Omnipotent decoding potential resides in eukaryotic translation termination factor eRF1 of variant-code organisms and is modulated by the interactions of amino acid sequences within domain 1

Ito, Koichi; Frolova, Ludmila; Seit-Nebi, Alim S.; Karamyshev, Andrey L.; Kisselev, Lev L.; Nakamura, Yoshikazu

doi:10.1073/pnas.142690099

Cited by 81 publications

(89 citation statements)

References 36 publications

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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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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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“…Normally, all three stop codons are bound and decoded by eRF1, which is a class I release factor with three functional domains (10, 42). Domain 1 binds to the stop codon and initiates the termination process (1,5,9,20,40). Domain 2 interacts with the peptidyl transferase center of the ribosome and mediates release of the completed polypeptide chain from the peptidyl-tRNA molecule in the ribosomal P site (12, 15).…”

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confidence: 99%

Distinct Paths To Stop Codon Reassignment by the Variant-Code Organisms Tetrahymena and Euplotes

Salas-Marco

Fan-Minogue

Kallmeyer

et al. 2006

Molecular and Cellular Biology

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The reassignment of stop codons is common among many ciliate species. For example, Tetrahymena species recognize only UGA as a stop codon, while Euplotes species recognize only UAA and UAG as stop codons. Recent studies have shown that domain 1 of the translation termination factor eRF1 mediates stop codon recognition. While it is commonly assumed that changes in domain 1 of ciliate eRF1s are responsible for altered stop codon recognition, this has never been demonstrated in vivo. To carry out such an analysis, we made hybrid proteins that contained eRF1 domain 1 from either Tetrahymena thermophila or Euplotes octocarinatus fused to eRF1 domains 2 and 3 from Saccharomyces cerevisiae. We found that the Tetrahymena hybrid eRF1 efficiently terminated at all three stop codons when expressed in yeast cells, indicating that domain 1 is not the sole determinant of stop codon recognition in Tetrahymena species. In contrast, the Euplotes hybrid facilitated efficient translation termination at UAA and UAG codons but not at the UGA codon. Together, these results indicate that while domain 1 facilitates stop codon recognition, other factors can influence this process. Our findings also indicate that these two ciliate species used distinct approaches to diverge from the universal genetic code.The near-universal nature of the standard genetic code implies that a barrier prevents organisms from easily evolving new coding strategies. However, exceptions to the standard code exist in mitochondria, ciliates, Mycoplasma, Candida, and other species (24). Among the ciliates, Tetrahymena species recognize UGA as a stop codon but have reassigned UAA and UAG to function as glutamine codons (16). Similarly, Euplotes species continue to recognize UAA and UAG as stop codons but have reassigned UGA to function as a cysteine codon (28). The existence of these alternate codes, which frequently include reassignment of the standard stop codons, raises obvious questions about how codon reassignment is carried out.In eukaryotes, the release factors eRF1 and eRF3 are required for translation termination (43,45). Normally, all three stop codons are bound and decoded by eRF1, which is a class I release factor with three functional domains (10, 42). Domain 1 binds to the stop codon and initiates the termination process (1,5,9,20,40). Domain 2 interacts with the peptidyl transferase center of the ribosome and mediates release of the completed polypeptide chain from the peptidyl-tRNA molecule in the ribosomal P site (12, 15). Domain 3 mediates an interaction between eRF1 and its functional partner, eRF3 (7,8,19,27). eRF3 is a class II release factor that contains a GTPase domain. GTP hydrolysis by eRF3 stimulates both polypeptide chain release and proper stop codon recognition by eRF1 (11,35).The eRF1 proteins from ciliates have the same basic domain structure as eRF1s from other eukaryotic species and also share significant sequence homology with them. For example, both Tetrahymena thermophila eRF1 and Euplotes octocarinatus eRF1 share ϳ56% overall a...

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“…A single RF is present in archaebacteria (aRF1) and the eukaryotic cytosol (eRF1), and each recognizes all three of the canonical stop codons used in these compartments (34,35). Eubacteria also use the three canonical stop codons but have two RFs; both recognize UAA, but RF1 alone has specificity for UAG, and only RF2 has specificity for UGA (29,36).…”

Section: What Are the Protein Factors That Recognize The Stop Codons?mentioning

confidence: 99%

Termination of Protein Synthesis in Mammalian Mitochondria

Chrzanowska-Lightowlers

Pajak

Lightowlers

2011

Journal of Biological Chemistry

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All mechanisms of protein synthesis can be considered in four stages: initiation, elongation, termination, and ribosome recycling. Remarkable progress has been made in understanding how these processes are mediated in the cytosol of many species; however, details of organellar protein synthesis remain sketchy. This is an important omission, as defects in human mitochondrial translation are known to cause disease and may contribute to the aging process itself. In this minireview, we focus on the recent advances that have been made in understanding how one of these processes, translation termination, occurs in the human mitochondrion.The synthesis of proteins is a fundamental mechanism of life. It is clearly essential that the process of mRNA translation, from which proteins are generated, is accurate and well controlled. Translation consists of four stages. The first is initiation, in which a repertoire of initiation factors coordinates the association of mRNA with the ribosomal subunits, recognition of the start codon, and its alignment with an fMet-tRNA Met in the ribosomal P-site. The second stage is elongation, which is facilitated by the action of elongation factors. These act in concert, causing the mRNA to move through the ribosome in steps corresponding to three nucleotides commonly referred to as a codon (1). This stepwise progression allows each codon to be decoded by the cognate aminoacylated tRNA, with the consequent addition of the corresponding amino acid to the nascent polypeptide (2). The third stage is termination, which occurs when a stop codon arrives in the ribosomal A-site and is recognized by a trans-acting protein termed a translation release (RF) 2 or termination factor. This acts in a ribosome-dependent manner, resulting in the nascent polypeptide being separated from the P-site tRNA, allowing the newly synthesized protein to be released from the ribosome. The final stage is that of ribosome recycling, in which the large (LSU) and small (SSU) ribosomal subunits are separated, and the mRNA is released so that the components can be used in a fresh cycle of translation.Extensive research on these individual steps has shown that, across the three domains of life, there are differences in both the cis-and trans-acting factors involved in carrying out these processes, resulting in mechanistic variations. Moreover, investigations into intraorganellar protein synthesis suggest that there are further subtleties to this process, with differences even between organelles from different organisms. To illustrate how the systems can differ as well as retain similarities, this minireview will concentrate on a single step in this process, namely translation termination, and focus on how mitochondria have organized their machinery to accomplish this process. TerminationTermination of translation occurs when a stop codon becomes positioned in the ribosomal A-site and is decoded by a protein moiety. This trans-acting factor (an RF) acts in an analogous fashion to the tRNAs, as it shows sequence-specific reco...

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Omnipotent decoding potential resides in eukaryotic translation termination factor eRF1 of variant-code organisms and is modulated by the interactions of amino acid sequences within domain 1

Cited by 81 publications

References 36 publications

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

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

Distinct Paths To Stop Codon Reassignment by the Variant-Code Organisms Tetrahymena and Euplotes

Termination of Protein Synthesis in Mammalian Mitochondria

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