Mixed-Function Supraoperons That Exhibit Overall Conservation, Albeit Shuffled Gene Organization, across Wide Intergenomic Distances within Eubacteria

Abstract

Nearly identical mixed-function supraoperons (defined as nested transcriptional units encoding gene products that function in more than one biochemical pathway) have been found recently in Pseudomonas stutzeri and Pseudomonas aeruginosa. The Pseudomonas serC(pdxF)aroQ_p.pheA-hisH_b-tyrA_c-aroF-cmk-rpsA supraoperon encodes 3-phosphoserine aminotransferase, a bidomain chorismate mutase/prephenate dehydratase, imidazole acetol-phosphate aminotransferase, cyclohexadienyl dehydrogenase, 5-enolpyruvylshikimate 3-phosphate synthase, cytidylate kinase, and 30S ribosomal protein SI. These enzymes participate in the biosynthesis of serine, pyridoxine, histidine, phenylalanine, tyrosine, tryptophan, and aromatic pathway vitamins and cytidylic acid, in addition to the general role of RpsA in the process of protein synthesis. Features that suggest supraoperon-wide translational coupling are the highly compressed intergenic spacing (including overlapping stop and start codons), as well as possible hairpin structures in mRNA, which could sequester many of the ribosome-binding sites. The hisH-tyrA-aroF segment corresponds to the distal genes of the classic Bacillus subtilis supraoperon. Extensive comparative analysis of the member genes of both the Bacillus and Pseudomonas supraoperons from organisms represented in the entire database revealed unmistakable organizational conservation of these genes across wide phylogenetic boundaries, although considerable gene shuffling was apparent. The persistence of aroE-aroB, hisH_b-tyrA-aroF, and cmk-rpsA throughout both the gram-negative and grampositive assemblages of bacteria, but the absence in Archaea, suggests an ancestral gene organization that occurred in bacteria after the separation of the bacterial and archaeal domains. In gram-negative bacteria, the hisH_b-tyrA_c-aroF grouping may have been expanded (as with the Pseudomonas supraoperon) and then subsequently collapsed (as with the Escherichia serC-aroF supraoperon) via gene shuffling that is herein equated with gene fusion events.