Interdisciplinary PhD in Structural and Computational Biology and Quantitative Biosciences

Paul G. Ahlquist

Paul J. Kaesberg Professor, Department of Oncology and Institute for Molecular Virology Lab Website ahlquist@wisc.edu(608) 263-5916

841A Bock Laboratories
1525 Linden Dr
Madison, WI 53706-1534

Education

B.S., Iowa State University
Ph.D., University of Wisconsin-Madison

Molecular mechanisms of virus replication and host interactions

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 yeast Saccharomyces 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.

Areas of Expertise

  • Computational Biology & Bioinformatics
  • Membrane & Cellular Biophysics
  • Microbial Biophysics & Virology
  • Structural Biology