During protein synthesis, the ribosome catalyzes peptide-bond formation. Biochemical and structural studies revealed that conserved nucleotides in the peptidyl-transferase center (PTC) and its proximity may play a key role in peptide-bond formation; the exact mechanism involved remains unclear. To more precisely define the functional importance of the highly conserved residues, we used a systematic genetic method, which we named SSER (systematic selection of functional sequences by enforced replacement), that allowed us to identify essential nucleotides for ribosomal function from randomized rRNA libraries in Escherichia coli cells. These libraries were constructed by complete randomization of the critical regions in and around the PTC. The selected variants contained natural rRNA sequences from other organisms and organelles as well as unnatural functional sequences; hence providing insights into the functional roles played by these essential bases and suggesting how the universal catalytic mechanism of peptide-bond formation could evolve in all living organisms. Our results highlight essential bases and interactions, which are shaping the PTC architecture and guiding the motions of the tRNA terminus from the A to the P site, found to be crucial not only for the formation of the peptide bond but also for nascent chain elongation.nucleotide essentiality ͉ protein biosynthesis ͉ symmetrical region R ibosomes are universally conserved ribonucleoproteins that translate the genetic information contained in mRNAs into proteins. The large (50S) ribosomal subunit catalyzes peptide-bond formation at the peptidyl-transferase center (PTC) between aminoacyl-tRNA (aa-tRNA) bound to the A site and peptidyl-tRNA (pep-tRNA) at the P site. In the crystal structures of 50S subunits of Haloarcula marismortui, H50S (1, 2), Deinococcus radiodurans, D50S (3, 4), and 70S ribosomes (5, 6), the PTC is composed solely of 23S rRNA and, hence, acts as a ribozyme, consistent with biochemical findings using deproteinized 50S subunit (7-10) for the formation of a single peptide bond.The PTC provides the frame for peptide-bond formation (11, 12) and plays a critical role in tRNA and nascent chain release (13-17), and the global ribosomal architecture is crucial for substrate positioning (18,19). Consistently, the hypothesis, based on structures of H50S complexed with minimum substrates, that the PTC acts as a general acid-base catalyst (2, 20-22), was contradicted by various mutagenesis and biochemical studies (12,(23)(24)(25)(26)(27)(28). The main catalytic contribution of the ribosomes, substrates positioning at proper orientation (4,28,29), is achieved by remote interactions, accompanied by symmetrical base-pairing of C75 of both tRNAs with G2553 (Escherichia coli numbering throughout) and G2251 (Fig. 4A, which is published as supporting information on the PNAS web site), respectively (2,4,31). The distinction between the rates of peptide-bond formation by full-length tRNAs and minimal substrates is also consistent with the essential role ...

Ribosomes translate the genetic information contained in mRNAs into proteins. The large (50 S) subunit of the ribosome catalyzes the formation of a peptide bond between the aminoacyl-tRNA (aa-tRNA) 3 bound to the A-site and the peptidyl-tRNA at the P-site. This peptide bond formation takes place at the peptidyltransferase center of the 50 S subunit. Codon-anticodon pairing occurs at the decoding center of the small (30 S) subunit. The aa-tRNA is delivered to the ribosome as a ternary complex of aa-tRNA, EF-Tu, and GTP. Cognate codon recognition is strictly monitored by 16 S rRNA and triggers GTP hydrolysis and dissociation of EF-Tu. This allows aa-tRNA to be accommodated by the A site of the 50 S subunit. Thus, accuracy of protein synthesis is based on the synergistic interplay of the large and small subunits of the ribosome. However, mechanistic insights into the ribosome dynamics during decoding are still rudimentary.The intersubunit bridges of the ribosome are functional sites that are not only necessary for subunit connection but also play roles in translation. Helix 69 (H69) (position 1906 -1924) is a highly conserved stemloop in domain IV of 23 S rRNA of the bacterial 50 S subunit (Fig. 1A). In fact, each base in the loop of H69 shows more than 98% conservation in 436 bacterial rRNAs (www.rna.icmb.utexas.edu). Crystallographic studies revealed that H69 is located on the surface involved in intersubunit association with the 30 S subunit by connecting with helix 44 (h44) of 16 S rRNA forming the bridge B2a; A1912, A1913, A1914, A1918 and A1919 in H69 make contact with positions 1407-1410 and 1494 -1495 in h44 and G1517 in h45 (1, 2) (see Fig. 7A). In the free 50 S subunit, H69 makes a compact structure and interacts with H71 of 23 S rRNA (3), whereas in the 70 S ribosome H69 stretches toward the small subunit and interacts with h44 of 16 S rRNA (1). The tip of H69 moves about 13.5 Å during this structural change. In addition, H69 directly interacts with A/T-, A-, and P-site tRNAs during each translation step (1). During the decoding step, aa-tRNA is brought into the A/T-site as a complex with EF-Tu/GTP (ternary complex). Cryoelectron microscopy analyses showed a kinked conformation for aa-tRNA at the A/T state (molecular spring) (4, 5). The tip of H69 makes a contact with the hinge of the kink between D-and anticodon-stems in tRNA. This interaction is supposed to facilitate the structural distortion of tRNA that enables the anticodon-stem to fit into the decoding center of 16 S rRNA. In the crystal structure of the 70 S ribosome complexed to both A-and P-site tRNAs, H69 is positioned between the two tRNAs (1). The minor groove of H69 (positions 1908 -1909, 1922-1923) interacts with the minor groove of the D-stem of the P-site tRNA (positions 12-13, 25-26) (Fig. 1B), whereas the conserved loop (positions 1913-1915) of H69 makes a contact with the D-stem of A-site tRNA (positions 11-12 and 25-26) (Fig. 1B). Moreover, it has been reported that H69 interacts with various translational factors. In the post-t...

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