USC.edu

Phuong Pham

Assistant Professor (Research) of Biological Sciences
Phuong Pham
Email ppham@usc.edu Office RRI 113 Office Phone (213) 740-5191

Education

  • Ph.D. Genetics, St. Petersburg State University, 5/1993
  • M.S. Biology, St. Peterburg State University, 6/1989
    • Visiting Fellow, National Institute of Environmental Health Sciences, 04/22/1999-04/22/2004

  • Summary Statement of Research Interests

    My research interest focuses on biological functions, structural and biochemical properties of “AID/Apobec” protein family of DNA dependent deoxycytidine deaminases. Members of this family include activation-induced cytidine deaminase (AID) and Apobec3G. By modifying DNA, AID and Apobec3G play an essential role in adaptive and innate immunity. AID is required for B cells to undergo somatic hypermutation (SHM) and class switch recombination (CSR), two processes that are needed to produce high-affinity antibodies. Apobec3G and other Apobec proteins are responsible for innate immunity against HIV infection by triggering the destruction of HIV-1 reverse transcribed DNA. My current studies focus on establishing the processive scanning and catalytic mechanisms of AID/Apobec proteins and on linking their biochemical features to the clustered mutational signature observed cancer genomes. I also work to develop eukaryotic transcription dependent AID-catalyzed deamination and error-prone DNA repair assays (mismatch repair and base excision repair) to investigate the enzymes involved in generating mutations at A and T sites resulting from the error-prone processing of AID-generated U•G mispairs.

  • Journal Article

    • Pham, P., Wood, E. A., Cox, M. M., Goodman, M. F. (2023). RecA and SSB genome-wide distribution in ssDNA gaps and ends in Escherichia coli. Nucleic Acids Res. Vol. 51 (112023/04/19), pp. 5527-5546.
    • Jeong, S. L., Zhang, H., Yamaki, S., Yang, C., McKemy, D. D., Lieber, M. R., Pham, P., Goodman, M. F. (2022). Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization. Nucleic Acids Res. Vol. 50 (202022/11/03), pp. 11738-11754.
    • Pham, P. T., Shao, Y., Cox, M. M., Goodman, M. F. (2022). Genomic Landscape of Single-stranded DNA Gapped Intermediates in Escherichia coli. Nucleic Acids Res. Vol. 50, pp. 937-951.
    • Liu, D., Goodman, M. F., Pham, P., Yu, K., Hsieh, C., Lieber, M. R. (2022). The mRNA Tether Model for Activation-Induced Deaminase and a Theory for Unifying Ig Somatic Hypermutation and Ig Class Switch Recombination. DNA Repair. Vol. 110, pp. 103271.
    • Henrikus, S. S., Henry, C., McGrath, A., Jergic, S., McDonald, J. P., Bruckbauer, S. T., Ritger, M., Cherry, M. E., Wood, E. A., Pham, P. T., Goodman, M. F., Woodgate, R., Cox, M. M., van Oijen, A. M., Ghodke, H., Robinson, A. (2020). Single-molecule live-cell imaging reveals RecB-Dependent Function of DNA Polymerase IV in Double Strand Break Repair. Nucleic Acids Res. Vol. 48, pp. 8490-8508.
    • Pham, P. T., Malik, S., Mak, C., Calabrese, P. C., Roeder, R. G., Goodman, M. F. (2019). AID-RNA polymerase II transcription-dependent deamination of IgV DNA. Nucleic Acids Res. (2019/10/01)
    • Mak, C. H., Pham, P. T., Goodman, M. F. (2019). Random Walk Enzymes: Information Theory, Quantum Isomorphism, and Entropy Dispersion. J Phys Chem A. Vol. 123 (132019/03/09), pp. 3030-3037.
    • Pham, P. T., Afif, S. A., Shimoda, M., Maeda, K., Sakaguchi, N., Pedersen, L. C., Goodman, M. F. (2017). Activation-induced deoxycytidine deaminase: Structural basis for favoring WRC hot motif specificities unique among APOBEC family members. DNA Repair (Amst). Vol. 54, pp. 8-12.
    • Eid, M. M., Shimoda, M., Singh, S. K., Almofty, S. A., Pham, P. T., Goodman, M. F., Maeda, K., Sakaguchi, N. (2017). Integrity of immunoglobulin variable regions is supported by GANP during AID-induced somatic hypermutation in germinal center B cells. Int Immunol. Vol. 29 (5), pp. 211-220.
    • Pham, P. T., Afif, S. A., Shimoda, M., Maeda, K., Sakaguchi, N., Pedersen, L. C., Goodman, M. F. (2016). Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification. DNA Repair (Amst). Vol. 43, pp. 48-56.
    • Senavirathne, G., Bertram, J. G., Jaszczur, M., Chaurasiya, K. R., Pham, P. T., Mak, C. H., Goodman, M. F., Rueda, D. (2015). Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution. Nat Commun. Vol. 6, pp. 10209.
    • Mak, C. H., Pham, P., Afif, S. A., Goodman, M. F. (2015). Random-walk enzymes. Phys. Review E. Vol. 92, pp. 032717.
    • Wei, L., Chahwan, R., Wang, S., Wang, X., Pham, P. T., Goodman, M. F., Bergman, A., Scharff, M. D., MacCarthy, T. (2015). Overlapping hotspots in CDRs are critical sites for V region diversification. Proc Natl Acad Sci U S A. Vol. 112 (72015/02/04), pp. E728-37.
    • Maeda, K., Almofty, S. A., Singh, S. K., Eid, M. M., Shimoda, M., Ikeda, T., Koito, A., Pham, P., Goodman, M. F., Sakaguchi, N. (2013). GANP interacts with APOBEC3G and facilitates its encapsidation into the virions to reduce HIV-1 infectivity. J. Immunol.. Vol. 191 (12), pp. 6030-6039.
    • Pham, P., Landolph, A., Mendez, C., Li, N., Goodman, M. F. (2013). A Biochemical Analysis Linking APOBEC3A to Disparate HIV-1 Restriction and Skin Cancer. J Biol Chem. Vol. 288 (412013/08/28), pp. 29294-304.
    • Mak, C. H., Pham, P., Afif, S. A., Goodman, M. F. (2013). A Mathematical Model for Scanning and Catalysis on Single-stranded DNA, Illustrated with Activation-induced Deoxycytidine Deaminase. J Biol Chem. Vol. 288 (412013/08/28), pp. 29786-95.
    • Jaszczur, M., Bertram, J. G., Pham, P., Scharff, M. D., Goodman, M. F. (2013). AID and Apobec3G haphazard deamination and mutational diversity. Cell Mol Life Sci. Vol. 70 (172012/11/28), pp. 3089-108.
    • Singh, S. K., Maeda, K., Eid, M. M., Almofty, S. A., Ono, M., Pham, P., Goodman, M. F., Sakaguchi, N. (2013). GANP regulates recruitment of AID to immunoglobulin variable regions by modulating transcription and nucleosome occupancy. Nat Commun. Vol. 4 (2013/05/09), pp. 1830.
    • Mu, Y., Prochnow, C., Pham, P., Chen, X. S., Goodman, M. F. (2012). A structural basis for the biochemical behavior of activation-induced deoxycytidine deaminase class-switch recombination-defective hyper-IgM-2 mutants. J Biol Chem. Vol. 287 (332012/06/21), pp. 28007-16.
    • Pham, P., Calabrese, P., Park, S., Goodman, M. F. (2011). Analysis of a single-stranded DNA-scanning process in which activation-induced deoxycytidine deaminase (AID) deaminates C to U haphazardly and inefficiently to ensure mutational diversity. J Biol Chem. Vol. 286 (282011/05/17), pp. 24931-42.
    • Maeda, K., Singh, S. K., Eda, K., Kitabatake, M., Pham, P., Goodman, M. F., Sakaguchi, N. (2010). GANP-mediated Recruitment of Activation-induced Cytidine Deaminase to Cell Nuclei and to Immunoglobulin Variable Region DNA. Journal of Biological Chemistry. Vol. 285 (31), pp. 23945-23953. PubMed Web Address
    • Chelico, L., Pham, P., Petruska, J., Goodman, M. F. (2009). Biochemical basis of immunological and retroviral responses to DNA-targeted cytosine deamination by activation-induced cytidine deaminase and APOBEC3G. Journal of Biological Chemistry. Vol. 284 (41), pp. 27761-27765.
    • Madia, F., Wei, M., Yuan, V., Hu, J., Gattazzo, C., Pham, P., Goodman, M. F., Longo, V. D. (2009). Oncogene homologue Sch9 promotes age-dependent mutations by a superoxide and Rev1/Polzeta-dependent mechanism. J Cell Biol. Vol. 186 (4), pp. 509-523. PubMed Web Address
    • Chelico, L., Pham, P., Goodman, M. F. (2009). Mechanisms of APOBEC3G-catalyzed processive deamination of deoxycytidine on single-stranded DNA. Nature Structural & Molecular Biology. Vol. 16 (5), pp. 454-455. PubMed Web Address
    • MacCarthy, T., Kalis, S. L., Roa, S., Pham, P., Goodman, M. F., Scharff, M. D., Bergman, A. (2009). V-region mutation in vitro, in vivo and in silico reveal the importance of the enzymatic properties of AID and the sequence environment. Proc Natl Acad Sci U S A. Vol. 106 (21), pp. 8629-8634.
    • Chelico, L., Pham, P., Goodman, M. F. (2009). Stochastic properties of processive cytidine DNA deaminases AID and APOBEC3G. Philosophical Transactions of the Royal Society B: Biological Sciences. Vol. 364 (1517), pp. 583-593.
    • Pham, P., Zhang, K., Goodman, M. F. (2008). Hypermutation at A/T sites during G.U mismatch repair in vitro by human B-cell lysates. Journal of Biological Chemistry. Vol. 283 (46), pp. 31754-31762.
    • Pham, P., Smolka, M., Calabrese, P., Landolph, A., Zhang, K., Zhou, H., Goodman, M. F. (2008). Impact of phosphorylation and phosphorylation-null mutants on the activity and deamination specificity of activation-induced cytidine deaminase. Journal of Biological Chemistry. Vol. 283 (25), pp. 17428-17439.
    • Gawel, D., Pham, P., Fijalkowska, I. J., Jonczyk, P., Schaaper, R. M. (2008). Role of Accessory DNA Polymerases in the Escherichia coli dnaX36 Mutator Mutant. Journal of Bacteriology. Vol. 190 (5), pp. 1730-1742.
    • Pham, P., Chelico, L., Goodman, M. F. (2007). DNA deaminases AID and APOBEC3G act processively on single-stranded DNA. DNA Repair (Amst). Vol. 6 (6), pp. 689-92.
    • Bransteitter, R. R., J, S. L., Allen, S., Pham, P. T., Goodman, M. F. (2006). First AID (activation-induced cytidine deaminase) is needed to produce high affinity isotype-switched antibodies. Journal of Biological Chemistry. Vol. 281, pp. 16833-16836.
    • Chelico, L., Pham, P. T., Calabrese, P., Goodman, M. F. (2006). APOBEC3G DNA deaminase acts processively 3′ –> 5′ on single-stranded DNA. Nature Structural & Molecular Biology/Nature Publishing Group. Vol. 13, pp. 392-399.
    • Pham, P. T., Zhao, W., Schaaper, R. M. (2006). Mutator mutants of Escherichia coli carrying a defect in the DNA polymerase III tau subunit. Molecular Microbiology/Blackwell Publishing. Vol. 59, pp. 1149-1161.
    • Schlacher, K., Pham, P. T., Cox, M., Goodman, M. F. (2006). Roles of DNA polymerase V and RecA protein in SOS damage-induced mutation. Chemical Reviews/American Chemical Society Press. Vol. 106, pp. 406-419.
    • Michell, D. L., Pham, P. T., Goodman, M. F., Nancy, M. (2005). AID binds to transcription-induced structures in c-MYC that map to regions associated with translocation and hypermutation. Oncogen/Nature Publishing Group. Vol. 24, pp. 5791-5798.
    • Pham, P. T., Bransteitter, R. R., Goodman, M. F. (2005). Reward versus Risk: DNA Cytidine Deaminases Triggering Immunity and Disease. Biochemistry/American Chemical Society. Vol. 44, pp. 2703-2715.
    • Bransteitter, R. R., Pham, P. T., Calabrese, P., Goodman, M. F. (2004). Biochemical analysis of hypermutational targeting by wild type and mutant activation-induced cytidine deaminase. Journal of Biological Chemistry. Vol. 279, pp. 51612-51621.
    • Tippin, B., Pham, P. T., Goodman, M. F. (2004). Error-prone replication for better or worse. Trends in Microbiology/Elsevier. Vol. 12, pp. 288-295.
    • Tippin, B., Pham, P. T., Bransteitter, R. R., Goodman, M. F. (2004). Somatic hypermutation: a mutational panacea. Advances in Protein Chemistry/Elsevier. Vol. 69, pp. 307-335.
    • Bransteitter, R., Pham, P., Scharff, M. D., Goodman, M. F. (2003). Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase. Proc Natl Acad Sci U S A. Vol. 100 (7), pp. 4102-4107.
    • Pham, P., Bransteitter, R., Petruska, J., Goodman, M. F. (2003). Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation. Nature. Vol. 424 (6944), pp. 103-107.
    • Kobayashi, S., Valentine, M. R., Pham, P., O’Donnell, M., Goodman, M. F. (2002). Fidelity of Escherichia coli DNA polymerase IV. Preferential generation of small deletion mutations by dNTP-stabilized misalignment. J Biol Chem. Vol. 277 (37), pp. 34198-34207.
    • Pham, P., Seitz, E. M., Saveliev, S., Shen, X., Woodgate, R., Cox, M. M., Goodman, M. F. (2002). Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis. Proc Natl Acad Sci U S A. Vol. 99 (17), pp. 11061-11066.
    • Pham, P., Bertram, J. G., O’Donnell, M., Woodgate, R., Goodman, M. F. (2001). A model for SOS-lesion-targeted mutations in Escherichia coli. Nature. Vol. 409 (6818), pp. 366-370.
    • Pham, P., Rangarajan, S., Woodgate, R., Goodman, M. F. (2001). Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli. Proc Natl Acad Sci U S A. Vol. 98 (15), pp. 8350-8354.
    • Silvian, L. F., Toth, E. A., Pham, P., Goodman, M. F., Ellenberger, T. (2001). Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus. Nat Struct Biol. Vol. 8 (11), pp. 984-989.
    • Song, M. S., Pham, P. T., Olson, M., Carter, J. R., Franden, M. A., Schaaper, R. M., McHenry, C. S. (2001). The delta and delta ‘ subunits of the DNA polymerase III holoenzyme are essential for initiation complex formation and processive elongation. J Biol Chem. Vol. 276 (37), pp. 35165-35175.
    • Tang, M., Pham, P., Shen, X., Taylor, J. S., O’Donnell, M., Woodgate, R., Goodman, M. F. (2000). Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis. Nature. Vol. 404 (6781), pp. 1014-1018.
    • Pham, P. T., Olson, M. W., McHenry, C. S., Schaaper, R. M. (1999). Mismatch extension by Escherichia coli DNA polymerase III holoenzyme. J Biol Chem. Vol. 274 (6), pp. 3705-3710.
    • Pham, P. T., Olson, M. W., McHenry, C. S., Schaaper, R. M. (1998). The base substitution and frameshift fidelity of Escherichia coli DNA polymerase III holoenzyme in vitro. J Biol Chem. Vol. 273 (36), pp. 23575-23584.