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

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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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REFERENCES

  1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 1997, vol. 25, pp. 3389–3402.

    Article  CAS  Google Scholar 

  2. Arndt, D., Grant, J.R., Marcu, A., Sajed, T., Pon, A., Liang, Y., and Wishart, D.S., PHASTER: a better, faster version of the PHAST phage search tool, Nucleic Acids Res., 2016, vol. 44, pp. 16–21.

    Article  Google Scholar 

  3. Baxter, N.J., Hirt, R.P., Bodrossy, L., Kovacs, K.L., Embley, M.T., Prosser, J.I., and Murrell, C.J., The ribulose-1,5-bisphosphate carboxylase/oxygenase gene cluster of Methylococcus capsulatus (Bath), Arch. Microbiol., 2002, vol. 177, pp. 279–289.

    Article  CAS  Google Scholar 

  4. Chistoserdova, L., Modularity of methylotrophy, revisited, Environ. Microbiol., 2011, vol. 13, pp. 2603–2622.

    Article  CAS  Google Scholar 

  5. Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D.R., da Costa, M.S., Rooney, A.P., Yi, H., Xu, X.W., De Meyer, S., and Trujillo, M.E., Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes, Int. J. Syst. Evol. Microbiol., 2018, vol. 68, pp. 461–466.

    Article  CAS  Google Scholar 

  6. Contreras-Moreira, B. and Vinuesa, P., GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis, Appl. Environ. Microbiol., 2013, vol. 79, pp. 7696–7701.

    Article  CAS  Google Scholar 

  7. Csáki, R., Bodrossy, L., Klem, J., Murrell, J.C., and Kovács, K.L., Genes involved in the copper-dependent regulation of soluble methane monooxygenase of Methylococcus capsulatus (Bath): Cloning, sequencing and mutational analysis, Microbiology (SGM), 2003, vol. 149, pp. 1785–1795.

    Article  Google Scholar 

  8. Foster, J.W. and Davis, R.H., A methane-dependent coccus, with notes on classification and nomenclature of obligate, methane-utilizing bacteria, J. Bacteriol., 1966, vol. 91, pp. 1924–1931.

    Article  CAS  Google Scholar 

  9. Galchenko, V.F., Metanotrofnye bakterii (Methanotrophic Bacteria), Moscow: GEOS, 2001.

  10. Grigoryan, A.N. and Gorskaya, L. Ispolzovanie prirodnogo gaza dlya mikrobiologicheskogo sinteza (Use of Natural Gas for Microbiological Synthesis), Moscow: ONTI Microbioprom, 1970.

  11. Hamer, G. and Harrison, D.E.F., Single cell protein: the technology, economics and future potential, in Hydrocarbons in Biotechnology, Harrison, D.E.F., Higgins, I.J., and London, W.R., Eds., London: Heyden Institute of Petroleum, 1980, pp. 59–73.

    Google Scholar 

  12. Hanson, R. and Hanson, T., Methanotrophic bacteria, Microbiol. Rev., 1996, vol. 60, pp. 439–471.

    Article  CAS  Google Scholar 

  13. Hartmann, T. and Leimkühler, S., The oxygen-tolerant and NAD+-dependent formate dehydrogenase from Rhodobacter capsulatus is able to catalyze the reduction of CO2 to formate, FEBS J., 2013, vol. 280, pp. 6083–6096.

    Article  CAS  Google Scholar 

  14. Henard, C.A., Smith, H.K., and Guarnieri, M.V., Phosphoketolase overexpression increases biomass and lipid yield from methane in an obligate methanotrophic biocatalyst, Metab. Eng., 2017, pp. 152–158.

  15. Hibi, Y., Asai, K., Arafuka, H., Hamajima, M., Iwama, T., and Kawai, K., Molecular structure of La3+-induced methanol dehydrogenase-like protein in Methylobacterium radiotolerans,J. Biosci. Bioeng., 2011, vol. 111, pp. 547–549.

    Article  CAS  Google Scholar 

  16. Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M., Data, information, knowledge and principle: back to metabolism in KEGG, Nucleic Acids Res., 2014, vol. 42, pp. D199–D205.

    Article  CAS  Google Scholar 

  17. Kanehisa, M., Sato, Y., and Morishima, K., BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences, J. Mol. Biol., 2016, vol. 428, pp. 726–731.

    Article  CAS  Google Scholar 

  18. Kao, W.C., Chen, Y.R., Yi, E.C., Lee, H., Tian, Q., Wu, K.M., Tsai, S.F., Yu, S.S.F., Chen, Y.J., Aebersold, R., and Chan, S.I., Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath), J. Biol. Chem., 2004, vol. 279, pp. 51554–51560.

    Article  CAS  Google Scholar 

  19. Khmelenina, V.N., Murrell, J.C., Smith, V.J., and Trotsenko, Y.A. Physiology and biochemistry of the aerobic methanotrophs, in Aerobic Utilization of Hydrocarbons, Oils and Lipids. Handbook of Hydrocarbon and Lipid Microbiology, Rojo, F., Ed., Cham: Springer, 2018, pp. 1–25.

    Google Scholar 

  20. Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J., and Marra, M.A., Circos: an information aesthetic for comparative genomics, Genome Res., 2009, vol. 19, pp. 1639–1645.

    Article  CAS  Google Scholar 

  21. Lagesen, K., Hallin, P., Rødland, E.A., Stærfeldt, H.H., Rognes, T., and Ussery D.W., RNAmmer: consistent and rapid annotation of ribosomal RNA genes, Nucleic Acids Res., 2007, vol. 35, pp. 3100–3108.

    Article  CAS  Google Scholar 

  22. Lalov, V.V., Analysis and synthesis of energotechnological systems for fodder protein production from natural gas, Extended abstract of Doctoral (Biol.) Dissertation, Moscow, 1991.

  23. Larsen, Ø. and Karlsen, O.A., Transcriptomic profiling of Methylococcus capsulatus (Bath) during growth with two different methane monooxygenases, MicrobiologyOpen, 2016, vol. 5, pp. 254–267.

    Article  CAS  Google Scholar 

  24. Lieven, C., Petersen, L.A.H., Jørgensen, S.B., Gernaey, K.V., Herrgard, M.J., and Sonnenschein, N.A., A genome-scale metabolic model for Methylococcus capsulatus predicts reduced efficiency uphill electron transfer to pMMO, bioRxiv., 2018, p. 329714.

  25. Linton, J. and Buckee, J., Interactions in a methane-utilising mixed culture in a chemostat, J. Gen. Microbiol., 1977, vol. 101, pp. 219–225.

    Article  Google Scholar 

  26. Lopes, A., Tavares, P., Petit, M.A., Guérois, R., and Zinn-Justin, S., Automated classification of tailed bacteriophages according to their neck organization, BMC Genomics, 2014, vol. 15, pp. 1–17.

    Article  Google Scholar 

  27. Lowe, V.M. and Eddy, S.R., TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res., 1996, vol. 25, pp. 955–964.

    Article  Google Scholar 

  28. Marçais, G., Delcher, A.L., Phillippy, A.M., Coston, R., Salzberg, S.L., and Zimin, A., MUMmer4: a fast and versatile genome alignment system, PLoS Comput. Biol., 2018, vol. 14, e1005944.

    Article  Google Scholar 

  29. Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.P., and Göker, M., Genome sequence-based species delimitation with confidence intervals and improved distance functions, BMC Bioinform., 2013, vol. 14, p. 60.

    Article  Google Scholar 

  30. Overbeek, R., Olson, R., Pusch, G.D., Olsen, G.J., Davis, J.J., Disz, T., Edwards, R.A., Gerdes, S., Parrello, B., Shukla, M., Vonstein, V., Wattam, A.R., Xia, F., and Stevens, R., The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST), Nucleic Acids Res., 2014, vol. 42, pp. 206–214.

    Article  Google Scholar 

  31. Parks, D.H., Chuvochina, M., Waite, D.W., Rinke, C., Skarshewski, A., Chaumeil, P.A., and Hugenholtz, P., A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life, Nat. Biotechnol., 2018, vol. 36, pp. 996‒1004.

    Article  CAS  Google Scholar 

  32. Reshetnikov, A.S., Rozova, O.N., Khmelenina, V.N., Mustakhimov, I.I., Beschastny, A.P., Murrell, J.C., and Trotsenko Y.A., Characterization of the pyrophosphate-dependent 6-phosphofructokinase from Methylococcus capsulatus Bath, FEMS Microbiol. Lett., 2008, vol. 288, pp. 202–210.

    Article  CAS  Google Scholar 

  33. Rodriguez-R, L.M. and Konstantinidis, K.V., Bypassing cultivation to identify bacterial species, Microbe, 2014, vol. 9, pp. 111–118.

    Google Scholar 

  34. Rozova, O.N., Khmelenina, V.N., Gavletdinova, J.Z., Mustakhimov, I.I., and Trotsenko, Y.A., Acetate kinase—an enzyme of the postulated phosphoketolase pathway in Methylomicrobium alcaliphilum 20Z, Antonie van Leeuwenhoek, 2015, vol. 108, pp. 965–974.

    Article  CAS  Google Scholar 

  35. Seemann, T., Prokka: rapid prokaryotic genome annotation, Bioinformatics, 2014, vol. 30, pp. 2068–2069.

    Article  CAS  Google Scholar 

  36. Sullivan, M.J., Petty, N.K., and Beatson, S.A., Easyfig: a genome comparison visualizer, Bioinformatics, 2011, vol. 27, pp. 1009–1010.

    Article  CAS  Google Scholar 

  37. Trotsenko Y.A. and Murrell J.C., Metabolic aspects of aerobic obligate methanotrophy, Adv. Appl. Microbiol., 2008, vol. 63, pp. 183–229.

    Article  CAS  Google Scholar 

  38. Varani, A.M., Siguier, P., Gourbeyre, E., Charneau, V., and Chandler, M., ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes, Genome Biol., 2011, vol. 12, no. 3, R30.

    Article  CAS  Google Scholar 

  39. Vuilleumier, S., Chistoserdova, L., Lee, M.C., Bringel, F., Lajus, A., Yang, Z., Gourion, B., Barbe, V., Chang, J., Cruveiller, S., Dossat, C., Gillett, W., Gruffaz, C., Haugen, E., Hourcade, E., et al., Methylobacterium genome sequences: A reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources, PLoS One, 2009, vol. 4, no. 5, e5584.

    Article  Google Scholar 

  40. Ward, N., Larsen, Ø., Sakwa, J., Bruseth, L., Khouri, H., Durkin, A.S., Dimitrov, G., Jiang, L., Scanlan, D., Kang, K.H., Lewis, M., Nelson, K.E., Methé, B., Wu, M., Heidelberg, J.F., et al., Genomic insights into methanotrophy: The complete genome sequence of Methylococcus capsulatus (Bath), PLoS Biol., 2004, vol. 2, pp. 707–713.

    Google Scholar 

  41. Wick, R.R., Judd, L.M., Gorrie, C.L., and Holt, K.E., Unicycler: resolving bacterial genome assemblies from short and long sequencing reads, PLoS Comput. Biol., 2017, vol. 13, no. 6, e1005595.

    Article  Google Scholar 

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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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Authors and Affiliations

  1. Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071, Moscow, Russia

    I. Yu. Oshkin, K. K. Miroshnikov, S. E. Belova, S. N. Dedysh & N. V. Pimenov

  2. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Biological Research Center, Russian Academy of Sciences, 142290, Pushchino, Russia

    V. N. Khmelenina & S. Yu. But

  3. Gazprom VNIIGAZ, 142717, Razvilka, Moscow oblast, Russia

    N. S. Khokhlachev

  4. NPO Biosintez, 107045, Moscow, Russia

    D. V. Chernushkin

  5. Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 119071, Moscow, Russia

    A. V. Beletsky, A. V. Mardanov & N. V. Ravin

  6. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, 119071, Moscow, Russia

    V. O. Popov

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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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