Evolution of double MutT/Nudix domain-containing proteins: similar domain architectures from independent gene duplication-fusion events

Jun Lin; Yihuai Hu; Bing Tian; Yuejin Hua

doi:10.1016/S1673-8527(08)60152-6

Volume 36 Issue 10

Oct. 2009

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Article Navigation > Journal of Genetics and Genomics > 2009 > 36(10): 603-610

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Evolution of double MutT/Nudix domain-containing proteins: similar domain architectures from independent gene duplication-fusion events

doi: 10.1016/S1673-8527(08)60152-6

Jun Lin^{a, b, #},
Yihuai Hu^{a, b, c, #},
Bing Tian^a,
Yuejin Hua^a

a
Key Laboratory for Nuclear-Agricultural Sciences of Chinese Ministry of Agriculture and Zhejiang Province, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
b
College of Life Sciences, Zhejiang University, Hangzhou 310029, China
c
College of Life Sciences and Chemical Engineering, Huaiyin Institute of Technology, Huai'an 223001, China

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Corresponding author: E-mail address: tianbing@zju.edu.cn (Bing Tian); E-mail address: yjhua@zju.edu.cn (Yuejin Hua)
Received Date: 2008-10-10
Accepted Date: 2009-03-12
Rev Recd Date: 2009-02-26

Available Online: 2009-10-17

Publish Date: 2009-10-20

Abstract

Abstract

The MutT/Nudix superfamily proteins repair DNA damage and play a role in human health and disease. In this study, we examined two different cases of double MutT/Nudix domain-containing proteins from eukaryotes and prokaryotes. Firstly, these double domain proteins were discovered in Drosophila, but only single Nudix domain proteins were found in other animals. The phylogenetic tree was constructed based on the protein sequence of Nudix_N and Nudix_C fromDrosophila, and Nudix from other animals. The phylogenetic analysis suggested that the double Nudix domain proteins might have undergone a gene duplication-speciation-fusion process. Secondly, two genes of the MutT family, DR0004 and DR0329, were fused by two mutT gene segments and formed double MutT domain protein genes in Deinococcus radiodurans. The evolutionary tree of bacterial MutT proteins suggested that the double MutT domain proteins in D. radiodurans probably resulted from a gene duplication-fusion event after speciation. Gene duplication-fusion is a basic and important gene innovation mechanism for the evolution of double MutT/Nudix domain proteins. Independent gene duplication-fusion events resulted in similar domain architectures of different double MutT/Nudix domain proteins.
- MutT/Nudix superfamily,
- DNA repair,
- gene duplication-fusion

These authors contributed equally to this work.

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References(47)

References

[1]	Altschul, S.F., Madden, T.L., Schaffer, A.A. et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res., 25 (1997),pp. 3389-3402
[2]	Bessman, M.J., Frick, D.N., O'Handley, S.F. The MutT proteins or “Nudix” hydrolases, a family of versatile, widely distributed, “housecleaning” enzymes J. Biol. Chem., 271 (1996),pp. 25059-25062
[3]	Brunelli, J.P., Robison, B.D., Thorgaard, G.H. Ancient and recent duplications of the rainbow trout Wilms' tumor gene Genome, 44 (2001),pp. 455-462
[4]	Cahuzac, B., Berthonneau, E., Birlirakis, N. et al. A recurrent RNA-binding domain is appended to eukaryotic aminoacyl-tRNA synthetases EMBO J., 19 (2000),pp. 445-452
[5]	Compaan, D.M., Ellington, W.R. Functional consequences of a gene duplication and fusion event in an arginine kinase J. Exp. Biol., 206 (2003),pp. 1545-1556
[6]	Cousineau, B., Leclerc, F., Cedergren, R. On the origin of protein synthesis factors: A gene duplication/fusion model J. Mol. Evol., 45 (1997),pp. 661-670
[7]	Finn, R.D., Mistry, J., Schuster-Bockler, B. et al. Pfam: Clans, web tools and services Nucleic Acids Res., 34 (2006),pp. D247-D251
[8]	Francki, M.G., Walker, E., Forster, J.W. et al. Fructosyltransferase and invertase genes evolved by gene duplication and rearrangements: Rice, perennial ryegrass, and wheat gene families Genome, 49 (2006),pp. 1081-1091
[9]	Galperin, M.Y., Moroz, O.V., Wilson, K.S. et al. House cleaning, a part of good housekeeping Mol. Microbiol., 59 (2006),pp. 5-19
[10]	Gu, X. Statistical methods for testing functional divergence after gene duplication Mol. Biol. Evol., 16 (1999),pp. 1664-1674
[11]	Gu, X. A site-specific measure for rate difference after gene duplication or speciation Mol. Biol. Evol., 18 (2001),pp. 2327-2330
[12]	Guerrucci, M.A., Monnier, A., Delalande, C. et al. The elongation factor-1delta (EF-1delta) originates from gene duplication of an EF-1beta ancestor and fusion with a protein-binding domain Gene, 233 (1999),pp. 83-87
[13]	Huang, J.F. Different protein tyrosine phosphatase superfamilies resulting from different gene reading frames Mol. Biol. Evol., 20 (2003),pp. 815-820
[14]	Hulo, N., Sigrist, C.J., Le Saux, V. et al. Recent improvements to the PROSITE database Nucleic Acids Res., 32 (2004),pp. 134-137
[15]	Koonin, E.V. A highly conserved sequence motif defining the family of MutT-related proteins from eubacteria, eukaryotes and viruses Nucleic Acids Res., 21 (1993),p. 4847
[16]	Kumar, S., Tamura, K., Nei, M. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment Brief Bioinform., 5 (2004),pp. 150-163
[17]	Lang, D., Thoma, R., Henn-Sax, M. et al. Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion Science, 289 (2000),pp. 1546-1550
[18]	Langkjaer, R.B., Cliften, P.F., Johnston, M. et al. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes Nature, 421 (2003),pp. 848-852
[19]	Lin, J., Chen, Z.Z., Tian, B. et al. Gene, 387 (2007),pp. 15-20
[20]	Lin, J., Tian, B., Hua, Y.J. Structural and functional diversity of Nudix Fold Protein Pept. Lett., 15 (2008),pp. 108-112
[21]	Livingstone, C.D., Barton, G.J. Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation Comput. Appl. Biosci., 9 (1993),pp. 745-756
[22]	Long, M. A new function evolved from gene fusion Genome Res., 10 (2000),pp. 1655-1657
[23]	Long, M., Thornton, K. Gene duplication and evolution Science, 293 (2001),p. 1551
[24]	Lynch, M. Genomics. Gene duplication and evolution Science, 297 (2002),pp. 945-947
[25]	Lynch, M., Conery, J.S. The evolutionary fate and consequences of duplicate genes Science, 290 (2000),pp. 1151-1155
[26]	Makarova, K.S., Aravind, L., Daly, M.J. et al. Genetica, 108 (2000),pp. 25-34
[27]	Makarova, K.S., Aravind, L., Wolf, Y.I. et al. Microbiol. Mol. Biol. Rev., 65 (2001),pp. 44-79
[28]	McKay, S.J., Trautner, J., Smith, M.J. et al. Evolution of duplicated growth hormone genes in autotetraploid salmonid fishes Genome, 47 (2004),pp. 714-723
[29]	McLennan, A.G. The MutT motif family of nucleotide phosphohydrolases in man and human pathogens Int. J. Mol. Med., 4 (1999),pp. 79-89
[30]	Mejean, V., Salles, C., Bullions, L.C. et al. Mol. Microbiol., 11 (1994),pp. 323-330
[31]	Michaels, M.L., Miller, J.H. The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8-oxoguanine) J. Bacteriol., 174 (1992),pp. 6321-6325
[32]	Murzin, A.G., Brenner, S.E., Hubbard, T. et al. SCOP: A structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol., 247 (1995),pp. 536-540
[33]	Ohno, S.
[34]	Ohta, T. Role of gene duplication in evolution Genome, 31 (1989),pp. 304-310
[35]	Sidow, A. Gen(om)e duplications in the evolution of early vertebrates Curr. Opin. Genet. Dev., 6 (1996),pp. 715-722
[36]	Suzuki, T., Kawasaki, Y., Unemi, Y. et al. Biochim. Biophys. Acta, 1388 (1998),pp. 253-259
[37]	Thompson, J.D., Higgins, D.G., Gibson, T.J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res., 22 (1994),pp. 4673-4680
[38]	Thomson, T.M., Lozano, J.J., Loukili, N. et al. Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene Genome Res., 10 (2000),pp. 1743-1756
[39]	Thornton, K., Long, M. Mol. Biol. Evol., 22 (2005),pp. 273-284
[40]	Wang, W., Yu, H., Long, M. Nat Genet., 36 (2004),pp. 523-527
[41]	Wang, W., Zhang, J., Alvarez, C. et al. Mol. Biol. Evol., 17 (2000),pp. 1294-1301
[42]	Weichenhan, D., Kunze, B., Traut, W. et al. Evolution by fusion and amplification: The murine Sp100-rs gene cluster Cytogenet. Cell. Genet., 80 (1998),pp. 226-231
[43]	Xu, W., Shen, J., Dunn, C.A. et al. Mol. Microbiol., 39 (2001),pp. 286-290
[44]	Yan, L., von Zitzewitz, J., Skinner, J.S. et al. Genome, 48 (2005),pp. 905-912
[45]	Zamocky, M., Janecek, S., Koller, F. Common phylogeny of catalase-peroxidases and ascorbate peroxidases Gene, 256 (2000),pp. 169-182
[46]	Zhang, L., Gaut, B.S., Vision, T.J. Gene duplication and evolution Science, 293 (2001),p. 1551
[47]	Zhou, Q., Wang, W. On the origin and evolution of new genes–a genomic and experimental perspective J. Genet. Genomics, 35 (2008),pp. 639-648