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Chapter 41 : rRNA Functional Sites and Structures for Peptide Chain Termination

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rRNA Functional Sites and Structures for Peptide Chain Termination, Page 1 of 2

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Abstract:

This chapter provides an overview of recent work that has demonstrated the roles of two rRNA functional sites, one in 16S rRNA (the small subunit) and the other in 23S rRNA (the large subunit), in release factor (RF) binding and in catalysis of peptidyl-tRNA hydrolysis and has implicated five other regions in termination, with one (in 23S rRNA) being a likely part of the hydrolytic center. The results thus far verify the validity of trying to isolate termination-defective mutants of rRNA by searching for nonsense suppressors that exhibit specificity for one or two of the termination codons, at least under some conditions. The major defect in RF2dependent termination caused by G1093A in vitro was consistent with the specific suppression of UGA (RF2-specific stop codon) seen in vivo in the presence of the mutation. In addition to G1093, other nucleotides in the GTPase center have been implicated in RF2-dependent termination based on UGA-specific suppressor mutations. After finding the G1093A mutation in the GTPase center of 23S rRNA, the authors asked whether they could find other codon-specific suppressors in 23S rRNA, particularly in the vicinity of nt 1093. The authors have suggested that an effective operational phenotype for potential termination-defective mutants is codon-specific nonsense suppression, at least under some conditions. It should be emphasized, however, that such a phenotype can be explained in other ways, less likely but indicative of other classes of very interesting mutants.

Citation: Murgola E, Arkov A, Chernyaeva N, Hedenstierna K, Pagel F. 2000. rRNA Functional Sites and Structures for Peptide Chain Termination, p 509-518. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch41

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Point Mutation
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Frameshift Mutation
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Deletion Mutation
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Missense Mutation
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Figures

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Figure 1

rRNA regions implicated in translation termination. (A) (Top) Secondary structure of 16S rRNA (small subunit). Indicated in boldface are helix 34; the base of helix 44, the major part of which is involved in the A site; a large unpaired region of helix 44 comprising nt 1431 to 1434 and 1467 to 1469; and the GAAA tetraloop at nt 159 to 162. (Bottom left) Detail of helix 34, with nucleotides implicated in termination circled. (Bottom right) Detail of the base, or A-site, portion of helix 44 (upper) and detail of the nonconserved internal loop in helix 44 (lower), with nucleotides implicated in termination circled. (B) (Top) Secondary structure of 23S rRNA (large subunit). Indicated in boldface are the GTPase center and the two UGA suppressor fragment-associated sites, nt 74 to 136 in domain I and nt 735 to 766 in domain II. A suggested general location of the RNA component of peptidyltransferase in domains IV and V ( ) is indicated (PT). The location of the 2-nt deletion that apparently compensates for termination defects caused by the mutation G1093A in the GTPase center is shown (ΔG2046 C2047). (Bottom) Detail of the GTPase center. The apparent RF2- interactive sites in the GTPase center RNA, based on UGA suppressor mutational analyses ( ) and analyses of the mutation G1093A in realistic in vitro termination assays ( ), are circled.

Citation: Murgola E, Arkov A, Chernyaeva N, Hedenstierna K, Pagel F. 2000. rRNA Functional Sites and Structures for Peptide Chain Termination, p 509-518. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch41
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Image of Figure 2
Figure 2

Possible functional interactions during transmission of a stop signal in the presence of RF2. The approximate ribosome locations of rRNA regions implicated in RF2-dependent termination are shown as either hatched rectangles (helix 34 and helix 44 of 16S rRNA) or hatched circles (23S rRNA regions, namely, the GTPase center and the hydrolytic center). A complete ribosome assembled from a 30S and a 50S subunit is viewed from the solvent side of the 30S subunit. Outlines of the 30S and 50S subunits are according to . Locations of helix 34, helix 44, and the A-site UGA codon were deduced from their proximities to the anticodon of the A-site tRNA, whose ribosome location has been presented ( ). The GTPase center is shown according to . The hydrolytic center is assumed to be situated near the acceptor end of the P-site tRNA, whose location has been presented ( ). Functional interactions between RF2 and RNA elements strongly suggested by the studies referred to in the text are shown as continuous arrows originating from RF2. Other interactions, for which there are few data available, are shown as dashed arrows.

Citation: Murgola E, Arkov A, Chernyaeva N, Hedenstierna K, Pagel F. 2000. rRNA Functional Sites and Structures for Peptide Chain Termination, p 509-518. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch41
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