Comparative Genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2440: Orthologs, Codon Usage, Repetitive Extragenic Palindromic Elements, and Oligonucleotide Motif Signatures

Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2440 were compared for global genome features. About half of the coding sequences share more than 50% amino acid sequence identity. The alignment of orthologs shows an X-type pattern, with large sections of conserved gene order indicative of symmetric inversions around the origin and terminus of replication since the two taxa diverged from a common ancestor. However, codon usage patterns are different in the two type I pseudomonads, as indicated by unrelated genome codon index and codon adaptation index profiles. The P. aeruginosa and P. putida chromosomes share similar fractions of global repeats and contain several hundred repetitive extragenic palindromic (REP) elements, part of which are organized in regularly spaced clusters as bacterial interspersed mosaic elements. The frequency and map position of all 2-meric to 14-meric oligonucleotides were determined in the two genomes. Among the short oligonucleotides the universally rare TA, CTA, TAG, and CTAG and stretches of oligoG and oligoC are strongly counterselected in the GC-rich pseudomonads. Frequent words encode peptides with strong codon bias, such as the tripeptide LLL.