Molecular evolution: Please release me, genetic code

Department of Biological Sciences, The University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA.
Current Biology (Impact Factor: 9.57). 02/2001; 11(2):R63-6. DOI: 10.1016/S0960-9822(01)00016-1
Source: PubMed


The genetic code is no longer universal, even in non-mitochondrial genomes. Recent studies have implicated the eukaryotic release factor eRF1 in mediating coding changes that are not as inconceivable as once thought. Specific residues in eRF1 proteins can be correlated with specific code changes in a wide variety of taxa.

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    • "Sequence alignment of eRF1s and the search for conserved residues within the N domain, which could vary following the reassignment of stop codons in ciliate eRF1, led to several hypotheses on eRF1 stop codon recognition (Inagaki and Doolittle, 2001; Lehman, 2001; Liang et al., 2001; Lozupone et al., 2001; Muramatsu et al., 2001; Inagaki et al., 2002). In vitro site-directed mutagenesis studies showed that the left part of the NIKS motif (positions 61 and 62) is important for the conservation of RF activity, whereas its right part (positions 63 and 64) and Arg residues in positions 65 and 68 are involved in ribosome binding (Frolova et al., 2002). "
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    ABSTRACT: To unravel the region of human eukaryotic release factor 1 (eRF1) that is close to stop codons within the ribosome, we used mRNAs containing a single photoactivatable 4-thiouridine (s(4)U) residue in the first position of stop or control sense codons. Accurate phasing of these mRNAs onto the ribosome was achieved by the addition of tRNA(Asp). Under these conditions, eRF1 was shown to crosslink exclusively to mRNAs containing a stop or s(4)UGG codon. A procedure that yielded (32)P-labeled eRF1 deprived of the mRNA chain was developed; analysis of the labeled peptides generated after specific cleavage of both wild-type and mutant eRF1s maps the crosslink in the tripeptide KSR (positions 63-65 of human eRF1) and points to K63 located in the conserved NIKS loop as the main crosslinking site. These data directly show the interaction of the N-terminal (N) domain of eRF1 with stop codons within the 40S ribosomal subunit and provide strong support for the positioning of the eRF1 middle (M) domain on the 60S subunit. Thus, the N and M domains mimic the tRNA anticodon and acceptor arms, respectively.
    The EMBO Journal 11/2002; 21(19):5302-11. DOI:10.1093/emboj/cdf484 · 10.43 Impact Factor
  • Cold Spring Harbor Symposia on Quantitative Biology 02/2001; 66:459-67. DOI:10.1101/sqb.2001.66.459
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    ABSTRACT: In eukaryotes, the polypeptide release factor 1 (eRF1) is involved in translation termination at all three stop codons. However, the mechanism for decoding stop codons remains unknown. A direct interaction of eRF1 with the stop codons has been postulated. Recent studies focus on eRF1 from ciliates in which some stop codons are reassigned to sense codons. Using an in vitro assay based on mammalian ribosomes, we show that eRF1 from the ciliate Euplotes aediculatus responds to UAA and UAG as stop codons and lacks the capacity to decipher the UGA codon, which encodes cysteine in this organism. This result strongly suggests that in ciliates with variant genetic codes eRF1 does not recognize the reassigned codons. Recent hypotheses describing stop codon discrimination by eRF1 are not fully consistent with the set of eRF1 sequences available so far and require direct experimental testing.
    EMBO Reports 09/2001; 2(8):680-4. DOI:10.1093/embo-reports/kve156 · 9.06 Impact Factor
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