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Rethinking biological activation of methane and conversion to liquid fuels

Abstract

If methane, the main component of natural gas, can be efficiently converted to liquid fuels, world reserves of methane could satisfy the demand for transportation fuels in addition to use in other sectors. However, the direct activation of strong C-H bonds in methane and conversion to desired products remains a difficult technological challenge. This perspective reveals an opportunity to rethink the logic of biological methane activation and conversion to liquid fuels. We formulate a vision for a new foundation for methane bioconversion and suggest paths to develop technologies for the production of liquid transportation fuels from methane at high carbon yield and high energy efficiency and with low CO2 emissions. These technologies could support natural gas bioconversion facilities with a low capital cost and at small scales, which in turn could monetize the use of natural gas resources that are frequently flared, vented or emitted.

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Figure 1: Macro-level data encourages methane as a liquid fuel feedstock.
Figure 2: Native enzymes capable of oxidizing C-H bonds.
Figure 3: Pathways for the conversion of methane or glucose to butanol in an engineered microorganism.
Figure 4: Selective routes for the activation of C-H bonds in hydrocarbons.
Figure 5: Metabolic pathways to butanol from metabolic intermediates derived from the efficient activation of methane.
Figure 6: Bioprocess considerations and techno-economics.

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References

  1. U.S. Energy Information Agency. Technically Recoverable Shale Oil and Shale Gas Resources: an Assessment of 137 Shale Formations in 41 Countries Outside the United States (U.S. Department of Energy, Washington, DC, 2013).

  2. Canadian Association of Petroleum Producers. Crude Oil: Forecast, Markets, and Transportation (Canadian Association of Petroleum Producers, Calgary, Canada, 2013).

  3. National Research Council. America's Energy Future: Technology and Transformation 211–270 (The National Academies Press, Washington, DC, 2009).

  4. U.S. Environmental Protection Agency. Summary Report: Global Anthropogenic Non-CO2 Greenhouse Gases Emissions: 1990–2030 (U.S. Environmental Protection Agency, Washington, DC, 2012).

  5. Global Gas Flaring Reduction Partnership. GGFR partners mark 10th anniversary by scaling up flaring reduction efforts. The World Bank, http://siteresources.worldbank.org/INTGGFR/Resources/GGFR_Gas_Flaring_Aug2012_a6.pdf (2012).

  6. National Petroleum Council. Advancing Technology for America's Transportation Future. Chapter 14 (National Petroleum Council, Washington, DC, 2012).

  7. Krishnan, M.S., Ho, N.W. & Tsao, G.T. Fermentation kinetics of ethanol production from glucose and xylose by recombinant Saccharomyces 1400 (pLNH33). Appl. Biochem. Biotechnol. 78, 373–388 (1999).

    Article  Google Scholar 

  8. Valdes, C. Brazil's Ethanol Industry: Looking Forward 4–7 (U.S. Department of Agriculture Economic Research Service, Washington, DC, 2011)

    Google Scholar 

  9. Trotsenko, Y.A. & Murrell, J.C. Metabolic aspects of aerobic obligate methanotrophy. Adv. Appl. Microbiol. 63, 183–229 (2008).

    Article  CAS  PubMed  Google Scholar 

  10. Hakemian, A.S. & Rosenzweig, A.C. The biochemistry of methane oxidation. Annu. Rev. Biochem. 76, 223–241 (2007).

    Article  CAS  PubMed  Google Scholar 

  11. Lee, S.J., Lippard, S.J. & Cho, U.S. Control of substrate access to the active site in methane monooxygenase. Nature 494, 380–384 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Balasubramanian, R. et al. Oxidation of methane by a biological dicopper centre. Nature 465, 115–119 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Li, J., Gan, J.H., Mathews, F.S. & Xia, Z.X. The enzymatic reaction–induced configuration change of the prosthetic group PQQ of methanol dehydrogenase. Biochem. Biophys. Res. Commun. 406, 621–626 (2011).

    Article  CAS  PubMed  Google Scholar 

  14. Orita, I. et al. The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis. J. Bacteriol. 188, 4698–4704 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Crowther, G.J., Kosály, G. & Lidstrom, M.E. Formate as the main branch point for methylotrophic metabolism in Methylobacterium extorquens AM1. J. Bacteriol. 190, 5057–5062 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Kato, N., Yurimoto, H. & Thauer, R.K. The physiological role of the ribulose monophosphate pathway in bacteria and archaea. Biosci. Biotechnol. Biochem. 70, 10–21 (2006).

    Article  CAS  PubMed  Google Scholar 

  17. Boden, R. et al. Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. J. Bacteriol. 193, 7001–7002 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Kalyuzhnaya, M.G. et al. Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. Nat. Commun. 4, 2785–2790 (2013).

    Article  CAS  PubMed  Google Scholar 

  19. Semrau, J.D., DiSpirito, A.A. & Yoon, S. Methanotrophs and copper. FEMS Microbiol. Rev. 34, 496–531 (2010).

    Article  CAS  PubMed  Google Scholar 

  20. Senior, P.J. & Windass, J. The ICI single cell protein process. Biotechnol. Lett. 2, 205–210 (1980).

    Article  CAS  Google Scholar 

  21. Ye, R.W. & Kelly, K. Construction of carotenoid biosynthetic pathways through chromosomal integration in methane-utilizing bacterium Methylomonas sp. strain 16a. Methods Mol. Biol. 2012, 85–195 ((2012).

    Google Scholar 

  22. Boll, M. & Heider, J. in Handbook of Hydrocarbon and Lipid Microbiology. Vol. 2 (ed. Timmins, K.N.) 1011–1024 (Springer, New York, 2010).

    Book  Google Scholar 

  23. Scheller, S., Goenrich, M., Boecher, R., Thauer, R.K. & Jaun, B. The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane. Nature 465, 606–608 (2010).

    Article  CAS  PubMed  Google Scholar 

  24. Shima, S. et al. Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically. Nature 481, 98–101 (2012).

    Article  CAS  Google Scholar 

  25. Atsumi, S., Hanai, T. & Liao, J.C. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451, 86–89 (2008).

    Article  CAS  PubMed  Google Scholar 

  26. Lan, E.I. & Liao, J.C. Microbial synthesis of n-butanol, isobutanol, and other higher alcohols from diverse resources. Bioresour. Technol. 135, 339–349 (2013).

    Article  CAS  PubMed  Google Scholar 

  27. Suenaga, H., Sato, M., Goto, M., Takeshita, M. & Furukawa, K. Steady state kinetic characterization of evolved biphenyl dioxygenase, which acquired novel degradation ability for benzene and toluene. Biosci. Biotechnol. Biochem. 70, 1021–1025 (2006).

    Article  CAS  PubMed  Google Scholar 

  28. Davico, G.E., Bierbaum, V.M., DePuy, C.H., Ellison, G.B. & Squires, R.R. The C-H bond energy of benzene. J. Am. Chem. Soc. 117, 2590–2599 (1995).

    Article  CAS  Google Scholar 

  29. Austin, R.N. & Groves, J.T. Alkane-oxidizing metallo enzymes in the carbon cycle. Metallomics 3, 775–787 (2011).

    Article  CAS  PubMed  Google Scholar 

  30. Callaghan, A.V., Wawrik, B., Ní Chadhain, S.M., Young, L.Y. & Zylstra, G.J. Anaerobic alkane-degrading strain AK-01 contains two alkylsuccinate synthase genes. Biochem. Biophys. Res. Commun. 366, 142–148 (2008).

    Article  CAS  PubMed  Google Scholar 

  31. Callaghan, A.V. et al. Diversity of benzyl- and alkylsuccinate synthase genes in hydrocarbon-impacted environments and enrichment cultures. Environ. Sci. Technol. 44, 7287–7294 (2010).

    Article  CAS  PubMed  Google Scholar 

  32. Duncan, K.E. et al. Biocorrosive thermophilic microbial communities in Alaskan North Slope oil facilities. Environ. Sci. Technol. 43, 7977–7984 (2009).

    Article  CAS  PubMed  Google Scholar 

  33. Gieg, L.M., Davidova, I.A., Duncan, K.E. & Suflita, J.M. Methanogenesis, sulfate reduction and crude oil biodegradation in hot Alaskan oilfields. Environ. Microbiol. 12, 3074–3086 (2010).

    Article  CAS  PubMed  Google Scholar 

  34. Johnson, H.A. & Spormann, A.M. In vitro studies on the initial reactions of anaerobic ethylbenzene mineralization. J. Bacteriol. 181, 5662–5668 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Johnson, H.A., Pelletier, D.A. & Spormann, A.M. Isolation and characterization of anaerobic ethylbenzene dehydrogenase, a novel Mo-Fe-S enzyme. J. Bacteriol. 183, 4536–4542 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Kniemeyer, O., Fischer, T., Wilkes, H., Glöckner, F.O. & Widdel, F. Anaerobic degradation of ethylbenzene by a new type of marine sulfate-reducing bacterium. Appl. Environ. Microbiol. 69, 760–768 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Szaleniec, M. et al. Kinetics and mechanism of oxygen independent hydrocarbon hydroxylation by ethylbenzene dehydrogenase. Biochemistry 46, 7637–7646 (2007).

    Article  CAS  PubMed  Google Scholar 

  38. Milucka, J. et al. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature 491, 541–546 (2012).

    Article  CAS  PubMed  Google Scholar 

  39. Musat, F. et al. Anaerobic degradation of naphthalene and 2-methylnaphthalene by strains of marine sulfate-reducing bacteria. Environ. Microbiol. 11, 209–219 (2009).

    Article  CAS  PubMed  Google Scholar 

  40. Kunapuli, U., Griebler, C., Beller, H.R. & Meckenstock, R.U. Identification of intermediates formed during anaerobic benzene degradation by an iron-reducing enrichment culture. Environ. Microbiol. 10, 1703–1712 (2008).

    Article  CAS  PubMed  Google Scholar 

  41. Ulrich, A.C., Beller, H.R. & Edwards, E.A. Metabolites detected during biogradation of 13C6-benzene in nitrate-reducing and methanogenic enrichment cultures. Environ. Sci. Technol. 39, 6681–6691 (2005).

    Article  CAS  PubMed  Google Scholar 

  42. Bogorad, I.W., Lin, T.-S. & Liao, J.C. Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature 502, 693–697 (2013).

    Article  CAS  PubMed  Google Scholar 

  43. Ragsdale, S.W. & Pierce, E. Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. Biochim. Biophys. Acta 1784, 1873–1898 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Ramos-Vera, W.H., Weiss, M., Strittmatter, E., Kockelkorn, D. & Fuchs, G. Identification of missing genes and enzymes for autotrophic carbon fixation in crenarchaeota. J. Bacteriol. 193, 1201–1211 (2011).

    Article  CAS  PubMed  Google Scholar 

  45. Appel, A.M. et al. Frontiers, opportunities, and challenges in biochemical and chemical catalysis of CO2 fixation. Chem. Rev. 113, 6621–6658 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Dellomonaco, C., Clomburg, J.M., Miller, E.N. & Gonzalez, R. Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals. Nature 476, 355–359 (2011).

    Article  CAS  PubMed  Google Scholar 

  47. Bar-Even, A., Noor, E., Lewis, N.E. & Milo, R. Design and analysis of synthetic carbon fixation pathways. Proc. Natl. Acad. Sci. USA 107, 8889–8894 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Fuchs, G. Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? Annu. Rev. Microbiol. 65, 631–658 (2011).

    Article  CAS  PubMed  Google Scholar 

  49. Kung, Y., Doukov, T.I., Seravalli, J., Ragsdale, S.W. & Drennan, C.L. Crystallographic snapshots of cyanide- and water-bound C-clusters from bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Biochemistry 48, 7432–7440 (2009).

    Article  CAS  PubMed  Google Scholar 

  50. Gaddis, E.S. Mass transfer in gas-liquid contactors. Chem. Eng. Process. 38, 503–510 (1999).

    Article  CAS  Google Scholar 

  51. Orgill, J.J. et al. A comparison of mass transfer coefficients between trickle-bed, hollow fiber membrane and stirred tank reactors. Bioresour. Technol. 133, 340–346 (2013).

    Article  CAS  PubMed  Google Scholar 

  52. Jang, Y.-S., Malaviya, A. & Lee, S.Y. Acetone-butanol-ethanol production with high productivity using Clostridium acetobutylicum BKM19. Biotechnol. Bioeng. 110, 1646–1653 (2013).

    Article  CAS  PubMed  Google Scholar 

  53. Conrado, R.J. & Gonzalez, R. Envisioning the bioconversion of methane to liquid fuels. Science 343, 621–623 (2014).

    Article  CAS  PubMed  Google Scholar 

  54. Keller, M.W. et al. Exploiting microbial hyperthermophilicity to produce an industrial chemical, using hydrogen and carbon dioxide. Proc. Natl. Acad. Sci. USA 110, 5840–5845 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Keil, F.J. Methane activation: oxidation goes soft. Nat. Chem. 5, 91–92 (2013).

    Article  CAS  PubMed  Google Scholar 

  56. Oelgeschläger, E. & Rother, M. Carbon monoxide–dependent energy metabolism in anaerobic bacteria and archaea. Arch. Microbiol. 190, 257–269 (2008).

    Article  CAS  PubMed  Google Scholar 

  57. United States Energy Information Agency. Annual Energy Review. http://www.eia.gov/totalenergy/data/annual/index.cfm (2012).

  58. Tijm, P.J.A. Gas to liquids, Fischer-Tropsch, Advanced Energy Technology, Future's Pathway (Peter Tijm, 2010).

    Google Scholar 

  59. Schmit, T.M., Luo, J. & Tauer, L.W. Ethanol plant investment using net present value and real options analyses. Biomass Bioenergy 33, 1442–1451 (2009).

    Article  Google Scholar 

  60. Smith, S.M. & Rosenzweig, A.C. Crystal structure and characterization of particulate methane monooxygenase from Methylocystis sp. strain M. Biochemistry 50, 10231–10240 (2011).

    Article  CAS  PubMed  Google Scholar 

  61. Porubsky, P.R., Battaile, K.P. & Scott, E.E. Human cytochrome P450 2E1 structures with fatty acid analogs reveal a previously unobserved binding mode. J. Biol. Chem. 285, 22282–22290 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Lin, T.Y., Werther, T., Jeoung, J.H. & Dobbek, H. Suppression of electron transfer to dioxygen by charge transfer and electron transfer complexes in the FAD-dependent reductase component of toluene dioxygenase. J. Biol. Chem. 287, 38338–38346 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. United States Energy Information Agency. Short-term Energy Outlook, http://www.eia.gov/forecasts/steo/ (2012).

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Acknowledgements

The authors would like to thank R.J. Conrado for his contributions to this work and E. Rohlfing for critically reading the manuscript.

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Correspondence to Ramon Gonzalez.

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Haynes, C., Gonzalez, R. Rethinking biological activation of methane and conversion to liquid fuels. Nat Chem Biol 10, 331–339 (2014). https://doi.org/10.1038/nchembio.1509

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