Alternative CUG Codon Usage in the Halotolerant Yeast <i>Debaryomyces hansenii</i>: Gene Expression Profiles Provide New Insights into Ambiguous Translation
The halotolerant yeast <i>Debaryomyces hansenii</i> belongs to the CTG-Ser1 clade of fungal species that use the CUG codon to translate as leucine or serine. The ambiguous decoding of the CUG codon is relevant for expanding protein diversity, but little is known about the role of leucine...
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| Format: | Article |
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MDPI AG
2022-09-01
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| Series: | Journal of Fungi |
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| Online Access: | https://www.mdpi.com/2309-608X/8/9/970 |
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| author | Daniel Ochoa-Gutiérrez Anya M. Reyes-Torres Ileana de la Fuente-Colmenares Viviana Escobar-Sánchez James González Rosario Ortiz-Hernández Nayeli Torres-Ramírez Claudia Segal-Kischinevzky |
| author_facet | Daniel Ochoa-Gutiérrez Anya M. Reyes-Torres Ileana de la Fuente-Colmenares Viviana Escobar-Sánchez James González Rosario Ortiz-Hernández Nayeli Torres-Ramírez Claudia Segal-Kischinevzky |
| author_sort | Daniel Ochoa-Gutiérrez |
| collection | DOAJ |
| description | The halotolerant yeast <i>Debaryomyces hansenii</i> belongs to the CTG-Ser1 clade of fungal species that use the CUG codon to translate as leucine or serine. The ambiguous decoding of the CUG codon is relevant for expanding protein diversity, but little is known about the role of leucine–serine ambiguity in cellular adaptations to extreme environments. Here, we examine sequences and structures of tRNA<sub>CAG</sub> from the CTG-Ser1 clade yeasts, finding that <i>D. hansenii</i> conserves the elements to translate ambiguously. Then, we show that <i>D. hansenii</i> has tolerance to conditions of salinity, acidity, alkalinity, and oxidative stress associated with phenotypic and ultrastructural changes. In these conditions, we found differential expression in both the logarithmic and stationary growth phases of tRNA<sup>Ser</sup>, tRNA<sup>Leu</sup>, tRNA<sub>CAG</sub>, LeuRS, and SerRS genes that could be involved in the adaptive process of this yeast. Finally, we compare the proteomic isoelectric points and hydropathy profiles, detecting that the most important variations among the physicochemical characteristics of <i>D. hansenii</i> proteins are in their hydrophobic and hydrophilic interactions with the medium. We propose that the ambiguous translation, i.e., leucylation or serynation, on translation of the CUG-encoded residues, could be linked to adaptation processes in extreme environments. |
| first_indexed | 2024-03-09T23:29:50Z |
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| institution | Directory Open Access Journal |
| issn | 2309-608X |
| language | English |
| last_indexed | 2024-03-09T23:29:50Z |
| publishDate | 2022-09-01 |
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| record_format | Article |
| series | Journal of Fungi |
| spelling | doaj.art-0153b23f8e49462eacbe6400167a7e872023-11-23T17:10:06ZengMDPI AGJournal of Fungi2309-608X2022-09-018997010.3390/jof8090970Alternative CUG Codon Usage in the Halotolerant Yeast <i>Debaryomyces hansenii</i>: Gene Expression Profiles Provide New Insights into Ambiguous TranslationDaniel Ochoa-Gutiérrez0Anya M. Reyes-Torres1Ileana de la Fuente-Colmenares2Viviana Escobar-Sánchez3James González4Rosario Ortiz-Hernández5Nayeli Torres-Ramírez6Claudia Segal-Kischinevzky7Laboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, MexicoLaboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, MexicoLaboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, MexicoLaboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, MexicoLaboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, MexicoLaboratorio de Microscopía Electrónica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, MexicoLaboratorio de Microscopía Electrónica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, MexicoLaboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, MexicoThe halotolerant yeast <i>Debaryomyces hansenii</i> belongs to the CTG-Ser1 clade of fungal species that use the CUG codon to translate as leucine or serine. The ambiguous decoding of the CUG codon is relevant for expanding protein diversity, but little is known about the role of leucine–serine ambiguity in cellular adaptations to extreme environments. Here, we examine sequences and structures of tRNA<sub>CAG</sub> from the CTG-Ser1 clade yeasts, finding that <i>D. hansenii</i> conserves the elements to translate ambiguously. Then, we show that <i>D. hansenii</i> has tolerance to conditions of salinity, acidity, alkalinity, and oxidative stress associated with phenotypic and ultrastructural changes. In these conditions, we found differential expression in both the logarithmic and stationary growth phases of tRNA<sup>Ser</sup>, tRNA<sup>Leu</sup>, tRNA<sub>CAG</sub>, LeuRS, and SerRS genes that could be involved in the adaptive process of this yeast. Finally, we compare the proteomic isoelectric points and hydropathy profiles, detecting that the most important variations among the physicochemical characteristics of <i>D. hansenii</i> proteins are in their hydrophobic and hydrophilic interactions with the medium. We propose that the ambiguous translation, i.e., leucylation or serynation, on translation of the CUG-encoded residues, could be linked to adaptation processes in extreme environments.https://www.mdpi.com/2309-608X/8/9/970CTG-Ser1 cladeambiguous translationCUG codonmistranslationserynationleucylation |
| spellingShingle | Daniel Ochoa-Gutiérrez Anya M. Reyes-Torres Ileana de la Fuente-Colmenares Viviana Escobar-Sánchez James González Rosario Ortiz-Hernández Nayeli Torres-Ramírez Claudia Segal-Kischinevzky Alternative CUG Codon Usage in the Halotolerant Yeast <i>Debaryomyces hansenii</i>: Gene Expression Profiles Provide New Insights into Ambiguous Translation Journal of Fungi CTG-Ser1 clade ambiguous translation CUG codon mistranslation serynation leucylation |
| title | Alternative CUG Codon Usage in the Halotolerant Yeast <i>Debaryomyces hansenii</i>: Gene Expression Profiles Provide New Insights into Ambiguous Translation |
| title_full | Alternative CUG Codon Usage in the Halotolerant Yeast <i>Debaryomyces hansenii</i>: Gene Expression Profiles Provide New Insights into Ambiguous Translation |
| title_fullStr | Alternative CUG Codon Usage in the Halotolerant Yeast <i>Debaryomyces hansenii</i>: Gene Expression Profiles Provide New Insights into Ambiguous Translation |
| title_full_unstemmed | Alternative CUG Codon Usage in the Halotolerant Yeast <i>Debaryomyces hansenii</i>: Gene Expression Profiles Provide New Insights into Ambiguous Translation |
| title_short | Alternative CUG Codon Usage in the Halotolerant Yeast <i>Debaryomyces hansenii</i>: Gene Expression Profiles Provide New Insights into Ambiguous Translation |
| title_sort | alternative cug codon usage in the halotolerant yeast i debaryomyces hansenii i gene expression profiles provide new insights into ambiguous translation |
| topic | CTG-Ser1 clade ambiguous translation CUG codon mistranslation serynation leucylation |
| url | https://www.mdpi.com/2309-608X/8/9/970 |
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