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Volumn 4, Issue , 2013, Pages

Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; MITOCHONDRIAL RELEASE FACTOR 1; MITOCHONDRIAL RELEASE FACTOR 1A; MITOCHONDRIAL RNA; RIBOSOME RNA; TRANSLATION TERMINATION FACTOR; UNCLASSIFIED DRUG;

EID: 84890916995     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms3940     Document Type: Article
Times cited : (43)

References (43)
  • 1
    • 0001515799 scopus 로고
    • Incorporation of labeled amino acids into the protein of muscle and liver mitochondri
    • McLean, J. R., Cohn, G. L., Brandt, I. K. & Simpson, A. M. Incorporation of labeled amino acids into the protein of muscle and liver mitochondria. J. Biol. Chem. 233, 657-663 (1958).
    • (1958) J. Biol. Chem. , vol.233 , pp. 657-663
    • McLean, J.R.1    Cohn, G.L.2    Brandt, I.K.3    Simpson, A.M.4
  • 2
    • 0019423856 scopus 로고
    • Sequence and organization of the human mitochondrial genome
    • DOI 10.1038/290457a0
    • Anderson, S. et al. Sequence and organization of the human mitochondrial genome. Nature 290, 457-465 (1981). (Pubitemid 11159074)
    • (1981) Nature , vol.290 , Issue.5806 , pp. 457-465
    • Anderson, S.1    Bankier, A.T.2    Barrell, B.G.3
  • 3
    • 78649513967 scopus 로고    scopus 로고
    • Current views of the structure of the mammalian mitochondrial ribosome
    • Koc, E. C., Haque, M. E. & Spremulli, L. L. Current views of the structure of the mammalian mitochondrial ribosome. Isr. J. Chem. 50, 45-59 (2010).
    • (2010) Isr. J. Chem. , vol.50 , pp. 45-59
    • Koc, E.C.1    Haque, M.E.2    Spremulli, L.L.3
  • 5
    • 0141953259 scopus 로고    scopus 로고
    • Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins
    • DOI 10.1016/S0092-8674(03)00762-1
    • Sharma, M. R. et al. Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins. Cell 115, 97-108 (2003). (Pubitemid 37255321)
    • (2003) Cell , vol.115 , Issue.1 , pp. 97-108
    • Sharma, M.R.1    Koc, E.C.2    Datta, P.P.3    Booth, T.M.4    Spremulli, L.L.5    Agrawal, R.K.6
  • 6
    • 0344012611 scopus 로고    scopus 로고
    • Properties of Human Mitochondrial Ribosomes
    • DOI 10.1080/15216540310001626610
    • O'Brien, T. W. Properties of human mitochondrial ribosomes. IUBMB Life 55, 505-513 (2003). (Pubitemid 37462706)
    • (2003) IUBMB Life , vol.55 , Issue.9 , pp. 505-513
    • O'Brien, T.W.1
  • 7
    • 34250704167 scopus 로고    scopus 로고
    • The mechanisms of codon reassignments in mitochondrial genetic codes
    • DOI 10.1007/s00239-006-0284-7
    • Sengupta, S., Yang, X. & Higgs, P. G. The mechanisms of codon reassignments in mitochondrial genetic codes. J. Mol. Evol. 64, 662-688 (2007). (Pubitemid 46956760)
    • (2007) Journal of Molecular Evolution , vol.64 , Issue.6 , pp. 662-688
    • Sengupta, S.1    Yang, X.2    Higgs, P.G.3
  • 9
    • 77949547496 scopus 로고    scopus 로고
    • A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome
    • Richter, R. et al. A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome. EMBO J. 29, 1116-1125 (2010).
    • (2010) EMBO J. , vol.29 , pp. 1116-1125
    • Richter, R.1
  • 10
    • 0032570020 scopus 로고    scopus 로고
    • Identification and cloning of human mitochondrial translational release factor 1 and the ribosome recycling factor
    • DOI 10.1016/S0167-4781(98)00223-1, PII S0167478198002231
    • Zhang, Y. & Spremulli, L. L. Identification and cloning of human mitochondrial translational release factor 1 and the ribosome recycling factor. Biochim. Biophys. Acta 1443, 245-250 (1998). (Pubitemid 29016032)
    • (1998) Biochimica et Biophysica Acta - Gene Structure and Expression , vol.1443 , Issue.1-2 , pp. 245-250
    • Zhang, Y.1    Spremulli, L.L.2
  • 11
    • 42449108199 scopus 로고    scopus 로고
    • HMRF1L is a human mitochondrial translation release factor involved in the decoding of the termination codons UAA and UAG
    • DOI 10.1111/j.1365-2443.2008.01181.x
    • Nozaki, Y., Matsunaga, N., Ishizawa, T., Ueda, T. & Takeuchi, N. HMRF1L is a human mitochondrial translation release factor involved in the decoding of the termination codons UAA and UAG. Genes Cells 13, 429-438 (2008). (Pubitemid 351567045)
    • (2008) Genes to Cells , vol.13 , Issue.5 , pp. 429-438
    • Nozaki, Y.1    Matsunaga, N.2    Ishizawa, T.3    Ueda, T.4    Takeuchi, N.5
  • 13
    • 77952729843 scopus 로고    scopus 로고
    • Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria
    • Young, D. J. et al. Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria. RNA 16, 1146-1155 (2010).
    • (2010) RNA , vol.16 , pp. 1146-1155
    • Young, D.J.1
  • 14
    • 49649099901 scopus 로고    scopus 로고
    • Structural basis for translation termination on the 70S ribosome
    • Laurberg, M. et al. Structural basis for translation termination on the 70S ribosome. Nature 454, 852-857 (2008).
    • (2008) Nature , vol.454 , pp. 852-857
    • Laurberg, M.1
  • 15
    • 77955082781 scopus 로고    scopus 로고
    • Mutations in C12orf65 in patients with encephalomyopathy and a mitochondrial translation defect
    • Antonicka, H. et al. Mutations in C12orf65 in patients with encephalomyopathy and a mitochondrial translation defect. Am. J. Hum. Genet. 87, 115-122 (2010).
    • (2010) Am. J. Hum. Genet. , vol.87 , pp. 115-122
    • Antonicka, H.1
  • 16
    • 84867222475 scopus 로고    scopus 로고
    • Solution structure and siRNA-mediated knockdown analysis of the mitochondrial disease-related protein C12orf65
    • Kogure, H. et al. Solution structure and siRNA-mediated knockdown analysis of the mitochondrial disease-related protein C12orf65. Proteins 80, 2629-2642 (2012).
    • (2012) Proteins , vol.80 , pp. 2629-2642
    • Kogure, H.1
  • 18
    • 84870390175 scopus 로고    scopus 로고
    • Bridging the gap between ribosome structure and biochemistry by mechanistic computations
    • Åqvist, J., Lind, C., Sund, J. & Wallin, G. Bridging the gap between ribosome structure and biochemistry by mechanistic computations. Curr. Opin. Struct. Biol. 22, 815-823 (2012).
    • (2012) Curr. Opin. Struct. Biol. , vol.22 , pp. 815-823
    • Åqvist, J.1    Lind, C.2    Sund, J.3    Wallin, G.4
  • 19
    • 34548227759 scopus 로고    scopus 로고
    • A Model for How Ribosomal Release Factors Induce Peptidyl-tRNA Cleavage in Termination of Protein Synthesis
    • DOI 10.1016/j.molcel.2007.06.032, PII S1097276507004443
    • Trobro, S. & Åqvist, J. A model for how ribosomal release factors induce peptidyl-tRNA cleavage in termination of protein synthesis. Mol. Cell 27, 758-766 (2007). (Pubitemid 47333221)
    • (2007) Molecular Cell , vol.27 , Issue.5 , pp. 758-766
    • Trobro, S.1    Aqvist, J.2
  • 20
    • 77953726745 scopus 로고    scopus 로고
    • Principles of stop-codon reading on the ribosome
    • Sund, J., Andér, M. & Åqvist, J. Principles of stop-codon reading on the ribosome. Nature 465, 947-950 (2010).
    • (2010) Nature , vol.465 , pp. 947-950
    • Sund, J.1    Andér, M.2    Åqvist, J.3
  • 22
    • 33846039881 scopus 로고    scopus 로고
    • Energetics of codon - Anticodon recognition on the small ribosomal subunit
    • DOI 10.1021/bi061713i
    • Almlöf, M., Andér, M. & Åqvist, J. Energetics of codon-anticodon recognition on the small ribosomal subunit. Biochemistry 46, 200-209 (2007). (Pubitemid 46067748)
    • (2007) Biochemistry , vol.46 , Issue.1 , pp. 200-209
    • Almlof, M.1    Ander, M.2    Aqvist, J.3
  • 23
    • 58149374559 scopus 로고    scopus 로고
    • Crystal structure of a translation termination complex formed with release factor RF2
    • Korostelev, A. et al. Crystal structure of a translation termination complex formed with release factor RF2. Proc. Natl Acad. Sci. USA 105, 19684-19689 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 19684-19689
    • Korostelev, A.1
  • 24
    • 84858309380 scopus 로고    scopus 로고
    • Structural basis for the rescue of stalled ribosomes: Structure of YaeJ bound to the ribosome
    • Gagnon, M. G., Seetharaman, S. V., Bulkley, D. & Steitz, T. A. Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome. Science 335, 1370-1372 (2012).
    • (2012) Science , vol.335 , pp. 1370-1372
    • Gagnon, M.G.1    Seetharaman, S.V.2    Bulkley, D.3    Steitz, T.A.4
  • 25
    • 79953142009 scopus 로고    scopus 로고
    • YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes
    • Handa, Y., Inaho, N. & Nameki, N. YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes. Nucleic Acids Res. 39, 1739-1748 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. 1739-1748
    • Handa, Y.1    Inaho, N.2    Nameki, N.3
  • 26
    • 77951974177 scopus 로고    scopus 로고
    • Structural aspects of messenger RNA reading frame maintenance by the ribosom
    • Jenner, L. B., Demeshkina, N., Yusupova, G. & Yusupov, M. Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nat. Struct. Mol. Biol. 17, 555-560 (2010).
    • (2010) Nat. Struct. Mol. Biol. , vol.17 , pp. 555-560
    • Jenner, L.B.1    Demeshkina, N.2    Yusupova, G.3    Yusupov, M.4
  • 27
    • 48449106792 scopus 로고    scopus 로고
    • The Jpred 3 secondary structure prediction server
    • Cole, C., Barber, J. D. & Barton, G. J. The Jpred 3 secondary structure prediction server. Nucleic Acids Res. 36, W197-W201 (2008).
    • (2008) Nucleic Acids Res. , vol.36
    • Cole, C.1    Barber, J.D.2    Barton, G.J.3
  • 28
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • DOI 10.1006/jmbi.1999.3091
    • Jones, D. T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202 (1999). (Pubitemid 29435759)
    • (1999) Journal of Molecular Biology , vol.292 , Issue.2 , pp. 195-202
    • Jones, D.T.1
  • 30
    • 79955394875 scopus 로고    scopus 로고
    • Bacterial toxin RelE mediates frequent codon-independent mRNA cleavage from 5' end of coding regions in vivo
    • Hurley, J. M., Cruz, J. W., Ouyang, M. & Woychik, N. A. Bacterial toxin RelE mediates frequent codon-independent mRNA cleavage from 5' end of coding regions in vivo. J. Biol. Chem. 286, 14770-14778 (2011).
    • (2011) J. Biol. Chem. , vol.286 , pp. 14770-14778
    • Hurley, J.M.1    Cruz, J.W.2    Ouyang, M.3    Woychik, N.A.4
  • 31
    • 84867817961 scopus 로고    scopus 로고
    • Evolution and diversification of the organellar release factor family
    • Duarte, I., Nabuurs, S. B., Magno, R. & Huynen, M. Evolution and diversification of the organellar release factor family. Mol. Biol. Evol. 29, 3497-3512 (2012).
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 3497-3512
    • Duarte, I.1    Nabuurs, S.B.2    Magno, R.3    Huynen, M.4
  • 33
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • DOI 10.1006/jmbi.1993.1626
    • Sali, A. & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815 (1993). (Pubitemid 24007801)
    • (1993) Journal of Molecular Biology , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 34
    • 78349313687 scopus 로고    scopus 로고
    • Solution structure of the catalytic domain of the mitochondrial protein ICT1 that is essential for cell vitality
    • Handa, Y. et al. Solution structure of the catalytic domain of the mitochondrial protein ICT1 that is essential for cell vitality. J. Mol. Biol. 404, 260-273 (2010).
    • (2010) J. Mol. Biol. , vol.404 , pp. 260-273
    • Handa, Y.1
  • 35
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • DOI 10.1021/ja9621760, PII S0002786396021762
    • Jorgensen, W. L., Maxwell, D. S. & Tirado-Rives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118, 11225-11236 (1996). (Pubitemid 26399746)
    • (1996) Journal of the American Chemical Society , vol.118 , Issue.45 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 37
    • 0032232405 scopus 로고    scopus 로고
    • Q: A molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems
    • DOI 10.1016/S1093-3263(99)00012-1, PII S1093326399000121
    • Marelius, J., Kolmodin, K., Feierberg, I. & Åqvist, J. Q. A molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. J. Mol. Graph. Model. 16, 213-225 (1998). (Pubitemid 30069589)
    • (1998) Journal of Molecular Graphics and Modelling , vol.16 , Issue.4-6 , pp. 213-225
    • Marelius, J.1    Kolmodin, K.2    Feierberg, I.3    Aqvist, J.4
  • 39
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell, A. D. et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586-3616 (1998).
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3586-3616
    • MacKerell, A.D.1
  • 40
    • 36549094414 scopus 로고
    • A surface constrained all-atom solvent model for effective simulations of polar solutions
    • King, G. & Warshel, A. A surface constrained all-atom solvent model for effective simulations of polar solutions. J. Chem. Phys. 91, 3647-3661 (1989).
    • (1989) J. Chem. Phys. , vol.91 , pp. 3647-3661
    • King, G.1    Warshel, A.2
  • 41
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J.-P., Ciccotti, G. & Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327-341 (1977).
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 42
    • 0000115003 scopus 로고
    • A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
    • Lee, F. S. & Warshel, A. A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations. J. Chem. Phys. 97, 3100-3107 (1992).
    • (1992) J. Chem. Phys. , vol.97 , pp. 3100-3107
    • Lee, F.S.1    Warshel, A.2


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