Polypeptide chain release factors

Abstract

SummaryNewly synthesized polypeptide chains are released from peptidyl-tRNA when the ribosome encounters a stop signal on mRNA. Extra-ribosomal proteins (release factors) play an essential role in this process. Although the termination process was first discovered in the late 1960s, much of the mechanism has remained obscure. However, important steps have recently been made in both prokaryotic and eukaryotic organisms in unlocking the secrets of this vital stage in protein synthesis. In this review we summarize these advances and focus attention on the remaining areas of uncertainty, particularly with respect to the models that have been proposed for the action of the GTP-hydrolysing termination factors in prokaryotes and eukaryotes, i.e. RF3 and eRF3.The codon-specific release factors

Suppression of eukaryotic translation termination by selected RNAs

“…Sense triplets are decoded on the ribosome by specific transfer RNAs via base pairing between codons in mRNA and anticodon triplets in tRNA+ In contrast, nonsense (termination, stop) codons are decoded in two canonical ways+ UGA can be decoded as selenocysteine by a specialized tRNA-translation factor complex (selenocysteinyl-tRNA Sec : SelB) that directs SectRNA Sec to a unique message structure (Hüttenhofer & Bock, 1998)+ More frequently UGA, UAA, and UAG are decoded as stop-translation signals+ A single-polypeptide release factor (RF) termed eRF1 performs this function in eukaryotes and two proteins, RF1 and RF2, do so in bacteria (reviewed in Tate et al+, 1996;Buckingham et al+, 1997;)+ The class-1 release factor proteins RF1, RF2, and eRF1, are distinguished by their ability to trigger peptidyl-tRNA hydrolysis, catalyzed by the ribosomal peptidyl transferase when a stop codon enters the A site+ Although the nature of this hydrolytic signal remains unknown, it is clear that class-1 RF proteins strongly compete with suppressor tRNAs in vitro and in vivo (Weiss et al+, 1984;Curran & Yarus, 1988;Eggertsson & Soll, 1988;Drugeon et al+, 1997;Le Goff et al+, 1997)+ They therefore probably overlap the ribosomal decoding site+ As has been suggested (Cantor, 1979;Nissen et al+, 1995;Ito et al+, 1996;Nakamura et al+, 1996;Kisselev et al+, 2000) and proven recently by crystallography (Song et al+, 2000), eRF1 adopts an extended, perhaps tRNA-like overall shape+ Other proteins acting at the ribosomal A site, such as elongation factor EF-G and bacterial ribosome recycling factor (RRF; Nyborg et al+, 1996;Selmer et al+, 1999), also emulate the tRNA shape+ These structural findings support a "tRNA-analog" hypothesis ; that is, that termination codons may be decoded directly by class-1 RFs, whose similar shape allows mimicry of tRNA action+ Thus RFs may contact stop codons in the decoding (A) site on the ribosome+ These facts suggest that RF action would be effectively inhibited by other strongly bound RNAs+ Selected RNA ligands for RF protein(s) therefore might act as highly specific inhibitors of stop codon translation+ This would be useful for biochemical dissection of the pathway for translation termination+ In addition, be-cause a single eRF1 protein decodes all termination codons, such RNA ligands would likely comprise a new type of omnipotent termination suppressor, increasing stop codon readthrough by interfering with the usual termination pathway+ Therefore we have isolated eRF ligands using selection-amplification (for review, see Wilson & Szostak, 1999)+ Starting with a randomized mixture of oligoribonucleotides, repetitive selection for RNA-RF binding yielded RNAs with high affinity ...…”

Amber (UAG) suppressors affected in UGA/UAA‐specific polypeptide release factor 2 of bacteria: genetic prediction of initial binding to ribosome preceding stop codon recognition

“…Translation termination requires two classes of polypeptide release factors (RFs): a class-I factor, codon-specific RFs (RF1 and RF2 in prokaryotes; eRF1 in eukaryotes), and a class-II factor, nonspecific RFs (RF3 in prokaryotes; eRF3 in eukaryotes) that bind guanine nucleotides and stimulate class-I RF activity (Capecchi & Klein 1969;Caskey et al 1969;Goldstein & Caskey 1970; reviewed by Tate & Brown 1992;Nakamura et al 1996;Buckingham et al 1997).…”

Three distinct peptides from the N domain of translation termination factor eRF1 surround stop codon in the ribosome

“…RFs are GTPases that stimulate in vitro activity of the respective class-1 RFs and promote their release from the ribosome after peptidyl-tRNA hydrolysis (see Buckingham et al 1997;Kisselev and Buckingham 2000;Zavialov et al 2001;Alkalaeva et al 2006). In prokaryotes, there are two class-1 RFs, RF1 and RF2, decoding UAA/UAG and UAA/ UGA, respectively.…”