1
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Kirsch R, Olzog VJ, Bonin S, Weinberg CE, Betat H, Stadler PF, Mörl M. A streamlined protocol for the detection of mRNA-sRNA interactions using AMT-crosslinking in vitro. Biotechniques 2019; 67:178-183. [PMID: 31462065 DOI: 10.2144/btn-2019-0047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Until recently, RNA-RNA interactions were mainly identified by crosslinking RNAs with interacting proteins, RNA proximity ligation and deep sequencing. Recently, AMT-based direct RNA crosslinking was established. Yet, several steps of these procedures are rather inefficient, reducing the output of identified interaction partners. To increase the local concentration of RNA ends, interacting RNAs are often fragmented. However, the resulting 2',3'-cyclic phosphate and 5'-OH ends are not accepted by T4 RNA ligase and have to be converted to 3'-OH and 5'-phosphate ends. Using an artificial mRNA/sRNA pair, we optimized the workflow downstream of the crosslinking reaction in vitro. The use of a tRNA ligase allows direct fusion of 2',3'-cyclic phosphate and 5'-OH RNA ends.
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Affiliation(s)
- Rebecca Kirsch
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany.,Center for Non-Coding RNA in Technology & Health, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark
| | - V Janett Olzog
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany
| | - Sonja Bonin
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany
| | | | - Heike Betat
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany
| | - Peter F Stadler
- Center for Non-Coding RNA in Technology & Health, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.,Bioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany.,Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany
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2
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Motorin Y, Muller S, Behm-Ansmant I, Branlant C. Identification of modified residues in RNAs by reverse transcription-based methods. Methods Enzymol 2007; 425:21-53. [PMID: 17673078 DOI: 10.1016/s0076-6879(07)25002-5] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Naturally occurring modified residues derived from canonical RNA nucleotides are present in most cellular RNAs. Their detection in RNA represents a difficult task because of their great diversity and their irregular distribution within RNA molecules. Over the decades, multiple experimental techniques were developed for the identification and localization of RNA modifications. Most of them are quite laborious and require purification of individual RNA to a homogeneous state. An alternative to these techniques is the use of reverse transcription (RT)-based approaches. In these approaches, purification of RNA to homogeneity is not necessary, because the selection of the analyzed RNA species is done by specific annealing of oligonucleotide DNA primers. However, results from primer extension analysis are difficult to interpret because of the unpredictable nature of RT pauses. They depend not only on the properties of nucleotides but also on the RNA primary and secondary structure. In addition, the degradation of cellular RNA during extraction, even at a very low level, may complicate the analysis of the data. RT-based techniques for the identification of modified residues were considerably improved by the development of selected chemical reagents specifically reacting with a given modified nucleotide. The RT profile obtained after such chemical modifications generally allows unambiguous identification of the chemical nature of the modified residues and their exact location in the RNA sequence. Here, we provide experimental protocols for selective chemical modification and identification of several modified residues: pseudouridine, inosine, 5-methylcytosine, 2'-O-methylations, 7-methylguanosine, and dihydrouridine. Advice for an optimized use of these methods and for correct interpretation of the data is also given. We also provide some helpful information on the ability of other naturally occurring modified nucleotides to generate RT pauses.
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Affiliation(s)
- Yuri Motorin
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, Faculté des Sciences et Techniques, Nancy Université, Vandouevre-les-Nancy, France
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3
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Abstract
The interaction of RNA-binding proteins (RBPs) with RNA is a crucial aspect of normal cellular metabolism. Yet, the diverse number of RBPs and RNA motifs to which they bind, the wide range of interaction strengths and the fact that RBPs associate in dynamic complexes have made it challenging to determine whether a particular RNA-binding protein binds a particular RNA. Recent work by three different laboratories has led to the development of new tools to query such interactions in the more physiological environs of cultured cells. The use of these methods has led to insights into (1) the networks of RNAs regulated by a particular protein, (2) the identification of new protein partners within messenger ribonucleoprotein particles and (3) the flux of RNA-binding proteins on an mRNA throughout its lifecycle. Here, I examine these new methods and discuss their relative strengths and current limitations.
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Affiliation(s)
- Robert B Denman
- Department of Molecular Biology, Laboratory of Biochemical Molecular Neurobiology, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314, USA.
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4
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Wodrich H, Guan T, Cingolani G, Von Seggern D, Nemerow G, Gerace L. Switch from capsid protein import to adenovirus assembly by cleavage of nuclear transport signals. EMBO J 2004; 22:6245-55. [PMID: 14633984 PMCID: PMC291855 DOI: 10.1093/emboj/cdg614] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Replication and assembly of adenovirus occurs in the nucleus of infected cells, requiring the nuclear import of all viral structural proteins. In this report we show that nuclear import of the major capsid protein, hexon, is mediated by protein VI, a structural protein located underneath the 12 vertices of the adenoviral capsid. Our data indicate that protein VI shuttles between the nucleus and the cytoplasm and that it links hexon to the nuclear import machinery via an importin alpha/beta-dependent mechanism. Key nuclear import and export signals of protein VI are located in a short C-terminal segment, which is proteolytically removed during virus maturation. The removal of these C-terminal transport signals appears to trigger a functional transition in protein VI, from a role in supporting hexon nuclear import to a structural role in virus assembly.
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Affiliation(s)
- Harald Wodrich
- Department of Cell Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
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5
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Juzumiene D, Shapkina T, Kirillov S, Wollenzien P. Short-range RNA-RNA crosslinking methods to determine rRNA structure and interactions. Methods 2001; 25:333-43. [PMID: 11860287 DOI: 10.1006/meth.2001.1245] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We describe details of procedures to analyze RNA-RNA crosslinks made by far-UV irradiation (< 300 nm) or made by irradiation with near-UV light (320-365 nm) on RNA containing photosensitive nucleotides, in the present case containing 4-thiouridine. Zero-length crosslinks of these types must occur because of the close proximity of the participants through either specific interactions or transient contacts in the folded RNA structure, so they are valuable monitors of the conformation of the RNA. Procedures to produce crosslinks in the 16S ribosomal RNA and between the 16S rRNA and mRNA or tRNA are described. Gel electrophoresis conditions are described that separate the products according to their structure to allow the determination of the number and frequency of the crosslinking products. Gel electrophoresis together with an ultracentrifugation procedure for the efficient recovery of RNA from the polyacrylamide gels allows the purification of molecules containing different crosslinks. These separation techniques allow the analysis of the sites of crosslinking by primer extension and RNA sequencing techniques. The procedures are applicable to other types of RNA molecules with some differences to control levels of crosslinking and separation conditions.
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Affiliation(s)
- D Juzumiene
- Department of Molecular and Structural Biochemistry, North Carolina State University, 126 Polk Hall, Raleigh, North Carolina 27695, USA
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6
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Abstract
Pseudouridine is present in ribosomal RNA, transfer RNA, tmRNA, and small nuclear and nucleolar RNAs. All are structured molecules. Pseudouridine is made by enzyme-catalyzed isomerization of specifically selected U residues after the polynucleotide chain is made. No energy input is required. Pseudouridine formation creates a hydrogen bond donor at the equivalent of uridine C-5. Therefore, a major role of pseudouridine may be to strengthen particular RNA conformations and/or RNA-RNA interactions because of this extra H-bond capability. Understanding the role of pseudouridine critically depends on knowledge of their location and number in RNA. The mapping method described here has greatly simplified this task and made it possible to survey many organisms. Procedures are described for mapping pseudouridines in large RNAs like ribosomal RNA and in small RNAs like tRNA. The method involves carbodiimide adduct formation with U, G, and pseudouridine followed by mild alkali to remove the adduct from U and G but not from the N-3 of pseudouridine. This results in attenuation of primed reverse transcription resulting in a stop band one residue 3' to the pseudouridine on sequencing gels. Use of primers means that purified RNAs are not needed, only knowledge of its primary sequence, but limit the sequence scanned to 30-40 residues from the 3' end. A poly(A) tailing procedure is described that allows extension of the method to within a few nucleotides of the 3' terminus.
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Affiliation(s)
- J Ofengand
- Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, Florida 33101, USA.
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7
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Dolzhanskaya N, Conti J, Schwenk V, Merz G, Denman RB. Self-Cleaving-Ribozyme-Mediated Reduction of βAPP in Human Rhabdomyosarcoma Cells. Arch Biochem Biophys 2001; 387:223-32. [PMID: 11370845 DOI: 10.1006/abbi.2000.2262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A self-cleaving hammerhead ribozyme targeted to codon 47 in beta-amyloid precursor protein (betaAPP) mRNA was cloned as a eucaryotic transcription cassette into the 3' UTR of enhanced green fluorescence protein (EGFP) mRNA, producing a C-terminal fusion mRNA. CMV promotor-driven vectors bearing this construct or a mutationally inactive ribozyme construct were transiently transfected into human embryonic rhabdomyosarcoma (A-204) cells and their effects studied. Ribozyme self-cleavage in vivo was demonstrated by Northern blotting and the site of self-cleavage was delineated using site-specific deoxyoligonucleotide probes and primer extension arrest. Using this ribozyme reporter we demonstrated that ribozyme expression correlated with lower betaAPP levels in the transfected cells. Control studies with the inactive ribozyme construct showed that both ribozyme cleavage and antisense mechanisms combined to produce the observed effect. Furthermore, production of truncated EGFP mRNA via ribozyme self-cleavage reduced EGFP-reporter expression compared to full-length EGFP control mRNAs, indicating that truncation affects the translatability of the reporter. This occurred because of a slight decrease in the stability of the fusion mRNA. The results of these studies suggest that self-cleaving ribozyme vectors may be an effective means of delivering and visualizing the expression of small active ribozymes in vivo.
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Affiliation(s)
- N Dolzhanskaya
- Department of Molecular Biology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island 10314, USA
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8
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Mundus D, Wollenzien P. Structure determination by directed photo-cross-linking in large RNA molecules with site-specific psoralen. Methods Enzymol 2001; 318:104-18. [PMID: 10889983 DOI: 10.1016/s0076-6879(00)18047-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Affiliation(s)
- D Mundus
- Magellan Labs, Research Triangle Park, North Carolina 27709, USA
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9
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Dolzhanskaya N, Conti J, Merz G, Denman RB. In vivo ribozyme targeting of betaAPP+ mRNAs. MOLECULAR CELL BIOLOGY RESEARCH COMMUNICATIONS : MCBRC 2000; 4:239-47. [PMID: 11409919 DOI: 10.1006/mcbr.2001.0287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Alzheimer's disease (AD) and Down's syndrome (DS) patients, posttranscriptional alterations of sequences encoded by exon 9 and exon 10 of the beta-amyloid precursor protein (betaAPP) mRNA result in mutant proteins (betaAPP+) that colocalize with neurofibrillary tangles and senile plaques. These aberrant messages may contribute to the development of sporadic or late-onset Alzheimer's disease; thus, eliminating them or attenuating their expression could significantly benefit AD patients. In the present work, self-cleaving hammerhead ribozymes targeted to betaAPP exon 9 (Rz9) and betaAPP+ mutant exon 10 (Rz10) were examined for their ability to distinguish between betaAPP and betaAPP+ mRNA. In transiently transfected A-204 cells, quantitative confocal fluorescence microscopy showed that Rz9 preferentially lowered endogenous betaAPP. In contrast, in transient cotransfection experiments with betaAPP+ mRNAs containing a wild-type exon 9 and mutant exon 10 (betaAPP-9/betaAPP-10+1), or a mutant exon 9 and wild-type exon 10 (betaAPP-9+1/betaAPP-10) we found that Rz9 and Rz10 preferentially reduced betaAPP+ -mutant exon 10 mRNA in a concentration and a ribozyme-dependent manner.
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Affiliation(s)
- N Dolzhanskaya
- Department of Molecular Biology, New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, New York 10314, USA
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10
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Leung SS, Koslowsky DJ. Mapping contacts between gRNA and mRNA in trypanosome RNA editing. Nucleic Acids Res 1999; 27:778-87. [PMID: 9889273 PMCID: PMC148247 DOI: 10.1093/nar/27.3.778] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
All guide RNAs (gRNAs) identified to date have defined 5' anchor sequences, guiding sequences and a non-encoded 3' uridylate tail. The 5' anchor is required for in vitro editing and is thought to be responsible for selection and binding to the pre-edited mRNA. Little is known, however, about how the gRNAs are used to direct RNA editing. Utilizing the photo-reactive crosslinking agent, azidophenacyl (APA), attached to the 5'- or 3'-terminus of the gRNA, we have begun to map the structural relationships between the different defined regions of the gRNA with the pre-edited mRNA. Analyses of crosslinked conjugates produced with a 5'-terminal APA group confirm that the anchor of the gRNA is correctly positioning the interacting molecules. 3' Crosslinks (X-linker placed at the 3'-end of a U10tail) have also been mapped for three different gRNA/mRNA pairs. In all cases, analyses indicate that the U-tail can interact with a range of nucleotides located upstream of the first edited site. It appears that the U-tail prefers purine-rich sites, close to the first few editing sites. These results suggest that the U-tail may act in concert with the anchor to melt out secondary structure in the mRNA in the immediate editing domain, possibly increasing the accessibility of the editing complex to the proper editing sites.
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Affiliation(s)
- S S Leung
- Department of Microbiology, Michigan State University, East Lansing, MI 48824, USA
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11
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Felden B, Hanawa K, Atkins JF, Himeno H, Muto A, Gesteland RF, McCloskey JA, Crain PF. Presence and location of modified nucleotides in Escherichia coli tmRNA: structural mimicry with tRNA acceptor branches. EMBO J 1998; 17:3188-96. [PMID: 9606200 PMCID: PMC1170657 DOI: 10.1093/emboj/17.11.3188] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Escherichia coli tmRNA functions uniquely as both tRNA and mRNA and possesses structural elements similar to canonical tRNAs. To test whether this mimicry extends to post-transcriptional modification, the technique of combined liquid chromatography/ electrospray ionization mass spectrometry (LC/ESIMS) and sequence data were used to determine the molecular masses of all oligonucleotides produced by RNase T1 hydrolysis with a mean error of 0.1 Da. Thus, this allowed for the detection, chemical characterization and sequence placement of modified nucleotides which produced a change in mass. Also, chemical modifications were used to locate mass-silent modifications. The native E.coli tmRNA contains two modified nucleosides, 5-methyluridine and pseudouridine. Both modifications are located within the proposed tRNA-like domain, in a seven-nucleotide loop mimicking the conserved sequence of T loops in canonical tRNAs. Although tmRNA acceptor branches (acceptor stem and T stem-loop) utilize different architectural rules than those of canonical tRNAs, their conformations in solution may be very similar. A comparative structural and functional analysis of unmodified tmRNA made by in vitro transcription and native E.coli tmRNA suggests that one or both of these post-transcriptional modifications may be required for optimal stability of the acceptor branch which is needed for efficient aminoacylation.
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Affiliation(s)
- B Felden
- Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112, USA
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12
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Baranov PV, Gurvich OL, Bogdanov AA, Brimacombe R, Dontsova OA. New features of 23S ribosomal RNA folding: the long helix 41-42 makes a "U-turn" inside the ribosome. RNA (NEW YORK, N.Y.) 1998; 4:658-68. [PMID: 9622125 PMCID: PMC1369648 DOI: 10.1017/s1355838298980104] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
23S rRNA from Escherichia coli was cleaved at single internucleotide bonds using ribonuclease H in the presence of appropriate chimeric oligonucleotides; the individual cleavage sites were between residues 384 and 385, 867 and 868, 1045 and 1046, and 2510 and 2511, with an additional fortuitous cleavage at positions 1117 and 1118. In each case, the 3' terminus of the 5' fragment was ligated to radioactively labeled 4-thiouridine 5'-,3'-biphosphate ("psUp"), and the cleaved 23S rRNA carrying this label was reconstituted into 50S subunits. The 50S subunits were able to associate normally with 30S subunits to form 70S ribosomes. Intra-RNA crosslinks from the 4-thiouridine residues were induced by irradiation at 350 nm, and the crosslink sites within the 23S rRNA were analyzed. The rRNA molecules carrying psUp at positions 867 and 1117 showed crosslinks to nearby positions on the opposite strand of the same double helix where the cleavage was located, and no crosslinking was detected from position 2510. In contrast, the rRNA carrying psUp at position 384 showed crosslinking to nt 420 (and sometimes also to 416 and 425) in the neighboring helix in 23S rRNA, and the rRNA with psUp at position 1045 gave a crosslink to residue 993. The latter crosslink demonstrates that the long helix 41-42 of the 23S rRNA (which carries the region associated with GTPase activity) must double back on itself, forming a "U-turn" in the ribosome. This result is discussed in terms of the topography of the GTPase region in the 50S subunit, and its relation to the locations of the 5S rRNA and the peptidyl transferase center.
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Affiliation(s)
- P V Baranov
- A.N. Belozersky Institute of Physico-Chemical Biology, Department of Chemistry, Moscow State University, Russia
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13
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Muralikrishna P, Alexander RW, Cooperman BS. Placement of the alpha-sarcin loop within the 50S subunit: evidence derived using a photolabile oligodeoxynucleotide probe. Nucleic Acids Res 1997; 25:4562-9. [PMID: 9358167 PMCID: PMC147071 DOI: 10.1093/nar/25.22.4562] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We report the synthesis of a radioactive, photolabile oligodeoxyribonucleotide probe and its exploitation in identifying 50S ribosomal subunit components neighboring the alpha-sarcin loop. The probe is complementary to 23S rRNA nt 2653-2674. Photolysis of the complex formed between the probe and 50S subunits leads to site-specific probe photoincorporation into proteins L2, the most highly labeled protein, L1, L15, L16 and L27, labeled to intermediate extents, and L5, L9, L17 and L24, each labeled to a minor extent. Portions of each of these proteins thus lie within 23 A of nt U2653. These results lead us to conclude that the alpha-sarcin loop is located at the base of the L1 projection within the 50S subunit. Such placement, near the peptidyl transferase center, provides a rationale for the extreme sensitivity of ribosomal function to cleavage of the alpha-sarcin loop.
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Affiliation(s)
- P Muralikrishna
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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14
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Denman RB. Facilitator oligonucleotides increase ribozyme RNA binding to full-length RNA substrates in vitro. FEBS Lett 1996; 382:116-20. [PMID: 8612731 DOI: 10.1016/0014-5793(96)00125-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Primer extension arrest (PEA) studies have demonstrated that antisense oligonucleotides (beta 112C, beta 114C), which lie upstream of a ribozyme targeted to beta-amyloid peptide precursor (beta APP) mRNA, but not sense oligonucleotides (beta 112S, beta 116S) or a scrambled oligonucleotide, beta 116 M, affect ribozyme-mediated cleavage in vitro. Substrate dissociation experiments revealed that the ribozyme binding site in this mRNA was masked; PEA kinetics showed the association of the ribozyme and substrate was enhanced by antisense oligonucleotide binding. These studies suggest that masked ribozyme cleavage sites that may occur in disease-causing mRNAs can be targeted for degradation using "facilitator" oligonucleotides.
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Affiliation(s)
- R B Denman
- Department of Molecular Biology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island 10314, USA
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15
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Lorsch JR, Bartel DP, Szostak JW. Reverse transcriptase reads through a 2'-5'linkage and a 2'-thiophosphate in a template. Nucleic Acids Res 1995; 23:2811-4. [PMID: 7544885 PMCID: PMC307115 DOI: 10.1093/nar/23.15.2811] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Avian myeloblastosis virus and Maloney murine leukemia virus RNase H-reverse transcriptases pause when they encounter a 2'-5' linkage or a 2'-thiophosphate in their template RNAs, but eventually read through these backbone modifications. Both reverse transcriptases pause after the 2'-5' linkage but before the 2'-thiophosphate. These results suggest that in the absence of precise information concerning the behavior of a given reverse transcriptase with respect to a particular lesion or modification, caution should be exercised in the interpretation of primer extension data that is being used to determine the existence of, or map the position of, a crosslink, site of chemical modification or non-standard linkage in an RNA template.
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Affiliation(s)
- J R Lorsch
- Department of Molecular Biology, Massachusetts General Hospital, Boston 02114, USA
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16
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17
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von Ahsen U, Noller HF. Identification of bases in 16S rRNA essential for tRNA binding at the 30S ribosomal P site. Science 1995; 267:234-7. [PMID: 7528943 DOI: 10.1126/science.7528943] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Previous studies suggest that the mechanism of action of the ribosome in translation involves crucial transfer RNA (tRNA)-ribosomal RNA (rRNA) interactions. Here, a selection scheme was developed to identify bases in 16S rRNA that are essential for tRNA binding to the P site of the small (30S) ribosomal subunit. Modification of the N-1 and N-2 positions of 2-methylguanine 966 and of the N-7 position of guanine 1401 interfered with messenger RNA (mRNA)-dependent binding of tRNA to the P site. Modification of the same positions as well as of the N-1 and N-2 positions of guanine 926 interfered with mRNA-independent binding of tRNA at high magnesium ion concentration. These results suggest that these three bases are involved in intermolecular contacts between ribosomes and tRNA.
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MESH Headings
- Aldehydes/pharmacology
- Base Composition
- Binding Sites
- Butanones
- CME-Carbodiimide/analogs & derivatives
- CME-Carbodiimide/pharmacology
- Codon
- Guanine/chemistry
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer, Leu/metabolism
- RNA, Transfer, Phe/metabolism
- Ribosomes/metabolism
- Sulfides/pharmacology
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Affiliation(s)
- U von Ahsen
- Sinsheimer Laboratories, University of California, Santa Cruz 95064
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18
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Stade K, Riens S, Bochkariov D, Brimacombe R. Contacts between the growing peptide chain and the 23S RNA in the 50S ribosomal subunit. Nucleic Acids Res 1994; 22:1394-9. [PMID: 8190630 PMCID: PMC307996 DOI: 10.1093/nar/22.8.1394] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Peptides of defined length carrying a diazirine photoaffinity label attached either to the alpha-NH2 group of the N-terminal methionine residue, or to the epsilon-NH2 group of an immediately adjacent lysine residue, were prepared in situ on Escherichia coli ribosomes in the presence of a synthetic mRNA analogue. Peptide growth was stopped simply by withholding the aminoacyl-tRNA cognate to an appropriate downstream codon. After photo-activation at 350 nm the sites of cross-linking to ribosomal RNA were determined by our standard procedures; the C-terminal amino acid of each peptide was labelled with tritium, in order to confirm whether the individual cross-linked complexes contained the expected 'full-length' peptide, as opposed to shorter products. The shortest peptides became cross-linked to sites within the 'peptidyl transferase ring' of the 23S RNA, namely to positions 2062, 2506, 2585 and 2609. However, already when the peptide was three or four residues long, a new cross-link was observed several hundred nucleotides away in another secondary structural domain; this site, at position 1781, lies within one of several RNA regions which have been implicated in other studies as being located close to the peptidyl transferase ring. Further application of this approach, combined with model-building studies, should enable the path of the nascent peptide through the large ribosomal subunit to be definitively mapped.
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Affiliation(s)
- K Stade
- Max-Planck-Institut für Molekulare Genetik, Abteilung Wittmann, Berlin, Germany
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19
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Sontheimer EJ, Steitz JA. The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science 1993; 262:1989-96. [PMID: 8266094 DOI: 10.1126/science.8266094] [Citation(s) in RCA: 280] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Five small nuclear RNAs (U1, U2, U4, U5, and U6) participate in precursor messenger RNA (pre-mRNA) splicing. To probe their interactions within the active center of the mammalian spliceosome, substrates containing a single photoactivatable 4-thiouridine residue adjacent to either splice site were synthesized, and crosslinks were induced during the course of in vitro splicing. An invariant loop sequence in U5 small nuclear RNA contacts exon 1 before and after the first step of splicing because a crosslink between U5 and the last residue of exon 1 appeared in the pre-mRNA and then in the cutoff exon 1 intermediate. Both of these crosslinked species could undergo subsequent splicing, indicating that the crosslinks reflect a functional interaction that is maintained through both reaction steps. The same U5 loop aligns the two exons for ligation since the first residue of exon 2 also became crosslinked to U5 in the lariat intermediate. An invariant sequence in U6 RNA became crosslinked to the conserved second position of the intron within both the lariat intermediate and the lariat intron product. On the basis of these results, several conformational arrangements of small nuclear RNAs within the spliceosomal active center can be distinguished, and additional mechanistic parallels between the spliceosome and self-splicing introns can be drawn.
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Affiliation(s)
- E J Sontheimer
- Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, Boyer Center for Molecular Medicine, New Haven, CT 06536-0812
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20
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Bakin A, Ofengand J. Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the application of a new sequencing technique. Biochemistry 1993; 32:9754-62. [PMID: 8373778 DOI: 10.1021/bi00088a030] [Citation(s) in RCA: 249] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A new technique has been developed for the facile location of pseudouridylate (psi) residues in any RNA molecule. The method uses two known modification procedures which in combination uniquely identify U residues which have been converted into psi. The first procedure involves reaction of all U-like and G-like residues with N-cyclohexyl-N'-beta-(4-methylmorpholinium)ethylcarbodiimide p-tosylate (CMC), followed by alkaline removal of all CMC groups except those linked to the N3 of psi. This stops reverse transcription, resulting in a gel band which identifies the U residue. The second procedure is uridine-specific hydrazinolysis which cleaves the RNA chain at all U residues and produces a gel band upon reverse transcription. psi residues, being resistant to hydrazinolysis, are not cleaved and do not stop reverse transcription. This leads to the absence of a band at psi residues. The combined method can also distinguish psi from 5-methyluridine, 4-thiouridine, uridine-5-oxyacetic acid, and 2-thio-5-methylaminomethyluridine as shown by treating rRNA and tRNA species known to contain these modified bases at defined sites. By this procedure, four new sites for psi in Escherichia coli 23S RNA were discovered, and one was disproven. The four new sites are at positions 2457, 2504, 2580, and 2605. The erroneous site is at position 2555. These four new psi residues, which are all in or within 2-3 residues of the peptidyltransferase ring, are thus in a position to play a functional and/or structural role at the peptidyltransferase center.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- A Bakin
- Roche Institute of Molecular Biology, Roche Research Center, Nutley, New Jersey 07110
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21
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Abstract
The sequences surrounding the first 5'GUC3' in the mRNA encoding the Alzheimer amyloid peptide precursor (beta APP) were used to construct a pair of transacting hammerhead ribozymes. Each ribozyme contained the conserved core bases of the hammerhead motif found in the positive strand of satellite RNA of tobacco ringspot virus [(+)sTRSV] and two stems, 7 and 8 bases long, complementary to the target, beta APP mRNA. However, one of the ribozyme cleaving strands was lengthened at its 3' end to include the early splicing and polyadenylation signal sequences of SV40 viral RNA. This RNA, therefore, more closely mimics transcripts produced by RNA polymerase II from eucaryotic expression vectors in vivo. RNA, prepared by run-off transcription of cDNA oligonucleotide or plasmid constructs containing a T7 RNA polymerase promoter was used to characterize several properties of the cleavage reaction. In the presence of both ribozyme cleaving strands magnesium-ion dependent cleavage of a model 26 base beta APP substrate RNA or full-length beta APP-751 mRNA was observed at the hammerhead consensus cleavage site. Neither ribozyme was active against non-message homologs of beta APP mRNA, nor was cleavage detected when point mutations were made in the conserved core sequences. However, the kcat/Km at 37 degrees C in 10 mM Mg+2 of the longer ribozyme was reduced twenty-fold when model and full-length substrates were compared. The use of short deoxyoligonucleotides (13-17 mers) that bind upstream of the ribozyme was found to enhance the rate of cleavage of the full-length but not beta APP model substrate RNAs. The rate of enhancement depended on both the length of the deoxyoligonucleotide used as well as its site of binding with respect to the ribozyme. These data demonstrate the utility of ribozymes to cleave target RNAs in a catalytic, site-specific fashion in vitro. Direct comparison of the efficiency of different ribozyme constructs and different modulating activities provide an experimental strategy for designing more effective ribozymes for therapeutic purposes.
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Affiliation(s)
- R B Denman
- New York Institute for Basic Research in Developmental Disabilities, Staten Island 10314
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22
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Cunningham PR, Nurse K, Bakin A, Weitzmann CJ, Pflumm M, Ofengand J. Interaction between the two conserved single-stranded regions at the decoding site of small subunit ribosomal RNA is essential for ribosome function. Biochemistry 1992; 31:12012-22. [PMID: 1280994 DOI: 10.1021/bi00163a008] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Formation of the tertiary base pair G1401:C1501, which brings together two universally present and highly sequence-conserved single-stranded segments of small subunit ribosomal RNA, is essential for ribosome function. It was previously reported that mutation of G1401 inactivated all in vitro functions of the ribosome [Cunningham et al. (1992) Biochemistry 31, 7629-7637]. Here we show that mutation of C1501 to G was equally inactivating but that the double mutant C1401:G1501 with the base pair reversed had virtually full activity for tRNA binding to the P, A, and I sites and for peptide bond formation. Initiation-dependent formation of the first peptide bond remained 70-85% inhibited, despite full 70S initiation complex formation ability as evidenced by the ability to form fMET-puromycin. These results suggest that the defect in formation of the first peptide bond lies in filling the initial A site, Ai, rather than the subsequent elongation A sites, Ae. An increased mobility around the anticodon was detected by UV cross-linking of the anticodon of P-site-bound tRNA to C1399 as well as to the expected C1400. These findings provide the first experimental evidence for the existence of the G1401:C1501 base pair and show that this base pair, located at the decoding site, is essential for function. The structural implications of tertiary base pair formation are discussed.
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MESH Headings
- Base Sequence
- Binding Sites
- Cross-Linking Reagents
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Molecular Sequence Data
- Mutation
- N-Formylmethionine/metabolism
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer/metabolism
- Ribosomes/metabolism
- Transcription, Genetic
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Affiliation(s)
- P R Cunningham
- Roche Institute of Molecular Biology, Roche Research Center, Nutley, New Jersey 07110
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23
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Sylvers LA, Kopylov AM, Wower J, Hixson SS, Zimmermann RA. Photochemical cross-linking of the anticodon loop of yeast tRNA(Phe) to 30S-subunit protein S7 at the ribosomal A and P sites. Biochimie 1992; 74:381-9. [PMID: 1637863 DOI: 10.1016/0300-9084(92)90116-v] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Yeast tRNA(Phe), containing the photoreactive nucleoside 2-azidoadenosine at position 37 within the anticodon loop, has been cross-linked to the aminoacyl-tRNA (A) and peptidyl-tRNA (P) binding sites of the Escherichia coli ribosome. The 30S subunit was exclusively labeled in each case, and cross-linking occurred to both protein and 16S rRNA. Electrophoretic and immunological analyses demonstrated that S7 was the only 30S-subunit protein covalently attached to the tRNA. However, digestion of the A and P site-labeled S7 with trypsin revealed a unique pattern of cross-linked peptide(s) at each site. Thus, while the anticodon loop of tRNA is in close proximity to protein S7 at both the A and P sites, it neighbors a different portion of the protein molecule in each. The placement of the aminoacyl- and peptidyl-tRNA binding sites is discussed in relationship to recent models of the 30S ribosomal subunit.
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Affiliation(s)
- L A Sylvers
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst 01003
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24
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Wollenzien P, Expert-Bezançon A, Favre A. Sites of contact of mRNA with 16S rRNA and 23S rRNA in the Escherichia coli ribosome. Biochemistry 1991; 30:1788-95. [PMID: 1993193 DOI: 10.1021/bi00221a009] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The locations of close encounter between ribosomal RNA (rRNA) and messenger RNA (mRNA) were determined by photochemical cross-linking experiments that employ an artificial mRNA, 51 nucleotides long, containing 14 U residues that were randomly substituted by 1-4 4-thiouridine (s4U) residues. The mRNA was bound to 70S ribosomes or 30S subunits and then was irradiated at 366 nm to activate cross-linking between the s4U residues and rRNA. Cross-linking occurred to both 16S rRNA and 23S RNA. The rRNA was then analyzed by a series of reverse transcriptase experiments to determine the locations of cross-linking. Twelve sites in the 16S rRNA and two sites in the 23S rRNA have been detected. In the 16S rRNA, two of the sites (U1381, C1395) are in the middle part of the secondary structure close to position C1400, and the remaining sites (G413, U421, G424; A532; G693; U723; A845; G1131/C1132; G1300; G1338) are distributed between six regions that are peripheral in the secondary structure. In the 23S rRNA, one site (U1065) is located in the GTPase center close to A1067, the site of thiostrepton-resistance methylation in domain II, and the other site (U887) is located a short distance away also in domain II. The distribution of these rRNA sites in the ribosome specifies an mRNA track that is consistent with other information. In addition, some of the contact points represent new constraints for the three-dimensional folding of the rRNA.
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Affiliation(s)
- P Wollenzien
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Medical Center, Missouri 63104
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25
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Downs WD, Cech TR. An ultraviolet-inducible adenosine-adenosine cross-link reflects the catalytic structure of the Tetrahymena ribozyme. Biochemistry 1990; 29:5605-13. [PMID: 2201409 DOI: 10.1021/bi00475a027] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
When a shortened enzymatic version of the Tetrahymena self-splicing intervening sequence (IVS) RNA is placed under catalytic conditions and irradiated at 254 nm, a covalent cross-link forms with high efficiency. The position of the cross-link was mapped by using three independent methods: RNase H digestion, primer extension with reverse transcriptase, and partial hydrolysis of end-labeled RNA. The cross-link is chemically unusual in that it joins two adenosines, A57 and A95. Formation of this cross-link depends upon the identity and concentration of divalent cations present and upon heat-cool renaturation of the IVS in a manner that parallels conditions required for optimal catalytic activity. Furthermore, cross-linking requires the presence of sequences within the core structure, which is conserved among group I intervening sequences and necessary for catalytic activity. Together these correlations suggest that a common folded structure permits cross-linking and catalytic activity. The core can form this structure independent of the presence of P1 and elements at the 3' end of the IVS. The cross-linked RNA loses catalytic activity under destabilizing conditions, presumably due to disruption of the folded structure by the cross-link. One of the nucleotides participating in this cross-link is highly conserved (86%) within the secondary structure of group I intervening sequences. We conclude that A57 and A95 are precisely aligned in a catalytically active conformation of the RNA. A model is presented for the tertiary arrangement in the vicinity of the cross-link.
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Affiliation(s)
- W D Downs
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Colorado, Boulder 80309-0215
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26
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Moazed D, Noller HF. Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16 S rRNA. J Mol Biol 1990; 211:135-45. [PMID: 2405162 DOI: 10.1016/0022-2836(90)90016-f] [Citation(s) in RCA: 209] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transfer RNA protects a characteristic set of bases in 16 S rRNA from chemical probes when it binds to ribosomes. We used several criteria, based on construction of well-characterized in vitro ribosome-tRNA complexes, to assign these proteins to A or P-site binding. All of these approaches lead to similar conclusions. In the A site, tRNA caused protection of G529, G530, A1492 and A1493 (strongly), and A1408 and G1494 (weakly). In the P site, the protected bases are G693, A794, C795, G926 and G1401 (strong), and A532, G966, G1338 and G1339 (weak). In contrast to what is observed for 23 S rRNA, blocking the release of EF-Tu.GDP from the ribosome by kirromycin has no detectable effect on the protection of bases in 16 S rRNA.
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Affiliation(s)
- D Moazed
- Thimann Laboratories, University of California Santa Cruz 95064
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27
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Abstract
Three sets of conserved nucleotides in 23 rRNA are protected from chemical probes by binding of tRNA to the ribosomal A, P, and E sites, respectively. They are located almost exclusively in domain V, primarily in or adjacent to the loop identified with the peptidyl transferase function. Some of these sites are also protected by antibiotics such as chloramphenicol, which could explain how these drugs interfere with protein synthesis. Certain tRNA-dependent protections are abolished when the 3'-terminal A or CA or 2',3'-linked acyl group is removed, providing direct evidence for the interaction of the conserved CCA terminus of tRNA with 23S rRNA. When the EF-Tu.GTP.aminoacyl-tRNA ternary complex is bound to the ribosome, no tRNA-dependent A site protections are detected in 23S rRNA until EF-Tu is released. Thus, EF-Tu prevents interaction of the 3' terminus of the incoming aminoacyl-tRNA with the peptidyl transferase region of the ribosome during anticodon selection, thereby permitting translational proofreading.
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MESH Headings
- Base Sequence
- Escherichia coli
- RNA, Bacterial/analysis
- RNA, Bacterial/metabolism
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 23S/analysis
- RNA, Ribosomal, 23S/metabolism
- RNA, Transfer/analysis
- RNA, Transfer/metabolism
- RNA, Transfer, Amino Acyl/analysis
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomes/metabolism
- Ribosomes/physiology
- Ribosomes/ultrastructure
- Transferases/physiology
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Affiliation(s)
- D Moazed
- Thimann Laboratories, University of California, Santa Cruz 95064
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28
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Ericson G, Wollenzien P. Use of reverse transcription to determine the exact locations of psoralen photochemical crosslinks in RNA. Anal Biochem 1988; 174:215-23. [PMID: 2464291 DOI: 10.1016/0003-2697(88)90538-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have studied the properties of avian myeloblastosis virus reverse transcriptase on Escherichia coli 16S ribosomal RNA that was known to contain a psoralen crosslink in a restricted region around residue 920. These crosslinked RNA molecules were purified on the basis of loop size by gel electrophoresis. Reverse transcription stopped at specific positions in the crosslinked molecules but not in control linear molecules. With the particular crosslink that was studied, at the earliest time of reverse transcription, the most frequent stopping site was G925. At later times two nearly equal stops at G925 and C924 were seen. The crosslinked site was an absolute stop since even at long times of incubation the reverse transcriptase was not able to proceed beyond G925/C924. An independent determination of the crosslinked site by directly sequencing a section of the crosslinked RNA indicated that C924 was the sole nucleotide involved in the crosslink. Therefore, reverse transcriptase was able to synthesize cDNA all the way up to and including the nucleotide that contained the psoralen crosslink. Thus, reverse transcription can be a rapid and precise method for determining psoralen crosslinking sites when prefractionated, crosslinked RNA templates are used.
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Affiliation(s)
- G Ericson
- E.A. Doisy Department of Biochemistry, St. Louis University Medical Center, Missouri 63104
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