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Volumn 18, Issue 4, 2012, Pages 752-758

Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state

Author keywords

Independent fold; Large subunit; Ribosomal evolution; Ribosome; SHAPE

Indexed keywords

LARGE SUBUNIT RIBOSOMAL RNA; MAGNESIUM; RIBOSOME PROTEIN; RNA 23S;

EID: 84858676366     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.030692.111     Document Type: Article
Times cited : (17)

References (47)
  • 2
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
    • DOI 10.1126/science.289.5481.905
    • Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289: 905-920. (Pubitemid 30659939)
    • (2000) Science , vol.289 , Issue.5481 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 4
    • 60549112849 scopus 로고    scopus 로고
    • A hierarchical model for evolution of 23S ribosomal RNA
    • Bokov K, Steinberg SV. 2009. A hierarchical model for evolution of 23S ribosomal RNA. Nature 457: 977-980.
    • (2009) Nature , vol.457 , pp. 977-980
    • Bokov, K.1    Steinberg, S.V.2
  • 5
    • 0020690563 scopus 로고
    • The structure of ribosomal RNA and its organization relative to ribosomal protein
    • Brimacombe R, Maly P, Zwieb C. 1983. The structure of ribosomal RNA and its organization relative to ribosomal protein. Prog Nucleic Acid Res Mol Biol 28: 1-48.
    • (1983) Prog Nucleic Acid Res Mol Biol , vol.28 , pp. 1-48
    • Brimacombe, R.1    Maly, P.2    Zwieb, C.3
  • 8
    • 23444449882 scopus 로고
    • Building protein structure and function from modular units
    • DOI 10.1016/0167-7799(94)90078-7
    • Campbell ID, Downing AK. 1994. Building protein structure and function from modular units. Trends Biotechnol 12: 168-172. (Pubitemid 24160423)
    • (1994) Trends in Biotechnology , vol.12 , Issue.5 , pp. 168-172
    • Campbell, I.D.1    Downing, A.K.2
  • 9
    • 2942571539 scopus 로고    scopus 로고
    • The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
    • doi: 10.1186/1471-2105-3-2
    • Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM, et al. 2002. The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2. doi: 10.1186/1471-2105-3-2.
    • (2002) BMC Bioinformatics , vol.3 , pp. 2
    • Cannone, J.J.1    Subramanian, S.2    Schnare, M.N.3    Collett, J.R.4    D'Souza, L.M.5    Du, Y.6    Feng, B.7    Lin, N.8    Madabusi, L.V.9    Muller, K.M.10
  • 10
    • 0014378880 scopus 로고
    • The origin of the genetic code
    • Crick FH. 1968. The origin of the genetic code. J Mol Biol 38: 367-379.
    • (1968) J Mol Biol , vol.38 , pp. 367-379
    • Crick, F.H.1
  • 12
    • 58749105663 scopus 로고    scopus 로고
    • RNA folding: Thermodynamic and molecular descriptions of the roles of ions
    • Draper DE. 2008. RNA folding: Thermodynamic and molecular descriptions of the roles of ions. Biophys J 95: 5489-5495.
    • (2008) Biophys J , vol.95 , pp. 5489-5495
    • Draper, D.E.1
  • 13
    • 0023645139 scopus 로고
    • Structure and accessibility of domain I of Escherichia coli 23S RNA in free RNA, in the L24-RNA complex and in 50S subunits. Implications for ribosomal assembly
    • Egebjerg J, Leffers H, Christensen A, Andersen H, Garrett RA. 1987. Structure and accessibility of domain I of Escherichia coli 23S RNA in free RNA, in the L24-RNA complex and in 50S subunits. Implications for ribosomal assembly. J Mol Biol 196: 125-136.
    • (1987) J Mol Biol , vol.196 , pp. 125-136
    • Egebjerg, J.1    Leffers, H.2    Christensen, A.3    Andersen, H.4    Garrett, R.A.5
  • 14
    • 33846266906 scopus 로고    scopus 로고
    • Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony
    • DOI 10.1016/j.jmb.2006.11.017, PII S0022283606015464
    • Fong JH, Geer LY, Panchenko AR, Bryant SH. 2007. Modeling the evolution of protein domain architectures using maximum parsimony. J Mol Biol 366: 307-315. (Pubitemid 46123330)
    • (2007) Journal of Molecular Biology , vol.366 , Issue.1 , pp. 307-315
    • Fong, J.H.1    Geer, L.Y.2    Panchenko, A.R.3    Bryant, S.H.4
  • 15
    • 78149403030 scopus 로고    scopus 로고
    • Origin and evolution of the ribosome
    • doi: 10.1101/cshperspect.a003483
    • Fox GE. 2010. Origin and evolution of the ribosome. Cold Spring Harb Perspect Biol 2: a003483. doi: 10.1101/cshperspect.a003483.
    • (2010) Cold Spring Harb Perspect Biol , vol.2
    • Fox, G.E.1
  • 16
    • 36849148382 scopus 로고
    • Origin of life: The RNA world
    • Gilbert W. 1986. Origin of life: The RNA world. Nature 319: 618.
    • (1986) Nature , vol.319 , pp. 618
    • Gilbert, W.1
  • 17
    • 0035977093 scopus 로고    scopus 로고
    • High resolution structure of the large ribosomal subunit from a mesophilic eubacterium
    • DOI 10.1016/S0092-8674(01)00546-3
    • Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A. 2001. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107: 679-688. (Pubitemid 34014868)
    • (2001) Cell , vol.107 , Issue.5 , pp. 679-688
    • Harms, J.1    Schluenzen, F.2    Zarivach, R.3    Bashan, A.4    Gat, S.5    Agmon, I.6    Bartels, H.7    Franceschi, F.8    Yonath, A.9
  • 18
    • 67249104874 scopus 로고    scopus 로고
    • A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center
    • Hsiao C, Williams LD. 2009. A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center. Nucleic Acids Res 37: 3134-3142.
    • (2009) Nucleic Acids Res , vol.37 , pp. 3134-3142
    • Hsiao, C.1    Williams, L.D.2
  • 19
    • 73349114907 scopus 로고    scopus 로고
    • Peeling the onion: Ribosomes are ancient molecular fossils
    • Hsiao C, Mohan S, Kalahar BK, Williams LD. 2009. Peeling the onion: Ribosomes are ancient molecular fossils. Mol Biol Evol 26: 2415-2425.
    • (2009) Mol Biol Evol , vol.26 , pp. 2415-2425
    • Hsiao, C.1    Mohan, S.2    Kalahar, B.K.3    Williams, L.D.4
  • 21
    • 33845328453 scopus 로고    scopus 로고
    • Size, shape, and flexibility of RNA structures
    • doi: 10.1063/1.2364190
    • Hyeon C, Dima RI, Thirumalai D. 2006. Size, shape, and flexibility of RNA structures. J Chem Phys 125: 194905. doi: 10.1063/1.2364190.
    • (2006) J Chem Phys , vol.125 , pp. 194905
    • Hyeon, C.1    Dima, R.I.2    Thirumalai, D.3
  • 22
    • 0024209174 scopus 로고
    • Domain VI of Escherichia coli 23 S ribosomal RNA structure, assembly and function
    • DOI 10.1016/0022-2836(88)90351-8
    • Leffers H, Egebjerg J, Andersen A, Christensen T, Garrett RA. 1988. Domain VI of Escherichia coli 23S ribosomal RNA. Structure, assembly and function. J Mol Biol 204: 507-522. (Pubitemid 19029957)
    • (1988) Journal of Molecular Biology , vol.204 , Issue.3 , pp. 507-522
    • Leffers, H.1    Egebjerg, J.2    Andersen, A.3    Christensen, T.4    Garrett, R.A.5
  • 23
    • 16244412610 scopus 로고    scopus 로고
    • RNA structure analysis at single nucleotide resolution by Selective 2′-Hydroxyl Acylation and Primer Extension (SHAPE)
    • DOI 10.1021/ja043822v
    • Merino EJ, Wilkinson KA, Coughlan JL, Weeks KM. 2005. RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE). J AmChem Soc 127: 4223-4231. (Pubitemid 40463047)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.12 , pp. 4223-4231
    • Merino, E.J.1    Wilkinson, K.A.2    Coughlan, J.L.3    Weeks, K.M.4
  • 24
    • 34247162792 scopus 로고    scopus 로고
    • A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry
    • DOI 10.1021/ja0704028
    • Mortimer SA, Weeks KM. 2007. A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J Am Chem Soc 129: 4144-4145. (Pubitemid 46595421)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.14 , pp. 4144-4145
    • Mortimer, S.A.1    Weeks, K.M.2
  • 25
    • 57149086080 scopus 로고    scopus 로고
    • Time-resolved RNA SHAPE chemistry
    • Mortimer SA, Weeks KM. 2008. Time-resolved RNA SHAPE chemistry. J Am Chem Soc 130: 16178-16180.
    • (2008) J Am Chem Soc , vol.130 , pp. 16178-16180
    • Mortimer, S.A.1    Weeks, K.M.2
  • 26
    • 0034637161 scopus 로고    scopus 로고
    • The structural basis of ribosome activity in peptide bond synthesis
    • DOI 10.1126/science.289.5481.920
    • Nissen P, Hansen J, Ban N, Moore PB, Steitz TA. 2000. The structural basis of ribosome activity in peptide bond synthesis. Science 289: 920-930. (Pubitemid 30659940)
    • (2000) Science , vol.289 , Issue.5481 , pp. 920-930
    • Nissen, P.1    Hansen, J.2    Ban, N.3    Moore, P.B.4    Steitz, T.A.5
  • 27
    • 24644437810 scopus 로고    scopus 로고
    • RNA structure: Reading the ribosome
    • DOI 10.1126/science.1111771
    • Noller HF. 2005. RNA structure: Reading the ribosome. Science 309: 1508-1514. (Pubitemid 41266466)
    • (2005) Science , vol.309 , Issue.5740 , pp. 1508-1514
    • Noller, H.F.1
  • 29
    • 0026639881 scopus 로고
    • Unusual resistance of peptidyl transferase to protein extraction procedures
    • Noller HF, Hoffarth V, Zimniak L. 1992. Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256: 1416-1419.
    • (1992) Science , vol.256 , pp. 1416-1419
    • Noller, H.F.1    Hoffarth, V.2    Zimniak, L.3
  • 31
    • 0014369024 scopus 로고
    • Evolution of the genetic apparatus
    • Orgel LE. 1968. Evolution of the genetic apparatus. J Mol Biol 38: 381-393.
    • (1968) J Mol Biol , vol.38 , pp. 381-393
    • Orgel, L.E.1
  • 33
    • 0003075565 scopus 로고
    • On the problems of evolution and biochemical information transfer
    • ed. M Kasha, B Pullman, Academic, New York
    • Rich A. 1962. On the problems of evolution and biochemical information transfer. In Horizons in biochemistry (ed. M Kasha, B Pullman), pp. 103-126. Academic, New York.
    • (1962) Horizons in Biochemistry , pp. 103-126
    • Rich, A.1
  • 34
    • 0027979072 scopus 로고
    • Independent in vitro assembly of a ribonucleoprotein particle containing the 3′ domain of 16S rRNA
    • Samaha RR, O'Brien B, O'Brien TW, Noller HF. 1994. Independent in vitro assembly of a ribonucleoprotein particle containing the 3′ domain of 16S rRNA. Proc Natl Acad Sci 91: 7884-7888.
    • (1994) Proc Natl Acad Sci , vol.91 , pp. 7884-7888
    • Samaha, R.R.1    O'Brien, B.2    O'Brien, T.W.3    Noller, H.F.4
  • 37
    • 0022423421 scopus 로고
    • Further characterization of the extremely small mitochondrial ribosomal RNAs from trypanosomes: A detailed comparison of the 9S and 12S RNAs from Crithidia fasciculata and Trypanosoma brucei with rRNAs from other organisms
    • Sloof P, Van den Burg J, Voogd A, Benne R, Agostinelli M, Borst P, Gutell R, Noller H. 1985. Further characterization of the extremely small mitochondrial ribosomal RNAs from trypanosomes: A detailed comparison of the 9S and 12S RNAs from Crithidia fasciculata and Trypanosoma brucei with rRNAs from other organisms. Nucleic Acids Res 13: 4171-4190.
    • (1985) Nucleic Acids Res , vol.13 , pp. 4171-4190
    • Sloof, P.1    Van Den Burg, J.2    Voogd, A.3    Benne, R.4    Agostinelli, M.5    Borst, P.6    Gutell, R.7    Noller, H.8
  • 38
    • 44149117720 scopus 로고    scopus 로고
    • The origin and evolution of the ribosome
    • doi: 10.1186/1745-6150-3-16
    • Smith TF, Lee JC, Gutell RR, Hartman H. 2008. The origin and evolution of the ribosome. Biol Direct 3: 16. doi: 10.1186/1745-6150-3-16.
    • (2008) Biol Direct , vol.3 , pp. 16
    • Smith, T.F.1    Lee, J.C.2    Gutell, R.R.3    Hartman, H.4
  • 39
    • 0028330508 scopus 로고
    • Visualization of protein-nucleic acid interactions involved in the in vitro assembly of the Escherichia coli 50 S ribosomal subunit
    • DOI 10.1006/jmbi.1994.1077
    • Tumminia SJ, Hellmann W, Wall JS, Boublik M. 1994. Visualization of protein-nucleic acid interactions involved in the in vitro assembly of the Escherichia coli 50S ribosomal subunit. J Mol Biol 235: 1239-1250. (Pubitemid 24148926)
    • (1994) Journal of Molecular Biology , vol.235 , Issue.4 , pp. 1239-1250
    • Tumminia, S.J.1    Hellmann, W.2    Wall, J.S.3    Boublik, M.4
  • 40
    • 0027532926 scopus 로고
    • Chemical evidence for domain assembly of the Escherichia coli 30S ribosome
    • Weitzmann CJ, Cunningham PR, Nurse K, Ofengand J. 1993. Chemical evidence for domain assembly of the Escherichia coli 30S ribosome. FASEB J 7: 177-180. (Pubitemid 23034031)
    • (1993) FASEB Journal , vol.7 , Issue.1 , pp. 177-180
    • Weitzmann, C.J.1    Cunningham, P.R.2    Nurse, K.3    Ofengand, J.4
  • 41
  • 44
    • 0034903851 scopus 로고    scopus 로고
    • Translation: In retrospect and prospect
    • DOI 10.1017/S1355838201010615
    • Woese CR. 2001. Translation: In retrospect and prospect. RNA 7: 1055-1067. (Pubitemid 32726905)
    • (2001) RNA , vol.7 , Issue.8 , pp. 1055-1067
    • Woese, C.R.1
  • 45
    • 0018936473 scopus 로고
    • Secondary structure model for bacterial 16S ribosomal RNA: Phylogenetic, enzymatic and chemical evidence
    • Woese CR, Magrum LJ, Gupta R, Siegel RB, Stahl DA, Kop J, Crawford N, Brosius J, Gutell R, Hogan JJ, et al. 1980. Secondary structure model for bacterial 16S ribosomal RNA: Phylogenetic, enzymatic and chemical evidence. Nucleic Acids Res 8: 2275-2293. (Pubitemid 10025762)
    • (1980) Nucleic Acids Research , vol.8 , Issue.10 , pp. 2275-2293
    • Woese, C.R.1    Magrum, L.J.2    Gupta, R.3
  • 46
    • 34347347191 scopus 로고    scopus 로고
    • On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
    • doi: 10.1186/1745-6150-2-14
    • Wolf YI, Koonin EV. 2007. On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biol Direct 2: 14. doi: 10.1186/1745-6150-2-14.
    • (2007) Biol Direct , vol.2 , pp. 14
    • Wolf, Y.I.1    Koonin, E.V.2


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