Graduate Program Information
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Professor of Biochemistry and Biophysics
Ph.D. State University of New York at Buffalo 1982

• URMC Researchers Form Company to Develop New Class of HIV Drugs.

Normal and cancer cells express more diversity in proteins than can be accounted for by the predicted number of expressed genomic DNA sequence. Expansion of the genomically encoded expressed sequences through alternative processing of RNA, such as mRNA editing, is a logical hypothesis for how protein diversity and variations seen as tissue-specific and regulated expression of proteins can be achieved. The specific focus of the research is to identify and characterize novel mammalian mRNA editing systems that employ a zinc-dependent deamination mechanism for the post-transcriptional conversion of cytidine to uridine at select sites within mRNAs. Computational modeling has suggested a family of mammalian enzymes known as Cytidine Deaminases Active on RNA or CDARs as responsible for C to U editing of mRNAs.

For more details see:

• A-to-I RNA editing website.
• IMB Jena Biocomputing Group

The expression of these enzymes in biology suggests that mRNA editing may be involved in numerous physiological processes and could be manipulated for the prevention of cardiovascular disease, HIV infection and cancer, and is also necessary for production of antibodies in B lymphocytes. Recent evidence indicates that the enzyme involved in suppressing HIV-1 infectivity (CEM15) and the enzyme that promotes antibody production (AID) may act to mutate deoxy cytidine in DNA rather than or in addition to RNA.

Our research involves molecular biology and protein techniques, DNA microarray analyses and computational biology to identify the mRNAs that are edited by CDARs and to determine the biological consequence of these editing events in terms of the predicted changes in the types of protein structures and functions that can be expressed. Our studies have demonstrated how cytidine to uridine mRNA editing contributes to expansion in the diversity of expressed mRNA sequences known collectively as the transcriptome.

We are also evaluating the regulatory mechanisms controlling the expression of editing factors and their localization in the cell nucleus. The development of this new information will establish an important new annotation of the human genome that will serve as a frame of reference for studies of proteins involved in health and disease and mechanisms regulating their expression.

APOBEC3G transfected into 293T cells showing cytoplasmic localization.  Superimposed is the molecular envelope of catalytically active APOBEC3G as a C-terminal homodimer determined by small angle X-ray scattering (SAXS). 

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APOBEC-1 distribution in liver cells
 

DAPI staining of nuclear DNA in the
liver cell shown above 

Recent Publications

Bennett RP, Presnyak V, Wedekind JE, Smith HC (2008) Nuclear Exclusion of the HIV-1 host defense factor APOBEC3G requires a novel cytoplasmic retention signal and is not dependent on RNA binding. J Biol Chem, 283:7320-7

Smith HC (2008) RNA and DNA Editing: Molecular Mechanisms and Their Integration into Biological Systems. (H.C. Smith, ed) 16 chapters, Wiley Press, NY, 2008.,

Lehmann DM, Galloway CA, Macelrevey C, Sowden MP, Wedekind JE, Smith HC (2007) Functional characterization of APOBEC-1 complementation factor phosphorylation sites. Biochim Biophys Acta, 1773:408-18

Smith HC (2007) Measuring editing activity and identifying cytidine-to-uridine mRNA editing factors in cells and biochemical isolates. In Methods in Enzymology, RNA Editing & Modification (Gott, J., eds) Academic Press, NY, 424:389-416

Jin X, Wu H, Smith HC (2007) APOBEC3G levels predict rates of progression to AIDS. Retrovirology, 4:20-7

Miller HJ, Presnyak V, Smith HC (2007) The dimerization domain of HIV-1 viral infectivity factor Vif is required to block virion incorporation of APOBEC3G. Retrovirology, 4:81-91

Bennett RP, Diner E, Sowden MP, Lees JA, Wedekind JE, Smith HC (2006) APOBEC-1 and AID are nucleo-cytoplasmic trafficking proteins but APOBEC3G cannot traffic. Biochem Biophys Res Commun, 350:214-9

Ichikawa HT, Sowden MP, Torelli AT, Bachl J, Huang P, Dance GS, Marr SH, Robert J, Wedekind JE, Smith HC, Bottaro A (2006) Structural phylogenetic analysis of activation-induced deaminase function. J Immunol, 177:355-61

Wedekind JE, Gillilan R, Janda A, Krucinska J, Salter JD, Bennett RP, Raina J, Smith HC (2006) Nanostructures of APOBEC3G support a hierarchical assembly model of high molecular mass ribonucleoprotein particles from dimeric subunits. J Biol Chem, 281:38122-6

Smith HC (2006) Editing Informational Content of Expressed DNA Sequences and Their Transcripts. The Implicit Genome (Caporale, L.H. ed.) Oxford University Press, NY, Chapter 14, 248-265

Lehmann DM, Galloway CA, Sowden MP, Smith HC (2006) Metabolic regulation of apoB mRNA editing is associated with phosphorylation of APOBEC-1 complementation factor. Nucleic Acids Res, 34:3299-308

Jin X, Brooks A, Chen H, Bennett R, Reichman R, Smith H (2005) APOBEC3G/CEM15 (hA3G) mRNA levels associate inversely with human immunodeficiency virus viremia. J Virol, 79:11513-6

Smith HC, Wedekind JE, Xie K, Sowden MP (2005) Mammalian C to U Editing. Topics in Current Genetics: "Fine-Tuning of RNA Functions by Modification and Editing"H. Grosjean (Ed.) Springer-Verlag, Berlin, 1610-2096

Xie K, Sowden MP, Dance GS, Torelli AT, Smith HC, Wedekind JE (2004) The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1. Proc Natl Acad Sci U S A, 101:8114-9

Smith HC, Bottaro A, Sowden MP, Wedekind JE (2004) Activation induced deaminase: the importance of being specific. Trends Genet, 20:224-7

Sowden MP, Lehmann DM, Lin X, Smith CO, Smith HC (2004) Identification of novel alternative splice variants of APOBEC-1 complementation factor with different capacities to support apolipoprotein B mRNA editing. J Biol Chem, 279:197-206

Galloway CA, Sowden MP, Smith HC (2003) Increasing the yield of soluble recombinant protein expressed in E. coli by induction during late log phase. Biotechniques, 34:524-6

Wedekind JE, Dance GS, Sowden MP, Smith HC (2003) Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business. Trends Genet, 19:207-16

Sowden MP, Ballatori N, Jensen KL, Reed LH, Smith HC (2002) The editosome for cytidine to uridine mRNA editing has a native complexity of 27S: identification of intracellular domains containing active and inactive editing factors. J Cell Sci, 115:1027-39

Yang Y, Ballatori N, Smith HC (2002) Apolipoprotein B mRNA editing and the reduction in synthesis and secretion of the atherogenic risk factor, apolipoprotein B100 can be effectively targeted through TAT-mediated protein transduction. Mol Pharmacol, 61:269-76

Smith HC (2002) A course director's perspectives on problem-based learning curricula in biochemistry. Acad Med, 77:1189-98

Dance GS, Sowden MP, Cartegni L, Cooper E, Krainer AR, Smith HC (2002) Two proteins essential for apolipoprotein B mRNA editing are expressed from a single gene through alternative splicing. J Biol Chem, 277:12703-9

Graduate students in my laboratory work toward a Ph.D. degree in the following program[s]:

Ph.D. in Biochemistry
Ph.D. in Biophysics
Ph.D. in Genetics
Ph.D. in Toxicology

Ph.D. candidates in my laboratory may also be affiliated with these programs:

Contact Information

E-Mail: Harold.Smith@rochester.edu

Harold Smith
Department of Biochemistry and Biophysics
University of Rochester School of Medicine and Dentistry
601 Elmwood Ave, Box 712
Rochester, New York 14642

Office: Medical Center G-7415
Telephone: Office:(585) 275-4267; Lab:(585) 275-1882; Fax: (585) 275-6007