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Kenan C Murphy PhD

TitleAssistant Professor
InstitutionUMass Chan Medical School
DepartmentMicrobiology and Physiological Systems
AddressUMass Chan Medical School
55 Lake Avenue North
Worcester MA 01655
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentMicrobiology and Physiological Systems

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentImmunology and Microbiology Program

    InstitutionUMass Chan Programs, Centers and Institutes
    DepartmentBacterial Genetics and Pathogenesis

    Collapse Biography 
    Collapse education and training
    Catholic University of America, Washington, DC, United StatesBAPhysics
    University of Maryland, College Park, College Park, MD, United StatesPHDBiochemistry

    Collapse Overview 
    Collapse Summary
    Focus: DNA Mismatch repair mechanisms in M. smegmatis; recombineering technology for gene replacement in bacterial pathogens, M. tuberculosis drug discovery.
    Collapse overview

    Academic Background

    Ph. D. (1983) University of Maryland

    Recombineering technology for gene replacement in bacterial pathogens

    Identification of Drug Targets in M. tuberculosis - creating regulatable strains for use in whole cell screens with small molecules

    My work invovles the use of Red recombineering technology for gene replacement in bacterial pathogens. My lab was the first to show that the lambda Red recombination system promotes gene replacement of electroporated linear DNA substrates into the Escherichia coliK-12 chromosome at a very high efficiency (Murphy, 1998). The system is also useful in pathogenic species of E. coli (Murphy & Campellone, 2003). Work continues to improve recombinering technology in pathogens such as Pseudomonas aeruginosa and Mycobacterium tuberculosis by expression of Red-lke recombination systems from phage known to infect these hosts.


    My lab is also interested in the mechnaism of the bacteriophage lambda Red recombination system. The system consist of two proteins, the ssDNA annealing Bet protein and the 5’-3’ dsDNA lambda exonuclease. These two proteins form a complex in vitro, and are thought to interact with each other in vivo. We have isolated various mutants of Bet that are deficient for both recombination and recombineering, and some that are deficient for one but not the other.   



    Proposed mechanism of Red Recombineering

    Lambda Exo's 5' exonuclease activity (red trapezoid)) generates ssDNA, which serves as a substrate for lambda Bet (blue oligomeric ring) to bind and promote annealing to ssDNA in the lagging strand of a replication fork. This structure is stabilized by the lambda Beta protein, unitl another fork comes by and generates both a wild type and a recombinant chromosome.

    replication Kenan Murphy figure page

    Collapse Rotation Projects

    Rotation Projects

    1. Study the interaction of the ssDNA annealing protein Bet and its cognate exonuclease with dsDNA ends. Compare wild type Bet with one or mutant Bet proteins.  Use both genetic and biochemical studies to answer the question of how this annealase binds to ssDNA and promotes recombination.


    2. Develop recombineering technologies for M. tuberculosis involving the electroporation of oligos containing clinically relevant single nucleotide polymorphisms (SNPs).


    3. Generate a recombineering system for Pseudomonas aeruginosa via the electroporation of PCR substrates into electrocompetent cells containing PA phage Red-like recombination systems. 


    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Vargas R, Luna MJ, Freschi L, Marin M, Froom R, Murphy KC, Campbell EA, Ioerger TR, Sassetti CM, Farhat MR. Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A. 2023 07 11; 120(28):e2301394120. PMID: 37399390.
      Citations:    Fields:    Translation:Cells
    2. Koh EI, Oluoch PO, Ruecker N, Proulx MK, Soni V, Murphy KC, Papavinasasundaram K, Reames CJ, Trujillo C, Zaveri A, Zimmerman MD, Aslebagh R, Baker RE, Shaffer SA, Guinn KM, Fitzgerald M, Dartois V, Ehrt S, Hung DT, Ioerger TR, Rubin EJ, Rhee KY, Schnappinger D, Sassetti CM. Chemical-genetic interaction mapping links carbon metabolism and cell wall structure to tuberculosis drug efficacy. Proc Natl Acad Sci U S A. 2022 04 12; 119(15):e2201632119. PMID: 35380903.
      Citations: 10     Fields:    Translation:HumansCells
    3. Smith CM, Baker RE, Proulx MK, Mishra BB, Long JE, Park SW, Lee HN, Kiritsy MC, Bellerose MM, Olive AJ, Murphy KC, Papavinasasundaram K, Boehm FJ, Reames CJ, Meade RK, Hampton BK, Linnertz CL, Shaw GD, Hock P, Bell TA, Ehrt S, Schnappinger D, Pardo-Manuel de Villena F, Ferris MT, Ioerger TR, Sassetti CM. Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice. Elife. 2022 02 03; 11. PMID: 35112666.
      Citations: 24     Fields:    Translation:AnimalsCells
    4. Murphy KC. Oligo-Mediated Recombineering and its Use for Making SNPs, Knockouts, Insertions, and Fusions in Mycobacterium tuberculosis. Methods Mol Biol. 2021; 2314:301-321. PMID: 34235660.
      Citations: 2     Fields:    Translation:Cells
    5. Sutiwisesak R, Hicks ND, Boyce S, Murphy KC, Papavinasasundaram K, Carpenter SM, Boucau J, Joshi N, Le Gall S, Fortune SM, Sassetti CM, Behar SM. A natural polymorphism of Mycobacterium tuberculosis in the esxH gene disrupts immunodomination by the TB10.4-specific CD8 T cell response. PLoS Pathog. 2020 10; 16(10):e1009000. PMID: 33075106.
      Citations: 14     Fields:    Translation:HumansAnimalsCells
    6. Poweleit N, Czudnochowski N, Nakagawa R, Trinidad DD, Murphy KC, Sassetti CM, Rosenberg OS. The structure of the endogenous ESX-3 secretion system. Elife. 2019 12 30; 8. PMID: 31886769.
      Citations: 28     Fields:    Translation:Cells
    7. Johnson EO, LaVerriere E, Office E, Stanley M, Meyer E, Kawate T, Gomez JE, Audette RE, Bandyopadhyay N, Betancourt N, Delano K, Da Silva I, Davis J, Gallo C, Gardner M, Golas AJ, Guinn KM, Kennedy S, Korn R, McConnell JA, Moss CE, Murphy KC, Nietupski RM, Papavinasasundaram KG, Pinkham JT, Pino PA, Proulx MK, Ruecker N, Song N, Thompson M, Trujillo C, Wakabayashi S, Wallach JB, Watson C, Ioerger TR, Lander ES, Hubbard BK, Serrano-Wu MH, Ehrt S, Fitzgerald M, Rubin EJ, Sassetti CM, Schnappinger D, Hung DT. Large-scale chemical-genetics yields new M. tuberculosis inhibitor classes. Nature. 2019 07; 571(7763):72-78. PMID: 31217586.
      Citations: 63     Fields:    Translation:Cells
    8. Murphy KC, Nelson SJ, Nambi S, Papavinasasundaram K, Baer CE, Sassetti CM. ORBIT: a New Paradigm for Genetic Engineering of Mycobacterial Chromosomes. mBio. 2018 12 11; 9(6). PMID: 30538179.
      Citations: 54     Fields:    Translation:Cells
    9. Prigozhin DM, Papavinasasundaram KG, Baer CE, Murphy KC, Moskaleva A, Chen TY, Alber T, Sassetti CM. Structural and Genetic Analyses of the Mycobacterium tuberculosis Protein Kinase B Sensor Domain Identify a Potential Ligand-binding Site. J Biol Chem. 2016 10 28; 291(44):22961-22969. PMID: 27601474.
      Citations: 12     Fields:    Translation:HumansCells
    10. Warrier T, Kapilashrami K, Argyrou A, Ioerger TR, Little D, Murphy KC, Nandakumar M, Park S, Gold B, Mi J, Zhang T, Meiler E, Rees M, Somersan-Karakaya S, Porras-De Francisco E, Martinez-Hoyos M, Burns-Huang K, Roberts J, Ling Y, Rhee KY, Mendoza-Losana A, Luo M, Nathan CF. N-methylation of a bactericidal compound as a resistance mechanism in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2016 08 02; 113(31):E4523-30. PMID: 27432954.
      Citations: 31     Fields:    Translation:Cells
    11. Murphy KC. ? Recombination and Recombineering. EcoSal Plus. 2016 05; 7(1). PMID: 27223821.
      Citations: 35     Fields:    Translation:Cells
    12. Murphy, KC. EcoSal Plus 2016; doi:10.1128/ecosalplus.ESP-0011-2015. Phage Lambda Recombination and Recombineering. 2016. View Publication.
    13. Nambi S, Long JE, Mishra BB, Baker R, Murphy KC, Olive AJ, Nguyen HP, Shaffer SA, Sassetti CM. The Oxidative Stress Network of Mycobacterium tuberculosis Reveals Coordination between Radical Detoxification Systems. Cell Host Microbe. 2015 Jun 10; 17(6):829-37. PMID: 26067605.
      Citations: 67     Fields:    Translation:AnimalsCells
    14. Murphy KC, Papavinasasundaram K, Sassetti CM. Mycobacterial recombineering. Methods Mol Biol. 2015; 1285:177-99. PMID: 25779316.
      Citations: 45     Fields:    Translation:Cells
    15. Meniche X, Otten R, Siegrist MS, Baer CE, Murphy KC, Bertozzi CR, Sassetti CM. Subpolar addition of new cell wall is directed by DivIVA in mycobacteria. Proc Natl Acad Sci U S A. 2014 Aug 05; 111(31):E3243-51. PMID: 25049412.
      Citations: 93     Fields:    Translation:Cells
    16. Carone BR, Xu T, Murphy KC, Marinus MG. High incidence of multiple antibiotic resistant cells in cultures of in enterohemorrhagic Escherichia coli O157:H7. Mutat Res. 2014 Jan; 759:1-8. PMID: 24361397.
      Citations: 8     Fields:    Translation:Cells
    17. Ioerger TR, O'Malley T, Liao R, Guinn KM, Hickey MJ, Mohaideen N, Murphy KC, Boshoff HI, Mizrahi V, Rubin EJ, Sassetti CM, Barry CE, Sherman DR, Parish T, Sacchettini JC. Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis. PLoS One. 2013; 8(9):e75245. PMID: 24086479.
      Citations: 112     Fields:    Translation:Cells
    18. Murphy KC, Volkert MR. Structural/functional analysis of the human OXR1 protein: identification of exon 8 as the anti-oxidant encoding function. BMC Mol Biol. 2012 Aug 08; 13:26. PMID: 22873401.
      Citations: 17     Fields:    Translation:HumansCells
    19. Murphy KC. Phage recombinases and their applications. Adv Virus Res. 2012; 83:367-414. PMID: 22748814.
      Citations: 41     Fields:    Translation:Cells
    20. Flockhart AF, Tree JJ, Xu X, Karpiyevich M, McAteer SP, Rosenblum R, Shaw DJ, Low CJ, Best A, Gannon V, Laing C, Murphy KC, Leong JM, Schneiders T, La Ragione R, Gally DL. Identification of a novel prophage regulator in Escherichia coli controlling the expression of type III secretion. Mol Microbiol. 2012 Jan; 83(1):208-23. PMID: 22111928.
      Citations: 19     Fields:    Translation:HumansAnimalsCells
    21. Brady MJ, Radhakrishnan P, Liu H, Magoun L, Murphy KC, Mukherjee J, Donohue-Rolfe A, Tzipori S, Leong JM. Enhanced Actin Pedestal Formation by Enterohemorrhagic Escherichia coli O157:H7 Adapted to the Mammalian Host. Front Microbiol. 2011; 2:226. PMID: 22102844.
    22. Tree JJ, Roe AJ, Flockhart A, McAteer SP, Xu X, Shaw D, Mahajan A, Beatson SA, Best A, Lotz S, Woodward MJ, La Ragione R, Murphy KC, Leong JM, Gally DL. Transcriptional regulators of the GAD acid stress island are carried by effector protein-encoding prophages and indirectly control type III secretion in enterohemorrhagic Escherichia coli O157:H7. Mol Microbiol. 2011 Jun; 80(5):1349-65. PMID: 21492263.
      Citations: 29     Fields:    Translation:AnimalsCells
    23. Wei JR, Krishnamoorthy V, Murphy K, Kim JH, Schnappinger D, Alber T, Sassetti CM, Rhee KY, Rubin EJ. Depletion of antibiotic targets has widely varying effects on growth. Proc Natl Acad Sci U S A. 2011 Mar 08; 108(10):4176-81. PMID: 21368134.
      Citations: 90     Fields:    Translation:Cells
    24. Murphy KC. Targeted chromosomal gene knockout using PCR fragments. Methods Mol Biol. 2011; 765:27-42. PMID: 21815084.
      Citations: 2     Fields:    Translation:Cells
    25. Murphy KC, Marinus MG. RecA-independent single-stranded DNA oligonucleotide-mediated mutagenesis. F1000 Biol Rep. 2010 Jul 22; 2:56. PMID: 20711416.
    26. Murphy KC, Ritchie JM, Waldor MK, L?bner-Olesen A, Marinus MG. Dam methyltransferase is required for stable lysogeny of the Shiga toxin (Stx2)-encoding bacteriophage 933W of enterohemorrhagic Escherichia coli O157:H7. J Bacteriol. 2008 Jan; 190(1):438-41. PMID: 17981979.
      Citations: 23     Fields:    Translation:Cells
    27. Murphy KC. The lambda Gam protein inhibits RecBCD binding to dsDNA ends. J Mol Biol. 2007 Aug 03; 371(1):19-24. PMID: 17583735.
      Citations: 19     Fields:    Translation:Cells
    28. Campellone KG, Roe AJ, L?bner-Olesen A, Murphy KC, Magoun L, Brady MJ, Donohue-Rolfe A, Tzipori S, Gally DL, Leong JM, Marinus MG. Increased adherence and actin pedestal formation by dam-deficient enterohaemorrhagic Escherichia coli O157:H7. Mol Microbiol. 2007 Mar; 63(5):1468-81. PMID: 17302821.
      Citations: 32     Fields:    Translation:HumansAnimalsCells
    29. Savage PJ, Leong JM, Murphy KC. Rapid allelic exchange in enterohemorrhagic Escherichia coli (EHEC) and other E. coli using lambda red recombination. Curr Protoc Microbiol. 2006 Jan; Chapter 5:Unit5A.2. PMID: 18770591.
      Citations: 1     Fields:    Translation:Cells
    30. Murphy KC, Campellone KG. Lambda Red-mediated recombinogenic engineering of enterohemorrhagic and enteropathogenic E. coli. BMC Mol Biol. 2003 Dec 13; 4:11. PMID: 14672541.
      Citations: 212     Fields:    Translation:Cells
    31. Loh T, Murphy KC, Marinus MG. Mutational analysis of the MutH protein from Escherichia coli. J Biol Chem. 2001 Apr 13; 276(15):12113-9. PMID: 11124943.
      Citations: 12     Fields:    Translation:Cells
    32. Murphy KC, Campellone KG, Poteete AR. PCR-mediated gene replacement in Escherichia coli. Gene. 2000 Apr 04; 246(1-2):321-30. PMID: 10767554.
      Citations: 139     Fields:    Translation:Cells
    33. Murphy KC. Use of bacteriophage lambda recombination functions to promote gene replacement in Escherichia coli. J Bacteriol. 1998 Apr; 180(8):2063-71. PMID: 9555887.
      Citations: 231     Fields:    Translation:Cells
    34. Murphy KC. Biochemical characterization of P22 phage-modified Escherichia coli RecBCD enzyme. J Biol Chem. 1994 Sep 09; 269(36):22507-16. PMID: 8077199.
      Citations: 2     Fields:    Translation:Cells
    35. Murphy KC, Lewis LJ. Properties of Escherichia coli expressing bacteriophage P22 Abc (anti-RecBCD) proteins, including inhibition of Chi activity. J Bacteriol. 1993 Mar; 175(6):1756-66. PMID: 8383665.
      Citations: 6     Fields:    Translation:Cells
    36. Murphy KC. Lambda Gam protein inhibits the helicase and chi-stimulated recombination activities of Escherichia coli RecBCD enzyme. J Bacteriol. 1991 Sep; 173(18):5808-21. PMID: 1653221.
      Citations: 62     Fields:    Translation:Cells
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