1999 Workshop Abstracts | Virus Evolution Home Page | Plant Biology Home Page

Bioinformatic analysis of dUTPase encoding genes in viruses and their hosts

Marcella A. McClure and Angela M. Baldo¹
Department of Microbiology and Center for Computational Biology,
Montana State University, Bozeman, MT 59717; mars@nervana.montana.edu
¹ Department of Plant Breeding, Cornell University, Ithaca, NY 14853

Bioinformatic analysis of sequence data can provide new knowledge regarding the evolution, function, and structure of proteins. The studies presented here, on the sequence analysis of the dut gene and it product, dUTPase, demonstrate the power of this approach in generating information regarding the horizontal transfer of genes between hosts and pathogens, gene location and architecture, and protein structure. dUTPase is a ubiquitous and essential enzyme responsible for regulating cellular levels of dUTP.

Phylogenetic analysis of dut sequences indicates five statistically supported gene transfers from host to virus. dut gene transfers have taken place in all three domains of life: from Eukaryotes to poxviruses, avian adenovirus, and Paramecium bursaria chlorella virus; from Eubacteria to bacteriophage SPb ; and from Archaea to Sulfobulus islandicus rod-shaped virus 1. Other cases of potential transfer have been identified among several Eubacteria, two between Eubacteria and their viruses, and one among retroviruses. Although statistical support for these latter cases cannot be generated with currently available data, the evidence of these transfers is independent of phylogenetic inference method and the manner in which the data are partitioned (conserved versus less conserved regions) for analyses. Further support for the movement of the dut gene comes from variable location in both host and viral genomes.

While it is well known that Retroviruses may acquire sequences relatively easily from their hosts, the studies presented here suggest that DNA viruses may have acquired the dut gene via a reverse transcription process. The human dut gene spans about 14kb and contains approximately five introns. Mouse and Rhesus monkey dut genes are also reported to have introns. To explain the presence of intron-less dut genes in DNA viruses, however, we hypothesize that these viruses acquired a cDNA of an RNA message analogous to the mechanism that results in v-oncogene acquisition in retroviruses.

The dut gene architecture is also variable. The majority of dUTPases considered in this study (62 out of 75 total) display a common arrangement of five accepted motifs, referred to as I, II, III, IV, and V. Fish herpes viruses and humans, for example, have a single-unit length dUTPase with the common arrangement of motifs. In alpha and gamma herpes viruses, however, the dUTPase is roughly twice as long as the common arrangement. In the amino portion of the dUTPase of these viruses, a clearly recognizable motif III is present, but only residual motifs I, II, and IV appear. The carboxy portion of the herpes virus dUTPase has recognizable motifs I, II, IV, and V, while a residual motif III is located between II and IV. In contrast, Caenorhabditis elegans has a triplication of the single arrangement such that there are fifteen complete motifs. The finding of three different gene archetectures for various dUTPases has implications for the three dimensional structure of these enzymes.

While the location of structural and functional residues has been determined by X-ray crystallography in single-copy dUTPases structures have not been reported for any dUTPases with other motif arrangements. Based on the conserved structural and functional residues in the alignment we hypothesize the type of folding and assembly that might occur in duplicated and triplicated dUTPases. Alpha and gamma herpes viruses have duplications such that the first copy conserves motif III, and the second copy conserves I, II, IV, and V. Available evidence indicates that herpes dUTPases function as monomers. Some residues involved in secondary structure are conserved as well, implying that much of the structure surrounding motifs I, II, IV, and V is similar. Although the structure of the amino portion of the alpha and gamma herpes virus dUTPase remains ambiguous, motif III is likely present in an active site as is found in homotrimers comprised of single copies. The dUTPase of C. elegans has a novel arrangement in that it is tandemly triplicated such that a single peptide could theoretically fold into a shape similar to that of a single copy homotrimer.

The patterns of dut horizontal transfer observed between Archaea, Eubacteria, and Eukaryotes and their viruses have important implications for clinical and genomic research. In terms of clinical implications, other DNA and RNA viruses may acquire the dut gene and thereby expand their pathology to include nondividing tissues. The dUTPase protein has been proposed as a target for anti-viral drugs and cancer chemotherapy. Already a common target for chemotherapy, thymidylate synthase is an enzyme downstream of dUTPase in the biochemical pathway for conversion of dUTP to TTP. Targeting the dUTPase protein may likewise have potential for controlling the rapid growth of tissue.

Abstract - Presented at the Virus Evolution Workshop
Ardmore, OK
October 21 - 24th, 1999

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e-mail: mroossinck@noble.org

Dr. Marilyn Roossinck
Plant Biology Division
The Noble Foundation
P.O. Box 2180
Ardmore, OK 73402

phone: 580 224-6630