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

Abstract

Plasmids play an important role in the adaptation of bacteria to changeable environmental conditions. As the main vectors of horizontal gene transfer, they can spread genetic information among bacteria, sometimes even across taxonomic boundaries. Some plasmids carry genes involved in the utilization of particular carbon compounds, which can provide a competitive advantage to their hosts in particular ecological niches. Analysis of the multireplicon genome of the soil bacterium P. aminovorans JCM 7685 revealed the presence of an extrachromosomal replicon pAMV1 (185 kb) with a unique structure and properties. This lifestyle-determining plasmid carries genes facilitating the metabolism of many different carbon compounds including sugars, short-chain organic acids and C1 compounds. Plasmid pAMV1 contains a large methylotrophy island (MEI) that is essential not only for the utilization of particular C1 compounds but also for the central methylotrophic metabolism required for the assimilation of C1 units (serine cycle). We demonstrate that the expression of the main serine cycle genes is induced in the presence of C1 compounds by the transcriptional regulator ScyR. The extrachromosomal localization of the MEI and the distribution of related genes in Paracoccus spp. indicate that it could have been acquired by HGT by an ancestor of P. aminovorans.

Molecular Mechanism of N , N -Dimethylformamide Degradation in Methylobacterium sp. Strain DM1

“…strain KUFA-1 and Paracoccus aminophilus strain JCM7685 (sharing Ͼ90% amino acid identity), while having lower levels of identity with those in Paracoccus aminophilus strain JCM7686 (84% and 73%, respectively) ( Fig. 4A and B) (19,20,31). A putative LuxR family transcriptional regulator was found upstream of dmfA1A2, displaying 57% amino acid identity with its homolog in Paracoccus aminophilus strain JCM7686 (19).…”

“…Plasmid pLVM1 in strain DM1 is unique among DMF degraders, with approximately 80% of its overall length representing genes involved in the initial steps of DMF degradation. The plasmid pAMV1 in the P. aminophilus isolate JCM7685 is not specific to DMF catabolism (20). In addition to a small proportion of ORFs encoding enzymes for DMF, DMA, and MA utilization, pAMV1 encodes genes facilitating the metabolism of other carbon sources, such as methanol and L-arabinose.…”

“…Comparative genomic analysis of methylotrophic pathways. To obtain a comprehensive understanding of methylotrophic pathways in strain DM1, we compared its genome with those of two other Methylobacterium strains (AM1 and DM4) and two well-studied DMF degraders (P. aminophilus JCM7685 and JCM7686) (19,20,26,30,39). Distinct from most Methylobacterium strains, strain DM1 possesses additional methylotrophic genes encoding DMFase, termed dmfA1 and dmfA2, within the plasmid pLVM1.…”

“…In Paracoccus, the reactions converting formaldehyde and CH 2 ϭTHF to formate are separate. Formaldehyde is catalyzed by S-(hydroxymethyl)glutathione synthase (Gfa), S-(hydroxymethyl) glutathione dehydrogenase (FlhA), and S-formylglutathione hydrolase (FghA), and the oxidation of CH 2 ϭTHF is performed by a bifunctional enzyme encoded by folD and a formyltetrahydrofolate deformylase encoded by purU; these enzymes have not been found in Methylobacterium (20). Although the genes involved in the serine cycle in these five strains are almost the same, they are dispersed on the chromosome of Methylobacterium sp.…”

“…Biodegradation of DMF has been established over the past 30 years. Several DMFdegrading bacteria, such as Pseudomonas (16), Paracoccus (6,(17)(18)(19)(20), Alcaligenes (21), Ochrobactrum (22), Mycobacterium, and Methylobacterium (23,24) strains, have been isolated and identified. However, except for Paracoccus aminophilus strains JCM7685 and JCM7686, little genomic information is available for these degraders.…”