Dept. of Plant Path.

Paul G. Ahlquist
Plant Pathology, Molecular Virology, and Oncology
Ph.D.: University of Wisconsin, Madison in Biophysics

Research Program

Our laboratory is studying the RNA-based pathways underlying the replication and evolution of positive-strand RNA viruses, a major class of viruses in humans, animals and plants.

Currently we are studying the mechanisms of RNA replication, gene expression/regulation, RNA-RNA recombination and host specificity in such RNA viruses to provide new insights into biochemistry and cell biology, new antiviral approaches, and new pathways for gene therapy and related applications. Our experiments integrate molecular genetic, biochemical, and cell biological studies of model virus-host systems that embody widely conserved features and have proven particularly tractable for genetic and biochemical studies.

Recently we identified the first and to date the only higher eukaryotic viruses that can direct genome replication, gene expression and virion assembly in the genetically tractable yeast Saccharomyces cerevisiae, allowing the use of yeast genetics to study virus replication. These yeast systems are proving extremely useful in studying the roles of both virus and host functions in infection. Using yeast genetics and genomics approaches, we have identified a growing number of host genes required for viral RNA replication and mRNA synthesis, and are studying how these function together with virus-encoded helicase- and polymerase-like replication factors and diverse cis-acting viral RNA signals to direct RNA template recruitment, assembly of the membrane-bound viral replication complex, and other steps. These studies also promise to shed light on infection cytopathology and, since the implicated host factors include a number of previously uncharacterized yeast genes, on general cell biology.

Selected Publications

Beckham, C. J., Light, H. R., Nissan, T. A., Ahlquist, P., Parker, R., and Noueiry, A. Interactions between Brome Mosaic Virus RNAs and Cytoplasmic Processing Bodies. J. Virol., 81: 9759-9768, 2007.

Kopek, B. G., Perkins, G., Miller, D. J., Ellisman, M. H., and P. Ahlquist. Three-Dimensional Analysis of a Viral RNA Replication Complex Reveals a Virus-induced Mini-Organelle. PLoS Biol., 5: 2022-2034, 2007.

Pyeon, D., Newton, M. A., Lambert, P. F., den Boon, J. A., Sengupta, S., Marsit, C. J., Woodworth, C. D., Connor, J. P., Haugen, T. H., Smith, E. M., Kelsey, K. T., Turek, L. P., and P. Ahlquist. Fundamental Differences in Cell Cycle Deregulation in Human Papillomavirus-positive and Human Papillomavirus-negative Head/Neck and Cervical Cancers. Cancer Res., 67: 4605-4619, 2007.

Van Wynsberghe, P. M., Chen, H.-R., and P. Ahlquist. Nodavirus RNA Replication Protein A Induces Membrane Association of Genomic RNA. J. Virol., 81: 4633-4644, 2007.

Watanabe, T., Sorensen, E. M., Naito, A., Schott, M., Kim, S., and P. Ahlquist. Involvement of Host Cellular Multivesicular Body Functions in Hepatitis B Virus Budding. Proc. Natl. Acad. Sci., USA, 104: 10205-10210, 2007.

Ahlquist, P. Parallels Among Positive-Strand RNA Viruses, Reverse-Transcribing Viruses and Double-Stranded RNA Viruses. Nat. Rev. Microbiol., 4: 371-382, 2006.

Dodd, L. E., Sengupta, S., Chen, I. H., den Boon, J. A., Cheng, Y.-J., Westra, W., Newton, M. A., Mittl, B. F., McShane, L., Chen, C.-J., Ahlquist, P., and Hildesheim, A. Genes Involved in DNA Repair and Nitrosamine Metabolism and Those Located on Chromosome 14q32 are Dysregulated in Nasopharyngeal Carcinoma. Cancer Epidemiol. Biomarkers Prev., 15: 2216-2225, 2006.

Garcia-Ruiz, H., and P. Ahlquist. Inducible Yeast System for Viral RNA Recombination Reveals Requirement for an RNA Replication Signal on Both Parental RNAs. J. Virol., 80: 8316-8328, 2006.

Mas, A., Alves-Rodrigues, I., Noueiry, A., Ahlquist, P., and Díez, J. Host Deadenylation-Dependent mRNA Decapping Factors Are Required for a Key Step in Brome Mosaic Virus RNA Replication. J. Virol., 80: 246-251, 2006.

Sengupta, S., den Boon, J. A., Chen, I.-H., Newton, M. A., Dahl, D. B., Chen, M., Cheng, Y.-J., Westra, W. H., Chen, C.-J., Hildesheim, A., Sugden, B., and P. Ahlquist. Genome-wide Expression Profiling Reveals EBV-associated Inhibition of MHC Class I Expression in Nasopharyngeal Carcinoma. Cancer Res., 66: 7999-8006, 2006.

Ahlquist, P. Virus Evolution: Fitting Lifestyles to a T. Curr. Biol., 15: R465-R467, 2005.

Ahlquist, P., Schwartz, M., Chen, J., Kushner, D., Hao, L., and Dye, B. T. Viral and Host Determinants of RNA Virus Vector Replication and Expression. Vaccine, 23: 1784-1787, 2005.

Bruce, J. W., Bradley, K. A., Ahlquist, P., and Young, J. A. T. Isolation of Cell Lines That Show Novel, Murine Leukemia Virus-Specific Blocks to Early Steps of Retroviral Replication. J. Virol., 79: 12969-12978, 2005.

Dye, B. T., Hao, L., and P. Ahlquist. High-Throughput Isolation of Saccharomyces cerevisiae RNA. BioTechniques, 38: 868-870, 2005.

Dye, B. T., Miller, D. J., and P. Ahlquist. In Vivo Self-Interaction of Nodavirus RNA Replicase Protein A Revealed by Fluorescence Resonance Energy Transfer. J. Virol., 79: 8909-8919, 2005.

Dye, B. T., Schell, K., Miller, D. J., and P. Ahlquist. Detecting Protein-Protein Interaction in Live Yeast by Flow Cytometry. Cytometry Part A, 63A: 77-86, 2005.

Grdzelishvili, V. Z., Garcia-Ruiz, H., Watanabe, T., and P. Ahlquist. Mutual Interference between Genomic RNA Replication and Subgenomic mRNA Transcription in Brome Mosaic Virus. J. Virol., 79: 1438-1451, 2005.

Perrigoue, J. G., den Boon, J. A., Friedl, A., Newton , M. A., Ahlquist, P., and Sugden, B. Lack of Association between EBV and Breast Carcinoma. Cancer Epidemiol. Biomarkers Prev., 14: 809-814, 2005.

Pyeon, D., Lambert, P. F., and P. Ahlquist. Production of Infectious Human Papillomavirus Independently of Viral Replication and Epithelial Cell Differentiation. Proc. Natl. Acad. Sci., U.S.A., 102: 9311-9316, 2005.

Wang, X., Lee, W.-M., Watanabe, T., Schwartz, M., Janda, M., and P. Ahlquist. Brome Mosaic Virus 1a Nucleoside Triphosphatase/Helicase Domain Plays Crucial Roles in Recruiting RNA Replication Templates. J. Virol., 79: 13747-13758, 2005.

Newton, M. A., Noueiry, A., Sarkar, D., and P. Ahlquist. Detecting Differential Gene Expression with a Semiparametric Hierarchical Mixture Method. Biostatistics, 5: 155-176, 2004.

Schwartz, M., Chen, J., Lee, W.-M., Janda, M., and P. Ahlquist. Alternate, Virus-induced Membrane Rearrangements Support Positive-Strand RNA Virus Genome Replication. Proc. Natl. Acad. Sci., U.S.A., 101: 11263-11268, 2004.

Ahlquist, P., Noueiry, A. O., Lee, W.-M., Kushner, D. B., and Dye, B. T. Host Factors in Positive-Strand RNA Virus Genome Replication. J. Virol., 77: 8181-8186, 2003.

Chen, J., Noueiry, A., and P. Ahlquist. An Alternate Pathway for Recruiting Template RNA to the Brome Mosaic Virus RNA Replication Complex. J. Virol., 77: 2568-2577, 2003.

Kushner, D. B., Lindenbach, B. D., Grdzelishvili, V. Z., Noueiry, A. O., Paul, S. M., and P. Ahlquist. Systematic, Genome-Wide Identification of Host Genes Affecting Replication of a Positive-Strand RNA Virus. Proc. Natl. Acad. Sci. USA, 100: 15764-15769, 2003.

Lee, W.-M., and P. Ahlquist. Membrane Synthesis, Specific Lipid Requirements, and Localized Lipid Composition Changes Associated with a Positive-Strand RNA Virus RNA Replication Protein. J. Virol., 77: 12819-12828, 2003.

Miller, D. J., Schwartz, M. D., Dye, B. T., and P. Ahlquist. Engineered Retargeting of Viral RNA Replication Complexes to an Alternative Intracellular Membrane. J. Virol., 77: 12193-12202, 2003.

Noueiry, A. O., and P. Ahlquist. Brome Mosaic Virus RNA Replication: Revealing the Role of the Host in RNA Virus Replication. Annu. Rev. Phytopathol., 41: 77-98, 2003.

Noueiry, A. O., Diez, J., Falk, S. P., Chen, J., and P. Ahlquist. Yeast Lsm1p-7p/Pat1p Deadenylation-Dependent mRNA-Decapping Factors Are Required for Brome Mosaic Virus Genomic RNA Translation. Mol. Cell Biol., 23: 4094-4106, 2003.

Tomita, Y., Mizuno, T., Díez, J., Naito, S., Ahlquist, P., and Ishikawa, M. Mutation of Host dnaJ Homolog Inhibits Brome Mosaic Virus Negative-Strand RNA Synthesis. J. Virol., 77: 2990-2997, 2003.

Ahlquist, P. RNA-Dependent RNA Polymerases, Viruses, and RNA Silencing. Science, 296:1270-1273, 2002.

Lindenbach, B. D., Sgro, J.-Y., and P. Ahlquist. Long-Distance Base Pairing in Flock House Virus RNA1 Regulates Subgenomic RNA3 Synthesis and RNA2 Replication. J. Virol., 76: 3905-3919, 2002.

Miller, D. J., and P. Ahlquist. Flock House Virus RNA Polymerase Is a Transmembrane Protein with Amino-Terminal Sequences Sufficient for Mitochondrial Localization and Membrane Insertion. J. Virol., 76: 9856-9867, 2002.

Price, B. D., Ahlquist, P., and Ball, L. A. DNA-Directed Expression of an Animal Virus RNA for Replication-Dependent Colony Formation in Saccharomyces cerevisiae. J. Virol., 76: 1610-1616, 2002.

Schwartz, M., Chen, J., Janda, M., Sullivan, M., den Boon, J., and P. Ahlquist. A Positive-Strand RNA Virus Replication Complex Parallels Form and Function of Retrovirus Capsids. Mol. Cell, 9: 505-514, 2002.

Baumstark, T., and P. Ahlquist. The Brome Mosaic Virus RNA3 Intergenic Replication Enhancer Folds to Mimic a tRNA TYC-Stem Loop and Is Modified in Vivo. RNA, 7: 1652-1670, 2001.

Chen J., Noueiry, A., and P. Ahlquist. Brome Mosaic Virus Protein 1a Recruits Viral RNA2 to RNA Replication through a 5´ Proximal RNA2 Signal. J. Virol., 75: 3207-3219, 2001.

den Boon, J. A., Chen, J., and P. Ahlquist. Identification of Sequences in Brome Mosaic Virus Replicase Protein 1a That Mediate Association with Endoplasmic Reticulum Membranes. J. Virol., 75: 12370-12381, 2001.

Lee, W.-M., Ishikawa, M., and P. Ahlquist. Mutation of Host D9 Fatty Acid Desaturase Inhibits Brome Mosaic Virus RNA Replication between Template Recognition and RNA Synthesis. J. Virol., 75: 2097-2106, 2001.

Miller, D. J., Schwartz, M. D., and P. Ahlquist. Flock. House Virus RNA Replicates on Outer Mitochondrial Membranes in Drosophila Cells. J. Virol., 75: 11664-11676, 2001.

Díez, J., M. Ishikawa, M. Kaido and P. Ahlquist. Identification and characterization of a host protein required for efficient template selection in viral RNA replication. Proc. Natl. Acad. Sci. USA 97:3913-3918, 2000

Ahola, T., den Boon, J. and P. Ahlquist. Helicase and capping enzyme active site mutations in brome mosaic virus protein 1a cause defects in template recruitment, negative-strand RNA synthesis and viral RNA capping. J. Virol. 74:8803-8811, 2000.

Price, B.D., Roeder, M. and P. Ahlquist. DNA-directed expression of functional flock house virus RNA1 derivatives in Saccharomyces cerevisiae, heterologous gene expression, and selective effects on subgenomic mRNA synthesis. J. Virol. 74:11724-11733, 2000.

Chen, J. and P. Ahlquist. Brome mosaic virus polymerase-like protein 2a is directed to the endoplasmic reticulum by helicase-like viral protein 1a.. J. Virol. 74:4310-4318, 2000.

Nouiery A., J. Chen and P. Ahlquist. A mutant allele of essential, general translation initiation factor DED1 selectively inhibits translation of a viral mRNA. Proc. Natl. Acad. Sci. USA. 97:12985-12990, 2000.

Sullivan, M. and P. Ahlquist. A brome mosaic virus intergenic RNA3 replication signal functions with viral replication protein 1a to dramatically stabilize RNA in vivo. J. Virol. 73:2622-2632, 1999.

Ahola, T. and P. Ahlquist. Putative RNA capping activities encoded by brome mosaic virus: methylation and covalent binding of guanylate by replicase protein 1a. J. Virol. 73:10061-10069, 1999.

Restrepo-Hartwig M. and P. Ahlquist. Brome mosaic virus RNA replication proteins 1a and 2a colocalize and 1a independently localizes on the yeast endoplasmic reticulum. J. Virol. 73:10303-10309, 1999.

Krol, M., N. Olson, J. Tate, J. Johnson, T. Baker and P. Ahlquist. RNA-controlled polymorphism in the in vivo assembly of 180-subunit and novel 120-subunit virions from a single capsid protein. Proc. Natl. Acad. Sci. USA 96:13650-13655, 1999.

Janda, M. and P Ahlquist. Brome mosaic virus RNA replication protein 1a dramatically increases in vivo stability but not translation of viral genomic RNA3. Proc. Natl. Acad. Sci. USA 95:2227-2232, 1998.

Sullivan, M. and P. Ahlquist. Cis-acting signals in bromovirus RNA replication and gene expression: networking with viral proteins and host factors. Seminars in Virol. 8: 221-230, 1997.