메뉴 건너뛰기




Volumn 118, Issue 2-3, 2003, Pages 171-182

Origin of new genes: Evidence from experimental and computational analyses

Author keywords

Domain shuffling; Evolutionary genomics; Exon shuffling; Exon intron evolution; Intron phases; New genes

Indexed keywords

CYTOCHROMES C1; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; EXONS; GENES; MUTANT CHIMERIC PROTEINS; RECOMBINANT FUSION PROTEINS; RETROELEMENTS;

EID: 0038645119     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1024153609285     Document Type: Article
Times cited : (50)

References (64)
  • 2
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant
    • AGI (The Arabidopsis Genome Initiative), 2000. Analysis of the genome sequence of the flowering plant. Nature 408: 796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 3
    • 0033762577 scopus 로고    scopus 로고
    • Ihe Babel of bioinformatics
    • Attwood, T.K., 2000. Ihe Babel of bioinformatics. Science 290: 471-473.
    • (2000) Science , vol.290 , pp. 471-473
    • Attwood, T.K.1
  • 4
    • 0031032101 scopus 로고    scopus 로고
    • Origin and evolution of a new gene descended from alcohol dehydrogenase in Drosophila
    • Begun, D.J., 1997. Origin and evolution of a new gene descended from alcohol dehydrogenase in Drosophila. Genetics 145: 375-382.
    • (1997) Genetics , vol.145 , pp. 375-382
    • Begun, D.J.1
  • 5
    • 0036021702 scopus 로고    scopus 로고
    • Expansion of genome coding regions by acquisition of new genes
    • Betrán, E. & M. Long, 2002. Expansion of genome coding regions by acquisition of new genes. Genetica 115: 65-80.
    • (2002) Genetica , vol.115 , pp. 65-80
    • Betrán, E.1    Long, M.2
  • 6
    • 0036097187 scopus 로고    scopus 로고
    • Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene
    • Betrán, E., W. Wang, L. Jin & M. Long, 2002. Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene. Mol. Biol. Evol. 19: 654-663.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 654-663
    • Betrán, E.1    Wang, W.2    Jin, L.3    Long, M.4
  • 7
    • 0033545669 scopus 로고    scopus 로고
    • Retroshuffling the genomic deck
    • Boeke, J.D. & O.K. Pickeral, 1999. Retroshuffling the genomic deck. Nature 398: 108-109, 111.
    • (1999) Nature , vol.398 , pp. 108-109
    • Boeke, J.D.1    Pickeral, O.K.2
  • 8
    • 0028348142 scopus 로고
    • Neutralism and selectionism face up to DNA data
    • Brookfield, J.F. & P.M. Sharp, 1994. Neutralism and selectionism face up to DNA data. Trends Genet. 10: 109-111.
    • (1994) Trends Genet. , vol.10 , pp. 109-111
    • Brookfield, J.F.1    Sharp, P.M.2
  • 9
    • 0032865868 scopus 로고    scopus 로고
    • RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements
    • Brosius, J., 1999. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238: 115-134.
    • (1999) Gene , vol.238 , pp. 115-134
    • Brosius, J.1
  • 10
    • 0013161988 scopus 로고    scopus 로고
    • The contribution of RNAs and retroposition to evolutionary novelties
    • Brosius, J., 2003. The contribution of RNAs and retroposition to evolutionary novelties. Genetica 118: 99-115.
    • (2003) Genetica , vol.118 , pp. 99-115
    • Brosius, J.1
  • 12
    • 0002219704 scopus 로고
    • The chimeric nature of nuclear genoms and the antiquity of introns as demonstrated by the GAPDH gene system
    • edited by M. Go & P. Schimmel. Elsevier, Amsterdam
    • Cerff, R., 1995. The chimeric nature of nuclear genoms and the antiquity of introns as demonstrated by the GAPDH gene system, pp. 205-228 in Tracing Biological Evolution in Protein and Gene Structures, edited by M. Go & P. Schimmel. Elsevier, Amsterdam.
    • (1995) Tracing Biological Evolution in Protein and Gene Structures , pp. 205-228
    • Cerff, R.1
  • 13
    • 0032509302 scopus 로고    scopus 로고
    • Genome sequence of the nematode C. elegans: A platform for investigating biology
    • CESC (The C. elegans Sequencing Consortium), 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-2018.
    • (1998) Science , vol.282 , pp. 2012-2018
  • 14
    • 0031200962 scopus 로고    scopus 로고
    • A gene fusion at a homeobox locus: Alterations in leaf shape and implications for morphological evolution
    • Chen, J.J., B.J. Janssen, A. Williams & N. Sinha, 1997. A gene fusion at a homeobox locus: alterations in leaf shape and implications for morphological evolution. Plant Cell 9: 1289-1304.
    • (1997) Plant Cell , vol.9 , pp. 1289-1304
    • Chen, J.J.1    Janssen, B.J.2    Williams, A.3    Sinha, N.4
  • 15
    • 0032574738 scopus 로고    scopus 로고
    • Toward a resolution of the introns early/late debate: Only phase zero introns are correlated with the structure of ancient proteins
    • De Souza, S.J., M. Long, R.J. Klein, S. Roy, S. Lin & W. Gilbert, 1998. Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins. Proc. Natl. Acad. Sci. USA 95: 5094-5099.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 5094-5099
    • De Souza, S.J.1    Long, M.2    Klein, R.J.3    Roy, S.4    Lin, S.5    Gilbert, W.6
  • 17
    • 0030722234 scopus 로고    scopus 로고
    • A phosphoglycerate mutase brain isoform (PGAM1) pseudogene is localized within the human Menkes disease gene (ATP7A)
    • Dierick, H.A., J.F.B. Mercer & T.W. Glover, 1997. A phosphoglycerate mutase brain isoform (PGAM1) pseudogene is localized within the human Menkes disease gene (ATP7A). Gene 198: 37-41.
    • (1997) Gene , vol.198 , pp. 37-41
    • Dierick, H.A.1    Mercer, J.F.B.2    Glover, T.W.3
  • 18
    • 0027967113 scopus 로고
    • Exon shuffling in anther-specific genes from sunflower
    • Domon, C. & A. Steinmetz, 1994. Exon shuffling in anther-specific genes from sunflower. Mol. Gen. Genet. 244: 312-317.
    • (1994) Mol. Gen. Genet. , vol.244 , pp. 312-317
    • Domon, C.1    Steinmetz, A.2
  • 19
    • 0025644510 scopus 로고
    • How big is the universe of exons?
    • Dorit, R.L., L. Schoenbach & W. Gilbert, 1991. How big is the universe of exons? Science 250: 1377-1382.
    • (1991) Science , vol.250 , pp. 1377-1382
    • Dorit, R.L.1    Schoenbach, L.2    Gilbert, W.3
  • 20
    • 0035656688 scopus 로고    scopus 로고
    • Non-coding RNA genes and the modern RNA world
    • Eddy, S.R., 2001. Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet. 2: 919-929.
    • (2001) Nat. Rev. Genet. , vol.2 , pp. 919-929
    • Eddy, S.R.1
  • 22
    • 0026579475 scopus 로고
    • Analysis of nonuniformity in intron phase distribution
    • Fedorov, A., G. Suboch, M. Bujakov & L. Fedorova, 1992. Analysis of nonuniformity in intron phase distribution. Nucl. Acids Res. 20(10): 2553-2557.
    • (1992) Nucl. Acids Res. , vol.20 , Issue.10 , pp. 2553-2557
    • Fedorov, A.1    Suboch, G.2    Bujakov, M.3    Fedorova, L.4
  • 24
    • 0018263844 scopus 로고
    • Why gene in pieces?
    • Gilbert, W., 1978. Why gene in pieces? Nature 271(5645): 501.
    • (1978) Nature , vol.271 , Issue.5645 , pp. 501
    • Gilbert, W.1
  • 28
    • 0001646661 scopus 로고
    • Distribution of two types of phosphoglyceric acid mutase, diphosphoglycerate mutase and D-2, 3-dipphosphoglyceric acid
    • Grisolia, S. & B.K. Joyce, 1959. Distribution of two types of phosphoglyceric acid mutase, diphosphoglycerate mutase and D-2, 3-dipphosphoglyceric acid. J. Biol. Chem. 234, 6: 1335-1337.
    • (1959) J. Biol. Chem. , vol.234 , Issue.6 , pp. 1335-1337
    • Grisolia, S.1    Joyce, B.K.2
  • 29
    • 0016416692 scopus 로고
    • Phosphoglycerate mutase from Yeast, chicken, breast muscle and kidney (2,3-PGA-dependent)
    • Grisolia, S. & J. Carreras, 1975. Phosphoglycerate mutase from Yeast, chicken, breast muscle and kidney (2,3-PGA-dependent). Meth. Enzymol. 42: 435-450.
    • (1975) Meth. Enzymol. , vol.42 , pp. 435-450
    • Grisolia, S.1    Carreras, J.2
  • 30
    • 0036187351 scopus 로고    scopus 로고
    • Extent of gene duplication in the genomes of Drosophila, nematode, and yeast
    • Gu, Z., A. Cavalcanti, F.C. Chen, P. Bouman & W.H. Li, 2002. Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol. Biol. Evol. 19: 256-262.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 256-262
    • Gu, Z.1    Cavalcanti, A.2    Chen, F.C.3    Bouman, P.4    Li, W.H.5
  • 32
    • 0028212966 scopus 로고
    • Mechanisms for selecting 5′ splice sites in mammalian pre-mRNA splicing
    • Horowitz, D.S. & A.R. Krainer, 1994. Mechanisms for selecting 5′ splice sites in mammalian pre-mRNA splicing. Trends Genet. 10: 100-106.
    • (1994) Trends Genet. , vol.10 , pp. 100-106
    • Horowitz, D.S.1    Krainer, A.R.2
  • 33
    • 0025910757 scopus 로고
    • Processed pseudogenes in Drosophila
    • Jeffs, P. & M. Ashburner, 1991. Processed pseudogenes in Drosophila. Proc. R. Soc. Lond. B. 244: 151-159.
    • (1991) Proc. R. Soc. Lond. B , vol.244 , pp. 151-159
    • Jeffs, P.1    Ashburner, M.2
  • 34
    • 0036851263 scopus 로고    scopus 로고
    • Signatures of domain shuffling in the human genome
    • Kaessmann, H., S. Zöllner, A. Nekrutenko & W.H. Li, 2002. Signatures of domain shuffling in the human genome. Genome Res. 12: 1642-1650.
    • (2002) Genome Res. , vol.12 , pp. 1642-1650
    • Kaessmann, H.1    Zöllner, S.2    Nekrutenko, A.3    Li, W.H.4
  • 35
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Lander, et al., 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander1
  • 37
    • 0035546224 scopus 로고    scopus 로고
    • Evolution of novel genes
    • Long, M., 2001. Evolution of novel genes. Curr. Opin. Genet. Dev. 11: 673-680.
    • (2001) Curr. Opin. Genet. Dev. , vol.11 , pp. 673-680
    • Long, M.1
  • 38
    • 0032753460 scopus 로고    scopus 로고
    • Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns
    • Long, M. & M. Deutsch, 1999. Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns. Mol. Biol. Evol. 16: 1528-1534.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1528-1534
    • Long, M.1    Deutsch, M.2
  • 39
    • 0032852328 scopus 로고    scopus 로고
    • Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila
    • Long, M., W. Wang & J. Zhang, 1999. Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila. Gene 238: 135-141.
    • (1999) Gene , vol.238 , pp. 135-141
    • Long, M.1    Wang, W.2    Zhang, J.3
  • 40
    • 0033637638 scopus 로고    scopus 로고
    • Testing the "proto-splice sites" model of intron origin: Evidence from analysis of intron phase correlations
    • Long, M. & C. Rosenberg, 2000. Testing the "proto-splice sites" model of intron origin: evidence from analysis of intron phase correlations. Mol. Biol. Evol. 17: 1789-1796.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1789-1796
    • Long, M.1    Rosenberg, C.2
  • 41
    • 0029586334 scopus 로고
    • Intron phase correlations and the evolution of the intron/exon structure of genes
    • Long, M., C. Rosenberg & W. Gilbert, 1995. Intron phase correlations and the evolution of the intron/exon structure of genes. Proc. Natl. Acad. Sci. USA 92(26): 12495-12499.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , Issue.26 , pp. 12495-12499
    • Long, M.1    Rosenberg, C.2    Gilbert, W.3
  • 42
    • 0029585511 scopus 로고
    • Evolution of intron/exon structure of eukaryotic genes
    • Long, M., S.J. de Souza & W. Gilbert, 1995. Evolution of intron/exon structure of eukaryotic genes. Curr. Opin. Genet. Dev. 5: 774-778.
    • (1995) Curr. Opin. Genet. Dev. , vol.5 , pp. 774-778
    • Long, M.1    De Souza, S.J.2    Gilbert, W.3
  • 43
    • 0029824258 scopus 로고    scopus 로고
    • Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome cl precursor
    • Long, M., S.J. de Souza, C. Rosenberg & W. Gilbert, 1996. Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome cl precursor. Proc. Natl. Acad. Sci. USA 93: 7727-7731.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 7727-7731
    • Long, M.1    De Souza, S.J.2    Rosenberg, C.3    Gilbert, W.4
  • 44
    • 0031915298 scopus 로고    scopus 로고
    • Relationship between "proto-splice sites" and intron phases: Evidence from dicodon analysis
    • Long, M., S.J. de Souza, C. Rosenberg & W. Gilbert, 1998. Relationship between "proto-splice sites" and intron phases: evidence from dicodon analysis. Proc. Natl. Acad. Sci. USA 95: 219-223.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 219-223
    • Long, M.1    De Souza, S.J.2    Rosenberg, C.3    Gilbert, W.4
  • 45
    • 0027905006 scopus 로고
    • Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila
    • Long, M. & C.H. Langley, 1993. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260: 91-95.
    • (1993) Science , vol.260 , pp. 91-95
    • Long, M.1    Langley, C.H.2
  • 46
    • 0037197986 scopus 로고    scopus 로고
    • Intron evolution as a population-genetic process
    • Lynch, M., 2002. Intron evolution as a population-genetic process. Proc. Natl. Acad. Sci. USA 99: 6118-6123.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 6118-6123
    • Lynch, M.1
  • 47
    • 0026091126 scopus 로고
    • RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution
    • Nugent, J.M. & J.D. Palmer, 1991. RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution. Cell 66: 473-481.
    • (1991) Cell , vol.66 , pp. 473-481
    • Nugent, J.M.1    Palmer, J.D.2
  • 48
    • 0032506534 scopus 로고    scopus 로고
    • Selective sweep of a newly evolved sperm-specific gene in Drosophila
    • Nurminsky, D.I., M.V. Nurminskaya, D. De Aguiar & D.L. Hartl, 1998. Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396: 572-575.
    • (1998) Nature , vol.396 , pp. 572-575
    • Nurminsky, D.I.1    Nurminskaya, M.V.2    De Aguiar, D.3    Hartl, D.L.4
  • 50
    • 0022294484 scopus 로고
    • Comparative organization of chloroplast genomes
    • Palmer, J.D., 1985. Comparative organization of chloroplast genomes. Annu. Rev. Genet. 19: 325-354.
    • (1985) Annu. Rev. Genet. , vol.19 , pp. 325-354
    • Palmer, J.D.1
  • 51
    • 0023646322 scopus 로고
    • Intron-dependent evolution: Preferred types of exons and introns
    • Patthy, L., 1987. Intron-dependent evolution: preferred types of exons and introns. FEBS Lett. 214: 1-7.
    • (1987) FEBS Lett. , vol.214 , pp. 1-7
    • Patthy, L.1
  • 52
    • 13244292544 scopus 로고
    • Modular exchange principles in proteins
    • Patthy, L., 1991. Modular exchange principles in proteins. Curr. Opin. Struct. Biol. 1: 351-361.
    • (1991) Curr. Opin. Struct. Biol. , vol.1 , pp. 351-361
    • Patthy, L.1
  • 53
    • 0003460189 scopus 로고
    • Molecular biology intelligence unit, edited by R.G. Landes. Springer, Austin, TX
    • Patthy, L., 1995. Protein Evolution by Exon-shuffling. Molecular biology intelligence unit, edited by R.G. Landes. Springer, Austin, TX.
    • (1995) Protein Evolution by Exon-Shuffling
    • Patthy, L.1
  • 54
    • 0028186046 scopus 로고
    • Using the FASTA program to search protein and DNA sequence databases
    • Pearson, W.R., 1994. Using the FASTA program to search protein and DNA sequence databases. Meth. Mol. Biol. 24: 307-331.
    • (1994) Meth. Mol. Biol. , vol.24 , pp. 307-331
    • Pearson, W.R.1
  • 55
    • 0029933504 scopus 로고    scopus 로고
    • Initial splice-site recognition and pairing during pre-mRNA splicing
    • Reed, R., 1996. Initial splice-site recognition and pairing during pre-mRNA splicing. Curr. Opin. Genet. Dev. 6: 215-220.
    • (1996) Curr. Opin. Genet. Dev. , vol.6 , pp. 215-220
    • Reed, R.1
  • 56
    • 0022725788 scopus 로고
    • A chemically synthesized pre-sequence of an imported mitochondrial protein can form an amphiphilic helix and perturb natural and artificial phospholipid bilayers
    • Roise, D., S.J. Horvath, J.M. Tomich, J.H. Richards & G. Schatz, 1986. A chemically synthesized pre-sequence of an imported mitochondrial protein can form an amphiphilic helix and perturb natural and artificial phospholipid bilayers. EMBO J. 5: 1327-1334.
    • (1986) EMBO J. , vol.5 , pp. 1327-1334
    • Roise, D.1    Horvath, S.J.2    Tomich, J.M.3    Richards, J.H.4    Schatz, G.5
  • 58
    • 0029979607 scopus 로고    scopus 로고
    • Common principles of protein translocation across membranes
    • Schatz, G. & B. Dobberstein, 1996. Common principles of protein translocation across membranes. Science 271: 1519-1526.
    • (1996) Science , vol.271 , pp. 1519-1526
    • Schatz, G.1    Dobberstein, B.2
  • 60
    • 0035895505 scopus 로고    scopus 로고
    • The sequence of the human genome
    • Venter, J.C. et al., 2001. The sequence of the human genome. Science 291: 1304-1351.
    • (2001) Science , vol.291 , pp. 1304-1351
    • Venter, J.C.1
  • 61
    • 0033850591 scopus 로고    scopus 로고
    • The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melonogaster
    • Wang, W., J. Zhang, C. Alvarez, A. Llopart & M. Long, 2000. The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melonogaster. Mol. Biol. Evol. 17: 1294-1301.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1294-1301
    • Wang, W.1    Zhang, J.2    Alvarez, C.3    Llopart, A.4    Long, M.5
  • 62
    • 0037007062 scopus 로고    scopus 로고
    • Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster
    • Wang, W., F.G. Brunet, E. Nevo & M. Long, 2002a. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 99: 4448-4453.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 4448-4453
    • Wang, W.1    Brunet, F.G.2    Nevo, E.3    Long, M.4
  • 63
    • 0037016489 scopus 로고    scopus 로고
    • Nucleotide variation along the Drosophila melanogaster fourth chromosome
    • Wang, W., K. Thornton, A. Berry & M. Long, 2002b. Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295: 134-137.
    • (2002) Science , vol.295 , pp. 134-137
    • Wang, W.1    Thornton, K.2    Berry, A.3    Long, M.4
  • 64
    • 0027340233 scopus 로고
    • The presequence of cytochrome cl from potato mitochondria is encoded on four exons
    • Wegener, S. & U.K. Schmitz, 1993. The presequence of cytochrome cl from potato mitochondria is encoded on four exons. Curr. Genet. 24: 256-259.
    • (1993) Curr. Genet. , vol.24 , pp. 256-259
    • Wegener, S.1    Schmitz, U.K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.