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Genome Editing in Methanotrophic Bacteria: Potential Targets and Available Tools

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Abstract

Aerobic methanotrophic bacteria are prokaryotic microorganisms possessing methane monooxygenases, unique enzymes that determine their ability to utilize methane (CH4) as a growth substrate. This metabolic capability makes methanotrophs attractive objects for biotechnological applications aimed at utilizing methane for production of microbial cell protein and various target metabolites. The current raise of interest to these biotechnologies is driven by high availability of methane, which is a major component of natural gas, as well as of the biogas produced in anaerobic fermentation processes. Since aerobic methanotrophs oxidize methane at the ambient temperature and pressure, they represent natural cell factories for converting CH4 into various value-added products. Further development of biotechnologies based on methane utilization requires application of genome editing techniques to obtain producer strains with improved characteristics. For a long time, the progress in metabolic engineering of methanotrophs was hampered by their specific metabolic properties and the difficulties of handling these bacteria. Here, we present an overview of the latest achievements in the field of metabolic engineering of methanotrophic bacteria and identify the potential targets as well as the currently available tools for genome editing of these microorganisms. These techniques open up the possibility of constructing strains with biotechnologically relevant characteristics and conducting in-depth research of the metabolic features of aerobic methanotrophs.

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REFERENCES

  1. Akberdin, I.R., Thompson, M., Hamilton, R., Desai, N., Alexander, D., Henard, C.A., Guarnieri, M.T., and Kalyuzhnaya, M.G., Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach, Sci. Rep., 2018, vol. 8, p. 2512.

    Article  Google Scholar 

  2. Ali, H. and Murrell, J.C., Development and validation of promoter-probe vectors for the study of methane monooxygenase gene expression in Methylococcus capsulatus Bath, Microbiology (Reading), 2009, vol. 155, pp. 761‒771.

    Article  CAS  Google Scholar 

  3. Bordel, S., Crombie, A.T., Muñoz, R., and Murrell, J.C., Genome Scale Metabolic Model of the versatile methanotroph Methylocella silvestris, Microb. Cell Fact., 2020, vol. 19, p. 144.

    Article  CAS  Google Scholar 

  4. Borodina, E., Nichol, T., Dumont, M.G., Smith, T.J., and Murrell, J.C., Mutagenesis of the “leucine gate” to explore the basis of catalytic versatility in soluble methane monooxygenase, Appl. Environ. Microbiol., 2007, vol. 73, pp. 6460–6467.

    Article  CAS  Google Scholar 

  5. Bosse, U. and Frenzel, P., Activity and distribution of methane-oxidizing bacteria in flooded rice soil microcosms and in rice plants (Oryza sativa), Appl. Environ. Microbiol., 1997, vol. 63, pp. 1199–1207.

    Article  CAS  Google Scholar 

  6. Bothe, H., Moller Jensen, K., Mergel, A., Larsen, J., Jorgensen, C., Bothe, H., and Jorgensen, L., Heterotrophic bacteria growing in association with Methylococcus capsulatus (Bath) in a single cell protein production process, Appl. Microbiol. Biotechnol., 2002, vol. 59, pp. 33‒39.

    Article  CAS  Google Scholar 

  7. But, S.Yu., Khmelenina, V.N., Mustakhimov, I.I., and Trotsenko, Yu.A., Construction and characterization of Methylomicrobium alcaliphilum 20Z knockout mutants defective in sucrose and ectoine biosynthesis genes, Microbiology (Moscow), 2013, vol. 82, pp. 253–255.

    Article  CAS  Google Scholar 

  8. But, S.Y., Egorova, S.V., Khmelenina, V.N., and Trotsenko, Y.A. Biochemical properties and phylogeny of hydroxypyruvate reductases from methanotrophic bacteria with different C1-assimilation pathways, Biochemistry (Moscow), 2017, vol. 82, pp. 1295–1303.

    CAS  Google Scholar 

  9. But, S.Yu., Dedysh, S.N., Popov, V.O., Pimenov, N.V., and Khmelenina, V.N., Construction of a Type-I methanotroph with reduced capacity for glycogen and sucrose accumulation, Appl. Biochem. Microbiol., 2020a, vol. 56, pp. 538–543.

    Article  CAS  Google Scholar 

  10. But, S.Y., Egorova, S.V., Khmelenina, V.N., and Mustakhimov, I.I., Malyl-CoA lyase provides glycine/glyoxylate synthesis in type I methanotrophs, FEMS Microbiol. Lett., 2020b, vol. 367, p. fnaa207.

  11. Chaumeil, P.-A., Mussig, A.J., Hugenholtz, P., and Parks, D.H., GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database, Bioinformatics, 2020, vol. 36, pp. 1925–1927.

    CAS  Google Scholar 

  12. Chistoserdova, L. and Lidstrom, M.E., Aerobic methylotrophic prokaryotes, in The Prokaryotes: Prokaryotic Physiology and Biochemistry, Rosenberg, E., DeLong, E.F., Lory, S., Stackebrandt, E., and Thompson, F., Eds., Berlin Heidelberg: Springer, 2013, pp. 267–285.

    Google Scholar 

  13. Chu, F., Beck, D.C., and Lidstrom, M.E., MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense, PeerJ., 2016, vol. 4, p. e2435.

    Article  Google Scholar 

  14. Chu, F. and Lidstrom, M.E., XoxF acts as the predominant methanol dehydrogenase in the type I methanotroph Methylomicrobium buryatense, J. Bacteriol., 2016, vol. 198, pp. 1317–1325.

    Article  CAS  Google Scholar 

  15. Conrad, R., The global methane cycle: recent advances in understanding the microbial processes involved, Environ. Microbiol. Rep., 2009, vol. 1, pp. 285–292.

    Article  CAS  Google Scholar 

  16. Crombie, A. and Murrell, J.C., Development of a system for genetic manipulation of the facultative methanotroph Methylocella silvestris BL2, Methods Enzymol., 2011, vol. 495, pp. 119‒133.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  18. Davamani, V., Parameswari, E., and Arulmani, S., Mitigation of methane gas emissions in flooded paddy soil through the utilization of methanotrophs, Sci. Total Environ., 2020, vol. 726, p. 138570.

    Article  CAS  Google Scholar 

  19. De la Torre, A., Metivier, A., Chu, F., Laurens, L.M., Beck, D.A., Pienkos, P.T., Lidsrom, M.E., and Kalyuzhnaya, M.G., Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1), Microb. Cell Fact., 2015, vol. 14, p. 188.

    Article  Google Scholar 

  20. Dedysh, S.N. and Dunfield, P.F., Facultative methane oxidizers, in Handbook of Hydrocarbon and Lipid Microbiology, Timmis, K.N., Ed., Berlin: Springer-Verlag, 2010, pp. 1967‒1976.

    Google Scholar 

  21. Dedysh, S.N. and Knief, C., Diversity and phylogeny of described aerobic methanotrophs, in Methane Biocatalysis: Paving the Way to Sustainability, Kalyuzhnaya, M. and Xing, X.H., Eds., Cham: Springer, 2018, pp. 17–42.

    Google Scholar 

  22. Dunfield, P.F. and Dedysh, S.N., Methylocella: a gourmand among methanotrophs, Trends Microbiol., 2014, vol. 22, pp. 368‒369.

    Article  CAS  Google Scholar 

  23. Eccleston, M. and Kelly, D.P., Assimilation and toxicity of some exogenous C1 compounds, alcohols, sugars and acetate in the methane-oxidizing bacterium Methylococcus capsulatus, J. Gen. Microbiol., 1973, vol. 75, pp. 211‒221.

    Article  CAS  Google Scholar 

  24. Egorov, I., Kupina, L., Aksyuk, I., and Murtazaeva, R., Gaprin—a protein source, Ptitsevidstvo, 1990, vol. 8, pp. 25‒27.

    Google Scholar 

  25. Eshinimaev, B.T., Khmelenina, V.N., Sakharovskii, V.G., Suzina, N.E., and Trotsenko, Y.A., Physiological, biochemical, and cytological characteristics of a haloalkalitolerant methanotroph grown on methanol, Microbiology (Moscow), 2002, vol. 71, pp. 512‒518.

    Article  CAS  Google Scholar 

  26. Espah Borujeni, A., Channarasappa, A.S., and Salis, H.M., Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites, Nucleic Acids Res., 2014, vol. 42, pp. 2646‒2659.

    Article  CAS  Google Scholar 

  27. Fu, Y., He, L., Reeve, J., Beck, D.A.C., and Lidstrom, M.E., Core metabolism shifts during growth on methanol versus methane in the methanotroph Methylomicrobium buryatense 5GB1, MBio, 2019, vol. 10, p. e00406-19.

    Article  CAS  Google Scholar 

  28. Fu, Y., Li, Y., and Lidstrom, M., The oxidative TCA cycle operates during methanotrophic growth of the Type I methanotroph Methylomicrobium buryatense 5GB1, Metab. Eng., 2017, vol. 42, pp. 43–51.

    Article  CAS  Google Scholar 

  29. Gal’chenko, V.F., Metanotrofnye bakterii (Methanotrophic Bacteria), Moscow: GEOS.

  30. Garg, S., Wu, H., Clomburg, J.M., and Bennett, G.N., Bioconversion of methane to C-4 carboxylic acids using carbon flux through acetyl-CoA in engineered Methylomicrobium buryatense 5GB1C, Metab. Eng., 2018, vol. 48, pp. 175‒183.

    Article  CAS  Google Scholar 

  31. Garneau, J.E., Dupuis, M.-È., Villion, M., Romero, D.A., Barrangou, R., Boyaval, P., Fremaux, C., Horvath, P., Magadán, A.H., and Moineau, S., The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA, Nature, 2010, vol. 468, pp. 67‒71.

    Article  CAS  Google Scholar 

  32. Gasiunas, G., Barrangou, R., Horvath, P., and Siksnys, V., Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria, Proc. Natl. Acad. Sci. USA, 2012, vol. 109, pp. E2579–E2586.

    Article  CAS  Google Scholar 

  33. Grigoryan, A.N. and Gorskaya, L.A., Ispol’zovanie prirodnogo gaza dlya mikrobiologicheskogo sinteza (Utilization of Natural Gas for Microbiological Synthesis), Moscow, ONTI Mikrobiopriom, 1970.

  34. Haque, M.F.U., Gu, W., DiSpirito, A.A., and Semrau, J.D., Marker exchange mutagenesis of mxaF, encoding the large subunit of the Mxa methanol dehydrogenase, in Methylosinus trichosporium OB3b, Appl. Environ. Microbiol., 2016, vol. 82, pp. 1549–1555.

    Article  Google Scholar 

  35. 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 

  36. Hanson, R.S. and Hanson, T.E., Methanotrophic bacteria, Microbiol. Rev., 1996, vol. 60, pp. 439‒471.

    Article  CAS  Google Scholar 

  37. Harwood, J.H., Williams, E., and Bainbridge, B.W., Mutation of the methane oxidizing bacterium Methylococcus capsulatus, J. Appl. Bacteriol., 1972, vol. 35, pp. 99–108.

    Article  CAS  Google Scholar 

  38. Henard, C.A., Franklin, T.G., Youhenna, B., But, S., Alexander, D., Kalyuzhnaya, M.G., and Guarnieri, M.T., Biogas biocatalysis: methanotrophic bacterial cultivation, metabolite profiling, and bioconversion to lactic acid, Front. Microbiol., 2018, vol. 9, p. 2610.

    Article  Google Scholar 

  39. Henard, C.A., Smith, H., Dowe, N., Kalyuzhnaya, M.G., Pienkos, P.T., and Guarnieri, M.T., Bioconversion of methane to lactate by an obligate methanotrophic bacterium, Sci. Rep., 2016, vol. 6, p. 21585.

    Article  CAS  Google Scholar 

  40. Henard, C.A., Wu, C., Xiong, W., Henard, J.M., Davidheiser-Kroll, B., Orata, F.D., and Guarnieri, M.T., Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is essential for growth of themethanotroph Methylococcus capsulatus strain Bath, Appl. Environ. Microbiol., 2021, vol. 87, p. e00881–21.

    Article  CAS  Google Scholar 

  41. Henard, C.A., Bourret, T.J., Song, M., and Vázquez-Torres, A., Control of redox balance by the stringent response regulatory protein promotes antioxidant defenses of Salmonella, J. Biol. Chem., 2010, vol. 285, pp. 36785–36793.

    Article  CAS  Google Scholar 

  42. Henard, C.A., Akberdin, I.R., Kalyuzhnaya, M.G., and Guarnieri, M.T., Muconic acid production from methane using rationally-engineered methanotrophic biocatalysts, Green Chem., 2019, vol. 21, pp. 6731–6737.

    Article  CAS  Google Scholar 

  43. Hu, L., Guo, S., Yan, X., Zhang, T., Xiang, J., and Fei, Q., Exploration of an efficient electroporation system for heterologous gene expression in the genome of methanotroph, Front. Microbiol., 2021, vol. 12, p. 717033.

    Article  Google Scholar 

  44. Ishikawa, M., Yokoe, S., Kato, S., and Hori, K., Efficient counterselection for Methylococcus capsulatus (Bath) by using a mutated pheS gene, Appl. Environ. Microbiol., 2018, vol. 84, p. e01875-18.

    Article  CAS  Google Scholar 

  45. Jiang, D., Kim, C.S., Hanson, R.S., and Wood, T.K., Optimization of trichloroethylene degradation using soluble methane monooxygenase of Methylosinus trichosporium OB3b expressed in recombinant bacteria, Biotechnol. Bioeng., 1996, vol. 51, pp. 349–359.

    Article  Google Scholar 

  46. Jiang, H., Chen, Y., Jiang, P., Zhang, C., Smith, T.J., Murrell, J.C., and Xing, X.H., Methanotrophs: multifunctional bacteria with promising applications in environmental bioengineering, Biochem. Eng J., 2010, vol. 49, pp. 277‒288.

    Article  CAS  Google Scholar 

  47. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A., and Charpentier, E., A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, 2012, vol. 337, pp. 816–821.

    Article  CAS  Google Scholar 

  48. Kalyuzhnaya, M.G., Kumaresan, D., Heimann, K., Caetano, N.S., Visvanathan, C., and Parthiba Karthikeyan, O., Editorial: Methane: a bioresource for fuel and biomolecules, Front. Environ. Sci., 2020, vol. 8, p. 9.

    Article  Google Scholar 

  49. Kalyuzhnaya, M.G., Puri, A.W., and Lidstrom, M.E., Metabolic engineering in methanotrophic bacteria, Metab. Engin., 2015, vol. 29, pp. 142‒152.

    Article  CAS  Google Scholar 

  50. Kalyuzhnaya, M.G., Yang, S., Rozova, O.N., Smalley, N.E., Clubb, J., Lamb, A., Gowda, G.N., Raftery, D., Fu, Y., Bringel, F., Vuilleumier, S., Beck, D.A.C., Trotsenko, Y.A., Khmelenina, V.N., and Lidstrom, M.E., Highly efficient methane biocatalysis revealed in a methanotrophic bacterium, Nat. Commun., 2013, vol. 4, p. 2785.

    Article  CAS  Google Scholar 

  51. Khadem, A.F., Pol, A., Wieczorek, A., Mohammadi, S.S., Francoijs, K.J., Stunnenberg, H.G., Jetten, M.S.M., and Op den Camp, H.J.M., Autotrophic methanotrophy in verrucomicrobia: Methylacidiphilum fumariolicum SolV uses the Calvin‒Benson‒Bassham cycle for carbon dioxide fixation, J. Bacteriol., 2011, vol. 193, pp. 4438–4446.

    Article  CAS  Google Scholar 

  52. Khider, M.L.K., Brautaset, T., and Irla, M., Methane monooxygenases: central enzymes in methanotrophy with promising biotechnological applications, World J. Microbiol. Biotechnol., 2021, vol. 37, p. 72.

    Article  CAS  Google Scholar 

  53. Khmelenina, V.N., But, S.Y., Rozova, O.N., and Trotsenko, Y.A., Metabolic features of aerobic methanotrophs: news and views, Curr. Issues Mol. Biol., 2019, vol. 33, pp. 85‒100.

    Article  Google Scholar 

  54. Khmelenina, V.N., Kalyuzhnaya, M.G., Sakharovsky, V.G., Suzina, N.E., Trotsenko, Y.A., and Gottschalk, G., Osmoadaptation in halophilic and alkaliphilic methanotrophs, Arch. Microbiol., 1999, vol. 172, pp. 321‒329.

    Article  CAS  Google Scholar 

  55. Knief, C., Diversity and habitat preferences of cultivated and uncultivated aerobic methanotrophic bacteria evaluated based on pmoA as molecular marker, Front. Microbiol., 2015, vol. 6, p. 1346.

    Article  Google Scholar 

  56. Lalov, V.V., Analysis and synthesis of energotechnological systems of fodder protein production from natural gas, Extended Abstract of Doctoral (Biology) Dissertation, Moscow, 1991.

  57. Le, H.T.Q., Nguyen, A.D., Park, Y.R., and Lee, E.Y., Sustainable biosynthesis of chemicals from methane and glycerol via reconstruction of multi-carbon utilizing pathway in obligate methanotrophic bacteria, Microb. Biotechnol., 2021, vol. 14, pp. 2552‒2565.

    Article  CAS  Google Scholar 

  58. Lee, J.K., Kim, S., Kim, W., Kim, S., Cha, S., Moon, H., Hur, D.H., Kim, S.Y., Na, J.G., Lee, J.W., Lee, E.Y., and Hahn, J.S., Efficient production of d-lactate from methane in a lactate-tolerant strain of Methylomonas sp. DH-1 generated by adaptive laboratory evolution, Biotechnol. Biofuels, 2019, vol. 12, pp. 234.

    Article  Google Scholar 

  59. Lee, H.M., Ren, J., Tran, K.M., Jeon, B.M., Park, W.U., Kim, H., Lee, K.E., Oh, Y., Choi, M., Kim, D.S., and Na, D., Identification of efficient prokaryotic cell-penetrating peptides with applications in bacterial biotechnology, Commun. Biol., 2021a, vol. 4, p. 205.

    Article  CAS  Google Scholar 

  60. Lee, H.M., Ren, J., Yu, M.S., Kim, H., Kim, W.Y., Shen, J., Yoo, S.M., Eyun, S.I., and Na, D., Construction of a tunable promoter library to optimize gene expression in Methylomonas sp. DH-1, a methanotroph, and its application to cadaverine production, Biotechnol. Biofuels, 2021b, vol. 14, p. 228.

    Article  CAS  Google Scholar 

  61. Lieven, C., Petersen, L.A.H., Jørgensen, S.B., Gernaey, K.V., Herrgard, M.J., and Sonnenschein, N., A genome-scale metabolic model for Methylococcus capsulatus (Bath) suggests reduced efficiency electron transfer to the particulate methane monooxygenase, Front. Microbiol., 2018, vol. 9, p. 2947.

    Article  Google Scholar 

  62. Liu, Y., He, X., Zhu, P., Cheng, M., Hong, Q., and Yan, X., pheSAG based rapid and efficient markerless mutagenesis in Methylotuvimicrobium, Front. Microbiol., 2020, vol. 11, p. 441.

    Article  Google Scholar 

  63. Liu, Y., Zhang, H., He, X., and Liu, J., Genetically engineered methanotroph as a platform for bioaugmentation of chemical pesticide contaminated soil, ACS Synth. Biol., 2021, vol. 10, pp. 487–494.

    Article  CAS  Google Scholar 

  64. Lloyd, J.S., Finch, R., Dalton, H., and Murrell, J.C. Homologous expression of soluble methane monooxygenase genes in Methylosinus trichosporium OB3b, Microbiology (Reading), 1999, vol. 145, pp. 461‒470.

    Article  CAS  Google Scholar 

  65. Marx, C.J. and Lidstrom, M.E., Development of improved versatile broad-host-range vectors for use in methylotrophs and other gram-negative bacteria, Microbiology, 2001, vol. 147, pp. 2065‒2075.

    Article  CAS  Google Scholar 

  66. Marx, C.J. and Lidstrom, M.E., Broad-host-range cre-lox system for antibiotic marker recycling in gram-negative bacteria, Biotechniques, 2002, vol. 33, pp. 1062‒1067.

    Article  CAS  Google Scholar 

  67. Marx, C.J., Development of a broad-host-range sacB-based vector for unmarked allelic exchange, BMC Res. Notes, 2008, vol. 1, p. 1. https://doi.org/10.1186/1756-0500-1-1

    Article  CAS  Google Scholar 

  68. Murrell, J.C., Gilbert, B., and McDonald, I.R., Molecular biology and regulation of methane monooxygenase, Arch. Microbiol., 2000, vol. 173, pp. 325–332.

    Article  CAS  Google Scholar 

  69. Murrell, J.C. and Smith, T.J., Biochemistry and molecular biology of methane monooxygenase, in Handbook of Hydrocarbon and Lipid Microbiology, Timmis, K.N., Ed., Berlin‒Heidelberg: Springer, 2010, pp. 1045–1055.

    Google Scholar 

  70. Mustakhimov, I.I., Reshetnikov, A.S., Glukhov, A.S., Khmelenina, V.N., Kalyuzhnaya, M.G., and Tro-tsenko, Y.A., Identification and characterization of EctR1, a new transcriptional regulator of the ectoine biosynthesis genes in the halotolerant methanotroph Methylomicrobium alcaliphilum 20Z, J. Bacteriol., 2010, vol. 192, pp. 410–417.

    Article  CAS  Google Scholar 

  71. Mustakhimov, I.I., But, S.Y., Reshetnikov, A.S., Khmelenina, V.N., and Trotsenko, Y.A., Homo- and heterologous reporter proteins for evaluation of promoter activity in Methylomicrobium alcaliphilum 20Z, Appl. Biochem. Microbiol., 2016, vol. 52, pp. 279‒286.

    Article  CAS  Google Scholar 

  72. Naizabekov, S. and Lee, E.Y., Genome-scale metabolic model reconstruction and in silico investigations of methane metabolism in Methylosinus trichosporium OB3b, Microorganisms, 2020, vol. 8, p. 437.

    Article  CAS  Google Scholar 

  73. Nguyen, A.D., Hwang, I.Y., Lee, O.K., Kim, D., Kalyuzhnaya, M.G., Mariyana, R., Hadiyati, S., Kim, M.S., and Lee, E.Y., Systematic metabolic engineering of Methylomicrobium alcaliphilum 20Z for 2,3-butanediol production from methane, Metab. Engin., 2018, vol. 47, pp. 323‒333.

    Article  CAS  Google Scholar 

  74. Nguyen, L.T. and Lee, E.Y., Biological conversion of methane to putrescine using genome-scale model-guided metabolic engineering of a methanotrophic bacterium Methylomicrobium alcaliphilum 20Z, Biotechnol. Biofuels, 2019, vol. 12, p. 147.

    Article  Google Scholar 

  75. Nguyen, D.T.N., Lee, O.K., Hadiyati, S., Affifah, A.N., Kim, M.S., and Lee, E.Y., Metabolic engineering of the type I methanotroph Methylomonas sp. DH-1 for production of succinate from methane, Metab. Engin., 2019, vol. 54, pp. 170‒179.

    Article  CAS  Google Scholar 

  76. Nguyen, D., Lee, O.K., Lim, C., Lee, J., Na, J.-G., and Lee, E.Y., Metabolic engineering of type II methanotroph, Methylosinus trichosporium OB3b, for production of 3-hydroxypropionic acid from methane via a malonyl-CoA reductase-dependent pathway, Metab. Engin., 2020a, vol. 59, pp. 142‒150.

    Article  CAS  Google Scholar 

  77. Nguyen, A.D., Kim, D., and Lee, E.Y., Unlocking the biosynthesis of sesquiterpenoids from methane via the methylerythritol phosphate pathway in methanotrophic bacteria, using α-humulene as a model compound, Metab. Engin., 2020b, vol. 61, pp. 69–78.

    Article  CAS  Google Scholar 

  78. Nguyen, A.D., Chau, T.H.T., and Lee, E.Y., Methanotrophic microbial cell factory platform for simultaneous conversion of methane and xylose to value-added chemicals, Chem. Eng. J., 2021, vol. 420, p. 127632.

    Article  Google Scholar 

  79. Op den Camp, H.J.M., Islam, T., Stott, M.B., Harhangi, H.R., Hynes, A., Schouten, S., Jetten, M.S.M., Birkeland, N.K., Pol, A., and Dunfield, P.F., Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia, Environ. Microbiol. Rep., 2009, vol. 1, pp. 293–306.

    Article  CAS  Google Scholar 

  80. Øverland, M., Tauson, A.H., Shearer, K., and Skrede, A., Evaluation of methane-utilising bacteria products as feed ingredients for monogastric animals, Arch. Anim. Nutr., 2010, vol. 64, pp. 171‒189.

    Article  Google Scholar 

  81. Parks, D.H., Chuvochina, M., Rinke, C., Mussig, A.J., Chaumeil, P.-A., and Hugenholtz, P., GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy, Nucleic Acids Res., 2022, vol. 50, pp. D785–D794.

    Article  CAS  Google Scholar 

  82. Pham, D.N., Nguyen, A.D., and Lee, E.Y., Outlook on engineering methylotrophs for one-carbon-based industrial biotechnology, Chem. Eng. J., 2022a, vol. 449, p. 137769.

    Article  CAS  Google Scholar 

  83. Pham, D.N., Nguyen, A.D., Oh, S.H., and Lee, E.Y., Bypassing the bottlenecks in the shikimate and methylerythritol phosphate pathways for enhancing the production of natural products from methane in Methylotuvimicrobium alcaliphilum 20Z, Green Chem., 2022b, vol. 24, pp. 2893‒2903.

    Article  CAS  Google Scholar 

  84. Pham, D.N., Mai, D.H.A., Nguyen, A.D., Chau, T.H.T., and Lee, E.Y., Development of an engineered methanotroph-based microbial platform for biocatalytic conversion of methane to phytohormone for sustainable agriculture, Chem. Eng. J., 2022c, vol. 429, p. 132522.

    Article  CAS  Google Scholar 

  85. Pieja, A.J., Morse, M.C., and Cal, A.J., Methane to bioproducts: the future of the bioeconomy?, Curr. Opin. Chem. Biol., 2017, vol. 41, pp. 123–131.

    Article  CAS  Google Scholar 

  86. Puri, A.W., Owen, S., Chu, F., Chavkin, T., Beck, D.A.C., and Kalyuzhnaya, M.G., Genetic tools for the industrially promising methanotroph Methylomicrobium buryatense, Appl. Environ. Microbiol., 2015, vol. 81, pp. 1775–1781.

    Article  Google Scholar 

  87. Recorbet, G., Robert, C., Givaudan, A., Kudla, B., Normand, P., and Faurie, G., Conditional suicide system of Escherichia coli released into soil that uses the Bacillus subtilis sacB gene, Appl. Environ. Microbiol., 1993, vol. 59, pp. 1356‒1365.

    Article  Google Scholar 

  88. Ren, J., Lee, H.‑M., Thai, T.D., and Na, D., Identification of a cytosine methyltransferase that improves transformation efficiency in Methylomonas sp. DH‑1, Biotechnol. Biofuels, 2020, vol. 13, p. 200.

    Article  CAS  Google Scholar 

  89. Ro, S.Y. and Rosenzweig, A.C., Recent advances in the genetic manipulation of Methylosinus trichosporium OB3b, Methods Enzymol., 2018, vol. 605, pp. 335‒349.

    Article  CAS  Google Scholar 

  90. Salis, H.M., Mirsky, E.A. and Voigt, C.A., Automated design of synthetic ribosome binding sites to control protein expression, Nat. Biotechnol., 2009, vol. 27, pp. 946‒950.

    Article  CAS  Google Scholar 

  91. Schmitz, R.A., Peeters, S.H., Versantvoort, W., Picone, N., Pol, A., Jetten, M.S.M., and Op Den Camp, H.J.M., Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles, FEMS Microbiol. Rev., 2021, vol. 45, p. fuab007.

  92. Shaner, N.C., Campbell, R.E., Steinbach, P.A., Giepmans, B.N.G., Palmer, A.E., and Tsien, R.Y., Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein, Nat. Biotechnol., 2004, vol. 22, pp. 1567‒1572.

    Article  CAS  Google Scholar 

  93. Stafford, G.P., Scanlan, J., McDonald, I.R., and Murrell, J.C., rpoN, mmoR and mmoG, genes involved in regulating the expression of soluble methane monooxygenase in Methylosinus trichosporium OB3b, Microbiology (Reading), 2003, vol. 149, pp. 1771–1784.

    Article  CAS  Google Scholar 

  94. Sternberg, N. and Hamilton, D., Bacteriophage P1 site-specific recombination: I. Recombination between loxP sites, J. Mol. Biol., 1981, vol. 150, pp. 467‒486.

    Article  CAS  Google Scholar 

  95. Strong, P.J., Xie, S., and Clarke, W.P., Methane as a resource: can the methanotrophs add value?, Environ Sci. Technol., 2015, vol. 49, pp. 4001–4018.

    Article  CAS  Google Scholar 

  96. Tapscott, T., Guarnieri, M.T., and Henard, C.A., Development of a CRISPR/Cas9 system for Methylococcus capsulatus in vivo gene editing, Appl. Environ. Microbiol., 2019, vol. 85, p. e00340-19.

    Article  CAS  Google Scholar 

  97. 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 

  98. Welander, P.V. and Summons, R.E., Discovery, taxonomic distribution, and phenotypic characterization of a gene required for 3-methylhopanoid production, Proc. Natl. Acad. Sci. USA, 2012, vol. 109, pp. 12905–12910.

    Article  CAS  Google Scholar 

  99. Williams, E., Shimmin, M.S., and Bainbridge, B.W., Mutation in the obligate methylotrophs Methylococcus capsulatus and Methylomonas albus, FEMS Microbiol. Lett., 1977, vol. 2, pp. 293–296.

    Article  CAS  Google Scholar 

  100. Wilson, E.H., Groom, J.D., Sarfatis, M.C., Ford, S.M., Lidstrom, M.E., and Beck, D.A., A computational framework for identifying promoter sequences in nonmodel organisms using RNA-seq data sets, ACS Synth. Biol., 2021, vol. 10, pp. 1394–1405.

    Article  CAS  Google Scholar 

  101. Yan, X., Chu, F., Puri, A.W., Fu, Y., and Lidstrom, M.E., Electroporation-based genetic manipulation in type I methanotrophs, Appl. Environ. Microbiol., 2016, vol. 82, pp. 2062–2069.

    Article  CAS  Google Scholar 

  102. Ye, R.W., Yao, H., Stead, K., Wang, T., Tao, L., Cheng, Q., Sharpe, P.L., Suh, W., Nagel, E., Arcilla, D., Dragotta, D., and Miller, E.S., Construction of the astaxanthin biosynthetic pathway in a methanotrophic bacterium Methylomonas sp. strain 16a, Ind. Microbiol. Biotechnol., 2007, vol. 34, pp. 289‒299.

    Article  CAS  Google Scholar 

  103. Zheng, Y., Huang, J., Zhao, F., and Chistoserdova, L., Physiological effect of XoxG(4) on lanthanide-dependent methanotrophy, mBio, 2018, vol. 9, p. e02430-17.

    Article  CAS  Google Scholar 

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Funding

The review was prepared as a part of the project no. 075-15-2021-1071 “Development of Genomic Editing Techniques for the Purposes of Innovation in Industrial and Food Biotechnologies” with financial support of the Ministry of Science and Higher Education of the Russian Federation.

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  1. Skryabin Institute of Biochemistry and Physiology of Microorganisms Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290, Pushchino, Moscow region, Russia

    V. N. Khmelenina, S. Yu. But & O. N. Rozova

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

    S. Yu. But, O. N. Rozova, I. Yu. Oshkin, N. V. Pimenov & S. N. Dedysh

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  1. V. N. Khmelenina
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  2. S. Yu. But
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  3. O. N. Rozova
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Correspondence to S. N. Dedysh.

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Translated by D. Timchenko

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Khmelenina, V.N., But, S.Y., Rozova, O.N. et al. Genome Editing in Methanotrophic Bacteria: Potential Targets and Available Tools. Microbiology 91, 613–630 (2022). https://doi.org/10.1134/S0026261722602196

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