Distinct eRF3 Requirements Suggest Alternate eRF1 Conformations Mediate Peptide Release during Eukaryotic Translation Termination

Fan-Minogue, Hua; Du, Ming; Pisarev, Andrey V.; Kallmeyer, Adam K.; Salas-Marco, Joe; Keeling, Kim M.; Thompson, Sunnie R.; Pestova, Tatyana V.; Bedwell, David M.

doi:10.1016/j.molcel.2008.03.020

Cited by 60 publications

(87 citation statements)

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“…In general, these species either utilize UGA as a stop codon (with UAA and UAG recoded to glutamine codons) (Horowitz and Gorovsky 1985;Lozupone et al 2001;Kim et al 2005) or UAA/UAG as stop codons (with UGA recoded to cysteine or tryptophan codons) (Meyer et al 1991;Lozupone et al 2001). Past studies found that fusion of eRF1 domain one from a variant code organism to eRF1 domains two and three from a standard code organism often conferred variant stop codon recognition (Kervestin et al 2001;SalasMarco et al 2006;Lekomtsev et al 2007a,b;Fan-Minogue et al 2008;Eliseev et al 2011). These results demonstrated that eRF1 domain one plays a key role in stop codon recognition.…”

Section: Introductionmentioning

confidence: 99%

“…1A; Knight et al 2000;Song et al 2000;Lozupone et al 2001;Kim et al 2005), suggesting that these sequence elements play a role in stop codon recognition. Mutagenesis studies examined the effects of changing amino acids within the TASNIKS and YCF motifs of eRF1 (Bertram et al 2000;Frolova et al 2002;Seit-Nebi et al 2002;Kolosov et al 2005;Fan-Minogue et al 2008;Cheng et al 2009). Those studies confirmed the general importance of both motifs in stop codon recognition.…”

Section: Introductionmentioning

confidence: 99%

“…In the current study, we used a previously established yeast system to determine the effects of different eRF1 mutations on stop codon selectivity (Keeling et al 2004;Salas-Marco and Bedwell 2004;Kallmeyer et al 2006;SalasMarco et al 2006;Fan-Minogue et al 2008). In particular, we compared the relative importance of the TASNIKS and YCF motifs in stop codon recognition.…”

Section: Introductionmentioning

confidence: 99%

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Identification of eRF1 residues that play critical and complementary roles in stop codon recognition

Conard

Buckley²,

Dang³

et al. 2012

RNA

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The initiation and elongation stages of translation are directed by codon-anticodon interactions. In contrast, a release factor protein mediates stop codon recognition prior to polypeptide chain release. Previous studies have identified specific regions of eukaryotic release factor one (eRF1) that are important for decoding each stop codon. The cavity model for eukaryotic stop codon recognition suggests that three binding pockets/cavities located on the surface of eRF1's domain one are key elements in stop codon recognition. Thus, the model predicts that amino acid changes in or near these cavities should influence termination in a stop codon-dependent manner. Previous studies have suggested that the TASNIKS and YCF motifs within eRF1 domain one play important roles in stop codon recognition. These motifs are highly conserved in standard code organisms that use UAA, UAG, and UGA as stop codons, but are more divergent in variant code organisms that have reassigned a subset of stop codons to sense codons. In the current study, we separately introduced TASNIKS and YCF motifs from six variant code organisms into eRF1 of Saccharomyces cerevisiae to determine their effect on stop codon recognition in vivo. We also examined the consequences of additional changes at residues located between the TASNIKS and YCF motifs. Overall, our results indicate that changes near cavities two and three frequently mediated significant effects on stop codon selectivity. In particular, changes in the YCF motif, rather than the TASNIKS motif, correlated most consistently with variant code stop codon selectivity.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification of eRF1 residues that play critical and complementary roles in stop codon recognition

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Buckley²,

Dang³

et al. 2012

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“…The M domain mimics the tRNA acceptor stem and contains a universal GGQ motif common to all class-1 RFs, which is located at the tip of the M domain of eRF1 and is essential for peptidyl-tRNA hydrolysis at the peptidyl transferase center Song et al 2000;Seit-Nebi et al 2001;Klaholz et al 2003;Mora et al 2003;Rawat et al 2003;Scarlett et al 2003;Petry et al 2005). The N domain mimics the tRNA anticodon arm and contains two loops with the highly conserved YxCxxxF (positions 125-131) and NIKS (positions 61-64) motifs that play a critical role in stop-codon recognition Ito et al 2002;Seit-Nebi et al 2002;Kolosov et al 2005;Fan-Minogue et al 2008;Cheng et al 2009). Evidence that the first nucleotide of a stop codon at the A site contacts K63 in the NIKS motif of human eRF1 has been obtained (Chavatte et al 2002) by cross-linking experiments with an mRNA analog containing a 4-thiouridine (s 4 U) residue at the first position of the stop codon phased on the ribosome by a tRNA Asp cognate to the Asp codon, which is located 59 to the stop codon (Chavatte et al 2001).…”

Section: Introductionmentioning

confidence: 99%

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

Bulygin¹,

Khairulina²,

Kolosov³

et al. 2010

RNA

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To study positioning of the polypeptide release factor eRF1 toward a stop signal in the ribosomal decoding site, we applied photoactivatable mRNA analogs, derivatives of oligoribonucleotides. The human eRF1 peptides cross-linked to these short mRNAs were identified. Cross-linkers on the guanines at the second, third, and fourth stop signal positions modified fragment 31-33, and to lesser extent amino acids within region 121-131 (the ''YxCxxxF loop'') in the N domain. Hence, both regions are involved in the recognition of the purines. A cross-linker at the first uridine of the stop codon modifies Val66 near the NIKS loop (positions 61-64), and this region is important for recognition of the first uridine of stop codons. Since the N domain distinct regions of eRF1 are involved in a stop-codon decoding, the eRF1 decoding site is discontinuous and is not of ''protein anticodon'' type. By molecular modeling, the eRF1 molecule can be fitted to the A site proximal to the P-site-bound tRNA and to a stop codon in mRNA via a large conformational change to one of its three domains. In the simulated eRF1 conformation, the YxCxxxF motif and positions 31-33 are very close to a stop codon, which becomes also proximal to several parts of the C domain. Thus, in the A-site-bound state, the eRF1 conformation significantly differs from those in crystals and solution. The model suggested for eRF1 conformation in the ribosomal A site and cross-linking data are compatible.

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“…The N domain is responsible for stop codon recognition, which is achieved through a 3D network of conserved residues that include apical TASNIKS (amino acid sequence: threonine-alanine-serine-asparagine-isoleucine-lysine-serine) and YxCxxxF motifs (e.g., refs. [9][10][11][12]. Domain M contains the universally conserved GGQ motif, which is critical for triggering peptide release: as shown for prokaryotes, its placement into the peptidyl transferase center (PTC) causes rRNA rearrangement, allowing a water molecule to enter (for review, see ref.…”

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confidence: 99%

Cryo-EM structure of the mammalian eukaryotic release factor eRF1–eRF3-associated termination complex

Taylor

Unbehaun

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Eukaryotic translation termination results from the complex functional interplay between two eukaryotic release factors, eRF1 and eRF3, and the ribosome, in which GTP hydrolysis by eRF3 couples codon recognition with peptidyl-tRNA hydrolysis by eRF1. Here, using cryo-electron microscopy (cryo-EM) and flexible fitting, we determined the structure of eRF1-eRF3-guanosine 5′- [β,γ-imido] triphosphate (GMPPNP)-bound ribosomal pretermination complex (pre-TC), which corresponds to the initial, pre-GTP hydrolysis stage of factor attachment. Our results show that eukaryotic translation termination involves a network of interactions between the two release factors and the ribosome. Our structure provides mechanistic insight into the coordination between GTP hydrolysis by eRF3 and subsequent peptide release by eRF1.T ermination of translation occurs when a ribosome reaches the end of the coding region and a stop codon (UAA, UAG, or UGA) enters the aminoacyl tRNA binding site (A site), leaving peptidyl-tRNA in the peptidyl tRNA binding site (P site). It entails stop codon recognition by specialized release factors followed by hydrolysis of peptidyl-tRNA. In eukaryotes, termination is mediated by the concerted action of two directly interacting release factors, eRF1 and eRF3. eRF1 is responsible for stop codon recognition and inducing hydrolysis of peptidyl-tRNA, whereas eRF3, a ribosome-dependent GTPase, strongly stimulates peptide release by eRF1 in a GTP-dependent manner (for review, see ref. 1).eRF1 also participates in ribosome recycling: after peptide release it remains associated with the ribosome and together with ATP-binding cassette sub-family E member 1 (ABCE1) promotes splitting the ribosome into free 60S and tRNA/mRNA-associated 40S subunits (2). eRF1 and eRF3 have paralogs, Dom34 (yeast)/ Pelota (mammals) and Hbs1, respectively, which do not participate in termination but instead play a key role in No-go and nonstop decay surveillance mechanisms (e.g., see refs. 3, 4). Dom34/Pelota and Hbs1 do not induce peptide release in a mechanism similar to eRFs. Instead, they cooperate with ABCE1 to promote dissociation of stalled elongation complexes, which is accompanied by peptidyltRNA drop off (5-7). eRF1 comprises N-terminal (N), middle (M), and C-terminal (C) domains (8). The N domain is responsible for stop codon recognition, which is achieved through a 3D network of conserved residues that include apical TASNIKS (amino acid sequence: threonine-alanine-serine-asparagine-isoleucine-lysine-serine) and YxCxxxF motifs (e.g., refs. 9-12). Domain M contains the universally conserved GGQ motif, which is critical for triggering peptide release: as shown for prokaryotes, its placement into the peptidyl transferase center (PTC) causes rRNA rearrangement, allowing a water molecule to enter (for review, see ref. 13). The rigid core of domain C forms an α-β sandwich (8) that deviates from the standard form by the presence of a small insertion, which forms a minidomain (14). eRF3 consists of an N-terminal sequence (residues 1-...

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Distinct eRF3 Requirements Suggest Alternate eRF1 Conformations Mediate Peptide Release during Eukaryotic Translation Termination

Cited by 60 publications

References 30 publications

Identification of eRF1 residues that play critical and complementary roles in stop codon recognition

Identification of eRF1 residues that play critical and complementary roles in stop codon recognition

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

Cryo-EM structure of the mammalian eukaryotic release factor eRF1–eRF3-associated termination complex

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