Structural arrangement of the decoding site of Escherichia coli ribosomes as revealed from the data on affinity labelling of ribosomes by analogs of mRNA - derivatives of oligoribonucleotides

Vladimirov, S.N.; Babkina, G.T.; Venijaminova, Alija G.; Gimautdinova, O. I.; Zenkova, Marina A.; Карпова, Г. Г.

doi:10.1016/0167-4781(90)90063-8

Cited by 30 publications

(14 citation statements)

References 23 publications

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“…These latter papers report cross-links to proteins S7, S18, and S21 from a 7-nt stretch (designated -4 to +3, where +1 to +3 correspond to the AUG initiation codon) within the mRNA. It is also pertinent that proteins S3 and S4, which we find as major sites of labeling in inactive rather than activated 30s subunits ( Figure 4, lower panel), are also found as minor labeling sites by Dontsova et al (1991) and that either S3 or S3 and S4 have been found as major sites of mRNA affinity labeling in several other studies [as reviewed in Cooperman (1987); more recent examples may be found in Vladimirov et al (1990), Dontsova et al (1992b), and Rinke-Appel et al…”

Section: Discussionmentioning

confidence: 87%

A Photolabile Oligodeoxyribonucleotide Probe of the Decoding Site in the Small Subunit of the Escherichia coli Ribosome: Identification of Neighboring Ribosomal Components

Muralikrishna

Cooperman²

1994

Biochemistry

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In this work we report the synthesis of a radioactive, photolabile oligodeoxyribonucleotide probe complementary to 16S rRNA nucleotides 1397-1405 and its exploitation in identifying 30S ribosomal subunit components neighboring its target site in 16S rRNA. Nucleotides 1397-1405 lie within a single-stranded sequence that has been linked to the decoding region of Escherichia coli ribosomes. On photolysis in the presence of activated 30S subunits, the photolabile oligodeoxyribonucleotide probe site-specifically incorporates into proteins S1, S7, S18, and S21 (identified by SDS-PAGE, RP-HPLC, and antibody affinity chromatography) and into three separate 16S rRNA regions, specifically, nucleotides A-1396, G-1405-A-1408, and A-1492 and A-1493. These results provide clear evidence that G-1405 in 16S rRNA is within 24 A (the distance between G-1405 and the photogenerated nitrene) of proteins S1, S7, S18, and S21 and each of the other nucleotides mentioned above, consistent with other studies of 30S internal structure. Although the probe binds to inactive 30S subunits about as well as to activated 30S subunits, photolysis of the inactive 30S.probe complex leads to a very different pattern of protein labeling, providing strong evidence, at the protein level, that the inactive to activated transition is accompanied by conformational change in the 1400 region of 16S rRNA.

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Section: Discussionmentioning

confidence: 87%

A Photolabile Oligodeoxyribonucleotide Probe of the Decoding Site in the Small Subunit of the Escherichia coli Ribosome: Identification of Neighboring Ribosomal Components

Muralikrishna

Cooperman²

1994

Biochemistry

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“…In earlier studies on affinity labeling of E. coli ribosomes by mRNA analogs, the environment of the codon-anticodon duplex on the ribosome had been shown to change at each step of translation (Vladimirov et al, 1990). Complexes 80s .…”

Section: Differences In Arrangement Of the Mrna Analogs Consisting Ofmentioning

confidence: 99%

“…The alkylating derivatives of oligoribonucleotides bearing alkylating groups at either the 3'-or the 5'-termini (mRNA analogs) have been successfully used in our laboratories for studying the structural arrangement of the decoding site of E. coli ribosomes (Vladimirov et al, 1990). Recently these derivatives were applied for affinity labeling of the human placental 80s ribosomes (Graifer et al 1990;Karpova et al, 1992) and 40s subunits Mundus et al, 1993) In these studies only regions of 18s rRNA containing sites of the reagents' covalent attachment had been determined.…”

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confidence: 99%

Arrangement of mRNA at the Decoding Site of Human Ribosomes

Malygin

Graifer

Bulygin

et al. 1994

European Journal of Biochemistry

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Affinity labeling of human placental 80S ribosomes with mRNA analogs of up to 12 uridyl residues, i.e. alkylating derivatives of oligouridylates bearing either 4-(N-2-chloroethyl-N-methylamino)benzylmethylphosphamide group at the 5'-termini or 2',3'-O-[4-(N-2-chloroethyl-N-methylamino)]benzylidene residue attached to the 3'-termini, in the presence of cognate Phe-tRNA(Phe) has been investigated. All the mRNA analogs modified only the 40S subunit. The fraction of 18S rRNA modified by the mRNA analogs with the alkylating group at the 5'-end decreased dramatically with extension of the reagent oligouridylate moiety. Nucleotides of 18S rRNA alkylated with the mRNA analogs were determined using a reverse transcription technique. For the mRNA analogs with the alkylating groups at the 3'-termini, G1702 and G1763/G1764 were identified as the cross-linking sites. The intensities of the bands corresponding to reverse transcriptase stops depended on the length of the reagent oligouridylate moieties. Cross-linking sites of the mRNA analogs with the alkylating group at the 5'-termini on 18S rRNA were A1023, C1026, C1057 and A1058 for the (pU)3 and (pU)4 derivatives and a single nucleotide C1057 for the (pU)6 one. Ribosomal protein S26 was found as the main target of modification with the same derivatives of (pU)6 and (pU)12.

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“…RpS7 controls translation of the str operon by binding to an intercistronic region of the mRNA (26). Affinity labeling experiments with mRNA analogues in bacterial ribosome systems revealed rpS7 as a frequent binding target (27,28). Cross-linking and immunological analysis of a 30 S ribosomal protein indicate that rpS7 is a primary target for binding to an upstream region of mRNA (29,30).…”

Section: Hcv Ires-s5 Interaction 20825mentioning

confidence: 99%

Ribosomal Protein S5 Interacts with the Internal Ribosomal Entry Site of Hepatitis C Virus

Fukushi

Okada

Stahl

et al. 2001

Journal of Biological Chemistry

102

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Translational initiation of hepatitis C virus (HCV) genome RNA occurs via its highly structured 5 noncoding region called the internal ribosome entry site (IRES).Recent studies indicate that HCV IRES and 40 S ribosomal subunit form a stable binary complex that is believed to be important for the subsequent assembly of the 48 S initiation complex. Ribosomal protein (rp) S9 has been suggested as the prime candidate protein for binding of the HCV IRES to the 40 S subunit. RpS9 has a molecular mass of ϳ25 kDa in UV cross-linking experiments. In the present study, we examined the ϳ25-kDa proteins of the 40 S ribosome that form complexes with the HCV IRES upon UV cross-linking. Immunoprecipitation with specific antibodies against two 25-kDa 40 S proteins, rpS5 and rpS9, clearly identified rpS5 as the protein bound to the IRES. Thus, our results support rpS5 as the critical element in positioning the HCV RNA on the 40 S ribosomal subunit during translation initiation.Translational initiation of most eukaryotic messenger RNAs is mediated by the binding of elongation initiation factor eIF-4 to the modified nucleotide cap on the 5Ј end of the mRNA and the binding of the 40 S ribosomal subunit and other initiation factors (1). However, in hepatitis C virus (HCV) 1 as well as in members of the picornavirus family, the positive-stranded RNA genome is not capped. In these viral genomes, the 5Ј noncoding region (NCR) contains an internal ribosomal entry site (IRES) (2, 3). Trans-acting cellular proteins regulate viral protein synthesis by binding to multiple sites within the IRES (2). For example, a polypyrimidine tract-binding protein (PTB) interacts with several sites in the IRES elements of picornaviruses (e.g. poliovirus (PV), encephalomyocarditis virus, foot-andmouth disease virus, and human rhinovirus) (4 -7). A 52-kDa nuclear factor, La protein, appears to be essential for PV translation initiation, because its addition to La-deficient rabbit reticulocyte lysates stimulates and corrects PV translation (8). In addition to these two proteins, other cellular factors (e.g. the 97-kDa protein and poly(rC)-binding protein-2) are likely to stimulate translation initiation directed by the picornavirus IRES (9, 10).Identification and characterization of IRES-binding proteins are important to the understanding of the mechanisms of internal initiation and, ultimately, to the development of novel therapies for HCV. The binding PTB and La are required for translation by HCV IRES (11, 12). However, Kaminski et al. (13) reported that recombinant PTB did not stimulate HCV IRES function, suggesting that PTB may not be necessary during HCV translation initiation under certain experimental conditions. Despite a considerably lower level of La protein in rabbit reticulocyte lysate, HCV IRES promotes efficient translation activity (14 -16). This clearly differs from the case of translation initiation on the PV genome. Thus, general models proposed for the process of 40 S ribosome entry to IRES elements on the picornavirus genome do not s...

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Structural arrangement of the decoding site of Escherichia coli ribosomes as revealed from the data on affinity labelling of ribosomes by analogs of mRNA - derivatives of oligoribonucleotides

Cited by 30 publications

References 23 publications

A Photolabile Oligodeoxyribonucleotide Probe of the Decoding Site in the Small Subunit of the Escherichia coli Ribosome: Identification of Neighboring Ribosomal Components

A Photolabile Oligodeoxyribonucleotide Probe of the Decoding Site in the Small Subunit of the Escherichia coli Ribosome: Identification of Neighboring Ribosomal Components

Arrangement of mRNA at the Decoding Site of Human Ribosomes

Ribosomal Protein S5 Interacts with the Internal Ribosomal Entry Site of Hepatitis C Virus

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