메뉴 건너뛰기




Volumn 382, Issue 4, 2001, Pages 661-668

Chemical accessibility of 18S rRNA in native ribosomal complexes: Interaction sites of mRNA, tRNA and translation factors

Author keywords

Eukaryotes; Footprinting; RRNA structure

Indexed keywords

LIGAND; MESSENGER RNA; NUCLEIC ACID BASE; NUCLEOTIDE; RNA 18S; TRANSFER RNA;

EID: 17344376222     PISSN: 14316730     EISSN: None     Source Type: Journal    
DOI: 10.1515/BC.2001.078     Document Type: Article
Times cited : (6)

References (43)
  • 1
    • 0024376144 scopus 로고
    • Probing the phosphates of the Escherichia coll ribosomal 16S RNA in its naked form, in the 30S subunit, and in the 70S ribosome
    • Baudin, F., Mougel, M., Romby, P., Eyermann, F., Ebel, J.P., Ehresmann, B., and Ehresmann, C. (1989). Probing the phosphates of the Escherichia coll ribosomal 16S RNA in its naked form, in the 30S subunit, and in the 70S ribosome. Biochemistry 28, 5847-5855.
    • (1989) Biochemistry , vol.28 , pp. 5847-5855
    • Baudin, F.1    Mougel, M.2    Romby, P.3    Eyermann, F.4    Ebel, J.P.5    Ehresmann, B.6    Ehresmann, C.7
  • 2
    • 0026043416 scopus 로고
    • Eukaryotic initiation factors elF-2 and elF-3: Interactions, structure and localization in ribosomal initiation complexes
    • Bommer, U.A., Lutsch, G., Stahl, J., and Bielka, H. (1991). Eukaryotic initiation factors elF-2 and elF-3: interactions, structure and localization in ribosomal initiation complexes. Biochimie 73, 1007-1019.
    • (1991) Biochimie , vol.73 , pp. 1007-1019
    • Bommer, U.A.1    Lutsch, G.2    Stahl, J.3    Bielka, H.4
  • 3
    • 0015507328 scopus 로고
    • A procedure for the isolation of mammalian messenger ribonucleic acid
    • Brawerman, G., Mendecki, J., and Lee, S.Y. (1972). A procedure for the isolation of mammalian messenger ribonucleic acid. Biochemistry 11, 637-641.
    • (1972) Biochemistry , vol.11 , pp. 637-641
    • Brawerman, G.1    Mendecki, J.2    Lee, S.Y.3
  • 4
    • 0028283123 scopus 로고
    • Specialized ribosomes allow for the study of mutations in functionally important regions in 16S rRNA, without affecting cell growth
    • Brink, M.F., Nels, R.N.M., Verbeet, M.P., and de Boer, H.A. (1994). Specialized ribosomes allow for the study of mutations in functionally important regions in 16S rRNA, without affecting cell growth. J. Mol. Biol. 237, 368-377.
    • (1994) J. Mol. Biol. , vol.237 , pp. 368-377
    • Brink, M.F.1    Nels, R.N.M.2    Verbeet, M.P.3    De Boer, H.A.4
  • 5
    • 0006572034 scopus 로고
    • Purification of eukaryotic messenger RNA
    • B.D. Hames and S.J. Higgins, eds. (Oxford, UK: IRL Press)
    • Clemens, M.J. (1984). Purification of eukaryotic messenger RNA. In: Transcription and Translation - A Practical Approach, B.D. Hames and S.J. Higgins, eds. (Oxford, UK: IRL Press), pp. 211-230.
    • (1984) Transcription and Translation - A Practical Approach , pp. 211-230
    • Clemens, M.J.1
  • 6
    • 0026681280 scopus 로고
    • Three widely separated positions in the 16S RNA lie in or close to the ribosomal decoding region; a site-directed cross-linking study with mRNA analogues
    • Dontsova, O., Dokudovskaya, S., Kopylov, A., Bogdanov, A., Rinke-Appel, A., Jünke, N., and Brimacombe, R. (1992). Three widely separated positions in the 16S RNA lie in or close to the ribosomal decoding region; a site-directed cross-linking study with mRNA analogues. EMBO J. 11, 3105-3116.
    • (1992) EMBO J. , vol.11 , pp. 3105-3116
    • Dontsova, O.1    Dokudovskaya, S.2    Kopylov, A.3    Bogdanov, A.4    Rinke-Appel, A.5    Jünke, N.6    Brimacombe, R.7
  • 7
    • 0024564403 scopus 로고
    • Use of lead (II) to probe the structure of large RNA's. Conformation of the 3′ terminal domain of E. coli 16S rRNA and its involvement in building the tRNA binding sites
    • Gornicki, P., Baudin, F., Romby, P., Wiewiorowski, M., Kryzosiak, W., Ebel, J.P., Ehresmann, C., and Ehresmann, B. (1989). Use of lead (II) to probe the structure of large RNA's. Conformation of the 3′ terminal domain of E. coli 16S rRNA and its involvement in building the tRNA binding sites. J. Biomol. Struct. Dyn. 6, 971-984.
    • (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 971-984
    • Gornicki, P.1    Baudin, F.2    Romby, P.3    Wiewiorowski, M.4    Kryzosiak, W.5    Ebel, J.P.6    Ehresmann, C.7    Ehresmann, B.8
  • 9
    • 0028221204 scopus 로고
    • mRNA binding track in the human 80S ribosome for mRNA analogues randomly substituted with 4-thiouridine residues
    • Graifer, D.M., Juzumiene, D.I., Karpova, G.G., and Wollenzien, P. (1994a). mRNA binding track in the human 80S ribosome for mRNA analogues randomly substituted with 4-thiouridine residues. Biochemistry 33, 6201-6206.
    • (1994) Biochemistry , vol.33 , pp. 6201-6206
    • Graifer, D.M.1    Juzumiene, D.I.2    Karpova, G.G.3    Wollenzien, P.4
  • 10
    • 0028210545 scopus 로고
    • Cross-linking of mRNA analogues containing 4-thiouridine residues on the 3′- or 5′-side of the coding triplet to the mRNA binding center of the human ribosome
    • Graifer, D.M., Juzumiene, D.I., Wollenzien, P., and Karpova, G.G. (1994b). Cross-linking of mRNA analogues containing 4-thiouridine residues on the 3′- or 5′-side of the coding triplet to the mRNA binding center of the human ribosome. Biochemistry 33, 3878-3884.
    • (1994) Biochemistry , vol.33 , pp. 3878-3884
    • Graifer, D.M.1    Juzumiene, D.I.2    Wollenzien, P.3    Karpova, G.G.4
  • 11
    • 0030970289 scopus 로고    scopus 로고
    • Ribosomes and translation
    • Green, R., and Noller, H.F. (1997). Ribosomes and translation. Annu. Rev. Biochem. 66, 679-716.
    • (1997) Annu. Rev. Biochem. , vol.66 , pp. 679-716
    • Green, R.1    Noller, H.F.2
  • 12
    • 0028071557 scopus 로고
    • Collection of small subunit (16S- and 16S-like) ribosomal RNA structures
    • Gutell, R.R. (1994). Collection of small subunit (16S- and 16S-like) ribosomal RNA structures. Nucleic Acids Res. 22, 3502-3507.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 3502-3507
    • Gutell, R.R.1
  • 13
    • 0026800847 scopus 로고
    • Ribosomebound eukaryotic elongation factor 2 protects 5s rRNA from modification
    • Holmberg, L., Melander, Y., and Nygård, O. (1992). Ribosomebound eukaryotic elongation factor 2 protects 5S rRNA from modification. J. Biol. Chem. 267, 21906-21910.
    • (1992) J. Biol. Chem. , vol.267 , pp. 21906-21910
    • Holmberg, L.1    Melander, Y.2    Nygård, O.3
  • 14
    • 0028102043 scopus 로고
    • Probing the conformational changes in 5.8S, 18S and 28S rRNA upon association of derived subunits into complete 80S ribosomes
    • Holmberg, L., Melander, Y., and Nygård, O. (1994a). Probing the conformational changes in 5.8S, 18S and 28S rRNA upon association of derived subunits into complete 80S ribosomes. Nucleic Acids Res. 22, 2776-2783.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 2776-2783
    • Holmberg, L.1    Melander, Y.2    Nygård, O.3
  • 15
    • 0028308319 scopus 로고
    • Probing the structure of mouse Ehrlich ascites cell 5.8S, 18S and 28S ribosomal RNA in situ
    • Holmberg, L., Melander, Y., and Nygård, O. (1994b). Probing the structure of mouse Ehrlich ascites cell 5.8S, 18S and 28S ribosomal RNA in situ. Nucleic Acids Res. 22, 1374-1382.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 1374-1382
    • Holmberg, L.1    Melander, Y.2    Nygård, O.3
  • 16
    • 0028609495 scopus 로고
    • Interaction sites of ribosome bound eukaryotic elongation factor 2 in 18S and 28S rRNA
    • Holmberg, L., and Nygård, O. (1994). Interaction sites of ribosome bound eukaryotic elongation factor 2 in 18S and 28S rRNA. Biochemistry 33, 15159-15167.
    • (1994) Biochemistry , vol.33 , pp. 15159-15167
    • Holmberg, L.1    Nygård, O.2
  • 17
    • 0030742891 scopus 로고    scopus 로고
    • Mapping of nuclease-sensitive sites in native reticulocyte ribosomes - An analysis of the accessibility of ribosomal RNA to enzymatic cleavage
    • Holmberg, L., and Nygård, O. (1997). Mapping of nuclease-sensitive sites in native reticulocyte ribosomes - an analysis of the accessibility of ribosomal RNA to enzymatic cleavage. Eur. J. Biochem. 247, 160-168.
    • (1997) Eur. J. Biochem. , vol.247 , pp. 160-168
    • Holmberg, L.1    Nygård, O.2
  • 18
    • 0028109924 scopus 로고
    • Arrangement of mRNA at the decoding site of human ribosomes: 18S rRNA nucleotides and ribosomal proteins cross-linked to oligouridulate derivatives with alkylating groups at either the 3′ or the 5′ termini
    • Malygin, A.A., Graifer, D.M., Bulygin, K.N., Zenkova, M.A., Yamkovoy, V.I., Stahl, J., and Karpova, G.G. (1994). Arrangement of mRNA at the decoding site of human ribosomes: 18S rRNA nucleotides and ribosomal proteins cross-linked to oligouridulate derivatives with alkylating groups at either the 3′ or the 5′ termini. Eur. J. Biochem. 226, 715-723.
    • (1994) Eur. J. Biochem. , vol.226 , pp. 715-723
    • Malygin, A.A.1    Graifer, D.M.2    Bulygin, K.N.3    Zenkova, M.A.4    Yamkovoy, V.I.5    Stahl, J.6    Karpova, G.G.7
  • 19
    • 0032571859 scopus 로고    scopus 로고
    • Nucleotides of 18S rRNA surrounding mRNA at the decoding site of translating human ribosome as revealed from the crosslinking data
    • Matassova, N.B., Venjaminova, A.G., and Karpova, G.G. (1998). Nucleotides of 18S rRNA surrounding mRNA at the decoding site of translating human ribosome as revealed from the crosslinking data. Biochim. Biophys. Acta 1397, 231-239.
    • (1998) Biochim. Biophys. Acta , vol.1397 , pp. 231-239
    • Matassova, N.B.1    Venjaminova, A.G.2    Karpova, G.G.3
  • 20
    • 0031031672 scopus 로고    scopus 로고
    • Structure of 18s ribosomal RNA in native 40S ribosomal subunits
    • Melander, Y., Holmberg, L., and Nygård, O. (1997). Structure of 18S ribosomal RNA in native 40S ribosomal subunits. J. Biol. Chem. 272, 3254-3258.
    • (1997) J. Biol. Chem. , vol.272 , pp. 3254-3258
    • Melander, Y.1    Holmberg, L.2    Nygård, O.3
  • 21
    • 0026718508 scopus 로고
    • Mechanism and regulation of eukaryotic protein synthesis
    • Merrick, W.C. (1992). Mechanism and regulation of eukaryotic protein synthesis. Microbiol. Rev. 56, 291-315.
    • (1992) Microbiol. Rev. , vol.56 , pp. 291-315
    • Merrick, W.C.1
  • 22
    • 0022916242 scopus 로고
    • Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes
    • Moazed, D., and Noller, H.F. (1986). Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell 47, 985-994.
    • (1986) Cell , vol.47 , pp. 985-994
    • Moazed, D.1    Noller, H.F.2
  • 23
    • 0025070318 scopus 로고
    • Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16S rRNA
    • Moazed, D., and Noller, H.F. (1990). Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16S rRNA. J. Mol. Biol. 217, 135-145.
    • (1990) J. Mol. Biol. , vol.217 , pp. 135-145
    • Moazed, D.1    Noller, H.F.2
  • 24
    • 0021832444 scopus 로고
    • Preparation and properties of an improved cell-free protein synthesis system from mammalian liver
    • Morley, S.J., and Jackson, R.J. (1985). Preparation and properties of an improved cell-free protein synthesis system from mammalian liver. Biochim. Biophys. Acta 825, 45-56.
    • (1985) Biochim. Biophys. Acta , vol.825 , pp. 45-56
    • Morley, S.J.1    Jackson, R.J.2
  • 25
    • 0018645825 scopus 로고
    • Early effects of dimethylnitrosamine on protein chain initiation and postmicrosomal polyadenylic acid-containing RNA content in mouse liver
    • Nygård, O., and Hultin, T. (1979). Early effects of dimethylnitrosamine on protein chain initiation and postmicrosomal polyadenylic acid-containing RNA content in mouse liver. Cancer Res. 39, 3349-3352.
    • (1979) Cancer Res. , vol.39 , pp. 3349-3352
    • Nygård, O.1    Hultin, T.2
  • 26
    • 0019448716 scopus 로고
    • Non-involvment of nucleolytic activities in the early effect of dimethylnitrosamine on the content of free mRNA in mouse liver
    • Nygård, O., and Hultin, T. (1981). Non-involvment of nucleolytic activities in the early effect of dimethylnitrosamine on the content of free mRNA in mouse liver. Biochem. J. 194, 475-480.
    • (1981) Biochem. J. , vol.194 , pp. 475-480
    • Nygård, O.1    Hultin, T.2
  • 27
    • 0020337793 scopus 로고
    • Identification by RNA-protein cross-linking of ribosomal proteins located at the interface between the small and the large subunits of mammalian ribosomes
    • Nygård, O., and Nika, H. (1982). Identification by RNA-protein cross-linking of ribosomal proteins located at the interface between the small and the large subunits of mammalian ribosomes. EMBO J. 1, 357-362.
    • (1982) EMBO J. , vol.1 , pp. 357-362
    • Nygård, O.1    Nika, H.2
  • 28
    • 0021705333 scopus 로고
    • Quantification of the different ribosomal phases during the translational elongation cycle in rabbit reticulocyte lysates
    • Nygård, O., and Nilsson, L. (1984). Quantification of the different ribosomal phases during the translational elongation cycle in rabbit reticulocyte lysates. Eur. J. Biochem. 145, 345-350.
    • (1984) Eur. J. Biochem. , vol.145 , pp. 345-350
    • Nygård, O.1    Nilsson, L.2
  • 29
    • 0023154926 scopus 로고
    • The ribosomal binding site for eukaryotic elongation factor EF-2 contains 5S ribosomal RNA
    • Nygård, O., and Nilsson, L. (1987). The ribosomal binding site for eukaryotic elongation factor EF-2 contains 5S ribosomal RNA. Biochim. Biophys. Acta 908, 46-53.
    • (1987) Biochim. Biophys. Acta , vol.908 , pp. 46-53
    • Nygård, O.1    Nilsson, L.2
  • 30
    • 0025291205 scopus 로고
    • Translational dynamics: Interactions between the translational factors, tRNA and ribosomes during eukaryotic protein synthesis
    • Nygård, O., and Nilsson, L. (1990). Translational dynamics: interactions between the translational factors, tRNA and ribosomes during eukaryotic protein synthesis. Eur. J. Biochem. 191, 1-17.
    • (1990) Eur. J. Biochem. , vol.191 , pp. 1-17
    • Nygård, O.1    Nilsson, L.2
  • 31
    • 0020490386 scopus 로고
    • Specific interaction of one subunit of eukaryotic initiation factor elF-3 with 18S ribosomal RNA within the binary complex, elF-3.small subunit, as shown by cross-linking experiments
    • Nygård, O., and Westermann, P. (1982). Specific interaction of one subunit of eukaryotic initiation factor elF-3 with 18S ribosomal RNA within the binary complex, elF-3.small subunit, as shown by cross-linking experiments. Nucleic Acids Res. 10, 1327-1334.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 1327-1334
    • Nygård, O.1    Westermann, P.2
  • 32
    • 0020364218 scopus 로고
    • Covalent crosslinking tRNAVal to 16S RNA at the ribosomal P-site: Identification of crosslinked residues
    • USA
    • Prince, J.B., Taylor, B.H., Thurlow, D.L., Ofengand, J., and Zimmermann, R.A. (1982). Covalent crosslinking tRNAVal to 16S RNA at the ribosomal P-site: identification of crosslinked residues. Proc. Natl. Acad. Sci. USA 79, 5450-5454.
    • (1982) Proc. Natl. Acad. Sci. , vol.79 , pp. 5450-5454
    • Prince, J.B.1    Taylor, B.H.2    Thurlow, D.L.3    Ofengand, J.4    Zimmermann, R.A.5
  • 33
    • 0025740497 scopus 로고
    • The path of mRNA through the Escherichia coli ribosome, site-directed crosslinking of mRNA analogoues carrying a photo-reactive label at various points 3′ to the decoding site
    • Rinke-Appel, J., Jünke, N., Stade, K., and Brimacombe, R. (1991). The path of mRNA through the Escherichia coli ribosome, site-directed crosslinking of mRNA analogoues carrying a photo-reactive label at various points 3′ to the decoding site. EMBO J. 10, 2195-2202.
    • (1991) EMBO J. , vol.10 , pp. 2195-2202
    • Rinke-Appel, J.1    Jünke, N.2    Stade, K.3    Brimacombe, R.4
  • 34
    • 0027214113 scopus 로고
    • Site-directed crosslinking of mRNA analogues to 16S ribosomal RNA; a complete scan of cross-links from all positions between +1 and +16 on the mRNA, downstream from the decoding site
    • Rinke-Appel, J., Jünke, N., Brimacombe, R., Dokudovskaya, S., Dontsova, O., and Bogdanov, A. (1993). Site-directed crosslinking of mRNA analogues to 16S ribosomal RNA; a complete scan of cross-links from all positions between +1 and +16 on the mRNA, downstream from the decoding site. Nucleic Acids Res. 21, 2853-2859.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 2853-2859
    • Rinke-Appel, J.1    Jünke, N.2    Brimacombe, R.3    Dokudovskaya, S.4    Dontsova, O.5    Bogdanov, A.6
  • 35
    • 0029085929 scopus 로고
    • A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome
    • Samaha, R.R., Green, R., and Noller, H.F. (1995). A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome. Nature 377, 309-314.
    • (1995) Nature , vol.377 , pp. 309-314
    • Samaha, R.R.1    Green, R.2    Noller, H.F.3
  • 36
    • 0019888811 scopus 로고
    • Affinity labeling of proteins at the mRNA binding site of rat liver ribosomes by an analogue of octauridylate containing an alkylating group attacked to the 3′-end
    • Stahl, J., and Kobets, N.D. (1981). Affinity labeling of proteins at the mRNA binding site of rat liver ribosomes by an analogue of octauridylate containing an alkylating group attacked to the 3′-end. FEBS Lett. 123, 269-272.
    • (1981) FEBS Lett. , vol.123 , pp. 269-272
    • Stahl, J.1    Kobets, N.D.2
  • 37
    • 0018791726 scopus 로고
    • Photoaffinity labeling of rat liver ribosomes by phenylalanine-tRNA N-acylated by 2-nitro-4-azidobenzoic acid
    • Stahl, J., Böhm, H., Pozdnjakov, V.A., and Girshovich, A.S. (1979). Photoaffinity labeling of rat liver ribosomes by phenylalanine-tRNA N-acylated by 2-nitro-4-azidobenzoic acid. FEBS Lett. 102, 273-276.
    • (1979) FEBS Lett. , vol.102 , pp. 273-276
    • Stahl, J.1    Böhm, H.2    Pozdnjakov, V.A.3    Girshovich, A.S.4
  • 38
    • 0021760787 scopus 로고
    • Crosslinking of mRNA to initiation factor elF-3, 24 kDa cap binding protein and ribosomal proteins S1, S3/3a, S6 and S11 within the 48S pre-initiation complex
    • Westermann, P., and Nygård, O. (1984). Crosslinking of mRNA to initiation factor elF-3, 24 kDa cap binding protein and ribosomal proteins S1, S3/3a, S6 and S11 within the 48S pre-initiation complex. Nucleic Acids Res. 12, 8887-8897.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 8887-8897
    • Westermann, P.1    Nygård, O.2
  • 39
    • 84886618482 scopus 로고
    • Crosslinking of initiation factor elF-2 to proteins of the small subunit of rat liver ribosomes
    • Westermann, P., Heumann, W., Bommer, U.A., Bielka, H., Nygård, O., and Hultin, T. (1979). Crosslinking of initiation factor elF-2 to proteins of the small subunit of rat liver ribosomes. FEBS Lett. 97, 101-104.
    • (1979) FEBS Lett. , vol.97 , pp. 101-104
    • Westermann, P.1    Heumann, W.2    Bommer, U.A.3    Bielka, H.4    Nygård, O.5    Hultin, T.6
  • 40
    • 0019332795 scopus 로고
    • The alpha and gamma subunits of initiation factor elF-2 can be crosslinked to 18S ribosomal RNA within the quaternary initiation complex, elF-2-Met-tRNAf-GDPCP-small ribosomal subunit
    • Westermann, P., Nygård, O., and Bielka, H. (1980). The alpha and gamma subunits of initiation factor elF-2 can be crosslinked to 18S ribosomal RNA within the quaternary initiation complex, elF-2-Met-tRNAf-GDPCP-small ribosomal subunit. Nucleic Acids Res. 8, 3065-3072.
    • (1980) Nucleic Acids Res. , vol.8 , pp. 3065-3072
    • Westermann, P.1    Nygård, O.2    Bielka, H.3
  • 43
    • 0024291322 scopus 로고
    • Phe containing 8-azidoadenosine at positions 73 and 76 to the Escherichia coli ribosome
    • Phe containing 8-azidoadenosine at positions 73 and 76 to the Escherichia coli ribosome. Biochemistry 27, 8114-8121.
    • (1988) Biochemistry , vol.27 , pp. 8114-8121
    • Wower, J.1    Hixson, S.S.2    Zimmermann, R.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.