Molecular characterization of virulent genes in Pseudomonas aeruginosa based on componential usage divergence

Abstract

Genetic characteristics of virulent genes in Pseudomonas aeruginosa attracted significant attention for they could govern their drug-resistances. Studies on the componential usage divergences in the virulent genes are beneficial for further explicating their molecular characteristics. In present study, one thousand complete genomes of Pseudomonas aeruginosa were considered to study the molecular characteristics of 21 typical virulent genes. The important componential usage patterns (i.e., the base usage pattern, the codon usage pattern and their divergences) of 21 specific virulent genes were counted and calculated. The results show that (1) most virulent genes concerned in the present study are high GC sequences (overall GC ratio > 50%), especially from the codon usage perspective, the virulent genes are obviously GC3-abundant sequences (GC3 ratio > 70%); (2) the relative synonymous codon usage of all concerned virulent genes are uneven, especially in the anvM and the lptA, there is no codon for some certain amino acids, which could reveal their obvious codon usage bias; (3) some genes (i.e., the oprF and the fadD1) with lower divergence have steady effective number of codons. The findings of the present work would improve novel insights on the genetic characteristics of virulent genes in Pseudomonas aeruginosa.

Keywords: Pseudomonas aeruginosa; Biodiversity; Codon usage bias; Evolutionary pressure; Virulent gene.

Fig. 1

Basic components of 21 virulent genes of P. aeruginosa genomes. (A) The PR2 plot of the virulent genes. (B) GC content (both GC₁₂ and GC₃) against their length. (C) Neutral plot for overall 21 virulent gene sequences and the quantity distribution of GC₁₂ and GC₃, and (D) Base component proportion of both human and virulent genes in P. aeruginosa genomes.

Fig. 2

Correlation analysis among the componential parameters. The color bar indicates the magnitude of the correlation among the parameters.

Fig. 3

ENC values of the virulent genes in P. aeruginosa genomes. (A) ENC-plot of all concerned virulent genes in P. aeruginosa. (B) The ENC values for each virulent genes in P. aeruginosa. (C) Relationship between ENC and CBI of all concerned virulent genes in P. aeruginosa.

Fig. 4

Overall RSCU values of virulent genes in P. aeruginosa. The names of codons are listed along the Y-axis. The codon quantity represents the total codons for all 5457 virulent gene sequences concerned in the present study.

Fig. 5

Base usage divergence of the virulent genes in P. aeruginosa genomes. Values of the bars represent the divergence degree of the virulent gene sequences, which equal to the summation of standard deviations of base components, G, C, A, T, GC, GC₃ and GC₁₂, etc. The numbers along the abscissa indicate the number of bases in the virulent gene sequences.

Fig. 6

Heat map of the RSCU values of virulent gene sequences in P. aeruginosa. The blank parts in the figure indicate that there is no corresponding codon for certain amino acid in the anvM and the lptA genes.