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How Changes in Anti-SD Sequences Would Affect SD Sequences in Escherichia coli and Bacillus subtilis. G3-GENES GENOMES GENETICS 2017; 7:1607-1615. [PMID: 28364038 PMCID: PMC5427494 DOI: 10.1534/g3.117.039305] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The 3' end of the small ribosomal RNAs (ssu rRNA) in bacteria is directly involved in the selection and binding of mRNA transcripts during translation initiation via well-documented interactions between a Shine-Dalgarno (SD) sequence located upstream of the initiation codon and an anti-SD (aSD) sequence at the 3' end of the ssu rRNA. Consequently, the 3' end of ssu rRNA (3'TAIL) is strongly conserved among bacterial species because a change in the region may impact the translation of many protein-coding genes. Escherichia coli and Bacillus subtilis differ in their 3' ends of ssu rRNA, being GAUCACCUCCUUA3' in E. coli and GAUCACCUCCUUUCU3' or GAUCACCUCCUUUCUA3' in B. subtilis Such differences in 3'TAIL lead to species-specific SDs (designated SDEc for E. coli and SDBs for B. subtilis) that can form strong and well-positioned SD/aSD pairing in one species but not in the other. Selection mediated by the species-specific 3'TAIL is expected to favor SDBs against SDEc in B. subtilis, but favor SDEc against SDBs in E. coli Among well-positioned SDs, SDEc is used more in E. coli than in B. subtilis, and SDBs more in B. subtilis than in E. coli Highly expressed genes and genes of high translation efficiency tend to have longer SDs than lowly expressed genes and genes with low translation efficiency in both species, but more so in B. subtilis than in E. coli Both species overuse SDs matching the bolded part of the 3'TAIL shown above. The 3'TAIL difference contributes to the host specificity of phages.
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2
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Mueller F, Brimacombe R. A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. I. Fitting the RNA to a 3D electron microscopic map at 20 A. J Mol Biol 1997; 271:524-44. [PMID: 9281424 DOI: 10.1006/jmbi.1997.1210] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recently published models of the Escherichia coli 70 S ribosome at 20 A resolution, obtained by cryo-electron microscopy (cryo-EM) combined with computerized image processing techniques, exhibit two features that are directly relevant to the in situ three-dimensional folding of the rRNA molecules. First, at this level of resolution many fine structural details are visible, a number of them having dimensions comparable to those of nucleic acid helices. Second, in reconstructions of ribosomes in the pre- and post-translocational states, density can be seen that corresponds directly to the A and P site tRNAs, and to the P and E site tRNAs, respectively, thus enabling the decoding region on the 30 S subunit to be located rather precisely. Accordingly, we have refined our previous model for the 16 S rRNA, based on biochemical evidence, by fitting it to the cryo-EM contour of ribosomes carrying A and P site tRNAs. For this purpose, the most immediately relevant evidence consists of new site-directed cross-linking data in the decoding region, which define sets of contacts between the 16 S rRNA and mRNA, or between 16 S rRNA and tRNA at the A, P and E sites; these contact sites can be correlated directly with the tRNA positions in the EM structure. The model is extended to other parts of the 16 S molecule by fitting individual elements of the well-established secondary structure of the 16 S rRNA into the appropriate fine structural elements of the EM contour, at the same time taking into account other data used in the previous model, such as intra-RNA cross-links within the 16 S rRNA itself. The large body of available RNA-protein cross-linking and foot-printing data is also considered in the model, in order to correlate the rRNA folding with the known distribution of the 30 S ribosomal proteins as determined by neutron scattering and immuno-electron microscopy. The great majority of the biochemical data points involve single-stranded regions of the rRNA, and therefore, in contrast to most previous models, the single-stranded regions are included in our structure, with the help of a specially developed modelling programme, ERNA-3D. This allows the various biochemical data sets to be displayed directly, in this and in the accompanying papers, on diagrams of appropriate parts of the rRNA structure within the cryo-EM contour.
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Affiliation(s)
- F Mueller
- AG-Ribosomen, Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, Berlin, 14195, Germany
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3
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Brandt R, Gualerzi CO. Ribosomal localization of the mRNA in the 30S initiation complex as revealed by UV crosslinking. FEBS Lett 1992; 311:199-202. [PMID: 1397315 DOI: 10.1016/0014-5793(92)81101-q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Translation initiation complexes consisting of 30S ribosomal subunits, 32P-labelled mRNA (002 mRNA), fMet-tRNA and the three initiation factors were subjected to UV-crosslinking to determine the protein and rRNA neighbors of the bound mRNA by immunochemical methods and by nucleic acid hybridization techniques. The mRNA was found to be crosslinked to a specific region of the 16S rRNA spanning from nucleotide 418 to 615 and to ribosomal proteins S1 and S21 (the main targets), S3, S10, S12 and S14; a low level of crosslinking was also detected with S2, S7, S13, S18 and S19.
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Affiliation(s)
- R Brandt
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
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4
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Brimacombe R. Structure-function correlations (and discrepancies) in the 16S ribosomal RNA from Escherichia coli. Biochimie 1992; 74:319-26. [PMID: 1379076 DOI: 10.1016/0300-9084(92)90109-r] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The published model for the three-dimensional arrangement of E coli 16S RNA is re-examined in the light of new experimental information, in particular cross-linking data with functional ligands and cross-links between the 16S and 23S RNA molecules. A growing body of evidence suggests that helix 18 (residues 500-545), helix 34 (residues 1046-1067/1189-1211) and helix 44 (residues 1409-1491) are incorrectly located in the model. It now appears that the functional sites in helices 18 and 34 may be close to the decoding site of the 30S subunit, rather than being on the opposite side of the 'head' of the subunit, as hitherto supposed. Helix 44 is now clearly located at the interface between the 30S and 50S subunits. Furthermore, almost all of the modified bases in both 16S and 23S RNA appear to form a tight cluster near to the upper end of this helix, surrounding the decoding site.
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Affiliation(s)
- R Brimacombe
- Max-Planck-Institut für Molekulare Genetik, Abteilung Wittmann, Berlin, Germany
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5
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McWilliams RA, Glitz DG. Localization of a segment of 16S RNA on the surface of the small ribosomal subunit by immune electron microscopy of complementary oligodeoxynucleotides. Biochimie 1991; 73:911-8. [PMID: 1720670 DOI: 10.1016/0300-9084(91)90132-k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Oligonucleotides that complement Escherichia coli 16S ribosomal RNA residues 685-696 and 694-705 have been synthesized so as to incorporate antibody-recognizable markers: a 3'-terminal residue of N6-delta 2-isopentenyladenosine, a 5'-dinitrophenyl group, or both. Each oligonucleotide is able to bind RNA within the small ribosomal subunit, whether free or in 70S ribosomes. Immune electron microscopy places probes at nucleotides 685, 694 and 705 within a single area, at the tip of the subunit platform, very near the position of the 3'-end of the 16S RNA.
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Affiliation(s)
- R A McWilliams
- Department of Biological Chemistry Institute, UCLA School of Medicine 90024-1737
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6
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Kössel H, Hoch B, Zeltz P. Alternative base pairing between 5'- and 3'-terminal sequences of small subunit RNA may provide the basis of a conformational switch of the small ribosomal subunit. Nucleic Acids Res 1990; 18:4083-8. [PMID: 2198532 PMCID: PMC331163 DOI: 10.1093/nar/18.14.4083] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The compiled sequences of small subunit ribosomal RNAs have been screened for base complementary between 5'- and 3'-terminal regions. Highly conserved complementary sequences are found which allow formation of a helix between the two ends of 5 or 6 base pairs. This helix is composed of sequences from the loop region of the first 5'-terminal stem and from sequences immediately distal to the last stem (the Me2A-stem) of the 3' terminus and therefore allows a coaxial stacking with either of these two flanking stems. Formation of the 5'/3'-helical arrangement is, however, only possible at the cost of dissolving the 'pseudo-knot' helix between the 5'-terminal region and the internal region of small subunit RNA. It is postulated that the mutually exclusive conformational states are in dynamic equilibrium and that they correlate with distinct functional states of the small ribosomal subunit. The 'pseudo-knot' containing conformation with the 3'-terminal sequences more exposed is likely to represent the initiating state, whereas the 5'/3' terminal paired 'closed' conformation may represent the elongating state in which interaction with fortuitous ribosomal binding sequences of mRNAs is avoided.
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Affiliation(s)
- H Kössel
- Institut für Biologie III, Universität Freiburg, FRG
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7
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Messenger RNA orientation on the ribosome. Placement by electron microscopy of antibody-complementary oligodeoxynucleotide complexes. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68164-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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8
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Nagano K, Harel M, Takezawa M. Prediction of three-dimensional structure of Escherichia coli ribosomal RNA. J Theor Biol 1988; 134:199-256. [PMID: 2468977 DOI: 10.1016/s0022-5193(88)80202-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A model for the tertiary structure of 23S, 16S and 5S ribosomal RNA molecules interacting with three tRNA molecules is presented using the secondary structure models common to E. coli, Z. mays chloroplast, and mammalian mitochondria. This ribosomal RNA model is represented by phosphorus atoms which are separated by 5.9 A in the standard A-form double helix conformation. The accumulated proximity data summarized in Table 1 were used to deduce the most reasonable assembly of helices separated from each other by at least 6.2 A. Straight-line approximation for single strands was adopted to describe the maximum allowed distance between helices. The model of a ribosome binding three tRNA molecules by Nierhaus (1984), the stereochemical model of codon-anticodon interaction by Sundaralingam et al. (1975) and the ribosomal transpeptidation model, forming an alpha-helical nascent polypeptide, by Lim & Spirin (1986), were incorporated in this model. The distribution of chemically modified nucleotides, cross-linked sites, invariant and missing regions in mammalian mitochondrial rRNAs are indicated on the model.
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MESH Headings
- Binding Sites
- Escherichia coli/genetics
- Models, Molecular
- Nucleic Acid Conformation
- Protein Conformation
- RNA, Bacterial/ultrastructure
- RNA, Ribosomal/ultrastructure
- RNA, Ribosomal, 16S/ultrastructure
- RNA, Ribosomal, 23S/ultrastructure
- RNA, Ribosomal, 5S/ultrastructure
- RNA, Transfer, Asp/ultrastructure
- RNA, Transfer, Phe/ultrastructure
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Affiliation(s)
- K Nagano
- Faculty of Pharmaceutical Sciences, University of Tokyo, Japan
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9
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Brimacombe R, Atmadja J, Stiege W, Schüler D. A detailed model of the three-dimensional structure of Escherichia coli 16 S ribosomal RNA in situ in the 30 S subunit. J Mol Biol 1988; 199:115-36. [PMID: 2451022 DOI: 10.1016/0022-2836(88)90383-x] [Citation(s) in RCA: 240] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A large body of intra-RNA and RNA-protein crosslinking data, obtained in this laboratory, was used to fold the phylogenetically and experimentally established secondary structure of Escherichia coli 16 S RNA into a three-dimensional model. All the crosslinks were induced in intact 30 S subunits (or in some cases in growing E. coli cells), and the sites of crosslinking were precisely localized on the RNA by oligonucleotide analysis. The RNA-protein crosslinking data (including 28 sites, and involving 13 of the 21 30S ribosomal were used to relate the RNA structure to the distribution of the proteins as determined by neutron scattering. The three-dimensional model of the 16 S RNA has overall dimensions of 220 A x 140 A x 90 A, in good agreement with electron microscopic estimates for the 30 S subunit. The shape of the model is also recognizably the same as that seen in electron micrographs, and the positions in the model of bases localized on the 30 S subunit by immunoelectron microscopy (the 5' and 3' termini, the m7G and m6(2)A residues, and C-1400) correspond closely to their experimentally observed positions. The distances between the RNA-protein crosslink sites in the model correlate well with the distances between protein centres of mass obtained by neutron scattering, only two out of 66 distances falling outside the expected tolerance limits. These two distances both involve protein S13, a protein noted for its anomalous behaviour. A comparison with other experimental information not specifically used in deriving the model shows that it fits well with published data on RNA-protein binding sites, mutation sites on the RNA causing resistance to antibiotics, tertiary interactions in the RNA, and a potential secondary structural "switch". Of the sites on 16 S RNA that have been found to be accessible to chemical modification in the 30 S subunit, 87% are at obviously exposed positions in the model. In contrast, 70% of the sites corresponding to positions that have ribose 2'-O-methylations in the eukaryotic 18 S RNA from Xenopus laevis are at non-exposed (i.e. internal) positions in the model. All nine of the modified bases in the E. coli 16 S RNA itself show a remarkable distribution, in that they form a "necklace" in one plane around the "throat" of the subunit. Insertions in eukaryotic 18 S RNA, and corresponding deletions in chloroplast or mammalian mitochondrial ribosomal RNA relative to E. coli 16 S RNA represent distinct sub-domains in the structure.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- R Brimacombe
- Max-Planck-Institut für Molekulare Genetik, Abteilung Wittmann, Berlin-Dahlem, Germany
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10
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Ehresmann C, Moine H, Mougel M, Dondon J, Grunberg-Manago M, Ebel JP, Ehresmann B. Cross-linking of initiation factor IF3 to Escherichia coli 30S ribosomal subunit by trans-diamminedichloroplatinum(II): characterization of two cross-linking sites in 16S rRNA; a possible way of functioning for IF3. Nucleic Acids Res 1986; 14:4803-21. [PMID: 2425339 PMCID: PMC311493 DOI: 10.1093/nar/14.12.4803] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The initiation factor IF3 is platinated with trans-diamminedichloroplatinum(II) and cross-linked to Escherichia coli 30S ribosomal subunit. Two cross-linking sites are unambiguously identified on the 16S rRNA: a major one, in the region 819-859 in the central domain, and a minor one, in the region 1506-1529 in the 3'-terminal domain. Specific features of these sequences together with their particular location within the 30S subunit lead us to postulate a role for IF3, that conciliates topographical and functional observations made so far.
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11
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12
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Nagano K, Harel M. Approaches to a three-dimensional model of E. coli ribosome. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1986; 48:67-101. [PMID: 3547502 DOI: 10.1016/0079-6107(86)90001-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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13
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Spitnik-Elson P, Elson D, Avital S, Abramowitz R. Long range RNA-RNA interactions in the 30 S ribosomal subunit of E. coli. Nucleic Acids Res 1985; 13:4719-38. [PMID: 2410855 PMCID: PMC321822 DOI: 10.1093/nar/13.13.4719] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We have attempted to identify long-range interactions in the tertiary structure of RNA in the E. coli 30 S ribosome. Native subunits were cleaved with ribonuclease and separated into nucleoprotein fragments which were deproteinized and fractionated into multi-oligonucleotide complexes under conditions intended to preserve RNA-RNA interactions. The final products were denatured by urea and heat and their constituent oligonucleotides resolved and sequenced. Many complexes contained complementary sequences known to be bound together in the RNA secondary structure, attesting to the validity of the technique. Other co-migrating oligonucleotides, not joined in the secondary structure, contained mutually complementary sequences in locations that allow base-pairing interaction without disrupting pre-existing secondary structure. In seven instances the complementary relationship was found to have been preserved during phylogenetic diversification.
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14
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Expert-Bezançon A, Wollenzien PL. Three-dimensional arrangement of the Escherichia coli 16 S ribosomal RNA. J Mol Biol 1985; 184:53-66. [PMID: 2411936 DOI: 10.1016/0022-2836(85)90043-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A model for the arrangement of the Escherichia coli 16 S ribosomal RNA in the 30 S ribosomal subunit is given. This model is based on the 16 S ribosomal RNA secondary structure, intramolecular RNA crosslinking results, protein-RNA interactions, and the locations of proteins within the 30 S subunit. These considerations allow placement of most of the RNA helices in approximate positions. The overall shape (that of an asymmetric Y) is very reminiscent of the description of the shape of the RNA made by direct determinations and is reasonably correlated to the appearance of the 30 S subunit. The identities of the three major secondary-structure domains of the 16 S ribosomal RNA are, for the most part, preserved. In addition, many close contacts between the 5' and middle RNA domains occur in the body of the particle. The 3'-terminal domain is situated in the central part of the model. This position corresponds to the region between the head and the platform structure in the 30 S subunit. The regions that represent the general locations of the messenger RNA and transfer RNA binding sites can be identified in the model.
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15
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Stöffler-Meilicke M, Epe B, Woolley P, Lotti M, Littlechild J, Stöffler G. Location of protein S4 on the small ribosomal subunit of E. coli and B. stearothermophilus with protein- and hapten-specific antibodies. MOLECULAR & GENERAL GENETICS : MGG 1984; 197:8-18. [PMID: 6083434 DOI: 10.1007/bf00327916] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In spite of considerable effort there is still serious disagreement in the literature about the question of whether epitopes of ribosomal protein S4 are accessible for antibody binding on the intact small ribosomal subunit. We have attempted to resolve this issue using three independent approaches: (i) a re-investigation of the exposure and the location of epitopes of ribosomal protein S4 on the surface of the 30S subunit and 30S core particles of the E. coli ribosome, including rigorous controls of antibody specificity, (ii) a similar investigation of protein S4 from Bacillus stearothermophilus and (iii) the labelling of residue Cys-31 of E. coli S4 with a fluorescein derivative the accessibility of which towards a fluorescein-specific antibody was demonstrated directly by fluorimetry. In each of the three cases the antigen (E. coli S4, B. stearothermophilus S4 or fluorescein) was found to reside on the small lobe.
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16
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Gornicki P, Nurse K, Hellmann W, Boublik M, Ofengand J. High resolution localization of the tRNA anticodon interaction site on the Escherichia coli 30 S ribosomal subunit. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(18)90990-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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17
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Meier N, Wagner R. Binding of tRNA alters the chemical accessibility of nucleotides within the large ribosomal RNAs of E. coli ribosomes. Nucleic Acids Res 1984; 12:1473-87. [PMID: 6366737 PMCID: PMC318590 DOI: 10.1093/nar/12.3.1473] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Functionally active 70S ribosomes were chemically modified with dimethylsulfate (DMS) in the presence and absence of bound tRNA. The ribosomal 16S RNA and 23S RNA were extracted, separated and labeled radioactively at their 3'-ends. DMS modification sites within the last 200 nucleotides from the 3'-ends were investigated on sequencing gels, after borohydride reduction and aniline catalyzed strand scission of the isolated RNA's. tRNA binding caused enhanced reactivity at 9 nucleotide positions while three sites showed decreased reactivity in the 16S RNA. The effects of bound tRNA on the modification of 23S RNA were limited. Only one enhancement was observed in the presence of bound tRNA. mRNA binding alone showed two more sites with enhanced reactivity, however. The results are consistent with the view that the sequence 1400-1500 of the 16S RNA plays an important functional role in the translating ribosome and possibly constitutes part of the tRNA binding site.
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18
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Lin FL, Boublik M, Ofengand J. Immunoelectron microscopic localization of the S19 site on the 30 S ribosomal subunit which is crosslinked to A site bound transfer RNA. J Mol Biol 1984; 172:41-55. [PMID: 6198524 DOI: 10.1016/0022-2836(84)90413-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Phe-tRNA of Escherichia coli, specifically derivatized at the S4U8 position with the 9 A long p-azidophenacyl photoaffinity probe, was crosslinked exclusively to protein S19 of the 30 S ribosomal subunit when the transfer RNA occupied the ribosomal A site (Lin et al., 1983). Two antigenic sites for S19 are known, on opposite sides of the head of the subunit. In this work, discrimination between these two sites was accomplished by affinity immunoelectron microscopy. A dinitrophenyl group was placed on the acp3U47 residue of the same tRNA molecules bearing the photoprobe on S4U8. Addition of this group affected neither aminoacylation, A site binding, nor crosslinking. It also made possible specific affinity purification of crosslinked tRNA-30 S complexes from unreactive 30 S. Reaction of the 2,4-dinitrophenyl-labeled tRNA-30 S complex with antibody was followed by immunoelectron microscopy to reveal the sites of attachment. All of the bound antibody was associated with the ribosome region corresponding to only one of the two known antigenic sites for S19, namely the one closer to the large side projection of the 30 S subunit. A site within this region must be within 10 A of the S4U8 residue of tRNA when it is bound in the ribosomal A site.
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19
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20
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Grant PG, Olson HM, Glitz DG, Cooperman BS. Puromycin binding to the small subunit of Escherichia coli ribosomes. Localization of the antibiotic in subunits reconstituted with puromycin-modified components. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44418-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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21
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Brimacombe R, Maly P, Zwieb C. The structure of ribosomal RNA and its organization relative to ribosomal protein. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1983; 28:1-48. [PMID: 6348873 DOI: 10.1016/s0079-6603(08)60081-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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22
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Epe B, Woolley P, Steinhäuser KG, Littlechild J. Distance measurement by energy transfer: the 3' end of 16-S RNA and proteins S4 and S17 of the ribosome of Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 129:211-9. [PMID: 6186486 DOI: 10.1111/j.1432-1033.1982.tb07042.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Escherichia coli ribosomal proteins S4 and S17 were specifically labelled at their thiol groups with the acetylaminoethyl-dansyl and/or bimane fluorophores. Each formed a complex with 16-S RNA and, when the other 30-S ribosomal proteins were added, a complete 30-S subunit with at least partial activity. If the 3' end of the RNA was also labelled (with fluorescein) then the distance between the two fluorophores could be measured by Förster-type energy transfer. The result for S4 was 6.0 nm (60 A) in the ribonucleoprotein complex and 5.6 nm (56 A) in the 30-S subunit, and for S17 6.3 nm (63 A) in the complex and 6.2 nm (62 A) in the subunit. There is no evidence for a major change in the relative disposition of the 3' and 5' ends of the 16-S RNA during formation of the 30-S subunit. Sources of error are discussed, including the question of multiple labelling. In order to measure more accurately the extent of energy transfer a procedure based upon enzymic digestion was developed and is detailed in this paper.
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23
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Stöffler G, Tate WP, Caskey CT. Ribosomal proteins cross-linked to peptide chain termination release factor 2. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34706-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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