Genomics of the ccoNOQP-encoded cbb3 oxidase complex in bacteria

Many bacteria adapt to microoxic conditions by synthesizing a particular cytochrome c oxidase (cbb(3)) complex with a high affinity for O-2, encoded by the ccoNOQP operon. A survey of genome databases indicates that ccoNOQP sequences are widespread in all sub-branches of Proteobacteria but otherwise are found only in bacteria of the CFB group (Cytophaga, Flexibacter, Bacteroides). Our analysis of available genome sequences suggests four major strategies of regulating ccoNOQP expression in response to O-2. The most widespread strategy involves direct regulation by the O-2-responsive protein Fnr. The second strategy involves an O-2-insensitive paralogue of Fnr, FixK, whose expression is regulated by the O-2-responding FixLJ two-component system. A third strategy of mixed regulation operates in bacteria carrying both fnr and fixLJ-fixK genes. Another, not yet identified, strategy is likely to operate in the epsilon-Proteobacteria Helicobacter pylori and Campylobacter jejuni which lack fnr and fixLJ-fixK genes. The FixLJ strategy appears specific for the alpha-subclass of Proteobacteria but is not restricted to rhizobia in which it was originally discovered.