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Volumn 65, Issue 5, 2007, Pages 529-540

Genomic evolution of the proteasome system among hemiascomycetous yeasts

Author keywords

Hemiascomycetes; In silico analysis; Proteasome; Regulation; Yeast

Indexed keywords

PROTEASOME; PROTEIN; RPN4P PROTEIN; UNCLASSIFIED DRUG;

EID: 36148943839     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-007-9031-y     Document Type: Article
Times cited : (15)

References (48)
  • 2
    • 17644425833 scopus 로고    scopus 로고
    • Aspergillus Sequencing Project. Broad Institute, MIT and Harvard Cambridge, MA
    • Aspergillus Sequencing Project (2003) Aspergillus Sequencing Project. Broad Institute, MIT and Harvard, Cambridge, MA
    • (2003) Aspergillus Sequencing Project
  • 3
    • 0037811432 scopus 로고    scopus 로고
    • Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
    • Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB (2003) Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol 4:R43
    • (2003) Genome Biol , vol.4 , pp. 43
    • Chiang, D.Y.1    Moses, A.M.2    Kellis, M.3    Lander, E.S.4    Eisen, M.B.5
  • 5
    • 0035986888 scopus 로고    scopus 로고
    • Evolution of transcription factor binding sites in Mammalian gene regulatory regions: Conservation and turnover
    • Dermitzakis ET, Clark AG (2002) Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover. Mol Biol Evol 19:1114-1121
    • (2002) Mol Biol Evol , vol.19 , pp. 1114-1121
    • Dermitzakis, E.T.1    Clark, A.G.2
  • 6
    • 11144355642 scopus 로고    scopus 로고
    • The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome
    • Dietrich FS, Voegeli S, Brachat S, Choi S, et al. (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304-307
    • (2004) Science , vol.304 , pp. 304-307
    • Dietrich, F.S.1    Voegeli, S.2    Brachat, S.3    Choi, S.4
  • 7
    • 33745736295 scopus 로고    scopus 로고
    • Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution
    • Dujon B (2006) Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution. Trends Genet. 22:375-387
    • (2006) Trends Genet. , vol.22 , pp. 375-387
    • Dujon, B.1
  • 8
    • 3042720475 scopus 로고    scopus 로고
    • Genome evolution in yeasts
    • Dujon B, Sherman D, Fischer G, et al. (2004) Genome evolution in yeasts. Nature 430:35-44
    • (2004) Nature , vol.430 , pp. 35-44
    • Dujon, B.1    Sherman, D.2    Fischer, G.3
  • 11
    • 33645787782 scopus 로고    scopus 로고
    • Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages
    • Fischer G, Rocha EP, Brunet F, Vergassola M, Dujon B (2006) Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages. PLoS Genet 2:e32
    • (2006) PLoS Genet , vol.2 , pp. 32
    • Fischer, G.1    Rocha, E.P.2    Brunet, F.3    Vergassola, M.4    Dujon, B.5
  • 12
    • 0037464589 scopus 로고    scopus 로고
    • The genome sequence of the filamentous fungus Neurospora crassa
    • Galagan JE, Calvo SE, Borkovitch KA, et al. (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859-868
    • (2003) Nature , vol.422 , pp. 859-868
    • Galagan, J.E.1    Calvo, S.E.2    Borkovitch, K.A.3
  • 16
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    • Hughes JD, Estep PW, Tavazoie S, Church GM (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296:1205-1214
    • (2000) J Mol Biol , vol.296 , pp. 1205-1214
    • Hughes, J.D.1    Estep, P.W.2    Tavazoie, S.3    Church, G.M.4
  • 17
    • 0033772765 scopus 로고    scopus 로고
    • Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes
    • Jelinsky SA, Estep P, Church GM, Samson LD (2000) Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol Cell Biol 20:8157-8167
    • (2000) Mol Cell Biol , vol.20 , pp. 8157-8167
    • Jelinsky, S.A.1    Estep, P.2    Church, G.M.3    Samson, L.D.4
  • 19
    • 2642560445 scopus 로고    scopus 로고
    • Proteasomal degradation of RPN4 via two distinct mechanisms, ubiquitin-dependent and -independent
    • Ju D, Xie Y (2004) Proteasomal degradation of RPN4 via two distinct mechanisms, ubiquitin-dependent and -independent. J Biol Chem 279:23851-23854
    • (2004) J Biol Chem , vol.279 , pp. 23851-23854
    • Ju, D.1    Xie, Y.2
  • 21
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 22
    • 1942452749 scopus 로고    scopus 로고
    • Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
    • Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-624
    • (2004) Nature , vol.428 , pp. 617-624
    • Kellis, M.1    Birren, B.W.2    Lander, E.S.3
  • 23
    • 0034704325 scopus 로고    scopus 로고
    • Genome rearrangements in yeasts. Genomic exploration of the hemiascomycetous yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae
    • Llorente B, Malpertuy A, Neuvéglise C, et al. (2000) Genome rearrangements in yeasts. Genomic exploration of the hemiascomycetous yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae. FEBS Lett 487:101-112
    • (2000) FEBS Lett , vol.487 , pp. 101-112
    • Llorente, B.1    Malpertuy, A.2    Neuvéglise, C.3
  • 24
    • 18944392199 scopus 로고    scopus 로고
    • Identification and characterization of a Drosophila proteasome regulatory network
    • Lundgren J, Masson P, Mirzaei Z, Young P (2005) Identification and characterization of a Drosophila proteasome regulatory network. Mol Cell Biol 25:4662-4675
    • (2005) Mol Cell Biol , vol.25 , pp. 4662-4675
    • Lundgren, J.1    Masson, P.2    Mirzaei, Z.3    Young, P.4
  • 25
    • 0032483028 scopus 로고    scopus 로고
    • Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences
    • Makalowski W, Boguski MS (1998) Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. Proc Natl Acad Sci USA 95:9407-9412
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 9407-9412
    • Makalowski, W.1    Boguski, M.S.2
  • 26
    • 0034704256 scopus 로고    scopus 로고
    • Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes
    • Malpertuy A, Tekaia F, Casaregola S, et al. (2000) Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes. FEBS Lett 487:113-121
    • (2000) FEBS Lett , vol.487 , pp. 113-121
    • Malpertuy, A.1    Tekaia, F.2    Casaregola, S.3
  • 27
    • 0033004441 scopus 로고    scopus 로고
    • Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast
    • Mannhaupt G, Schnall R, Karpov V, Vetter I, Feldmann H (1999) Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast. FEBS Lett 450:27-34
    • (1999) FEBS Lett , vol.450 , pp. 27-34
    • Mannhaupt, G.1    Schnall, R.2    Karpov, V.3    Vetter, I.4    Feldmann, H.5
  • 28
    • 0037821846 scopus 로고    scopus 로고
    • Inhibition of proteasome activity induces concerted expression of proteasome genes and de novo formation of mammalian proteasomes
    • Meiners S, Heyken D, Weller A, Ludwig A, Stangl K, Kloetzel K-P, Kruger E (2003) Inhibition of proteasome activity induces concerted expression of proteasome genes and de novo formation of mammalian proteasomes. J Biol Chem 278:21517-21525
    • (2003) J Biol Chem , vol.278 , pp. 21517-21525
    • Meiners, S.1    Heyken, D.2    Weller, A.3    Ludwig, A.4    Stangl, K.5    Kloetzel, K.-P.6    Kruger, E.7
  • 30
    • 0642368358 scopus 로고    scopus 로고
    • Position specific variation in the rate of evolution in transcription factor binding sites
    • Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB (2003) Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol Biol 3:19
    • (2003) BMC Evol Biol , vol.3 , pp. 19
    • Moses, A.M.1    Chiang, D.Y.2    Kellis, M.3    Lander, E.S.4    Eisen, M.B.5
  • 31
    • 22144491990 scopus 로고    scopus 로고
    • MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
    • Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB (2004) MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol 5:R98
    • (2004) Genome Biol , vol.5 , pp. 98
    • Moses, A.M.1    Chiang, D.Y.2    Pollard, D.A.3    Iyer, V.N.4    Eisen, M.B.5
  • 33
    • 0036226237 scopus 로고    scopus 로고
    • Control of 26S proteasome expression by transcription factors regulating multidrug resistance in Saccharomyces cerevisiae
    • Owsianik G, Balzi L, Ghislain M (2002) Control of 26S proteasome expression by transcription factors regulating multidrug resistance in Saccharomyces cerevisiae. Mol Microbiol 43:1295-1308
    • (2002) Mol Microbiol , vol.43 , pp. 1295-1308
    • Owsianik, G.1    Balzi, L.2    Ghislain, M.3
  • 34
    • 0034923498 scopus 로고    scopus 로고
    • Design and selection of novel Cys2His2 zinc finger proteins
    • Pabo CO, Peisach E, Grant RA (2001) Design and selection of novel Cys2His2 zinc finger proteins. Annu Rev Biochem 70:313-340
    • (2001) Annu Rev Biochem , vol.70 , pp. 313-340
    • Pabo, C.O.1    Peisach, E.2    Grant, R.A.3
  • 37
    • 33645023614 scopus 로고    scopus 로고
    • Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts
    • Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH (2006) Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440:341-345
    • (2006) Nature , vol.440 , pp. 341-345
    • Scannell, D.R.1    Byrne, K.P.2    Gordon, J.L.3    Wong, S.4    Wolfe, K.H.5
  • 38
    • 0034704310 scopus 로고    scopus 로고
    • Genomic exploration of the hemiascomycetous yeasts: 1. a set of yeast species for molecular evolution studies
    • Souciet JL, Aigle M, Artiguenave F, et al. (2000) Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies. FEBS Lett 487:3-12
    • (2000) FEBS Lett , vol.487 , pp. 3-12
    • Souciet, J.L.1    Aigle, M.2    Artiguenave, F.3
  • 39
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • The Arabidopsis Genome Initiative
    • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
    • (2000) Nature , vol.408 , pp. 796-815
  • 40
    • 0041620271 scopus 로고    scopus 로고
    • Regulatory sequence analysis tools
    • van Helden J (2003) Regulatory sequence analysis tools. Nucleic Acids Res 31:3593-3596
    • (2003) Nucleic Acids Res , vol.31 , pp. 3593-3596
    • Van Helden, J.1
  • 41
    • 11244343965 scopus 로고    scopus 로고
    • Rpn4 is a physiological substrate of the Ubr2 ubiquitin ligase
    • Wang L, Mao X, Ju D, Xie Y (2004) Rpn4 is a physiological substrate of the Ubr2 ubiquitin ligase. J Biol Chem 279:55218-55223
    • (2004) J Biol Chem , vol.279 , pp. 55218-55223
    • Wang, L.1    Mao, X.2    Ju, D.3    Xie, Y.4
  • 42
    • 9644300915 scopus 로고    scopus 로고
    • The proteasome: A proteolytic nanomachine of cell regulation and waste disposal
    • Wolf DH, Hilt W (2004) The proteasome: a proteolytic nanomachine of cell regulation and waste disposal. Biochim Biophys Acta 1695:19-31
    • (2004) Biochim Biophys Acta , vol.1695 , pp. 19-31
    • Wolf, D.H.1    Hilt, W.2
  • 43
    • 0030947344 scopus 로고    scopus 로고
    • Molecular evidence for an ancient duplication of the entire yeast genome
    • Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713
    • (1997) Nature , vol.387 , pp. 708-713
    • Wolfe, K.H.1    Shields, D.C.2
  • 45
    • 0037155196 scopus 로고    scopus 로고
    • Analysis of Drosophila 26 S proteasome using RNA interference
    • Wojcik C, DeMartino GN (2002) Analysis of Drosophila 26 S proteasome using RNA interference. J Biol Chem 277:6188-6197
    • (2002) J Biol Chem , vol.277 , pp. 6188-6197
    • Wojcik, C.1    Demartino, G.N.2
  • 46
    • 0037148758 scopus 로고    scopus 로고
    • The genome sequence of Schizosaccharomyces pombe
    • Wood V, Gwilliam R, Rajandream MA, et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415:871-880
    • (2002) Nature , vol.415 , pp. 871-880
    • Wood, V.1    Gwilliam, R.2    Rajandream, M.A.3
  • 48
    • 0035853037 scopus 로고    scopus 로고
    • RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: A negative feedback circuit
    • Xie Y, Varshavsky A (2001) RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: a negative feedback circuit. Proc Natl Acad Sci USA 98:3056-3061
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 3056-3061
    • Xie, Y.1    Varshavsky, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.