Two distinct conformations of the conserved RNA-rich decoding center of the small ribosomal subunit are recognized by tRNAs and release factors

Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk

The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNAVal. The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed us to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transitions in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide a description of the structure and function of the human mitoribosome.

Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications

The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNA Val . The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transition in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide the most complete description so far of the structure and function of the human mitoribosome.

Mechanisms that ensure speed and fidelity in eukaryotic translation termination

Translation termination, which liberates a nascent polypeptide from the ribosome specifically at stop codons, must occur accurately and rapidly. We established single-molecule fluorescence assays to track the dynamics of ribosomes and two requisite release factors (eRF1 and eRF3) throughout termination using an in vitro-reconstituted yeast translation system. We found that the two eukaryotic release factors bound together to recognize stop codons rapidly and elicit termination through a tightly regulated, multistep process that resembles transfer RNA selection during translation elongation. Because the release factors are conserved from yeast to humans, the molecular events that underlie yeast translation termination are likely broadly fundamental to eukaryotic protein synthesis.

Dual interaction of the Hsp70 J-protein cochaperone Zuotin with the 40S and 60S ribosomal subunits

Ribosome-associated J protein-Hsp70 chaperones promote nascent polypeptide folding and normal translational fidelity. Though known to span the ribosome subunits, understanding of J protein Zuo1 function is limited. New structural and crosslinking data allow more precise positioning of Saccharomyces cerevisiae Zuo1 near the 60S polypeptide exit site, pointing to interactions with ribosomal protein eL31 and 25S rRNA helix 24. The junction between the 60S-interacting and subunit-spanning helices is a hinge, positioning Zuo1 on the 40S, yet accommodating subunit rotation. Interaction between C-terminus of Zuo1 and 40S occurs via 18S rRNA expansion segment 12 (ES12) of helix 44, which originates at the decoding site. Deletions in either ES12 or C-terminus of Zuo1 alter stop codon readthrough and −1 frameshifting. Our study offers insight into how this cotranslational chaperone system may monitor decoding site activity and nascent polypeptide transit, thereby coordinating protein translation and folding.

Distinct roles for release factor 1 and release factor 2 in translational quality control

In bacteria, stop codons are recognized by two similar class 1 release factors, release factor 1 (RF1) and release factor 2 (RF2). Normally, during termination, the class 2 release factor 3 (RF3), a GTPase, functions downstream of peptide release where it accelerates the dissociation of RF1/RF2 prior to ribosome recycling. In addition to their canonical function in termination, both classes of release factor are also involved in a post peptidyl transfer quality control (post PT QC) mechanism where the termination factors recognize mismatched (i.e. error-containing) ribosome complexes and promote premature termination. Here, using a well defined in vitro system, we explored the role of release factors in canonical termination and post PT QC. As reported previously, during canonical termination, RF1 and RF2 recognize stop codons in a similar manner, and RF3 accelerates their rate of dissociation. During post PT QC, only RF2 (and not RF1) effectively binds to mismatched ribosome complexes; and whereas the addition of RF3 to RF2 increased its rate of release on mismatched complexes, the addition of RF3 to RF1 inhibited its rate of release but increased the rate of peptidyl-tRNA dissociation. Our data strongly suggest that RF2, in addition to its primary role in peptide release, functions as the principle factor for post PT QC.

Distinct response of yeast ribosomes to a miscoding event during translation

Numerous mechanisms have evolved to control the accuracy of translation, including a recently discovered retrospective quality control mechanism in bacteria. This quality control mechanism is sensitive to perturbations in the codon:anticodon interaction in the P site of the ribosome that trigger a dramatic loss of fidelity in subsequent tRNA and release factor selection events in the A site. These events ultimately lead to premature termination of translation in response to an initial miscoding error. In this work, we extend our investigations of this mechanism to an in vitro reconstituted Saccharomyces cerevisiae translation system. We report that yeast ribosomes do not respond to mismatches in the P site by loss of fidelity in subsequent substrate recognition events. We conclude that retrospective editing, as initially characterized in Escherichia coli, does not occur in S. cerevisiae. These results highlight potential mechanistic differences in the functional core of highly conserved ribosomes.

Fidelity at the molecular level: lessons from protein synthesis

The faithful and rapid translation of genetic information into peptide sequences is an indispensable property of the ribosome. The mechanistic understanding of strategies used by the ribosome to achieve both speed and fidelity during translation results from nearly a half century of biochemical and structural studies. Emerging from these studies is the common theme that the ribosome uses local as well as remote conformational switches to govern induced-fit mechanisms that ensure accuracy in codon recognition during both tRNA selection and translation termination.

Biological implications of the ribosome's stunning stereochemistry

The ribosome's striking architecture is ingeniously designed for its efficient polymerase activity in the biosynthesis of proteins, which is a prerequisite for cell vitality. This elaborate architecture is comprised of a universal symmetrical region that connects all of the ribosomal functional centers involved in protein biosynthesis. Assisted by the mobility of selected ribosomal nucleotides, the symmetrical region provides the structural tools that are required not only for peptide bond formation, but also for fast and smooth successive elongation of nascent proteins. It confines the path along which the A-tRNA 3'-end is rotated into the P-site in concert with the overall tRNA/mRNA sideways movement, thus providing the required stereochemistry for peptide bond formation and substrate-mediated catalysis. The extreme flexibility of the nucleotides that facilitate peptide bond formation is being exploited to promote antibiotic selectivity and synergism, as well as to combat antibiotic resistance.

Precise alignment of peptidyl tRNA by the decoding center is essential for EF-G-dependent translocation

Translocation is an essential step in the elongation cycle of the protein synthesis that allows for the continual incorporation of new amino acids to the growing polypeptide. Movement of mRNA and tRNAs within the ribosome is catalyzed by EF-G binding and GTP hydrolysis. The 30S subunit decoding center is crucial for the selection of the cognate tRNA. However, it is not clear whether the decoding center participates in translocation. We disrupted the interactions in the decoding center by mutating the universally conserved 16S rRNA bases G530, A1492, and A1493, and the effects of these mutations on translocation were studied. Our results show that point mutation of any of these 16S rRNA bases inhibits EF-G-dependent translocation. Furthermore, the mutant ribosomes showed increased puromycin reactivity in the pretranslocation complexes, indicating that the dynamic equilibrium of the peptidyl tRNA between the classical and hybrid-state configurations is influenced by contacts in the decoding center.

Structural basis for translation termination on the 70S ribosome

At termination of protein synthesis, type I release factors promote hydrolysis of the peptidyl-transfer RNA linkage in response to recognition of a stop codon. Here we describe the crystal structure of the Thermus thermophilus 70S ribosome in complex with the release factor RF1, tRNA and a messenger RNA containing a UAA stop codon, at 3.2 A resolution. The stop codon is recognized in a pocket formed by conserved elements of RF1, including its PxT recognition motif, and 16S ribosomal RNA. The codon and the 30S subunit A site undergo an induced fit that results in stabilization of a conformation of RF1 that promotes its interaction with the peptidyl transferase centre. Unexpectedly, the main-chain amide group of Gln 230 in the universally conserved GGQ motif of the factor is positioned to contribute directly to peptidyl-tRNA hydrolysis.

The termination of translation

Recent results from cryoelectron microscopy, crystallography, and biochemical experiments have shed considerable light on the process by which protein synthesis is terminated when a stop codon is reached. However, a detailed understanding of the underlying mechanisms will require higher-resolution structures of the various states involved.

Stop codon recognition by release factors induces structural rearrangement of the ribosomal decoding center that is productive for peptide release

Peptide release on the ribosome is catalyzed in the large subunit peptidyl transferase center by release factors on recognition of stop codons in the small subunit decoding center. Here we examine the role of the decoding center in this process. Mutation of decoding center nucleotides or removal of 2'OH groups from the codon--deleterious in the related process of tRNA selection--has only mild effects on peptide release. The miscoding antibiotic paromomycin, which binds the decoding center and promotes the critical steps of tRNA selection, instead dramatically inhibits peptide release. Differences in the kinetic mechanism of paromomycin inhibition on stop and sense codons, paired with correlated structural changes monitored by chemical footprinting, suggest that recognition of stop codons by release factors induces specific structural rearrangements in the small subunit decoding center. We propose that, like other steps in translation, the specificity of peptide release is achieved through an induced-fit mechanism.

Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion

In vivo incorporation of unnatural amino acids by amber codon suppression is limited by release factor-1-mediated peptide chain termination. Orthogonal ribosome-mRNA pairs function in parallel with, but independent of, natural ribosomes and mRNAs. Here we show that an evolved orthogonal ribosome (ribo-X) improves tRNA(CUA)-dependent decoding of amber codons placed in orthogonal mRNA. By combining ribo-X, orthogonal mRNAs and orthogonal aminoacyl-tRNA synthetase/tRNA pairs in Escherichia coli, we increase the efficiency of site-specific unnatural amino acid incorporation from approximately 20% to >60% on a single amber codon and from <1% to >20% on two amber codons. We hypothesize that these increases result from a decreased functional interaction of the orthogonal ribosome with release factor-1. This technology should minimize the functional and phenotypic effects of truncated proteins in experiments that use unnatural amino acid incorporation to probe protein function in vivo.