Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection Force

Kumar, Utsang; Khandia, Rekha; Singhal, Shailja; Puranik, Nidhi; Tripathi, Meghna; Pateriya, Atul Kumar; Khan, Raju; Emran, Talha Bin; Dhama, Kuldeep; Munjal, Ashok; Alqahtani, Taha; Alqahtani, Ali

doi:10.3390/cancers13112739

Cited by 24 publications

(11 citation statements)

References 66 publications

(92 reference statements)

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“…It indicates the frequency with which a codon is used among all codons coding for the same amino acid. The codons with RSCU values below 0.6 are underrepresented, while those above 1.6 are overrepresented [14]. We performed RSCU analysis using CodonW 1.4.4 software (http://codonw.sourceforge.net (accessed on 28 June 2021)).…”

Section: Relative Synonymous Codon Usage (Rscu) Analysismentioning

confidence: 99%

Genes Common in Primary Immunodeficiencies and Cancer Display Overrepresentation of Codon CTG and Dominant Role of Selection Pressure in Shaping Codon Usage

Khandia

Alqahtani

2021

Biomedicines

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Primary immunodeficiencies (PIDs) are disorders of the immune system that involve faulty cellular, humoral, or both cellular and humoral functions. PIDs are present at the crossroad between infections, immune dysregulation, and cancers. A panel encompassing 42 genes involved in both PIDs and cancer has been investigated for the genes’ compositional properties, codon usage patterns, various forces affecting codon choice, protein properties, and gene expression profiles. In the present study, the codon choice of genes was found to be dependent upon the richness of the nucleotide; the viz AT nucleotide rich genome preferred AT ending codons. The dinucleotide TpA adversely affected protein expression, while CpG did not. The CTG codon was the most overrepresented codon in 80.95% of genes. Analysis of various protein properties, including GRAVY, AROMA, isoelectric point, aliphatic index, hydrophobicity, instability index, and numbers of acidic, basic, and neutral amino acid residues revealed that the hydrophobicity index, instability index, and numbers of acidic and basic amino acid residues are the factors affecting gene expression. Based on neutrality analysis, parity analysis, ENc-GC3 analysis, and regression analysis of nucleotides present at the first and third positions of the codon, it was determined that selection pressure, mutation pressure, and compositional constraints all participated in shaping codon usage. The study will help determine the various evolutionary forces acting on genes common to both PIDs and cancer. Codon usage analysis might be helpful in the future to augment both diseases simultaneously. The research also indicates a peculiar pattern adapted by a set of genes involved in any disease.

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Section: Relative Synonymous Codon Usage (Rscu) Analysismentioning

confidence: 99%

Genes Common in Primary Immunodeficiencies and Cancer Display Overrepresentation of Codon CTG and Dominant Role of Selection Pressure in Shaping Codon Usage

Khandia

Alqahtani

2021

Biomedicines

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“…Overall analysis revealed the importance of compositional, mutational, and selectional pressure. However, the role of selection pressure was dominant over others (49).…”

Section: Discussionmentioning

confidence: 99%

The G nucleotide guides codon usage bias in genes associated with depression

Khandia

Puranik

Pandey

et al. 2022

Preprint

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Depression or major depressive disorder is a psychiatric disorder affecting mood, behavior, and mental and physical health. Depression runs in families, suggestive of the genetic basis of the disease. Much research is going to understand the molecular basis of depression. In the present work, we tried to envisage the codon usage pattern analysis of genes involved in depression. The investigation revealed that all the genes were highly expressed, and codon usage bias (CUB) is influenced by the length of the gene, nucleotide disproportion, nucleotide compositional constraints, and CAI. The detailed investigation related to the effect of codon composition of CUB revealed that out of 20 compositional constraints, only G nucleotide showed a relationship at overall %G, %G2, %G3 and %GC2 positions. E of composition is further evidenced by the relationship between CUB and nucleotide skew. Neutrality, parity, P2 analysis, suppression of CpG, and TpA dinucleotide and over-representation of TpG dinucleotide followed by under abundance of TpA and CpG encompassing codons and over-representation of CTG and GTG codons all indicated towards the selectional force in shaping codon usage in genes linked to depression. The genes showed a significant positive correlation with each other based on RSCU value indicative of similar codon usage. Based on protein properties, all genes correlated with each other except for the CYP3A4 gene. The association is suggestive of identical protein properties also of genes involved. The analysis helps unveil the compositional features and various forces affecting codon usage of the gene.

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“…RSCU analysis was done by CodonW 1.4.4 software available at http://codonw.sourceforge.net . The codons with RSCU values above 1.6 are called over-represented and below 0.6 are called under-represented ( Kumar et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia

Alqahtani¹,

Khandia²,

Puranik³

et al. 2022

Front. Genet.

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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. 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 towards GC-ending codons enhanced the gene expression level, evidenced by the positive association between CAI and GC-ending codons. The unusual behavior of TTG codon showing an inverse relationship with GC-ending codon and negative influence of gene expression, a behavior contrary to all other GC-ending codons, shows operative selectional force. Furthermore, parity analysis, higher translational selection value, preference of GC-ending codons over AT-ending codons, and the association of gene length with gene expression refer to the dominant role of selection pressure with compositional constraint and mutational force shaping codon usage.

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Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection Force

Cited by 24 publications

References 66 publications

Genes Common in Primary Immunodeficiencies and Cancer Display Overrepresentation of Codon CTG and Dominant Role of Selection Pressure in Shaping Codon Usage

Genes Common in Primary Immunodeficiencies and Cancer Display Overrepresentation of Codon CTG and Dominant Role of Selection Pressure in Shaping Codon Usage

The G nucleotide guides codon usage bias in genes associated with depression

Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia

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