Molecular Genetics of the GenusParacoccus: Metabolically Versatile Bacteria with Bioenergetic Flexibility

Abstract

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.

Lifestyle‐determining extrachromosomal replicon pAMV1 and its contribution to the carbon metabolism of the methylotrophic bacterium Paracoccus aminovorans JCM 7685

“…P. aminovorans JCM 7685 and P. denitrificans Pd1222 carry separate sets of genes involved in methylotrophy and the biochemical basis of their C1 metabolism is different (Calvin cycle or serine cycle as the central C1 assimilation process). As genes of the Calvin cycle are conserved in many Paracoccus species (Baker et al, 1998;Supporting Information Table S7), they seem to be inherited vertically as a part of their genetic repertoire. However, in some strains (P. aminovorans and P. aminophilus) Calvin cycle genes have apparently been replaced by horizontally-acquired serine cycle genes.…”

“…Interestingly, about 50% of known Paracoccus spp. are described as methylotrophs, i.e., organisms utilizing C1 compounds (reduced carbon compounds lacking carboncarbon bonds) as their sole carbon and energy sources (Baker et al, 1998). Methylotrophs are extremely widespread and are found in diverse environments (Chistoserdova, 2015;Butterfield et al, 2016), where they play a crucial role in the global cycling of carbon, nitrogen and sulfur (Chistoserdova, 2011).…”

Methylophilaceae link methanol oxidation to denitrification in freshwater lake sediment as suggested by stable isotope probing and pure culture analysis

“…However, no strong correlation exists between the presence of xox genes and the denitrifying capability in bacteria. For example, the classic denitrifier Paracoccus denitrificans possesses the Xox system but does not appear to be able to use methanol as an electron donor (Baker et al, 1998). The specific connection between the Xox system and the denitrification capability of Methylotenera and other Methylophilaceae remains enigmatic and will be the focus of our future studies.…”

“…While denitrification capabilities of Paracoccus and Hyphomicrobium species have been extensively described, pure cultures of the former are not known for denitrification with methanol (Baker et al, 1998), and of the latter, few strains have been described that were capable of methanol-dependent denitrification (Sperl and Hoare, 1971). Denitrification by pure cultures of Methyloversatilis or species belonging to Methylophilaceae has not been reported so far.…”

Mycobacterial genomes for all tastes: from BCG to biodegradation of naphtalene and pyrene

“…Paracoccus denitrificans, first described in 1910 by Beijerinck, has a respiratory chain that is very similar to the one in mitochondria and has long been a popular model organism for studies of membrane energy transformation (Maklashina et al, 2003). It has also been used for studying the mechanisms of denitrification, ammonia oxidation, reduction of thiosulfate and utilization of methylamine, carbon disulfide and other C1 compounds (Baker et al, 1998). Thanks to the availability of the complete genome sequence, this easy-to-grow non-pathogenic metabolically flexible bacterium will now become an even more useful model organism.…”