Synthetic methylotrophy: Engineering the production of biofuels and chemicals based on the biology of aerobic methanol utilization

Current Opinion in Biotechnology

Volumn 33, Issue , 2015, Pages 165-175

  Whitaker, William B ^a   Sandoval, Nicholas R ^a   Bennett, Robert K ^a   Fast, Alan G ^a   Papoutsakis, Eleftherios T ^a  

^a UNIVERSITY OF DELAWARE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOFUELS; BIOLOGY; CARBOHYDRATES; ESCHERICHIA COLI; METABOLIC ENGINEERING; METABOLITES; METHANE;

CO-SUBSTRATE; ENERGY SOURCE; FERMENTATION SUBSTRATES; METHANOL UTILIZATION; NON-NATIVE; OXIDATION PRODUCTS; SOLE CARBON; SYNTHETIC BIOLOGY;

METHANOL;

CARBOHYDRATE; CARBON; FORMALDEHYDE; METHANE; METHANOL; METHANOL DEHYDROGENASE; NICOTINAMIDE ADENINE DINUCLEOTIDE; PYRROLOQUINOLINEQUINONE; BIOFUEL;

BACTERIAL GROWTH; BACTERIAL STRAIN; BIOFUEL PRODUCTION; CARBON SOURCE; CHEMICAL STRUCTURE; ENERGY RESOURCE; ESCHERICHIA COLI; FERMENTATION; GRAM NEGATIVE BACTERIUM; METABOLIC ENGINEERING; METHYLOTROPH; NONHUMAN; OXIDATION; PRIORITY JOURNAL; REVIEW; SYNTHESIS; SYNTHETIC BIOLOGY; SYNTHETIC METHYLOTROPHY; AEROBIC METABOLISM; METABOLISM; OXIDATION REDUCTION REACTION;

ESCHERICHIA COLI;

AEROBIOSIS; BIOFUELS; FERMENTATION; METABOLIC ENGINEERING; METHANOL; OXIDATION-REDUCTION;

EID: 84924958721     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2015.01.007     Document Type: Review

References (50)

1. Blohm A., Peichel J., Smith C., Kougentakis A. The significance of regulation and land use patterns on natural gas resource estimates in the Marcellus shale. Energy Policy 2012, 50:358-369.
2. Haynes C.A., Gonzalez R. Rethinking biologocal activation of methane and conversion to liquid fuels. Nat Chem Biol 2014, 10:331-339.
3. Fei Q., Guarnieri M.T., Tao L., Laurens L.M.L., Dowe N., Pienkos P.T. Bioconversion of natural gas to liquid fuel: opportunities and challenges. Biotechnol Adv 2014, 32:596-614.
4. Balk M., Weijma J., Friedrich M.W., Stams A.J. Methanol utilization by a novel thermophilic homoacetogenic bacterium, Moorella mulderi sp. nov., isolated from a bioreactor. Arch Microbiol 2003, 179:315-320.
5. Hakemian A.S., Rosenzweig A.C. The biochemistry of methane oxidation. Annu Rev Biochem 2007, 76:223-241.
6. Anthony C. The Biochemistry of Methylotrophs 1982, Academic Press.
7. Krog A., Heggeset T.M.B., Muller J.E.N., Kupper C.E., Schneider O., Vorholt J.A., Ellingsen T.E., Brautaset T. Methylotrophic Bacillus methanolicus encodes two chromosomal and one plasmid born NAD(+) dependent methanol dehydrogenase paralogs with different catalytic and biochemical properties. PLoS One 2013, 8.
8. Yurimoto H., Oku M., Sakai Y. Yeast methylotrophy: metabolism, gene regulation and peroxisome homeostasis. Int J Microbiol 2011, 2011:101298.
9. Kalyuzhnaya M.G., Hristova K.R., Lidstrom M.E., Chistoserdova L. Characterization of a novel methanol dehydrogenase in representatives of Burkholderiales: implications for environmental detection of methylotrophy and evidence for convergent evolution. J Bacteriol 2008, 190:3817-3823.
10. Matsushita K., Arents J.C., Bader R., Yamada M., Adachi O., Postma P.W. Escherichia coli is unable to produce pyrroloquinoline quinone (PQQ). Microbiology 1997, 143(Pt 10):3149-3156.
11. Puehringer S., Metlitzky M., Schwarzenbacher R. The pyrroloquinoline quinone biosynthesis pathway revisited: a structural approach. BMC Biochem 2008, 9:8.
12. Velterop J.S., Sellink E., Meulenberg J.J.M., David S., Bulder I., Postma P.W. Synthesis of pyrroloquinoline quinone in-vivo and in-vitro and detection of an intermediate in the biosynthetic-pathway. J Bacteriol 1995, 177:5088-5098.
13. Sheehan M.C., Bailey C.J., Dowds B.C.A., Mcconnell D.J. A new alcohol-dehydrogenase, reactive towards methanol, from Bacillus stearothermophilus. Biochem J 1988, 252:661-666.
14. Brautaset T, Heggeset TMB, Krog A, Quax WJ, Sibbald MJJB, Vorholt J, Müller J, Kiefer P, Potthoff E, Wendisch VF: Novel methanol dehydrogenase enzymes from bacillus. World patent publication WO/2013/110797 A1. 2013, Assignees: Sinvent As, Rijksuniversiteit Groningen, Eth Zurich.
15. Burgard AP, Osterhout RE, Van Dien SJ, Tracewell CA, Pharkya P, Andrae S: Microorganisms and methods for enhancing the availability of reducing equivalents in the presence of methanol, and for producing 1,4-butanediol related thereto. US Patent Publication 20140058056. 2014, Assignee: Genomatica, Inc. (San Diego, CA, US).
16. Kato N., Yurimoto H., Thauer R.K. The physiological role of the ribulose monophosphate pathway in bacteria and archaea. Biosci Biotechnol Biochem 2006, 70:10-21.
17. Yurimoto H., Kato N., Sakai Y. Genomic organization and biochemistry of the ribulose monophosphate pathway and its application in biotechnology. Appl Microbiol Biotechnol 2009, 84:407-416.
18. Chistoserdova L., Lapidus A., Han C., Goodwin L., Saunders L., Brettin T., Tapia R., Gilna P., Lucas S., Richardson P.M., et al. Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. J Bacteriol 2007, 189:4020-4027.
19. Taylor E.J., Smith N.L., Colby J., Charnock S.J., Black G.W. The gene encoding the ribulose monophosphate pathway enzyme, 3-hexulose-6-phosphate synthase, from Aminomonas aminovorus C2A1 is adjacent to coding sequences that exhibit similarity to histidine biosynthesis enzymes. Antonie Van Leeuwenhoek 2004, 86:167-172.
20. Mitsui R., Sakai Y., Yasueda H., Kato N. A novel operon encoding formaldehyde fixation: the ribulose monophosphate pathway in the gram-positive facultative methylotrophic bacterium Mycobacterium gastri MB19. J Bacteriol 2000, 182:944-948.
21. Brautaset T., Jakobsen M.O., Flickinger M.C., Valla S., Ellingsen T.E. Plasmid-dependent methylotrophy in thermotolerant Bacillus methanolicus. J Bacteriol 2004, 186:1229-1238.
22. Jakobsen O.M., Benichou A., Flickinger M.C., Valla S., Ellingsen T.E., Brautaset T. Upregulated transcription of plasmid and chromosomal ribulose monophosphate pathway genes is critical for methanol assimilation rate and methanol tolerance in the methylotrophic bacterium Bacillus methanolicus. J Bacteriol 2006, 188:3063-3072.
23. Muller J.E., Litsanov B., Bortfeld-Miller M., Trachsel C., Grossmann J., Brautaset T., Vorholt J.A. Proteomic analysis of the thermophilic methylotroph Bacillus methanolicus MGA3. Proteomics 2014, 14:725-737.
24. Markert B., Stolzenberger J., Brautaset T., Wendisch V.F. Characterization of two transketolases encoded on the chromosome and the plasmid pBM19 of the facultative ribulose monophosphate cycle methylotroph Bacillus methanolicus. BMC Microbiol 2014, 14:7.
25. Stolzenberger J., Lindner S.N., Persicke M., Brautaset T., Wendisch V.F. Characterization of fructose 1,6-bisphosphatase and sedoheptulose 1,7-bisphosphatase from the facultative ribulose monophosphate cycle methylotroph Bacillus methanolicus. J Bacteriol 2013, 195:5112-5122.
26. Stolzenberger J., Lindner S.N., Wendisch V.F. The methylotrophic Bacillus methanolicus MGA3 possesses two distinct fructose 1,6-bisphosphate aldolases. Microbiology 2013, 159:1770-1781.
27. Orita I., Sakamoto N., Kato N., Yurimoto H., Sakai Y. Bifunctional enzyme fusion of 3-hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase. Appl Microbiol Biotechnol 2007, 76:439-445.
28. Koopman F.W., de Winde J.H., Ruijssenaars H.J. C(1) compounds as auxiliary substrate for engineered Pseudomonas putida S12. Appl Microbiol Biotechnol 2009, 83:705-713.
29. Mitsui R., Kusano Y., Yurimoto H., Sakai Y., Kato N., Tanaka M. Formaldehyde fixation contributes to detoxification for growth of a nonmethylotroph, Burkholderia cepacia TM1, on vanillic acid. Appl Environ Microbiol 2003, 69:6128-6132.
30. Yurimoto H., Kato N., Sakai Y. Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism. Chem Rec 2005, 5:367-375.
31. Gutheil W.G., Holmquist B., Vallee B.L. Purification, characterization, and partial sequence of the glutathione-dependent formaldehyde dehydrogenase from Escherichia coli: a class III alcohol dehydrogenase. Biochemistry 1992, 31:475-481.
32. Herring C.D., Blattner F.R. Global transcriptional effects of a suppressor tRNA and the inactivation of the regulator frmR. J Bacteriol 2004, 186:6714-6720.
33. Fast A.G., Papoutsakis E.T. Stoichiometric and energetic analyses of non-photosynthetic CO2-fixation pathways to support synthetic biology strategies for production of fuels and chemicals. Curr Opin Chem Eng 2012, 1:380-395.
34. Papoutsakis E.T. Equations and calculations for fermentations of butyric-acid bacteria. Biotechnol Bioeng 1984, 26:174-187.
35. Bastian S., Liu X., Meyerowitz J.T., Snow C.D., Chen M.M., Arnold F.H. Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli. Metab Eng 2011, 13:345-352.
36. Song J.K., Chung B., Oh Y.H., Rhee J.S. Construction of DNA-shuffled and incrementally truncated libraries by a mutagenic and unidirectional reassembly method: changing from a substrate specificity of phospholipase to that of lipase. Appl Environ Microbiol 2002, 68:6146-6151.
37. Short JM: Directed evolution of thermophilic enzymes. US Patent 2002, US6335179 B1.
38. Hendrickson E.L., Beck D.A., Wang T., Lidstrom M.E., Hackett M., Chistoserdova L. Expressed genome of Methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophy. J Bacteriol 2010, 192:4859-4867.
39. Ravin N.V., Eldarov M.A., Kadnikov V.V., Beletsky A.V., Schneider J., Mardanova E.S., Smekalova E.M., Zvereva M.I., Dontsova O.A., Mardanov A.V., et al. Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. BMC Genomics 2013, 14:837.
40. van Zutphen T., Baerends R.J., Susanna K.A., de Jong A., Kuipers O.P., Veenhuis M., van der Klei I.J. Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis. BMC Genomics 2010, 11:1.
41. Hua Q., Yang C., Baba T., Mori H., Shimizu K. Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts. J Bacteriol 2003, 185:7053-7067.
42. Zhao J., Baba T., Mori H., Shimizu K. Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on 13C-labeling experiments and the measurement of enzyme activities. Appl Microbiol Biotechnol 2004, 64:91-98.
43. Kim Y.M., Cho H.S., Jung G.Y., Park J.M. Engineering the pentose phosphate pathway to improve hydrogen yield in recombinant Escherichia coli. Biotechnol Bioeng 2011, 108:2941-2946.
44. Agrawal P., Flores G.E. A study of methanol transport/uptake by a methanol-utilizing bacterium L3 in a batch bioreactor. Biotechnol Bioeng 1989, 33:104-114.
45. Papoutsakis E., Lim H.C. Role of formaldehyde in utilization of C-1 compounds via ribulose monophosphate cycle. Biotechnol Bioeng 1978, 20:421-442.
46. Bennett B.D., Kimball E.H., Gao M., Osterhout R., Van Dien S.J., Rabinowitz J.D. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol 2009, 5:593-599.
47. Potzkei J., Kunze M., Drepper T., Gensch T., Jaeger K.E., Buchs J. Real-time determination of intracellular oxygen in bacteria using a genetically encoded FRET-based biosensor. BMC Biol 2012, 10:28.
48. Watts R.J., Washington D., Howsawkeng J., Loge F.J., Teel A.L. Comparative toxicity of hydrogen peroxide, hydroxyl radicals, and superoxide anion to Escherichia coli. Adv Environ Res 2003, 7:961-968.
49. Zheng Y.J., Xia Z., Chen Z., Mathews F.S., Bruice T.C. Catalytic mechanism of quinoprotein methanol dehydrogenase: a theoretical and X-ray crystallographic investigation. Proc Natl Acad Sci U S A 2001, 98:432-434.
50. Reddy S.Y., Bruice T.C. Determination of enzyme mechanisms by molecular dynamics: studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase. Protein Sci 2004, 13:1965-1978.