Molecular evolution: Please release me, genetic code
ABSTRACT 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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ABSTRACT: We previously employed a combinatorial approach to identify the most efficient suppressors of four-base codons in E. coli. We have now examined the suppression of two-, three-, four-, five-, and six-base codons with tRNAs containing 6-10 nt in their anticodon loops. We found that the E. coli translational machinery tolerates codons of 3-5 bases and that tRNAs with 6-10 nt anticodon loops can suppress these codons. However, N-length codons were found to prefer N + 4-length anticodon loops. Additionally, sequence preferences, including the requirement of Watson-Crick complementarity to the codon, were evident in the loops. These selections have yielded efficient suppressors of four-base and five-base codons for our ongoing efforts to expand the genetic code. They also highlight some of the parameters that underlie the fidelity of frame maintenance.Chemistry & Biology 03/2002; 9(2):237-44. DOI:10.1016/S1074-5521(02)00094-7 · 6.59 Impact Factor
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ABSTRACT: The discovery in the 1960s of an identical genetic code in Escherichia coli viruses and mammalian cells suggested that all living organisms use the same genetic code. The existence of a universal genetic code prompted Crick to propose the “Frozen Accident Theory” which states that the genetic code does not evolve. This theory was based on the assumption that in the last common ancestor, life-forms had reached a level of complexity that would not tolerate alterations in the identity of their codons. That is, once proteins had ac-quired a certain level of functionality, any alteration in codon identity would introduce struc-tural and functional disruption with a high probability that this would be lethal or highly detrimental.04/2007: pages 183-200;
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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 · 7.86 Impact Factor