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Phuong Pham

Assistant Professor (Research) of Biological Sciences

Contact Information
E-mail: ppham@usc.edu
Phone: (213) 740-5191
Office: RRI 113

 

Education

Ph.D. Genetics, St. Petersburg State University, 5/1993
M.S. Biology, St. Peterburg State University, 6/1989
 

Postdoctoral Training

Visiting Fellow, National Institute of Environmental Health Sciences, 04/22/1999-04/22/2004  
 

Description of Research

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.
 

Publications

Journal Article

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.
 
 
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