I'm a PhD grad Student in Ken Stedmans Lab at Portland State University. My research focuses on understanding the replication and integration of the extremely thermophilic and acidophilic virus family Fuselloviridae, commonly called the SSV or spindle–shaped viruses. These viruses are among a diverse group of unique viruses infecting the Archaeon genus Sulfolobus in which little is known. Specifically my research explores the role of the integrase protein in viral replication, its localization and specificity of site specific recombination, and its relationship to other integrases in the tyrosine recombinase family of proteins.
The Sulfolobales and their many viruses live in terrestrial hot springs at temperatures around 80 C and pH that is often below 2. In these harsh conditions very few organisms are able to survive, the vast majority being Archaea. Like bacteria theses organisms are single celled and reproduce clonally. Viral integration is particularly important in systems because it provides a method of recombination, allowing organisms to escape the detrimental effects of Muller’s Ratchet
The importance of integration is seen in the conservation of the integrase gene in the viruses in the family Fueslloviridae. Of the 30-some putative genes found in each of the sequenced Fusellovirus genomes only one gene, the integrase, shows homology to genes found outside of this virus family.
My first experiment concerning integration was to determine if the integrase gene itself was needed in the replication of the viral type species, SSV1. I developed a technique called Long Inverse PCR to create deletion mutants in the circular viral genome and removed the integrase gene completely. To our surprise this virus was still able to replicate (but not integrate) into the genome of its host. I also showed that the integrase lacking virus is less competitive than its integrase containing relative. Details of this experiment are described in our publication in Virology
Further work to characterize Fueslloviruse integrases and compare theses to well known proteins such as Lambda integrase and Cre recombinase are underway in our lab.
Phylogenetic analysis of the integrases thought to be in the tyrosine recombinase family are under investigation. The sequencing of a new Fusellovirus from Lassen National Volcanic Park is underway and will hopefully aid in this analysis.