Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology
Tóm tắt
The microbial production of biofuels is a promising avenue for the development of viable processes for the generation of fuels from sustainable resources. In order to become cost and energy effective, these processes must utilize organisms that can be optimized to efficiently produce candidate fuels from a variety of feedstocks. Escherichia coli has become a promising host organism for the microbial production of biofuels in part due to the ease at which this organism can be manipulated. Advancements in metabolic engineering and synthetic biology have led to the ability to efficiently engineer E. coli as a biocatalyst for the production of a wide variety of potential biofuels from several biomass constituents. This review focuses on recent efforts devoted to engineering E. coli for the production of biofuels, with emphasis on the key aspects of both the utilization of a variety of substrates as well as the synthesis of several promising biofuels. Strategies for the efficient utilization of carbohydrates, carbohydrate mixtures, and noncarbohydrate carbon sources will be discussed along with engineering efforts for the exploitation of both fermentative and nonfermentative pathways for the production of candidate biofuels such as alcohols and higher carbon biofuels derived from fatty acid and isoprenoid pathways. Continued advancements in metabolic engineering and synthetic biology will help improve not only the titers, yields, and productivities of biofuels discussed herein, but also increase the potential range of compounds that can be produced.
Tài liệu tham khảo
Aristidou A, Penttila M (2000) Metabolic engineering applications to renewable resource utilization. Curr Opin Biotechnol 11:187–198
Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJY, Hanai T, Liao JC (2008a) Metabolic engineering of Escherichia coli for 1-butanol production. Metab Eng 10:305–311
Atsumi S, Hanai T, Liao JC (2008b) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451:86–89
Atsumi S, Liao JC (2008a) Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli. Appl Environ Microbiol 74:7802–7808
Atsumi S, Liao JC (2008b) Metabolic engineering for advanced biofuels production from Escherichia coli. Curr Opin Biotechnol 19:414–419
Babitzke P, Romeo T (2007) CsrB sRNA family: sequestration of RNA-binding regulatory proteins. Curr Opin Microbiol 10:156–163
Bailey JE (1991) Toward a Science of Metabolic Engineering. Science 252:1668–1675
Bermejo LL, Welker NE, Papoutsakis ET (1998) Expression of Clostridium acetobutylicum ATCC 824 genes in Escherichia coli for acetone production and acetate detoxification. Appl Environ Microbiol 64:1079–1085
Cann AF, Liao JC (2008) Production of 2-methyl-1-butanol in engineered Escherichia coli. Appl Microbiol Biotechnol 81:89–98
Carothers JM, Goler JA, Keasling JD (2009) Chemical synthesis using synthetic biology. Curr Opin Biotechnol 20:498–503
Chen JS, Hiu SF (1986) Acetone butanol isopropanol production by Clostridium beijerinckii. Biotechnol Lett 8:371–376
Chisti Y (2007) Biodiesel from microalgae. Biotechnol Adv 25:294–306
Christianson DW (2008) Unearthing the roots of the terpenome. Curr Opin Chem Biol 12:141–150
Connor MR, Liao JC (2008) Engineering of an Escherichia coli strain for the production of 3-methyl-1-butanol. Appl Environ Microbiol 74:5769–5775
Connor MR, Liao JC (2009) Microbial production of advanced transportation fuels in non-natural hosts. Curr Opin Biotechnol 20:307–315
Daniel R, Gottschalk G (1992) Growth temperature-dependent acitivity of glycerol dehydratase in Escherichia coli expressing the Citrobacter freundii dha Regulon. FEMS Microbiol Lett 100:281–285
Decker K, Plumbridge J, Boos W (1998) Negative transcriptional regulation of a positive regulator: the expression of malT, encoding the transcriptional activator of the maltose regulon of Escherichia coli, is negatively controlled by Mlc. Mol Microbiol 27:381–390
Dewick PM (2002) The biosynthesis of C-5-C-25 terpenoid compounds. Nat Prod Rep 19:181–222
Dharmadi Y, Murarka A, Gonzalez R (2006) Anaerobic fermentation of glycerol by Escherichia coli: a new platform for metabolic engineering. Biotechnol Bioeng 94:821–829
Doan TTP, Carlsson AS, Hamberg M, Bulow L, Stymne S, Olsson P (2009) Functional expression of five Arabidopsis fatty acyl-CoA reductase genes in Escherichia coli. J Plant Physiol 166:787–796
Durnin G, Clomburg J, Yeates Z, Alvarez PJJ, Zygourakis K, Campbell P, Gonzalez R (2009) Understanding and harnessing the microaerobic metabolism of glycerol in Escherichia coli. Biotechnol Bioeng 103:148–161
Durrett TP, Benning C, Ohlrogge J (2008) Plant triacylglycerols as feedstocks for the production of biofuels. Plant J 54:593–607
Ezeji TC, Qureshi N, Blaschek HP (2005) Continuous butanol fermentation and feed starch retrogradation: butanol fermentation sustainability using Clostridium beijerinckii BA101. J Biotechnol 115:179–187
Fischer CR, Klein-Marcuschamer D, Stephanopoulos G (2008) Selection and optimization of microbial hosts for biofuels production. Metab Eng 10:295–304
Flores N, Xiao J, Berry A, Bolivar F, Valle F (1996) Pathway engineering for the production of aromatic compounds in Escherichia coli. Nat Biotechnol 14:620–623
Fortman JL, Chhabra S, Mukhopadhyay A, Chou H, Lee TS, Steen E, Keasling JD (2008) Biofuel alternatives to ethanol: pumping the microbial well. Trends Biotechnol 26:375–381
Friedman L, Rude M (2008) Process for producing low molecular weight hydrocarbons from renewable resources. WO/2008/113041
Goerke B, Stulke J (2008) Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 6:613–624
Gonzalez R, Campbell P, Wong M (2009) Production of ethanol from thin stillage by metabolically engineered Escherichia coli. Biotechnol Lett 32. doi:10.1007/s10529-009-0159-2
Gonzalez R, Murarka A, Dharmadi Y, Yazdani SS (2008) A new model for the anaerobic fermentation of glycerol in enteric bacteria: trunk and auxiliary pathways in Escherichia coli. Metab Eng 10:234–245
Gonzalez R, Tao H, Purvis JE, York SW, Shanmugam KT, Ingram LO (2003) Gene array-based identification of changes that contribute to ethanol tolerance in ethanologenic Escherichia coli: Comparison of KO11 (Parent) to LY01 (resistant mutant). Biotechnol Prog 19:612–623
Hanai T, Atsumi S, Liao JC (2007) Engineered synthetic pathway for isopropanol production in Escherichia coli. Appl Environ Microbiol 73:7814–7818
Hardiman T, Lemuth K, Keller MA, Reuss M, Siemann-Herzberg M (2007) Topology of the global regulatory network of carbon limitation in Escherichia coli. J Biotechnol 132:359–374
Hernandez-Montalvo V, Martinez A, Hernandez-Chavez G, Bolivar F, Valle F, Gosset G (2003) Expression of galP and glk in a Escherichia coli PTS mutant restores glucose transport and increases glycolytic flux to fermentation products. Biotechnol Bioeng 83:687–694
Hernandez-Montalvo V, Valle F, Bolivar F, Gosset G (2001) Characterization of sugar mixtures utilization by an Escherichia coli mutant devoid of the phosphotransferase system. Appl Microbiol Biotechnol 57:186–191
Himmel ME, Ding SY, Johnson DK, Adney WS, Nimlos MR, Brady JW, Foust TD (2007) Biomass recalcitrance: engineering plants and enzymes for biofuels production. Science 315:804–807
Hirsch RL, Bezdek R, Wendling R (2006) Peaking of world oil production and its mitigation. AIChE J 52:2–8
Hu Q, Sommerfeld M, Jarvis E, Ghirardi M, Posewitz M, Seibert M, Darzins A (2008) Microalgal triacylglycerols as feedstocks for biofuel production: perspectives and advances. Plant J 54:621–639
Ideker T, Galitski T, Hood L (2001) A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2:343–372
Ingram LO, Conway T, Clark DP, Sewell GW, Preston JF (1987) Genetic engineering of ethanol production in Escherichia coli. Appl Environ Microbiol 53:2420–2425
Inui M, Suda M, Kimura S, Yasuda K, Suzuki H, Toda H, Yamamoto S, Okino S, Suzuki N, Yukawa H (2008) Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli. Appl Microbiol Biotechnol 77:1305–1316
Jones DT, Woods DR (1986) Acetone-butanol fermentation revisited. Microbiol Rev 50:484–524
Kalscheuer R, Stolting T, Steinbuchel A (2006) Microdiesel: Escherichia coli engineered for fuel production. Microbiology 152:2529–2536
Keasling JD, Hu Z, Somerville C, Church G, Berry D, Friedman L, Schirmer A, Brubaker S, Del Cardayre SB (2007) Production of fatty acids and derivatives thereof. WO/2007/136762
Kerr RA (2007) Global warming is changing the world. Science 316:188–190
Khankal R, Chin JW, Ghosh D, Cirino PC (2009) Transcriptional effects of CRP* expression in Escherichia coli. J Biol Eng 3:13
Kim Y, Ingram LO, Shanmugam KT (2007) Construction of an Escherichia coli K-12 mutant for homoethanologenic fermentation of glucose or xylose without foreign genes. Appl Environ Microbiol 73:1766–1771
Kimata K, Inada T, Tagami H, Aiba H (1998) A global repressor (MIc) is involved in glucose induction of the ptsG gene encoding major glucose transporter in Escherichia coli. Mol Microbiol 29:1509–1519
Knoshaug EP, Zhang M (2009) Butanol tolerance in a selection of microorganisms. Appl Biochem Biotechnol 153:13–20
Lee SK, Chou H, Ham TS, Lee TS, Keasling JD (2008) Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels. Curr Opin Biotechnol 19:556–563
Lu XF, Vora H, Khosla C (2008) Overproduction of free fatty acids in E. coli: implications for biodiesel production. Metab Eng 10:333–339
Ma FR, Hanna MA (1999) Biodiesel production: a review. Bioresour Technol 70:1–15
Martin VJJ, Pitera DJ, Withers ST, Newman JD, Keasling JD (2003) Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 21:796–802
Mukhopadhyay A, Redding AM, Rutherford BJ, Keasling JD (2008) Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol 19:228–234
Murarka A, Dharmadi Y, Yazdani SS, Gonzalez R (2008) Fermentative utilization of glycerol by Escherichia coli and its implications for the production of fuels and chemicals. Appl Environ Microbiol 74:1124–1135
Nichols NN, Dien BS, Bothast RJ (2001) Use of catabolite repression mutants for fermentation of sugar mixtures to ethanol. Appl Microbiol Biotechnol 56:120–125
Nielsen DR, Leonard E, Yoon SH, Tseng HC, Yuan C, Jones Prather KL (2009) Engineering alternative butanol production platforms in heterologous bacteria. Metab Eng 11:262–273
Ohta K, Beall DS, Mejia JP, Shanmugam KT, Ingram LO (1991) Genetic improvement of Escherichia coli for ehtnao, production: chromosomal integration of Zymomonas mobilis genes enconding pyruvate decarboxylase and alcohol dehydrogenase II. Appl Environ Microbiol 57:893–900
Oren A (2005) A hundred years of Dunaliella research: 1905–2005. Saline Syst 1:2
Pleiss J (2006) The promise of synthetic biology. Appl Microbiol Biotechnol 73:735–739
Rude MA, Schirmer A (2009) New microbial fuels: a biotech perspective. Curr Opin Microbiol 12:274–281
Rodriguez-Moya M, Gonzalez R (2009) Systems biology approaches for the microbial production of biofuels. Biofuels 1. doi:10.4155/BFS.10.5
Sawers RG, Clark DP (2004) Fermentative pyruvate and acetyl-CoA metabolism. In: Neidhardt FC, Curtiss R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE (eds) Escherichia coli and Salmonella: cellular and molecular biology, Webth edn. ASM Press, Washington
Schubert C (2006) Can biofuels finally take center stage? Nat Biotechnol 24:777–784
Service RF (2009) Biofuels: ExxonMobil fuels venter’s efforts to run vehicles on algae-based oil. Science 325:379–379
Shen CR, Liao JC (2008) Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways. Metab Eng 10:312–320
Skraly FA, Lytle BL, Cameron DC (1998) Construction and characterization of a 1,3-propanediol operon. Appl Environ Microbiol 64:98–105
Stephanopoulos G (2002) Metabolic engineering: perspective of a chemical engineer. AIChE J 48:920–926
Stephanopoulos G (2007) Challenges in engineering microbes for biofuels production. Science 315:801–804
Stulke J, Hillen W (1999) Carbon catabolite repression in bacteria. Curr Opin Microbiol 2:195–201
Tao H, Gonzalez R, Martinez A, Rodriguez M, Ingram LO, Preston JF, Shanmugam KT (2001) Engineering a homo-ethanol pathway in Escherichia coli: Increased glycolytic flux and levels of expression of glycolytic genes during xylose fermentation. J Bacteriol 183:2979–2988
Totemeyer S, Booth NA, Nichols WW, Dunbar B, Booth IR (1998) From famine to feast: the role of methylglyoxal production in Escherichia coli. Mol Microbiol 27:553–562
Trinh CT, Srienc F (2009) Metabolic Engineering of Escherichia coli for Efficient Conversion of Glycerol to Ethanol. Appl Environ Microbiol 75:6696–6705
Trinh CT, Unrean P, Srienc F (2008) Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses. Appl Environ Microbiol 74:3634–3643
Withers ST, Gottlieb SS, Lieu B, Newman JD, Keasling JD (2007) Identification of isopentenol biosynthetic genes from Bacillus subtilis by a screening method based on isoprenoid precursor toxicity. Appl Environ Microbiol 73:6277–6283
Yazdani SS, Gonzalez R (2007) Anaerobic fermentation of glycerol: a path to economic viability for the biofuels industry. Curr Opin Biotechnol 18:213–219
Yazdani SS, Gonzalez R (2008) Engineering Escherichia coli for the efficient conversion of glycerol to ethanol and co-products. Metab Eng 10:340–351
Yomano LP, York SW, Ingram LO (1998) Isolation and characterization of ethanol-tolerant mutants of Escherichia coli KO11 for fuel ethanol production. J Ind Microbiol Biotech 20:132–138
Yomano LP, York SW, Shanmugam KT, Ingram LO (2009) Deletion of methylglyoxal synthase gene (mgsA) increased sugar co-metabolism in ethanol-producing Escherichia coli. Biotechnol Lett 31:1389–1398
Yomano LP, York SW, Zhou S, Shanmugam KT, Ingram LO (2008) Re-engineering Escherichia coli for ethanol production. Biotechnol Lett 30:2097–2103
Zhang KC, Sawaya MR, Eisenberg DS, Liao JC (2008) Expanding metabolism for biosynthesis of nonnatural alcohols. Proc Natl Acad Sci USA 105:20653–20658
Zhu MM, Skraly FA, Cameron DC (2001) Accumulation of methylglyoxal in anaerobically grown Escherichia coli and its detoxification by expression of the Pseudomonas putida glyoxalase I gene. Metab Eng 3:218–225