This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The major goal of this research endeavor is to search for novel genes among the Nucleocytoplasmic Large DNA Viruses (NCLDV). The model virus of this group, Paramecium bursaria chlorella virus-1 (PBVC-1), which infect a green alga, has been sequenced, as have 7 other viruses of this group. These viruses contain many novel genes/proteins, some of which are the smallest known, several of which have commercial applications (next paragraph and section B.3.). PBCV-1 belongs to an ancient family of eukaryotic viruses that infect a chlorella-like green alga, a symbiont of Paramecium bursaria. PBVC-1 is a plaque-forming virus that has proven to be very amenable to laboratory study. James Van Etten, (JVE) the mentor/collaborator for this project (see section E below), has 25+ years working on this virus and has current NIH funding to investigate the DNA replication and gene expression of this virus. Furthermore, JVE has a network of collaborators who are studying a wide variety of PBVC-1 properties. This virus will be used as a reference against all newly sequenced viruses. The reasons for focusing on the NCLDV group of viruses are that they have, by definition, large genomes (the mimivirus encodes over 1000 proteins) and they are ancient. Their large genomes have come about by high jacking genes from a variety of sources and by gene duplication. Their ancient history and short life cycles have enabled them to evolve some of the smallest functional proteins, while other proteins have been shown to have medical importance (see section B.3.). For example, PBCV-1 has genes that encode proteins involved in DNA replication, recombination and repair, cell signaling, DNA restriction/modification, to name a few. The PBCV-1 type II DNA topoisomerase is the smallest one to be described to date and yet has very high activity levels (Lavrukhin et al., 2000). Topoisomerase II from PBCV-1 has been of interest in the study of cancer cells. Its restriction and methylation enzymes are commercially sold by New England Biolabs. This virus also encodes the smallest K+ channel protein. Plugge et al. (2000) have extensively characterized this protein from PBCV-1. Ion channel proteins affect ion concentrations and are the target of channel blockers for muscles, including the heart. As well, potassium ion (K+) channels play a key role in the proliferations of breast cancer (Abdul, Santo, and Hoosein, 2003). The primary objectives towards this proposal are: (i.) sequence additional viruses from this group;(ii.) conduct genomic, bioinformatic and phylogenetic analyses of these newly sequenced genomes. The analyses will be ongoing as new databanks and methods emerge. (iii.) Upon identification of novel or unusual genes, hand them off to others in the Van Etten lab and their colleagues who will clone, express and characterize them.

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
Exploratory Grants (P20)
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Special Emphasis Panel (ZRR1-RI-4 (01))
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University of Nebraska Medical Center
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