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Abstract
Ribosomes are biological nanomachine that synthesise all proteins within a cell. It took decades to reveal the architecture of this essential cellular component. To understand the structure -function relationship of this nanomachine needed the utilisisation of different biochemical, biophysical and structural techniques. Structural studies combined with mutagenesis of the different ribosomal complexes comprising various RNAs and proteins enabled us to understand how this machine works inside a cell. Nowadays quite a number of ribosomal structures were published that confirmed biochemical studies on particular steps of protein synthesis by the ribosome . Four major steps were identified: initiation , elongation, termination and recycling. These steps lead us to the important question how the ribosome function can be regulated. Advances in technology for cryo electron microscopy: sample preparations, image recording, developments in algorithms for image analysis and processing significantly helped in revelation of structural details of the ribosome . We now have a library of ribosome structures from prokaryotes to eukaryotes that enable us to understand the complex mechanics of this nanomachine. As this structural library continues to grow, we gradually improve our understanding of this process and how it can be regulated and how the specific ribosomes can be stalled or activated, or completely disabled. This article provides a comprehensive overview of ribosomal structures that represent structural snapshots of the ribosome at its different functional states. Better understanding rises more particular questions that have to be addressed by determination structures of more complexes.Synopsis: Structural biology of the ribosome.
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Affiliation(s)
- Abid Javed
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK
| | - Elena V Orlova
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK.
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Javed A, Christodoulou J, Cabrita LD, Orlova EV. The ribosome and its role in protein folding: looking through a magnifying glass. Acta Crystallogr D Struct Biol 2017; 73:509-521. [PMID: 28580913 PMCID: PMC5458493 DOI: 10.1107/s2059798317007446] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/19/2017] [Indexed: 11/21/2022] Open
Abstract
Protein folding, a process that underpins cellular activity, begins co-translationally on the ribosome. During translation, a newly synthesized polypeptide chain enters the ribosomal exit tunnel and actively interacts with the ribosome elements - the r-proteins and rRNA that line the tunnel - prior to emerging into the cellular milieu. While understanding of the structure and function of the ribosome has advanced significantly, little is known about the process of folding of the emerging nascent chain (NC). Advances in cryo-electron microscopy are enabling visualization of NCs within the exit tunnel, allowing early glimpses of the interplay between the NC and the ribosome. Once it has emerged from the exit tunnel into the cytosol, the NC (still attached to its parent ribosome) can acquire a range of conformations, which can be characterized by NMR spectroscopy. Using experimental restraints within molecular-dynamics simulations, the ensemble of NC structures can be described. In order to delineate the process of co-translational protein folding, a hybrid structural biology approach is foreseeable, potentially offering a complete atomic description of protein folding as it occurs on the ribosome.
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Affiliation(s)
- Abid Javed
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
- Institute of Structural and Molecular Biology, University College London (UCL), Gower Street, London WC1E 6BT, England
| | - John Christodoulou
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
- Institute of Structural and Molecular Biology, University College London (UCL), Gower Street, London WC1E 6BT, England
| | - Lisa D. Cabrita
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
- Institute of Structural and Molecular Biology, University College London (UCL), Gower Street, London WC1E 6BT, England
| | - Elena V. Orlova
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
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3
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Hartmann RK, Vogel DW, Walker RT, Erdmann VA. In vitro incorporation of eubacterial, archaebacterial and eukaryotic 5S rRNAs into large ribosomal subunits of Bacillus stearothermophilus. Nucleic Acids Res 1988; 16:3511-24. [PMID: 2453840 PMCID: PMC336509 DOI: 10.1093/nar/16.8.3511] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bacillus stearothermophilus large ribosomal subunits were reconstituted in the presence of 5S rRNAs from different origins and tested for their biological activities. The results obtained have shown that eubacterial and archaebacterial 5S rRNAs can easily substitute for B. stearothermophilus 5S rRNA in the reconstitution, while eukaryotic 5S rRNAs yield ribosomal subunits with reduced biological activities. From our results we propose an interaction between nucleotides 42-47 of 5S rRNA and nucleotides 2603-2608 of 23S rRNA during the assembly of the 50S ribosomal subunit. Other experiments with eukaryotic 5.8S rRNAs reveal, if at all, a very low incorporation of these RNA species into the reconstituted ribosomes.
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Affiliation(s)
- R K Hartmann
- Institut für Biochemie, Freie Universität Berlin, FRG
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4
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Romaniuk PJ, de Stevenson IL, Ehresmann C, Romby P, Ehresmann B. A comparison of the solution structures and conformational properties of the somatic and oocyte 5S rRNAs of Xenopus laevis. Nucleic Acids Res 1988; 16:2295-312. [PMID: 3357778 PMCID: PMC338217 DOI: 10.1093/nar/16.5.2295] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The secondary and tertiary structures of Xenopus oocyte and somatic 5S rRNAs were investigated using chemical and enzymatic probes. The accessibility of both RNAs towards single-strand specific nucleases (T1, T2, A and S1) and a helix-specific ribonuclease from cobra venom (RNase V1) was determined. The reactivity of nucleobase N7, N3 and N1 positions towards chemical probes was investigated under native (5 mM MgCl2, 100 mM KCl, 20 degrees C) and semi-denaturing (1 mM EDTA, 20 degrees C) conditions. Ethylnitrosourea was used to identify phosphates not reactive towards alkylation under native conditions. The results obtained confirm the presence of the five helical stems predicted by the consensus secondary structure model of 5S rRNA. The chemical reactivity data indicate that loops C and D are involved in a number of tertiary interactions, and loop E folds into an unusual secondary structure. A comparison of the data obtained for the two types of Xenopus 5S rRNA indicates that the conformations of the oocyte and somatic 5S rRNAs are very similar. However, the data obtained with nucleases under native conditions, and chemical probes under semi-denaturing conditions, reveal that helices III and IV in the somatic 5S rRNA are less stable than the same structures in oocyte 5S rRNA. Using chimeric 5S rRNAs, it was possible to demonstrate that the relative resistance of oocyte 5S rRNA to partial denaturation in 4 M urea is conferred by the five oocyte-specific nucleotide substitutions in loop B/helix III. In contrast, the superior stability of oocyte 5S rRNA in the presence of EDTA is related to a single C substitution at position 79.
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Affiliation(s)
- P J Romaniuk
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
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5
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Silberklang M, RajBhandary UL, Lück A, Erdmann VA. Chemical reactivity of E. coli 5S RNA in situ in the 50S ribosomal subunit. Nucleic Acids Res 1983; 11:605-17. [PMID: 6340064 PMCID: PMC325740 DOI: 10.1093/nar/11.3.605] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
E. coli 50S ribosomal subunits were reacted with monoperphthalic acid under conditions in which non-base paired adenines are modified to their 1-N-oxides. 5S RNA was isolated from such chemically reacted subunits and the two modified adenines were identified as A73 and A99. The modified 5S RNA, when used in reconstitution of 50S subunits, yielded particles with reduced biological activity (50%). The results are discussed with respect to a recently proposed three-dimensional structure for 5S RNA, the interaction of the RNA with proteins E-L5, E-L18 and E-L25 and previously proposed interactions of 5S RNA with tRNA, 16S and 23S ribosomal RNAs.
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6
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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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7
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Pieler T, Erdmann VA. Three-dimensional structural model of eubacterial 5S RNA that has functional implications. Proc Natl Acad Sci U S A 1982; 79:4599-603. [PMID: 6181508 PMCID: PMC346722 DOI: 10.1073/pnas.79.15.4599] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli 5S RNA and its specific protein complexes were hydrolyzed with the single-strand-specific nuclease S1. Based on the results, a tertiary structural model for E. coli 5S RNA is proposed in which ribosomal proteins E-L5, E-L18, and E-L25 influence the conformation of the RNA. This may be of significance for ribosomal function. Comparison of the proposed E. coli 5S RNA structure with those of 18 other prokaryotic 5S RNAs led to a generalized eubacterial 5S RNA tertiary structure in which the majority of the conserved nucleotides are in non-base-paired regions and several conserved "looped-out" adenines (in E. coli, adenines -52, -53, -57, -58, and -66) are implied to be important for protein recognition or interaction or both.
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8
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Loughney K, Lund E, Dahlberg JE. tRNA genes are found between 16S and 23S rRNA genes in Bacillus subtilis. Nucleic Acids Res 1982; 10:1607-24. [PMID: 6280153 PMCID: PMC320553 DOI: 10.1093/nar/10.5.1607] [Citation(s) in RCA: 133] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
There are at least nine, and probably ten, ribosomal RNA gene sets in the genome of Bacillus subtilis. Each gene set contains sequences complementary to 16S, 23S and 5S rRNAs. We have determined the nucleotide sequences of two DNA fragments which each contain 165 base pairs of the 16S rRNA gene, 191 base pairs of the 23S rRNA gene, and the spacer region between them. The smaller space region is 164 base pairs in length and the larger one includes an additional 180 base pairs. The extra nucleotides could be transcribed in tRNAIIe and tRNA Ala sequences. Evidence is also presented for the existence of a second spacer region which also contains tRNAIIe and tRNA Ala sequences. No other tRNAs appear to be encoded in the spacer regions between the 16S and 23S rRNA genes. Whereas the nucleotide sequences corresponding to the 16S rRNA, 23S rRNA and the spacer tRNAs are very similar to those of E. coli, the sequences between these structural genes are very different.
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9
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Noller HF, Kop J, Wheaton V, Brosius J, Gutell RR, Kopylov AM, Dohme F, Herr W, Stahl DA, Gupta R, Waese CR. Secondary structure model for 23S ribosomal RNA. Nucleic Acids Res 1981; 9:6167-89. [PMID: 7031608 PMCID: PMC327592 DOI: 10.1093/nar/9.22.6167] [Citation(s) in RCA: 313] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A secondary structure model for 23S ribosomal RNA has been constructed on the basis of comparative sequence data, including the complete sequences from E. coli. Bacillus stearothermophilis, human and mouse mitochondria and several partial sequences. The model has been tested extensively with single strand-specific chemical and enzymatic probes. Long range base-paired interactions organize the molecule into six major structural domains containing over 100 individual helices in all. Regions containing the sites of interaction with several ribosomal proteins and 5S RNA have been located. Segments of the 23S RNA structure corresponding to eucaryotic 5.8S and 25 RNA have been identified, and base paired interactions in the model suggest how they are attached to 28S RNA. Functionally important regions, including possible sites of contact with 30S ribosomal subunits, the peptidyl transferase center and locations of intervening sequences in various organisms are discussed. Models for molecular 'switching' of RNA molecules based on coaxial stacking of helices are presented, including a scheme for tRNA-23S RNA interaction.
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10
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Hinnebusch AG, Klotz LC, Blanken RL, Loeblich AR. An evaluation of the phylogenetic position of the dinoflagellate Crypthecodinium cohnii based on 5S rRNA characterization. J Mol Evol 1981; 17:334-7. [PMID: 7197304 DOI: 10.1007/bf01734355] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Partial nucleotide sequences for the 5S and 5.8S rRNAs from the dinoflagellate Crypthecodinium cohnii have been determined, using a rapid chemical sequencing method, for the purpose of studying dinoflagellate phylogeny. The 5S RNA sequence shows the most homology (75%) with the 5S sequences of higher animals and the least homology (less than 60%) with prokaryotic sequences. In addition, it lacks certain residues which are highly conserved in prokaryotic molecules but are generally missing in eukaryotes. These findings suggest a distant relationship between dinoflagellates and the prokaryotes. Using two different sequence alignments and several different methods for selecting an optimum phylogenetic tree for selecting an optimum phylogenetic tree for a collection of 5S sequences including higher plants and animals, fungi, and bacteria in addition to the C. cohnii sequence, the dinoflagellate lineage was joined to the tree at the point of the plant-animal divergence well above the branching point of the fungi. This result is of interest because it implies that the well-documented absence in dinoflagellates of histones and the typical nucleosomal subunit structure of eukaryotic chromatin is the result of secondary loss, and not an indication of an extremely primitive state, as was previously suggested. Computer simulations of 5S RNA evolution have been carried out in order to demonstrate that the above-mentioned phylogenetic placement is not likely to be the result of random sequence convergence. We have also constructed a phylogeny for 5.8S RNA sequences in which plants, animals, fungi and the dinoflagellates are again represented. While the order of branching on this tree is the same as in the 5S tree for the organisms represented, because it lacks prokaryotes, the 5.8S tree cannot be considered a strong independent confirmation of the 5S result. Moreover, 5.8S RNA appears to have experienced very different rates of evolution in different lineages indicating that it may not be the best indicator of evolutionary relationships. We have also considered the existing biological data regarding dinoflagellate evolution in relation to our molecular phylogenetic evidence.
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11
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Hori H, Sawada M, Osawa S, Murao K, Ishikura H. The nucleotide sequence of 5S rRNA from Mycoplasma capricolum. Nucleic Acids Res 1981; 9:5407-10. [PMID: 7301591 PMCID: PMC327528 DOI: 10.1093/nar/9.20.5407] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The nucleotide sequence of 5S rRNA from Mycoplasma capricolum is UUGGUGGUAUAGCAUAGAGGUCACACCUGUUCCCAUGCCGAACACAGAAGUUAAGCUCUAUUACGGUGAAGAUAUUACU GAUGUGAGAAAAUAGCAAGCUGCCAGUUOH. The length is 107 nucleotides long, and the shortest in all the 5S rRNAs so far known. The sequence is more similar to those of the gram-positive bacteria than those of the gram-negative bacteria.
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12
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Jacq B. Sequence homologies between eukaryotic 5.8S rRNA and the 5' end of prokaryotic 23S rRNa: evidences for a common evolutionary origin. Nucleic Acids Res 1981; 9:2913-32. [PMID: 7024907 PMCID: PMC326902 DOI: 10.1093/nar/9.12.2913] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The question of the evolutionary origin of eukaryotic 5.8S rRNA was re-examined after the recent publication of the E. coli 23S rRNA sequence (26,40). A region of the 23S RNA located at its 5' end was found to be approximately 50% homologous to four different eukaryotic 5.8S rRNAs. A computer comparison analysis indicates that no other region of the E. coli ribosomal transcription unit (greater than 5 000 nucleotides in length) shares a comparable homology with 5.8S rRNA. Homology between the 5' end of e. coli 23S and four different eukaryotic 5.8S rRNAs falls within the same range as that between E. coli 5S RNA from the same four eukaryotic species. All these data strongly suggest that the 5' end of prokaryotic 23S rRNA and eukaryotic 5.8S RNA have a common evolutionary origin. Secondary structure models are proposed for the 5' region of E. coli 23S RNA.
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13
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Mashkova TD, Serenkova TI, Mazo AM, Avdonina TA, Kisselev LL. The primary structure of oocyte and somatic 5S rRNAs from the loach Misgurnus fossilis. Nucleic Acids Res 1981; 9:2141-51. [PMID: 7197777 PMCID: PMC326831 DOI: 10.1093/nar/9.9.2141] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Somatic and oocyte 5S rRNAs from the liver and unfertilized eggs of the loach (Misgurnus fossilis have been sequenced and found to differ in six nucleotides. All the substitutions are confined to the 5'-half of the molecules; 4 of them are pyrimidine-pyrimidine substitutions, and 2 are purine-pyrimidine ones. Considerable differences, both in the position and the character of substitutions, have been established when these 5S rRNAs were compared with somatic and oocyte 5S rRNAs from Xenopus borealis and Xenopus laevis. Among the known primary structures, somatic 5S rRNA of M. fossilis is most similar to trout 5S rRNA.
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14
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Garrett R, Douthwaite S, Noller H. Structure and role of 5S RNA-protein complexes in protein biosynthesis. Trends Biochem Sci 1981. [DOI: 10.1016/0968-0004(81)90051-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Newberry V, Garrett RA. The role of the basic N-terminal region of protein L18 in 5S RNA-23S RNA complex formation. Nucleic Acids Res 1980; 8:4131-42. [PMID: 6159586 PMCID: PMC324224 DOI: 10.1093/nar/8.18.4131] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Of the three proteins, L5, L18 and L25, which bind to 5S RNA, the former two effect the interaction of 5S RNA with 23S RNA. We have used trypsin as a probe to investigate the roles of the proteins in this RNA-RNA assembly, with the following results: (1) In complexes with 5S RNA, the highly basic N-terminal region of L18 is accessible to trypsin. This accessibility is unaffected by L25. However, its presence is essential for stimulating L5 binding. (2) In 5S RNA-protein-23S RNA complexes proteins L5 and L18 are both strongly resistant to proteolysis. (3) No 5S RNA-23S RNA complex formation occurs in the presence of L5 and the C-terminal L18 fragment. Two possible models for the mechanism of RNA-RNA assembly are proposed.
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16
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Brosius J, Dull TJ, Noller HF. Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A 1980; 77:201-4. [PMID: 6153795 PMCID: PMC348236 DOI: 10.1073/pnas.77.1.201] [Citation(s) in RCA: 289] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The complete nucleotide sequence of the 23S RNA gene from the rrnB operon of Escherichia coli has been determined. The sequences of both strands of the entire gene were determined, most of the sequence was independently confirmed by use of alternate restriction fragments, and all restriction cuts overlapped. The DNA region corresponding to mature 23S rRNA contains 2904 nucleotides. Kethoxal-reactive sites protected by 30S subunits are found between positions 2300 and 28000, placing the subunit interface in this region of the molecule. The functional importance of this region is further supported by studies by other investigators, including homology with chloroplast and mitochondrial rRNA.
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17
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Abstract
An immediate precursor of 5S ribosomal RNA (rRNA) from Bacillus subtilis has 21 and 42 nucleotide precursor-specific segments associated with its 5' and 3' termini, respectively. On the basis of its nucleotide sequence, predicted secondary structure and location in the rRNA transcriptional unit, the 3' precursor element apparently functions during the termination of transcription. A portion of the 5' precursor element is shown to facilitate the native folding of the mature domain of the precursor. Precursor 5S rRNA molecules which lack the 5' terminal 8-9 nucleotides of the 5' precursor elements were fabricated. These abbreviated constructs assume a non-native conformation, as revealed by their behavior during polyacrylamide gel electrophoresis. The aberrant conformation is evidently forced upon the abbreviated constructs by the residual 5' precursor sequence, since its removal by the maturation endonuclease RNAase M5 precipitates the reordering of the mature domain into its native conformation. Inspection of the nucleotide sequence of the 5S precursor suggested the nature of the conformational aberration, and gel electrophoresis analyses of limited nuclease digests of end-labeled precursors in the native and aberrant conformations are consistent with the derived model. We conclude taht the 5' terminal six nucleotides in the intact 5S precursor assist in the folding of the mature domain by forming a base-paired duplex with neighboring nucleotides, thereby preventing that adjacent sequence from engendering the abnormal conformation. The involvement of precursor-specific sequences and conformational dynamics in RNA function are discussed.
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18
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Noller HF, Garrett RA. Structure of 5 S ribosomal RNA from Escherichia coli: identification of kethoxal-reactive sites in the A and B conformations. J Mol Biol 1979; 132:621-36. [PMID: 393828 DOI: 10.1016/0022-2836(79)90378-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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19
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Garrett RA, Noller HF. Structures of complexes of 5S RNA with ribosomal proteins L5, L18 and L25 from Escherichia coli: identification of kethoxal-reactive sites on the 5S RNA. J Mol Biol 1979; 132:637-48. [PMID: 393829 DOI: 10.1016/0022-2836(79)90379-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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20
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Hori H, Osawa S. Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species. Proc Natl Acad Sci U S A 1979; 76:381-5. [PMID: 284354 PMCID: PMC382943 DOI: 10.1073/pnas.76.1.381] [Citation(s) in RCA: 257] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Secondary structure models of 54 5S RNA species are constructed based on the comparative analyses of their primary structure. All 5S RNAs examined have essentially the same secondary structure. However, there are revealing characteristic differences between eukaryotic and prokaryotic types. The prokaryotic 5S RNAs may be further classified into two types, one having 120 nucleotides (120-N type) and another having 116 (116-N type). A possible mechanism for the conversion of the prokaryotic 116-N type to the 120-N type 5S RNAs (or vice versa) is discussed on the basis of their nucleotide alignments. Finally, by comparing the nucleotide alignments, we propose a phylogenic tree of the 54 5S RNA species.
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21
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Wrede P, Pongs O, Erdmann VA. Binding oligonucleotides to Escherichia coli and Bacillus stearothermophilus 5 S RNA. J Mol Biol 1978; 120:83-96. [PMID: 347090 DOI: 10.1016/0022-2836(78)90296-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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22
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Herr W, Noller HF. Nucleotide sequences of accessible regions of 23S RNA in 50S ribosomal subunits. Biochemistry 1978; 17:307-15. [PMID: 339946 DOI: 10.1021/bi00595a018] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleotide sequences around kethoxal-reactive guanine residues of 23S RNA in 50S ribosomal subunits have been determined. By use of the diagonal paper electrophoresis method )Noller, H.F. (1974), Biochemistry 13, 4694-4703), 41 ribonuclease T1 oligonucleotides, originating from about 25 sites, were identified and sequenced. These sites are single stranded and accessible in free 50S subunits, and are thus potential sites for interaction with functional ligands during protein synthesis. Examination of these sequences for potential intermolecular base-pairing reveals the following: (1) There are 19 possible complementary combinations between exposed sequences in 16S and 23S RNA containing more than 4 base pairs: 15 containing 5 base pairs and 4 containing 6 base pairs. Nine of these complementary combinations contain 16S RNA sequences which we have previously shown to be protected from kethoxall by 50S subunits (Chapman, N.M., and Noller, H.F. (1977), J. Mol. Biol. 109, 131-149). (2) One of the exposed sites in 23S RNA has a sequence which is complementary to the invariant GT psi CR sequence in tRNA.
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23
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Fox J, Wong K. Changes in the conformation and stability of 5 S RNA upon the binding of ribosomal proteins. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)38259-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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24
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Structure and function of prokaryotic and eukaryotic ribosomes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1978. [DOI: 10.1016/0079-6107(78)90020-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Bermek E. Mechanisms in polypeptide chain elongation on ribosomes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1978; 21:63-100. [PMID: 358280 DOI: 10.1016/s0079-6603(08)60267-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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Vigne R, Jordan BR. Partial enzyme digestion studies on Escherichia coli, Pseudomonas, Chlorella, Drosophila, HeLa and yeast 5S RNAs support a general class of 5S RNA models. J Mol Evol 1977; 10:77-86. [PMID: 409850 DOI: 10.1007/bf01796136] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fox and Woese (1975a) have shown that a model of 5S RNA secondary structure similar to the one originally derived for Chlorella 5S RNA can be generalized with relatively minor variations to all sequenced 5S RNA molecules, i.e. that corresponding base paired regions can be formed at approximately the same positions. We present experimental data in favour of this hypothesis and show that the points at which ribonucleases T1, T2 and pancreatic ribonuclease cleave six different 5S RNA molecules under 'mild' conditions (high ionic strength, low temperature, low RNAase concentration) nearly always fall in the proposed single-stranded regions. We conclude that this model is a good approximation to the conformation of 5S RNA in solution.
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Osterberg R, Garrett RA. Small-angle X-ray titration study on the complex formation between 5-S RNA and the L18 protein of the Escherichia coli 50-S ribosome particle. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 79:56-72. [PMID: 334548 DOI: 10.1111/j.1432-1033.1977.tb11784.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The 5-S RNA (A) and the L18 protein (B) from Escherichia coli ribosomes form one single AB complex in the concentration ranges supposed to prevail in vivo; at concentrations of L18 higher than 40 mM there is some indication for a minor species, most probably an AB2 species. This is indicated from the X-ray scattering titration data of the 5-S RNA/L18 system recorded at 21 degrees C in ribosomal reconstitution buffer. As a result of the 1:1 complex formation, there is a relatively small but defined increase in the radius of gyration from 3.61 to 3.85 nm. This result as well as the experimental scattering curve can be explained by models where it is assumed that the elongated L18 model is quite far from the electron density centre and where protein L18 interacts with one or both of the minor arms of the supposed Y-shaped 5-S RNA molecule.
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Leon V, Altman S, Crothers DM. Influence of the A15 mutation on the conformational energy balance in Escherichia coli tRNA Tyr. J Mol Biol 1977; 113:253-65. [PMID: 328897 DOI: 10.1016/0022-2836(77)90053-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Branlant C, Ebel JP. Studies on the primary structure of Escherichia coli 23 SRNA. Nucleotide sequence of the ribonuclease T1 digestion products containing more than one uridine residue. J Mol Biol 1977; 111:215-56. [PMID: 325211 DOI: 10.1016/s0022-2836(77)80050-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Branlant C, Sri Widada J, Krol A, Ebel JP. RNA sequences in ribonucleoprotein fragments of the complex formed from ribosomal 23-S RNA and ribosomal protein L24 of Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 74:155-70. [PMID: 404143 DOI: 10.1111/j.1432-1033.1977.tb11377.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Upon digestion of the complex formed from the 23-S ribosomal RNA and the 50-S ribosomal protein L24 of Escherichia coli, two fragments resistant to ribonuclease were recovered; these fragments contained RNA sections belonging to the 480 nucleotides at the 5' end of 23-S RNA. By determining the sequence of 70% of this latter region we were able to localise the sections which, in the presence of the protein, are resistant to ribonuclease. Our results suggest that the region encompassing the 480 nucleotides starting at the 9th nucleotide from the 5' end of 23-S RNA has a compact tertiary structure, which is stabilised by protein L24.
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31
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Weidner H, Yuan R, Crothers DM. Does 5S RNA function by a switch between two secondary structures? Nature 1977; 266:193-4. [PMID: 859597 DOI: 10.1038/266193a0] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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32
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Chen-Schmeisser U, Garrett RA. A new method for the isolation of a 5 S RNA complex with proteins L5, L18 and L25 from Escherichia coli ribosomes. FEBS Lett 1977; 74:287-91. [PMID: 321249 DOI: 10.1016/0014-5793(77)80866-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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33
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Walker TA, Pace NR. Transcriptional organization of the 5.8S ribosomal RNA cistron in Xenopus laevis ribosomal DNA. Nucleic Acids Res 1977; 4:595-601. [PMID: 559301 PMCID: PMC342465 DOI: 10.1093/nar/4.3.595] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Hybridization of purified, 32p-labeled 5.8S ribosomal RNA from Xenopus laevis to fragments generated from X. laevis rDNA by the restriction endonuclease, EcoRI, demonstrates that the 5.8S rRNA cistron lies within the transcribed region that links the 18S and 28S rRNA cistrons.
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Woese CR, Luehrsen KR, Pribula CD, Fox GE. Sequence characterization of 5S ribosomal RNA from eight gram positive procaryotes. J Mol Evol 1976; 8:143-53. [PMID: 823342 DOI: 10.1007/bf01739100] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The available comparative data on procaryotic 5S rRNA was extended through sequencing studies of eight gram positive procaryotes. Complete nucleotide sequences were presented for 5S rRNA from Bacillus subtilis, B. firmus, B. pasteurii, B. brevis, Lactobacillus brevis and Streptococcus faecalis. In addition, 5S rRNA oligonucleotide catalogs and partial sequence data were provided for B. cereus and Sporosarcina ureae. These sequences and catalogs were discussed in terms of known features of procaryotic 5S rRNA architecture.
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Abstract
Based on the comparative analyses of the primary structure of 5S RNAs from 19 organisms, a secondary structure model of 5S RNA is proposed. 5S RNA has essentially the same structure among all prokaryotic species. The same is true for eukaryotic 5S RNAs. Prokaryotic and eukaryotic 5S RNAs are also quite similar to each other, except for a difference in a specific region. By comparing the nucleotide alignment from the juxtaposed 5S RNA secondary structures, a phylogenic tree of nineteen organisms was constructed. The time of divergence between prokaryotes and eukaryotes was estimated to be 2.5 X 10(9) years ago (minimum estimate: 2.1 X 10(9).
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Raué HA, Stoof TJ, Planta RJ. Nucleotide sequence of 5-S RNA from Bacillus licheniformis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 59:35-42. [PMID: 1204617 DOI: 10.1111/j.1432-1033.1975.tb02421.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The complete nucleotide sequence of 5-S RNA from Bacillus licheniformis was determined by analysis of complete and partial digests obtained with either T1 or pancreatic ribonuclease. The molecule was found to have a length of 116 nucleotides and may possess a minor sequence heterogeneity. There is a large degree of homology between the sequence of B. licheniformis 5-S RNA and those published for 5-S RNA from B. megatherium and B. stearothermophilus. The difference between the three 5-S RNA species are limited mainly to the two terminal and one internal sequence. B. licheniformis 5-S RNA contains the sequence U95-G-A-G-A-G100, which in B. subtilis has been implicated in the processing of precursor 5-S RNA. Possible models for the secondary structure of prokaryotic 5-S RNA are discussed on the basis of the results of limited digestion of B. licheniformis 5-S RNA by ribonuclease T1.
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