A tandem gene duplication followed by recruitment of a retrotransposon created the paralogous bucentaur gene (bcntp97) in the ancestral ruminant

Molecular Biology and Evolution

Volumn 23, Issue 4, 2006, Pages 798-806

  Iwashita, Shintaro ^a,b   Ueno, Sadao ^a,b   Nakashima, Kentaro ^a,b   Song, Si Young ^a   Ohshima, Kenshiro ^c   Tanaka, Kazuaki ^d   Endo, Hideki ^e   Kimura, Junpei ^f   Kurohmaru, Masamichi ^g   Fukuta, Katsuhiro ^h   David, Lior ⁱ   Osada, Naoki ^j  

^a Mitsubishi Kagaku Institute of Life Sciences (MITILS)   (Japan)

^b YOKOHAMA NATIONAL UNIVERSITY   (Japan)

^c HITACHI LTD   (Japan)

^d AZABU UNIVERSITY   (Japan)

^e DEPARTMENT OF BOTANY   (Japan)

^f NIHON UNIVERSITY   (Japan)

^g UNIVERSITY OF TOKYO   (Japan)

^h NAGOYA UNIVERSITY   (Japan)

ⁱ STANFORD UNIVERSITY   (United States)

^j NATIONAL INSTITUTE OF BIOMEDICAL INNOVATION   (Japan)

more..

Author keywords

Adaptive evolution; AP endonuclease domain; Exonization; Gene duplication; Reverse transcriptase domain; Ruminant

Indexed keywords

NUCLEOTIDE;

ARTICLE; BOVIDS; CAMEL; CONTROLLED STUDY; EXON; GENE; GENE BCNT P97; GENE DUPLICATION; GENE EXPRESSION; GENE FUNCTION; GENE SEQUENCE; GENETIC ANALYSIS; GENOME ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PARALOGY; PHYLOGENY; RADIATION; RETROPOSON; SOUTHERN BLOTTING; SWINE;

ANIMALIA; BOVIDAE; BOVINAE; CAMELIDAE; SUS SCROFA; TRAGULUS JAVANICUS;

EID: 33644920974     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj088     Document Type: Article

References (42)

1. Beernink, P. T., B. W. Segelke, M. Z. Hadi, J. P. Erzberger, D. M. Wilson III, and B. Rupp. 2001. Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: implications for the catalytic mechanism. J. Mol. Biol. 307:1023-1034.
2. Breukelman, H. J., P. A. Jekel, J.-Y. Dubois, P. P. M. F. A. Mulder, H. W. Warmels, and J. J. Beintema. 2001. Secretory ribonucleases in the primitive ruminant chevrotain (Tragulus javanicus). Eur. J. Biochem. 268:3890-3897.
3. Brosius, J. 2005. Echoes from the past - are we still in an RNP world? Cytogenet. Genome Res. 110:8-24.
4. Diekwisch, T. G., and X. Luan. 2002. CP27 function is necessary for cell survival and differentiation during tooth morphogenesis in organ culture. Gene 287:141-147.
5. Endo, H., J. Kimura, M. Sasaki, M. Matsuzaki, H. Matsubayashi, K. Tanaka, and K. Fukuta. 2002. Functional morphology of the mastication muscles in the lesser and greater mouse deer. J. Vet. Med. Sci. 64:901-905.
6. Force, A., M. Lynch, F. B. Pickett, A. Amores, Y.-L. Yan, and J. Postlethwait. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.
7. Francino, M. P. 2005. An adaptive radiation model for the origin of new gene functions. Nat. Genet. 37:573-577.
8. Fritz, G., and B. Kaina. 1999. Phosphorylation of the DNA repair protein APE/REF-1 by CKII affects redox regulation of AP-1. Oncogene 18:1033-1040.
9. Han, J. S., S. T. Szak, and J. D. Boeke. 2004. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429:268-274.
10. Hassanin, A., and E. J. Douzery. 2003. Molecular and morphological phylogenies of ruminantia and the alternative position of the moschidae. Syst. Biol. 52:206-228.
11. Hon-Nami, K., S. Ueno, H. Endo, H. Nishimura, H. Igarashi, L. David, and S. Iwashita. 2004. A novel Giraffidae-specific interspersed repeat with a microsatellite, originally found in an intron of a ruminant paralogous p97bcnt gene. Gene 340:283-290.
12. Hughes, A. L. 2002. Adaptive evolution after gene duplication. Trends Genet. 18:433-434.
13. Iwashita, S., T. Nobukuni, S. Tanaka, M. Kobayashi, T. Iwanaga, H. B. Tamate, T. Masui, I. Takahashi, and K. Hashimoto. 1999. Partial nuclear localization of a bovine phosphoprotein, BCNT, that includes a region derived from a LINE repetitive sequence in Ruminantia. Biochim. Biophys. Acta 1427:408-416.
14. Iwashita, S., N. Osada, T. Itoh et al. (11 co-authors). 2003. A transposable element-mediated gene divergence that directly produces a novel type bovine Bcnt protein including the endonuclease domain of RTE-1. Mol. Biol. Evol. 20:1556-1563.
15. Jordan, I. K., Y. I. Wolf, and E. V. Koonin. 2004. Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol. Biol. 4:22.
16. Kishino, H., and M. Hasegawa. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol. 29:170-179.
17. Kordis, D., and F. Gubensek. 1998. Unusual horizontal transfer of a long interspersed nuclear element between distant vertebrate classes. Proc. Natl. Acad. Sci. USA 95:10704-10709.
18. Lev-Maor, G., R. Sorek, N. Shomron, and G. Ast. 2003. The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons. Science 300:1288-1291.
19. Liu, W.-M., W.-M. Chu, P. V. Choudary, and C. W. Schmid. 1995. Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res. 23:1758-1765.
20. Long, M. 2001. Evolution of novel genes. Curr. Opin. Genet. Dev. 11:673-680.
21. Lynch, M., and V. Katju. 2004. The altered evolutionary trajectories of gene duplicates. Trends Genet. 20:544-549.
22. Makalowski, W. 2000. Genomic scrap yard: how genomes utilize all that junk. Gene 259:61-67.
23. _. 2003. Not junk after all. Science 300:1246-1247.
24. Malik, H. S., and T. H. Eickbush. 1998. The RTE class of non-LTR retrotransposons is widely distributed in animals and is the origin of many SINEs. Mol. Biol. Evol. 15:1123-1134.
25. Modi, W. S., D. S. Gallagher, and J. E. Womack. 1996. Evolutionary histories of highly repeated DNA families among the Artiodactyla (Mammalia). J. Mol. Evol. 42:337-349.
26. Morales, J. F., E. T. Snow, J. P. Murnane. 2003. Environmental factors affecting transcription of the human L1 retrotransposon. II. Stressors. Mutagenesis 18:151-158.
27. Nekrutenko, A., and W.-H. Li. 2001. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 17:619-621.
28. Nikaido, M., A. P. Rooney, and N. Okada. 1999. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales. Proc. Natl. Acad. Sci. USA 96:10261-10266.
29. Nobukuni, T., M. Kobayashi, A. Omori et al. (12 co-authors). 1997. An Alu-linked repetitive sequence corresponding to 280 amino acids is expressed in a novel bovine protein, but not in its human homologue. J. Biol. Chem. 272:2801-2807.
30. Ohno, S. 1970. Evolution by gene duplication. Allen and Unwin, Springer-Verlag, London.
31. Poulter, R., M. Butler, and J. Ormandy. 1999. A LINE element from the pufferfish (fugu) Fugu rubripes which shows similarity to the CR1 family of non-LTR retrotransposons. Gene 227:169-179.
32. Suzuki, K., S. Asakawa, M. Iida, S. Shimanuki, N. Fujishima, H. Hiraiwa, Y. Murakami, N. Shimizu, and H. Yasue. 2000. Construction and evaluation of a porcine bacterial artificial chromosome library. Anim. Genet. 31:8-12.
33. Szemraj, J., G. Plucienniczak, J. Jaworski, and A. Plucienniczak. 1995. Bovine Alu-like sequences mediate transposition of a new site-specific retroelement. Gene 152:261-264.
34. Takahashi, I., T. Nobukuni, H. Ohmori, M. Kobayashi, S. Tanaka, K. Ohshima, N. Okada, T. Masui, K. Hashimoto, and S. Iwashita. 1998. Existence of a bovine LINE repetitive insert that appears in the cDNA of bovine protein BCNT in ruminant, but not in human, genomes. Gene 211:387-394.
35. Tatusova, T. A., and T. L. Madden. 1999. Blast 2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174:247-250.
36. Tell, G., G. Damante, D. Caldwell, and M. R. Kelley. 2005. The intracellular localization of APE1/Ref-1: more than a passive phenomenon? Antioxid. Redox Signal. 7:367-384.
37. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
38. Wen, Y., and D. M. Irwin. 1999. Mosaic evolution of ruminant stomach lysozyme genes. Mol. Phylogenet. Evol. 13:474-482.
39. Wisniewski, T. P., C. L. Tanzi, and J. G. Gindhart. 2003. The Drosophila kinesin-I associated protein YETI binds both kinesin subunits. Biol. Cell. 95:595-602.
40. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
41. Zhang, J., A. M. Dean, F. Brunet, and M. Long. 2004. Evolving protein functional diversity in new genes of Drosophila. Proc. Natl. Acad. Sci. USA 101:16246-16250.
42. Zupunski, V., F. Gubensek, and D. Kordis. 2001. Evolutionary dynamics and evolutionary history in the RTE clade of non-LTR retrotransposons. Mol. Biol. Evol. 18:1849-1863.