Next generation biofuel engineering in prokaryotes

Current Opinion in Chemical Biology

Volumn 17, Issue 3, 2013, Pages 462-471

  Gronenberg, Luisa S ^a   Marcheschi, Ryan J ^a   Liao, James C ^a,b  

^a University of California   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETONE; ALCOHOL; BUTANOL; CARBON DIOXIDE; CELLULASE; COENZYME A; FATTY ACID DERIVATIVE; ISOPRENOID; LIGNOCELLULOSE; OXOACID; RECOMBINANT ENZYME;

ALCOHOL PRODUCTION; AUTOTROPH; BACILLUS SUBTILIS; BACTERIAL METABOLISM; BIOENGINEERING; BIOFUEL PRODUCTION; CLOSTRIDIUM; CLOSTRIDIUM ACETOBUTYLICUM; CLOSTRIDIUM BEIJERINCKII; ESCHERICHIA COLI; FATTY ACID SYNTHESIS; FERMENTATION; GEOBACILLUS; GEOBACILLUS THERMOGLUCOSIDASIUS; METABOLIC ENGINEERING; MOLECULAR MODEL; NONHUMAN; PROKARYOTE; REVIEW; SPECIES; SUSTAINABLE DEVELOPMENT; SYNECHOCOCCUS ELONGATUS; THERMOPHILIC BACTERIUM; WASTE;

AUTOTROPHIC PROCESSES; BACTERIA; BIOFUELS; HOT TEMPERATURE; LIGNIN; METABOLIC ENGINEERING;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 84878854426     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2013.03.037     Document Type: Review

References (90)

1. Tuck C.O., Perez E., Horvath I.T., Sheldon R.A., Poliakoff M. Valorization of biomass: deriving more value from waste. Science 2012, 337:695-699.
2. Peralta-Yahya P.P., Zhang F., del Cardayre S.B., Keasling J.D. Microbial engineering for the production of advanced biofuels. Nature 2012, 488:320-328.
3. Inokuma K., Liao J.C., Okamoto M., Hanai T. Improvement of isopropanol production by metabolically engineered Escherichia coli using gas stripping. Journal of Bioscience and Bioengineering 2010, 110:696-701.
4. Bond-Watts B.B., Bellerose R.J., Chang M.C. Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways. Nat Chem Biol 2011, 7:222-227.
5. Shen C.R., Lan E.I., Dekishima Y., Baez A., Cho K.M., Liao J.C. Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli. Appl Environ Microbiol 2011, 77:2905-2915.
6. Dekishima Y., Lan E.I., Shen C.R., Cho K.M., Liao J.C. Extending carbon chain length of 1-butanol pathway for 1-hexanol synthesis from glucose by engineered Escherichia coli. J Am Chem Soc 2011, 133:11399-11401.
7. Machado H.B., Dekishima Y., Luo H., Lan E.I., Liao J.C. A selection platform for carbon chain elongation using the CoA-dependent pathway to produce linear higher alcohols. Metab Eng 2012, 14:504-511.
8. Dellomonaco C., Clomburg J.M., Miller E.N., Gonzalez R. Engineered reversal of the beta-oxidation cycle for the synthesis of fuels and chemicals. Nature 2011, 476:355-359.
9. Atsumi S., Hanai T., Liao J.C. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008, 451:86-89.
10. Huo Y.X., Cho K.M., Rivera J.G., Monte E., Shen C.R., Yan Y., Liao J.C. Conversion of proteins into biofuels by engineering nitrogen flux. Nat Biotechnol 2011, 29:346-351.
11. Baez A., Cho K.M., Liao J.C. High-flux isobutanol production using engineered Escherichia coli: a bioreactor study with in situ product removal. Appl Microbiol Biotechnol 2011, 90:1681-1690.
12. 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.
13. Marcheschi R.J., Li H., Zhang K., Noey E.L., Kim S., Chaubey A., Houk K.N., Liao J.C. A synthetic recursive '+1' pathway for carbon chain elongation. ACS Chem Biol 2012, 7:689-697.
14. Atsumi S., Liao J.C. Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli. Appl Environ Microbiol 2008, 74:7802-7808.
15. Li S., Wen J., Jia X. Engineering Bacillus subtilis for isobutanol production by heterologous Ehrlich pathway construction and the biosynthetic 2-ketoisovalerate precursor pathway overexpression. Appl Microbiol Biotechnol 2011, 91:577-589.
16. Connor M.R., Cann A.F., Liao J.C. 3-Methyl-1-butanol production in Escherichia coli: random mutagenesis and two-phase fermentation. Appl Microbiol Biotechnol 2010, 86:1155-1164.
17. Meylemans H.A., Quintana R.L., Harvey B.G. Efficient conversion of pure and mixed terpene feedstocks to high density fuels. Fuel 2012, 97:560-568.
18. Tsuruta H., Paddon C.J., Eng D., Lenihan J.R., Horning T., Anthony L.C., Regentin R., Keasling J.D., Renninger N.S., Newman J.D. High-level production of amorpha-4,11-diene, a precursor of the antimalarial agent artemisinin, in Escherichia coli. PLoS One 2009, 4:e4489.
19. Peralta-Yahya P.P., Ouellet M., Chan R., Mukhopadhyay A., Keasling J.D., Lee T.S. Identification and microbial production of a terpene-based advanced biofuel. Nat Commun 2011, 2:483.
20. Wang C., Yoon S.H., Jang H.J., Chung Y.R., Kim J.Y., Choi E.S., Kim S.W. Metabolic engineering of Escherichia coli for alpha-farnesene production. Metab Eng 2011, 13:648-655.
21. Bokinsky G., Peralta-Yahya P.P., George A., Holmes B.M., Steen E.J., Dietrich J., Soon Lee T., Tullman-Ercek D., Voigt C.A., Simmons B.A., et al. Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. Proc Natl Acad Sci U S A 2011, 108:19949-19954.
22. Dunlop M.J., Dossani Z.Y., Szmidt H.L., Chu H.C., Lee T.S., Keasling J.D., Hadi M.Z., Mukhopadhyay A. Engineering microbial biofuel tolerance and export using efflux pumps. Mol Syst Biol 2011, 7:487.
23. Zhao Y., Yang J., Qin B., Li Y., Sun Y., Su S., Xian M. Biosynthesis of isoprene in Escherichia coli via methylerythritol phosphate (MEP) pathway. Appl Microbiol Biotechnol 2011, 90:1915-1922.
24. Yang J., Xian M., Su S., Zhao G., Nie Q., Jiang X., Zheng Y., Liu W. Enhancing production of bio-isoprene using hybrid MVA pathway and isoprene synthase in E. coli. PLoS One 2012, 7:e33509.
25. Lennen R.M., Pfleger B.F. Engineering Escherichia coli to synthesize free fatty acids. Trends Biotechnol 2012, 30:659-667.
26. Handke P., Lynch S.A., Gill R.T. Application and engineering of fatty acid biosynthesis in Escherichia coli for advanced fuels and chemicals. Metab Eng 2011, 13:28-37.
27. Liu T., Vora H., Khosla C. Quantitative analysis and engineering of fatty acid biosynthesis in E. coli. Metab Eng 2010, 12:378-386.
28. Liu H., Yu C., Feng D., Cheng T., Meng X., Liu W., Zou H., Xian M. Production of extracellular fatty acid using engineered Escherichia coli. Microb Cell Fact 2012, 11:41.
29. Xu P., Ranganathan S., Fowler Z.L., Maranas C.D., Koffas M.A. Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. Metab Eng 2011, 13:578-587.
30. Zhang F., Carothers J.M., Keasling J.D. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 2012, 30:354-359.
31. Yu X., Liu T., Zhu F., Khosla C. In vitro reconstitution and steady-state analysis of the fatty acid synthase from Escherichia coli. Proc Natl Acad Sci U S A 2011, 108:18643-18648.
32. Steen E.J., Kang Y., Bokinsky G., Hu Z., Schirmer A., McClure A., del Cardayre S.B., Keasling J.D. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 2010, 463:559-562.
33. Zheng Y.N., Li L.L., Liu Q., Yang J.M., Wang X.W., Liu W., Xu X., Liu H., Zhao G., Xian M. Optimization of fatty alcohol biosynthesis pathway for selectively enhanced production of C12/14 and C16/18 fatty alcohols in engineered Escherichia coli. Microb Cell Fact 2012, 11:65.
34. Lennen R.M., Pfleger B.F. Modulating membrane composition alters free fatty acid tolerance in Escherichia coli. PLoS One 2013, 8:e54031.
35. Goh E.B., Baidoo E.E., Keasling J.D., Beller H.R. Engineering of bacterial methyl ketone synthesis for biofuels. Appl Environ Microbiol 2012, 78:70-80.
36. Park J., Rodriguez-Moya M., Li M., Pichersky E., San K.Y., Gonzalez R. Synthesis of methyl ketones by metabolically engineered Escherichia coli. J Ind Microbiol Biotechnol 2012, 39:1703-1712.
37. Clomburg J.M., Vick J.E., Blankschien M.D., Rodríguez-Moyaó M., Gonzalez R. A synthetic biology approach to engineer a functional reversal of the β oxidation cycle. ACS Synth Biol 2013, 1:541-554.
38. Lennen R.M., Braden D.J., West R.A., Dumesic J.A., Pfleger B.F. A process for microbial hydrocarbon synthesis: Overproduction of fatty acids in Escherichia coli and catalytic conversion to alkanes. Biotechnol Bioeng 2010, 106:193-202.
39. Schirmer A., Rude M.A., Li X., Popova E., del Cardayre S.B. Microbial biosynthesis of alkanes. Science 2010, 329:559-562.
40. Li N., Chang W.C., Warui D.M., Booker S.J., Krebs C., Bollinger J.M. Evidence for only oxygenative cleavage of aldehydes to alk(a/e)nes and formate by cyanobacterial aldehyde decarbonylases. Biochemistry 2012, 51:7908-7916.
41. Das D., Eser B.E., Han J., Sciore A., Marsh E.N. Oxygen-independent decarbonylation of aldehydes by cyanobacterial aldehyde decarbonylase: a new reaction of diiron enzymes. Angew Chem 2011, 50:7148-7152.
42. Das D., Eser B.E., Han J., Sciore A., Marsh E.N. Corrigendum: Oxygen-independent decarbonylation of aldehydes by cyanobacterial aldehyde decarbonylase: a new reaction of diiron enzymes. Angew Chem 2012, 51:7881.
43. Eser B.E., Das D., Han J., Jones P.R., Marsh E.N. Oxygen-independent alkane formation by non-heme iron-dependent cyanobacterial aldehyde decarbonylase: investigation of kinetics and requirement for an external electron donor. Biochemistry 2011, 50:10743-10750.
44. Eser B.E., Das D., Han J., Jones P.R., Marsh E.N. Correction to oxygen-independent alkane formation by non-heme iron-dependent cyanobacterial aldehyde decarbonylase: investigation of kinetics and requirement for an external electron donor. Biochemistry 2012, 51:5703.
45. Rude M.A., Baron T.S., Brubaker S., Alibhai M., del Cardayre S.B., Schirmer A. Terminal olefin (1-alkene) biosynthesis by a novel p450 fatty acid decarboxylase from Jeotgalicoccus species. Appl Environ Microbiol 2011, 77:1718-1727.
46. Nakashima N., Tamura T. A new carbon catabolite repression mutation of Escherichia coli, mlc*, and its use for producing isobutanol. J Biosci Bioeng 2012, 114:38-44.
47. Groff D., Benke P.I., Batth T.S., Bokinsky G., Petzold C.J., Adams P.D., Keasling J.D. Supplementation of intracellular XylR leads to coutilization of hemicellulose sugars. Appl Environ Microbiol 2012, 78:2221-2229.
48. Mazzoli R., Lamberti C., Pessione E. Engineering new metabolic capabilities in bacteria: lessons from recombinant cellulolytic strategies. Trends Biotechnol 2012, 30:111-119.
49. Soma Y., Inokuma K., Tanaka T., Ogino C., Kondo A., Okamoto M., Hanai T. Direct isopropanol production from cellobiose by engineered Escherichia coli using a synthetic pathway and a cell surface display system. J Biosci Bioeng 2012, 114:80-85.
50. Zhang X.Z., Sathitsuksanoh N., Zhu Z., Percival Zhang Y.H. One-step production of lactate from cellulose as the sole carbon source without any other organic nutrient by recombinant cellulolytic Bacillus subtilis. Metab Eng 2011, 13:364-372.
51. Anderson T.D., Robson S.A., Jiang X.W., Malmirchegini G.R., Fierobe H.P., Lazazzera B.A., Clubb R.T. Assembly of minicellulosomes on the surface of Bacillus subtilis. Appl Environ Microbiol 2011, 77:4849-4858.
52. Almeida J.R., Favaro L.C., Quirino B.F. Biodiesel biorefinery: opportunities and challenges for microbial production of fuels and chemicals from glycerol waste. Biotechnol Biofuels 2012, 5:48.
53. Clomburg J.M., Gonzalez R. Anaerobic fermentation of glycerol: a platform for renewable fuels and chemicals. Trends Biotechnol 2013, 31:20-28.
54. Lutke-Eversloh T., Bahl H. Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production. Curr Opin Biotechnol 2011, 22:634-647.
55. Kuehne S.A., Heap J.T., Cooksley C.M., Cartman S.T., Minton N.P. ClosTron-mediated engineering of Clostridium. Methods Mol Biol 2011, 765:389-407.
56. Lee J., Jang Y.S., Choi S.J., Im J.A., Song H., Cho J.H., Seung do Y., Papoutsakis E.T., Bennett G.N., Lee S.Y. Metabolic engineering of Clostridium acetobutylicum ATCC 824 for isopropanol-butanol-ethanol fermentation. Appl Environ Microbiol 2012, 78:1416-1423.
57. Collas F., Kuit W., Clement B., Marchal R., Lopez-Contreras A.M., Monot F. Simultaneous production of isopropanol, butanol, ethanol and 2,3-butanediol by Clostridium acetobutylicum ATCC 824 engineered strains. AMB Express 2012, 2:45.
58. Dai Z., Dong H., Zhu Y., Zhang Y., Li Y., Ma Y. Introducing a single secondary alcohol dehydrogenase into butanol-tolerant Clostridium acetobutylicum Rh8 switches ABE fermentation to high level IBE fermentation. Biotechnol Biofuels 2012, 5:44.
59. Lee J.Y., Jang Y.S., Lee J., Papoutsakis E.T., Lee S.Y. Metabolic engineering of Clostridium acetobutylicum M5 for highly selective butanol production. Biotechnol J 2009, 4:1432-1440.
60. Yu M., Zhang Y., Tang I.C., Yang S.T. Metabolic engineering of Clostridium tyrobutyricum for n-butanol production. Metab Eng 2011, 13:373-382.
61. Chanal A., Mingardon F., Bauzan M., Tardif C., Fierobe H.P. Scaffoldin modules serving as 'cargo' domains to promote the secretion of heterologous cellulosomal cellulases by Clostridium acetobutylicum. Appl Environ Microbiol 2011, 77:6277-6280.
62. Xiao H., Li Z., Jiang Y., Yang Y., Jiang W., Gu Y., Yang S. Metabolic engineering of d-xylose pathway in Clostridium beijerinckii to optimize solvent production from xylose mother liquid. Metab Eng 2012.
63. Xiao H., Gu Y., Ning Y., Yang Y., Mitchell W.J., Jiang W., Yang S. Confirmation and elimination of xylose metabolism bottlenecks in glucose phosphoenolpyruvate-dependent phosphotransferase system-deficient Clostridium acetobutylicum for simultaneous utilization of glucose, xylose, and arabinose. Appl Environ Microbiol 2011, 77:7886-7895.
64. Agrawal M., Wang Y., Chen R.R. Engineering efficient xylose metabolism into an acetic acid-tolerant Zymomonas mobilis strain by introducing adaptation-induced mutations. Biotechnol Lett 2012, 34:1825-1832.
65. Yanase H., Miyawaki H., Sakurai M., Kawakami A., Matsumoto M., Haga K., Kojima M., Okamoto K. Ethanol production from wood hydrolysate using genetically engineered Zymomonas mobilis. Appl Microbiol Biotechnol 2012, 94:1667-1678.
66. Vasan P.T., Piriya P.S., Prabhu D.I., Vennison S.J. Cellulosic ethanol production by Zymomonas mobilis harboring an endoglucanase gene from Enterobacter cloacae. Bioresour Technol 2011, 102:2585-2589.
67. Becker J., Wittmann C. Bio-based production of chemicals, materials and fuels-Corynebacterium glutamicum as versatile cell factory. Curr Opin Biotechnol 2012, 23:631-640.
68. Smith K.M., Cho K.M., Liao J.C. Engineering Corynebacterium glutamicum for isobutanol production. Appl Microbiol Biotechnol 2010, 87:1045-1055.
69. Blombach B., Riester T., Wieschalka S., Ziert C., Youn J.W., Wendisch V.F., Eikmanns B.J. Corynebacterium glutamicum tailored for efficient isobutanol production. Appl Environ Microbiol 2011, 77:3300-3310.
70. Hyeon J.E., Jeon W.J., Whang S.Y., Han S.O. Production of minicellulosomes for the enhanced hydrolysis of cellulosic substrates by recombinant Corynebacterium glutamicum. Enzyme Microb Technol 2011, 48:371-377.
71. Higashide W., Li Y., Yang Y., Liao J.C. Metabolic engineering of Clostridium cellulolyticum for production of isobutanol from cellulose. Appl Environ Microbiol 2011, 77:2727-2733.
72. Olson D.G., McBride J.E., Shaw A.J., Lynd L.R. Recent progress in consolidated bioprocessing. Curr Opin Biotechnol 2012, 23:396-405.
73. Joe Shaw A., Covalla S.F., Miller B.B., Firliet B.T., Hogsett D.A., Herring C.D. Urease expression in a Thermoanaerobacterium saccharolyticum ethanologen allows high titer ethanol production. Metab Eng 2012, 14:528-532.
74. Gardner J.G., Keating D.H. Genetic and functional genomic approaches for the study of plant cell wall degradation in Cellvibrio japonicus. Methods Enzymol 2012, 510:331-347.
75. Tolonen A.C., Chilaka A.C., Church G.M. Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367. Mol Microbiol 2009, 74:1300-1313.
76. Tripathi S.A., Olson D.G., Argyros D.A., Miller B.B., Barrett T.F., Murphy D.M., McCool J.D., Warner A.K., Rajgarhia V.B., Lynd L.R., et al. Development of pyrF-based genetic system for targeted gene deletion in Clostridium thermocellum and creation of a pta mutant. Appl Environ Microbiol 2010, 76:6591-6599.
77. Argyros D.A., Tripathi S.A., Barrett T.F., Rogers S.R., Feinberg L.F., Olson D.G., Foden J.M., Miller B.B., Lynd L.R., Hogsett D.A., et al. High ethanol titers from cellulose by using metabolically engineered thermophilic, anaerobic microbes. Appl Environ Microbiol 2011, 77:8288-8294.
78. Li Y., Tschaplinski T.J., Engle N.L., Hamilton C.Y., Rodriguez M., Liao J.C., Schadt C.W., Guss A.M., Yang Y., Graham D.E. Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations. Biotechnol Biofuels 2012, 5:2.
79. Cripps R.E., Eley K., Leak D.J., Rudd B., Taylor M., Todd M., Boakes S., Martin S., Atkinson T. Metabolic engineering of Geobacillus thermoglucosidasius for high yield ethanol production. Metab Eng 2009, 11:398-408.
80. Machado I.M., Atsumi S. Cyanobacterial biofuel production. J Biotechnol 2012, 162:50-56.
81. Atsumi S., Higashide W., Liao J.C. Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde. Nat Biotechnol 2009, 27:1177-1180.
82. Lan E.I., Liao J.C. Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide. Metab Eng 2011, 13:353-363.
83. Lan E.I., Liao J.C. ATP drives direct photosynthetic production of 1-butanol in cyanobacteria. Proc Natl Acad Sci U S A 2012, 109:6018-6023.
84. Gao Z., Zhao H., Li Z., Tana X., Lu X. Photosynthetic production of ethanol from carbon dioxide in genetically engineered cyanobacteria. Energy Environ Sci 2012, 5:9857-9865.
85. Lindberg P., Park S., Melis A. Engineering a platform for photosynthetic isoprene production in cyanobacteria, using Synechocystis as the model organism. Metab Eng 2010, 12:70-79.
86. Mendez-Perez D., Begemann M.B., Pfleger B.F. Modular synthase-encoding gene involved in alpha-olefin biosynthesis in Synechococcus sp. strain PCC 7002. Appl Environ Microbiol 2011, 77:4264-4267.
87. Liu X., Sheng J., Curtiss R. Fatty acid production in genetically modified cyanobacteria. Proc Natl Acad Sci U S A 2011, 108:6899-6904.
88. 2-limitation-inducible Green Recovery of fatty acids from cyanobacterial biomass. Proc Natl Acad Sci U S A 2011, 108:6905-6908.
89. Lu J., Brigham C.J., Gai C.S., Sinskey A.J. Studies on the production of branched-chain alcohols in engineered Ralstonia eutropha. Appl Microbiol Biotechnol 2012, 96:283-297.
90. 2 to higher alcohols. Science 2012, 335:1596.