-Denomy J. Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies. Nat Methods. 2020 Mar 16. PMID: 32203383.
      View in: PubMed
    7. Roux S, Krupovic M, Daly RA, Borges AL, Nayfach S, Schulz F, Sharrar A, Matheus Carnevali PB, Cheng JF, Ivanova NN, Bondy-Denomy J, Wrighton KC, Woyke T, Visel A, Kyrpides NC, Eloe-Fadrosh EA. Author Correction: Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes. Nat Microbiol. 2020 Mar; 5(3):527. PMID: 32047285.
      View in: PubMed
    8. Mendoza SD, Nieweglowska ES, Govindarajan S, Leon LM, Berry JD, Tiwari A, Chaikeeratisak V, Pogliano J, Agard DA, Bondy-Denomy J. A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases. Nature. 2020 01; 577(7789):244-248. PMID: 31819262.
      View in: PubMed
    9. Crowley VM, Catching A, Taylor HN, Borges AL, Metcalf J, Bondy-Denomy J, Jackson RN. A Type IV-A CRISPR-Cas System in Pseudomonas aeruginosa Mediates RNA-Guided Plasmid Interference In Vivo. CRISPR J. 2019 12; 2(6):434-440. PMID: 31809194.
      View in: PubMed
    10. Hooda Y, Sajib MSI, Rahman H, Luby SP, Bondy-Denomy J, Santosham M, Andrews JR, Saha SK, Saha S. Molecular mechanism of azithromycin resistance among typhoidal Salmonella strains in Bangladesh identified through passive pediatric surveillance. PLoS Negl Trop Dis. 2019 11; 13(11):e0007868. PMID: 31730615.
      View in: PubMed
    11. Soto-Perez P, Bisanz JE, Berry JD, Lam KN, Bondy-Denomy J, Turnbaugh PJ. CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog. Cell Host Microbe. 2019 Sep 11; 26(3):325-335.e5. PMID: 31492655.
      View in: PubMed
    12. Stanley SY, Borges AL, Chen KH, Swaney DL, Krogan NJ, Bondy-Denomy J, Davidson AR. Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription. Cell. 2019 Sep 05; 178(6):1452-1464.e13. PMID: 31474367.
      View in: PubMed
    13. Roux S, Krupovic M, Daly RA, Borges AL, Nayfach S, Schulz F, Sharrar A, Matheus Carnevali PB, Cheng JF, Ivanova NN, Bondy-Denomy J, Wrighton KC, Woyke T, Visel A, Kyrpides NC, Eloe-Fadrosh EA. Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth's biomes. Nat Microbiol. 2019 11; 4(11):1895-1906. PMID: 31332386.
      View in: PubMed
    14. Mendoza SD, Bondy-Denomy J. Cas13 Helps Bacteria Play Dead when the Enemy Strikes. Cell Host Microbe. 2019 07 10; 26(1):1-2. PMID: 31295418.
      View in: PubMed
    15. Nakamura M, Srinivasan P, Chavez M, Carter MA, Dominguez AA, La Russa M, Lau MB, Abbott TR, Xu X, Zhao D, Gao Y, Kipniss NH, Smolke CD, Bondy-Denomy J, Qi LS. Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells. Nat Commun. 2019 01 14; 10(1):194. PMID: 30643127.
      View in: PubMed
    16. Jiang F, Liu JJ, Osuna BA, Xu M, Berry JD, Rauch BJ, Nogales E, Bondy-Denomy J, Doudna JA. Temperature-Responsive Competitive Inhibition of CRISPR-Cas9. Mol Cell. 2019 02 07; 73(3):601-610.e5. PMID: 30595438.
      View in: PubMed
    17. Tsao YF, Taylor VL, Kala S, Bondy-Denomy J, Khan AN, Bona D, Cattoir V, Lory S, Davidson AR, Maxwell KL. Phage Morons Play an Important Role in Pseudomonas aeruginosa Phenotypes. J Bacteriol. 2018 11 15; 200(22). PMID: 30150232.
      View in: PubMed
    18. Bondy-Denomy J, Davidson AR, Doudna JA, Fineran PC, Maxwell KL, Moineau S, Peng X, Sontheimer EJ, Wiedenheft B. A Unified Resource for Tracking Anti-CRISPR Names. CRISPR J. 2018 10; 1:304-305. PMID: 31021273.
      View in: PubMed
    19. Marino ND, Zhang JY, Borges AL, Sousa AA, Leon LM, Rauch BJ, Walton RT, Berry JD, Joung JK, Kleinstiver BP, Bondy-Denomy J. Discovery of widespread type I and type V CRISPR-Cas inhibitors. Science. 2018 10 12; 362(6411):240-242. PMID: 30190308.
      View in: PubMed
    20. Borges AL, Zhang JY, Rollins MF, Osuna BA, Wiedenheft B, Bondy-Denomy J. Bacteriophage Cooperation Suppresses CRISPR-Cas3 and Cas9 Immunity. Cell. 2018 08 09; 174(4):917-925.e10. PMID: 30033364.
      View in: PubMed
    21. Bondy-Denomy J. Protein Inhibitors of CRISPR-Cas9. ACS Chem Biol. 2018 02 16; 13(2):417-423. PMID: 29251498.
      View in: PubMed
    22. Leon LM, Mendoza SD, Bondy-Denomy J. How bacteria control the CRISPR-Cas arsenal. Curr Opin Microbiol. 2018 04; 42:87-95. PMID: 29169146.
      View in: PubMed
    23. Harvey H, Bondy-Denomy J, Marquis H, Sztanko KM, Davidson AR, Burrows LL. Pseudomonas aeruginosa defends against phages through type IV pilus glycosylation. Nat Microbiol. 2018 Jan; 3(1):47-52. PMID: 29133883.
      View in: PubMed
    24. Borges AL, Davidson AR, Bondy-Denomy J. The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs. Annu Rev Virol. 2017 09 29; 4(1):37-59. PMID: 28749735.
      View in: PubMed
    25. Shin J, Jiang F, Liu JJ, Bray NL, Rauch BJ, Baik SH, Nogales E, Bondy-Denomy J, Corn JE, Doudna JA. Disabling Cas9 by an anti-CRISPR DNA mimic. Sci Adv. 2017 07; 3(7):e1701620. PMID: 28706995.
      View in: PubMed
    26. Rollins MF, Chowdhury S, Carter J, Golden SM, Wilkinson RA, Bondy-Denomy J, Lander GC, Wiedenheft B. Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity. Proc Natl Acad Sci U S A. 2017 06 27; 114(26):E5113-E5121. PMID: 28438998.
      View in: PubMed
    27. Chowdhury S, Carter J, Rollins MF, Golden SM, Jackson RN, Hoffmann C, Nosaka L, Bondy-Denomy J, Maxwell KL, Davidson AR, Fischer ER, Lander GC, Wiedenheft B. Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex. Cell. 2017 03 23; 169(1):47-57.e11. PMID: 28340349.
      View in: PubMed
    28. Wiedenheft B, Bondy-Denomy J. CRISPR control of virulence in Pseudomonas aeruginosa. Cell Res. 2017 02; 27(2):163-164. PMID: 28084330.
      View in: PubMed
    29. Rauch BJ, Silvis MR, Hultquist JF, Waters CS, McGregor MJ, Krogan NJ, Bondy-Denomy J. Inhibition of CRISPR-Cas9 with Bacteriophage Proteins. Cell. 2017 Jan 12; 168(1-2):150-158.e10. PMID: 28041849.
      View in: PubMed
    30. Høyland-Kroghsbo NM, Paczkowski J, Mukherjee S, Broniewski J, Westra E, Bondy-Denomy J, Bassler BL. Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system. Proc Natl Acad Sci U S A. 2017 01 03; 114(1):131-135. PMID: 27849583.
      View in: PubMed
    31. Maxwell KL, Garcia B, Bondy-Denomy J, Bona D, Hidalgo-Reyes Y, Davidson AR. The solution structure of an anti-CRISPR protein. Nat Commun. 2016 10 11; 7:13134. PMID: 27725669.
      View in: PubMed
    32. Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS, Davidson AR, Maxwell KL. Prophages mediate defense against phage infection through diverse mechanisms. ISME J. 2016 12; 10(12):2854-2866. PMID: 27258950.
      View in: PubMed
    33. van Houte S, Ekroth AK, Broniewski JM, Chabas H, Ashby B, Bondy-Denomy J, Gandon S, Boots M, Paterson S, Buckling A, Westra ER. The diversity-generating benefits of a prokaryotic adaptive immune system. Nature. 2016 Apr 21; 532(7599):385-8. PMID: 27074511.
      View in: PubMed
    34. Rao C, Guyard C, Pelaz C, Wasserscheid J, Bondy-Denomy J, Dewar K, Ensminger AW. Active and adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen. Cell Microbiol. 2016 10; 18(10):1319-38. PMID: 26936325.
      View in: PubMed
    35. Vorontsova D, Datsenko KA, Medvedeva S, Bondy-Denomy J, Savitskaya EE, Pougach K, Logacheva M, Wiedenheft B, Davidson AR, Severinov K, Semenova E. Foreign DNA acquisition by the I-F CRISPR-Cas system requires all components of the interference machinery. Nucleic Acids Res. 2015 Dec 15; 43(22):10848-60. PMID: 26586803.
      View in: PubMed
    36. Bondy-Denomy J, Garcia B, Strum S, Du M, Rollins MF, Hidalgo-Reyes Y, Wiedenheft B, Maxwell KL, Davidson AR. Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins. Nature. 2015 Oct 01; 526(7571):136-9. PMID: 26416740.
      View in: PubMed
    37. Westra ER, van Houte S, Oyesiku-Blakemore S, Makin B, Broniewski JM, Best A, Bondy-Denomy J, Davidson A, Boots M, Buckling A. Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense. Curr Biol. 2015 Apr 20; 25(8):1043-9. PMID: 25772450.
      View in: PubMed
    38. Pawluk A, Bondy-Denomy J, Cheung VH, Maxwell KL, Davidson AR. A new group of phage anti-CRISPR genes inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa. mBio. 2014 Apr 15; 5(2):e00896. PMID: 24736222.
      View in: PubMed
    39. Bondy-Denomy J, Davidson AR. When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness. J Microbiol. 2014 Mar; 52(3):235-42. PMID: 24585054.
      View in: PubMed
    40. Bondy-Denomy J, Davidson AR. To acquire or resist: the complex biological effects of CRISPR-Cas systems. Trends Microbiol. 2014 Apr; 22(4):218-25. PMID: 24582529.
      View in: PubMed
    41. Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature. 2013 Jan 17; 493(7432):429-32. PMID: 23242138.
      View in: PubMed
    42. Phee A, Bondy-Denomy J, Kishen A, Basrani B, Azarpazhooh A, Maxwell K. Efficacy of bacteriophage treatment on Pseudomonas aeruginosa biofilms. J Endod. 2013 Mar; 39(3):364-9. PMID: 23402508.
      View in: PubMed
    43. Cady KC, Bondy-Denomy J, Heussler GE, Davidson AR, O'Toole GA. The CRISPR/Cas adaptive immune system of Pseudomonas aeruginosa mediates resistance to naturally occurring and engineered phages. J Bacteriol. 2012 Nov; 194(21):5728-38. PMID: 22885297.
      View in: PubMed
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