Endless possibilities: translation termination and stop codon recognition

Abstract

OverviewThe process of protein synthesis can be divided into three main phases : initiation, during which the ribosomal subunits join the mRNA and locate the AUG initiator codon ; elongation, during which sense codons are decoded and the bulk of the polypeptide is made ; and termination, during which a stop codon directs the release of the completed polypeptide from the ribosome. Whereas the general principles of sense codon decoding by transfer RNAs are well established, a clear picture of translation termination and stop codon recognition has hitherto been lacking. Recently however, the use of optimized, complex, reconstituted in vitro termination reactions to identify the roles of key termination factors, and the solution of tertiary structures of termination factors, has allowed a reappraisal of termination factor structure and function. This review will describe these recent advances, many of which have resulted from studies of termination in micro-organisms, and in the light of the new information, discuss models for the mechanism of termination and recognition of the stop codon. While the mechanism of peptide chain termination is normally effective, stop codons are not always recognized efficiently, and during the translation of certain viral RNAs can be suppressed or read through, resulting in the expression of additional coding information. How stop codons are reassigned to encode ' sense ' at a given frequency in some RNAs will be reviewed in the context of current understanding of termination and stop codon recognition mechanisms. The translation termination apparatus in eukaryotes and prokaryotesDuring translation termination, a stop codon located in the ribosomal A-site is recognized by a release factor or release factor complex, which binds the ribosome and triggers release of the nascent peptide. In eukaryotes, translation is terminated by a heterodimer consisting of two proteins, release factors eRF1 and eRF3, which interact in vivo (Frolova et al., 1994 ;Zhouravleva et al., 1995 ;Stansfield et al., 1995). eRF1 recognizes all three stop codons and triggers peptidyl-tRNA hydrolysis by the ribosome, releasing the nascent peptide (Frolova et al., 1994 ; Drugeon et al., 1997). Eukaryote termination efficiency is enhanced by the GTPase release factor eRF3, the second component of the heterodimer eRF complex. In response to a stop codon in the ribosomal A-site, formation of a quaternary complex comprising the ribosome, eRF1, GTP and eRF3 triggers GTP hydrolysis and enhances the rate of peptidyl release (Zhouravleva et al., 1995 ; Frolova et al., 1994 ; Fig. 1). In yeast, eRF1 and eRF3 are encoded by essential genes (SUP35 and SUP45, respectively), mutations in which produce nonsense suppression phenotypes (Stansfield & Tuite, 1994).In contrast to eukaryotes, the role of stop codon recognition during translation termination in eubacteria is divided between two so-called class 1 release factors, RF1 and RF2, which in Escherichia coli are encoded by the essential prfA and prfB genes, respectively (Scolni...

Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code

“…Interestingly, tRNA Ile (UAU) is commonly utilized in eukaryotes, although tRNA Ile (UAU) can potentially be ambiguous with tRNA Met (CAU). Trp (CCA) shares a 2-codon sector with a stop codon, which is read in mRNA by a protein rather than a tRNA [15]. …”

“…Primitive archaea have 46 tRNAs and 3 stop codons. Translation termination signals are recognized by proteins (not tRNA) that bind to an mRNA stop codon in the ribosome decoding center and reach into the ribosome peptidyl transferase center to terminate translation [15]. Included in sets of 46 tRNAs are encoded 44 unique tRNA anticodons.…”

Eukaryotic release factors (eRFs) history

“…Possibly eRF3 has arisen in the early step of eukaryotic evolution because neither bacterial nor archaebacterial genomes contain any homologs of eRF3. The function of the class-2 release factors in translation termination has been extensively reviewed (Kisselev and Buckingham, 2000;Poole and Tate, 2000;Bertram et al, 2001;Kisselev et al, 2003). A model in which the GTPase activity of RF3 on ribosomes is stimulated by the presence of RF1 or RF2 suggests that both RF3 and eRF3 function in a similar way (Zavialov et al, 2001(Zavialov et al, , 2002.…”

“…However, the precise mechanisms of this process are still under investigation especially in relation to the crystal structure of the class-1 RFs. This aspect has been extensively reviewed over the last few years (Kisselev and Buckingham, 2000;Poole and Tate, 2000;Bertram et al, 2001;Kisselev et al, 2003).…”

“…This is the case of translation termination even though our knowledge has largely improved over the last few years. Several reviews described the recent findings in this field (Kisselev and Buckingham, 2000;Poole and Tate, 2000;Bertram et al, 2001;Kisselev et al, 2003). A general scheme of the translation termination complex in eukaryotes is shown in Fig.…”