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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 the tmm1 and tmm2 mutations on growth of P. aminophilus JCM 7686 on trimethylamine (A), dimethylamine (B), methylamine (C), and L-arabinose (D). wt, wild type; tmm1, tmm1 insertional mutant; tmm2, tmm2 insertional mutant; tmm12, double insertional mutant in tmm1 and tmm2 genes. The values are means of three replicates, and the error bars indicate the standard deviations.
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Figure 4: Effect of the tmm1 and tmm2 mutations on growth of P. aminophilus JCM 7686 on trimethylamine (A), dimethylamine (B), methylamine (C), and L-arabinose (D). wt, wild type; tmm1, tmm1 insertional mutant; tmm2, tmm2 insertional mutant; tmm12, double insertional mutant in tmm1 and tmm2 genes. The values are means of three replicates, and the error bars indicate the standard deviations.

Mentions: TMA oxidation via TMAO depends on the activity of three enzymes: (i) TMA monooxygenase, (ii) TMAO demethylase, and (iii) DMA monooxygenase. Interestingly, pAMI6 carries two genes, tmm1 (JCM7686_pAMI6p076) and tmm2 (JCM7686_pAMI6p102), encoding putative TMA monooxygenases. The predicted Tmm1 and Tmm2 proteins show high amino acid (aa) sequence similarity (75%) to one another and share about 60% identity with the Tmm protein of Methylocella silvestris BL2 (Chen et al., 2011). To analyze the role of the tmm genes in the TMA metabolism of JCM 7686, three mutant strains were constructed lacking either tmm1 or tmm2, or both genes. The growth rate of the strains containing single mutations (tmm1 or tmm2) in minimal medium with TMA as the sole carbon and energy source was identical to that of the wild type strain (Figure 4). In contrast, the double mutant strain (tmm1tmm2) was no longer able to utilize TMA, but it still had the ability to grow on medium supplemented with DMA or MA (the products of TMA utilization) (Figure 4). The growth on TMA was restored when tmm1 or tmm2 gene cloned in vector pBBR1MCS-5 was introduced into the double mutant strain (data not shown). These results indicated that both identified tmm genes encode enzymes with the same specificity and that they are both involved in the first stage of TMA metabolism. Additionally, the contribution of two tmm genes in TMA oxidation was confirmed by RT-qPCR. It was shown that transcript levels of both genes are increased in a similar degree during growth on TMA in comparison with non-methylotrophic conditions (Table 1).


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 the tmm1 and tmm2 mutations on growth of P. aminophilus JCM 7686 on trimethylamine (A), dimethylamine (B), methylamine (C), and L-arabinose (D). wt, wild type; tmm1, tmm1 insertional mutant; tmm2, tmm2 insertional mutant; tmm12, double insertional mutant in tmm1 and tmm2 genes. 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 4: Effect of the tmm1 and tmm2 mutations on growth of P. aminophilus JCM 7686 on trimethylamine (A), dimethylamine (B), methylamine (C), and L-arabinose (D). wt, wild type; tmm1, tmm1 insertional mutant; tmm2, tmm2 insertional mutant; tmm12, double insertional mutant in tmm1 and tmm2 genes. The values are means of three replicates, and the error bars indicate the standard deviations.
Mentions: TMA oxidation via TMAO depends on the activity of three enzymes: (i) TMA monooxygenase, (ii) TMAO demethylase, and (iii) DMA monooxygenase. Interestingly, pAMI6 carries two genes, tmm1 (JCM7686_pAMI6p076) and tmm2 (JCM7686_pAMI6p102), encoding putative TMA monooxygenases. The predicted Tmm1 and Tmm2 proteins show high amino acid (aa) sequence similarity (75%) to one another and share about 60% identity with the Tmm protein of Methylocella silvestris BL2 (Chen et al., 2011). To analyze the role of the tmm genes in the TMA metabolism of JCM 7686, three mutant strains were constructed lacking either tmm1 or tmm2, or both genes. The growth rate of the strains containing single mutations (tmm1 or tmm2) in minimal medium with TMA as the sole carbon and energy source was identical to that of the wild type strain (Figure 4). In contrast, the double mutant strain (tmm1tmm2) was no longer able to utilize TMA, but it still had the ability to grow on medium supplemented with DMA or MA (the products of TMA utilization) (Figure 4). The growth on TMA was restored when tmm1 or tmm2 gene cloned in vector pBBR1MCS-5 was introduced into the double mutant strain (data not shown). These results indicated that both identified tmm genes encode enzymes with the same specificity and that they are both involved in the first stage of TMA metabolism. Additionally, the contribution of two tmm genes in TMA oxidation was confirmed by RT-qPCR. It was shown that transcript levels of both genes are increased in a similar degree during growth on TMA in comparison with non-methylotrophic conditions (Table 1).

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