Chemical modifications of messenger RNA (mRNA) may regulate many aspects of mRNA processing and protein synthesis. Recently, 2′-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acid. Here, using single-molecule, bulk kinetics and structural methods, we show that 2′-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate transfer RNA (tRNA) selection. Our results suggest that 2′-O-methylation sterically perturbs interactions of ribosomal monitoring bases (G530, A1492 and A1493) with cognate codon-anticodon helices, thereby inhibiting downstream GTP-hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated-tRNAs in initial selection and proofreading. Our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation.

We have studied the pH dependence of the rate of termination of bacterial protein synthesis catalyzed by a class-1 release factor (RF1 or RF2). We used a classical quench-flow technique and a newly developed stopped-flow technique that relies on the use of fluorescently labeled peptides. We found the termination rate to increase with increasing pH and, eventually, to saturate at about 70 s(-1) with an apparent pKa value of about 7.6. From our data, we suggest that class-1 RF termination is rate limited by the chemistry of ester bond hydrolysis at low pH and by a stop-codon-dependent and pH-independent conformational change of RFs at high pH. We propose that RF-dependent termination depends on the participation of a hydroxide ion rather than a water molecule in the hydrolysis of the ester bond between the P-site tRNA and its peptide chain. We provide a simple explanation for why the rate of termination saturated at high pH in our experiments but not in those of others.

When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away. Surprisingly, free RF2 is compact, with only 20 Å between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.

70S E-coli ribosomes bound to a trans-translation inhibitor. Using cryogenic electron microscopy, we have resolved the binding site of the drug and have observed novel conformational changes in the ribosomal protein L27. We will discuss how these observations help explain the mechanism by which drugs can target trans-translation without affecting normal translation. These studies will further help to improve the design of antibiotics that target rescue pathways in bacteria.

We used quench flow to study how N6-methylated adenosines (m6A) affect the accuracy ratio between kcat/Km (i.e. association rate constant (ka) times probability (Pp) of product formation after enzyme-substrate complex formation) for cognate and near-cognate substrate for mRNA reading by tRNAs and peptide release factors 1 and 2 (RFs) during translation with purified Escherichia coli components. We estimated kcat/Km for Glu-tRNAGlu, EF-Tu and GTP forming ternary complex (T3) reading cognate (GAA and Gm6AA) or near-cognate (GAU and Gm6AU) codons. ka decreased 10-fold by m6A introduction in cognate and near-cognate cases alike, while Pp for peptidyl transfer remained unaltered in cognate but increased 10-fold in near-cognate case leading to 10-fold amino acid substitution error increase. We estimated kcat/Km for ester bond hydrolysis of P-site bound peptidyl-tRNA by RF2 reading cognate (UAA and Um6AA) and near-cognate (UAG and Um6AG) stop codons to decrease 6-fold or 3-fold by m6A introduction, respectively. This 6-fold effect on UAA reading was also observed in a single-molecule termination assay. Thus, m6A reduces both sense and stop codon reading accuracy by decreasing cognate significantly more than near-cognate kcat/Km, in contrast to most error inducing agents and mutations, which increase near-cognate at unaltered cognate kcat/Km.

13When the mRNA translating ribosome encounters a stop codon in its aminoacyl site (A site), 14 it recruits a class-1 release factor (RF) to induce hydrolysis of the ester bond between 15 peptide chain and peptidyl-site (P-site) tRNA. This process, called termination of translation, 16 is under strong selection pressure for high speed and accuracy. Class-1 RFs (RF1, RF2 in 17 bacteria, eRF1 in eukarya and aRF1 in archaea), have structural motifs that recognize stop 18 codons in the decoding center (DC) and a universal GGQ motif for induction of ester bond 19 hydrolysis in the peptidyl transfer center (PTC) 70 Å away from the DC. The finding that free 20 RF2 is compact with only 20 Å between its codon reading and GGQ motifs came therefore as 21 a surprise 1 . Cryo-electron microscopy (cryo-EM) then showed that ribosome-bound RF1 and 22 RF2 have extended structures 2,3 , suggesting that bacterial RFs are compact when entering 23 the ribosome and switch to the extended form in a stop signal-dependent manner 3 . FRET 4 , 24 cryo-EM 5,6 and X-ray crystallography 7 , along with a rapid kinetics study suggesting a pre-25 termination conformational change on the millisecond time-scale of ribosome-bound RF1 26 and RF2 8 , have lent indirect support to this proposal. However, direct experimental evidence 27 for such a short-lived compact conformation on the native pathway to RF-dependent 28 termination is missing due to its transient nature. Here we use time-resolved cryo-29 EM 9,10,11,12,13 to visualize compact and extended forms of RF1 and RF2 at 3.5 and 4 Å 30 resolution, respectively, in the codon-recognizing complex on the pathway to termination. 31 About 25% of ribosomal complexes have RFs in the compact state at 24 ms reaction time 32 after mixing RF and ribosomes, and within 60 ms virtually all ribosome-bound RFs are 33 transformed to their extended forms. 34 Main 35 Most intracellular functions are carried out by proteins, assembled as chains of peptide-bond 36 linked amino acid (aa) residues on large ribonucleoprotein particles called ribosomes. The 37 aa-sequences are specified by information stored as deoxyribonucleic acid (DNA) sequences 38 in the genome and transcribed into sequences of messenger RNAs (mRNAs). The mRNAs are 39 translated into aa-sequences with the help of transfer RNAs (tRNAs) reading any of their 61 40 aa-encoding ribonucleotide triplets (codons). In termination of translation, the complete 41 protein is released from the ribosome by a class-1 release factor (RF) recognizing one of the 42 universal stop codons (UAA, UAG, and UGA), signaling the end of the amino acid encoding 43 open reading frame (ORF) of the mRNA. There are two RFs in bacteria, RF1 and RF2, one in 44 eukarya, eRF1, and one in archaea, aRF1.RF1 and RF2 read UAA, UAG, and UAA, UGA, 45 respectively, while the omnipotent eRF1 and aRF1 factors read all -codons. Stop codon-46 reading by RFs is aided by class-2 RFs, the GTPases RF3, eRF3 and aRF3 in bacteria, eukarya 47

In bacteria, release of newly synthesized proteins from ribosomes during translation termination is catalyzed by class-I release factors (RFs) RF1 or RF2, reading UAA and UAG or UAA and UGA codons, respectively. Class-I RFs are recycled from the post-termination ribosome by a class-II RF, the GTPase RF3, which accelerates ribosome intersubunit rotation and class-I RF dissociation. How conformational states of the ribosome are coupled to the binding and dissociation of the RFs remains unclear and the importance of ribosome-catalyzed guanine nucleotide exchange on RF3 for RF3 recycling in vivo has been disputed. Here, we profile these molecular events using a single-molecule fluorescence assay to clarify the timings of RF3 binding and ribosome intersubunit rotation that trigger class-I RF dissociation, GTP hydrolysis, and RF3 dissociation. These findings in conjunction with quantitative modeling of intracellular termination flows reveal rapid ribosome-dependent guanine nucleotide exchange to be crucial for RF3 action in vivo.

When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away. Surprisingly, free RF2 is compact, with only 20 Å between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.