Highly expressed and alien genes of the Synechocystis genome

Abstract

Comparisons of codon frequencies of genes to several gene classes are used to characterize highly expressed and alien genes on the SYNECHOCYSTIS: PCC6803 genome. The primary gene classes include the ensemble of all genes (average gene), ribosomal protein (RP) genes, translation processing factors (TF) and genes encoding chaperone/degradation proteins (CH). A gene is predicted highly expressed (PHX) if its codon usage is close to that of the RP/TF/CH standards but strongly deviant from the average gene. Putative alien (PA) genes are those for which codon usage is significantly different from all four classes of gene standards. In SYNECHOCYSTIS:, 380 genes were identified as PHX. The genes with the highest predicted expression levels include many that encode proteins vital for photosynthesis. Nearly all of the genes of the RP/TF/CH gene classes are PHX. The principal glycolysis enzymes, which may also function in CO(2) fixation, are PHX, while none of the genes encoding TCA cycle enzymes are PHX. The PA genes are mostly of unknown function or encode transposases. Several PA genes encode polypeptides that function in lipopolysaccharide biosynthesis. Both PHX and PA genes often form significant clusters (operons). The proteins encoded by PHX and PA genes are described with respect to functional classifications, their organization in the genome and their stoichiometry in multi-subunit complexes.

Figure 1

Distribution of PHX and PA genes on the Synechocystis genome. PHX genes are indicated as thin red bars immediately above and below the scale axis. The genes above the axis are transcribed from left to right (direct strand), whereas the genes below the axis are transcribed from right to left (complementary strand). The three levels of the bars indicate three possible reading frames for each orientation. PHX genes are shown in red, PA genes in blue and all other genes (not PHX or PA) in gray. The bars below indicate significant clusters of PHX (red) and PA (blue) genes investigated by r-scan statistics (20). The thick bars correspond to the 99% confidence level and the thin bars are significant at the 95% confidence level.