Bioinformatic Prediction of an tRNA<sup>Sec</sup> Gene Nested inside an Elongation Factor SelB Gene in Alphaproteobacteria
In bacteria, selenocysteine (Sec) is incorporated into proteins via the recoding of a particular codon, the UGA stop codon in most cases. Sec-tRNA<sup>Sec</sup> is delivered to the ribosome by the Sec-dedicated elongation factor SelB that also recognizes a Sec-insertion sequence element...
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| Format: | Article |
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MDPI AG
2021-04-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/9/4605 |
| _version_ | 1797536081819729920 |
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| author | Takahito Mukai |
| author_facet | Takahito Mukai |
| author_sort | Takahito Mukai |
| collection | DOAJ |
| description | In bacteria, selenocysteine (Sec) is incorporated into proteins via the recoding of a particular codon, the UGA stop codon in most cases. Sec-tRNA<sup>Sec</sup> is delivered to the ribosome by the Sec-dedicated elongation factor SelB that also recognizes a Sec-insertion sequence element following the codon on the mRNA. Since the excess of SelB may lead to sequestration of Sec-tRNA<sup>Sec</sup> under selenium deficiency or oxidative stress, the expression levels of SelB and tRNA<sup>Sec</sup> should be regulated. In this bioinformatic study, I analyzed the Rhizobiales SelB species because they were annotated to have a non-canonical C-terminal extension. I found that the open reading frame (ORF) of diverse Alphaproteobacteria <i>selB</i> genes includes an entire tRNA<sup>Sec</sup> sequence (<i>selC</i>) and overlaps with the start codon of the downstream ORF. A remnant tRNA<sup>Sec</sup> sequence was found in the <i>Sinorhizobium meliloti</i><i>selB</i> genes whose products have a shorter C-terminal extension. Similar overlapping traits were found in Gammaproteobacteria and Nitrospirae. I hypothesized that once the tRNA<sup>Sec</sup> moiety is folded and processed, the expression of the full-length SelB may be repressed. This is the first report on a nested tRNA gene inside a protein ORF in bacteria. |
| first_indexed | 2024-03-10T11:54:34Z |
| format | Article |
| id | doaj.art-ebea7aa4fbc449d98a082f5327aed934 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T11:54:34Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-ebea7aa4fbc449d98a082f5327aed9342023-11-21T17:26:23ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-04-01229460510.3390/ijms22094605Bioinformatic Prediction of an tRNA<sup>Sec</sup> Gene Nested inside an Elongation Factor SelB Gene in AlphaproteobacteriaTakahito Mukai0Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, JapanIn bacteria, selenocysteine (Sec) is incorporated into proteins via the recoding of a particular codon, the UGA stop codon in most cases. Sec-tRNA<sup>Sec</sup> is delivered to the ribosome by the Sec-dedicated elongation factor SelB that also recognizes a Sec-insertion sequence element following the codon on the mRNA. Since the excess of SelB may lead to sequestration of Sec-tRNA<sup>Sec</sup> under selenium deficiency or oxidative stress, the expression levels of SelB and tRNA<sup>Sec</sup> should be regulated. In this bioinformatic study, I analyzed the Rhizobiales SelB species because they were annotated to have a non-canonical C-terminal extension. I found that the open reading frame (ORF) of diverse Alphaproteobacteria <i>selB</i> genes includes an entire tRNA<sup>Sec</sup> sequence (<i>selC</i>) and overlaps with the start codon of the downstream ORF. A remnant tRNA<sup>Sec</sup> sequence was found in the <i>Sinorhizobium meliloti</i><i>selB</i> genes whose products have a shorter C-terminal extension. Similar overlapping traits were found in Gammaproteobacteria and Nitrospirae. I hypothesized that once the tRNA<sup>Sec</sup> moiety is folded and processed, the expression of the full-length SelB may be repressed. This is the first report on a nested tRNA gene inside a protein ORF in bacteria.https://www.mdpi.com/1422-0067/22/9/4605genetic codeselenocysteinenon-coding RNA |
| spellingShingle | Takahito Mukai Bioinformatic Prediction of an tRNA<sup>Sec</sup> Gene Nested inside an Elongation Factor SelB Gene in Alphaproteobacteria International Journal of Molecular Sciences genetic code selenocysteine non-coding RNA |
| title | Bioinformatic Prediction of an tRNA<sup>Sec</sup> Gene Nested inside an Elongation Factor SelB Gene in Alphaproteobacteria |
| title_full | Bioinformatic Prediction of an tRNA<sup>Sec</sup> Gene Nested inside an Elongation Factor SelB Gene in Alphaproteobacteria |
| title_fullStr | Bioinformatic Prediction of an tRNA<sup>Sec</sup> Gene Nested inside an Elongation Factor SelB Gene in Alphaproteobacteria |
| title_full_unstemmed | Bioinformatic Prediction of an tRNA<sup>Sec</sup> Gene Nested inside an Elongation Factor SelB Gene in Alphaproteobacteria |
| title_short | Bioinformatic Prediction of an tRNA<sup>Sec</sup> Gene Nested inside an Elongation Factor SelB Gene in Alphaproteobacteria |
| title_sort | bioinformatic prediction of an trna sup sec sup gene nested inside an elongation factor selb gene in alphaproteobacteria |
| topic | genetic code selenocysteine non-coding RNA |
| url | https://www.mdpi.com/1422-0067/22/9/4605 |
| work_keys_str_mv | AT takahitomukai bioinformaticpredictionofantrnasupsecsupgenenestedinsideanelongationfactorselbgeneinalphaproteobacteria |