Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa.

Codon usage biases of all DNA sequences (length greater than or equal to 300 bp) from the complete genome of Pseudomonas aeruginosa have been analyzed. As P. aeruginosa is a GC-rich organism, G and/or C are expected to predominate in their codons. Overall codon usage data analysis indicates that indeed codons ending in G and/or C are predominant in this organism. But multivariate statistical analysis indicates that there is a single major trend in the codon usage variation among the genes in this organism, which has a strong negative correlation with the expressivities of the genes. The majority of the lowly expressed genes are scattered towards the positive end of the major axis whereas the highly expressed genes are clustered towards the negative end. This is the first report where the prokaryotic organism having highly skewed base composition is dictated mainly by translational selection, though some other factors such as the lengths of the genes as well as the hydrophobicity of genes also influence the codon usage variation among the genes in this organism in a minor way.

[1]  P. Sharp,et al.  Systematic base composition variation around the genome of Mycoplasma genitalium, but not Mycoplasma pneumoniae , 1997, Molecular microbiology.

[2]  Etsuko N. Moriyama,et al.  Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli , 1998, Nucleic Acids Res..

[3]  P. Sharp,et al.  Codon usage in the Mycobacterium tuberculosis complex. , 1996, Microbiology.

[4]  M. Vignali,et al.  Evolution of codon usage and base contents in kinetoplastid protozoans. , 1994, Molecular biology and evolution.

[5]  Manolo Gouy,et al.  Codon catalog usage is a genome strategy modulated for gene expressivity , 1981, Nucleic Acids Res..

[6]  J. Bennetzen,et al.  Codon selection in yeast. , 1982, The Journal of biological chemistry.

[7]  R. Clarke,et al.  Theory and Applications of Correspondence Analysis , 1985 .

[8]  T. Ikemura.  Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. , 1981, Journal of molecular biology.

[9]  J O McInerney,et al.  Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Antonio Marín,et al.  Preference for guanosine at first codon position in highly expressed Escherichia coli genes. A relationship with translational efficiency , 1996, Nucleic Acids Res..

[11]  S. Lory,et al.  Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen , 2000, Nature.

[12]  T. Ikemura.  Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. , 1981, Journal of molecular biology.

[13]  H. Romero,et al.  Heterogeneity in Codon Usage in the Flatworm Schistosoma mansoni , 1998, Journal of Molecular Evolution.

[14]  Y. Nakamura,et al.  Codon-anticodon assignment and detection of codon usage trends in seven microbial genomes. , 1997, Microbial & comparative genomics.

[15]  P. Sharp,et al.  Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. , 1986, Nucleic acids research.

[16]  Kamel Jabbari,et al.  Synonymous Codon Choices in the Extremely GC-Poor Genome of Plasmodium falciparum: Compositional Constraints and Translational Selection , 1999, Journal of Molecular Evolution.

[17]  T. Ikemura.  Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. , 1982, Journal of molecular biology.

[18]  K. H. Wolfe,et al.  Base Composition Skews, Replication Orientation, and Gene Orientation in 12 Prokaryote Genomes , 1998, Journal of Molecular Evolution.

[19]  F Wright,et al.  Codon usage in the G+C-rich Streptomyces genome. , 1992, Gene.

[20]  M. Gouy,et al.  Codon usage in bacteria: correlation with gene expressivity. , 1982, Nucleic acids research.

[21]  P. Sharp,et al.  Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. , 1999, Nucleic acids research.

[22]  T. Sicheritz-Pontén,et al.  The genome sequence of Rickettsia prowazekii and the origin of mitochondria , 1998, Nature.

[23]  E. Tillier,et al.  The Contributions of Replication Orientation, Gene Direction, and Signal Sequences to Base-Composition Asymmetries in Bacterial Genomes , 2000, Journal of Molecular Evolution.

[24]  F. Wright.  The 'effective number of codons' used in a gene. , 1990, Gene.

[25]  J. Lobry,et al.  Origin of Replication of Mycoplasma genitalium , 1996, Science.

[26]  G. Bernardi,et al.  Gene Expression, Amino Acid Conservation, and Hydrophobicity Are the Main Factors Shaping Codon Preferences in Mycobacterium tuberculosis and Mycobacterium leprae , 2000, Journal of Molecular Evolution.

[27]  H. Romero,et al.  Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. , 2000, Nucleic acids research.

[28]  T C Ghosh,et al.  Studies on codon usage in Entamoeba histolytica. , 2000, International journal for parasitology.

[29]  T. Ohama,et al.  Role of GC-biased mutation pressure on synonymous codon choice in Micrococcus luteus, a bacterium with a high genomic GC-content. , 1990, Nucleic acids research.

[30]  T Gojobori,et al.  Codon usage tabulated from the GenBank Genetic Sequence Data. , 1988, Nucleic acids research.

[31]  P. Sharp,et al.  The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. , 1987, Nucleic acids research.

[32]  H. Romero,et al.  Compositional pressure and translational selection determine codon usage in the extremely GC-poor unicellular eukaryote Entamoeba histolytica. , 2000, Gene.

[33]  Paul M. Sharp,et al.  Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases , 1994, Nucleic Acids Res..

[34]  C. Dutta,et al.  Codon usage in highly expressed genes of Haemophillus influenzae and Mycobacterium tuberculosis: translational selection versus mutational bias. , 1998, Gene.