Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection Force
Uneven codon usage within genes as well as among genomes is a usual phenomenon across organisms. It plays a significant role in the translational efficiency and evolution of a particular gene. EPB41L3 is a tumor suppressor protein-coding gene, and in the present study, the pattern of codon usage was...
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MDPI AG
2021-06-01
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| Series: | Cancers |
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| author | Utsang Kumar Rekha Khandia Shailja Singhal Nidhi Puranik Meghna Tripathi Atul Kumar Pateriya Raju Khan Talha Bin Emran Kuldeep Dhama Ashok Munjal Taha Alqahtani Ali M. Alqahtani |
| author_facet | Utsang Kumar Rekha Khandia Shailja Singhal Nidhi Puranik Meghna Tripathi Atul Kumar Pateriya Raju Khan Talha Bin Emran Kuldeep Dhama Ashok Munjal Taha Alqahtani Ali M. Alqahtani |
| author_sort | Utsang Kumar |
| collection | DOAJ |
| description | Uneven codon usage within genes as well as among genomes is a usual phenomenon across organisms. It plays a significant role in the translational efficiency and evolution of a particular gene. EPB41L3 is a tumor suppressor protein-coding gene, and in the present study, the pattern of codon usage was envisaged. The full-length sequences of the EPB41L3 gene for the human, brown rat, domesticated cattle, and Sumatran orangutan available at the NCBI were retrieved and utilized to analyze CUB patterns across the selected mammalian species. Compositional properties, dinucleotide abundance, and parity analysis showed the dominance of A and G whilst RSCU analysis indicated the dominance of G/C-ending codons. The neutrality plot plotted between GC12 and GC3 to determine the variation between the mutation pressure and natural selection indicated the dominance of selection pressure (R = 0.926; <i>p</i> < 0.00001) over the three codon positions across the gene. The result is in concordance with the codon adaptation index analysis and the ENc-GC3 plot analysis, as well as the translational selection index (P2). Overall selection pressure is the dominant pressure acting during the evolution of the EPB41L3 gene. |
| first_indexed | 2024-03-10T10:48:32Z |
| format | Article |
| id | doaj.art-256fe9736ad1462ba4299c346ba774a9 |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-10T10:48:32Z |
| publishDate | 2021-06-01 |
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| series | Cancers |
| spelling | doaj.art-256fe9736ad1462ba4299c346ba774a92023-11-21T22:22:39ZengMDPI AGCancers2072-66942021-06-011311273910.3390/cancers13112739Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection ForceUtsang Kumar0Rekha Khandia1Shailja Singhal2Nidhi Puranik3Meghna Tripathi4Atul Kumar Pateriya5Raju Khan6Talha Bin Emran7Kuldeep Dhama8Ashok Munjal9Taha Alqahtani10Ali M. Alqahtani11Department of Biochemistry and Genetics, Barkatullah University, Bhopal 462026, IndiaDepartment of Biochemistry and Genetics, Barkatullah University, Bhopal 462026, IndiaDepartment of Biochemistry and Genetics, Barkatullah University, Bhopal 462026, IndiaDepartment of Biochemistry and Genetics, Barkatullah University, Bhopal 462026, IndiaICAR-National Institute of High Security Animal Diseases, Bhopal 462043, IndiaICAR-National Institute of High Security Animal Diseases, Bhopal 462043, IndiaMicrofluidics & MEMS Center, (MRS & CFC), CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal 462026, IndiaDepartment of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, BangladeshDivision of Pathology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, IndiaDepartment of Biochemistry and Genetics, Barkatullah University, Bhopal 462026, IndiaDepartment of Pharmacology, College of Pharmacy, King Khalid University, Abha 62529, Saudi ArabiaDepartment of Pharmacology, College of Pharmacy, King Khalid University, Abha 62529, Saudi ArabiaUneven codon usage within genes as well as among genomes is a usual phenomenon across organisms. It plays a significant role in the translational efficiency and evolution of a particular gene. EPB41L3 is a tumor suppressor protein-coding gene, and in the present study, the pattern of codon usage was envisaged. The full-length sequences of the EPB41L3 gene for the human, brown rat, domesticated cattle, and Sumatran orangutan available at the NCBI were retrieved and utilized to analyze CUB patterns across the selected mammalian species. Compositional properties, dinucleotide abundance, and parity analysis showed the dominance of A and G whilst RSCU analysis indicated the dominance of G/C-ending codons. The neutrality plot plotted between GC12 and GC3 to determine the variation between the mutation pressure and natural selection indicated the dominance of selection pressure (R = 0.926; <i>p</i> < 0.00001) over the three codon positions across the gene. The result is in concordance with the codon adaptation index analysis and the ENc-GC3 plot analysis, as well as the translational selection index (P2). Overall selection pressure is the dominant pressure acting during the evolution of the EPB41L3 gene.https://www.mdpi.com/2072-6694/13/11/2739EPB41L3codon usage biasRSCUGC contentstranslational efficiencymutational pressure |
| spellingShingle | Utsang Kumar Rekha Khandia Shailja Singhal Nidhi Puranik Meghna Tripathi Atul Kumar Pateriya Raju Khan Talha Bin Emran Kuldeep Dhama Ashok Munjal Taha Alqahtani Ali M. Alqahtani Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection Force Cancers EPB41L3 codon usage bias RSCU GC contents translational efficiency mutational pressure |
| title | Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection Force |
| title_full | Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection Force |
| title_fullStr | Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection Force |
| title_full_unstemmed | Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection Force |
| title_short | Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection Force |
| title_sort | insight into codon utilization pattern of tumor suppressor gene epb41l3 from different mammalian species indicates dominant role of selection force |
| topic | EPB41L3 codon usage bias RSCU GC contents translational efficiency mutational pressure |
| url | https://www.mdpi.com/2072-6694/13/11/2739 |
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