Cytochrome P450 genes in coronary artery diseases: Codon usage analysis reveals genomic GC adaptation

Malakar, Arup Kumar; Halder, Binata; Pavlidis, Paul; Chakraborty, Supriyo

doi:10.1016/j.gene.2016.06.011

Cited by 11 publications

(7 citation statements)

References 49 publications

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“…These findings suggest that the expression of photolyase encoding genes in cyanobacteria inhabiting fresh water and marine habitats is not affected by the codon bias pattern. Similar findings have been reported for enterovirus (Ma et al 2014) and for cytochrome P450 genes which are associated with coronary artery disease in human (Malakar et al 2016). However, the expressions of photolyase encoding genes in hot spring cyanobacteria were found to be affected by pattern of codon bias.…”

Section: Gene Expression Level Of Photolyase Encoding Genessupporting

confidence: 85%

“…In this study, the abundance of GARP was found. Recently, Malakar et al (2016) showed that mutational pressure and natural selection could be the main factors accounting for codon usage bias in cytochrome P450 (CYP) genes. In Actinobacteria, mutation is a main driving force than natural selection for extreme GC content and codon bias (Lal et al 2016).…”

Section: Discussionmentioning

confidence: 99%

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Codon usage analysis of photolyase encoding genes of cyanobacteria inhabiting diverse habitats

et al. 2017

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Nucleotide and amino acid compositions were studied to determine the genomic and structural relationship of photolyase gene in freshwater, marine and hot spring cyanobacteria. Among three habitats, photolyase encoding genes from hot spring cyanobacteria were found to have highest GC content. The genomic GC content was found to influence the codon usage and amino acid variability in photolyases. The third position of codon was found to have more effect on amino acid variability in photolyases than the first and second positions of codon. The variation of amino acids Ala, Asp, Glu, Gly, His, Leu, Pro, Gln, Arg and Val in photolyases of three different habitats was found to be controlled by first position of codon (G1C1). However, second position (G2C2) of codon regulates variation of Ala, Cys, Gly, Pro, Arg, Ser, Thr and Tyr contents in photolyases. Third position (G3C3) of codon controls incorporation of amino acids such as Ala, Phe, Gly, Leu, Gln, Pro, Arg, Ser, Thr and Tyr in photolyases from three habitats. Photolyase encoding genes of hot spring cyanobacteria have 85% codons with G or C at third position, whereas marine and freshwater cyanobacteria showed 82 and 60% codons, respectively, with G or C at third position. Principal component analysis (PCA) showed that GC content has a profound effect in separating the genes along the first major axis according to their RSCU (relative synonymous codon usage) values, and neutrality analysis indicated that mutational pressure has resulted in codon bias in photolyase genes of cyanobacteria.

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Section: Gene Expression Level Of Photolyase Encoding Genessupporting

confidence: 85%

Section: Discussionmentioning

confidence: 99%

Codon usage analysis of photolyase encoding genes of cyanobacteria inhabiting diverse habitats

et al. 2017

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“…In most of the species a significant negative correlation between Nc and GC3 was depicted, a trend well in line with the standard notion of Nc-GC3 relationship (Hassan et al, 2009;Pandit and Sinha, 2011;Prabha et al, 2012;Malakar et al, 2016Malakar et al, , 2019Song et al, 2017b). The results of the correlation analysis is shown in Supplementary Table 3.…”

Section: Analysis Of Cub Pattern Of Whole Genomesupporting

confidence: 81%

Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes

Saha

Sarkar

et al. 2019

Front. Microbiol.

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“…nuclear encoded CYP 450 gene was GC‐rich. The mean ENC value of CYP450 gene was 47.61, which suggested a low CUB similar to the mitochondrial CO genes in fishes, birds, and mammals (Malakar, Halder, Paul, & Chakraborty, ).…”

Section: Discussionmentioning

confidence: 97%

“…The ENC values were high, that is, low CUB supporting our current study . Further, we compared the CO genes of fishes, (Malakar, Halder, Paul, & Chakraborty, 2016).…”

Section: Discussionmentioning

confidence: 99%

Understanding molecular biology of codon usage in mitochondrial complex IV genes of electron transport system: Relevance to mitochondrial diseases

Uddin¹,

Mazumder

Chakraborty

2018

Journal Cellular Physiology

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The mitochondrial cytochrome oxidase (CO) genes are involved in complex IV of the electron transport system, and dysfunction of CO genes leads to several diseases.However, no work has been reported on the codon usage pattern of these genes. We used bioinformatic methods to analyze the compositional properties and the codon usage pattern of the COI, COII, and COIII genes in fishes, birds, and mammals to understand the similarities and dissimilarities of codon usage in these genes, which gave an insight into the molecular biology of these genes. The effective number of codons (ENC) value of genes was high in different species of fishes, birds and mammals, which indicates that the codon bias of CO genes was low and the ENC values were significantly different among fishes, birds, and mammals, as revealed from the t test. The overall guanine and cytosine (GC) content in fishes, birds, and mammals was lower than 50% in all genes, indicating that the genes were AT-rich and significantly different among fishes, birds, and mammals. The TCA codon was overrepresented in fishes, birds, and mammals for the COI gene, in birds and mammals for the COII gene, but it was not overrepresented in others. Only three codons, namely CTA, CGA, and AAA, were overrepresented in all three groups for the COI, COII, and COIII genes, repectively. From the neutrality plot in fishes, birds, and mammals, it was observed that the slopes of the regression lines (regression coefficients) in the COI, COII, and COIII genes were <0.5, suggesting that natural selection played a major role, whereas mutation pressure played a minor role.

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Cytochrome P450 genes in coronary artery diseases: Codon usage analysis reveals genomic GC adaptation

Cited by 11 publications

References 49 publications

Codon usage analysis of photolyase encoding genes of cyanobacteria inhabiting diverse habitats

Codon usage analysis of photolyase encoding genes of cyanobacteria inhabiting diverse habitats

Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes

Understanding molecular biology of codon usage in mitochondrial complex IV genes of electron transport system: Relevance to mitochondrial diseases

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