RNA–Magnesium–Protein Interactions in Large Ribosomal Subunit

Petrov, Anton S.; Bernier, Chad R.; Hsiao, Chiaolong; Okafor, C. Denise; Tannenbaum, Emmanuel; Stern, Joshua; Gaucher, Eric A.; Schneider, Dana; Hud, Nicholas V.; Harvey, Stephen C.; Williams, Loren Dean

doi:10.1021/jp304723w

Cited by 45 publications

(58 citation statements)

References 56 publications

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“…4). It is known that the association of 30S and 50S ribosomal subunits requires Mg 2ϩ ions (25)(26)(27) and that Mg 2ϩ stabilizes the secondary structure of rRNA and the binding of the ribosomal proteins to the rRNA (28)(29)(30). These results raise the possibility that restoration of the Mg 2ϩ concentration by the disruption of yhdP and overexpression of mgtE suppresses the defect in 70S ribosome formation that is observed in the ⌬rpmH mutant.…”

Section: Resultsmentioning

confidence: 99%

“…One probable reason is stabilization of the 50S subunit. Mg 2ϩ stabilizes the binding of ribosomal proteins to the rRNA and the secondary structure of rRNA in the ribosome (28)(29)(30). Moreover, it has been demonstrated that Mg 2ϩ concentration controls the dynamics of the ribosome exquisitely through altering ribosome stability and flexibility (66).…”

Section: Discussionmentioning

confidence: 99%

“…The in vitro association of the 30S and 50S ribosomal subunits to form intact 70S ribosomes depends strongly on the concentration of Mg 2ϩ ions within the cell (25)(26)(27). Mg 2ϩ is also required for both stabilization of the secondary structure of rRNA and binding of the ribosomal proteins to the rRNA (28)(29)(30). Furthermore, Mg 2ϩ stabilizes the codon-anticodon interaction in the A site and influences the binding of ribosome recycling factor (RRF) to the ribosome (31)(32)(33)(34).…”

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confidence: 99%

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Defect in the Formation of 70S Ribosomes Caused by Lack of Ribosomal Protein L34 Can Be Suppressed by Magnesium

et al. 2014

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dTo elucidate the biological functions of the ribosomal protein L34, which is encoded by the rpmH gene, the rpmH deletion mutant of Bacillus subtilis and two suppressor mutants were characterized. Although the ⌬rpmH mutant exhibited a severe slowgrowth phenotype, additional mutations in the yhdP or mgtE gene restored the growth rate of the ⌬rpmH strain. Either the disruption of yhdP, which is thought to be involved in the efflux of Mg 2؉ , or overexpression of mgtE, which plays a major role in the import of Mg 2؉ , could suppress defects in both the formation of the 70S ribosome and growth caused by the absence of L34. Interestingly, the Mg 2؉ content was lower in the ⌬rpmH cells than in the wild type, and the Mg 2؉ content in the ⌬rpmH cells was restored by either the disruption of yhdP or overexpression of mgtE. In vitro experiments on subunit association demonstrated that 50S subunits that lacked L34 could form 70S ribosomes only at a high concentration of Mg 2؉ . These results showed that L34 is required for efficient 70S ribosome formation and that L34 function can be restored partially by Mg 2؉ . In addition, the Mg 2؉ content was consistently lower in mutants that contained significantly reduced amounts of the 70S ribosome, such as the ⌬rplA (L1) and ⌬rplW (L23) strains and mutant strains with a reduced number of copies of the rrn operon. Thus, the results indicated that the cellular Mg 2؉ content is influenced by the amount of 70S ribosomes.T he eubacterial ribosome (70S), which plays a central role in protein synthesis, is composed of a small (30S) subunit and a large (50S) subunit. The small subunit is comprised of the 16S rRNA and more than 20 proteins, whereas the large subunit is comprised of the 23S and 5S rRNAs and more than 30 proteins (1, 2). The molecular mechanisms of translation have been elucidated in detail by the convergence of various approaches, including crystal structure analysis (3-8). The individual functions of several ribosomal proteins have also been elucidated by biochemical and genetic analyses, including reconstitution and mutational analysis. For example, ribosomal protein L2 plays important roles in the assembly of the ribosomal subunits, binding of the tRNA to the A and P sites, peptidyltransferase activity, and formation of the peptide bond (9-13). However, in general, disruption of the genes that encode the ribosomal proteins has been avoided as a means of identifying protein function, because these genes, which are highly conserved in bacteria, have been considered essential for cell proliferation (14). Nonetheless, recently, it was found that 22 of the 54 Escherichia coli genes for ribosomal proteins could be deleted on an individual basis (15,16). We have also shown that out of the 57 ribosomal-protein-encoding genes that have been annotated in the Gram-positive bacterium Bacillus subtilis, at least 22 genes are not individually essential for cell proliferation (17). The rpmH gene encoding ribosomal protein L34, which is a component of the large subunit, is one of the...

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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Defect in the Formation of 70S Ribosomes Caused by Lack of Ribosomal Protein L34 Can Be Suppressed by Magnesium

et al. 2014

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“…We have aligned 23S/28S rRNA sequences from 122 organisms (29) that represent, as far as available data allow, a complete and non-biased sampling of the phylogenetic tree, including to all three domains of life. This alignment suggests that the pairing interactions of Helix 26a are conserved over the entire phylogenetic tree.…”

Section: Resultsmentioning

confidence: 99%

“…We aligned 23S rRNA/28S sequences from 122 organisms (29) intended to represent, as far as available data allow, a broad sampling of the phylogenetic tree of life including all three domains of life. Sequences came from 19 eukaryotic species, 67 bacterial species and 36 archaeal species.…”

Section: Methodsmentioning

confidence: 99%

Secondary structure and domain architecture of the 23S and 5S rRNAs

Petrov

Bernier

Hershkovits

et al. 2013

Nucleic Acids Research

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We present a de novo re-determination of the secondary (2°) structure and domain architecture of the 23S and 5S rRNAs, using 3D structures, determined by X-ray diffraction, as input. In the traditional 2° structure, the center of the 23S rRNA is an extended single strand, which in 3D is seen to be compact and double helical. Accurately assigning nucleotides to helices compels a revision of the 23S rRNA 2° structure. Unlike the traditional 2° structure, the revised 2° structure of the 23S rRNA shows architectural similarity with the 16S rRNA. The revised 2° structure also reveals a clear relationship with the 3D structure and is generalizable to rRNAs of other species from all three domains of life. The 2° structure revision required us to reconsider the domain architecture. We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness. The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed. Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted. Editable 2° structures mapped with various data are provided (http://apollo.chemistry.gatech.edu/RibosomeGallery).

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