Polyamine binding sites on Escherichia coli ribosomes

Kakegawa, Tomohito; Sato, Emi; Hirose, Sachiko; Igarashi, Kazuei

doi:10.1016/0003-9861(86)90347-4

Cited by 23 publications

(19 citation statements)

References 27 publications

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“…However, consistent with that observation, polyamines also stimulate readthrough in vitro of termination codons, both UGA (82) and UAG (140). In addition to binding tRNAs, polyamines are known to bind ribosomes (97) and polynucleotides (124); it is unclear how polyamines might stimulate mistranslation by readthrough or frameshifting.…”

Section: The Rat Ornithine Decarboxylase Antizyme Genementioning

confidence: 74%

Programmed Translational Frameshifting

1996

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▪ Abstract Errors that alter the reading frame occur extremely rarely during translation, yet some genes have evolved sequences that efficiently induce frameshifting. These sequences, termed programmed frameshift sites, manipulate the translational apparatus to promote non-canonical decoding. Frameshifts are mechanistically diverse. Most cause a −1 shift of frames; the first such site was discovered in a metazoan retrovirus, but they are now known to be dispersed quite widely among evolutionarily diverse species. +1 frameshift sites are much less common, but again dispersed widely. The rarest form are the translational hop sites which program the ribosome to bypass a region of several dozen nucleotides. Each of these types of events are stimulated by distinct mechanisms. All of the events share a common phenomenology in which the programmed frameshift site causes the ribosome to pause during elongation so that the kinetically unfavorable alternative decoding event can occur. During this pause most frameshifts occur because one or more ribosome-bound tRNAs slip between cognate or near-cognate codons. However, even this generalization is not entirely consistent, since some frameshifts occur without slippage. Because of their similarity to rarer translational errors, programmed frameshift sites provide a tool with which to probe the mechanism of frame maintenance.

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Section: The Rat Ornithine Decarboxylase Antizyme Genementioning

confidence: 74%

Programmed Translational Frameshifting

1996

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“…The rationale is that photoprobe cross-linking acts as a barrier for reverse transcriptase. This technique bypasses all disadvantages of other cross-linking methods utilizing homo-bifunctional reagents (17–19), and has been successfully applied so far for mapping spermine binding sites in AcPhe-tRNA bound to the P-site of poly(U)-programmed 70S ribosomes (29), in ribosomal proteins (20), or in 16S rRNA from E.coli (34). The results of the present study represent the first unambiguous and complete mapping of spermine binding sites in 23S rRNA.…”

Section: Introductionmentioning

confidence: 99%

Localization of spermine binding sites in 23S rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50S subunit functions

Xaplanteri

Πετρόπουλος

Dinos

et al. 2005

Nucleic Acids Research

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Polyamine binding to 23S rRNA was investigated, using a photoaffinity labeling approach. This was based on the covalent binding of a photoreactive analog of spermine, N1-azidobenzamidino (ABA)-spermine, to Escherichia coli ribosomes or naked 23S rRNA under mild irradiation conditions. The cross-linking sites of ABA-spermine in 23S rRNA were determined by RNase H digestion and primer-extension analysis. Domains I, II, IV and V in naked 23S rRNA were identified as discrete regions of preferred cross-linking. When 50S ribosomal subunits were targeted, the interaction of the photoprobe with the above 23S rRNA domains was elevated, except for helix H38 in domain II whose susceptibility to cross-linking was greatly reduced. In addition, cross-linking sites were identified in domains III and VI. Association of 30S with 50S subunits, poly(U), tRNAPhe and AcPhe-tRNA to form a post-translocation complex further altered the cross-linking, in particular to helices H11–H13, H21, H63, H80, H84, H90 and H97. Poly(U)-programmed 70S ribosomes, reconstituted from photolabeled 50S subunits and untreated 30S subunits, bound AcPhe-tRNA in a similar fashion to native ribosomes. However, they exhibited higher reactivity toward puromycin and enhanced tRNA-translocation efficiency. These results suggest an essential role for polyamines in the structural and functional integrity of the large ribosomal subunit.

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“…Studies using a photoreactive analogue of spermine, ABA-spermine, have shown that spermine binds to several sites of 23S rRNA that are located into the PTase centre (24) as well as with the ribosomal proteins L2, L3, L6, L15, L17, and L18 that are topographically adjacent to the PTase centre (25,26). It was speculated that polyamines may influence the conformation of specific 'PTase proteins', which, in turn, affect the conformation of ribosomal RNA residues involved in the catalysis of peptide bond formation.…”

Section: Modulation Of Ribosomal Activitymentioning

confidence: 99%

Insights into functional modulation of catalytic RNA activity

et al. 2008

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SummaryRNA molecules play critical roles in cell biology, and novel findings continuously broaden their functional repertoires. Apart from their well-documented participation in protein synthesis, it is now apparent that several noncoding RNAs (i.e., micro-RNAs and riboswitches) also participate in the regulation of gene expression. The discovery of catalytic RNAs had profound implications on our views concerning the evolution of life on our planet at a molecular level. A characteristic attribute of RNA, probably traced back to its ancestral origin, is the ability to interact with and be modulated by several ions and molecules of different sizes. The inhibition of ribosome activity by antibiotics has been extensively used as a therapeutical approach, while activation and substrate-specificity alteration have the potential to enhance the versatility of ribozyme-based tools in translational research. In this review, we will describe some representative examples of such modulators to illustrate the potential of catalytic RNAs as tools and targets in research and clinical approaches.

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Polyamine binding sites on Escherichia coli ribosomes

Cited by 23 publications

References 27 publications

Programmed Translational Frameshifting

Programmed Translational Frameshifting

Localization of spermine binding sites in 23S rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50S subunit functions

Insights into functional modulation of catalytic RNA activity

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