The ‘polysemous’ codon—a codon with multiple amino acid assignment caused by dual specificity of tRNA identity

Abstract

In some Candida species, the universal CUG leucine codon is translated as serine. However, in most cases, the serine tRNAs responsible for this non‐universal decoding (tRNASerCAG) accept in vitro not only serine, but also, to some extent, leucine. Nucleotide replacement experiments indicated that m1G37 is critical for leucylation activity. This finding was supported by the fact that the tRNASerCAGs possessing the leucylation activity always have m1G37, whereas that of Candida cylindracea, which possesses no leucylation activity, has A37. Quantification of defined aminoacetylated tRNAs in cells demonstrated that 3% of the tRNASerCAGs possessing m1G37 were, in fact, charged with leucine in vivo. A genetic approach using an auxotroph mutant of C.maltosa possessing this type of tRNASerCAG also suggested that the URA3 gene inactivated due to the translation of CUG as serine was rescued by a slight incorporation of leucine into the polypeptide, which demonstrated that the tRNA charged with multiple amino acids could participate in the translation. These findings provide the first evidence that two distinct amino acids are assigned by a single codon, which occurs naturally in the translation process of certain Candida species. We term this novel type of codon a ‘polysemous codon’.

A Proteogenomic Pipeline for the Analysis of Protein Biosynthesis Errors in the Human Pathogen Candida albicans

“…The findings presented in our study are thus in agreement with previous research conducted using various MS approaches, fluorescence, and in vitro tRNA charging methods ( 16 , 17 , 27 ), which collectively refute the study by Mühlhausen et al. ( 54 ).…”

A Proteogenomic Pipeline for the Analysis of Protein Biosynthesis Errors in the Human Pathogen Candida albicans

“…The findings presented in our study are thus in agreement with previous research conducted using various MS approaches, fluorescence, and in vitro tRNA charging methods ( 16 , 17 , 27 ), which collectively refute the study by Mühlhausen et al. ( 54 ).…”

A proteogenomic pipeline for the analysis of protein biosynthesis errors in the human pathogen Candida albicans

“…The findings presented in our study are thus in agreement with previous research conducted using various MS approaches, fluorescence, and in vitro tRNA charging methods (Suzuki et al ., 1997, Gomes et al ., 2007, Bezerra et al ., 2013), which collectively refute the study by Mühlhausen et al . (Mühlhausen et al ., 2021).…”

“…The findings presented in our study are thus in agreement with previous research conducted using various MS approaches, fluorescence, and in vitro tRNA charging methods (Suzuki et al, 1997, Gomes et al, 2007, Bezerra et al, 2013, which collectively refute the study by Mühlhausen et al (Mühlhausen et al, 2021). Despite the low sensitivity and high variability among datasets and even between replicates from the same dataset, we found that whenever CUG mistranslation was identified, the associated error frequency was always higher than the global error of the sample (Figure 8).…”

Predicting the Binding Affinities of Misacylated tRNAs for Thermus thermophilus EF-Tu·GTP

“…Thus, the small amount (3%) of Leu-tRNA Ser observed in vivo is unlikely to be incorporated into protein. This conclusion is consistent with the fact that insertion of Leu at CUG codons could not be detected in two Candida species (41).…”

A Proteogenomic Pipeline for the Analysis of Protein Biosynthesis Errors in the Human Pathogen Candida albicans

“…The findings presented in our study are thus in agreement with previous research conducted using various MS approaches, fluorescence, and in vitro tRNA charging methods ( 16 , 17 , 27 ), which collectively refute the study by Mühlhausen et al. ( 54 ).…”

A proteogenomic pipeline for the analysis of protein biosynthesis errors in the human pathogen Candida albicans

“…The findings presented in our study are thus in agreement with previous research conducted using various MS approaches, fluorescence, and in vitro tRNA charging methods (Suzuki et al ., 1997, Gomes et al ., 2007, Bezerra et al ., 2013), which collectively refute the study by Mühlhausen et al . (Mühlhausen et al ., 2021).…”

“…The findings presented in our study are thus in agreement with previous research conducted using various MS approaches, fluorescence, and in vitro tRNA charging methods (Suzuki et al, 1997, Gomes et al, 2007, Bezerra et al, 2013, which collectively refute the study by Mühlhausen et al (Mühlhausen et al, 2021). Despite the low sensitivity and high variability among datasets and even between replicates from the same dataset, we found that whenever CUG mistranslation was identified, the associated error frequency was always higher than the global error of the sample (Figure 8).…”

Predicting the Binding Affinities of Misacylated tRNAs for Thermus thermophilus EF-Tu·GTP

“…Thus, the small amount (3%) of Leu-tRNA Ser observed in vivo is unlikely to be incorporated into protein. This conclusion is consistent with the fact that insertion of Leu at CUG codons could not be detected in two Candida species (41).…”

A Proteogenomic Pipeline for the Analysis of Protein Biosynthesis Errors in the Human Pathogen Candida albicans

“…The findings presented in our study are thus in agreement with previous research conducted using various MS approaches, fluorescence, and in vitro tRNA charging methods ( 16 , 17 , 27 ), which collectively refute the study by Mühlhausen et al. ( 54 ).…”

A proteogenomic pipeline for the analysis of protein biosynthesis errors in the human pathogen Candida albicans

“…The findings presented in our study are thus in agreement with previous research conducted using various MS approaches, fluorescence, and in vitro tRNA charging methods (Suzuki et al ., 1997, Gomes et al ., 2007, Bezerra et al ., 2013), which collectively refute the study by Mühlhausen et al . (Mühlhausen et al ., 2021).…”

“…The findings presented in our study are thus in agreement with previous research conducted using various MS approaches, fluorescence, and in vitro tRNA charging methods (Suzuki et al, 1997, Gomes et al, 2007, Bezerra et al, 2013, which collectively refute the study by Mühlhausen et al (Mühlhausen et al, 2021). Despite the low sensitivity and high variability among datasets and even between replicates from the same dataset, we found that whenever CUG mistranslation was identified, the associated error frequency was always higher than the global error of the sample (Figure 8).…”

Predicting the Binding Affinities of Misacylated tRNAs for Thermus thermophilus EF-Tu·GTP

“…Thus, the small amount (3%) of Leu-tRNA Ser observed in vivo is unlikely to be incorporated into protein. This conclusion is consistent with the fact that insertion of Leu at CUG codons could not be detected in two Candida species (41).…”