Molecular genetics of the genus Paracoccus: Metabolically versatile bacteria with bioenergetic flexibility

Paracoccus denitrificans and its near relative Paracoccus versutus (formerl y known as Thiobacillus versutus) have been attracting increasing attention because the aerobic respiratory system of P. denitrificans has long been r egarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa(3) oxidase) in common. Members of the genu s 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 o xide as alternative electron acceptors to oxygen and the ability to use C-1 compounds (e.g., methanol and methylamine) as electron donors to the respi ratory chains. The proteins required for these respiratory processes are no t 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 suc h as P. denitrificans involves a conventional sigma(70)-type RNA polymerase , especially since canonical -35 and -10 DNA binding sites have not been re adily identified. In this review, we argue that many genes, in particular t hose encoding constitutive proteins, may be under the control of a sigma(70 ) RNA polymerase very closely related to that of Rhodobacter capsulatus. Wh ile the main focus is on the structure and regulation of genes coding for p roducts involved in respiratory processes in Paracoccus, the current state of knowledge of the components of such respiratory pathways, and their biog enesis, is also reviewed.