Analysis of the Complete Genome Sequence of Strain Concept-8, a Novel Representative of the Genus Methylococcus

Abstract

The complete genome sequence of a thermotolerant obligate methanotroph Methylococcus sp. Concept-8 was determined and analyzed. This strain was obtained by long-term storage, selection, and purification of an industrial culture of Methylococcus capsulatus BSV-874, which was used for methane-based protein biosynthesis in the Soviet Union. The size of the Concept-8 genome is 3.46 Mb. Genome annotation identified 3266 open reading frames that encode proteins. The closest phylogenetic relative of strain Concept-8 is Methylococcus capsulatus Bath (98.7% identity of 16S rRNA gene sequences). Comparison of the genomic sequences of these methanotrophs revealed 88.39% average nucleotide sequence identity, indicating that Concept-8 represents a novel species of the genus Methylococcus. The genomes of the strains Bath and Concept-8 both contain two copies of rRNA operons and pmoBAC operons for particulate methane monooxygenase, as well as a single copy of the soluble methane monooxygenase operon mmoXYBZDC. Growth on methanol was possible due to the presence of two complementary methanol dehydrogenases: MxaFJGIRACKLD and XoxF. The two methanotrophs also possess highly similar sets of genes encoding enzymes of the major pathways of the metabolism of C1 compounds. The genome of Methylococcus sp. Concept-8 was found to contain two regions associated with prophages of the family Siphoviridae. The prophage regions detected in the genome of Mc. capsulatus Bath are also homologous to viral sequences of the family Siphoviridae but differ from those identified in the genome of Concept-8.

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Funding

This work was supported by the Ministry of Science and High Education of Russia, project no. 075-15-2019-1830 of the Federal Targeted Program; unique identifier (UID) of the project: RFMEFI60719X0297.

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Correspondence to S. N. Dedysh.

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Conflict of interests. The authors declare that they have no conflict of interest.

The authors’ contribution. N.S. Khokhlachev and D.V. Chernushkin provided the original culture of strain Concept-8. S.E. Belova was in charge of purification of the strain and biomass harvesting for genome sequencing. A.V. Mardanov, A.V. Beletsky, and N.V. Ravin were in charge of DNA isolation, sequencing, and genome assembly. I.Yu. Oshkin, V.N. Khmelenina, and S.Yu. But performed the comparative analysis of Concept-8 and Bath genome sequences and the analysis of central metabolic pathways. K.K. Miroshnikov analyzed the genome for the presence of prophage. The text of the manuscript was written by S.N. Dedysh, V.N. Khmelenina, V.O. Popov, and N.V. Pimenov. All authors participated in the discussion of the results.

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Oshkin, I.Y., Khmelenina, V.N., But, S.Y. et al. Analysis of the Complete Genome Sequence of Strain Concept-8, a Novel Representative of the Genus Methylococcus. Microbiology 89, 309–317 (2020). https://doi.org/10.1134/S0026261720030121

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Keywords:

  • methanotrophic bacteria
  • Methylococcus
  • genome analysis
  • methane monooxygenase
  • metabolism of C1 compounds
  • prophage