Escherichia coli ribosome unfolding in low Mg<sup>2+</sup>solutions observed by laser Raman spectroscopy and electron microscopy

King, Thomas C.; Rucinsky, Tom; Schlessinger, David; Milanovich, F. P.

doi:10.1093/nar/9.3.647

Cited by 8 publications

(13 citation statements)

References 23 publications

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“…Electron microscopic analysis of unfolded 50S subunits or partially denatured 23S RMA has shown characteristic structural features that can be compared with our secondary structure scheme. 50S subunits unfolded by removal of magnesium ions appear as asterisk-like shapes, with five prominent arms radiating from a common center (28). These could well correspond to the five largest domains (I-V; Fig.…”

Section: Resultsmentioning

confidence: 88%

Secondary structure model for 23S ribosomal RNA

et al. 1981

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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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Section: Resultsmentioning

confidence: 88%

Secondary structure model for 23S ribosomal RNA

et al. 1981

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“…The slightly higher rate for the 50S subunits may reflect the presence of small amounts of partially denatured ribosomes. Indeed, control experiments where the ribosomes or 50S subunits were disrupted by treatment with 100 mM EDTA (42) prior to assay gave full ATPase activity (Figure 6 and data not shown). Remarkably, the kinetic constants for the EDTA-treated ribosomes were identical to those for naked rRNA (Table 3).…”

Section: Resultsmentioning

confidence: 93%

Kinetic Analysis of the RNA-Dependent Adenosinetriphosphatase Activity of DbpA, an Escherichia coli DEAD Protein Specific for 23S Ribosomal RNA

Tsu

Uhlenbeck

1998

Biochemistry

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The adenosinetriphosphatase (ATPase) activity of the Escherichia coli DEAD protein DbpA is unusual in that it is specifically stimulated by 23S ribosomal RNA (rRNA). A coupled spectroscopic ATPase assay was used to investigate the interaction of DbpA with RNA and ATP. A 153-base fragment of domain V of 23S rRNA is kinetically identical to intact, native rRNA in activating DbpA: kcat = 600 min-1, Kapp(RNA) = 10 nM, and Km(ATP) = 120 microM. The ATPase turnover in the absence of RNA is 0.25 min-1. Fragments of 23S rRNA lacking this site (nucleotides 2454-2606) are essentially inactive, as are other RNAs such as poly(A) and tRNA. The relative RNA specificity of DbpA ranges from 10(3) to 10(6) [kmax/Kapp(RNA)]. The interaction with this small RNA fragment was further investigated with regard to stoichiometry, pH, salt and temperature. DbpA is not activated by E. coli ribosomes, nor by large subunits, while denatured ribosomes stimulate full ATPase activity. Taken together with the tight, site-specific binding to naked, unmodified 23S rRNA, this suggests a role for DbpA in ribosome biogenesis rather than translation.

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“…Ribosomes, transfer RNA, and many enzymes involved in these processes lose their biological activity in the absence of this ion. Furthermore, it is known that the magnesium ion maintains the tertiary structure of transfer RNA (Lindahl et al, 1966;Lynch & Schimmel, 1974a;Quigley et al, 1978) and the folding of ribosomal particles (Weiss & Morris, 1973a,b;King et al, 1981). The stability of double-helical DNA against thermal denaturation is also greatly enhanced by magnesium ions.…”

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confidence: 99%

Magnesium binding and conformational change of DNA in chromatin

Watanabe¹,

Iso²

1984

Biochemistry

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The structure of chromatin in the presence of Mg2+ ions was examined by circular dichroism and equilibrium dialysis. Circular dichroism (CD) shows that above 260 nm the intensity of the spectrum of DNA in nucleoproteins decreases as the Mg2+ concentration increases. This change is an intrinsic characteristic of DNA since it is also observed in protein-free DNA and has been attributed to a change in the winding angle of base pairs around the DNA axis. Some structural elements of the DNA in the nucleosome core, therefore, are as movable as those of protein-free DNA. The basic organization of H1-depleted chromatin, 146 base pairs (bp) of DNA wound around core histones and a residual 49 bp in the linker region in the repeating unit, is maintained both in the presence and in the absence of Mg2+ ions, as shown by the fact that the CD spectrum of H1-depleted chromatin has the same type of linear combination between the spectrum of protein-free DNA and that of the nucleosome core in 0.2 mM MgCl2-10 mM triethanolamine (pH 7.8) as it has in 1 mM ethylenediaminetetraacetic acid-10 mM tris(hydroxymethyl) aminomethane (pH 7.8). The ellipticity of chromatin shows a smaller decrease relative to the other nucleoproteins and protein-free DNA upon the addition of Mg2+ ions. Therefore, some structural elements of chromatin are apparently somewhat protected against the conformational change induced by these ions. The spectrum of chromatin becomes almost indistinguishable from that of H1-depleted chromatin in 0.2 mM MgCl2.(ABSTRACT TRUNCATED AT 250 WORDS)

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Escherichia coli ribosome unfolding in low Mg²⁺solutions observed by laser Raman spectroscopy and electron microscopy

Cited by 8 publications

References 23 publications

Secondary structure model for 23S ribosomal RNA

Secondary structure model for 23S ribosomal RNA

Kinetic Analysis of the RNA-Dependent Adenosinetriphosphatase Activity of DbpA, an Escherichia coli DEAD Protein Specific for 23S Ribosomal RNA

Magnesium binding and conformational change of DNA in chromatin

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Escherichia coli ribosome unfolding in low Mg2+solutions observed by laser Raman spectroscopy and electron microscopy

Cited by 8 publications

References 23 publications

Secondary structure model for 23S ribosomal RNA

Secondary structure model for 23S ribosomal RNA

Kinetic Analysis of the RNA-Dependent Adenosinetriphosphatase Activity of DbpA, an Escherichia coli DEAD Protein Specific for 23S Ribosomal RNA

Magnesium binding and conformational change of DNA in chromatin

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Escherichia coli ribosome unfolding in low Mg²⁺solutions observed by laser Raman spectroscopy and electron microscopy