Biofuels and bio-based chemicals from lignocellulose: metabolic engineering strategies in strain development

Biotechnology Letters

Volumn 38, Issue 2, 2016, Pages 213-221

  Chen, Rachel ^a   Dou, Jennifer ^b  

^a Georgia Institute of Technology   (United States)

^b RICE UNIVERSITY   (United States)

Author keywords

Catabolite repression; Inhibitor tolerance; Laboratory evolution; Lignocellulose biomass; Metabolic engineering; Microbial consortium; Strain development; Xylose metabolism

Indexed keywords

BIOLOGY; CELLULOSE; GENE EXPRESSION; GENES; LIGNIN; METABOLISM; XYLOSE;

BIO-BASED CHEMICALS; CATABOLITE REPRESSION; COMMODITY PRODUCTS; EVOLUTIONARY ENGINEERING; INHIBITOR TOLERANCES; MICROBIAL CONSORTIA; STRAIN DEVELOPMENT; SUSTAINABLE TECHNOLOGY;

METABOLIC ENGINEERING;

BIOFUEL; LIGNIN; LIGNOCELLULOSE;

METABOLIC ENGINEERING; METABOLISM; MICROBIOLOGY; PROCEDURES;

BIOFUELS; INDUSTRIAL MICROBIOLOGY; LIGNIN; METABOLIC ENGINEERING;

EID: 84958780549     PISSN: 01415492     EISSN: 15736776     Source Type: Journal    
DOI: 10.1007/s10529-015-1976-0     Document Type: Review

References (52)

1. Agrawal M, Mao Z, Chen R (2011) Adaptation yields a highly efficient xylose-fermenting Zymomonas mobilis strain. Biotechnol Bioeng 108:777–805
2. Almario MP, Reyes LH, Kao KC (2013) Evolutionary engineering of Saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass. Biotechnol Bioeng 110:2616–2623
3. Bae YH, Yang KH, Jin YS, Seo JH (2014) Molecular cloning and expression of fungal cellobiose transporters and β-glucosidases conferring efficient cellobiose fermentation in Saccharomyces cerevisiae. J Biotechnol 169:34–41
4. Bokinsky G, Peralta-Yahya PP, George A, Holmes BM, Steen EJ, Dietrich J, Lee TS, Tullman-Ercek D, Voigt CA, Simmons BA, Keasling JD (2011) Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. Proc Natl Acad Sci USA 108:19949–19954
5. Bootten TJ, Joblin KN, McArdle BH, Harris PJ (2011) Degradation of lignified secondary cell walls of lucerne (Medicago sativa L.) by rumen fungi growing in methanogenic co-culture. J Appl Microbiol 111:1086–1096
6. Cheirsilp B, Suwannarat W, Niyomdecha R (2011) Mixed culture of oleaginous yeast Rhodotorula glutinis and microalga Chlorella vulgaris for lipid production from industrial wastes and its use as biodiesel feedstock. Nat Biotechnol 28:362–368
7. Chen R (2015) A paradigm shift in biomass technology from complete to partial cellulose hydrolysis: lessons learned from nature. Bioengineered 6:69–72
8. Dunn KL, Rao CV (2015) Expression of a xylose-specific transporter improves ethanol production by metabolically engineered Zymomonas mobilis. Appl Microbiol Biotechnol 98:6897–6905
9. Frederix M, Hutter K, Leu J, Batth TS, Turner WJ, Ruegg TL, Blanch HW, Simmons BA, Keasling JD, Thelen MP, Dunlop MJ, Petzold CJ, Mukhopadhyay A (2014) Development of a native Escherichia coli induction system for ionic liquid tolerance. PLoS One 9:e101115
10. Gaida SM, Al-Hinai MA, Indurthi DC, Nicolaou SA, Papoutsakis ET (2013) Synthetic tolerance: three noncoding small RNAs, DsrA, ArcZ and RprA, acting supra-additively against acid stress. Nucleic Acid Res 41:8726–8737
11. Galazka JM, Tian C, Beeson WT, Martinez B, Glass NL, Cate JH (2010) Cellodextrin transport in yeast for improved biofuel production. Science 330:84–86
12. Geng H, Jiang R (2015) cAMP receptor protein (CRP)-mediated resistance/tolerance in bacteria: mechanism and utilization in biotechnology. Appl Microbiol Biotechnol 99:4533–4543
13. Ha SJ, Wei Q, Kim SR, Galazka JM, Cate JH, Jin YS (2011) Cofermentation of cellobiose and galactose by an engineered Saccharomyces cerevisiae strain. Appl Environ Microbiol 77:5822–5825
14. Ha SJ, Kim SR, Kim H, Du J, Cate JH, Jin YS (2013) Continuous co-fermentation of cellobiose and xylose by engineered Saccharomyces cerevisiae. Bioresour Technol 149:525–531
15. Hanly TJ, Urello M, Henson MA (2012) Dynamic flux balance modeling of S. cerevisiae and E. coli co-cultures for efficient consumption of glucose/xylose mixtures. Appl Microbiol Biotechnol 93:2529–2541
16. Hou J, Suo F, Wang C, Li X, Shen Y, Bao X (2014) Fine-tuning of NADH oxidase decreases byproduct accumulation in respiration deficient xylose metabolic Saccharomyces cerevisiae. BMC Biotechnol 14:13
17. Kaczmaryk D, Anfelt J, Sarnegrim A, Hudson EP (2014) Overexpression of sigma factor SigB improves temperature and butanol tolerance of Synechocystis sp. PCC6803. J Biotechnol 182–183:54–60
18. Kang A, Chang MW (2012) Identification and reconstitution of genetic regulatory networks for improved microbial tolerance to isooctane. Mol BioSyst 8:1350–1358
19. Kerner A, Park J, Williams A, Lin XN (2012) A programmable Escherichia coli consortium via tunable symbiosis. PLoS One 7:e34032
20. Kim H, Lee WH, Galazka JM, Cate JH, Jin YS (2014) Analysis of cellodextrin transporters from Neurospora crassa in Saccharomyces cerevisiae for cellobiose fermentation. Appl Microbiol Biotechnol 98:1087–1094
21. Kim SK, Jin YS, Choi IG, Park YC, Seo JH (2015) Enhanced tolerance of Saccharomyces cerevisiae to multiple lignocellulose-derived inhibitors through modulation of spermidine contents. Metab Eng 29:46–55
22. Kurosawa K, Debono AC, Sinskey AJ (2015) Lignocellulose-derived inhibitors improve lipid extraction from wet Rhodococcus opacus cells. Bioresour Technol 193:206–212
23. Lane S, Zhang S, Wei N, Rao C, Jin YS (2015) Development and physiological characterization of cellobiose-consuming Yarrowia lipolytica. Biotechnol Bioeng 112(5):1012–1022
24. le Bui M, Lee JY, Geraldi A, Rahman Z, Lee JH, Kim SC (2015) Improved n-butanol tolerance in Escherichia coli by controlling membrane related functions. J Biotechnol 204:33–44
25. Lee WH, Nan H, Kim HJ, Jin YS (2013) Simultaneous saccharification and fermentation by engineered Saccharomyces cerevisiae without supplementing extracellular β-glucosidase. J Biotechnol 167:316–322
26. Lee SM, Jellison T, Alper HS (2014) Systematic and evolutionary engineering of a xylose isomerase-based pathway in Saccharomyces cerevisiae for efficient conversion yields. Biotechnol Biofuels 7:122
27. Lennen RM, Pfleger BF (2013) Modulating membrane composition alters free fatty acid tolerance in Escherichia coli. PLoS One 8:e54031
28. Li L, Li K, Wang Y, Chen C, Xu Y, Zhang L, Han B, Gao C, Tao F, Ma C, Xu P (2015a) Metabolic engineering of Enterobacter cloacae for high-yield production of enantiopure (2R,3R)-2,3-butanediol from lignocellulose-derived sugars. Metab Eng 28:19–27
29. Li P, Sun H, Chen Z, Li Y, Zhu T (2015b) Construction of efficient xylose utilizing Pichia pastoris for industrial enzyme production. Microb Cell Fact 14:22
30. Miller EN, Turner PC, Jarboe LR, Ingram LO (2010) Genetic changes that increase 5-hydroxymethyl furfural resistance in ethanol-producing Escherichia coli LY180. Biotechnol Lett 32(5):661–667
31. Minty JJ, Singer ME, Scholz SA, Bae CH, Ahn JH, Foster CE, Liao JC, Lin XN (2013) Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc Natl Acad Sci USA 110:14592–14597
32. Morais S, Shterzer N, Grinberg IR, Mathiesen G, Eijsink VG, Axelsson L, Lamed R, Bayer EA, Mizrahi I (2013) Establishment of a simple Lactobacillus plantarum cell consortium for cellulase-xylanase synergistic interactions. Appl Environ Microbiol 79:5242–5249
33. Oide S, Gunji W, Moteki Y, Yamamoto S, Suda M, Jojima T, Yukawa H, Inui M (2015) Thermal and solvent stress cross-tolerance conferred to Corynebacterium glutamicum by adaptive laboratory evolution. Appl Environ Microbiol 81(7):2284–2298
34. Pereira FB, Teixeira MC, Mira NP, Sa-Correia I, Domingues L (2014) Genome-wide screening of Saccharomyces cerevisiae genes required to foster tolerance towards industrial wheat straw hydrolysates. J Ind Microbiol Biotechnol 41:1753–1756
35. Radek AK, Krumbach J, Gatgens V, Wendisch F, Wiechert W, Bott M, Noack S, Marienhagen J (2014) Engineering of Corynebacterium glutamicum for minimized carbon loss during utilization of d-xylose containing substrates. J Biotechnol 192A:156–160
36. Rutter C, Chen R (2014) Improved cellobiose utilization in E. coli by including both hydrolysis and phosphorolysis mechanisms. Biotechnol Lett 36:301–307
37. Rutter C, Mao Z, Chen R (2013) Periplasmic expression of a Saccharophagus cellodextrinase enables E. coli to ferment cellodextrin. Appl Microbiol Biotechnol 97:8129–8138
38. Salimi F, Mahadevan R (2013) Characterizing metabolic interactions in a Clostridial co-culture for consolidated bioprocessing. BMC Biotechnol 13:95
39. Sekar R, Shin HD, Chen R (2012) Engineering Escherichia coli cells for cellobiose assimilation through a phosphorolytic mechanism. Appl Environ Microbiol 78:1611–1614
40. Shin HD, McClendon S, Vo T, Chen RR (2010) Escherichia coli binary culture engineered for direct fermentation of hemicellulose to a biofuel. Appl Environ Microbiol 76:8150–8159
41. Shin HD, Yoon SH, Wu J, Rutter C, Kim SW, Chen RR (2012) High-yield production of meso-2,3-butanediol from cellodextrin by engineered E. coli biocatalysts. Bioresour Technol 118:367–373
42. Shin HD, Wu J, Chen R (2014) Comparative engineering of Escherichia coli for cellobiose utilization: hydrolysis versus phosphorolysis. Metab Eng 24:9–17
43. Vargus-Tah A, Martinex LM, Hernandex-Chavex G, Rocha M, Martinex A, Bolivar F, Gosset G (2015) Production of cinnamic and p-hydroxycinnamic acid from sugar mixtures with engineered Escherichia coli. Micro Cell Fact 14:6
44. Villela L, de Araujo VP, Paredes R, Bon EP, Torres FA, Neves BC, Eleutherio EC (2015) Enhanced xylose fermentation and ethanol production by engineered Saccharomyces cerevisiae strain. AMB Express 5:16
45. Wang X, Yomano LP, Lee JY, York SW, Zhen H, Mullinnix MT, Shanmugam KT, Ingram LO (2013a) Engineering furfural tolerance in Escherichia coli improves the fermentation of lignocellulosic sugars into renewable chemicals. Proc Natl Acad Sci USA 110:4021–4026
46. Wang X, Li BZ, Ding MZ, Zhang WW, Yuan YJ (2013b) Metabolomic analysis reveals key metabolites related to the rapid adaptation of Saccharomyce cerevisiae to multiple inhibitors of furfural, acetic acid, and phenol. OMICS 17:150–159
47. Wang C, Bao X, Li Y, Jiao C, Hou J, Zhang Q, Zhang W, Liu W, Shen Y (2015) Cloning and characterization of heterologous transporters in Saccharomyces cerevisiae and identification of important amino acids for xylose utilization. Metab Eng 30:79–88
48. Wu Y, Yang Y, Ren C, Yang C, Yang S, Gu Y, Jiang W (2015) Molecular modulation of pleiotropic regulator CcpA for glucose and xylose coutilization by solvent-producing Clostridium acetobutylicum. Metab Eng 28:169–179
49. Yang S, Pelletier DA, Lu TY, Brown SD (2010) The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors. BMC Microbiol 10:135
50. Yu L, Xu M, Tang IC, Yang ST (2015) Metabolic engineering of Clostridium tyrobutyricum for n-butanol production through co-utilization of glucose and xylose. Biotechnol Bioeng 112:2134–2141
51. Zhang J, Hu B (2012) A novel method to harvest microalgae via co-culture of filamentous fungi to form cell pellets. Bioresour Technol 114:529–535
52. Zhang B, Li N, Wang N, Tang YJ, Chen T, Zhao X (2015) Inverse metabolic engineering of Bacillus subtilis for xylose utilization based on adaptive evolution and whole-genome sequencing. Appl Microbio Biotechnol 99:885–896