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Teaching Fields:
- Molecular Biology
- Virology
- Nucleic Acids Biochemistry
- Protein Structure
Research Interests: 
The overall goal of our research is to understand the
structure and function of RNA molecules. Most of our work has focused
on ribosomal RNA (rRNA), characterizing the role of the RNA in protein
synthesis (Thompson et al 2001, Vila et al 1994). We have recently embarked
on a new area of investigation studying the structure and function of
viral RNA molecules.
Our current projects on rRNA seek to understand the dynamic
nature of the RNA during protein synthesis. One of our projects investigates
the interaction of initiation factor 3 (IF3) on the small ribosomal subunit.
Using chemical probes, we have pinpointed nucleotides that shift conformation
during IF3 binding. Mutations in rRNA that preclude these shifts are deleterious
to IF3 interaction and cell viability. A second set of projects uses mutagenesis
of rRNA to investigate the importance of tertiary interactions in rRNA.
This analysis has revealed a number of critically important lone pair
interactions in both small subunit and large subunit rRNA. Over the last
several years, crystallographic analysis has generated atomic resolution
models of the ribosome and rRNA (Figure 1). This has greatly enhanced
our understanding of rRNA and protein synthesis. By focusing on rRNA dynamics
we hope to contribute elements of movement to the current rRNA models.
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Figure1 Crystal structure of the small ribosomal subunit. From:Brian
T. Wimberly, Ditlev E. Broderson, William M. Clemons Jr, Robert J. Morgan-Warren,
Andrew P. Carter, Clemens Vonrhein, Thomas Hartsch and V. Ramakrishnan.
Nature 407, 327 - 339 (2000)
Many of the approaches that we use for determining the structure of rRNA
are also applicable to viral RNA. We have initiated studies to learn the
structure of the internal ribosome entry site (IRES) RNA found in picornaviruses
and flaviviruses (Figure 2 and Figure 3). This work is significant because
virulence is determined by IRES structure. In our initial studies we have
used chemical modification and primer extension to deduce the secondary
structure of the IRES elements in coxsackievirus B3 and bovine diarrhea
virus. This analysis has been completed for virulent wild type viruses
and for attenuated mutant viruses. We have shown localized structural
changes in the IRES RNA that correlate with virulence. Theses shifts in
structure occur in regions of the IRES known to be important for the binding
of key cellular proteins. The results show that viral replication and
viral virulence is critically dependent on discrete structures in the
RNA. Further characterization of these structures will lead to strategies
to develop antiviral compounds and vaccines.
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Figure 2. Crystal structure of a picornavirus virion
Figure 3. Secondary structure model for the IRES element of coxsackievirus
B3
Selected Publications:
- Bailey, J. M. and Tapprich, W. E. (2007) “Structure of the 5’ Nontranslated Region of the Coxsackievirus B3 Genome: Chemical Modification and Comparative Sequence Analysis” J. Virol. 81:650-668.
- Tracy, S, Chapman, N. M., Drescher, K. M. and Tapprich, W. (2006) “Evolution of Virulence in Picornaviruses.” Curr. Top. Micro. and Immonol. 299:193-210
- Kim, K-S, Tracy S, Tapprich, W.E., Bailey, J., Lee, C-G, Kim K, Barry, WH and Chapman, NM (2005) “5’ Terminal Deletions Occur in Coxsackievirus B3 During Replication in Murine Hearts and Cardiac Myocyte Cultures and Correlate with Encapsidation of Negative Strand Viral DNA.” J. Virol. 79:7024-7041.
- Xiong W., Tapprich W.E. and Cox G.S. (2002) “Mechanism of Gonadotropin
Gene Expression: Identification of a Novel Negative Regulatory Element
at the Transcription Start Site of the Glycoprotein Hormone alpha Subunit
Gene”.J Biol Chem 277(43):40235-46.
- Thompson, J., Tapprich, W.E., Munger, C. and Dahlberg, A.E. (2001)
“Staphlococcus aureus domain V functions in E. coli ribosomes
provided a conserved interaction with domain IV is restored.”
RNA 8:1076-83.
- Vila, A., Viril-Farley, J. and Tapprich, W. E. (1994) "Pseudoknot
in the Central Domain of Small Subunit Ribosomal RNA is Essential for
Translation." Proc. Natl. Acad. Sci. USA 91: 11148-11152.
- Lodmell, J. S., Tapprich, W. E. and Hill, W. E. (1993) "Evidence
for a Conformational Change in the Exit site of the Escherichia coli
Ribosome upon tRNA Binding." Biochemistry 32: 4067-4072.
- Melancon, P., Tapprich, W. E. and Brakier-Gingras, L. (1992) "Single-Base
Mutations at Position 2661 of Eschericia coli 23S rRNA Increase Efficiency
of Translational Proofreading." J. Bacteriology, 174: 7896-7901.Hill,
W. E., Tassanakajohn, A. and Tapprich, W. E. (1990) "Interaction
of tRNA with domain II of 23S rRNA." Biochim, Biophys. ACTA, 1050:
45-50.
- Tapprich, W. E. and Dahlberg, A. E. (1990). "A Single Base Mutation
at Position 2661 in Escherichia coli 23S Ribosomal RNA Affects the Binding
of Ternary Complex to the Ribosome." EMBO J., 9: 2649-2655.
- Tapprich, W. E., Göringer, H. U., De Stasio, E. A., Prescott,
C. and Dahlberg, A. E. (1990) "Studies of Ribosome Function by
Mutagenesis of Escerichia coli rRNA" In: The Ribosome: Structure,
Function and Evolution, W. Hill, A. Dahlberg, R. A. Garrett, P. B. Moore,
D. Schlessinger, J. R. Warner eds. ASM Press, Washington DC.
- Hill, W. E., Gluick, T., Marconi, R. T., Merryman, C., Tassanakajohn,
A., Weller, J. and Tapprich, W. E. (1990) "Probing Ribosome Structure
and Function by using Short, Complementary DNA Oligonucleotides"
In: The Ribosome: Structure, Function and Evolution, W. Hill, A. Dahlberg,
R. A. Garrett, P. B. Moore, D. Schlessinger, J. R. Warner eds. ASM Press,
Washington DC.
- Tapprich, W. E., Göringer, H. U., De Stasio, E. A. and Dahlberg,
A. E. (1990) "Site-Directed Mutagenesis of Ribosomal RNA."
In: Ribosomes a Practical Approach, G. Spedding ed. IRL Press, Oxford,
UK.
- Tapprich, W. E., Goss, D. J. and Dahlberg, A. E. (1989) "A Mutation
at Position 791 in Escherichia coli 16S Ribosomal RNA Affects Processes
Involved in the Initiation of Protein Synthesis." Proc. Natl. Acad.
Sci. USA 86: 4927-4931.
- De Stasio, E. A., Göringer, H. U., Tapprich, W. E. and Dahlberg
A. E. (1988) "Probing Ribosomal Function Through Mutagenesis of
Ribosomal RNA" In: Genetics of Translation. Tuite, M. F., Picard,
M. and Bolotin-Fukuhara eds. Springer-Verlag, Berlin.
- Hill, W. E., Tapprich, W. E., Camp, D. G. and Tassanakajohn, A. (1988)
"Probing Ribosomal Structure and Function using Complementary Oligonucleotides."
Meth. Enz. 164, 605-625.
- Hill, W. E., Tapprich, W. E. and Tassanakajohn, A. (1986) "Probing
Ribosomal Structure and Function." In: Structure, Function and
Genetics of Ribosomes. Hardesty, B. etc eds. Springer-Verlag, Berlin.
- Tapprich, W. E. and Hill W. E. (1986) "The Involvement of Bases
787-795 of Escherichia coli 16S Ribosomal RNA in Ribosomal Subunit Association."
Proc. Natl. Acad. Sci. USA 83, 556-560.
Thesis Titles
(recent students):
- Missak, Johanna M. 2005. Structural Analysis of the 5’ Nontranslated Region on the Genomic RNA of Virulent and Nonvirulent Strains of the Coxsackievirus B3.
- Bailey, Jennifer M. 2004. Structure of 5'Nontranslated
Region RNA in Virulent and Nonvirulent Coxsackievirus B3 Genomes.
- Martinsen, Angela. 2003. Molecular Analysis of Structural
Alterations of E. coli 16S rRNA Induced by IF3.
- Park, John M. 2001. Molecular Detail of the Binding
Interaction Between IF3 and 16S rRNA.
- Ihrig, Timothy G. 2000. Probing the Structure of the
5' NTR of Coxsackievirus B3 RNA.
- Munger, Corey M. 2000. Analysis of a Potential Base
Pair Between 1782U and 2586U in Eschericia coli 23S Ribosomal
RNA.
- Carden, Bruce M. 1998. Analysis of Potential Base-Pairs
Between 16S and 23S Ribosomal RNA in Eschericia coli.
- Yu, Ni 1998. Development of Ovarian Follicles in situ
.
- Brown, Kirk M. 1997. Exploring a Lone Pair Interaction
in Escherichia coli 16S Ribosomal RNA Using Site-Directed
Mutagenesis.
- Loyd, Gregory R. 1996. Probing the Extreme 3' End
of 16S Ribosomal RNA from Escherichia coli.
- Bellah, Susan P. 1995. Effects of 5-Fluorouracil on
Escherichia coli
Ribosomes.
- Staplin, William R. 1995. Analysis of Subunit Association
using Mutations at Position 790 of Escherichia coli rRNA.
Other Responsibilities:
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