Highly conserved NIKS tetrapeptide is functionally essential in eukaryotic translation termination factor eRF1

Frolova, Ludmila; Seit-Nebi, Alim S.; Kisselev, Lev L.

doi:10.1017/s1355838202013262

Cited by 127 publications

(140 citation statements)

References 28 publications

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“…Structural studies of human RF1 suggest that its N-terminal domain interacts with mRNA during stop codon recognition (30). Numerous studies demonstrated that the sequences near the highly conserved NIKS motif in this domain are critical for stop codon recognition (31)(32)(33). If UAG codons were reassigned to code for Pyl in Pyl-containing archaea, their release factors would have specific changes responsible for the alteration of their specificity.…”

Section: Analysis Of Class I Release Factors In Archaeamentioning

confidence: 99%

Pyrrolysine and Selenocysteine Use Dissimilar Decoding Strategies

Zhang

Baranov

Atkins

et al. 2005

Journal of Biological Chemistry

116

106

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Selenocysteine (Sec) and pyrrolysine (Pyl) are known as the 21st and 22nd amino acids in protein. Both are encoded by codons that normally function as stop signals. Sec specification by UGA codons requires the presence of a cis-acting selenocysteine insertion sequence (SECIS) element. Similarly, it is thought that Pyl is inserted by UAG codons with the help of a putative pyrrolysine insertion sequence (PYLIS) element. Herein, we analyzed the occurrence of Pyl-utilizing organisms, Pylassociated genes, and Pyl-containing proteins. The Pyl trait is restricted to several microbes, and only one organism has both Pyl and Sec. We found that methanogenic archaea that utilize Pyl have few genes that contain in-frame UAG codons, and many of these are followed with nearby UAA or UGA codons. In addition, unambiguous UAG stop signals could not be identified. This bias was not observed in Sec-utilizing organisms and non-Pyl-utilizing archaea, as well as with other stop codons. These observations as well as analyses of the coding potential of UAG codons, overlapping genes, and release factor sequences suggest that UAG is not a typical stop signal in Pyl-utilizing archaea. On the other hand, searches for conserved Pyl-containing proteins revealed only four protein families, including methylamine methyltransferases and transposases. Only methylamine methyltransferases matched the Pyl trait and had conserved Pyl, suggesting that this amino acid is used primarily by these enzymes. These findings are best explained by a model wherein UAG codons may have ambiguous meaning and Pyl insertion can effectively compete with translation termination for UAG codons obviating the need for a specific PYLIS structure. Thus, Sec and Pyl follow dissimilar decoding and evolutionary strategies.

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Section: Analysis Of Class I Release Factors In Archaeamentioning

confidence: 99%

Pyrrolysine and Selenocysteine Use Dissimilar Decoding Strategies

Zhang

Baranov

Atkins

et al. 2005

Journal of Biological Chemistry

116

106

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“…It was proposed that the N and M domains could form a functionally active "core" domain (Frolova et al, 2000). Possibly, all domains contain ribosome-interacting sites (Eurwilaichitr et al, 1999;Frolova et al, 1999Frolova et al, , 2002.…”

Section: Eukaryotic Release Factors 1 (Erf1)mentioning

confidence: 99%

Eukaryotic release factors (eRFs) history

Инге-Вечтомов

Zhouravleva

Maury

2003

Biology of the Cell

114

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In the present review, we describe the history of the identification of the eukaryotic translation termination factors eRF1 and eRF3. As in the case of several proteins involved in general and essential processes in all cells (e.g., DNA replication, gene expression regulation...) the strategies and methodologies used to identify these release factors were first established in prokaryotes. The genetic investigations in Saccharomyces cerevisiae have made a major contribution in the field. A large amount of data have been produced, from which it was concluded that the SUP45 and SUP35 genes were controlling translation termination but were also involved in other functions important for the cell organization and the cell cycle accomplishment. This does not seem to be restricted to yeast but is also probably the case in eukaryotes in general. The biochemical studies of the proteins encoded by the higher eukaryote homologs of SUP45 and SUP35 were efficient and permitted the identification of eRF1 as being the key protein in the termination process, eRF3 having a stimulating role. Around 25 years were needed after the identification of sup45 and sup35 mutants for the characterization of their gene products as eRF1 and eRF3, respectively. It also has to be pointed out that if the results came first from bacteria, the identification of RF3 and eRF3 was made practically at the same time. Moreover, eRF1 was the first crystal structure obtained for a class-1 release factor, the bacterial RF2 structure came later. The goal is now to understand at the molecular level the roles of both eRF1 and eRF3 in addition to their translation termination functions.

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“…The ciliate-specific diversity at TAS and NIKS sites also has been pointed out independently (1,22,23). Recently, the role of NIKS motif in RF activity and ribosome binding has been shown for human eRF1 in in vitro experiments (24). Therefore, it is tempting to speculate that the TASNIKS heptapeptide region is functionally essential and can modulate stop codon discrimination in eukaryotes.…”

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confidence: 91%

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

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Frolova

Seit-Nebi

et al. 2002

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

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In eukaryotes, a single translational release factor, eRF1, deciphers three stop codons, although its decoding mechanism remains puzzling. In the ciliate Tetrahymena thermophila, UAA and UAG codons are reassigned to Gln codons. A yeast eRF1-domain swap containing Tetrahymena domain 1 responded only to UGA in vitro and failed to complement a defect in yeast eRF1 in vivo at 37°C. This finding demonstrates that decoding specificity of eRF1 from variant code organisms resides at domain 1. However, the wild-type eRF1 hybrid fully restored the growth of eRF1-deficient yeast at 30°C. Tetrahymena eRF1 contains a variant sequence, KATNIKD, at the tip of domain 1. The TASNIKD variant of hybrid eRF1 rendered the eRF1-nullified yeast viable, although in an in vitro assay, the same hybrid eRF1 responded only to UGA. Nevertheless, the yeast eRF1 bearing the KATNIKD motif instead of the TASNIKS heptapeptide present in higher eukaryotes remains omnipotent in vivo. Collectively, these data suggest that variant genetic code organisms like Tetrahymena have an intrinsic potential to decode three stop codons in vivo, and that interaction within domain 1 between the KAT tripeptide and other sequences modulates the decoding specificity of Tetrahymena eRF1.

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Highly conserved NIKS tetrapeptide is functionally essential in eukaryotic translation termination factor eRF1

Cited by 127 publications

References 28 publications

Pyrrolysine and Selenocysteine Use Dissimilar Decoding Strategies

Pyrrolysine and Selenocysteine Use Dissimilar Decoding Strategies

Eukaryotic release factors (eRFs) history

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

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