메뉴 건너뛰기




Volumn 12, Issue , 2011, Pages

Detection of Fused Genes in Eukaryotic Genomes using Gene deFuser: Analysis of the Tetrahymena thermophila genome

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTIC GENOME; GENE ANNOTATION; GENE FUSION; NUCLEAR EXPORT; PROTEIN FUNCTIONS; PROTEIN SEQUENCE FILES; SURFACE ANTIGEN; TETRAHYMENA THERMOPHILA;

EID: 79960074591     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-279     Document Type: Article
Times cited : (11)

References (39)
  • 1
    • 0003838721 scopus 로고    scopus 로고
    • Oxford: Blackwell Science, Malden MA, 2
    • Patthy L. Protein evolution 2008, Oxford: Blackwell Science, Malden MA, 2.
    • (2008) Protein evolution
    • Patthy, L.1
  • 2
    • 0036046771 scopus 로고    scopus 로고
    • Evolution of gene fusions: horizontal transfer versus independent events
    • 115226, 12049665
    • Yanai I, Wolf YI, Koonin EV. Evolution of gene fusions: horizontal transfer versus independent events. Genome Biol 2002, 3:research0024. 115226, 12049665.
    • (2002) Genome Biol , vol.3
    • Yanai, I.1    Wolf, Y.I.2    Koonin, E.V.3
  • 3
    • 0034625235 scopus 로고    scopus 로고
    • The impact of comparative genomics on our understanding of evolution
    • 10.1016/S0092-8674(00)80867-3, 10892642
    • Koonin EV, Aravind L, Kondrashov AS. The impact of comparative genomics on our understanding of evolution. Cell 2000, 101:573-576. 10.1016/S0092-8674(00)80867-3, 10892642.
    • (2000) Cell , vol.101 , pp. 573-576
    • Koonin, E.V.1    Aravind, L.2    Kondrashov, A.S.3
  • 4
    • 0034084865 scopus 로고    scopus 로고
    • Who's your neighbor? New computational approaches for functional genomics
    • 10.1038/76443, 10835597
    • Galperin MY, Koonin EV. Who's your neighbor? New computational approaches for functional genomics. Nat Biotechnol 2000, 18:609-613. 10.1038/76443, 10835597.
    • (2000) Nat Biotechnol , vol.18 , pp. 609-613
    • Galperin, M.Y.1    Koonin, E.V.2
  • 5
    • 0018371786 scopus 로고
    • Gene fusion during the evolution of the tryptophan operon in enterobacteriaceae
    • 10.1038/277486a0, 368647
    • Miozzari GF, Yanofsky C. Gene fusion during the evolution of the tryptophan operon in enterobacteriaceae. Nature 1979, 277:486-489. 10.1038/277486a0, 368647.
    • (1979) Nature , vol.277 , pp. 486-489
    • Miozzari, G.F.1    Yanofsky, C.2
  • 6
    • 0033621536 scopus 로고    scopus 로고
    • Genome evolution. Gene fusion versus gene fission
    • Snel B, Bork P, Huynen M. Genome evolution. Gene fusion versus gene fission. Trends Genet 2000, 16:9-11.
    • (2000) Trends Genet , vol.16 , pp. 9-11
    • Snel, B.1    Bork, P.2    Huynen, M.3
  • 7
    • 0037841805 scopus 로고    scopus 로고
    • The deep roots of eukaryotes
    • 10.1126/science.1085544, 12805537
    • Baldauf SL. The deep roots of eukaryotes. Science 2003, 300:1703-1706. 10.1126/science.1085544, 12805537.
    • (2003) Science , vol.300 , pp. 1703-1706
    • Baldauf, S.L.1
  • 8
    • 13144259695 scopus 로고    scopus 로고
    • Relative rates of gene fusion and fission in multi-domain proteins
    • 10.1016/j.tig.2004.11.007, 15680510
    • Kummerfeld SK, Teichmann SA. Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet 2005, 21:25-30. 10.1016/j.tig.2004.11.007, 15680510.
    • (2005) Trends Genet , vol.21 , pp. 25-30
    • Kummerfeld, S.K.1    Teichmann, S.A.2
  • 9
    • 0037025197 scopus 로고    scopus 로고
    • Rooting the eukaryote tree by using a derived gene fusion
    • 10.1126/science.1071196, 12098695
    • Stechmann A, Cavalier-Smith T. Rooting the eukaryote tree by using a derived gene fusion. Science 2002, 297:89-91. 10.1126/science.1071196, 12098695.
    • (2002) Science , vol.297 , pp. 89-91
    • Stechmann, A.1    Cavalier-Smith, T.2
  • 10
    • 0041919404 scopus 로고    scopus 로고
    • The root of the eukaryote tree pinpointed
    • 10.1016/S0960-9822(03)00602-X, 12956967
    • Stechmann A, Cavalier-Smith T. The root of the eukaryote tree pinpointed. Curr Biol 2003, 13:R665-666. 10.1016/S0960-9822(03)00602-X, 12956967.
    • (2003) Curr Biol , vol.13
    • Stechmann, A.1    Cavalier-Smith, T.2
  • 11
    • 14544283723 scopus 로고    scopus 로고
    • Root of the Eukaryota tree as inferred from combined maximum likelihood analyses of multiple molecular sequence data
    • Arisue N, Hasegawa M, Hashimoto T. Root of the Eukaryota tree as inferred from combined maximum likelihood analyses of multiple molecular sequence data. Mol Biol Evol 2005, 22:409-420.
    • (2005) Mol Biol Evol , vol.22 , pp. 409-420
    • Arisue, N.1    Hasegawa, M.2    Hashimoto, T.3
  • 12
    • 33645456207 scopus 로고    scopus 로고
    • Eukaryotic evolution, changes and challenges
    • 10.1038/nature04546, 16572163
    • Embley TM, Martin W. Eukaryotic evolution, changes and challenges. Nature 2006, 440:623-630. 10.1038/nature04546, 16572163.
    • (2006) Nature , vol.440 , pp. 623-630
    • Embley, T.M.1    Martin, W.2
  • 13
    • 0036180314 scopus 로고    scopus 로고
    • Rosetta Stone proteins: "chance and necessity"?
    • 139009, 11864366
    • Veitia RA. Rosetta Stone proteins: "chance and necessity"?. Genome Biol 2002, 3:interactions1001. 139009, 11864366.
    • (2002) Genome Biol , vol.3
    • Veitia, R.A.1
  • 16
    • 20444393401 scopus 로고    scopus 로고
    • Reciprocal fusions of two genes in the formaldehyde detoxification pathway in ciliates and diatoms
    • 10.1093/molbev/msi151, 15858209
    • Stover NA, Cavalcanti ARO, Li AJ, Richardson BC, Landweber LF. Reciprocal fusions of two genes in the formaldehyde detoxification pathway in ciliates and diatoms. Mol Biol Evol 2005, 22:1539-1542. 10.1093/molbev/msi151, 15858209.
    • (2005) Mol Biol Evol , vol.22 , pp. 1539-1542
    • Stover, N.A.1    Cavalcanti, A.R.O.2    Li, A.J.3    Richardson, B.C.4    Landweber, L.F.5
  • 17
    • 73449103212 scopus 로고    scopus 로고
    • 1 + 1 = 3: a fusion of 2 enzymes in the methionine salvage pathway of Tetrahymena thermophila creates a trifunctional enzyme that catalyzes 3 steps in the pathway
    • 10.1371/journal.pgen.1000701, 2759508, 19851454
    • Salim HMW, Negritto MC, Cavalcanti ARO. 1 + 1 = 3: a fusion of 2 enzymes in the methionine salvage pathway of Tetrahymena thermophila creates a trifunctional enzyme that catalyzes 3 steps in the pathway. PLoS Genet 2009, 5:e1000701. 10.1371/journal.pgen.1000701, 2759508, 19851454.
    • (2009) PLoS Genet , vol.5
    • Salim, H.M.W.1    Negritto, M.C.2    Cavalcanti, A.R.O.3
  • 18
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 19
    • 0042902833 scopus 로고    scopus 로고
    • The COG database: an updated version includes eukaryotes
    • 10.1186/1471-2105-4-41, 222959, 12969510
    • Tatusov RL, et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4:41. 10.1186/1471-2105-4-41, 222959, 12969510.
    • (2003) BMC Bioinformatics , vol.4 , pp. 41
    • Tatusov, R.L.1
  • 20
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • 10.1126/science.278.5338.631, 9381173
    • Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science 1997, 278:631-637. 10.1126/science.278.5338.631, 9381173.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 21
    • 34547596639 scopus 로고    scopus 로고
    • BLASTO: a tool for searching orthologous groups
    • 10.1093/nar/gkm278, 1933156, 17483516
    • Zhou Y, Landweber LF. BLASTO: a tool for searching orthologous groups. Nucleic Acids Res 2007, 35:W678-682. 10.1093/nar/gkm278, 1933156, 17483516.
    • (2007) Nucleic Acids Res , vol.35
    • Zhou, Y.1    Landweber, L.F.2
  • 24
    • 0033517147 scopus 로고    scopus 로고
    • Guanylyl cyclases with the topology of mammalian adenylyl cyclases and an N-terminal P-type ATPase-like domain in Paramecium, Tetrahymena and Plasmodium
    • 10.1093/emboj/18.15.4222, 1171498, 10428960
    • Linder JU, Engel P, Reimer A, Krüger T, Plattner H, Schultz A, Schultz JE. Guanylyl cyclases with the topology of mammalian adenylyl cyclases and an N-terminal P-type ATPase-like domain in Paramecium, Tetrahymena and Plasmodium. EMBO J 1999, 18:4222-4232. 10.1093/emboj/18.15.4222, 1171498, 10428960.
    • (1999) EMBO J , vol.18 , pp. 4222-4232
    • Linder, J.U.1    Engel, P.2    Reimer, A.3    Krüger, T.4    Plattner, H.5    Schultz, A.6    Schultz, J.E.7
  • 25
    • 61949285138 scopus 로고    scopus 로고
    • Role of an ancestral d-bifunctional protein containing two sterol-carrier protein-2 domains in lipid uptake and trafficking in Toxoplasma
    • 2626556, 19005217
    • Lige B, Jayabalasingham B, Zhang H, Pypaert M, Coppens I. Role of an ancestral d-bifunctional protein containing two sterol-carrier protein-2 domains in lipid uptake and trafficking in Toxoplasma. Mol Biol Cell 2009, 20:658-672. 2626556, 19005217.
    • (2009) Mol Biol Cell , vol.20 , pp. 658-672
    • Lige, B.1    Jayabalasingham, B.2    Zhang, H.3    Pypaert, M.4    Coppens, I.5
  • 26
    • 1542373671 scopus 로고    scopus 로고
    • Nuclear protein phosphatases with Kelch-repeat domains modulate the response to brassinosteroids in Arabidopsis
    • 10.1101/gad.1174204, 359398, 14977918
    • Mora-García S, Vert G, Yin Y, Caño-Delgado A, Cheong H, Chory J. Nuclear protein phosphatases with Kelch-repeat domains modulate the response to brassinosteroids in Arabidopsis. Genes Dev 2004, 18:448-460. 10.1101/gad.1174204, 359398, 14977918.
    • (2004) Genes Dev , vol.18 , pp. 448-460
    • Mora-García, S.1    Vert, G.2    Yin, Y.3    Caño-Delgado, A.4    Cheong, H.5    Chory, J.6
  • 27
    • 0036015165 scopus 로고    scopus 로고
    • Protein Ser/Thr phosphatases with kelch-like repeat domains
    • 10.1016/S0898-6568(02)00018-9, 12034355
    • Kutuzov MA, Andreeva AV. Protein Ser/Thr phosphatases with kelch-like repeat domains. Cell Signal 2002, 14:745-750. 10.1016/S0898-6568(02)00018-9, 12034355.
    • (2002) Cell Signal , vol.14 , pp. 745-750
    • Kutuzov, M.A.1    Andreeva, A.V.2
  • 28
    • 68149126705 scopus 로고    scopus 로고
    • In silico analysis of the cyclophilin repertoire of apicomplexan parasites
    • 10.1186/1756-3305-2-27, 2713222, 19555495
    • Krücken J, Greif G, von Samson-Himmelstjerna G. In silico analysis of the cyclophilin repertoire of apicomplexan parasites. Parasit Vectors 2009, 2:27. 10.1186/1756-3305-2-27, 2713222, 19555495.
    • (2009) Parasit Vectors , vol.2 , pp. 27
    • Krücken, J.1    Greif, G.2    von Samson-Himmelstjerna, G.3
  • 29
    • 22044439908 scopus 로고    scopus 로고
    • The domain architecture of large guanine nucleotide exchange factors for the small GTP-binding protein Arf
    • 10.1186/1471-2164-6-20, 553965, 15717927
    • Mouratou B, Biou V, Joubert A, Cohen J, Shields DJ, Geldner N, Jürgens G, Melançon P, Cherfils J. The domain architecture of large guanine nucleotide exchange factors for the small GTP-binding protein Arf. BMC Genomics 2005, 6:20. 10.1186/1471-2164-6-20, 553965, 15717927.
    • (2005) BMC Genomics , vol.6 , pp. 20
    • Mouratou, B.1    Biou, V.2    Joubert, A.3    Cohen, J.4    Shields, D.J.5    Geldner, N.6    Jürgens, G.7    Melançon, P.8    Cherfils, J.9
  • 30
    • 0032825306 scopus 로고    scopus 로고
    • Cell type-specific gene expression in the cell cycle of the dimorphic ciliate Eufolliculina uhligi
    • 10.1007/s004380051098, 10517337
    • Markmann-Mulisch U, Reiss B, Mulisch M. Cell type-specific gene expression in the cell cycle of the dimorphic ciliate Eufolliculina uhligi. Mol Gen Genet 1999, 262:390-399. 10.1007/s004380051098, 10517337.
    • (1999) Mol Gen Genet , vol.262 , pp. 390-399
    • Markmann-Mulisch, U.1    Reiss, B.2    Mulisch, M.3
  • 31
    • 33644853063 scopus 로고    scopus 로고
    • Modulation of nuclear factor E2-related factor 2-mediated gene expression in mice liver and small intestine by cancer chemopreventive agent curcumin
    • Shen G, Xu C, Hu R, Jain MR, Gopalkrishnan A, Nair S, Huang M-T, Chan JY, Kong A-NT. Modulation of nuclear factor E2-related factor 2-mediated gene expression in mice liver and small intestine by cancer chemopreventive agent curcumin. Mol Cancer Ther 2006, 5:39-51.
    • (2006) Mol Cancer Ther , vol.5 , pp. 39-51
    • Shen, G.1    Xu, C.2    Hu, R.3    Jain, M.R.4    Gopalkrishnan, A.5    Nair, S.6    Huang, M.-T.7    Chan, J.Y.8    Kong, A.-N.T.9
  • 33
    • 0026555495 scopus 로고
    • Dual-specificity protein kinases: will any hydroxyl do?
    • 10.1016/0968-0004(92)90248-8, 1412695
    • Lindberg RA, Quinn AM, Hunter T. Dual-specificity protein kinases: will any hydroxyl do?. Trends Biochem Sci 1992, 17:114-119. 10.1016/0968-0004(92)90248-8, 1412695.
    • (1992) Trends Biochem Sci , vol.17 , pp. 114-119
    • Lindberg, R.A.1    Quinn, A.M.2    Hunter, T.3
  • 35
    • 0032559260 scopus 로고    scopus 로고
    • Kinesin and dynein superfamily proteins and the mechanism of organelle transport
    • 10.1126/science.279.5350.519, 9438838
    • Hirokawa N. Kinesin and dynein superfamily proteins and the mechanism of organelle transport. Science 1998, 279:519-526. 10.1126/science.279.5350.519, 9438838.
    • (1998) Science , vol.279 , pp. 519-526
    • Hirokawa, N.1
  • 36
    • 45049086435 scopus 로고    scopus 로고
    • The RCC1 superfamily: from genes, to function, to disease
    • 10.1016/j.bbamcr.2008.03.015, 18442486
    • Hadjebi O, Casas-Terradellas E, Garcia-Gonzalo FR, Rosa JL. The RCC1 superfamily: from genes, to function, to disease. Biochim Biophys Acta 2008, 1783:1467-1479. 10.1016/j.bbamcr.2008.03.015, 18442486.
    • (2008) Biochim Biophys Acta , vol.1783 , pp. 1467-1479
    • Hadjebi, O.1    Casas-Terradellas, E.2    Garcia-Gonzalo, F.R.3    Rosa, J.L.4
  • 37
    • 75149170545 scopus 로고    scopus 로고
    • Nuclear myosin 1 is in complex with mature rRNA transcripts and associates with the nuclear pore basket
    • 10.1096/fj.09-135863, 19729515
    • Obrdlik A, Louvet E, Kukalev A, Naschekin D, Kiseleva E, Fahrenkrog B, Percipalle P. Nuclear myosin 1 is in complex with mature rRNA transcripts and associates with the nuclear pore basket. FASEB J 2010, 24:146-157. 10.1096/fj.09-135863, 19729515.
    • (2010) FASEB J , vol.24 , pp. 146-157
    • Obrdlik, A.1    Louvet, E.2    Kukalev, A.3    Naschekin, D.4    Kiseleva, E.5    Fahrenkrog, B.6    Percipalle, P.7
  • 38
    • 0142188569 scopus 로고    scopus 로고
    • Ran in the spindle checkpoint: a new function for a versatile GTPase
    • 10.1016/j.tcb.2003.09.003, 14573347
    • Li H-Y, Cao K, Zheng Y. Ran in the spindle checkpoint: a new function for a versatile GTPase. Trends Cell Biol 2003, 13:553-557. 10.1016/j.tcb.2003.09.003, 14573347.
    • (2003) Trends Cell Biol , vol.13 , pp. 553-557
    • Li, H.-Y.1    Cao, K.2    Zheng, Y.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.