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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

The methylotrophy-linked metabolic capabilities encoded by the genomes of Paracoccus spp. Tmm, trimethylamine monooxygenase; Dmm, putative dimethylamine monooxygenase; NMGP, N-methylglutamate pathway; Mau, methylamine dehydrogenase; Mxa, Mxa-type methanol dehydrogenase; Xox, Xox-type methanol dehydrogenase; GSH, glutathione; CH2 = THF, 5,10-methylene-tetrahydrofolate; FolD, 5,10-methylene-tetrahydrofolate dehydrogenase/5,10-methylene-tetrahydrofolate cyclohydrolase; PurU, formyltetrahydrofolate deformylase; FtfL, formate-tetrahydrofolate ligase. The accession numbers of Paracoccus complete genomes: JCM7686 – GQ410978, GQ468939, GQ468938, CP006650–CP006655, and Pd1222 – CP000489–CP000491. The accession numbers of Paracoccus draft genomes: J39 – JAEN01000001–JAEN01000050, J55 – AZVA01000001–AZVA01000069, N5 – AQUO01000001–AQUO01000003, ATCC BAA-599 – JHWH01000001– JHWH01000073, DSM 582 – JRKO01000001– JRKO01000187, TRP – AEPN01000001– AEPN01000119, J40 – JAGK01000001– JAGK01000119, J46 – JAEM01000001– JAEM01000105, HAMBI 3106 – JRKS01000001– JRKS01000137, 10990 – JRKR01000001– JRKR01000309, 39524 – JRKP01000001– JRKP01000273, 4681 – JRKT01000001– JRKT01000176, 5503 – JRKQ01000001– JRKQ01000265, JCM 14014 – JRKN01000001– JRKN01000122, and ATCC 21588 – ATUJ01000001– ATUJ01000035.
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Figure 6: The methylotrophy-linked metabolic capabilities encoded by the genomes of Paracoccus spp. Tmm, trimethylamine monooxygenase; Dmm, putative dimethylamine monooxygenase; NMGP, N-methylglutamate pathway; Mau, methylamine dehydrogenase; Mxa, Mxa-type methanol dehydrogenase; Xox, Xox-type methanol dehydrogenase; GSH, glutathione; CH2 = THF, 5,10-methylene-tetrahydrofolate; FolD, 5,10-methylene-tetrahydrofolate dehydrogenase/5,10-methylene-tetrahydrofolate cyclohydrolase; PurU, formyltetrahydrofolate deformylase; FtfL, formate-tetrahydrofolate ligase. The accession numbers of Paracoccus complete genomes: JCM7686 – GQ410978, GQ468939, GQ468938, CP006650–CP006655, and Pd1222 – CP000489–CP000491. The accession numbers of Paracoccus draft genomes: J39 – JAEN01000001–JAEN01000050, J55 – AZVA01000001–AZVA01000069, N5 – AQUO01000001–AQUO01000003, ATCC BAA-599 – JHWH01000001– JHWH01000073, DSM 582 – JRKO01000001– JRKO01000187, TRP – AEPN01000001– AEPN01000119, J40 – JAGK01000001– JAGK01000119, J46 – JAEM01000001– JAEM01000105, HAMBI 3106 – JRKS01000001– JRKS01000137, 10990 – JRKR01000001– JRKR01000309, 39524 – JRKP01000001– JRKP01000273, 4681 – JRKT01000001– JRKT01000176, 5503 – JRKQ01000001– JRKQ01000265, JCM 14014 – JRKN01000001– JRKN01000122, and ATCC 21588 – ATUJ01000001– ATUJ01000035.

Mentions: Annotated genomic sequences of 17 strains of Paracoccus spp. (including P. aminophilus JCM 7686) are currently available in the GenBank database (Figure 6). The genomes of these strains were screened for the presence of 67 genes encoding enzymes involved in methylotrophy that have been identified in P. aminophilus and other methylotrophic Alphaproteobacteria. It is important to note that for 15 Paracoccus spp. strains only draft genomes were available, thus some data may be missing. Therefore, the lack of the particular genes has to be verified after obtaining complete genome sequences of those strains.


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)

The methylotrophy-linked metabolic capabilities encoded by the genomes of Paracoccus spp. Tmm, trimethylamine monooxygenase; Dmm, putative dimethylamine monooxygenase; NMGP, N-methylglutamate pathway; Mau, methylamine dehydrogenase; Mxa, Mxa-type methanol dehydrogenase; Xox, Xox-type methanol dehydrogenase; GSH, glutathione; CH2 = THF, 5,10-methylene-tetrahydrofolate; FolD, 5,10-methylene-tetrahydrofolate dehydrogenase/5,10-methylene-tetrahydrofolate cyclohydrolase; PurU, formyltetrahydrofolate deformylase; FtfL, formate-tetrahydrofolate ligase. The accession numbers of Paracoccus complete genomes: JCM7686 – GQ410978, GQ468939, GQ468938, CP006650–CP006655, and Pd1222 – CP000489–CP000491. The accession numbers of Paracoccus draft genomes: J39 – JAEN01000001–JAEN01000050, J55 – AZVA01000001–AZVA01000069, N5 – AQUO01000001–AQUO01000003, ATCC BAA-599 – JHWH01000001– JHWH01000073, DSM 582 – JRKO01000001– JRKO01000187, TRP – AEPN01000001– AEPN01000119, J40 – JAGK01000001– JAGK01000119, J46 – JAEM01000001– JAEM01000105, HAMBI 3106 – JRKS01000001– JRKS01000137, 10990 – JRKR01000001– JRKR01000309, 39524 – JRKP01000001– JRKP01000273, 4681 – JRKT01000001– JRKT01000176, 5503 – JRKQ01000001– JRKQ01000265, JCM 14014 – JRKN01000001– JRKN01000122, and ATCC 21588 – ATUJ01000001– ATUJ01000035.
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Figure 6: The methylotrophy-linked metabolic capabilities encoded by the genomes of Paracoccus spp. Tmm, trimethylamine monooxygenase; Dmm, putative dimethylamine monooxygenase; NMGP, N-methylglutamate pathway; Mau, methylamine dehydrogenase; Mxa, Mxa-type methanol dehydrogenase; Xox, Xox-type methanol dehydrogenase; GSH, glutathione; CH2 = THF, 5,10-methylene-tetrahydrofolate; FolD, 5,10-methylene-tetrahydrofolate dehydrogenase/5,10-methylene-tetrahydrofolate cyclohydrolase; PurU, formyltetrahydrofolate deformylase; FtfL, formate-tetrahydrofolate ligase. The accession numbers of Paracoccus complete genomes: JCM7686 – GQ410978, GQ468939, GQ468938, CP006650–CP006655, and Pd1222 – CP000489–CP000491. The accession numbers of Paracoccus draft genomes: J39 – JAEN01000001–JAEN01000050, J55 – AZVA01000001–AZVA01000069, N5 – AQUO01000001–AQUO01000003, ATCC BAA-599 – JHWH01000001– JHWH01000073, DSM 582 – JRKO01000001– JRKO01000187, TRP – AEPN01000001– AEPN01000119, J40 – JAGK01000001– JAGK01000119, J46 – JAEM01000001– JAEM01000105, HAMBI 3106 – JRKS01000001– JRKS01000137, 10990 – JRKR01000001– JRKR01000309, 39524 – JRKP01000001– JRKP01000273, 4681 – JRKT01000001– JRKT01000176, 5503 – JRKQ01000001– JRKQ01000265, JCM 14014 – JRKN01000001– JRKN01000122, and ATCC 21588 – ATUJ01000001– ATUJ01000035.
Mentions: Annotated genomic sequences of 17 strains of Paracoccus spp. (including P. aminophilus JCM 7686) are currently available in the GenBank database (Figure 6). The genomes of these strains were screened for the presence of 67 genes encoding enzymes involved in methylotrophy that have been identified in P. aminophilus and other methylotrophic Alphaproteobacteria. It is important to note that for 15 Paracoccus spp. strains only draft genomes were available, thus some data may be missing. Therefore, the lack of the particular genes has to be verified after obtaining complete genome sequences of those strains.

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