Paul Ahlquist

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Phone: 608-263-5916

841a Robert M Bock Lab
1525 Linden Dr
Madison, WI 53706

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Ph.D. University of Wisconsin-Madison in Biophysics


We are studying the novel, RNA-based pathways and virus-host interactions underlying replication, gene expression and evolution by positive-strand RNA viruses, the largest class of viruses. Positive strand RNA viruses include many important human pathogens such as hepatitis C virus, which chronically infects nearly 3% of the world population, causing progressive liver damage and liver cancer, and the new SARS coronavirus. We are also studying selected replication processes of a reverse-transcribing virus, hepatitis B virus, which is also a major human tumor virus. Our studies integrate molecular genetics, genomics, biochemistry and cell biology to address fundamental questions in virus replication and virus-cell interactions.

Viruses are divided into six distinct classes differing in the type of nucleic acid in the virus particle and its replication pathways. Recently, we discovered multiple, detailed structural and functional parallels among the replication complexes of three of these six virus classes: positive-strand RNA viruses, retroviruses and dsRNA viruses. These results imply a significant functional and evolutionary unification within virology, and have opened the door to many exciting new experimental questions and approaches that we are now pursuing.

We also have identified the first higher eukaryotic viruses that can direct genome replication, gene expression and virion assembly in the genetically tractable yeastSaccharomyces cerevisiae. Using yeast genetics and genomics, we are identifying a growing number of host genes required for viral RNA replication and are studying how these function with virus-encoded helicase- and polymerase-like replication factors and diverse cis-acting viral RNA signals to direct assembly and function of the membrane-bound viral genome replication complexes and other processes.

Courses Taught

Oncology/Microbiology/Plant Pathology 640 General Virology-Multiplication


Diaz, A., Gallei, A., and Ahlquist, P.  Bromovirus RNA Replication Compartment Formation Requires Concerted Action of 1a’s Self-Interacting RNA Capping and Helicase Domains.  J. Virol., 86:  821-834, 2012.

Huang, H.-S., Pyeon, D., Pearce, S. M., Lank, S. M., Griffin, L. M., Ahlquist, P., and Lambert, P. F.  Novel Antivirals Inhibit Early Steps in HPV Infection.  Antiviral Res.,93:  280-287, 2012.

Wen, Z., Pyeon, D., Wang, Y., Lambert, P., Xu, W., and Ahlquist, P.  Orphan Nuclear Receptor PNR/NR2E3 Stimulates p53 Functions by Enhancing p53 Acetylation.  Mol. Cell. Biol., 32:  26-35, 2012.

Zhang, J., Diaz, A., Mao, L., Ahlquist, P., and Wang, X.  Host Acyl-CoA Binding Protein Regulates Replication Complex Assembly and Activity of a Positive-Strand RNA Virus.  J. Virol., in press, 2012 [Epub ahead of print Feb 15 2012].

Gancarz, B. L., Hao, L., He, Q., Newton, M. A., and Ahlquist, P.  Systematic Identification of Novel, Essential Host Genes Affecting Bromovirus RNA Replication.  PLoS One, 6(8):e23988, 2011.

Scholthof, K.-B. G., Adkins, S., Czosnek, H., Palukaitis, P., Jacquot, E., Ho