RESEARCH ARTICLE Copyright © 2002 American Scientic Publishers. All rights reserved Printed in the United States of America GENOME LETTERS 2002, 4, 175–187 www.aspbs.com/genomelett Comparative Genomics of Pseudomonas aeruginosa PAO1 and Pseudomonas putida KT2440: Orthologs, Codon Usage, Repetitive Extragenic Palindromic Elements, and Oligonucleotide Motif Signatures Christian Weinel, 1, ¤ David W. Ussery, 2 Hakan Ohlsson, 2 Thomas Sicheritz-Ponten, 2 Claudia Kiewitz, 1 and Burkhard Tümmler 1 1 Klinische Forschergruppe,OE 6711, Medizinische Hochschule Hannover, D-30625 Hannover, Germany 2 Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Lyngby, Denmark ABSTRACT: 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 proles. The P. aeruginosa and P. putida chromosomes share similar fractions of global repeats and contain several hundred repet- itive 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. Keywords: Codon Adaptation Index, Genome Codon Index, Genome Evolution, Synteny, Oligonucleotide, Ortholog, Pseudomonas aeruginosa, Pseudomonas putida, Repetitive Extragenic Palindromic Sequence, Bacterial Interspersed Mosaic Elements. 1. INTRODUCTION Pseudomonads are ubiquitous, metabolically versatile Gram-negative bacteria [1]. Pseudomonas putida is able to colonize soil, water, and the plant rhizosphere [2]. This nonpathogenic saprophytic species is considered to be innocuous for the environment, and hence P. putida strain KT2440 is the rst Gram-negative soil bacterium to be cer- tied as a safety strain by the Recombinant DNA Advisory Committee [3] and is the preferred host for cloning and gene expression for Gram-negative soil bacteria [4]. The ¤ Author to whom correspondence should be addressed. type species of the genus Pseudomonas aeruginosa is also extremely versatile metabolically and is found in numer- ous aquatic and soil habitats in the environment [5], but in contrast to P. putida it is also an important opportunistic pathogen for plants, animals, and humans [5]. P. aerug- inosa causes disease in cystic brosis, burn, cancer, and intensive-care patients associated with substantial morbid- ity and mortality [5]. The 6.2-Mb large genomes of the reference strains P. putida KT2440 [6] and P. aeruginosa PAO1 [7] were recently completely sequenced. The two strains share homology for 77% of the predicted coding regions [6]. Nel- son et al. [6] performed a comparative metabolic analysis Genome Letters 2002, Vol. 1, No. 4 1537-3053/2002/01/175/187/$17.00+.25 doi:10.1166/gl.2002.021 175