Abstract
CH4 offers a promising, high-volume petroleum replacement for fuel and chemical bioprocesses. Recent advances in gas recovery technologies have facilitated access to previously inaccessible natural gas reserves, while biogas generated from anaerobic digestion of waste streams offers a versatile, renewable CH4 source. Importantly, CH4 is also the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. However, the gaseous state of CH4 makes for a lack of compatibility with current transportation and industrial manufacturing infrastructure, limiting its utilization as a transportation fuel and intermediate in biochemical processes. Resurgent interest in CH4 upgrading has pushed microbial conversion of CH4 to fuels and value-added chemicals to the forefront of industrial bioprocessing. CH4 bioconversion offers both CH4 valorization and GHG emission reduction potential and importantly offers a scalable, modular, and selective approach to CH4 utilization compared to conventional physical and chemical conversion strategies. However, as noted above, advances in CH4 biocatalysis have been constrained by limited genetic tractability of natural CH4-consuming microbes. In this chapter, we review recent advances in methanotrophic genetic and genomic tool development and metabolic engineering.
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References
Akberdin IR, Thompson M, Hamilton R, Desai N, Alexander D, Henard CA, Guarnieri MT, Kalyuzhnaya MG (2018) Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach. Sci Rep 8(1):2512
Anthony C, Williams P (2003) The structure and mechanism of methanol dehydrogenase. Biochim Biophys Acta 1647:18–23. https://doi.org/10.1016/S1570-9639(03)00042-6
Baani M, Liesack W (2008) Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2. Proc Natl Acad Sci USA 105:10203–10208. https://doi.org/10.1073/pnas.0702643105
Baxter NJ, Hirt RP, Bodrossy L et al (2002) The ribulose-1,5-bisphosphate carboxylase/oxygenase gene cluster of Methylococcus capsulatus (Bath). Arch Microbiol 177:279–289. https://doi.org/10.1007/s00203-001-0387-x
Boden R, Cunliffe M, Scanlan J et al (2011) Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. J Bacteriol 193:7001–7002. https://doi.org/10.1128/JB.06267-11
Clomburg JM, Crumbley AM, Gonzalez R (2017) Industrial biomanufacturing: the future of chemical production. Science 355:aag0804. https://doi.org/10.1126/science.aag0804
Conrado RJ, Gonzalez R (2014) Chemistry. Envisioning the bioconversion of methane to liquid fuels. Science 343:621–623. https://doi.org/10.1126/science.1246929
Crombie A, Murrell JC (2011) Development of a system for genetic manipulation of the facultative methanotroph Methylocella silvestris BL2. Methods Enzymol 495:119–133. https://doi.org/10.1016/B978-0-12-386905-0.00008-5
Culpepper MA, Rosenzweig AC (2014) Structure and protein-protein interactions of methanol dehydrogenase from Methylococcus capsulatus (Bath). Biochemistry 53:6211–6219. https://doi.org/10.1021/bi500850j
Fei Q, Guarnieri MT, Tao L et al (2014) Bioconversion of natural gas to liquid fuel: opportunities and challenges. Biotechnol Adv 32:596–614. https://doi.org/10.1016/j.biotechadv.2014.03.011
Flynn JD, Hirayama H, Sakai Y et al (2016) Draft genome sequences of gammaproteobacterial methanotrophs isolated from marine ecosystems. Genome Announc 4:e01629–e01615. https://doi.org/10.1128/genomeA.01629-15
Garst AD, Bassalo MC, Pines G et al (2017) Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering. Nat Biotechnol 35:48–55. https://doi.org/10.1038/nbt.3718
Gilman A, Laurens LM, Puri AW et al (2015) Bioreactor performance parameters for an industrially-promising methanotroph Methylomicrobium buryatense 5GB1. Microb Cell Fact 14:1–8. https://doi.org/10.1186/s12934-015-0372-8
Hamilton R, Kits KD, Ramonovskaya VA et al (2015) Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. Genome Announc 3(3). https://doi.org/10.1128/genomeA.00515-15
Harwood JH, Williams E, Bainbridge BW (1972) Mutation of the methane oxidizing bacterium, Methylococcus capsulatus. J Appl Microbiol 35:99–108. https://doi.org/10.1111/j.1365-2672.1972.tb03678.x
Haynes CA, Gonzalez R (2014) Rethinking biological activation of methane and conversion to liquid fuels. Nat Chem Biol 10:331–339. https://doi.org/10.1038/nchembio.1509
Henard CA, Freed EF, Guarnieri MT (2015) Phosphoketolase pathway engineering for carbon-efficient biocatalysis. Curr Opin Biotechnol 36:183–188. https://doi.org/10.1016/j.copbio.2015.08.018
Henard CA, Smith H, Dowe N et al (2016) Bioconversion of methane to lactate by an obligate methanotrophic bacterium. Sci Rep 6:1–9. https://doi.org/10.1038/srep21585
Henard CA, Smith HK, Guarnieri MT (2017) Phosphoketolase overexpression increases biomass and lipid yield from methane in an obligate methanotrophic biocatalyst. Metab Eng 41:152–158
Kalyuzhanaya MG, Yang S, Matsen JB et al (2013) Global molecular analyses of methane metabolism in Methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. Metabolomics and 13C-labeling study. Front Microbiol. https://doi.org/10.3389/fmicb.2013.00070
Kalyuzhnaya MG (2013) Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. metabolomics and 13C-labeling study. Front Microbiol:1–13. https://doi.org/10.3389/fmicb.2013.00070/abstract
Kalyuzhnaya MG, Yang S, Rozova ON et al (2013) Highly efficient methane biocatalysis revealed in a methanotrophic bacterium. Nat Commun 4. https://doi.org/10.1038/ncomms3785
Kalyuzhnaya MG, Puri AW, Lidstrom ME (2015) Metabolic engineering in methanotrophic bacteria. Metabolic Engineering 29:142–152. https://doi.org/10.1016/j.ymben.2015.03.010
Khadem AF, Pol A, Wieczorek A et al (2011) Autotrophic methanotrophy in verrucomicrobia: Methylacidiphilum fumariolicumSolV uses the Calvin-Benson-Bassham cycle for carbon dioxide fixation. J Bacteriol 193:4438–4446. https://doi.org/10.1128/JB.00407-11
Khmelenina VN, Beck DAC, Munk C et al (2013) Draft genome sequence of Methylomicrobium buryatense Strain 5G, a Haloalkaline-Tolerant Methanotrophic Bacterium. Genome Announc 1(4). https://doi.org/10.1128/genomeA.00053-13
Komor AC, Badran AH, Liu DR (2017) CRISPR-based technologies for the manipulation of eukaryotic genomes. Cell 168:20–36. https://doi.org/10.1016/j.cell.2016.10.044
la Torre de A, Metivier A, Chu F et al (2015) Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1). Microb Cell Fact 14:188. https://doi.org/10.1186/s12934-015-0377-3
Larsen Ø, Karlsen OA (2016) Transcriptomic profiling of Methylococcus capsulatus (Bath) during growth with two different methane monooxygenases. MicrobiologyOpen 5:254–267. https://doi.org/10.1002/mbo3.324
Lawton TJ, Rosenzweig AC (2016) Methane-oxidizing enzymes: an upstream problem in biological gas-to-liquids conversion. J Am Chem Soc 138:9327–9340. https://doi.org/10.1021/jacs.6b04568
Lee OK, Hur DH, Nguyen D (2016) Metabolic engineering of methanotrophs and its application to production of chemicals and biofuels from methane. Biofuels Bioprod Biorefin 10(6):848–863. https://doi.org/10.1002/bbb.1678/pdf
Lidstrom ME, Wopat AE (1984) Plasmids in methanotrophic bacteria: isolation, characterization and DNA hybridization analysis. Arch Microbiol 140:27–33. https://doi.org/10.1007/BF00409767
Lynch MD, Gill RT (2006) Broad host range vectors for stable genomic library construction. Biotechnol Bioeng 94:151–158. https://doi.org/10.1002/bit.20836
Makarova KS, Wolf YI, Alkhnbashi OS et al (2015) An updated evolutionary classification of CRISPR–Cas systems. Nat Rev Microbiol 13:722–736. https://doi.org/10.1038/nrmicro3569
Malashenko YR, Pirog TP, Romanovskaya VA et al (2001) Search for methanotrophic producers of exopolysaccharides. Appl Biochem Microbiol 37:599–602. https://doi.org/10.1023/A:1012307202011
Marraffini LA (2016) The CRISPR-Cas system of Streptococcus pyogenes: function and applications. In: Ferretti JJ, Stevens DL, Fischetti VA (eds) Streptococcus pyogenes: basic biology to clinical manifestations. University of Oklahoma Health Sciences Center, Oklahoma
Marx CJ (2008) Development of a broad-host-range sacB-based vector for unmarked allelic exchange. BMC Res Notes 1(1). https://doi.org/10.1186/1756-0500-1-1
Marx CJ, Lidstrom ME (2002) Broad-host-range cre-lox system for antibiotic marker recycling in gram-negative bacteria. Biotechniques 33(5):1062–1067
Matsen JB, Yang S, Stein LY et al (2013) Global molecular analyses of methane metabolism in Methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: Transcriptomic study. Front Microbiol. https://doi.org/10.3389/fmicb.2013.00040
McPheat WL, Mann NH, Dalton H (1987) Isolation of mutants of the obligate methanotroph Methylomonas albus defective in growth on methane. Arch Microbiol 148:40–43. https://doi.org/10.1007/BF00429645
Mohanraju P, Makarova KS, Zetsche B et al (2016) Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science 353:aad5147. https://doi.org/10.1126/science.aad5147
Murrell JC (1992) Genetics and molecular biology of methanotrophs. FEMS Microbiol Rev 8:233–248. https://doi.org/10.1111/j.1574-6968.1992.tb04990.x
Mustakhimov II, But SY, Reshetnikov AS et al (2016) Homo- and heterologous reporter proteins for evaluation of promoter activity in Methylomicrobium alcaliphilum 20Z. Appl Biochem Microbiol 52:263–268. https://doi.org/10.1134/S0003683816030157
Nicolaidis AA, Sargent AW (1987) Isolation of methane monooxygenase-deficient mutants from Methylosinus trichosporium OB3b using dichloromethane. FEMS Microbiol Lett 41:47–52. https://doi.org/10.1111/j.1574-6968.1987.tb02139.x
Ojala DS, Beck DAC, Kalyuzhnaya MG (2011) Genetic systems for moderately halo(alkali)philic bacteria of the genus Methylomicrobium. Methods Enzymol 495:99–118. https://doi.org/10.1016/B978-0-12-386905-0.00007-3
Puri AW, Owen S, Chu F et al (2015) Genetic Tools for the Industrially Promising Methanotroph Methylomicrobium buryatense. Appl Environ Microbiol 81:1775–1781. https://doi.org/10.1128/AEM.03795-14
Puri AW, Schaefer AL, Fu Y et al (2016) Quorum sensing in a methane-oxidizing bacterium. J Bacteriol 199(5). https://doi.org/10.1128/JB.00773-16
Rasigraf O, Kool DM, Jetten MSM et al (2014) Autotrophic carbon dioxide fixation via the Calvin-Benson-Bassham cycle by the denitrifying methanotroph “Candidatus Methylomirabilis oxyfera”. Appl Environ Microbiol 80:2451–2460. https://doi.org/10.1128/AEM.04199-13
Rohr LM, Teuber M, Meile L (2002) Phosphoketolase, a neglected enzyme of microbial carbohydrate metabolism. Chimia 56:270–273
Rozova ON, Khmelenina VN, Gavletdinova JZ et al (2015) Acetate kinase-an enzyme of the postulated phosphoketolase pathway in Methylomicrobium alcaliphilum 20Z. Antonie Van Leeuwenhoek 108:965–974. https://doi.org/10.1007/s10482-015-0549-5
Sánchez B, Zúñiga M, González-Candelas F (2010) Bacterial and eukaryotic phosphoketolases: phylogeny, distribution and evolution. J Mol Microbiol Biotechnol 18:37–51
Sharan SK, Thomason LC, Kuznetsov SG, Court DL (2009) Recombineering: a homologous recombination-based method of genetic engineering. Nat Protoc 4:206–223. https://doi.org/10.1038/nprot.2008.227
Sharpe PL, Dicosimo D, Bosak MD et al (2007) Use of transposon promoter-probe vectors in the metabolic engineering of the obligate methanotroph Methylomonas sp. strain 16a for enhanced C40 carotenoid synthesis. Appl Environ Microbiol 73:1721–1728. https://doi.org/10.1128/AEM.01332-06
Sirajuddin S, Rosenzweig AC (2015) Enzymatic oxidation of methane. Biochemistry 54:2283–2294. https://doi.org/10.1021/acs.biochem.5b00198
Strong PJ, Xie S, Clarke WP (2015) Methane as a resource: can the methanotrophs add value? Environ Sci Technol 49:4001–4018. https://doi.org/10.1021/es504242n
Toukdarian AE, Lidstrom ME (1984) Molecular construction and characterization of nif mutants of the obligate methanotroph Methylosinus sp. strain 6. J Bacteriol 157:979–983
Ungerer J, Pakrasi HB (2016) Cpf1 is a versatile tool for CRISPR genome editing across diverse species of Cyanobacteria. Sci Rep:1–9. https://doi.org/10.1038/srep39681
Vorobev A, Jagadevan S, Jain S et al (2014) Genomic and transcriptomic analyses of the facultative methanotroph Methylocystis sp. strain SB2 grown on methane or ethanol. Appl Environ Microbiol 80:3044–3052. https://doi.org/10.1128/AEM.00218-14
Vuilleumier S, Khmelenina VN, Bringel F et al (2012) Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z. J Bacteriol 194(2):551–552
Wang HH, Isaacs FJ, Carr PA et al (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature 460:894–898. https://doi.org/10.1038/nature08187
Williams E (1977) Mutation in the obligate methylotrophs Methylococcus capsulatus and Methylomonas albus. FEMS Microbiol Lett 2:293–296
Williams E, Bainbridge BW (1976) Mutation, repair mechanisms and transformation in the methane-utilizing bacterium, Methylococcus capsulatus. Proceedings of international symposium on the genetics of industrial microorganisms
Woolston BM, Edgar S, Stephanopoulos G (2013) Metabolic engineering: past and future. Annu Rev Chem Biomol Eng 4:259–288. https://doi.org/10.1146/annurev-chembioeng-061312-103312
Yan X, Chu F, Puri AW et al (2016) Electroporation-based genetic manipulation in Type I Methanotrophs. Appl Environ Microbiol 82:2062–2069. https://doi.org/10.1128/AEM.03724-15
Zetsche B, Gootenberg JS, Abudayyeh OO et al (2015) Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-CAS system. Cell 163:759–771. https://doi.org/10.1016/j.cell.2015.09.038
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Henard, C.A., Guarnieri, M.T. (2018). Metabolic Engineering of Methanotrophic Bacteria for Industrial Biomanufacturing. In: Kalyuzhnaya, M., Xing, XH. (eds) Methane Biocatalysis: Paving the Way to Sustainability. Springer, Cham. https://doi.org/10.1007/978-3-319-74866-5_8
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