Genome-guided insight into the methylotrophy of Paracoccus aminophilus JCM 7686

Abstract

Paracoccus aminophilus JCM 7686 (Alphaproteobacteria) is a facultative, heterotrophic methylotroph capable of utilizing a wide range of C1 compounds as sole carbon and energy sources. Analysis of the JCM 7686 genome revealed the presence of genes involved in the oxidation of methanol, methylamine, dimethylamine, trimethylamine, N,N-dimethylformamide, and formamide, as well as the serine cycle, which appears to be the only C1 assimilatory pathway in this strain. Many of these genes are located in different extrachromosomal replicons and are not present in the genomes of most members of the genus Paracoccus, which strongly suggests that they have been horizontally acquired. When compared with Paracoccus denitrificans Pd1222 (type strain of the genus Paracoccus), P. aminophilus JCM 7686 has many additional methylotrophic capabilities (oxidation of dimethylamine, trimethylamine, N,N-dimethylformamide, the serine cycle), which are determined by the presence of three separate gene clusters. Interestingly, related clusters form compact methylotrophy islands within the genomes of Paracoccus sp. N5 and many marine bacteria of the Roseobacter clade.

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

“…The predicted GS genetic module of pAMV1 consists of the genes aceBA (JCM7685_pAMV1p0018 and JCM7685_pAMV1p0017) encoding malate synthase and isocitrate lyase respectively. The sequences of these proteins show moderate similarity to the respective GS proteins of E. coli (AceB -45%, AceA -28%), but they are more closely related to the ace genes of P. aminophilus JCM 7686 (AceB -69%, AceA -88%), whose involvement in GS was indicated previously (Dziewit et al, 2015).…”

“…A similar topology of C1 metabolic routes is found in P . aminophilus JCM 7685, which experienced the same selective forces (Dziewit et al ., ), but not in P . denitrificans Pd1222, which was isolated from a different environment (Fig.…”

“…coli (AceB – 45%, AceA – 28%), but they are more closely related to the ace genes of P . aminophilus JCM 7686 (AceB – 69%, AceA – 88%), whose involvement in GS was indicated previously (Dziewit et al ., ).…”

“…). Similar ‘methylotrophy islands’ are present in the chromosomes of bacteria of the marine Roseobacter clade and in some representatives of the genus Paracoccus (Dziewit et al ., ).…”

“…The spatial organization of this cluster differs from well‐known serine cycle gene clusters (e.g., from Methylbacterium extorquens ) (Vuilleumier et al ., ) and is very similar to putative serine cycle gene clusters of P . aminophilus (Dziewit et al ., ), Paracoccus sp. N5 (Beck et al ., ) and R .…”