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

Abstract

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; p < 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.

Keywords: EPB41L3; GC contents; RSCU; codon usage bias; mutational pressure; natural selection; translational efficiency.

Figure 1

(a) Minimum, maximum, and average values of nucleobases A, C, T, and G of the EPB41L3 gene. (b) Minimum, maximum, and average of nucleobases at third position %A3, %C3, %T3, and %G3 of the EPB41L3 gene.

Figure 2

Relative dinucleotide frequencies among the EPB41L3 transcripts.

Figure 3

(a) Matrix plot of the average RSCU values against the distribution of G/C-ending and A/T-ending codons. The overrepresented (RSCU > 1.6), underrepresented (RSCU < 0.6), more frequently (RSCU > 1), and less frequently used codons (RSCU < 1) are shown. (b) Clustering of RSCU values of the EPB41L3 gene across the selected mammals. Heat map comparing the average RSCU value of a codon (rows) corresponding to the gene transcripts across the mammalian species (columns). The map indicates differing codon preferences within the gene itself (higher RSCU values with more frequent codon usage depicted in dark red and lower RSCU values depicted in dark blue).

Figure 3

(a) Matrix plot of the average RSCU values against the distribution of G/C-ending and A/T-ending codons. The overrepresented (RSCU > 1.6), underrepresented (RSCU < 0.6), more frequently (RSCU > 1), and less frequently used codons (RSCU < 1) are shown. (b) Clustering of RSCU values of the EPB41L3 gene across the selected mammals. Heat map comparing the average RSCU value of a codon (rows) corresponding to the gene transcripts across the mammalian species (columns). The map indicates differing codon preferences within the gene itself (higher RSCU values with more frequent codon usage depicted in dark red and lower RSCU values depicted in dark blue).

Figure 4

Neutrality plot analysis (GC12 vs. GC3) for the entire coding sequences of EPB41L3. GC12 stands for the average value of GC contents at the first and second positions of the codons (GC1 and GC2), while GC3 refers to the GC contents at the third codon position. The red line is the linear regression of GC12 against GC3, R = 0.926, relative neutrality is 30.21%. The blue dots are assigned for Homo sapiens while the yellow dots are assigned for other mammals.

Figure 5

Parity analysis showing preference of purine over pyrimidine. A disproportionate distribution shows the preference towards codon choices is shaped by both mutational pressure and natural selection.

Figure 6

ENc-GC3 plot (selection curve) analysis. ENc denotes the effective number of codons and GC3s denotes the GC content in the third synonymous codon position. The red line curve represents the expected curve when the codon usage was only determined by the GC3 composition.

Figure 7

Graphical representation of CAI, ENc, GC3%, and GC% with their mean values.

Figure 8

Regression analysis of the ratio of the ENc and the compositional properties, %GC3, and CAI.

Figure 9

Phylogenetic analysis based on the Kimura two-parameter (K2P) distances of the mRNA coding sequences of the EPB41L3 gene of different mammalian species. The evolutionary analyses were performed in MEGA7, whereas the evolutionary distances were calculated using the Kimura two-parameter method and are presented in the number of base substitutions per site.