TRNA translocation

Macrolides, lincosamides and streptogramins are protein biosynthesis inhibitors that bind to 50S subunit of the ribosome and inhibit peptidyl tRNA translocation from the A-site to the P-site." Macrolides have a glycosylated 14-, 15- or 16-membered lactone ring structure and are produced by several species of Streptomyces. Lincosamide antibiotics were isolated initially from Streptomyces lincolnensis but later isolated from different species of Streptomcyces. Streptogramins were also isolated from Streptomycesgraminofaciens and subsequently from several different Streptomyces species. There are two structurally different streptogramins, A and B they are bacteriostatic individually and can be bactericidal when combined. 

The translocation reaction in E. coli. The translocation reaction occurs immediately after peptide synthesis. It involves displacement of the discharged tRNA from the P site and concerted movement of the peptidyl-tRNA and mRNA so that the peptidyl-tRNA is bound to the P site and the same three nucleotides in the mRNA. The A site is vacated and ready for the addition of another aminoacyl-tRNA. Translocation in eukaryotes is similar except that the EF-2 factor is involved instead of the EF-G factor. 

The process of tRNA translocation occurs in two discrete steps (Figure 13.16) ... 

Elongation is a cycUc process on the ribosome in which one amino acid at a time is added to the nascent peptide chain. The peptide sequence is determined by the order of the codons in the mRNA. Elongation involves several steps catalyzed by proteins called elongation factors (EFs). These steps are (1) binding of aminoacyl-tRNA to the A site, (2) peptide bond formation, and (3) translocation. 

The charging of the tRNA molecule with the aminoacyl moiety requires the hydrolysis of an ATP to an AMP, equivalent to the hydrolysis of two ATPs to two ADPs and phosphates. The entry of the aminoacyl-tRNA into the A site results in the hydrolysis of one GTP to GDP. Translocation of the newly formed pep-tidyl-tRNA in the A site into the P site by EF2 similarly results in hydrolysis of GTP to GDP and phosphate. Thus, the energy requirements for the formation of one peptide bond include the equivalent of the hydrolysis of two ATP molecules to ADP and of two GTP molecules to GDP, or the hydrolysis of four high-energy phosphate bonds. A eukaryotic ribosome can incorporate as many as six amino acids per second prokaryotic ribosomes incorporate as many as 18 per second. Thus, the process of peptide synthesis occurs with great speed and accuracy until a termination codon is reached. 

Bacterial ribosome function Aminoglycosides Tetracyclines Chloramphenicol Macrolides, azalides Fusidic acid Mupirocin Distort SOS ribosomal subunit Block SOS ribosomal subunit Inhibits peptidyl transferase Block translocation Inhibits elongation factor Inhibits isoleucyl-tRNA synthesis No action on 40S subunit Excluded by mammalian cells No action on mammalian equivalent No action on mammalian equivalent Excluded by mammalian cells No action on mammalian equivalent... 

After formation of the initiation dipeptide, the first EF-G-dependent translocation allows binding of the third aminoacyl-tRNA in the A-site so that a tripeptide is formed. The apparent rate of this event may depend upon the nature of the initiation complex initially formed, being slower, for instance, with those containing mRNAs with an extended SD sequence than with those having either very short or no SD complementarity (C. O. G. and M. Rodnina, unpublished results). Furthermore, very powerful translocation inhibitors may block tripeptide formation to such an extent that they mimic translation initiation inhibitors. 

Several key concepts are worth remembering. GTP is used as an energy source for translation, but ATP is used to form the aminoacyl-tRNA. The ribosome effectively has two kinds of tRNA binding sites. Only tRNAMet can bind to the P (for peptide) site, and this only occurs during the initial formation of the functional ribosome (initiation). All other aminoacyl-tRNAs enter at the A (for amino acid) binding site. After formation of the peptide bond (this doesn t require GTP hydrolysis), the tRNA with the growing peptide attached is moved (translocated) to the other site (this does require GTP hydrolysis). 

For processive peptide polymerization, the rihosome has to move along the mRNA. Following peptide bond formation, the rihosomal A site is occupied hy a peptidyl-tRNA whereas the P site contains a deacylated tRNA. During translocation, the complex of the two tRNAs with the mRNA has to move relative to the ribosome to... 

In order to allow for translocation of the tRNA-mRNA complex, the ribosome will have to undergo conformational changes as well. The contacts described above between the decoding center and the codon-anticodon helix as well as the base pairs between the SOS A and P loops and the tRNA acceptor stems will have... 

Figure 8 EF-G-catalyzed translocation of the tRNA-mRNA complex within the ribosome, (a) Hybrid state formation and intersubunit rotation. Upon peptide bond formation, the ribosome fluctuates between the classical state and a hybrid state. In the classical state, the tRNAs are bound to the A and P site on both the 308 and 508 subunit. In the hybrid state, the anticodons remain in the A and P site on the 308 subunit whereas the acceptor ends move into the P and E site on the 508 subunit, respectively. 8imultaneously to hybrid state formation, the 308 subunit rotates relative to the 508 subunit as shown on the right site, (b) Kinetic mechanism of EF-G-catalyzed translocation. Upon GTP hydrolysis, unlocking occurs through a ribosomal rearrangement. Only subsequently, tRNA and mRNA movement as well as dissociation of the inorganic phosphate from EF-G take place.

The intersubunit rotation is required for translocation as ribosomes trapped in the nonrotated state by an engineered intersubunit disulfide bridge fail in tRNA-mRNA movement. Real-time observation of intersubunit movement by fluorescence resonance energy transfer (FRET) showed that intersubunit movement occurs concomitantly with hybrid state formation, and that the rotated state can be trapped by the antibiotic viomycin. Similarly to the fluctuation of tRNAs between classical and hybrid states, single-molecule studies have detected spontaneous intersubunit movement where the 3 OS subunit fluctuates between a rotated... 

In the translocation step, the ribosome moves exactly three nudeotides (one codon) along the message. This moves the growing peptidyl-tRNA into the P site and aligns the next codon to be translated with the empty A site. 

A nasopharyngeal swab obtained from a 4-month-old infrint with rhinitis and paroxysmal coughing tested positive upon culture for Bordetella pertussis. He was admitted to the hospital for therapy with an antibiotic that inhibits the translocation of peptidyl-tRNA on 70S ribosomes, This patient was most likely treated with... 

Then the peptidyl-tRNA at the A site is translocated to the P site by the ribosome moving along the mRNA a codon at a time, exposing the A site for a new aminoacyl-tRNA appropriate for the particular codon, and a repeat of the elongation process occurs. The cycles of elongation and translocation continue until a termination codon is reached, and the peptide or protein is then hydrolysed and released... 

The ribosome then translocates to the next codon, with the peptidyl-tRNA shifting from the A site to the P site and the now uncharged tRNA exiting the ribosome from the E site. 

Macrolides bind to the SOS ribosomal subunit of bacteria but not to the SOS mammalian ribosome this accounts for its selective toxicity. Binding to the ribosome occurs at a site near peptidyltransferase, with a resultant inhibition of translocation, peptide bond formation, and release of oligopeptidyl tRNA. However, unlike chloramphenicol, the macrolides do not inhibit protein synthesis by intact mitochondria, and this suggests that the mitochondrial membrane is not permeable to erythromycin. 

Emetine and dehydroemetine are natural alkaloid obtained from Cephaelis ipecacuanha and synthetic analog respectively. They are effective against tissue trophozoites of . histolytica. It has no effect on cysts but effective in amoebic liver abscess also. It acts by inhibiting protein synthesis by arresting intraribosome translocation of tRNA-amino acid complex. Dehydroemetine is less toxic than emetine and very effective drug for tissue amoebiasis. It is more rapidly eliminated from the body than emetine. 

Elongation Step 3 Translocation In the final step of the elongation cycle, translocation, the ribosome moves one codon toward the 3 end of the mRNA (Fig. 27-25a). This movement shifts the anticodon of the dipeptidyl-tRNA, which is still attached to the second codon of the mRNA, from the A site to the P site, and shifts the de-acylated tRNA from the P site to the E site, from where the tRNA is released into the cytosol. The third codon of the mRNA now lies in the A site and the second codon in the P site. Movement of the ribosome along the mRNA requires EF-G (also known as translocase) and the energy provided by hydrolysis of another molecule of GTP. 

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