UGA is translated as cysteine in pheromone 3 of Euplotes octocarinatus.

Meyer, F. A.; Schmidt, Helmut; Plümper, Evelyn; Hasilík, Andrej; Mersmann, Günther; Meyer, Helmut E.; Engström, Åke; Heckmann, Klaus

doi:10.1073/pnas.88.9.3758

Cited by 157 publications

(90 citation statements)

References 28 publications

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“…1). Their sequences include multiple ATG start codons and multiple TAA and TAG stop codons, which (it is worth recalling) some ciliates may use unconventionally to specify glutamine or glutamic acid so as, Euplotes in particular, may use TGA to specify cysteine instead of signaling stop to translation [16][17][18][19].…”

Section: Nucleotide Sequencesmentioning

confidence: 99%

Characterization of the pheromone gene family of an Antarctic and Arctic protozoan ciliate, Euplotes nobilii

Vallesi¹,

Alimenti²,

Terza³

et al. 2009

Marine Genomics

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Allelic genes encoding water-borne signal proteins (pheromones) were amplified and sequenced from the somatic (macronuclear) sub-chromosomic genome of Antarctic and Arctic strains of the marine ciliate, Euplotes nobilii. Their open reading frames appeared to be specific for polypeptide sequences of 83 to 94 amino acids identifiable with cytoplasmic pheromone precursors (pre-pro-pheromones), requiring two proteolytic steps to remove the pre-and pro-segments and secrete the mature pheromones. Differently from most of the macronuclear genes that have so far been characterized from Euplotes and other hypotrich ciliates, the 5' and 3' non-coding regions of all the seven E. nobilii pheromone genes are much longer than the coding regions (621 to 700 versus 214 to 285 nucleotides), and the 5' regions in particular show nearly identical sequences across the whole set of pheromone genes. These structural peculiarities of the non-coding regions are likely due to the presence of intron sequences and provide presumptive evidence that they are site of basic, conserved activities in the mechanism that regulates the expression of the E. nobilii pheromone genes. AbstractAllelic genes encoding water-borne signal proteins (pheromones) were amplified and sequenced from the somatic (macronuclear) sub-chromosomic genome of Antarctic and Arctic strains of the marine ciliate, Euplotes nobilii. Their open reading frames appeared to be specific for polypeptide sequences of 83 to 94 amino acids identifiable with cytoplasmic pheromone precursors (pre-propheromones), requiring two proteolytic steps to remove the pre-and pro-segments and secrete the mature pheromones. Differently from most of the macronuclear genes that have so far been characterized from Euplotes and other hypotrich ciliates, the 5' and 3' non-coding regions of all the seven E. nobilii pheromone genes are much longer than the coding regions (621 to 700 versus 214 to 285 nucleotides), and the 5' regions in particular show nearly identical sequences across the whole set of pheromone genes. These structural peculiarities of the non-coding regions are likely due to the presence of intron sequences and provide presumptive evidence that they are site of basic, conserved activities in the mechanism that regulates the expression of the E. nobilii pheromone genes.3

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Section: Nucleotide Sequencesmentioning

confidence: 99%

Characterization of the pheromone gene family of an Antarctic and Arctic protozoan ciliate, Euplotes nobilii

Vallesi¹,

Alimenti²,

Terza³

et al. 2009

Marine Genomics

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“…While the genome of M. genitalium contains a prfA gene encoding RF1, there is no homologue of the gene encoding UGA-decoding RF2 (prfB ; Fraser et al, 1995). Amongst eukaryote micro-organisms, the ciliate species of the genera Paramecium and Tetrahymena use UAA and UAG to encode glutamine (Caron & Meyer, 1985), while Euplotes species signal stop using UAA and UAG only, with UGA encoding cysteine (Meyer et al, 1991). Recently, an unclassified diplomonad species from the Hexamitidae has been discovered with an apparent stop codon reassignment to glutamine (Keeling & Doolittle, 1997).…”

Section: Release Factors and The Reassignment Of Stop Codons To Sensementioning

confidence: 99%

Endless possibilities: translation termination and stop codon recognition

et al. 2001

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OverviewThe process of protein synthesis can be divided into three main phases : initiation, during which the ribosomal subunits join the mRNA and locate the AUG initiator codon ; elongation, during which sense codons are decoded and the bulk of the polypeptide is made ; and termination, during which a stop codon directs the release of the completed polypeptide from the ribosome. Whereas the general principles of sense codon decoding by transfer RNAs are well established, a clear picture of translation termination and stop codon recognition has hitherto been lacking. Recently however, the use of optimized, complex, reconstituted in vitro termination reactions to identify the roles of key termination factors, and the solution of tertiary structures of termination factors, has allowed a reappraisal of termination factor structure and function. This review will describe these recent advances, many of which have resulted from studies of termination in micro-organisms, and in the light of the new information, discuss models for the mechanism of termination and recognition of the stop codon. While the mechanism of peptide chain termination is normally effective, stop codons are not always recognized efficiently, and during the translation of certain viral RNAs can be suppressed or read through, resulting in the expression of additional coding information. How stop codons are reassigned to encode ' sense ' at a given frequency in some RNAs will be reviewed in the context of current understanding of termination and stop codon recognition mechanisms. The translation termination apparatus in eukaryotes and prokaryotesDuring translation termination, a stop codon located in the ribosomal A-site is recognized by a release factor or release factor complex, which binds the ribosome and triggers release of the nascent peptide. In eukaryotes, translation is terminated by a heterodimer consisting of two proteins, release factors eRF1 and eRF3, which interact in vivo (Frolova et al., 1994 ;Zhouravleva et al., 1995 ;Stansfield et al., 1995). eRF1 recognizes all three stop codons and triggers peptidyl-tRNA hydrolysis by the ribosome, releasing the nascent peptide (Frolova et al., 1994 ; Drugeon et al., 1997). Eukaryote termination efficiency is enhanced by the GTPase release factor eRF3, the second component of the heterodimer eRF complex. In response to a stop codon in the ribosomal A-site, formation of a quaternary complex comprising the ribosome, eRF1, GTP and eRF3 triggers GTP hydrolysis and enhances the rate of peptidyl release (Zhouravleva et al., 1995 ; Frolova et al., 1994 ; Fig. 1). In yeast, eRF1 and eRF3 are encoded by essential genes (SUP35 and SUP45, respectively), mutations in which produce nonsense suppression phenotypes (Stansfield & Tuite, 1994).In contrast to eukaryotes, the role of stop codon recognition during translation termination in eubacteria is divided between two so-called class 1 release factors, RF1 and RF2, which in Escherichia coli are encoded by the essential prfA and prfB genes, respectively (Scolni...

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“…Capture of an eRF1 variant of stop-codon selectivity or of preference in other organisms would facilitate the study of eRF1s. Ciliates might provide us with such a tool based on the fact that some of them are known to possess UAA and UAG (or UGA) reassigned as a sense codon instead of a stop codon during evolution; for example, in Euplotes octacarinatus, UGA is decoded as Cys (12), and UAA and UAG are decoded as Gln in Tetrahymena thermophila (13)(14)(15)(16). Kervestin et al (17) showed recently, in an in vitro assay based on mammalian ribosomes, that eRF1 from the ciliate Euplotes aediculatus responds to UAA and UAG as stop codons and lacks the capacity to decipher UGA, which encodes Cys in this organism.…”

mentioning

confidence: 99%

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

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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UGA is translated as cysteine in pheromone 3 of Euplotes octocarinatus.

Cited by 157 publications

References 28 publications

Characterization of the pheromone gene family of an Antarctic and Arctic protozoan ciliate, Euplotes nobilii

Characterization of the pheromone gene family of an Antarctic and Arctic protozoan ciliate, Euplotes nobilii

Endless possibilities: translation termination and stop codon recognition

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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