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Volumn 41, Issue 18, 2013, Pages 8444-8451

Minimal genome encoding proteins with constrained amino acid repertoire

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE; PROTEOME;

EID: 84885915478     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt610     Document Type: Article
Times cited : (4)

References (48)
  • 3
    • 0029789824 scopus 로고    scopus 로고
    • A minimal gene set for cellular life derived by comparison of complete bacterial genomes
    • Mushegian, A.R. and Koonin, E.V. (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl Acad. Sci. USA, 93, 10268-10273.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 10268-10273
    • Mushegian, A.R.1    Koonin, E.V.2
  • 5
    • 0032785020 scopus 로고    scopus 로고
    • The minimal genome concept
    • Mushegian, A. (1999) The minimal genome concept. Curr. Opin. Genet. Dev., 9, 709-714.
    • (1999) Curr. Opin. Genet. Dev , vol.9 , pp. 709-714
    • Mushegian, A.1
  • 6
    • 10944248427 scopus 로고    scopus 로고
    • Computing prokaryotic gene ubiquity: Rescuing the core from extinction
    • Charlebois, R.L. and Doolittle, W.F. (2004) Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res., 14, 2469-2477.
    • (2004) Genome Res , vol.14 , pp. 2469-2477
    • Charlebois, R.L.1    Doolittle, W.F.2
  • 7
    • 80053098802 scopus 로고    scopus 로고
    • Essence of life: Essential genes of minimal genomes
    • Juhas, M., Eberl, L. and Glass, J.I. (2011) Essence of life: Essential genes of minimal genomes. Trends Cell Biol., 21, 562-568.
    • (2011) Trends Cell Biol , vol.21 , pp. 562-568
    • Juhas, M.1    Eberl, L.2    Glass, J.I.3
  • 8
    • 1542272747 scopus 로고    scopus 로고
    • Comparative genomics minimal gene-sets and the last universal common ancestor
    • Koonin, E.V. (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat. Rev. Microbiol., 1, 127-136.
    • (2003) Nat. Rev. Microbiol , vol.1 , pp. 127-136
    • Koonin, E.V.1
  • 9
    • 77954198131 scopus 로고    scopus 로고
    • A lowpolynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches
    • Kristensen, D.M., Kannan, L., Coleman, M.K., Wolf, Y.I., Sorokin, A., Koonin, E.V. and Mushegian, A.R. (2010) A lowpolynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics, 26, 1481-1487.
    • (2010) Bioinformatics , vol.26 , pp. 1481-1487
    • Kristensen, D.M.1    Kannan, L.2    Coleman, M.K.3    Wolf, Y.I.4    Sorokin, A.5    Koonin, E.V.6    Mushegian, A.R.7
  • 10
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Edgar, R.C. (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 12
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • So? ding, J., Biegert, A. and Lupas, A.N. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res., 33, W244-W248.
    • (2005) Nucleic Acids Res , vol.33
    • So Ding, J.1    Biegert, A.2    Lupas, A.N.3
  • 13
    • 77951557120 scopus 로고    scopus 로고
    • Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution
    • Omelchenko, M.V., Galperin, M.Y., Wolf, Y.I. and Koonin, E.V. (2010) Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution. Biol. Direct., 5, 31.
    • (2010) Biol. Direct , vol.5 , pp. 31
    • Omelchenko, M.V.1    Galperin, M.Y.2    Wolf, Y.I.3    Koonin, E.V.4
  • 16
    • 0035830860 scopus 로고    scopus 로고
    • Principles for the buffering of genetic variation
    • Hartman, J.L. 4th, Garvik, B. and Hartwell, L. (2001) Principles for the buffering of genetic variation. Science, 291, 1001-1004.
    • (2001) Science , vol.291 , pp. 1001-1004
    • Hartman, I.V.J.L.1    Garvik, B.2    Hartwell, L.3
  • 18
    • 0035225012 scopus 로고    scopus 로고
    • Two C or not two C: Recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins
    • RESEARCH0033
    • Makarova, K.S., Ponomarev, V.A. and Koonin, E.V. (2001) Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. Genome Biol., 2, RESEARCH0033.
    • (2001) Genome Biol , vol.2
    • Makarova, K.S.1    Ponomarev, V.A.2    Koonin, E.V.3
  • 19
    • 0035965270 scopus 로고    scopus 로고
    • NAD+- dependent DNA ligase encoded by a eukaryotic virus
    • Sriskanda, V., Moyer, R.W. and Shuman, S. (2001) NAD+- dependent DNA ligase encoded by a eukaryotic virus. J. Biol. Chem., 276, 36100-36109.
    • (2001) J. Biol. Chem , vol.276 , pp. 36100-36109
    • Sriskanda, V.1    Moyer, R.W.2    Shuman, S.3
  • 20
    • 79956197903 scopus 로고    scopus 로고
    • Probing the role of the fully conserved Cys126 in triosephosphate isomerase by site-specific mutagenesis-distal effects on dimer stability
    • Samanta, M., Banerjee, M., Murthy, M.R.N., Balaram, H. and Balaram, P. (2011) Probing the role of the fully conserved Cys126 in triosephosphate isomerase by site-specific mutagenesis-distal effects on dimer stability. FEBS J., 278, 1932-1943.
    • (2011) FEBS J , vol.278 , pp. 1932-1943
    • Samanta, M.1    Banerjee, M.2    Murthy, M.R.N.3    Balaram, H.4    Balaram, P.5
  • 22
    • 0033558785 scopus 로고    scopus 로고
    • The active site of phosphorylating glyceraldehyde-3-phosphate dehydrogenase is not designed to increase the nucleophilicity of a serine residue
    • Boschi-Muller, S. and Branlant, G. (1999) The active site of phosphorylating glyceraldehyde-3-phosphate dehydrogenase is not designed to increase the nucleophilicity of a serine residue. Arch. Biochem. Biophys., 363, 259-266.
    • (1999) Arch. Biochem. Biophys , vol.363 , pp. 259-266
    • Boschi-Muller, S.1    Branlant, G.2
  • 23
    • 79953268441 scopus 로고    scopus 로고
    • Versatile metabolic adaptations of Ralstonia eutropha H16 to a loss of PdhL, the E3 component of the pyruvate dehydrogenase complex
    • Raberg, M., Bechmann, J., Brandt, U., Schlu? ter, J., Uischner, B., Voigt, B., Hecker, M. and Steinbu? chel, A. (2011) Versatile metabolic adaptations of Ralstonia eutropha H16 to a loss of PdhL, the E3 component of the pyruvate dehydrogenase complex. Appl. Environ. Microbiol., 77, 2254-2263.
    • (2011) Appl. Environ. Microbiol , vol.77 , pp. 2254-2263
    • Raberg, M.1    Bechmann, J.2    Brandt, U.3    Schlu Ter, J.4    Uischner, B.5    Voigt, B.6    Hecker, M.7    Steinbu Chel, A.8
  • 25
    • 77950229275 scopus 로고    scopus 로고
    • Critical role of dispensable genes in Mycoplasma agalactiae interaction with mammalian cells
    • Baranowski, E., Guiral, S., Sagné , E., Skapski, A. and Citti, C. (2010) Critical role of dispensable genes in Mycoplasma agalactiae interaction with mammalian cells. Infect. Immun., 78, 1542-1551.
    • (2010) Infect. Immun , vol.78 , pp. 1542-1551
    • Baranowski, E.1    Guiral, S.2    Sagné, E.3    Skapski, A.4    Citti, C.5
  • 26
    • 2442669151 scopus 로고    scopus 로고
    • Structural, kinetic, and mutational studies of the zinc ion environment in tetrameric cytidine deaminase
    • Johansson, E., Neuhard, J., Willemoe's, M. and Larsen, S. (2004) Structural, kinetic, and mutational studies of the zinc ion environment in tetrameric cytidine deaminase. Biochemistry, 43, 6020-6029.
    • (2004) Biochemistry , vol.43 , pp. 6020-6029
    • Johansson, E.1    Neuhard, J.2    Willemoes, M.3    Larsen, S.4
  • 28
    • 0017904146 scopus 로고    scopus 로고
    • Thioredoxin from Escherichia coli. Radioimmunological and enzymatic determinations in wild type cells and mutants defective in phage T7 DNA replication
    • Holmgren, A., Ohlsson, I. and Grankvist, M.L. Thioredoxin from Escherichia coli. Radioimmunological and enzymatic determinations in wild type cells and mutants defective in phage T7 DNA replication. J. Biol. Chem., 253, 430-436.
    • J. Biol. Chem , vol.253 , pp. 430-436
    • Holmgren, A.1    Ohlsson, I.2    Grankvist, M.L.3
  • 29
    • 0023845261 scopus 로고
    • Construction and characterization of glutaredoxin-negative mutants of Escherichia coli
    • Russel, M. and Holmgren, A. (1988) Construction and characterization of glutaredoxin-negative mutants of Escherichia coli. Proc. Natl Acad. Sci. USA, 85, 990-994.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 990-994
    • Russel, M.1    Holmgren, A.2
  • 30
    • 78049374613 scopus 로고    scopus 로고
    • The use of thiols by ribonucleotide reductase
    • Holmgren, A. and Sengupta, R. (2010) The use of thiols by ribonucleotide reductase. Free Radic. Biol. Med., 49, 1617-1628.
    • (2010) Free Radic. Biol. Med , vol.49 , pp. 1617-1628
    • Holmgren, A.1    Sengupta, R.2
  • 31
    • 84885926803 scopus 로고    scopus 로고
    • Decoding in Candidatus Riesia pediculicola, close to a minimal tRNA modification set?
    • de Crécy-Lagard, V., Marck, C. and Grosjean, H. (2012) Decoding in Candidatus Riesia pediculicola, close to a minimal tRNA modification set? Trends Cell Molec. Biol., 7, 12-39.
    • (2012) Trends Cell Molec. Biol , vol.7 , pp. 12-39
    • De Crécy-Lagard, V.1    Marck, C.2    Grosjean, H.3
  • 32
    • 34648840096 scopus 로고    scopus 로고
    • Comparative RNomics and modomics in Mollicutes: Prediction of gene function and evolutionary implications
    • de Crécy-Lagard, V., Marck, C., Brochier-Armanet, C. and Grosjean, H. (2007) Comparative RNomics and modomics in Mollicutes: prediction of gene function and evolutionary implications. IUBMB Life, 59, 634-658.
    • (2007) IUBMB Life , vol.59 , pp. 634-658
    • De Crécy-Lagard, V.1    Marck, C.2    Brochier-Armanet, C.3    Grosjean, H.4
  • 33
    • 0036955843 scopus 로고    scopus 로고
    • The cysteine desulfurase IscS is required for synthesis of all five thiolated nucleosides present in tRNA from Salmonella enterica serovar typhimurium
    • Nilsson, K., Lundgren, H.K., Hagervall, T.G. and Bjo? rk, G.R. (2002) The cysteine desulfurase IscS is required for synthesis of all five thiolated nucleosides present in tRNA from Salmonella enterica serovar typhimurium. J. Bacteriol., 184, 6830-6835.
    • (2002) J. Bacteriol , vol.184 , pp. 6830-6835
    • Nilsson, K.1    Lundgren, H.K.2    Hagervall, T.G.3    Bjo Rk, G.R.4
  • 34
    • 0043210520 scopus 로고    scopus 로고
    • The GTPase activity and C-terminal cysteine of the Escherichia coli MnmE protein are essential for its tRNA modifying function
    • Yim, L., Mart́nez-Vicente, M., Villarroya, M., Aguado, C., Knecht, E. and Armengod, M.E. (2003) The GTPase activity and C-terminal cysteine of the Escherichia coli MnmE protein are essential for its tRNA modifying function. J. Biol. Chem., 278, 28378-28387.
    • (2003) J. Biol. Chem , vol.278 , pp. 28378-28387
    • Yim, L.1    Mart́nez-Vicente, M.2    Villarroya, M.3    Aguado, C.4    Knecht, E.5    Armengod, M.E.6
  • 35
    • 65149088650 scopus 로고    scopus 로고
    • Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon
    • Osawa, T., Ito, K., Inanaga, H., Nureki, O., Tomita, K. and Numata, T. (2009) Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon. Structure, 17, 713-724.
    • (2009) Structure , vol.17 , pp. 713-724
    • Sawa, T.1    Ito, K.2    Inanaga, H.3    Nureki, O.4    Tomita, K.5    Numata, T.6
  • 36
    • 8844277667 scopus 로고    scopus 로고
    • Key players involved in bacterial disulfide-bond formation
    • Tan, J.T. and Bardwell, J.C.A. (2004) Key players involved in bacterial disulfide-bond formation. Chembiochem, 5, 1479-1487.
    • (2004) Chembiochem , vol.5 , pp. 1479-1487
    • Tan, J.T.1    Bardwell, J.C.A.2
  • 37
    • 39549122002 scopus 로고    scopus 로고
    • Efficient coupling of catalysis and dynamics in the E1 component of Escherichia coli pyruvate dehydrogenase multienzyme complex
    • Kale, S., Ulas, G., Song, J., Brudvig, G.W., Furey, W. and Jordan, F. (2008) Efficient coupling of catalysis and dynamics in the E1 component of Escherichia coli pyruvate dehydrogenase multienzyme complex. Proc. Natl Acad. Sci. USA, 105, 1158-1163.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 1158-1163
    • Kale, S.1    Ulas, G.2    Song, J.3    Brudvig, G.W.4    Furey, W.5    Jordan, F.6
  • 38
    • 80054756682 scopus 로고    scopus 로고
    • Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli
    • Babu, M., Gagarinova, A. and Emili, A. (2011) Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli. Methods Mol. Biol., 781, 99-126.
    • (2011) Methods Mol. Biol , vol.781 , pp. 99-126
    • Babu, M.1    Gagarinova, A.2    Emili, A.3
  • 40
    • 84876808409 scopus 로고    scopus 로고
    • From essential to persistent genes: A functional approach to constructing synthetic life
    • Acevedo-Rocha, C.G., Fang, G., Schmidt, M., Ussery, D.W. and Danchin, A. (2013) From essential to persistent genes: A functional approach to constructing synthetic life. Trends Genet., 29, 273-279.
    • (2013) Trends Genet , vol.29 , pp. 273-279
    • Acevedo-Rocha, C.G.1    Fang, G.2    Schmidt, M.3    Ussery, D.W.4    Danchin, A.5
  • 42
    • 84878617116 scopus 로고    scopus 로고
    • Characterization of genome-reduced fission yeast strains
    • Sasaki, M., Kumagai, H., Takegawa, K. and Tohda, H. (2013) Characterization of genome-reduced fission yeast strains. Nucleic Acids Res., 41, 5382-5399.
    • (2013) Nucleic Acids Res , vol.41 , pp. 5382-5399
    • Sasaki, M.1    Kumagai, H.2    Takegawa, K.3    Tohda, H.4
  • 43
    • 0034736513 scopus 로고    scopus 로고
    • Consensus temporal order of amino acids and evolution of the triplet code
    • Trifonov, E.N. (2000) Consensus temporal order of amino acids and evolution of the triplet code. Gene, 261, 139-151.
    • (2000) Gene , vol.261 , pp. 139-151
    • Trifonov, E.N.1
  • 44
    • 42549096025 scopus 로고    scopus 로고
    • Gene content of LUCA, the last universal common ancestor
    • Mushegian, A. (2008) Gene content of LUCA, the last universal common ancestor. Front Biosci., 13, 4657-4666.
    • (2008) Front Biosci , vol.13 , pp. 4657-4666
    • Mushegian, A.1
  • 46
    • 84885918811 scopus 로고    scopus 로고
    • Vol Verba Mundi Jaffrey NH
    • Perec, G. and Adair, G. (2005) A Void, Vol. Verba Mundi, Jaffrey, NH.
    • (2005) A Void
    • Perec, G.1    Adair, G.2
  • 48
    • 33746151994 scopus 로고    scopus 로고
    • Evolution of protein lipograms: A bioinformatics problem
    • White, H.B. 3rd and Dhurjati, P. (2006) Evolution of protein lipograms: A bioinformatics problem. Biochem. Mol. Biol. Educ., 34, 262-266.
    • (2006) Biochem. Mol. Biol. Educ , vol.34 , pp. 262-266
    • White Iii., H.B.1    Dhurjati, P.2


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