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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

Comparison of clustering of the serine pathway genes with other methylotrophy-linked genes in P. aminophilus JCM 7686, Paracoccus sp. N5, and three selected strains of the Roseobacter clade. Colored bars show shuffling of specific DNA regions when compared to P. aminophilus JCM 7686. In P. aminophilus JCM 7686, the presented set of methylotrophy genes is divided into three clusters, two located within pAMI6 and one within the chromosome. In the other strains all these genes constitute a single methylotrophy island, which may be located within the chromosome (R. pomeroyi DSS-3 and L. methylohalidivorans DSM 14336), or in putative extrachromosomal replicons (Paracoccus sp. N5). In some cases, certain genes of the methylotrophy island may be found in a distant location in a genome (e.g., the tmm and tdm genes of R. denitrificans Och 114). The full names of enzymes encoded by most of the genes presented in the figure are summarized in Table S4. The others are tmoP—TMAO permease gene (Zhu et al., 2014), and tmoXWV—TMAO ABC-transporter system genes (Lidbury et al., 2014). The accession numbers of particular replicons are as follows: JCM 7686 – CP006654 (pAMI6) and CP006650 (chromosome), N5 – AQUO01000003, Och 114 – CP000362, DSM 14336 – CP006773, DSS-3 – CP000031.
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Figure 7: Comparison of clustering of the serine pathway genes with other methylotrophy-linked genes in P. aminophilus JCM 7686, Paracoccus sp. N5, and three selected strains of the Roseobacter clade. Colored bars show shuffling of specific DNA regions when compared to P. aminophilus JCM 7686. In P. aminophilus JCM 7686, the presented set of methylotrophy genes is divided into three clusters, two located within pAMI6 and one within the chromosome. In the other strains all these genes constitute a single methylotrophy island, which may be located within the chromosome (R. pomeroyi DSS-3 and L. methylohalidivorans DSM 14336), or in putative extrachromosomal replicons (Paracoccus sp. N5). In some cases, certain genes of the methylotrophy island may be found in a distant location in a genome (e.g., the tmm and tdm genes of R. denitrificans Och 114). The full names of enzymes encoded by most of the genes presented in the figure are summarized in Table S4. The others are tmoP—TMAO permease gene (Zhu et al., 2014), and tmoXWV—TMAO ABC-transporter system genes (Lidbury et al., 2014). The accession numbers of particular replicons are as follows: JCM 7686 – CP006654 (pAMI6) and CP006650 (chromosome), N5 – AQUO01000003, Och 114 – CP000362, DSM 14336 – CP006773, DSS-3 – CP000031.

Mentions: What is noteworthy, in all strains possessing the serine cycle genes, a co-occurrence of the genes involved in TMA oxidation via TMAO and the NMGP was observed. In P. aminophilus JCM 7686, these genes are present within three separate clusters. Two of them are located in pAMI6 (genes involved in TMA oxidation and in the NMGP) and the other (involved in the serine cycle) in the chromosome (Figure 7). In Paracoccus sp. N5 all the aforementioned genes form a single methylotrophy island, which is most probably extrachromosomally located (Figure 7).


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)

Comparison of clustering of the serine pathway genes with other methylotrophy-linked genes in P. aminophilus JCM 7686, Paracoccus sp. N5, and three selected strains of the Roseobacter clade. Colored bars show shuffling of specific DNA regions when compared to P. aminophilus JCM 7686. In P. aminophilus JCM 7686, the presented set of methylotrophy genes is divided into three clusters, two located within pAMI6 and one within the chromosome. In the other strains all these genes constitute a single methylotrophy island, which may be located within the chromosome (R. pomeroyi DSS-3 and L. methylohalidivorans DSM 14336), or in putative extrachromosomal replicons (Paracoccus sp. N5). In some cases, certain genes of the methylotrophy island may be found in a distant location in a genome (e.g., the tmm and tdm genes of R. denitrificans Och 114). The full names of enzymes encoded by most of the genes presented in the figure are summarized in Table S4. The others are tmoP—TMAO permease gene (Zhu et al., 2014), and tmoXWV—TMAO ABC-transporter system genes (Lidbury et al., 2014). The accession numbers of particular replicons are as follows: JCM 7686 – CP006654 (pAMI6) and CP006650 (chromosome), N5 – AQUO01000003, Och 114 – CP000362, DSM 14336 – CP006773, DSS-3 – CP000031.
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Figure 7: Comparison of clustering of the serine pathway genes with other methylotrophy-linked genes in P. aminophilus JCM 7686, Paracoccus sp. N5, and three selected strains of the Roseobacter clade. Colored bars show shuffling of specific DNA regions when compared to P. aminophilus JCM 7686. In P. aminophilus JCM 7686, the presented set of methylotrophy genes is divided into three clusters, two located within pAMI6 and one within the chromosome. In the other strains all these genes constitute a single methylotrophy island, which may be located within the chromosome (R. pomeroyi DSS-3 and L. methylohalidivorans DSM 14336), or in putative extrachromosomal replicons (Paracoccus sp. N5). In some cases, certain genes of the methylotrophy island may be found in a distant location in a genome (e.g., the tmm and tdm genes of R. denitrificans Och 114). The full names of enzymes encoded by most of the genes presented in the figure are summarized in Table S4. The others are tmoP—TMAO permease gene (Zhu et al., 2014), and tmoXWV—TMAO ABC-transporter system genes (Lidbury et al., 2014). The accession numbers of particular replicons are as follows: JCM 7686 – CP006654 (pAMI6) and CP006650 (chromosome), N5 – AQUO01000003, Och 114 – CP000362, DSM 14336 – CP006773, DSS-3 – CP000031.
Mentions: What is noteworthy, in all strains possessing the serine cycle genes, a co-occurrence of the genes involved in TMA oxidation via TMAO and the NMGP was observed. In P. aminophilus JCM 7686, these genes are present within three separate clusters. Two of them are located in pAMI6 (genes involved in TMA oxidation and in the NMGP) and the other (involved in the serine cycle) in the chromosome (Figure 7). In Paracoccus sp. N5 all the aforementioned genes form a single methylotrophy island, which is most probably extrachromosomally located (Figure 7).

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