The long term objective of this proposal is to study the origin(s) and evolution of RNA virus systems via computer-based sequence analysis. RNA viruses are the major causative agents of human, animal and plant viral diseases. Knowledge of sequence relationships within RNA virus groups, between such groups and to potential cellular homologues is of primary interest in tracing the origins of viruses as well as elucidating mechanisms of emergence of new pathogenic strains. The use of computer-assisted comparisons of primary sequence data (nucleic acid or protein) is a powerful approach to questions of this nature. In addition, RNA viruses represent a highly divergent set of biologically related sequences and therefore provide a model database for development of new computer programs and strategies necessary for determining the most distant relationships between the genes of other organisms.
Our specific aims are the following: 1) analysis of relationships between viruses known to utilize reverse transcriptase (RT) in their lifecycle and cellular elements with RT-like sequences; 2) quantitation of evolutionary relationships among picornaviruses and related plant viruses; and 3) development of computer-assisted methodologies for quantitation of the most distant protein sequence relationships.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
3R01AI028309-06S1
Application #
2064361
Study Section
Experimental Virology Study Section (EVR)
Project Start
1993-06-01
Project End
1996-02-29
Budget Start
1993-12-01
Budget End
1996-02-29
Support Year
6
Fiscal Year
1995
Total Cost
Indirect Cost
Name
University of Nevada Las Vegas
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
City
Las Vegas
State
NV
Country
United States
Zip Code
89154
Werren, John H; Richards, Stephen; Desjardins, Christopher A et al. (2010) Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science 327:343-8
Basta, Holly A; Cleveland, Sean B; Clinton, Rochelle A et al. (2009) Evolution of teleost fish retroviruses: characterization of new retroviruses with cellular genes. J Virol 83:10152-62
McClure, Marcella A; Richardson, Hugh S; Clinton, Rochelle A et al. (2005) Automated characterization of potentially active retroid agents in the human genome. Genomics 85:512-23
Franklin, Michael J; Douthit, Stephanie A; McClure, Marcella A (2004) Evidence that the algI/algJ gene cassette, required for O acetylation of Pseudomonas aeruginosa alginate, evolved by lateral gene transfer. J Bacteriol 186:4759-73
McClure, Marcella A; Donaldson, Eric; Corro, Seanna (2002) Potential multiple endonuclease functions and a ribonuclease H encoded in retroposon genomes. Virology 296:147-58
McClure, M A (2001) Evolution of the DUT gene: horizontal transfer between host and pathogen in all three domains of life. Curr Protein Pept Sci 2:313-24
McClure, M A (2000) The complexities of genome analysis, the Retroid agent perspective. Bioinformatics 16:79-95
Mcclure, M A; Kowalski, J (1999) The effects of ordered-series-of-motifs anchoring and sub-class modeling on the generation of HMMs representing highly divergent protein sequences. Pac Symp Biocomput :162-70
Baldo, A M; McClure, M A (1999) Evolution and horizontal transfer of dUTPase-encoding genes in viruses and their hosts. J Virol 73:7710-21
Hudak, J; Mcclure, M A (1999) A comparative analysis of computational motif-detection methods. Pac Symp Biocomput :138-49

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