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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

Effect of mutations in genes encoding four putative subunits of dimethylamine monooxygenase (dmmDABC) on growth of P. aminophilus JCM 7686 on dimethylamine (A), N,N-dimethylformamide (B), trimethylamine (C), methylamine (D), and L-arabinose (E). wt, wild type; dmmA, dmmA insertional mutant; dmmB, dmmB insertional mutant; dmmC, dmmC insertional mutant; dmmD, dmmD insertional mutant. The values are means of three replicates, and the error bars indicate the standard deviations.
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Figure 5: Effect of mutations in genes encoding four putative subunits of dimethylamine monooxygenase (dmmDABC) on growth of P. aminophilus JCM 7686 on dimethylamine (A), N,N-dimethylformamide (B), trimethylamine (C), methylamine (D), and L-arabinose (E). wt, wild type; dmmA, dmmA insertional mutant; dmmB, dmmB insertional mutant; dmmC, dmmC insertional mutant; dmmD, dmmD insertional mutant. The values are means of three replicates, and the error bars indicate the standard deviations.

Mentions: To verify the function of the P. aminophilus dmmDABC genes, their mutational analysis was performed. The four mutant strains carrying deletions of the individual dmm genes failed to grow on dimethylamine as the sole carbon and energy source, while they showed the same growth rate as the wild-type strain when cultivated on methylamine or L-arabinose (Figure 5). The wild-type phenotype was restored when the dmmDABC module cloned in vector pBBR1MCS-3 was introduced into the mutant strains (data not shown). The mutations also influenced growth on C1 compounds that are metabolized via DMA, i.e., N,N-dimethylformamide and trimethylamine (Figure 5). Interestingly, inactivation of dmmD had a much weaker effect on growth on TMA than the inactivation of the other dmm genes (Figure 5). This observation is consistent with the hypothesis that the DmmD protein is not necessary for the conversion of DMA into MA and formaldehyde, but is an auxiliary subunit of the DMA monooxygenase which may convert formaldehyde into methylene-THF (Zhu et al., 2014).


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)

Effect of mutations in genes encoding four putative subunits of dimethylamine monooxygenase (dmmDABC) on growth of P. aminophilus JCM 7686 on dimethylamine (A), N,N-dimethylformamide (B), trimethylamine (C), methylamine (D), and L-arabinose (E). wt, wild type; dmmA, dmmA insertional mutant; dmmB, dmmB insertional mutant; dmmC, dmmC insertional mutant; dmmD, dmmD insertional mutant. The values are means of three replicates, and the error bars indicate the standard deviations.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: Effect of mutations in genes encoding four putative subunits of dimethylamine monooxygenase (dmmDABC) on growth of P. aminophilus JCM 7686 on dimethylamine (A), N,N-dimethylformamide (B), trimethylamine (C), methylamine (D), and L-arabinose (E). wt, wild type; dmmA, dmmA insertional mutant; dmmB, dmmB insertional mutant; dmmC, dmmC insertional mutant; dmmD, dmmD insertional mutant. The values are means of three replicates, and the error bars indicate the standard deviations.
Mentions: To verify the function of the P. aminophilus dmmDABC genes, their mutational analysis was performed. The four mutant strains carrying deletions of the individual dmm genes failed to grow on dimethylamine as the sole carbon and energy source, while they showed the same growth rate as the wild-type strain when cultivated on methylamine or L-arabinose (Figure 5). The wild-type phenotype was restored when the dmmDABC module cloned in vector pBBR1MCS-3 was introduced into the mutant strains (data not shown). The mutations also influenced growth on C1 compounds that are metabolized via DMA, i.e., N,N-dimethylformamide and trimethylamine (Figure 5). Interestingly, inactivation of dmmD had a much weaker effect on growth on TMA than the inactivation of the other dmm genes (Figure 5). This observation is consistent with the hypothesis that the DmmD protein is not necessary for the conversion of DMA into MA and formaldehyde, but is an auxiliary subunit of the DMA monooxygenase which may convert formaldehyde into methylene-THF (Zhu et al., 2014).

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