Characterizations of highly expressed genes of four fast-growing bacteria

Predicted highly expressed (PHX) genes are characterized for the completely sequenced genomes of the four fast-growing bacteria Escherichia coli, Haem ophilus influenzae, Vibrio cholerae, and Bacillus subtilis. Our approach to ascertaining gene expression levels relates to codon usage differences amo ng certain gene classes: the collection of all genes (average gene), the en semble of ribosomal protein genes, major translation/transcription processi ng factors, and genes for polypeptides of chaperone/degradation complexes. A gene is predicted highly expressed (PHX) if its codon frequencies are clo se to those of the ribosomal proteins, major translation/transcription proc essing factor, and chaperone/degradation standards but strongly deviant fro m the average gene codon frequencies. PHX genes identified by their codon u sage frequencies among prokaryotic genomes commonly include those for ribos omal proteins, major transcription/translation processing factors (several occurring in multiple copies), and major chaperone/degradation proteins. Al so PHX genes generally include those encoding enzymes of essential energy m etabolism pathways of glycolysis, pyruvate oxidation, and respiration (aero bic and anaerobic), genes of fatty acid biosynthesis, and the principal gen es of amino acid and nucleotide biosyntheses. Gene classes generally not PH X include most repair protein genes, virtually all vitamin biosynthesis gen es, genes of two-component sensor systems, most regulatory genes, and most genes expressed in stationary phase or during starvation. Members of the se t of PHX aminoacyl-tRNA synthetase genes contrast sharply between genomes. There are also subtle differences among the PHX energy metabolism genes bet ween E. coli and B. subtilis, particularly with respect to genes of the tri carboxylic acid cycle. The good agreement of PHX genes of E. coli and B. su btilis with high protein abundances, as assessed by two-dimensional gel det ermination, is verified. Relationships of PHX genes with stoichiometry, mul tifunctionality, and operon structures are also examined. The spatial distr ibution of PHX genes within each genome reveals clusters and significantly long regions without PHX genes.