Evolution and horizontal transfer of dUTPase-encoding genes in viruses and their hosts

Journal of Virology

Volumn 73, Issue 9, 1999, Pages 7710-7721

  Baldo, Angela M ^a,b   McClure, Marcella A ^a,c  

^a UNIVERSITY OF NEVADA   (United States)

^b MONTANA STATE UNIVERSITY   (United States)

^c Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

URIDINE TRIPHOSPHATE; VIRUS ENZYME;

AMINO ACID SEQUENCE; ARTICLE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME STRUCTURE; EVOLUTION; GENE TRANSFER; NONHUMAN; PRIORITY JOURNAL; SPECIES DIFFERENTIATION;

EID: 0032837333     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.73.9.7710-7721.1999     Document Type: Article

References (77)

1. Abergel, C., D. L. Robertson, and J.-M. Claverie. 1999. "Hidden" dUTPase sequence in human immunodeficiency virus type 1 gp120. J. Virol. 73:751-753.
2. Altschul, S., W. Gish, W. Miller, E. Myers, and D. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. Baer, R., A. T. Bankier, M. D. Biggin, P. L. Deininger, P. J. Farrell, T. J. Gibson, G. Hatfull, G. S. Hudson, S. C. Satchwell, and C. Seguin. 1984. DNA sequence and expression of the B95-8 Epstein-Barr virus genome. Nature 310:207-211.
4. Camacho, A., R. Arrebola, J. Peña-Diaz, L. M. Ruiz-Pérez, and D. González-Pacanowska. 1997. Description of a novel eukaryotic deoxyuridine 5′-triphosphate nucleotidohydrolase in Leishmania major. Biochem. J. 325:441-447.
5. Caradonna, S. J., and D. M. Adamkiewicz. 1984. Purification and properties of the deoxyuridine triphosphate nucleotidohydrolase enzyme derived from HeLa S3 cells. J. Biol. Chem. 259:5459-5464.
6. Cedergren-Zeppezauer, E. S., G. Larsson, P. O. Nyman, Z. Dauter, and K. S. Wilson. 1992. Crystal structure of a dUTPase. Nature 355:740-743.
7. Coffin, J. M., S. H. Hughes, and H. E. Varmus (ed.). 1997. Retroviruses, 1st ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
8. Cordonnier, A., J.-F. Casella, and T. Heidmann. 1995. Isolation of novel human endogenous retrovirus-like elements with foamy virus-related pol sequence. J. Virol. 69:5890-5897.
9. Dauter, Z., R. Persson, A. M. Rosengren, P. O. Nyman, K. S. Wilson, and E. S. Cedergren-Zeppezauer. 1999. Crystal structure of dUTPase from equine infectious anaemia virus: active site metal binding in a substrate analogue complex. J. Mol. Biol. 285:655-673.
10. Davison, A. J. 1998. The genome of salmonid herpesvirus 1. J. Virol. 72: 1974-1982.
11. Davison, A. J., and J. E. Scott. 1986. The complete DNA sequence of varicella-zoster virus. J. Gen. Virol. 67:1759-1816.
12. Dayhoff, M. O., R. M. Schwartz, and B. C. Orcutt. 1978. A model of evolutionary change in proteins, p. 345-352. In M. O. Dayhoff (ed.), Atlas of protein sequence and structure, vol. 5, suppl. 3. National Biomedical Research Foundation, Washington, D.C.
13. Eisen, J. A. 1995. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J. Mol. Evol. 41:1105-1123.
14. El-Hajj, H. H., H. Zhang, and B. Weiss. 1988. Lethality of a dut (deoxyuridine triphosphatase) mutation in Escherichia coli. J. Bacteriol. 170:1069-1075.
15. Felsenstein, J. 1989. PHYLIP - phylogeny inference package (version 3.2). Cladistics 5:164-166.
16. Feng, D. F., and R. F. Doolittle. 1987. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25:351-360.
17. Fitch, W. M., and J. S. Farris. 1974. Evolutionary trees with minimum nucleotide replacements from amino acid sequences. J. Mol. Evol. 3:263-278.
18. Fitch, W. M., and E. Margoliash. 1967. Construction of phylogenetic trees. Science 155:279-284.
19. Fleming, S. B., D. J. Lyttle, J. T. Sullivan, A. A. Mercer, and A. J. Robinson. 1995. Genomic analysis of a transposition-deletion variant of ORF virus reveals a 3.3 kbp region of non-essential DNA. J. Gen. Virol. 76:2969-2978.
20. Fraser, C. M., S. J. Norris, G. M. Weinstock, O. White, G. G. Sutton, R. Dodson, M. Gwinn, E. K. Hickey, R. Clayton, K. A. Ketchum, E. Sodergren, J. M. Hardham, M. P. McLeod, S. Salzberg, J. Peterson, H. Khalak, D. Richardson, J. K. Howell, M. Chidambaram, T. Utterback, L. McDonald, P. Artiach, C. Bowman, M. D. Cotton, C. Fujii, S. Garland, B. Hatch, K. Horst, L. Roberts, L. Watthey, W. Janice, H. O. Smith, and C. J. Venter. 1998. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 281:375-388.
21. Gadsen, M., E. McIntosh, J. Game, P. Wilson, and R. Haynes. 1993. dUTP pyrophosphatase is an essential enzyme in Saccharomyces cerevisiae. EMBO J. 12:4425-4431.
22. Ghim, S.-Y., S.-K. Choi, B.-S. Shin, and S.-H. Park. 1998. An 8 kb nucleotide sequence at the 3′ flanking region of the sspC gene (184°) on the Bacillus subtilis 168 chromosome containing an intein and an intron. DNA Res. 5:121-126.
23. Hajjar, A. M., and M. L. Linial. 1993. A model system for nonhomologous recombination between retroviral and cellular RNA. J. Virol. 67:3845-3853.
24. Hannenhalli, S., C. Chappey, E. V. Koonin, and P. A. Pevzner. 1995. Genome sequence comparison and scenarios for gene rearrangements: a test case. Genomics 30:299-311.
25. Higgins, D., A. J. Bleasby, and R. Fuchs. 1991. Clustal V: improved software for multiple sequence alignment. CABIOS 8:189-191.
26. Hill, F., D. Loakes, and D. M. Brown. 1998. Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases. Proc. Natl. Acad. Sci. USA 95:4258-4263.
27. Hughey, R., and A. Krogh. 1996. Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput. Appl. Biosci. 12:95-107.
28. Kaliman, A. V. 1996. Identification of the bacteriophage T5 dUTPase by protein sequence comparisons. DNA Seq. 6:347-350.
29. Krogh, A., I. Brown, S. Mian, K. Sjolander, and D. Haussler. 1994. Hidden Markov models in computational biology: applications to protein modeling. J. Mol. Biol. 235:1501-1531.
30. Kuzio, J., M. N. Pearson, S. H. Harwood, J. C. Funk, J. T. Evans, J. M. Slavicek, and G. F. Rohrmann. 1999. Sequence and analysis of the genome of a baculovirus pathogenic for Lymantria dispar. Virology 253:17-34.
31. Ladner, R. Personal communication.
32. Ladner, R. D., D. E. McNulty, S. A. Carr, G. D. Roberts, and S. J. Caradonna. 1996. Characterization of distinct nuclear and mitochondrial forms of human deoxyuridine triphosphate nucleotidohydrolase. J. Biol. Chem. 271: 7745-7751.
33. Larsson, G., L. A. Svensson, and P. O. Nyman. 1996. Crystal structure of the Escherichia coli dUTPase in complex with a substrate analogue (dUTP). Nat. Struct. Biol. 3:532-538.
34. Lazarevic, V., B. Soldo, A. Düsterhöft, H. Hilbert, C. Mauël, and D. Karamata. 1998. Introns and intein coding sequence in the ribonucleotide reductase genes of Bacillus subtilis temperate bacteriophage SPbeta. Proc. Natl. Acad. Sci. USA 95:1692-1697.
35. Li, Y., Z. Lu, L. Sun, S. Ropp, G. F. Kutish, D. L. Rock, and J. L. van Etten. 1997. Analysis of 74 kb of DNA located at the right end of the 330-kb chlorella virus PBCV-1 genome. Virology 237:360-377.
36. Liang, X., M. Tang, B. Manns, L. A. Babiuk, and T. J. Zamb. 1993. Identification and deletion mutagenesis of the bovine herpesvirus 1 dUTPase gene and a gene homologous to herpes simplex virus UL49.5′. Virology 195:42-50.
37. Lichtenstein, D. L., K. E. Rushlow, R. F. Cook, M. L. Raabe, C. J. Swardson, G. J. Kociba, C. J. Issel, and R. C. Montelaro. 1995. Replication in vitro and in vivo of an equine infectious anemia virus mutant deficient in dUTPase activity. J. Virol. 69:2881-2888.
38. Massung, R. F., V. Jayarama, and R. W. Moyer. 1993. DNA sequence analysis of conserved and unique regions of swinepox virus: identification of genetic elements supporting phenotypic observations including a novel G protein-coupled receptor homologue. Virology 197:511-528.
39. McClure, M. A. 1991. Evolution of retroposons by acquisition or deletion of retrovirus-like genes. Mol. Biol. Evol. 8:835-856.
40. McClure, M. A., J. Hudak, and J. M. Kowalski. 1998. Low identity, low similarity protein sequences: independent modeling of the ordered-series-of-motifs and motif-intervening-regions, p. 183-192. In S. Miyano and T. Takagi (ed.), Genome informatics 1998. Universal Academy Press, Inc., Tokyo, Japan.
41. McClure, M. A., M. S. Johnson, and R. F. Doolittle. 1987. Relocation of a protease-like gene segment between two retroviruses. Proc. Natl. Acad. Sci. USA 84:2693-2697.
42. McClure, M. A., M. S. Johnson, D.-F. Feng, and R. F. Doolittle. 1988. Sequence comparisons of retroviral proteins: relative rates of change and general phylogeny. Proc. Natl. Acad. Sci. USA 85:2469-2473.
43. McClure, M. A., and J. Kowalski. 1999. The effects of ordered-series-of-motifs anchoring and subclass modeling on the generation of HMMs representing highly divergent protein sequences, p. 162-170. In R. B. Altman, A. K. Dunker, L. Hunter, T. E. Klein, and K. Lauderdale (ed.), Proceedings of the Pacific Symposium on Biocomputing, 1999. World Scientific, River Edge, N.J.
44. McClure, M. A., and R. Raman. 1995. Parameterization studies of hidden Markov models representing highly divergent protein sequences, p. 184-193. In L. Hunter and B. D. Shriver (ed.), Proceedings of the 28th Hawaii International Conference on System Sciences, vol. V. IEEE Computer Society Press, Washington, D.C.
45. McGeoch, D. J. 1990. Protein sequences, comparisons show that the 'pseudoproteases' encoded by poxviruses and certain retroviruses belong to the deoxyuridine triphosphatase family. Nucleic Acids Res. 18:4105-4110.
46. McGeoch, D. J., M. A. Dalrymple, A. J. Davison, A. Dolan, M. C. Frame, D. McNab, L. J. Perry, J. E. Scott, and P. Taylor. 1988. The complete DNA sequence of the long unique region in the genome of herpes simplex virus type 1. J. Gen. Virol. 69:1531-1574.
47. McIntosh, E. M., D. D. Ager, M. H. Gadsden, and R. H. Haynes. 1992. Human dUTP pyrophosphatase: cDNA sequence and potential biological importance of the enzyme. Proc. Natl. Acad. Sci. USA 89:8020-8024.
48. McIntosh, E. M., and R. H. Haynes. 1997. dUTP pyrophosphatase as a potential target for chemotherapeutic drug development. Acta Biochim. Pol. 44:159-171.
49. McIntosh, E. M., and R. H. Haynes. 1996. HIV and human endogenous retroviruses: an hypothesis with therapeutic implications. Acta Biochim. Pol. 43:583-592.
50. Mercer, A. A., K. M. Fraser, P. A. Stockwell, and A. J. Robinson. 1989. A homologue of retroviral pseudoproteases in the paraoxvirus, ORF virus. Virology 172:665-668.
51. Mol, C. D., J. M. Harris, E. M. McIntosh, and J. A. Tainer. 1996. Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits. Structure 4:1077-1092.
52. Needleman, S. B., and C. D. Wunsch. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443-453.
53. Petursson, G., P. Turelli, M. Sigridur, G. Georgsson, O. S. Andresson, S. Torsteinsdottir, R. Vigne, V. Andresdottir, E. Gunnarsson, G. Agnarsdottir, and G. Querat. 1998. Visna virus dUTPase is dispensable for neuropathogenicity. J. Virol. 72:1657-1661.
54. Phillips, T. R., O. Prospero-Garcia, D. W. Wheeler, P. C. Wagaman, D. L. Lerner, H. S. Fox, L. R. Whalen, F. E. Bloom, J. H. Elder, and S. J. Henriksen. 1996. Neurologic dysfunctions caused by a molecular clone of feline immunodeficiency virus, FIV-PPR. J. Neurovirol. 2:388-396.
55. Prangisvili, D., H.-P. Klenk, G. Jakobs, A. Schmiechen, C. Hanselmann, I. Holz, and W. Zillig. 1998. Biochemical and phylogenetic characterization of the dUTPase from the archaeal virus SIRV. J. Biol. Chem. 273:6024-6029.
56. Prasad, S. G., E. A. Stura, D. E. McRee, G. S. Laco, C. Hasselkus-Light, J. H. Elder, and C. D. Stout. 1996. Crystal structure of dUTP pyrophosphatase from feline immunodeficiency virus. Protein Sci. 5:2429-2437.
57. Pyles, R. B., N. M. Sawtell, and R. L. Thompson. 1992. Herpes simplex virus type 1 dUTPase mutants are attenuated for neurovirulence, neuroinvasiveness, and reactivation from latency. J. Virol. 66:6706-6713.
58. Ross, J., M. Williams, and J. I. Cohen. 1997. Disruption of the varicella-zoster virus dUTPase and the adjacent ORF9A gene results in impaired growth and reduced syncytia formation in vitro. Virology 234:186-195.
59. Senkevich, T. G., E. V. Koonin, J. J. Bugert, G. Darai, and B. Moss. 1997. The genome of Molluscum contagiosum virus: analysis and comparison with other poxviruses. Virology 233:19-42.
60. Shao, H., M. D. Robek, D. S. Threadgill, L. S. Mankowski, C. E. Cameron, F. J. Fuller, and S. L. Payne. 1997. Characterization and mutational studies of equine infectious anemia virus dUTPase. Biochem. Biophys. Acta 1339: 181-191.
61. Slabaugh, M. B., and N. A. Roseman. 1989. Retroviral protease-like gene in the vaccinia virus genome. Proc. Natl. Acad. Sci. USA 86:4152-4155.
62. Stephens, R. S., S. Kalman, C. Lammel, J. Fan, R. Marathe, L. Aravind, W. Mitchell, L. Olinger, R. L. Tatusov, Q. Zhao, E. V. Koonin, and R. W. Davis. 1998. Genome sequence of a obligate intracellular pathogen of humans: Chlamydia trachomatis, Science 282:754-759.
63. Tamames, J., G. Casari, C. Ouzounis, and A. Valencie. 1997. Conserved clusters of functionally related genes in two bacterial genomes. J. Mol. Evol. 44:66-73.
64. The Chlamydia Genome Project. [Online.] University of California, Berkeley. http://chlamydia-www.berkeley.edu:4231. [20 January 1999, last date accessed.]
65. The Gonococcal Genome Sequencing Project. [Online.] http://dna1.chem.ou .edu/gono.html. [20 January 1999, last date accessed.]
66. The Microbial Genome Project. [Online.] Genome therapeutics, http://www.genomecorp.com/genesequences/clostridium/clospage.html. [20 January 1999, last date accessed.]
67. The Pseudomonas Genome Project. [Online.] University of Washington Genome Center/PathoGenesis Corp./U.S. Cystic Fibrosis Foundation, http://www.pseudomonas.com. [20 January 1999, last date accessed.]
68. Tomb, J.-F., O. White, A. R. Kerlavage, R. A. Clayton, G. G. Sutton, R. D. Fleischmann, K. A. Ketchum, H. P. Klenk, S. Gill, B. A. Dougherty, K. Nelson, J. Quackenbush, L. Zhou, E. F. Kirkness, S. Peterson, B. Loftus, D. Richardson, R. Dodson, H. G. Khalak, A. Glodek, K. McKenney, L. M. Fitzgerald, N. Lee, M. D. Adams, E. K. Hickey, D. E. Berg, J. D. Gocayne, T. R. Utterback, J. D. Peterson, J. M. Kelley, M. D. Cotton, J. M. Weidman, C. Fuji, C. Bowman, L. Watthey, E. Wallin, W. S. Hayes, M. Borodovsky, P. D. Karp, H. O. Smith, C. M. Fraser, and C. J. Venter. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388: 539-547.
69. Turelli, P., F. Guiguen, J.-F. Mornex, R. Vigne, and G. Querat. 1997. dUTPase-minus Caprine arthritis-encephalitis virus is attenuated for pathogenesis and accumulates G-to-A substitutions. J. Virol. 71:4522-4530.
70. van Sinderen, D., H. Karsens, J. Kok, P. Terpstra, M. H. J. Ruiters, G. Venema, and A. Nauta. 1996. Sequence analysis and molecular characterization of the temperate lactococcal bacteriophage rlt. Mol. Microbiol. 19: 1343-1355.
71. Vertessy, B. G. 1997. Flexible glycine rich motif of Escherichia coli deoxyuridine triphosphate nucleotidohydrolase is important for functional but not for structural integrity of the enzyme. Proteins 28:568-579.
72. Vertessy, B. G., G. Larsson, T. Persson, A.-C. Bergman, R. Persson, and P. O. Nyman. 1998. The complete triphosphate moiety of non-hydrolyzable substrate analogues is required for a conformational shift of the flexible C-terminus in Escherichia coli dUTP pyrophosphatase. FEBS Lett. 421:83-88.
73. Vertessy, B. G., R. Persson, A.-M. Rosengren, M. Zeppezauer, and N. P. Olof. 1996. Specific derivatization of the active site tyrosine in dUTPase perturbs ligand binding to the active site. Biochem. Biophys. Res. Commun. 219:294-300.
74. Vertessy, B. G., P. Zalud, P. O. Nyman, and M. Zeppezauer. 1994. Identification of tyrosine as a functional residue in the active site of Escherichia coli dUTPase. Biochem. Biophys. Acta 1295:146-150.
75. Wagaman, P. C., C. S. Hasselkus-Light, M. Henson, D. L. Lerner, T. R. Phillips, and J. H. Elder. 1993. Molecular cloning and characterization of deoxyuridine triphosphatase from feline immunodeficiency virus (FIV). Virology 196:451-457.
76. Weiss, R. S., S. S. Lee, B. V. V. Prasad, and R. T. Javier. 1997. Human adenovirus early region 4 open reading frame 1 genes encode growth-transforming proteins that may be distantly related to dUTP pyrophosphatase enzymes. J. Virol. 71:1857-1870.
77. Wheeler, L. J., N. F. Ray, C. Ungermann, S. P. Hendricks, M. A. Bernard, E. S. Hanson, and C. K. Mathews. 1996. T4 phage gene 32 protein as a candidate organizing factor for the deoxyribonucleoside triphosphate synthetase complex. J. Biol. Chem. 271:11156-11162.