Our understanding of Archaea as a third domain of life is incomplete because of their relatively recent discovery. Archaea are often found in extreme environments and provide good model systems for understanding the adaptations needed to sustain life in such conditions. The viruses that replicate in thermophilic Archaea have been studied recently in an attempt to understand the biochemistry and molecular biology of their hosts. Using advanced tools of bioinformatics, our lab has tentatively assigned functions to about one third of proteins found in Fuselloviridae isolated from Sulfolobus species. Somewhat surprisingly, almost 20% of viral open reading frames are predicted to code for DNA-binding proteins. This finding strongly implies that the viruses have developed mechanisms for tight regulation of their own transcription, and possibly that of their hosts. Our goal is to characterize these proteins in order to increase our understanding of the mechanisms of transcriptional regulation in these viruses and their hosts.

We found that Sulfolobus spindle-shaped viruses (SSVs) code for ribbon-helix-helix (RHH), winged helix-turn-helix (wHTH) and zinc-finger DNA-binding proteins. Interestingly, at least one protein from each of the three groups of DNA-binding proteins is shared between all four SSV species, clearly indicating common functions for these proteins in all SSVs. We cloned several DNA-binding proteins and tested them in gel-shift and in vitro selection experiments. We showed that one of RHH proteins binds to tandem-repeated DNA sites found in two viral promoters. A long-term goal of this work, and a likely direct outcome of the experimental results obtained, will be greater understanding of transcriptional regulation by DNA-binding proteins of SSVs.

There are several important questions to be answered:
1) What are the effects of expression of these proteins on transcription in both viral and host genomes?
2) Are these proteins activators or repressors of transcription, and what is the molecular nature of their action?

Our results are likely to converge with other research groups interested in thermophilic viruses at Montana State University and will provide more detailed picture of viral and host transcriptional regulation.

Current Lab Personnel:

Katie Basham, Research Assistant

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