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Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly.

Polikanov YS, Melnikov SV, Söll D, Steitz TA - Nat. Struct. Mol. Biol. (2015)

Bottom Line: We report crystal structures of the Thermus thermophilus ribosome at 2.3- to 2.5-Å resolution, which have enabled modeling of rRNA modifications.The structures reveal contacts of modified nucleotides with mRNA and tRNAs or protein pY, and contacts within the ribosome interior stabilizing the functional fold of rRNA.Our work provides a resource to explore the roles of rRNA modifications and yields a more comprehensive atomic model of a bacterial ribosome.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA. [2] Howard Hughes Medical Institute at Yale University, New Haven, Connecticut, USA.

ABSTRACT
We report crystal structures of the Thermus thermophilus ribosome at 2.3- to 2.5-Å resolution, which have enabled modeling of rRNA modifications. The structures reveal contacts of modified nucleotides with mRNA and tRNAs or protein pY, and contacts within the ribosome interior stabilizing the functional fold of rRNA. Our work provides a resource to explore the roles of rRNA modifications and yields a more comprehensive atomic model of a bacterial ribosome.

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Modified nucleotides form numerous molecular contacts with the ribosome ligands and within the ribosome interior(a) Categorization of modified rRNA nucleotides into three groups based on their molecular contacts: (i) interacting with the ribosome ligands (orange), (ii) forming the inter-subunit bridges (light blue), and (iii) strengthening RNA-RNA and RNA-protein interactions within ribosomal interior (yellow). The actual sites of modifications are shown as red spheres. Modifications specific only to T. thermophilus are labeled in red (see Supplementary Table 2). (b-c)rRNA modifications that directly interact with either mRNA and tRNAs (b), or with protein pY (c). (d) rRNA modifications that maintain structure of the helix 44 in the mRNA channel (mRNA is not shown for clarity). In panels (b-d), modified residues of 16S rRNA are shown in orange, unmodified residues are in in light yellow.
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Figure 3: Modified nucleotides form numerous molecular contacts with the ribosome ligands and within the ribosome interior(a) Categorization of modified rRNA nucleotides into three groups based on their molecular contacts: (i) interacting with the ribosome ligands (orange), (ii) forming the inter-subunit bridges (light blue), and (iii) strengthening RNA-RNA and RNA-protein interactions within ribosomal interior (yellow). The actual sites of modifications are shown as red spheres. Modifications specific only to T. thermophilus are labeled in red (see Supplementary Table 2). (b-c)rRNA modifications that directly interact with either mRNA and tRNAs (b), or with protein pY (c). (d) rRNA modifications that maintain structure of the helix 44 in the mRNA channel (mRNA is not shown for clarity). In panels (b-d), modified residues of 16S rRNA are shown in orange, unmodified residues are in in light yellow.

Mentions: The structures revealed three major types of contacts formed by rRNA modifications: (1) with the ribosome ligands; (2) between the ribosomal subunits; and (3) within the interior of the ribosomal RNA (Fig. 3a). The first group comprises nucleotides m22G966, m5C1400, m4Cm1402 of the 16S rRNA, which are all located within the P site of the small ribosomal subunit. In the complex of 70S ribosomes with mRNA and tRNAs, the methyl groups of these residues surround the mRNA-tRNA duplex and contact the mRNA codon (m4Cm1402) and the wobble base-pair (m22G966, m5C1400), as predicted earlier14,15 (Fig. 3b). These contacts rationalize why loss of m22G966 methylation affects recruitment of the initiator tRNA and the initiation of translation16-18. One of these modifications, 5-C-methylation of C1400, is absent in E. coli ribosomes and thereby may reflect adaptation of Tth ribosomes to high temperature via the extended stacking between m5C1400 base and the wobble-pair (Supplementary Table 1). In the complex of 70S ribosomes with protein pY, the methyl groups of m22G966, m5C1400, and m4Cm1402 form hydrophobic contacts with pY (Fig. 3c). These contacts suggest that loss of the rRNA modifications could not only alter the ribosome affinity to the P-site tRNA but also could reduce its affinity to the hibernation factor pY and, thus, impair translational response to stress and stationary phase.


Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly.

Polikanov YS, Melnikov SV, Söll D, Steitz TA - Nat. Struct. Mol. Biol. (2015)

Modified nucleotides form numerous molecular contacts with the ribosome ligands and within the ribosome interior(a) Categorization of modified rRNA nucleotides into three groups based on their molecular contacts: (i) interacting with the ribosome ligands (orange), (ii) forming the inter-subunit bridges (light blue), and (iii) strengthening RNA-RNA and RNA-protein interactions within ribosomal interior (yellow). The actual sites of modifications are shown as red spheres. Modifications specific only to T. thermophilus are labeled in red (see Supplementary Table 2). (b-c)rRNA modifications that directly interact with either mRNA and tRNAs (b), or with protein pY (c). (d) rRNA modifications that maintain structure of the helix 44 in the mRNA channel (mRNA is not shown for clarity). In panels (b-d), modified residues of 16S rRNA are shown in orange, unmodified residues are in in light yellow.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401423&req=5

Figure 3: Modified nucleotides form numerous molecular contacts with the ribosome ligands and within the ribosome interior(a) Categorization of modified rRNA nucleotides into three groups based on their molecular contacts: (i) interacting with the ribosome ligands (orange), (ii) forming the inter-subunit bridges (light blue), and (iii) strengthening RNA-RNA and RNA-protein interactions within ribosomal interior (yellow). The actual sites of modifications are shown as red spheres. Modifications specific only to T. thermophilus are labeled in red (see Supplementary Table 2). (b-c)rRNA modifications that directly interact with either mRNA and tRNAs (b), or with protein pY (c). (d) rRNA modifications that maintain structure of the helix 44 in the mRNA channel (mRNA is not shown for clarity). In panels (b-d), modified residues of 16S rRNA are shown in orange, unmodified residues are in in light yellow.
Mentions: The structures revealed three major types of contacts formed by rRNA modifications: (1) with the ribosome ligands; (2) between the ribosomal subunits; and (3) within the interior of the ribosomal RNA (Fig. 3a). The first group comprises nucleotides m22G966, m5C1400, m4Cm1402 of the 16S rRNA, which are all located within the P site of the small ribosomal subunit. In the complex of 70S ribosomes with mRNA and tRNAs, the methyl groups of these residues surround the mRNA-tRNA duplex and contact the mRNA codon (m4Cm1402) and the wobble base-pair (m22G966, m5C1400), as predicted earlier14,15 (Fig. 3b). These contacts rationalize why loss of m22G966 methylation affects recruitment of the initiator tRNA and the initiation of translation16-18. One of these modifications, 5-C-methylation of C1400, is absent in E. coli ribosomes and thereby may reflect adaptation of Tth ribosomes to high temperature via the extended stacking between m5C1400 base and the wobble-pair (Supplementary Table 1). In the complex of 70S ribosomes with protein pY, the methyl groups of m22G966, m5C1400, and m4Cm1402 form hydrophobic contacts with pY (Fig. 3c). These contacts suggest that loss of the rRNA modifications could not only alter the ribosome affinity to the P-site tRNA but also could reduce its affinity to the hibernation factor pY and, thus, impair translational response to stress and stationary phase.

Bottom Line: We report crystal structures of the Thermus thermophilus ribosome at 2.3- to 2.5-Å resolution, which have enabled modeling of rRNA modifications.The structures reveal contacts of modified nucleotides with mRNA and tRNAs or protein pY, and contacts within the ribosome interior stabilizing the functional fold of rRNA.Our work provides a resource to explore the roles of rRNA modifications and yields a more comprehensive atomic model of a bacterial ribosome.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA. [2] Howard Hughes Medical Institute at Yale University, New Haven, Connecticut, USA.

ABSTRACT
We report crystal structures of the Thermus thermophilus ribosome at 2.3- to 2.5-Å resolution, which have enabled modeling of rRNA modifications. The structures reveal contacts of modified nucleotides with mRNA and tRNAs or protein pY, and contacts within the ribosome interior stabilizing the functional fold of rRNA. Our work provides a resource to explore the roles of rRNA modifications and yields a more comprehensive atomic model of a bacterial ribosome.

Show MeSH
Related in: MedlinePlus