Evolutionary Methods for Improving the Production of Biorenewable Fuels and Chemicals

Biotechnology for Biofuel Production and Optimization

Volumn , Issue , 2016, Pages 265-290

  Jin, Tao ^a   Chen, Yingxi ^a   Jarboe, Laura R ^a  

^a Iowa State University of Science and Technology   (United States)

Author keywords

Biofuels; Directed evolution; Mutations; Orgel's rule; Reverse engineering

Indexed keywords

EID: 84966800334     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-444-63475-7.00010-8     Document Type: Chapter

References (154)

1. Bailey J.E. Toward a science of metabolic engineering. Science 1991, 252(5013):1668-1675.
2. Stephanopoulos G., Vallino J.J. Network rigidity and metabolic engineering in metabolite overproduction. Science 1991, 252(5013):1675-1681.
3. McKenna R., Nielsen D.R. Styrene biosynthesis from glucose by engineered E. coli. Metab Eng 2011, 13(5):544-554.
4. Ranganathan S., Tee T.W., Chowdhury A., Zomorrodi A.R., Yoon J.M., Fu Y., et al. An integrated computational and experimental study for overproducing fatty acids in Escherichia coli. Metab Eng 2012, 14(6):687-704.
5. Bankar S.B., Survase S.A., Ojamo H., Granstrom T. Biobutanol: the outlook of an academic and industrialist. RSC Adv 2013, 3(47):24734-24757.
6. Liang Y., Zhao X., Chi Z., Rover M., Johnston P., Brown R., et al. Utilization of acetic acid-rich pyrolytic bio-oil by microalga Chlamydomonas reinhardtii: reducing bio-oil toxicity and enhancing algal toxicity tolerance. Bioresour Technol 2013, 133:500-506.
7. Kim S.R., Ha S.-J., Wei N., Oh E.J., Jin Y.-S. Simultaneous co-fermentation of mixed sugars: a promising strategy for producing cellulosic ethanol. Trends Biotechnol 2012, 30(5):274-282.
8. Kim S.R., Park Y.-C., Jin Y.-S., Seo J.-H. Strain engineering of Saccharomyces cerevisiae for enhanced xylose metabolism. Biotechnol Adv 2013, 31(6):851-861.
9. Madhavan A., Srivastava A., Kondo A., Bisaria V.S. Bioconversion of lignocellulose-derived sugars to ethanol by engineered Saccharomyces cerevisiae. Crit Rev Biotechnol 2012, 32(1):22-48.
10. Layton D.S., Ajjarapu A., Choi D.W., Jarboe L.R. Engineering ethanologenic Escherichia coli for levoglucosan utilization. Bioresour Technol 2011, 102(17):8318-8322.
11. Bengelsdorf F.R., Straub M., Duerre P. Bacterial synthesis gas (syngas) fermentation. Environ Technol 2013, 34(13-14):1639-1651.
12. Daniell J., Koepke M., Simpson S.D. Commercial biomass syngas fermentation. Energies 2012, 5(12):5372-5417.
13. Jarboe L.R., Wen Z., Choi D., Brown R.C. Hybrid thermochemical processing: fermentation of pyrolysis-derived bio-oil. Appl Microbiol Biotechnol 2011, 91(6):1519-1523.
14. Jonsson L.J., Alriksson B., Nilvebrant N.-O. Bioconversion of lignocellulose: inhibitors and detoxification. Biotechnol Biofuels 2013, 6:13.
15. Lo T.-M., Teo W.S., Ling H., Chen B., Kang A., Chang M.W. Microbial engineering strategies to improve cell viability for biochemical production. Biotechnol Adv 2013, 31(6):903-914.
16. Mills T.Y., Sandoval N.R., Gill R.T. Cellulosic hydrolysate toxicity and tolerance mechanisms in Escherichia coli. Biotechnol Biofuels 2009, 2:26.
17. Nicolaou S.A., Gaida S.M., Papoutsakis E.T. A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: from biofuels and chemicals, to biocatalysis and bioremediation. Metab Eng 2010, 12(4):307-331.
18. Jarboe L.R., Royce L.A., Liu P. Understanding biocatalyst inhibition by carboxylic acids. Front Microbiol 2013, 4:272.
19. Dunlop M.J. Engineering microbes for tolerance to next-generation biofuels. Biotechnol Biofuels 2011, 4:32.
20. Chen Y., Ren H., Liu D., Zhao T., Shi X., Cheng H., et al. Enhancement of n-butanol production by in situ butanol removal using permeating-heating-gas stripping in acetone-butanol-ethanol fermentation. Bioresour Technol 2014, 164:276-284.
21. Hemavathy R.V., Sankaran K., Vadanasundari V., Rangabhashiyam S. in situ separation of ethanol with aqueous two-phase system and assessment of K(L)a for yeast growth in batch cultivation. Prep Biochem Biotechnol 2014, 44(6):633-644.
22. Huang H.-J., Ramaswamy S., Liu Y. Separation and purification of biobutanol during bioconversion of biomass. Sep Purif Technol 2014, 132:513-540.
23. Teh A.L., Layton D.S., Hyduke D.R., Jarboe L.R., Rollins D.K. Data mining based on principal component analysis: application to the nitric oxide response in Escherichia coli. J Stat Sci Appl 2014, 2:1-18.
24. Lopez-Garzon C.S., Straathof A.J.J. Recovery of carboxylic acids produced by fermentation. Biotechnol Adv 2014, 32(5):873-904.
25. Xu K., Xu P. Efficient calcium lactate production by fermentation coupled with crystallization-based in situ product removal. Bioresour Technol 2014, 163:33-39.
26. Chan J.K.S., Duff S.J.B. Methods for mitigation of bio-oil extract toxicity. Bioresour Technol 2010, 101(10):3755-3759.
27. Chi Z., Rover M., Jun E., Deaton M., Johnston P., Brown R.C., et al. Overliming detoxification of pyrolytic sugar syrup for direct fermentation of levoglucosan to ethanol. Bioresour Technol 2013, 150:220-227.
28. Datta S., Lin Y.J., Schell D.J., Millard C.S., Ahmad S.F., Henry M.P., et al. Removal of acidic impurities from corn stover hydrolysate liquor by resin wafer based electrodeionization. Ind Eng Chem Res 2013, 52(38):13777-13784.
29. Fakhrudin J., Setyaningsih D., Rahayuningsih M. Bioethanol production from seaweed Eucheuma cottonii by neutralization and detoxification of acidic catalyzed hydrolysate. Int J Environ Sci Dev 2014, 5(5):455-458.
30. Grzenia D.L., Wickramasinghe S.R., Schell D.J. Fermentation of reactive-membrane-extracted and ammonium-hydroxide-conditioned dilute-acid-pretreated corn stover. Appl Biochem Biotechnol 2012, 166(2):470-478.
31. Guo X., Cavka A., Jonsson L.J., Hong F. Comparison of methods for detoxification of spruce hydrolysate for bacterial cellulose production. Microb Cell Factories 2013, 12:93.
32. Hodge D.B., Andersson C., Berglund K.A., Rova U. Detoxification requirements for bioconversion of softwood dilute acid hydrolyzates to succinic acid. Enzym Microb Technol 2009, 44(5):309-316.
33. Mateo S., Roberto I.C., Sanchez S., Moya A.J. Detoxification of hemicellulosic hydrolyzate from olive tree pruning residue. Ind Crop Prod 2013, 49:196-203.
34. Rover M.R., Johnston P.A., Jin T., Smith R.G., Brown R.C., Jarboe L. Production of clean pyrolytic sugars for fermentation. Chemsuschem 2014, 7(6):1662-1668.
35. Stoutenburg R.M., Perrotta J.A., Nakas J.P. Overcoming inhibitors in a hemicellulosic hydrolysate: improving fermentability by feedstock detoxification and adaptation of Pichia stipitis. J Ind Microbiol Biotechnol 2011, 38(12):1939-1945.
36. Dunlop M.J., Dossani Z.Y., Szmidt H.L., Chu H.C., Lee T.S., Keasling J.D., et al. Engineering microbial biofuel tolerance and export using efflux pumps. Mol Syst Biol 2011, 7:487.
37. Frederix M., Huetter K., Leu J., Batth T.S., Turner W.J., Rueegg T.L., et al. Development of a native Escherichia coli induction system for ionic liquid tolerance. PLoS ONE 2014, 9(7):e101115.
38. Lennen R.M., Pfleger B.F. Modulating membrane composition alters free fatty acid tolerance in Escherichia coli. PLoS ONE 2013, 8(1):e54031.
39. Luo L.H., Seo P.-S., Seo J.-W., Heo S.-Y., Kim D.-H., Kim C.H. Improved ethanol tolerance in Escherichia coli by changing the cellular fatty acids composition through genetic manipulation. Biotechnol Lett 2009, 31(12):1867-1871.
40. Anfelt J., Hallstrom B., Nielsen J., Uhlen M., Hudson E.P. Using transcriptomics to improve butanol tolerance of Synechocystis sp strain PCC 6803. Appl Environ Microbiol 2013, 79(23):7419-7427.
41. He M.-X., Wu B., Shui Z.-X., Hu Q.-C., Wang W.-G., Tan F.-R., et al. Transcriptome profiling of Zymomonas mobilis under furfural stress. Appl Microbiol Biotechnol 2012, 95(1):189-199.
42. Brynildsen M.P., Liao J.C. An integrated network approach identifies the isobutanol response network of Escherichia coli. Mol Syst Biol 2009, 5:277.
43. Miller E.N., Jarboe L.R., Turner P.C., Pharkya P., Yomano L.P., York S.W., et al. Furfural inhibits growth by limiting sulfur assimilation in ethanologenic Escherichia coli strain LY180. Appl Environ Microbiol 2009, 75(19):6132-6141.
44. Abatemarco J., Hill A., Alper H.S. Expanding the metabolic engineering toolbox with directed evolution. Biotechnol J 2013, 8(12):1397-1410.
45. Cakar Z.P., Turanli-Yildiz B., Alkim C., Yilmaz U. Evolutionary engineering of Saccharomyces cerevisiae for improved industrially important properties. FEMS Yeast Res 2012, 12(2):171-182.
46. Conrad T.M., Lewis N.E., Palsson B.O. Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol 2011, 7:509.
47. Dragosits M., Mattanovich D. Adaptive laboratory evolution-principles and applications for biotechnology. Microb Cell Factories 2013, 12:64.
48. Furusawa C., Horinouchi T., Hirasawa T., Shimizu H. Systems Metabolic Engineering: The Creation of Microbial Cell Factories by Rational Metabolic Design and Evolution. Future Trends Biotechnol 2013, 131:1-23.
49. Kumar A., Singh S. Directed evolution: tailoring biocatalysts for industrial applications. Crit Rev Biotechnol 2013, 33(4):365-378.
50. Pal C., Papp B., Posfai G. The dawn of evolutionary genome engineering. Nat Rev Genet 2014, 15(7):504-512.
51. Portnoy V.A., Bezdan D., Zengler K. Adaptive laboratory evolution-harnessing the power of biology for metabolic engineering. Curr Opin Biotechnol 2011, 22(4):590-594.
52. Soyer O.S., O'Malley M.A. Evolutionary systems biology: what it is and why it matters. Bioessays 2013, 35(8):696-705.
53. Tee K.L., Wong T.S. Polishing the craft of genetic diversity creation in directed evolution. Biotechnol Adv 2013, 31(8):1707-1721.
54. Allewell N.M. Thematic minireview series on enzyme evolution in the post-genomic era. J Biol Chem 2012, 287(1):1-2.
55. Goldsmith M., Tawfik D.S. Directed enzyme evolution: beyond the low-hanging fruit. Curr Opin Struct Biol 2012, 22(4):406-412.
56. Jarboe L.R., Liu P., Kautharapu K.B., Ingram L.O. Optimization of enzyme parameters for fermentative production of biorenewable fuels and chemicals. Comput Struct Biotechnol J 2012, 3:e201210005.
57. Austad S.N. An experimental paradigm for the study of slowly aging organisms. Exp Gerontol 2001, 36(4-6):599-605.
58. Dennett D.C. Darwin's dangerous idea: evolution and meanings of life 1996, Touchstone, New York.
59. Wright B.E. Stress-directed adaptive mutations and evolution. Mol Microbiol 2004, 52(3):643-650.
60. Galhardo R.S., Hastings P.J., Rosenberg S.M. Mutation as a stress response and the regulation of evolvability. Crit Rev Biochem Mol Biol 2007, 42(5):399-435.
61. Foster P.L. Stress-induced mutagenesis in bacteria. Crit Rev Biochem Mol Biol 2007, 42(5):373-397.
62. Steinborn G. Uvm mutants of Escherichia coli K 12 deficient in UV mutagenesis. Mol Gen Genet MGG 1978, 165(1):87-93.
63. Ohta T., Nakamura N., Moriya M., Shirasu Y., Kada T. The SOS-function-inducing activity of chemical mutangens in Escherichia coli. Mutat Res 1984, 131(3-4):101-109.
64. Radman M. Fidelity and infidelity. Nature 2001, 413(6852):115.
65. Loeb L.A., Cheng K.C. Errors in DNA-synthesis-a source of spontaneous mutations. Mutat Res 1990, 238(3):297-304.
66. Zhang Z., Saier M.H. Transposon-mediated adaptive and directed mutations and their potential evolutionary benefits. J Mol Microbiol Biotechnol 2011, 21(1-2):59-70.
67. Turner P.C., Yomano L.P., Jarboe L.R., York S.W., Baggett C.L., Moritz B.E., et al. Optical mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements, and multiple tandem copies of the Zymomonas mobilis pdc and adhB genes. J Ind Microbiol Biotechnol 2012, 39(4):629-639.
68. Haft R.J.F., Keating D.H., Schwaegler T., Schwalbach M.S., Vinokur J., Tremaine M., et al. Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria. Proc Natl Acad Sci U S A 2014, 111(25):E2576-E2585.
69. Drake J.W., Charlesworth B., Charlesworth D., Crow J.F. Rates of spontaneous mutation. Genetics 1998, 148(4):1667-1686.
70. Foster P.L., Gudmundsson G., Trimarchi J.M., Cai H., Goodman M.F. Proofreading-defective DNA-polymerase-II increases adaptive mutation in Escherichia coli. Proc Natl Acad Sci U S A 1995, 92(17):7951-7955.
71. Weber H., Polen T., Heuveling J., Wendisch V.F., Hengge R. Genome-wide analysis of the general stress response network in Escherichia coli: sigma(S)-dependent genes, promoters, and sigma factor selectivity. J Bacteriol 2005, 187(5):1591-1603.
72. Cortazzo P., Cervenansky C., Marin M., Reiss C., Ehrlich R., Deana A. Silent mutations affect in vivo protein folding in Escherichia coli. Biochem Biophys Res Commun 2002, 293(1):537-541.
73. Deana A., Ehrlich R., Reiss C. Silent mutations in the Escherichia coli ompA leader peptide region strongly affect transcription and translation in vivo. Nucleic Acids Res 1998, 26(20):4778-4782.
74. Zhu X., Tan Z., Xu H., Chen J., Tang J., Zhang X. Metabolic evolution of two reducing equivalent-conserving pathways for high-yield succinate production in Escherichia coli. Metab Eng 2014, 24:87-96.
75. Notley-McRobb L., Ferenci T. Adaptive mgl-regulatory mutations and genetic diversity evolving in glucose-limited Escherichia coli populations. Environ Microbiol 1999, 1(1):33-43.
76. Turner P.C., Miller E.N., Jarboe L.R., Baggett C.L., Shanmugam K.T., Ingram L.O. YqhC regulates transcription of the adjacent Escherichia coli genes yqhD and dkgA that are involved in furfural tolerance. J Ind Microbiol Biotechnol 2011, 38(3):431-439.
77. Tsui H.C.T., Leung H.C.E., Winkler M.E. Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K12. Mol Microbiol 1994, 13(1):35-49.
78. Giel M., Desnoyer M., Lopilato J. A mutation in a new gene, bglJ, activates the bgl operon in Escherichia coli K-12. Genetics 1996, 143(2):627-635.
79. Kishimoto T., Iijima L., Tatsumi M., Ono N., Oyake A., Hashimoto T., et al. Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution. PLoS Genet 2010, 6(10):e1001164.
80. Wang Y., Manow R., Finan C., Wang J., Garza E., Zhou S. Adaptive evolution of nontransgenic Escherichia coli KC01 for improved ethanol tolerance and homoethanol fermentation from xylose. J Ind Microbiol Biotechnol 2011, 38(9):1371-1377.
81. Lenski R.E., Travisano M. Dynamics of adaptation and diversifcation-a 10,000-generation experiment with bacterial-populations. Proc Natl Acad Sci U S A 1994, 91(15):6808-6814.
82. Yomano L.P., York S.W., Ingram L.O. Isolation and characterization of ethanol-tolerant mutants of Escherichia coli KO11 for fuel ethanol production. J Ind Microbiol Biotechnol 1998, 20(2):132-138.
83. Reyes L.H., Winkler J., Kao K.C. Visualizing evolution in real-time method for strain engineering. Front Microbiol 2012, 3:198.
84. Huang M., McClellan M., Berman J., Kao K.C. Evolutionary dynamics of candida albicans during in vitro evolution. Eukaryot Cell 2011, 10(11):1413-1421.
85. Alper H., Stephanopoulos G. Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab Eng 2007, 9(3):258-267.
86. Alper H., Moxley J., Nevoigt E., Fink G.R., Stephanopoulos G. Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 2006, 314(5805):1565-1568.
87. Liu H.M., Yan M., Lai C.G., Xu L., Ouyang P.K. gTME for improved xylose fermentation of Saccharomyces cerevisiae. Appl Biochem Biotechnol 2010, 160(2):574-582.
88. Zhang H., Chong H., Ching C.B., Song H., Jiang R. Engineering global transcription factor cyclic AMP receptor protein of Escherichia coli for improved 1-butanol tolerance. Appl Microbiol Biotechnol 2012, 94(4):1107-1117.
89. Lynch M.D., Warnecke T., Gill R.T. SCALEs: multiscale analysis of library enrichment. Nat Methods 2007, 4(1):87-93.
90. Sandoval N.R., Mills T.Y., Zhang M., Gill R.T. Elucidating acetate tolerance in E. coli using a genome-wide approach. Metab Eng 2011, 13(2):214-224.
91. Singh A., Lynch M.D., Gill R.T. Genes restoring redox balance in fermentation-deficient E. coli NZN111. Metab Eng 2009, 11(6):347-354.
92. Yuan Y., Du J., Zhao H. Customized optimization of metabolic pathways by combinatorial transcriptional engineering. Methods Mol Biol (Clifton, NJ) 2013, 985:177-209.
93. Sandoval N.R., Kim J.Y.H., Glebes T.Y., Reeder P.J., Aucoin H.R., Warner J.R., et al. Strategy for directing combinatorial genome engineering in Escherichia coli. Proc Natl Acad Sci U S A 2012, 109(26):10540-10545.
94. Garcia V., Pakkila J., Ojamo H., Muurinen E., Keiski R.L. Challenges in biobutanol production: how to improve the efficiency?. Renew Sustain Energy Rev 2011, 15(2):964-980.
95. Ezeji T., Milne C., Price N.D., Blaschek H.P. Achievements and perspectives to overcome the poor solvent resistance in acetone and butanol-producing microorganisms. Appl Microbiol Biotechnol 2010, 85(6):1697-1712.
96. Warnecke T., Gill R.T. Organic acid toxicity, tolerance, and production in Escherichia coli biorefining applications. Microb Cell Factories 2005, 4:25.
97. Ingram L.O., Buttke T.M. Effects of alcohols on microorganisms. Adv Microb Physiol 1984, 25:253-300.
98. Ramos J.L., Duque E., Gallegos M.T., Godoy P., Ramos-Gonzalez M.I., Rojas A., et al. Mechanisms of solvent tolerance in gram-negative bacteria. Annu Rev Microbiol 2002, 56:743-768.
99. Klinke H.B., Thomsen A.B., Ahring B.K. Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomass. Appl Microbiol Biotechnol 2004, 66(1):10-26.
100. McKenna R., Moya L., McDaniel M., Nielsen D.R. Comparing in situ removal strategies for improving styrene bioproduction. Bioprocess Biosyst Eng 2014, 38:1-10.
101. Roffler S.R., Blanch H.W., Wilke C.R. In situ extractive fermentation of acetone and butanol. Biotechnol Bioeng 1988, 31(2):135-143.
102. Inokuma K., Liao J.C., Okamoto M., Hanai T. Improvement of isopropanol production by metabolically engineered Escherichia coli using gas stripping. J Biosci Bioeng 2010, 110(6):696-701.
103. Jarboe L.R., Liu P., Royce L.A. Engineering inhibitor tolerance for the production of biorenewable fuels and chemicals. Curr Opin Chem Eng 2011, 1(1):38-42.
104. Atsumi S., Wu T.-Y., Machado I.M.P., Huang W.-C., Chen P.-Y., Pellegrini M., et al. Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol Syst Biol 2010, 6:449.
105. Ward RJ, McConnell CA, Minty JJ, Rouillard J-M, Lin F, Chen Y, et al. Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli. ArrayExpress Archive; 2012.
106. Ghiaci P., Norbeck J., Larsson C. Physiological adaptations of Saccharomyces cerevisiae evolved for improved butanol tolerance. Biotechnol Biofuels 2013, 6:101.
107. Ni Y., Song L., Qian X., Sun Z. Proteomic analysis of Pseudomonas putida reveals an organic solvent tolerance-related gene mmsB. PLoS ONE 2013, 8(2):e55858.
108. Miller E.N., Jarboe L.R., Yomano L.P., York S.W., Shanmugam K.T., Ingram L.O. Silencing of NADPH-dependent oxidoreductase genes (yqhD and dkgA) in furfural-resistant ethanologenic Escherichia coli. Appl Environ Microbiol 2009, 75(13):4315-4323.
109. Miller E.N., Turner P.C., Jarboe L.R., Ingram L.O. Genetic changes that increase 5-hydroxymethyl furfural resistance in ethanol-producing Escherichia coli LY180. Biotechnol Lett 2010, 32(5):661-667.
110. Koppram R., Albers E., Olsson L. Evolutionary engineering strategies to enhance tolerance of xylose utilizing recombinant yeast to inhibitors derived from spruce biomass. Biotechnol Biofuels 2012, 5:32.
111. Isken S., de Bont J.A.M. Bacteria tolerant to organic solvents. Extremophiles 1998, 2(3):229-238.
112. Sardessai Y., Bhosle S. Tolerance of bacteria to organic solvents. Res Microbiol 2002, 153(5):263-268.
113. Shah A.A., Wang C., Chung Y.-R., Kim J.-Y., Choi E.-S., Kim S.-W. Enhancement of geraniol resistance of Escherichia coli by MarA overexpression. J Biosci Bioeng 2013, 115(3):253-258.
114. Zingaro K.A., Papoutsakis E.T. GroESL overexpression imparts Escherichia coli tolerance to i-, n-, and 2-butanol, 1,2,4-butanetriol and ethanol with complex and unpredictable patterns. Metab Eng 2013, 15:196-205.
115. Ohta K., Beall D.S., Mejia J.P., Shanmugam K.T., Ingram L.O. Genetic improvement of Escherichia coli for ethanol-production-chromosomal integration of Zymomonas mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase-II. Appl Environ Microbiol 1991, 57(4):893-900.
116. Trinh C.T., Srienc F. Metabolic engineering of Escherichia coli for efficient conversion of glycerol to ethanol. Appl Environ Microbiol 2009, 75(21):6696-6705.
117. Demeke M.M., Dietz H., Li Y., Foulquie-Moreno M.R., Mutturi S., Deprez S., et al. Development of a d-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering. Biotechnol Biofuels 2013, 6:89.
118. Guimaraes P.M.R., Francois J., Parrou J.L., Teixeira J.A., Domingues L. Adaptive evolution of a lactose-consuming Saccharomyces cerevisiae recombinant. Appl Environ Microbiol 2008, 74(6):1748-1756.
119. Zhou S.D., Causey T.B., Hasona A., Shanmugam K.T., Ingram L.O. Production of optically pure d-lactic acid in mineral salts medium by metabolically engineered Escherichia coli W3110. Appl Environ Microbiol 2003, 69(1):399-407.
120. Zhou S., Yomano L.P., Shanmugam K.T., Ingram L.O. Fermentation of 10% (w/v) sugar to d(-)-lactate by engineered Escherichia coli B. Biotechnol Lett 2005, 27(23-24):1891-1896.
121. Zhou S., Shanmugam K.T., Yomano L.P., Grabar T.B., Ingram L.O. Fermentation of 12% (w/v) glucose to 1.2M lactate by Escherichia coli strain SZ194 using mineral salts medium. Biotechnol Lett 2006, 28(9):663-670.
122. Zhou S.D., Shanmugam K.T., Ingram L.O. Functional replacement of the Escherichia colid-(-)-lactate dehydrogenase gene (ldhA) with the l-(+)-lactate dehydrogenase gene (ldhL) from Pediococcus acidilactici. Appl Environ Microbiol 2003, 69(4):2237-2244.
123. Jantama K., Haupt M.J., Svoronos S.A., Zhang X., Moore J.C., Shanmugam K.T., et al. Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate. Biotechnol Bioeng 2008, 99(5):1140-1153.
124. Zhang X., Jantama K., Moore J.C., Shanmugam K.T., Ingram L.O. Production of L-alanine by metabolically engineered Escherichia coli. Appl Microbiol Biotechnol 2007, 77(2):355-366.
125. Cobb R.E., Si T., Zhao H. Directed evolution: an evolving and enabling synthetic biology tool. Curr Opin Chem Biol 2012, 16(3-4):285-291.
126. Smith K.M., Liao J.C. An evolutionary strategy for isobutanol production strain development in Escherichia coli. Metab Eng 2011, 13(6):674-681.
127. Kabara J.J., Marshall D.L. Medium-chain fatty acids and esters. Antimicrobials in food 2010, 327-360. BocaRaton, CRC Press. 3rd ed.
128. Russell A.D. Mechanisms of bacterial-resistance to non-antibiotics- food-additives and food and pharmaceutical preservatives. J Appl Bacteriol 1991, 71(3):191-201.
129. Lennen R.M., Kruziki M.A., Kumar K., Zinkel R.A., Burnum K.E., Lipton M.S., et al. Membrane stresses induced by overproduction of free fatty acids in Escherichia coli. Appl Environ Microbiol 2011, 77(22):8114-8128.
130. Royce L.A., Liu P., Stebbins M.J., Hanson B.C., Jarboe L.R. The damaging effects of short chain fatty acids on Escherichia coli membranes. Appl Microbiol Biotechnol 2013, 97(18):8317-8327.
131. Sherkhanov S., Korman T.P., Bowie J.U. Improving the tolerance of Escherichia coli to medium-chain fatty acid production. Metab Eng 2014, 25:1-7.
132. Royce L.A., Yoon J.M., Chen Y., Rickenbach E., Shanks J.V., Jarboe L.R. Evolution for exogenous octanoic acid tolerance improves carboxylic acid production and membrane integrity. Metab Eng 2015, 29:180-188.
133. Stephanopoulos G. Challenges in engineering microbes for biofuels production. Science 2007, 315(5813):801-804.
134. Jorgensen H., Kristensen J.B., Felby C. Enzymatic conversion of lignocellulose into fermentable sugars: challenges and opportunities. Biofuels Bioprod Bior 2007, 1(2):119-134.
135. Almeida J.R.M., Modig T., Petersson A., Hahn-Hagerdal B., Liden G., Gorwa-Grauslund M.F. Increased tolerance and conversion of inhibitors in lignocellulosic hydrolysates by Saccharomyces cerevisiae. J Chem Technol Biotechnol 2007, 82(4):340-349.
136. Sanchez B., Bautista J. Effects of furfural and 5-hydroxymethylfurfural on the fermentation of Saccharomyces cerevisiae and biomass production from Candida guilliermondii. Enzym Microb Technol 1988, 10(5):315-318.
137. Zaldivar J., Ingram L.O. Effect of organic acids on the growth and fermentation of ethanologenic Escherichia coli LY01. Biotechnol Bioeng 1999, 66(4):203-210.
138. Zaldivar J., Martinez A., Ingram L.O. Effect of selected aldehydes on the growth and fermentation of ethanologenic Escherichia coli. Biotechnol Bioeng 1999, 65(1):24-33.
139. Glebes T.Y., Sandoval N.R., Reeder P.J., Schilling K.D., Zhang M., Gill R.T. Genome-wide mapping of furfural tolerance genes in Escherichia coli. PLoS ONE 2014, 9(1). e87540.
140. Glebes T.Y., Sandoval N.R., Gillis J.H., Gill R.T. Comparison of genome-wide selection strategies to identify furfural tolerance genes in Escherichia coli. Biotechnol Bioeng 2014, 112:129-140.
141. Luhe A.L., Lim C.Y., Gerken H., Wu J., Zhao H. Furfural and HMF tolerance in Escherichia coli ΔacrR regulatory mutants. Biotechnol Appl Biochem 2014, 62:32-36.
142. Miller E.N., Jarboe L.R., Turner P.C., Pharkya P., Yomano L.P., York S.W., et al. Furfural inhibits growth by limiting sulfur assimilation in ethanologenic Escherichia coli strain LY180. Appl Environ Microbiol 2009, 75(19):6132-6141.
143. Wang X., Miller E.N., Yomano L.P., Zhang X., Shanmugam K.T., Ingram L.O. Increased furfural tolerance due to overexpression of NADH-dependent oxidoreductase FucO in Escherichia coli strains engineered for the production of ethanol and lactate. Appl Environ Microbiol 2011, 77(15):5132-5140.
144. Geddes R.D., Wang X., Yomano L.P., Miller E.N., Zheng H., Shanmugam K.T., et al. Polyamine transporters and polyamines increase furfural tolerance during xylose fermentation with ethanologenic Escherichia coli strain LY180. Appl Environ Microbiol 2014, 80(19):5955-5964. p. AEM. 01913-14.
145. Chong H., Geng H., Zhang H., Song H., Huang L., Jiang R. Enhancing E. coli isobutanol tolerance through engineering its global transcription factor cAMP Receptor Protein (CRP). Biotechnol Bioeng 2014, 111(4):700-708.
146. Reyes L.H., Almario M.P., Winkler J., Orozco M.M., Kao K.C. Visualizing evolution in real time to determine the molecular mechanisms of n-butanol tolerance in Escherichia coli. Metab Eng 2012, 14(5):579-590.
147. Almario M.P., Reyes L.H., Kao K.C. Evolutionary engineering of saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass. Biotechnol Bioeng 2013, 110(10):2616-2623.
148. Fong S.S., Burgard A.P., Herring C.D., Knight E.M., Blattner F.R., Maranas C.D., et al. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng 2005, 91(5):643-648.
149. Zhang X., Jantama K., Moore J.C., Jarboe L.R., Shanmugam K.T., Ingram L.O. Metabolic evolution of energy-conserving pathways for succinate production in Escherichia coli. Proc Natl Acad Sci U S A 2009, 106(48):20180-20185.
150. Royce L., Boggess E., Jin T., Dickerson J., Jarboe L. Identification of mutations in evolved bacterial genomes. Methods Mol Biol (Clifton, NJ) 2013, 985:p. 249-p. 267.
151. Jarboe L.R. YqhD: a broad-substrate range aldehyde reductase with various applications in production of biorenewable fuels and chemicals. Appl Microbiol Biotechnol 2011, 89(2):249-257.
152. Conrad T.M., Joyce A.R., Applebee M.K., Barrett C.L., Xie B., Gao Y., et al. Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol 2009, 10(10):R118.
153. Unrean P., Srienc F. Metabolic networks evolve towards states of maximum entropy production. Metab Eng 2011, 13(6):666-673.
154. Unrean P., Srienc F. Predicting the adaptive evolution of Thermoanaerobacterium saccharolyticum. J Biotechnol 2012, 158(4):259-266.