The Change Rate of the <i>Fbxl21</i> Gene and the Amino Acid Composition of Its Protein Correlate with the Species-Specific Lifespan in Placental Mammals
This article proposes a methodology for establishing a relationship between the change rate of a given gene (relative to a given taxon) together with the amino acid composition of the proteins encoded by this gene and the traits of the species containing this gene. The methodology is illustrated bas...
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2024-10-01
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| author | Vassily A. Lyubetsky Gregory A. Shilovsky Jian-Rong Yang Alexandr V. Seliverstov Oleg A. Zverkov |
| author_facet | Vassily A. Lyubetsky Gregory A. Shilovsky Jian-Rong Yang Alexandr V. Seliverstov Oleg A. Zverkov |
| author_sort | Vassily A. Lyubetsky |
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| description | This article proposes a methodology for establishing a relationship between the change rate of a given gene (relative to a given taxon) together with the amino acid composition of the proteins encoded by this gene and the traits of the species containing this gene. The methodology is illustrated based on the mammalian genes responsible for regulating the circadian rhythms that underlie a number of human disorders, particularly those associated with aging. The methods used are statistical and bioinformatic ones. A systematic search for orthologues, pseudogenes, and gene losses was performed using our previously developed methods. It is demonstrated that the least conserved <i>Fbxl21</i> gene in the Euarchontoglires superorder exhibits a statistically significant connection of genomic characteristics (the median of <i>dN</i>/<i>dS</i> for a gene relative to all the other orthologous genes of a taxon, as well as the preference or avoidance of certain amino acids in its protein) with species-specific lifespan and body weight. In contrast, no such connection is observed for <i>Fbxl21</i> in the Laurasiatheria superorder. This study goes beyond the protein-coding genes, since the accumulation of amino acid substitutions in the course of evolution leads to pseudogenization and even gene loss, although the relationship between the genomic characteristics and the species traits is still preserved. The proposed methodology is illustrated using the examples of circadian rhythm genes and proteins in placental mammals, e.g., longevity is connected with the rate of <i>Fbxl21</i> gene change, pseudogenization or gene loss, and specific amino acid substitutions (e.g., asparagine at the 19th position of the CRY-binding domain) in the protein encoded by this gene. |
| format | Article |
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| issn | 2079-7737 |
| language | English |
| publishDate | 2024-10-01 |
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| series | Biology |
| spelling | doaj-art-e7a98a31d69748a292e5d666ea7e88ca2025-08-20T02:11:12ZengMDPI AGBiology2079-77372024-10-01131079210.3390/biology13100792The Change Rate of the <i>Fbxl21</i> Gene and the Amino Acid Composition of Its Protein Correlate with the Species-Specific Lifespan in Placental MammalsVassily A. Lyubetsky0Gregory A. Shilovsky1Jian-Rong Yang2Alexandr V. Seliverstov3Oleg A. Zverkov4Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 127051 Moscow, RussiaInstitute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 127051 Moscow, RussiaDepartment of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, ChinaInstitute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 127051 Moscow, RussiaInstitute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 127051 Moscow, RussiaThis article proposes a methodology for establishing a relationship between the change rate of a given gene (relative to a given taxon) together with the amino acid composition of the proteins encoded by this gene and the traits of the species containing this gene. The methodology is illustrated based on the mammalian genes responsible for regulating the circadian rhythms that underlie a number of human disorders, particularly those associated with aging. The methods used are statistical and bioinformatic ones. A systematic search for orthologues, pseudogenes, and gene losses was performed using our previously developed methods. It is demonstrated that the least conserved <i>Fbxl21</i> gene in the Euarchontoglires superorder exhibits a statistically significant connection of genomic characteristics (the median of <i>dN</i>/<i>dS</i> for a gene relative to all the other orthologous genes of a taxon, as well as the preference or avoidance of certain amino acids in its protein) with species-specific lifespan and body weight. In contrast, no such connection is observed for <i>Fbxl21</i> in the Laurasiatheria superorder. This study goes beyond the protein-coding genes, since the accumulation of amino acid substitutions in the course of evolution leads to pseudogenization and even gene loss, although the relationship between the genomic characteristics and the species traits is still preserved. The proposed methodology is illustrated using the examples of circadian rhythm genes and proteins in placental mammals, e.g., longevity is connected with the rate of <i>Fbxl21</i> gene change, pseudogenization or gene loss, and specific amino acid substitutions (e.g., asparagine at the 19th position of the CRY-binding domain) in the protein encoded by this gene.https://www.mdpi.com/2079-7737/13/10/792bioinformaticsmammalscircadian rhythmslongevityrate of changeamino acid composition |
| spellingShingle | Vassily A. Lyubetsky Gregory A. Shilovsky Jian-Rong Yang Alexandr V. Seliverstov Oleg A. Zverkov The Change Rate of the <i>Fbxl21</i> Gene and the Amino Acid Composition of Its Protein Correlate with the Species-Specific Lifespan in Placental Mammals Biology bioinformatics mammals circadian rhythms longevity rate of change amino acid composition |
| title | The Change Rate of the <i>Fbxl21</i> Gene and the Amino Acid Composition of Its Protein Correlate with the Species-Specific Lifespan in Placental Mammals |
| title_full | The Change Rate of the <i>Fbxl21</i> Gene and the Amino Acid Composition of Its Protein Correlate with the Species-Specific Lifespan in Placental Mammals |
| title_fullStr | The Change Rate of the <i>Fbxl21</i> Gene and the Amino Acid Composition of Its Protein Correlate with the Species-Specific Lifespan in Placental Mammals |
| title_full_unstemmed | The Change Rate of the <i>Fbxl21</i> Gene and the Amino Acid Composition of Its Protein Correlate with the Species-Specific Lifespan in Placental Mammals |
| title_short | The Change Rate of the <i>Fbxl21</i> Gene and the Amino Acid Composition of Its Protein Correlate with the Species-Specific Lifespan in Placental Mammals |
| title_sort | change rate of the i fbxl21 i gene and the amino acid composition of its protein correlate with the species specific lifespan in placental mammals |
| topic | bioinformatics mammals circadian rhythms longevity rate of change amino acid composition |
| url | https://www.mdpi.com/2079-7737/13/10/792 |
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