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Cytochome c oxidase is the terminal member of the electron transport chains of mitochondria and many bacteria. Providing an efficient mechanism for dioxygen reduction on the one hand, it also acts as a redox-linked proton pump, coupling the free energy of water formation to the generation of a transmembrane electrochemical gradient to eventually drive ATP synthesis. The overall complexity of the mitochondrial enzyme is also reflected by its subunit structure and assembly pathway, whereas the diversity of the bacterial enzymes has fostered the notion of a large family of heme-copper terminal oxidases. Moreover, the successful elucidation of 3-D structures for both the mitochondrial and several bacterial oxidases has greatly helped in designing mutagenesis approaches to study functional aspects in these enzymes.

SUMMARY Paracoccus denitrificans and its near relative Paracoccus versutus (formerly known as Thiobacilllus versutus) have been attracting increasing attention because the aerobic respiratory system of P. denitrificans has long been regarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa3 oxidase) in common. Members of the genus exhibit a great range of metabolic flexibility, particularly with respect to processes involving respiration. Prominent examples of flexibility are the use in denitrification of nitrate, nitrite, nitrous oxide, and nitric oxide as alternative electron acceptors to oxygen and the ability to use C1 compounds (e.g., methanol and methylamine) as electron donors to the respiratory chains. The proteins required for these respiratory processes are not constitutive, and the underlying complex regulatory systems that regulate their expression are beginning to be unraveled. There has been uncertainty about whether transcription in a member of the alpha-3 Proteobacteria such as P. denitrificans involves a conventional ς70-type RNA polymerase, especially since canonical −35 and −10 DNA binding sites have not been readily identified. In this review, we argue that many genes, in particular those encoding constitutive proteins, may be under the control of a ς70 RNA polymerase very closely related to that of Rhodobacter capsulatus. While the main focus is on the structure and regulation of genes coding for products involved in respiratory processes in Paracoccus, the current state of knowledge of the components of such respiratory pathways, and their biogenesis, is also reviewed.

Despite the existence of several three-dimensional structures of cytochrome c oxidases, a detailed understanding of pathways involved in proton movements through the complex remains largely elusive. Next to the two well-established pathways (termed D and K), an additional proton-conducting network ('H-channel') has been proposed for the beef heart enzyme. Yet, our recent mutational studies on corresponding residues of the Paracoccus denitrificans cytochrome c oxidase provide no clues that such a pathway operates in the prokaryotic enzyme.

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