Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia
Dementia is a clinical syndrome characterized by progressive cognitive decline, and the symptoms could be gradual, persistent, and progressive. In the present study, we investigated 47 genes that have been linked to dementia. Compositional, selectional, and mutational forces were seen to be involved...
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Frontiers Media S.A.
2022-08-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.884348/full |
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| author | Taha Alqahtani Rekha Khandia Nidhi Puranik Ali M. Alqahtani Yahia Alghazwani Saad Ali Alshehri Kumarappan Chidambaram Mohammad Amjad Kamal Mohammad Amjad Kamal Mohammad Amjad Kamal Mohammad Amjad Kamal |
| author_facet | Taha Alqahtani Rekha Khandia Nidhi Puranik Ali M. Alqahtani Yahia Alghazwani Saad Ali Alshehri Kumarappan Chidambaram Mohammad Amjad Kamal Mohammad Amjad Kamal Mohammad Amjad Kamal Mohammad Amjad Kamal |
| author_sort | Taha Alqahtani |
| collection | DOAJ |
| description | Dementia is a clinical syndrome characterized by progressive cognitive decline, and the symptoms could be gradual, persistent, and progressive. In the present study, we investigated 47 genes that have been linked to dementia. Compositional, selectional, and mutational forces were seen to be involved. Nucleotide components that influenced A- and GC-affected codon usages bias at all three codon positions. The influence of these two compositional constraints on codon usage bias (CUB) was positive for nucleotide A and negative for GC. Nucleotide A also experienced the highest mutational force, and GC-ending codons were preferred over AT-ending codons. A high bias toward GC-ending codons enhances the gene expression level, evidenced by the positive association between CAI- and GC-ending codons. Unusual behavior of the TTG codon showing an inverse relationship with the GC-ending codon and negative influence of gene expression, behavior contrary to all other GC-ending codons, shows an operative selectional force. Furthermore, parity analysis, higher translational selection value, preference of GC-ending codons over AT-ending codons, and association of gene length with gene expression refer to the dominant role of selection pressure with compositional constraint and mutational force-shaping codon usage. |
| format | Article |
| id | doaj-art-94c9a54e38984df38e0e791dfd77a9f9 |
| institution | Kabale University |
| issn | 1664-8021 |
| language | English |
| publishDate | 2022-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj-art-94c9a54e38984df38e0e791dfd77a9f92025-01-24T15:06:25ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-08-011310.3389/fgene.2022.884348884348Codon Usage is Influenced by Compositional Constraints in Genes Associated with DementiaTaha Alqahtani0Rekha Khandia1Nidhi Puranik2Ali M. Alqahtani3Yahia Alghazwani4Saad Ali Alshehri5Kumarappan Chidambaram6Mohammad Amjad Kamal7Mohammad Amjad Kamal8Mohammad Amjad Kamal9Mohammad Amjad Kamal10Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi ArabiaDepartment of Biochemistry and Genetics, Barkatullah University, Bhopal, IndiaDepartment of Biochemistry and Genetics, Barkatullah University, Bhopal, IndiaDepartment of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi ArabiaDepartment of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi ArabiaDepartment of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi ArabiaDepartment of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi ArabiaInstitutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, ChinaKing Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi ArabiaDepartment of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, BangladeshEnzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, AustraliaDementia is a clinical syndrome characterized by progressive cognitive decline, and the symptoms could be gradual, persistent, and progressive. In the present study, we investigated 47 genes that have been linked to dementia. Compositional, selectional, and mutational forces were seen to be involved. Nucleotide components that influenced A- and GC-affected codon usages bias at all three codon positions. The influence of these two compositional constraints on codon usage bias (CUB) was positive for nucleotide A and negative for GC. Nucleotide A also experienced the highest mutational force, and GC-ending codons were preferred over AT-ending codons. A high bias toward GC-ending codons enhances the gene expression level, evidenced by the positive association between CAI- and GC-ending codons. Unusual behavior of the TTG codon showing an inverse relationship with the GC-ending codon and negative influence of gene expression, behavior contrary to all other GC-ending codons, shows an operative selectional force. Furthermore, parity analysis, higher translational selection value, preference of GC-ending codons over AT-ending codons, and association of gene length with gene expression refer to the dominant role of selection pressure with compositional constraint and mutational force-shaping codon usage.https://www.frontiersin.org/articles/10.3389/fgene.2022.884348/fulldementiaGC compositioncompositional constraintcodon usagenucleotide skew |
| spellingShingle | Taha Alqahtani Rekha Khandia Nidhi Puranik Ali M. Alqahtani Yahia Alghazwani Saad Ali Alshehri Kumarappan Chidambaram Mohammad Amjad Kamal Mohammad Amjad Kamal Mohammad Amjad Kamal Mohammad Amjad Kamal Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia Frontiers in Genetics dementia GC composition compositional constraint codon usage nucleotide skew |
| title | Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia |
| title_full | Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia |
| title_fullStr | Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia |
| title_full_unstemmed | Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia |
| title_short | Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia |
| title_sort | codon usage is influenced by compositional constraints in genes associated with dementia |
| topic | dementia GC composition compositional constraint codon usage nucleotide skew |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.884348/full |
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