USC College Department of Biology

Faculty

Biological Sciences has more than 60 full-time faculty members, as well as more than 20 faculty with joint appointments and 15 visiting or adjunct professors. Among its many distinctions and honors, the Ph.D. program faculty includes two members of the National Academy of Sciences, four members of the American Academy of Arts and Sciences, and 18 holders of endowed chairs and professorships.

Phuong Pham

Assistant Professor (research) of Biological Sciences

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

Education

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

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 and biochemical properties of “Apobec” protein family of DNA dependent cytosine 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 and Apobec3G. I also work to develop 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

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.