Metabolic engineering in methanotrophic bacteria

Metabolic Engineering

Volumn 29, Issue , 2015, Pages 142-152

  Kalyuzhnaya, Marina G ^a,c   Puri, Aaron W ^b   Lidstrom, Mary E ^b,c  

^a SAN DIEGO STATE UNIVERSITY   (United States)

^b Department of Chemical Engineering ^*  (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Metabolic engineering; Methanotroph; Natural gas

Indexed keywords

AGRICULTURE; BIOLOGICAL WATER TREATMENT; METABOLISM; METHANE; NATURAL GAS; WASTEWATER TREATMENT;

BIO-INDUSTRY; BIOLOGICAL ENGINEERING; ENVIRONMENTAL FOOTPRINTS; METABOLIC SYSTEMS; METHANOTROPHIC BACTERIA; METHANOTROPHS; SUSTAINABLE SOLUTION; SYSTEMS BIOLOGY;

METABOLIC ENGINEERING;

ACETYL COENZYME A; FATTY ACID; METHANE; METHANE MONOOXYGENASE; METHANOL; OXYGEN; PYRUVIC ACID; WASTE WATER;

AIR POLLUTION CONTROL; ARTICLE; BACTERIUM CULTURE; BIOCATALYSIS; BIOSYNTHESIS; BIOTECHNOLOGY; BIOTRANSFORMATION; ELECTRON; ELECTRON TRANSPORT; FERMENTATION; GENE VECTOR; GENETIC ANALYSIS; GENOME; INDEL MUTATION; METABOLIC ENGINEERING; METHANOTROPH; METHANOTROPHIC BACTERIUM; MUTANT; NONHUMAN; OXIDATION; PRECURSOR; PRIORITY JOURNAL; BACTERIUM; GENETICS; METABOLISM; MICROBIOLOGY; PROCEDURES; WASTE WATER; WATER MANAGEMENT;

BACTERIA; METABOLIC ENGINEERING; METHANE; WASTE WATER; WATER MICROBIOLOGY; WATER PURIFICATION;

EID: 84926364931     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2015.03.010     Document Type: Article

References (129)

1. Adedayo M.R., Ajiboye E.A., Akintunde J.K., Obaibo A. Single cell proteins: as nutritional enhancer. Adv. Appl. Sci. Res. 2011, 2:396-409.
2. Ali H., Murrell J.C. Development and validation of promoter-probe vectors for the study of methane monooxygenase gene expression in Methylococcus capsulatus Bath. Microbiology (Reading, England) 2009, 155:761-771.
3. Anthony C. The Biochemistry of Methylotrophs 1982, 431. Academic Press, London; New York.
4. Anthony C. The quinoprotein dehydrogenases for methanol and glucose. Arch. Biochem. Biophys. 2004, 428:2-9.
5. Arp D.J., Chain P.S.G., Klotz M.G. The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annu. Rev. Microbiol. 2007, 61:503-528.
6. Baani M., Liesack W. Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:10203-10208.
7. Balasubramanian R., Smith S.M., Rawat S., Yatsunyk L.A., Stemmler T.L., Rosenzweig A.C. Oxidation of methane by a biological dicopper centre. Nature 2010, 465:115-119.
8. Bayer T.S., Widmaier D.M., Temme K., Mirsky E.A., Santi D.V., Voigt C.A. Synthesis of methyl halides from biomass using engineered microbes. J. Am. Chem. Soc. 2009, 131:6508-6515.
9. Beck D.A., Kalyuzhnaya M.G., Malfatti S., Tringe S.G., Glavina Del Rio T., Ivanova N., Lidstrom M.E., Chistoserdova L. A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae. PeerJ 2013, 1:e23.
10. Berson O., Lidstrom M.E. Cloning and characterization of corA, a gene encoding a copper-repressible polypeptide in the type I methanotroph, Methylomicrobium albus BG8. FEMS Microbiol. Lett. 1997, 148:169-174.
11. Bogorad I.W., Lin T.S., Liao J.C. Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature 2013, 502:693-697.
12. Bothe H., Møller Jensen K., Mergel A., Larsen J., Jørgensen C., Bothe H., Jørgensen L. Heterotrophic bacteria growing in association with Methylococcus capsulatus (Bath) in a single cell protein production process. Appl. Microbiol. Biotechnol. 2002, 59:33-39.
13. But S., Khmelenina V.N., Reshetnikov A.S., Mustakhimov II, Kalyuzhnaya M.G., Trotsenko Y.A. Sucrose metabolism in halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. Arch. Microbiol. 2015, (PMID: 25577257).
14. Campbell M.A., Nyerges G., Kozlowski J.A., Poret-Peterson A.T., Stein L.Y., Klotz M.G. Model of the molecular basis for hydroxylamine oxidation and nitrous oxide production in methanotrophic bacteria. FEMS Microbiol. Lett. 2011, 322:82-89.
15. Cantrell K.B., Ducey T., Ro K.S., Hunt P.G. Livestock waste-to-bioenergy generation opportunities. Bioresour. Technol. 2008, 99:7941-7953.
16. Choi D.W., DiSpirito A.A., Chipman D.C., Brown R.C. Hybrid processing. Thermochemical Processing of Biomass: Conversion into Fuels, Chemicals and Power. Wiley Series in Renewable Resources 2011, 280-303. John Wiley & Sons. Ltd., R. Brown (Ed.).
17. Choi D.W., Do Y.S., Zea C.J., McEllistrem M.T., Lee S.-W., Semrau J.D., Pohl N.L., Kisting C.J., Scardino L.L., Hartsel S.C., et al. Spectral and thermodynamic properties of Ag(I), Au(III), Cd(II), Co(II), Fe(III), Hg(II), Mn(II), Ni(II), Pb(II), U(IV), and Zn(II) binding by methanobactin from Methylosinus trichosporium OB3b. J. Inorg. Biochem. 2006, 100:2150-2161.
18. Choi D.W., Kunz R.C., Boyd E.S., Semrau J.D., Antholine W.E., Han J.-I., Zahn J.A., Boyd J.M., de la Mora A.M., DiSpirito A.A. The membrane-associated methane monooxygenase (pMMO) and pMMO-NADH:quinone oxidoreductase complex from Methylococcus capsulatus Bath. J. Bacteriol. 2003, 185:5755-5764.
19. Conrado R.J., Gonzalez R. Chemistry. Envisioning the bioconversion of methane to liquid fuels. Science 2014, 343:621-623.
20. Cook S.A., Shiemke A.K. Evidence that a type-2 NADH:quinone oxidoreductase mediates electron transfer to particulate methane monooxygenase in Methylococcus capsulatus. Arch. Biochem. Biophys. 2002, 398:32-40.
21. Corder R.E., Johnson E.R., Vega J.L., Clausen E.C., Gaddy J.L. Biological production of methanol from methane. Prepr. Pap. Am. Chem. Soc., Div. Fuel. Chem. 1988, 33:469-478.
22. Criddle, C.S., Hart, J.R., Wu, W.M., Sundstrom, E.R., Morse, M.C., Billington, S.L., Rostkowski, K.H., Frank, C.W. 2013. Production of PHA Using Biogas as Feedstock and Power Source. US20130071890 A1.
23. Crombie A.T., Murrell J.C. Development of a system for genetic manipulation of the facultative methanotroph Methylocella silvestris BL2. Methods Enzymol. 2011, 495:119-133.
24. Crombie A.T., Murrell J.C. Trace-gas metabolic versatility of the facultative methanotroph Methylocella silvestris. Nature 2014, 510:148-151.
25. Csaki R., Bodrossy L., Klem J., Murrell J.C., Kovacs 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, 149:1785-1795.
26. Culpepper M.A., Rosenzweig A.C. Structure and protein-protein interactions of methanol dehydrogenase from Methylococcus capsulatus (Bath). Biochemistry 2014, 53:6211-6219.
27. Dedysh S.N., Dunfield P.F. Facultative and obligate methanotrophs: how to identify and differentiate them. Methods Enzymol. 2011, 495:31-44.
28. Dedysh S.N., Horz H.P., Dunfield P.F., Liesack W. A novel pmoA lineage represented by the acidophilic methanotrophic bacterium Methylocapsa acidiphila (correction of acidophila) B2. Arch. Microbiol. 2001, 177:117-121.
29. DiSpirito A.A., Choi, D.D., Semrau, J.D., Keeney, D. 2011. Use of Methanobactin. US7932052 B1.
30. Doronina N.V., Ezhov V.A., Trotsenko Yu.A. Growth of Methylosinus trichosporium OB3b on methane and poly-beta-hydroxybutyrate biosynthesis. Appl. Biochem. Microbiol. (Russian) 2008, 44:182-185.
31. Dunfield P.F., Dedysh S.N. Methylocella: a gourmand among methanotrophs. Trends Microbiol. 2014, 22:368-369.
32. Egorov I., Kupina L., Aksyuk I., Murtazaeva R. Gaprin-a protein source. Ptitsevodstvo (Russian) 1990, 8:25-27.
33. El Ghazouani A., Basle A., Firbank S.J., Knapp C.W., Gray J., Graham D.W., Dennison C. Copper-binding properties and structures of methanobactins from Methylosinus trichosporium OB3b. Inorg. Chem. 2011, 50:1378-1391.
34. Eshinimaev B.T., Khmelenina V.N., Sakharovskii V.G., Suzina N.E., Trotsenko Y.A. Physiological, biochemical, and cytological characteristics of a haloalkalitolerant methanotroph grown on methanol. Mikrobiologiia (Russian) 2002, 71:512-518.
35. Esvelt K.M., Wang H.H. Genome-scale engineering for systems and synthetic biology. Mol. Sys. Biol. 2013, 9:641.
36. Etiope G., Ciccioli P. Earth's degassing: a missing ethane and propane source. Science 2009, 323:478.
37. Ettwig K.F., van Alen T., van de Pas-Schoonen K.T., Jetten M.S., Strous M. Enrichment and molecular detection of denitrifying methanotrophic bacteria of the NC10 phylum. Appl. Environ. Microbiol. 2009, 75:3656-3662.
38. Fassel T.A., Buchholz L.A., Collins M.L., Remsen C.C. Localization of methanol dehydrogenase in two strains of methylotrophic bacteria detected by immunogold labeling. Appl. Environ. Microbiol. 1992, 58:2302-2307.
39. Fei Q., Guarnieri M.T., Tao L., Laurens L.M., Dowe N., Pienkos P.T. Bioconversion of natural gas to liquid fuel: opportunities and challenges. Biotechnol. Adv. 2014, 32:596-614.
40. Figurski D.H., Helinski D.R. Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc. Natl. Acad. Sci. U.S.A. 1979, 76:1648-1652.
41. Furuto T., Takeguchi M., Okura I. Semicontinuous methanol biosynthesis by Methylosinus trichosporium OB3b. J. Mol. Catal. A: Chem. 1999, 144:257-261.
42. Guiot S.R., Cimpoia R., Kuhn R., Alaplantive A. Electrolytic methanogenic-methanotrophic coupling for tetrachloroethylene bioremediation: proof of concept. Environ. Sci. Technol. 2008, 42:3011-3017.
43. Haynes C.A., Gonzalez R. Rethinking biological activation of methane and conversion to liquid fuels. Nat. Chem. Biol. 2014, 10:331-339.
44. Holmes A.J., Costello A., Lidstrom M.E., Murrell J.C. Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol. Lett. 1995, 132:203-208.
45. Hou C.T. Oxidation of gaseous hydrocarbons by methanotrophs: heterogeneous bioreactor. Ann. N.Y. Acad. Sci. 1984, 434:541-548.
46. Huang Q., Zhang Q., Cicek N., Mann D. Biofilter: a promising tool for mitigating methane emission from manure storage. J. Arid Land 2011, 3:61-70.
47. Jagmann N., Philipp B. Design of synthetic microbial communities for biotechnological production processes. J. Biotechnol. 2014, 184:209-218.
48. Jahng D., Kim C.S., Hanson R.S., Wood T.K. Optimization of trichloroethylene degradation using soluble methane monooxygenase of Methylosinus trichosporium OB3b expressed in recombinant bacteria. Biotechnol. Bioeng. 1996, 51:349-359.
49. Janssen H.J., Steinbuchel A. Production of triacylglycerols in Escherichia coli by deletion of the diacylglycerol kinase gene and heterologous overexpression of atfA from Acinetobacter baylyi ADP1. Appl. Microbiol. Biotechnol. 2014, 98:1913-1924.
50. Jiang H., Chen Y., Zhang C., Smith T.J., Murrell J.C., Xing X-H. Methanotrophs: multifunctional bacteria with promising applications in environmental bioengineering. Biochem. Eng. J. 2010, 49:277-288.
51. Kao W.C., Chen Y.R., Yi E.C., Lee H., Tian Q., Wu K.M., Tsai S.F., Yu S.S., Chen Y.J., Aebersold R., Chan S.I. Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath). J. Biol. Chem. 2004, 279:51554-51560.
52. Kalyuzhnaya M.G., But S., Lidstrom M.E., Khmelenina V.N. 2015. US 61/993,636 // Conversion of Methane into Chemicals via Dry Fermentation // UW [IP: 46694.01US1].
53. Kalyuzhnaya M.G., Khmelenina V.N., Lysenko A.M., Suzina N.E., Trotsenko Yu.A. New methanotrophic isolates from soda lakes of the southern Transbaikal region. Mikrobiologiia (Russian) 1999, 68:689-697.
54. Kalyuzhnaya M.G., Lapidus A., Ivanova N., Copeland A.C., McHardy A.C., Szeto E., Salamov A., Grigoriev I.V., Suciu D., Levine S.R., et al. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat. Biotech 2008, 26:1029-1034.
55. Kalyuzhnaya M.G., Yang S., Rozova O.N., Smalley N.E., Clubb J., Lamb A., Nagana Gowda G.A., Raftery D., Fu Y., Bringel F., Vuilleumier S., Beck D., Trotsenko Y.A., Khmelenina V.N., Lidstrom M.E. Highly efficient methane biocatalysis revealed in methanotrophic bacterium. Nat. Commun. 2013, 4:2785.
56. Karr J.R., Sanghvi J.C., Macklin D.N., Gutschow M.V., Jacobs J.M., Bolival B., Assad-Garcia N., Glass J.I., Covert M.W. A whole-cell computational model predicts phenotype from genotype. Cell 2012, 150:389-401.
57. Khadem A.F., Pol A., Wieczorek A., Mohammadi S.S., Francoijs K.J., Stunnenberg H.G., Jetten M.S., Op den Camp H.J. Autotrophic methanotrophy in verrucomicrobia: Methylacidiphilum fumariolicum SolV uses the Calvin-Benson-Bassham cycle for carbon dioxide fixation. J. Bacteriol. 2011, 193:4438-4446.
58. Khmelenina V.N., Gayazov R.R., Suzina N.E., Doronina V.N., Mshensky Yu.N., Trotsenko Yu.A. The synthesis of polysaccarides by Methylococcus capsulatus under various conditions of cultivation. Mikrobiologiia (Russian) 1992, 61:404-410.
59. Kim H.J., Graham D.W., DiSpirito A.A., Alterman M.A., Galeva N., Larive C.K., Asunskis D., Sherwood P.M.A. Methanobactin, a copper-acquisition compound from methane-oxidizing bacteria. Science 2004, 305:1612-1615.
60. Kitmitto A., Myronova N., Basu P., Dalton H. Characterization and structural analysis of an active particulate methane monooxygenase trimer from Methylococcus capsulatus (Bath). Biochemistry 2005, 44:10954-10965.
61. Knittel K., Boetius A. Anaerobic oxidation of methane: progress with an unknown process. Annu. Rev. Microbiol. 2009, 63:311-334.
62. Koffas M., Odom, J. M., Schenzle, A. 2001. High Growth Methanotrophic Bacterial Strain Methylomonas 16a. EP1320579 A2/ WO2002020728 A2.
63. Koffas, M., Odom, J.M., Schenzle, A. 2005. Methane or Methanol as Sole Carbon Source; Embden-Meyerhof Carbon Pathway Comprising a Gene Encoding a Pyrophosphate Dependent Phosphofructokinase; Biomass Contains Protein, Carbohydrates and Pigment on Industrial Scale. US6958222 B2.
64. Labinger J.A. Tuning into better catalysts. Science 1995, 269:1833.
65. Leak D.J., Dalton H. Growth yields of methanotrophs. 1. Effect of copper on the growth yields of methanotrophs. Appl. Microbiol. Biotechnol. 1986, 23:470-476.
66. Lee D., Smallbone K., Dunn W.B., Murabito E., Winder C.L., Kell D.B., Mendes P., Swainston N. Improving metabolic flux predictions using absolute gene expression data. BMC Syst. Biol. 2012, 6:73.
67. Lee, G.J., Hu, Z. 2010. Systems and Methods for the Production of Mixed Fatty Esters. WO2010021711 A1.
68. Lee J., Yun H., Feist A.M., Palsson B.O., Lee S.Y. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl. Microbiol. Biotechnol. 2008, 80:849-862.
69. Liu X., Sheng J., Curtiss R. Fatty acid production in genetically modified cyanobacteria. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:6899-6904.
70. Lloyd J.S., Finch R., Dalton H., Murrell J.C. Homologous expression of soluble methane monooxygenase genes in Methylosinus trichosporium OB3b. Microbiology (UK) 1999, 145:461-470.
71. Lontoh S., Zahn J.A., DiSpirito A.A., Semrau J.D. Identification of intermediates of in vivo trichloroethylene oxidation by the membrane-associated methane monooxygenase. FEMS Microbiol. Lett. 2000, 186:109-113.
72. Marx C.J., Lidstrom M.E. Broad-host-range cre-lox system for antibiotic marker recycling in gram-negative bacteria. BioTechniques 2002, 33:1062-1067.
73. Matsen J.B., Yang S., Stein L.Y., Beck D., Kalyuzhnaya M.G. Global molecular analyses of methane metabolism in methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b. Part I: Transcriptomic study. Front. Microbiol. 2013, 4:40.
74. Mehta P.K., Mishra S., Ghose T.K. Methanol biosynthesis by covalently immobilized cells of M. trichosporium: batch and continuous studies. Biotechnol. Bioeng. 1991, 37:551-556.
75. Milucka J., Ferdelman T.G., Polerecky L., Franzke D., Wegener G., Schmid M., Lieberwirth I., Wagner M., Widdel F., Kuypers M.M. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature 2012, 491:541-546.
76. Minty J.J., Singer M.E., Scholz S.A., Bae C.H., Ahn J.H., Foster C.E., Liao J.C., Lin X.N. Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:14592-14597.
77. Müller J.E., Meyer F., Litsanov B., Kiefer P., Potthoff E., Heux S., Quax W.J., Wendisch V.F., Brautaset T., Portais J.C., Vorholt J.A. Engineering Escherichia coli for methanol conversion. Metab.Eng. 2015, 28C:190-201.
78. Murrell J.C. Genomics of Methylococcus capsulatus (Bath). Handbook of Hydrocarbon and Lipid Microbiology 2010, 36:1328-1333. Springer, Heidelberg, Germany.
79. Murrell J.C., Jetten M.S.M. The microbial methane cycle. Environ. Microbiol. Rep. 2009, 1:279-284.
80. Nguyen, H.H., Chan, S. 2003. Protein and Nucleic Acid Expression Systems. US20030032141 A1.
81. Nikiema J., Bibeau L., Lavoie J., Brzezinski R., Vigneux J., Heitz M.. Biofiltration of methane: an experimental study. Chem. Eng. J. 2005, 113:1385-8947.
82. Ojala D.S., Beck D.A., Kalyuzhnaya M.G. Genetic systems for moderately halo(alkali)philic bacteria of the genus Methylomicrobium. Methods Enzymol. 2011, 495:99-118.
83. Park, S., Brown, K.W., Thomas, J.C., Lee, I., Sung, K. 2008. Comparison study of methane emissions from landfills with different landfill covers. Environ. Earth Sci. 10.1007/s12665-009-0229-8.
84. Park D., Lee J. Biological conversion of methane to methanol. Korean J. Chem. Eng. 2013, 30:977-987.
85. Peyraud R., Schneider K., Kiefer P., Massou S., Vorholt J., Portais J.P. Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1. BMC Syst. Biol 2011, 5:189.
86. Puri A.W., Owen S., Chu F., Chavkin T., Beck D.A., Kalyuzhnaya M.G., Lidstrom M.E. Genetic tools for the industrially promising methanotroph Methylomicrobium buryatense. Appl. Environ. Microbiol. 2015, 81:1775-1781.
87. Santos F., Boele J., Teusink B. A practical guide to genome-scale metabolic models and their analysis. Methods Enzymol. 2011, 500:509-532.
88. Scheutz C., Kjeldsen P., Bogner J.E., De Vissche A., Gebert J., Hilger H.A., Huber-Humer M., Spokas K. Microbial methane oxidation processes and technologies for mitigation of landfill gas emissions. Waste Manage. Res. 2009, 27:409-455.
89. Semrau J.D. Bioremediation via methanotrophy: overview of recent findings and suggestions for future research. Front. Microbiol. 2011, 2:209.
90. Semrau J.D., DiSpirito A.A., Vuilleumier S. Facultative methanotrophy: false leads, true results, and suggestions for future research. FEMS Microbiol. Lett. 2011, 323:1-12.
91. Semrau J.D., DiSpirito A.A., Yoon S. Methanotrophs and copper. FEMS Microbiol. Rev. 2010, 34:496-531.
92. Semrau J.D., Jagadevan S., DiSpirito A.A., Khalifa A., Scanlan J., Bergman B.H., Freemeier B.C., Baral B.S., Bandow N.L., Vorobev A., et al. Methanobactin and MmoD work in concert to act as the 'copper-switch' in methanotrophs. Environ. Microbiol. 2013, 15:3077-3086.
93. Sharpe P.L., Dicosimo D., Bosak M.D., Knoke K., Tao L., Cheng Q., Ye R.W. 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. 2007, 73:1721-1728.
94. Shiemke A.K., Arp D.J., Sayavedra-Soto L.A. Inhibition of membrane-bound methane monooxygenase and ammonia monooxygenase by diphenyliodonium: implications for electron transfer. J. Bacteriol. 2004, 186:928-937.
95. Shindell D., Kuylenstierna J.C.I., Vignati E., Dingenen R., Amann M., Klimont Z., Anenberg S., Muller N., Janssens-Maenhout G., Raes F., Schwartz J., Faluvegi G., Pozzoli L., Kupiainen K., Höglund-Isaksson L., Emberson L., Streets D., Ramanathan V., Hicks K., Oanh N.T., Milly G., Williams M., Demkine V., Fowler D. Simultaneously mitigating near-term climate change and improving human health and food security. Science 2012, 335:183-189.
96. Simon J., Klotz M.G. Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations. Biochim. Biophys. Acta 2013, 1827:114-135.
97. Simon R., Priefer U., Pühler A. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram negative bacteria. BioTechnology 1983, 1:784-791.
98. Sipkema E.M., de Koning W., Ganzeveld K.J., Janssen D.B., Beenackers A.A. NADH-regulated metabolic model for growth of Methylosinus trichosporium OB3b. Model presentation, parameter estimation, and model validation. Biotechnol. Prog. 2000, 16:176-188.
99. Smith T.J., Murrell J.C. Microbial biotechnology meets environmental microbiology. Microb. Biotechnol. 2009, 2:142-143.
100. Smith T.J., Murrell J.C. Methanotrophs. Encyclopaedia of Industrial Biotechnology, Bioprocess, Bioseparation and Cell Technology 2010, 1-13. Wiley. M. Flickinger (Ed.).
101. Stafford G.P., Scanlan J., McDonald I.R., Murrell J.C. rpoN, mmoR and mmoG, genes involved in regulating the expression of soluble methane monooxygenase in Methylosinus trichosporium OB3b. Microbiology-SGM 2003, 149:1771-1784.
102. Steen E.J., Kang Y., Bokinsky G., Hu Z., Schirmer A., McClure A., del Cardayré S.B., Keasling J.D. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 2010, 463:559-562.
103. Streese J., Stegmann R. Microbial oxidation of methane from old landfills in biofilters. Waste Manage. 2003, 23:573-580.
104. Summer K.H., Lichtmannegger J., Bandow N., Choi D.W., DiSpirito A.A., Michalke B. The biogenic methanobactin is an effective chelator for copper in a rat model for Wilson disease. J. Trace Elem. Med. Biol. 2011, 25:36-41.
105. Tamas I., Smirnova A.V., He Z., Dunfield P.F. The (d)evolution of methanotrophy in the Beijerinckiaceae-a comparative genomics analysis. ISME J. 2014, 8:369-382.
106. Theisen A.R., Ali M.H., Radajewski S., Dumont M.G., Dunfield P.F., McDonald I.R., Dedysh S.N., Miguez C.B., Murrell J.C. Regulation of methane oxidation in the facultative methanotroph Methylocella silvestris BL2. Mol. Microbiol. 2005, 58:682-692.
107. Toukdarian A.E., Lidstrom M.E. Molecular construction and characterization of nif mutants of the obligate methanotroph Methylosinus sp. strain 6. J. Bacteriol. 1984, 157:979-983.
108. Trotsenko Y.A., Khmelenina V.N. Extremophilic Methanotrophs 2008, 206. ONTI PNTs RAN, Pushchino.
109. Trotsenko Y.A., Murrell J.C. Metabolic aspects of aerobic obligate methanotrophy. Adv. Appl. Microbiol. 2008, 63:183-229.
110. Van Dien S.J., Lidstrom M.E. Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C(3) and C(4) metabolism. Biotechnol. Bioeng. 2002, 78:296-312.
111. Vorholt J.A. Cofactor-dependent pathways of formaldehyde oxidation in methylotrophic bacteria. Arch. Microbiol. 2002, 178:239-249.
112. Vorobev A., Jagadevan S., Baral B.S., Dispirito A.A., Freemeier B.C., Bergman B.H., Bandow N.L., Semrau J.D. Detoxification of mercury by methanobactin from Methylosinus trichosporium OB3b. Appl. Environ. Microbiol. 2013, 79:5918-5926.
113. Vorobev A., Jagadevan S., Jain S., Anantharaman K., Dick G.J., Vuilleumier S., Semrau J.D. Genomic and transcriptomic analyses of the facultative methanotroph Methylocystis sp. strain SB2 grown on methane or ethanol. Appl. Environ. Microbiol. 2014, 80:3044-3052.
114. Welander P.V., Summons R.E. Discovery, taxonomic distribution, and phenotypic characterization of a gene required for 3-methylhopanoid production. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:12905-12910.
115. West C.A., Salmond G.P., Dalton H., Murrell J.C. Functional expression in Escherichia coli of proteins B and C from soluble methane monooxygenase of Methylococcus capsulatus (Bath). J. Gen. Microbiol. 1992, 138:1301-1307.
116. Whittenbury R., Phillips K.C., Wilkinson J.F. Enrichment, isolation and some properties of methane-utilizing bacteria. J. Gen. Microbiol. 1970, 61:205-218.
117. Winder R. Methane to biomass: Norferm, Norway, uses Methylococcus capsulatus bacteria to convert methane to bioprotein in a continuous loop fermentation process. Chem. Ind. 2010, http://findarticles.com/p/articles/mi_hb5255/is_17/ai_n29124852/.
118. Xin J.Y., Cui J.R., Niu J.Z., Hua S.F., Xia C.G., Li S.B, Zhu I.M. Production of methanol from methane by methanotrophic bacteria. Biocatal. Biotransform. 2004, 22:225-229.
119. Xin J.Y., Cui J.R., Niu J.Z., Hua S.F., Xia C.G., Li S.B, Zhu I.M. Biosynthesis of methanol from CO2 and CH4 by methanotrophic bacteria. Biotechnology 2004, 3:67-71.
120. Yang S., Matsen J.B., Konopka M., Green-Saxena A., Clubb J., Sadilek M., Orphan V.J., Beck D., Kalyuzhnaya M.G. Global molecular analyses of methane metabolism in methanotrophic alphaproteobacterium, Methylosinus trichosporium OB3b. Part II. Metabolomics and 13C-labeling study. Front. Microbiol. 2013, 4:70.
121. Yazdian F., Hajizadeh S., Shojaosadati S.A., Khalilzadeh R., Jahanshahi M., Nosrati M. Production of single cell protein from natural gas: parameter optimization and RNA evaluation. Iran. J. Biotechnol. 2005, 3:235-242.
122. 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, 892:185-195.
123. Ye R.W., Yao H., Stead K., Wang T., Tao L., Cheng Q., Sharpe P.L., Suh W., Nagel E., Arcilla D., Dragotta D., Miller E.S. Construction of the astaxanthin biosynthetic pathway in a methanotrophic bacterium Methylomonas sp. strain 16a. J. Ind. Microbiol. Biotechnol. 2007, 34(4):289-299.
124. Yoon S., Carey J.N., Semrau J.D. Feasibility of atmospheric methane removal using methanotrophic biotrickling filters. Appl. Microbiol. Biotechnol. 2009, 83:949-956.
125. Yoon S., Semrau J.D. Measurement and modeling of multiple substrate oxidation by methanotrophs at 20 degrees C. FEMS Microbiol. Lett. 2008, 287:156-162.
126. Zelle R.M., de Hulster E., van Winden W.A., de Waard P., Dijkema C., Winkler A.A., Geertman J.M., van Dijken J.P., Pronk J.T., van Maris A.J. Malic acid production by Saccharomyces cerevisiae: engineering of pyruvate carboxylation, oxaloacetate reduction, and malate export. Appl. Environ. Microbiol. 2008, 74:2766-2777.
127. Zhang Y., Xin J., Chen L., Xia C. The methane monooxygenase intrinsic activity of kinds of methanotrophs. Appl. Biochem. Biotechnol. 2009, 157:431-441.
128. Zimin, B.A. 2008. Method for Production of Aerobic Microorganism Biomass. Russian Federation RU 2322488 C2.
129. Zischka H., Lichtmannegger J., Schmitt S., Jagemann N., Schulz S., Wartini D., Jennen L., Rust C., Larochette N., Galluzzi L., et al. Liver mitochondrial membrane crosslinking and destruction in a rat model of Wilson disease. J. Clin. Invest. 2011, 121:1508-1518.