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

Dziewit L, Czarnecki J, Prochwicz E, Wibberg D, Schlüter A, Pühler A, Bartosik D - Front Microbiol (2015)

Bottom Line: 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.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.Interestingly, related clusters form compact methylotrophy islands within the genomes of Paracoccus sp.

View Article: PubMed Central - PubMed

Affiliation: Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland.

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.

No MeSH data available.


Related in: MedlinePlus

Growth of P. aminophilus JCM 7686 on various C1 compounds or L-arabinose as a sole carbon and energy source. (A) Growth on L-arabinose (L-ara), N,N-dimethylformamide (DMF), and trimethylamine (TMA), (B) Growth on methanol (MeOH), dimethylamine (DMA), formamide (FAM), and methylamine (MA). The values are means of three replicates, and the error bars indicate the standard deviations.
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Figure 1: Growth of P. aminophilus JCM 7686 on various C1 compounds or L-arabinose as a sole carbon and energy source. (A) Growth on L-arabinose (L-ara), N,N-dimethylformamide (DMF), and trimethylamine (TMA), (B) Growth on methanol (MeOH), dimethylamine (DMA), formamide (FAM), and methylamine (MA). The values are means of three replicates, and the error bars indicate the standard deviations.

Mentions: P. aminophilus JCM 7686 was isolated in Japan from soil contaminated with N,N-dimethylformamide (DMF) as a strain able to utilize many C1 compounds (Figure S1) (Urakami et al., 1990). However, no further analysis regarding the methylotrophy of this strain was performed. In the initial stage of this study we confirmed that, besides DMF, JCM 7686 can utilize methylamine, dimethylamine, trimethylamine, and formamide. We also found that it is able to utilize methanol (Figure 1), which is contrary to the original observations of Urakami et al. (1990). To determine the genetic basis of these phenotypes we examined the JCM 7686 genome (Dziewit et al., 2014) for the presence of genes linked to C1 metabolism and we performed functional analysis of selected genes to confirm our predictions. The collected data permitted reconstruction of the complex C1 metabolic pathway of this strain (Figure 2, Table S4).


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

Dziewit L, Czarnecki J, Prochwicz E, Wibberg D, Schlüter A, Pühler A, Bartosik D - Front Microbiol (2015)

Growth of P. aminophilus JCM 7686 on various C1 compounds or L-arabinose as a sole carbon and energy source. (A) Growth on L-arabinose (L-ara), N,N-dimethylformamide (DMF), and trimethylamine (TMA), (B) Growth on methanol (MeOH), dimethylamine (DMA), formamide (FAM), and methylamine (MA). The values are means of three replicates, and the error bars indicate the standard deviations.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4543880&req=5

Figure 1: Growth of P. aminophilus JCM 7686 on various C1 compounds or L-arabinose as a sole carbon and energy source. (A) Growth on L-arabinose (L-ara), N,N-dimethylformamide (DMF), and trimethylamine (TMA), (B) Growth on methanol (MeOH), dimethylamine (DMA), formamide (FAM), and methylamine (MA). The values are means of three replicates, and the error bars indicate the standard deviations.
Mentions: P. aminophilus JCM 7686 was isolated in Japan from soil contaminated with N,N-dimethylformamide (DMF) as a strain able to utilize many C1 compounds (Figure S1) (Urakami et al., 1990). However, no further analysis regarding the methylotrophy of this strain was performed. In the initial stage of this study we confirmed that, besides DMF, JCM 7686 can utilize methylamine, dimethylamine, trimethylamine, and formamide. We also found that it is able to utilize methanol (Figure 1), which is contrary to the original observations of Urakami et al. (1990). To determine the genetic basis of these phenotypes we examined the JCM 7686 genome (Dziewit et al., 2014) for the presence of genes linked to C1 metabolism and we performed functional analysis of selected genes to confirm our predictions. The collected data permitted reconstruction of the complex C1 metabolic pathway of this strain (Figure 2, Table S4).

Bottom Line: 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.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.Interestingly, related clusters form compact methylotrophy islands within the genomes of Paracoccus sp.

View Article: PubMed Central - PubMed

Affiliation: Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland.

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.

No MeSH data available.


Related in: MedlinePlus