Abstract
Sustainable development of the world’s economy would require a paradigm shift from the current fossil fuel-based energy and chemical production model to that of a renewable supply-based model, where lignocellulosic biorefinery has a great potential. In this chapter, we review and discuss the current knowledge and progress on biorefinery of lignocellulosics for the production of biofuels and biochemicals, along with the socio-economic and technical problems this industry has to tackle. The chemical, microbiological, and technical aspects for the enzymatic conversion of lignocellulose to the platform sugars were examined in detail. In particular, we addressed the cost reduction issue of lignocellulose degradation, which is otherwise a major impediment of the biorefinery industry. We further discussed the biotechnological and bioengineering efforts to convert lignocellulosic sugars to biofuels and biochemicals. These include the predominant biofuel ethanol, advanced biofuels such as butanol with better compatibility to current infrastructure, and bulk and fine chemicals such as organic acids and isoprenoids. Various metabolic engineering strategies were also summarized to enable further development of microbial strains for biofuel and biochemical production. We believe that the renewable lignocellulosic biofuel and biochemical industry are critical contributors to a sustainable future that is independent of the fossil fuels and their derived products.
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References
Durand JD (1977) Historical estimates of world population: an evaluation. Popul Dev Rev 3(3):253–296
Riley JC (2005) Estimates of regional and global life expectancy, 1800–2001. Popul Dev Rev 31(3):537–543
Bowman DM, Balch JK, Artaxo P, Bond WJ, Carlson JM, Cochrane MA, D’Antonio CM, Defries RS, Doyle JC, Harrison SP, Johnston FH, Keeley JE, Krawchuk MA, Kull CA, Marston JB, Moritz MA, Prentice IC, Roos CI, Scott AC, Swetnam TW, van der Werf GR, Pyne SJ (2009) Fire in the Earth system. Science 324(5926):481–484
Conti J, Holtberg P, Beamon JA, Napolitano S, Schaal AM, Turnure JT, Westfall L (2013) International energy outlook 2013. U.S. Energy Information Administration, Washington, DC
Shafiee S, Topal E (2009) When will fossil fuel reserves be diminished? Energy Policy 37:181–189
Demain AL, Newcomb M, Wu JH (2005) Cellulase, clostridia, and ethanol. Microbiol Mol Biol Rev 69(1):124–154
Xie G, Wang X, Ren L (2010) China’s crop residues resources evaluation. Chin J Biotechnol 26(7):855–863
Zhu C, Zhang H, Xiao R, Chen Y, Liu D, Du F, Ying H, Ouyang P (2015) Research progress in catalytic valorization of lignocellulose. Sci Chin Chem 45(5):454–478
Plan for comprehensive utilization of agricultural straws in the 12th Five-Year Plan (2011)
Parikka M (2004) Global biomass fuel resources. Biomass Bioenergy 27:613–620
Sorrell S, Speirs J, Bentley R, Brandt A, Miller R (2010) Global oil depletion: a review of the evidence. Energy Policy 38:5290–5295
Bornscheuer U, Buchholz K, Seibel J (2014) Enzymatic degradation of (ligno)cellulose. Angew Chem Int Ed Engl 53(41):10876–10893
Wang M, Liu K, Dai L, Zhang J, Fang X (2013) The structural and biochemical basis for cellulose biodegradation. J Chem Technol Biotechnol 88:491–500
Sánchez C (2009) Lignocellulosic residues: biodegradation and bioconversion by fungi. Biotechnol Adv 27(2):185–194
Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66(3):506–577
Peng F, Peng P, Xu F, Sun RC (2012) Fractional purification and bioconversion of hemicelluloses. Biotechnol Adv 30(4):879–903
Zeng Y, Zhao S, Yang S, Ding SY (2014) Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels. Curr Opin Biotechnol 27:38–45
Voxeur A, Wang Y, Sibout R (2015) Lignification: different mechanisms for a versatile polymer. Curr Opin Plant Biol 23:83–90
Iiyama K, Lam T, Stone BA (1994) Covalent cross-links in the cell wall. Plant Physiol 104(2):315–320
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(5813):804–807
Wang M, Li Z, Fang X, Wang L, Qu Y (2012) Cellulolytic enzyme production and enzymatic hydrolysis for second-generation bioethanol production. Adv Biochem Eng Biotechnol 128:1–24
Shallom D, Shoham Y (2003) Microbial hemicellulases. Curr Opin Microbiol 6(3):219–228
Brown ME, Chang MC (2014) Exploring bacterial lignin degradation. Curr Opin Chem Biol 19:1–7
Pollegioni L, Tonin F, Rosini E (2015) Lignin-degrading enzymes. FEBS J 282(7):1190–1213
Divne C, Stahlberg J, Reinikainen T, Ruohonen L, Pettersson G, Knowles JK, Teeri TT, Jones TA (1994) The three-dimensional crystal structure of the catalytic core of cellobiohydrolase I from Trichoderma reesei. Science 265(5171):524–528
Davies GJ, Brzozowski AM, Dauter M, Varrot A, Schülein M (2000) Structure and function of Humicola insolens family 6 cellulases: structure of the endoglucanase, Cel6B, at 1.6 Å resolution. Biochem J 348(Pt 1):201–207
Karkehabadi S, Helmich KE, Kaper T, Hansson H, Mikkelsen NE, Gudmundsson M, Piens K, Fujdala M, Banerjee G, Scott-Craig JS, Walton JD, Phillips GN Jr, Sandgren M (2014) Biochemical characterization and crystal structures of a fungal family 3 β-glucosidase, Cel3A from Hypocrea jecorina. J Biol Chem 289(45):31624–31637
Törrönen A, Rouvinen J (1995) Structural comparison of two major endo-1,4-xylanases from Trichoderma reesei. Biochemistry 34(3):847–856
Yang JK, Yoon HJ, Ahn HJ, Lee BI, Pedelacq JD, Liong EC, Berendzen J, Laivenieks M, Vieille C, Zeikus GJ, Vocadlo DJ, Withers SG, Suh SW (2004) Crystal structure of β-d-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase. J Mol Biol 335(1):155–165
Golan G, Shallom D, Teplitsky A, Zaide G, Shulami S, Baasov T, Stojanoff V, Thompson A, Shoham Y, Shoham G (2004) Crystal structures of Geobacillus stearothermophilus α-glucuronidase complexed with its substrate and products: mechanistic implications. J Biol Chem 279(4):3014–3024
Taylor EJ, Gloster TM, Turkenburg JP, Vincent F, Brzozowski AM, Dupont C, Shareck F, Centeno MS, Prates JA, Puchart V, Ferreira LM, Fontes CM, Biely P, Davies GJ (2006) Structure and activity of two metal ion-dependent acetylxylan esterases involved in plant cell wall degradation reveals a close similarity to peptidoglycan deacetylases. J Biol Chem 281(16):10968–10975
Hermoso JA, Sanz-Aparicio J, Molina R, Juge N, Gonzalez R, Faulds CB (2004) The crystal structure of feruloyl esterase A from Aspergillus niger suggests evolutive functional convergence in feruloyl esterase family. J Mol Biol 338(3):495–506
Miki Y, Calviño FR, Pogni R, Giansanti S, Ruiz-Dueñas FJ, Martinez MJ, Basosi R, Romero A, Martinez AT (2011) Crystallographic, kinetic, and spectroscopic study of the first ligninolytic peroxidase presenting a catalytic tyrosine. J Biol Chem 286(17):15525–15534
Osipov E, Polyakov K, Kittl R, Shleev S, Dorovatovsky P, Tikhonova T, Hann S, Ludwig R, Popov V (2014) Effect of the L499 M mutation of the ascomycetous Botrytis aclada laccase on redox potential and catalytic properties. Acta Crystallogr D Biol Crystallogr 70(Pt 11):2913–2923
Li XL, Špániková S, de Vries RP, Biely P (2007) Identification of genes encoding microbial glucuronoyl esterases. FEBS Lett 581(21):4029–4035
Quinlan RJ, Sweeney MD, Lo Leggio L, Otten H, Poulsen JC, Johansen KS, Krogh KB, Jorgensen CI, Tovborg M, Anthonsen A, Tryfona T, Walter CP, Dupree P, Xu F, Davies GJ, Walton PH (2011) Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components. Proc Natl Acad Sci USA 108(37):15079–15084
Harris PV, Welner D, McFarland KC, Re E, Navarro Poulsen JC, Brown K, Salbo R, Ding H, Vlasenko E, Merino S, Xu F, Cherry J, Larsen S, Lo Leggio L (2010) Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: structure and function of a large, enigmatic family. Biochemistry 49(15):3305–3316
Langston JA, Shaghasi T, Abbate E, Xu F, Vlasenko E, Sweeney MD (2011) Oxidoreductive cellulose depolymerization by the enzymes cellobiose dehydrogenase and glycoside hydrolase 61. Appl Environ Microbiol 77(19):7007–7015
Hemsworth GR, Henrissat B, Davies GJ, Walton PH (2014) Discovery and characterization of a new family of lytic polysaccharide monooxygenases. Nat Chem Biol 10(2):122–126
Cherry JR, Fidantsef AL (2003) Directed evolution of industrial enzymes: an update. Curr Opin Biotechnol 14(4):438–443
Li Z, Yao G, Wu R, Gao L, Kan Q, Liu M, Yang P, Liu G, Qin Y, Song X, Zhong Y, Fang X, Qu Y (2015) Synergistic and dose-controlled regulation of cellulase gene expression in Penicillium oxalicum. PLoS Genet 11(9):e1005509
van Zyl WH, Lynd LR, den Hann R, McBride JE (2007) Consolidated bioprocessing for bioethanol production using Saccharomyces cerevisiae. Adv Biochem Eng Biot 108:205–235
Olson DG, McBride JE, Shaw AJ, Lynd LR (2012) Recent progress in consolidated bioprocessing. Curr Opin Biotechnol 23(3):396–405
Biswas R, Zheng T, Olson DG, Lynd LR, Guss AM (2015) Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum. Biotechnol Biofuels 8:20
Shen Y, Jarboe L, Brown R, Wen Z (2015) A thermochemical-biochemical hybrid processing of lignocellulosic biomass for producing fuels and chemicals. Biotechnol Adv 33(8):1799–1813
Martin ME, Richter H, Saha S, Angenent LT (2015) Traits of selected Clostridium strains for syngas fermentation to ethanol. Biotechnol Bioeng 113(3):531–539
Ahmed A, Cateni BG, Huhnke RL, Lewis RS (2006) Effects of biomass-generated producer gas constituents on cell growth, product distribution and hydrogenase activity of Clostridium carboxidivorans P7T. Biomass Bioenerg 30(7):665–672
Macrelli S, Mogensen J, Zacchi G (2012) Techno-economic evaluation of 2nd generation bioethanol production from sugar cane bagasse and leaves integrated with the sugar-based ethanol process. Biotechnol Biofuels 5:22
Klein-Marcuschamer D, Oleskowicz-Popiel P, Simmons BA, Blanch HW (2012) The challenge of enzyme cost in the production of lignocellulosic biofuels. Biotechnol Bioeng 109(4):1083–1087
Littlewood J, Wang L, Turnbull C, Murphy RJ (2013) Techno-economic potential of bioethanol from bamboo in China. Biotechnol Biofuels 6(1):173
Galbe M, Sassner P, Wingren A, Zacchi G (2007) Process engineering economics of bioethanol production. Adv Biochem Eng Biotechnol 108:303–327
Kim SR, Park YC, Jin YS, Seo JH (2013) Strain engineering of Saccharomyces cerevisiae for enhanced xylose metabolism. Biotechnol Adv 31(6):851–861
Grimmler C, Held C, Liebl W, Ehrenreich A (2010) Transcriptional analysis of catabolite repression in Clostridium acetobutylicum growing on mixtures of d-glucose and d-xylose. J Biotechnol 150(3):315–323
Sun S, Sun S, Cao X, Sun R (2015) The role of pretreatment in improving the enzymatic hydrolysis of lignocellulosic materials. Bioresour Technol 199:49–58
Jonsson LJ, Martin C (2015) Pretreatment of lignocellulose: Formation of inhibitory by-products and strategies for minimizing their effects. Bioresour Technol 199:103–112
Gnansounou E, Dauriat A (2010) Techno-economic analysis of lignocellulosic ethanol: a review. Bioresour Technol 101:4980–4991
Liu W, Yan J, Li J, Sang T (2012) Yield potential of Miscanthus energy crops in the Loess Plateu of China. GCB Energy 4:545–554
Peterson R, Nevalainen H (2012) Trichoderma reesei RUT-C30-thirty years of strain improvement. Microbiology 158(Pt 1):58–68
Gusakov AV (2011) Alternatives to Trichoderma reesei in biofuel production. Trends Biotechnol 29(9):419–425
Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol 26(5):553–560
Murphy L, Bohlin C, Baumann MJ, Olsen SN, Sorensen TH, Anderson L, Borch K, Westh P (2013) Product inhibition of five Hypocrea jecorina cellulases. Enzyme Microb Technol 52(3):163–169
Ma L, Zhang J, Zou G, Wang C, Zhou Z (2011) Improvement of cellulase activity in Trichoderma reesei by heterologous expression of a β-glucosidase gene from Penicillium decumbens. Enzyme Microb Technol 49(4):366–371
Chen M, Qin Y, Liu Z, Liu K, Wang F, Qu Y (2010) Isolation and characterization of a β-glucosidase from Penicillium decumbens and improving hydrolysis of corncob residue by using it as cellulase supplementation. Enzyme Microb Technol 46(6):444–449
Gold ND, Martin VJ (2007) Global view of the Clostridium thermocellum cellulosome revealed by quantitative proteomic analysis. J Bacteriol 189(19):6787–6795
Qu Y, Gao P, Wang Z (1984) Screening of catabolite repression-resistant mutants of cellulase producing Penicillium spp. Acta Mycol Sinica 3:238–243
Liu G, Zhang L, Qin Y, Zou G, Li Z, Yan X, Wei X, Chen M, Chen L, Zheng K, Zhang J, Ma L, Li J, Liu R, Xu H, Bao X, Fang X, Wang L, Zhong Y, Liu W, Zheng H, Wang S, Wang C, Xun L, Zhao GP, Wang T, Zhou Z, Qu Y (2013) Long-term strain improvements accumulate mutations in regulatory elements responsible for hyper-production of cellulolytic enzymes. Sci Rep 3:1569
Fang X, Shen Y, Zhao J, Bao X, Qu Y (2010) Status and prospect of lignocellulosic bioethanol production in China. Bioresour Technol 101(13):4814–4819
Wang M, He D, Liang Y, Liu K, Jiang B, Wang F, Hou S, Fang X (2013) Factors involved in the response to change of agitation rate during cellulase production from Penicillium decumbens JUA10-1. J Ind Microbiol Biotechnol 40(9):1077–1082
Liu G, Zhang L, Wei X, Zou G, Qin Y, Ma L, Li J, Zheng H, Wang S, Wang C, Xun L, Zhao GP, Zhou Z, Qu Y (2013) Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens. PLoS ONE 8(2):e55185
Shen Y, Zhang Y, Ma T, Bao X, Du F, Zhuang G, Qu Y (2008) Simultaneous saccharification and fermentation of acid-pretreated corncobs with a recombinant Saccharomyces cerevisiae expressing β-glucosidase. Bioresour Technol 99(11):5099–5103
Jiang Y, Duarte AV, van den Brink J, Wiebenga A, Zou G, Wang C, de Vries RP, Zhou Z, Benoit I (2015) Enhancing saccharification of wheat straw by mixing enzymes from genetically-modified Trichoderma reesei and Aspergillus niger. Biotechnol Lett 38(1):65–70
Mehboob N, Asad MJ, Asgher M, Gulfraz M, Mukhtar T, Mahmood RT (2014) Exploring thermophilic cellulolytic enzyme production potential of Aspergillus fumigatus by the solid-state fermentation of wheat straw. Appl Biochem Biotechnol 172(7):3646–3655
Lan TQ, Wei D, Yang ST, Liu X (2013) Enhanced cellulase production by Trichoderma viride in a rotating fibrous bed bioreactor. Bioresour Technol 133:175–182
Rahnama N, Foo HL, Abdul Rahman NA, Ariff A, Md Shah UK (2014) Saccharification of rice straw by cellulase from a local Trichoderma harzianum SNRS3 for biobutanol production. BMC Biotechnol 14:103
Singhania RR, Saini JK, Saini R, Adsul M, Mathur A, Gupta R, Tuli DK (2014) Bioethanol production from wheat straw via enzymatic route employing Penicillium janthinellum cellulases. Bioresour Technol 169:490–495
dos Reis L, Fontana RC, Delabona Pda S, da Silva Lima DJ, Camassola M, Pradella JG, Dillon AJ (2013) Increased production of cellulases and xylanases by Penicillium echinulatum S1M29 in batch and fed-batch culture. Bioresour Technol 146:597–603
Karlsson J, Momcilovic D, Wittgren B, Schulein M, Tjerneld F, Brinkmalm G (2002) Enzymatic degradation of carboxymethyl cellulose hydrolyzed by the endoglucanases Cel5A, Cel7B, and Cel45A from Humicola insolens and Cel7B, Cel12A and Cel45A core from Trichoderma reesei. Biopolymers 63(1):32–40
Fang X, Yano S, Inoue H, Sawayama S (2009) Strain improvement of Acremonium cellulolyticus for cellulase production by mutation. J Biosci Bioeng 107(3):256–261
Roche CM, Glass NL, Blanch HW, Clark DS (2014) Engineering the filamentous fungus Neurospora crassa for lipid production from lignocellulosic biomass. Biotechnol Bioeng 111(6):1097–1107
Currie DH, Herring CD, Guss AM, Olson DG, Hogsett DA, Lynd LR (2013) Functional heterologous expression of an engineered full length CipA from Clostridium thermocellum in Thermoanaerobacterium saccharolyticum. Biotechnol Biofuels 6(1):32
Messner R, Kubicek CP (1991) Carbon source control of Cellobiohydrolase I and II formation by Trichoderma reesei. Appl Environ Microbiol 57(3):630–635
Conrad M, Schothorst J, Kankipati HN, Van Zeebroeck G, Rubio-Texeira M, Thevelein JM (2014) Nutrient sensing and signaling in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 38(2):254–299
Leisola MS, Ulmer DC, Pitkanen K, Fiechter A (1985) Induction of cellulases in Chaetomium cellulolyticum by cellobiose. Biotechnol Bioeng 27(9):1389–1391
Ilmén M, Saloheimo A, Onnela ML, Penttilä ME (1997) Regulation of cellulase gene expression in the filamentous fungus Trichoderma reesei. Appl Environ Microbiol 63(4):1298–1306
Sternberg D, Mandels GR (1979) Induction of cellulolytic enzymes in Trichoderma reesei by sophorose. J Bacteriol 139(3):761–769
Tisch D, Schmoll M (2013) Targets of light signalling in Trichoderma reesei. BMC Genom 14:657
Tisch D, Schuster A, Schmoll M (2014) Crossroads between light response and nutrient signalling: ENV1 and PhLP1 act as mutual regulatory pair in Trichoderma reesei. BMC Genom 15:425
Dror TW, Rolider A, Bayer EA, Lamed R, Shoham Y (2005) Regulation of major cellulosomal endoglucanases of Clostridium thermocellum differs from that of a prominent cellulosomal xylanase. J Bacteriol 187(7):2261–2266
Stevenson DM, Weimer PJ (2005) Expression of 17 genes in Clostridium thermocellum ATCC 27405 during fermentation of cellulose or cellobiose in continuous culture. Appl Environ Microbiol 71(8):4672–4678
Newcomb M, Chen CY, Wu JH (2007) Induction of the celC operon of Clostridium thermocellum by laminaribiose. Proc Natl Acad Sci USA 104(10):3747–3752
Johnson EA, Bouchot F, Demain AL (1985) Regulation of cellulase formation in Clostridium thermocellum. J Gen Microbiol 131:2303–2308
Dror TW, Morag E, Rolider A, Bayer EA, Lamed R, Shoham Y (2003) Regulation of the cellulosomal CelS (cel48A) gene of Clostridium thermocellum is growth rate dependent. J Bacteriol 185(10):3042–3048
Dror TW, Rolider A, Bayer EA, Lamed R, Shoham Y (2003) Regulation of expression of scaffoldin-related genes in Clostridium thermocellum. J Bacteriol 185(17):5109–5116
Felenbok B, Flipphi M, Nikolaev I (2001) Ethanol catabolism in Aspergillus nidulans: a model system for studying gene regulation. Prog Nucleic Acid Res Mol Biol 69:149–204
Strauss J, Mach RL, Zeilinger S, Hartler G, Stoffler G, Wolschek M, Kubicek CP (1995) Cre1, the carbon catabolite repressor protein from Trichoderma reesei. FEBS Lett 376(1–2):103–107
Portnoy T, Margeot A, Linke R, Atanasova L, Fekete E, Sandor E, Hartl L, Karaffa L, Druzhinina IS, Seiboth B, Le Crom S, Kubicek CP (2011) The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation. BMC Genom 12:269
Antoniêto AC, dos Santos Castro L, Silva-Rocha R, Persinoti GF, Silva RN (2014) Defining the genome-wide role of CRE1 during carbon catabolite repression in Trichoderma reesei using RNA-Seq analysis. Fungal Genet Biol 73:93–103
Nakari-Setälä T, Paloheimo M, Kallio J, Vehmaanperä J, Penttilä M, Saloheimo M (2009) Genetic modification of carbon catabolite repression in Trichoderma reesei for improved protein production. Appl Environ Microbiol 75(14):4853–4860
Stricker AR, Grosstessner-Hain K, Wurleitner E, Mach RL (2006) Xyr1 (xylanase regulator 1) regulates both the hydrolytic enzyme system and d-xylose metabolism in Hypocrea jecorina. Eukaryot Cell 5(12):2128–2137
Lichius A, Bidard F, Buchholz F, Le Crom S, Martin J, Schackwitz W, Austerlitz T, Grigoriev IV, Baker SE, Margeot A, Seiboth B, Kubicek CP (2015) Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype. BMC Genom 16:326
Portnoy T, Margeot A, Seidl-Seiboth V, Le Crom S, Ben Chaabane F, Linke R, Seiboth B, Kubicek CP (2011) Differential regulation of the cellulase transcription factors XYR1, ACE2, and ACE1 in Trichoderma reesei strains producing high and low levels of cellulase. Eukaryot Cell 10(2):262–271
Coradetti ST, Xiong Y, Glass NL (2013) Analysis of a conserved cellulase transcriptional regulator reveals inducer-independent production of cellulolytic enzymes in Neurospora crassa. Microbiology Open 2(4):595–609
Coradetti ST, Craig JP, Xiong Y, Shock T, Tian C, Glass NL (2012) Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi. Proc Natl Acad Sci USA 109(19):7397–7402
Aro N, Saloheimo A, Ilmén M, Penttilä M (2001) ACEII, a novel transcriptional activator involved in regulation of cellulase and xylanase genes of Trichoderma reesei. J Biol Chem 276(26):24309–24314
Aro N, Ilmén M, Saloheimo M, Penttilä M (2003) ACEI of Trichoderma reesei is a repressor of cellulase and xylanase expression. Appl Environ Microbiol 69(1):56–65
Saloheimo A, Aro N, Ilmén M, Penttilä M (2000) Isolation of the ace1 gene encoding a Cys2-His2 transcription factor involved in regulation of activity of the cellulase promoter cbh1 of Trichoderma reesei. J Biol Chem 275(8):5817–5825
He R, Ma L, Li C, Jia W, Li D, Zhang D, Chen S (2014) Trpac1, a pH response transcription regulator, is involved in cellulase gene expression in Trichoderma reesei. Enzyme Microb Technol 67:17–26
Lockington RA, Rodbourn L, Barnett S, Carter CJ, Kelly JM (2002) Regulation by carbon and nitrogen sources of a family of cellulases in Aspergillus nidulans. Fungal Genet Biol 37(2):190–196
Zeilinger S, Ebner A, Marosits T, Mach R, Kubicek CP (2001) The Hypocrea jecorina HAP 2/3/5 protein complex binds to the inverted CCAAT-box (ATTGG) within the cbh2 (cellobiohydrolase II-gene) activating element. Mol Genet Genom 266(1):56–63
Würleitner E, Pera L, Wacenovsky C, Cziferszky A, Zeilinger S, Kubicek CP, Mach RL (2003) Transcriptional regulation of xyn2 in Hypocrea jecorina. Eukaryot Cell 2(1):150–158
Cziferszky A, Mach RL, Kubicek CP (2002) Phosphorylation positively regulates DNA binding of the carbon catabolite repressor Cre1 of Hypocrea jecorina (Trichoderma reesei). J Biol Chem 277(17):14688–14694
Strauss J, Horvath HK, Abdallah BM, Kindermann J, Mach RL, Kubicek CP (1999) The function of CreA, the carbon catabolite repressor of Aspergillus nidulans, is regulated at the transcriptional and post-transcriptional level. Mol Microbiol 32(1):169–178
Mach-Aigner AR, Pucher ME, Steiger MG, Bauer GE, Preis SJ, Mach RL (2008) Transcriptional regulation of xyr1, encoding the main regulator of the xylanolytic and cellulolytic enzyme system in Hypocrea jecorina. Appl Environ Microbiol 74(21):6554–6562
Ries L, Belshaw NJ, Ilmén M, Penttilä ME, Alapuranen M, Archer DB (2014) The role of CRE1 in nucleosome positioning within the cbh1 promoter and coding regions of Trichoderma reesei. Appl Microbiol Biotechnol 98(2):749–762
Mello-de-Sousa TM, Rassinger A, Pucher ME, dos Santos Castro L, Persinoti GF, Silva-Rocha R, Pocas-Fonseca MJ, Mach RL, Nascimento Silva R, Mach-Aigner AR (2015) The impact of chromatin remodelling on cellulase expression in Trichoderma reesei. BMC Genom 16:588
Xin Q, Gong Y, Lv X, Chen G, Liu W (2013) Trichoderma reesei histone acetyltransferase Gcn5 regulates fungal growth, conidiation, and cellulase gene expression. Curr Microbiol 67(5):580–589
Zhou Q, Xu J, Kou Y, Lv X, Zhang X, Zhao G, Zhang W, Chen G, Liu W (2012) Differential involvement of β-glucosidases from Hypocrea jecorina in rapid induction of cellulase genes by cellulose and cellobiose. Eukaryot Cell 11(11):1371–1381
Xu J, Zhao G, Kou Y, Zhang W, Zhou Q, Chen G, Liu W (2014) Intracellular β-glucosidases CEL1a and CEL1b are essential for cellulase induction on lactose in Trichoderma reesei. Eukaryot Cell 13(8):1001–1013
Chen M, Qin Y, Cao Q, Liu G, Li J, Li Z, Zhao J, Qu Y (2013) Promotion of extracellular lignocellulolytic enzymes production by restraining the intracellular β-glucosidase in Penicillium decumbens. Bioresour Technol 137:33–40
Li J, Liu G, Chen M, Li Z, Qin Y, Qu Y (2013) Cellodextrin transporters play important roles in cellulase induction in the cellulolytic fungus Penicillium oxalicum. Appl Microbiol Biotechnol 97(24):10479–10488
Kubicek CP (2013) Systems biological approaches towards understanding cellulase production by Trichoderma reesei. J Biotechnol 163(2):133–142
Karaffa L, Coulier L, Fekete E, Overkamp KM, Druzhinina IS, Mikus M, Seiboth B, Novak L, Punt PJ, Kubicek CP (2013) The intracellular galactoglycome in Trichoderma reesei during growth on lactose. Appl Microbiol Biotechnol 97(12):5447–5456
Hu Y, Liu G, Li Z, Qin Y, Qu Y, Song X (2013) G protein-cAMP signaling pathway mediated by PGA3 plays different roles in regulating the expressions of amylases and cellulases in Penicillium decumbens. Fungal Genet Biol 58–59:62–70
Schuster A, Tisch D, Seidl-Seiboth V, Kubicek CP, Schmoll M (2012) Roles of protein kinase A and adenylate cyclase in light-modulated cellulase regulation in Trichoderma reesei. Appl Environ Microbiol 78(7):2168–2178
Tisch D, Kubicek CP, Schmoll M (2011) New insights into the mechanism of light modulated signaling by heterotrimeric G-proteins: ENVOY acts on gna1 and gna3 and adjusts cAMP levels in Trichoderma reesei (Hypocrea jecorina). Fungal Genet Biol 48(6):631–640
Seiboth B, Karimi RA, Phatale PA, Linke R, Hartl L, Sauer DG, Smith KM, Baker SE, Freitag M, Kubicek CP (2012) The putative protein methyltransferase LAE1 controls cellulase gene expression in Trichoderma reesei. Mol Microbiol 84(6):1150–1164
Karimi-Aghcheh R, Németh Z, Atanasova L, Fekete E, Paholcsek M, Sandor E, Aquino B, Druzhinina IS, Karaffa L, Kubicek CP (2014) The VELVET A orthologue VEL1 of Trichoderma reesei regulates fungal development and is essential for cellulase gene expression. PLoS ONE 9(11):e112799
Liu K, Dong Y, Wang F, Jiang B, Wang M, Fang X (2015) Regulation of cellulase expression, sporulation and morphogenesis by velvet family proteins in Trichoderma reesei. Appl Microbiol Biotechnol 100(2):769–779
Wang M, Zhao Q, Yang J, Jiang B, Wang F, Liu K, Fang X (2013) A mitogen-activated protein kinase Tmk3 participates in high osmolarity resistance, cell wall integrity maintenance and cellulase production regulation in Trichoderma reesei. PLoS ONE 8(8):e72189
Lei Y, Liu G, Li Z, Gao L, Qin Y, Qu Y (2014) Functional characterization of protein kinase CK2 regulatory subunits regulating Penicillium oxalicum asexual development and hydrolytic enzyme production. Fungal Genet Biol 66:44–53
Wang M, Dong Y, Zhao Q, Wang F, Liu K, Jiang B, Fang X (2014) Identification of the role of a MAP kinase Tmk2 in Hypocrea jecorina (Trichoderma reesei). Sci Rep 4:6732
Wang M, Yang H, Zhang M, Liu K, Wang H, Luo Y, Fang X (2015) Functional analysis of Trichoderma reesei CKIIα2, a catalytic subunit of casein kinase II. Appl Microbiol Biotechnol 99(14):5929–5938
Nataf Y, Bahari L, Kahel-Raifer H, Borovok I, Lamed R, Bayer EA, Sonenshein AL, Shoham Y (2010) Clostridium thermocellum cellulosomal genes are regulated by extracytoplasmic polysaccharides via alternative sigma factors. Proc Natl Acad Sci USA 107(43):18646–18651
Harrison MJ, Nouwens AS, Jardine DR, Zachara NE, Gooley AA, Nevalainen H, Packer NH (1998) Modified glycosylation of cellobiohydrolase I from a high cellulase-producing mutant strain of Trichoderma reesei. Eur J Biochem 256(1):119–127
Zhou F, Olman V, Xu Y (2009) Large-scale analyses of glycosylation in cellulases. Genom Proteom Bioinform 7(4):194–199
Chen L, Drake MR, Resch MG, Greene ER, Himmel ME, Chaffey PK, Beckham GT, Tan Z (2014) Specificity of O-glycosylation in enhancing the stability and cellulose binding affinity of Family 1 carbohydrate-binding modules. Proc Natl Acad Sci USA 111(21):7612–7617
Wei W, Chen L, Zou G, Wang Q, Yan X, Zhang J, Wang C, Zhou Z (2013) N-glycosylation affects the proper folding, enzymatic characteristics and production of a fungal ß-glucosidase. Biotechnol Bioeng 110(12):3075–3084
Payne CM, Resch MG, Chen L, Crowley MF, Himmel ME, Taylor LE 2nd, Sandgren M, Stahlberg J, Stals I, Tan Z, Beckham GT (2013) Glycosylated linkers in multimodular lignocellulose-degrading enzymes dynamically bind to cellulose. Proc Natl Acad Sci USA 110(36):14646–14651
Beckham GT, Dai Z, Matthews JF, Momany M, Payne CM, Adney WS, Baker SE, Himmel ME (2012) Harnessing glycosylation to improve cellulase activity. Curr Opin Biotechnol 23(3):338–345
Taylor CB, Talib MF, McCabe C, Bu L, Adney WS, Himmel ME, Crowley MF, Beckham GT (2012) Computational investigation of glycosylation effects on a family 1 carbohydrate-binding module. J Biol Chem 287(5):3147–3155
Gao L, Gao F, Wang L, Geng C, Chi L, Zhao J, Qu Y (2012) N-glycoform diversity of cellobiohydrolase I from Penicillium decumbens and synergism of nonhydrolytic glycoform in cellulose degradation. J Biol Chem 287(19):15906–15915
Xu L, Shen Y, Hou J, Peng B, Tang H, Bao X (2014) Secretory pathway engineering enhances secretion of cellobiohydrolase I from Trichoderma reesei in Saccharomyces cerevisiae. J Biosci Bioeng 117(1):45–52
Qin Y, Wei X, Liu X, Wang T, Qu Y (2008) Purification and characterization of recombinant endoglucanase of Trichoderma reesei expressed in Saccharomyces cerevisiae with higher glycosylation and stability. Protein Expr Purif 58(1):162–167
Mandels M, Weber J, Parizek R (1971) Enhanced cellulase production by a mutant of Trichoderma viride. Appl Microbiol 21(1):152–154
Montenecourt BS, Eveleigh DE (1977) Preparation of mutants of Trichoderma reesei with enhanced cellulase production. Appl Environ Microbiol 34(6):777–782
Ribeiro O, Magalhães F, Aguiar TQ, Wiebe MG, Penttilä M, Domingues L (2013) Random and direct mutagenesis to enhance protein secretion in Ashbya gossypii. Bioengineered 4(5):322–331
Shafique S, Bajwa R, Shafique S (2010) Molecular characterisation of UV and chemically induced mutants of Trichoderma reesei FCBP-364. Nat Prod Res 24(15):1438–1448
Abdullah R, Zafar W, Nadeem M, Iqtedar M, Naz S, Syed Q, Butt ZA (2015) Random mutagenesis and media optimisation for hyperproduction of cellulase from Bacillus species using proximally analysed Saccharum spontaneum in submerged fermentation. Nat Prod Res 29(4):336–344
Iwakuma H, Koyama Y, Miyachi A, Nasukawa M, Matsumoto H, Yano S, Ogihara J, Kasumi T (2015) Generation of a glucose de-repressed mutant of Trichoderma reesei using disparity mutagenesis. Biosci Biotechnol Biochem 80(3):486–492
Cheng Y, Song X, Qin Y, Qu Y (2009) Genome shuffling improves production of cellulase by Penicillium decumbens JU-A10. J Appl Microbiol 107(6):1837–1846
Zi Z, Shi W, Li Y, Zhai Z, Han L, Wang M, Fang X (2013) Modification of celllulose-producing industrial filamentous fungi with plasma induced mutation. Chin Brew 32(S1):5–8
Qin Y, Wei X, Song X, Qu Y (2008) Engineering endoglucanase II from Trichoderma reesei to improve the catalytic efficiency at a higher pH optimum. J Biotechnol 135(2):190–195
Nakazawa H, Okada K, Onodera T, Ogasawara W, Okada H, Morikawa Y (2009) Directed evolution of endoglucanase III (Cel12A) from Trichoderma reesei. Appl Microbiol Biotechnol 83(4):649–657
Mahadevan SA, Wi SG, Lee DS, Bae HJ (2008) Site-directed mutagenesis and CBM engineering of Cel5A (Thermotoga maritima). FEMS Microbiol Lett 287(2):205–211
Becker D, Braet C, Brumer H 3rd, Claeyssens M, Divne C, Fagerstrom BR, Harris M, Jones TA, Kleywegt GJ, Koivula A, Mahdi S, Piens K, Sinnott ML, Stahlberg J, Teeri TT, Underwood M, Wohlfahrt G (2001) Engineering of a glycosidase Family 7 cellobiohydrolase to more alkaline pH optimum: the pH behaviour of Trichoderma reesei Cel7A and its E223S/ A224H/L225 V/T226A/D262G mutant. Biochem J 356(Pt 1):19–30
Chokhawala HA, Roche CM, Kim TW, Atreya ME, Vegesna N, Dana CM, Blanch HW, Clark DS (2015) Mutagenesis of Trichoderma reesei endoglucanase I: impact of expression host on activity and stability at elevated temperatures. BMC Biotechnol 15:11
Nordwald EM, Brunecky R, Himmel ME, Beckham GT, Kaar JL (2014) Charge engineering of cellulases improves ionic liquid tolerance and reduces lignin inhibition. Biotechnol Bioeng 111(8):1541–1549
Akcapinar GB, Venturini A, Martelli PL, Casadio R, Sezerman UO (2015) Modulating the thermostability of Endoglucanase I from Trichoderma reesei using computational approaches. Protein Eng Des Sel 28(5):127–135
Yao G, Li Z, Gao L, Wu R, Kan Q, Liu G, Qu Y (2015) Redesigning the regulatory pathway to enhance cellulase production in Penicillium oxalicum. Biotechnol Biofuels 8:71
Liu C, Cai M, Ma X (1993) Secreening of a β-glucosidase product repression resistant Penicillium decumbens strain. Microbiol Res Appl 613:5–8
Kim JJ, Kwon YK, Kim JH, Heo SJ, Lee Y, Lee SJ, Shim WB, Jung WK, Hyun JH, Kwon KK, Kang DH, Oh C (2014) Effective microwell plate-based screening method for microbes producing cellulase and xylanase and its application. J Microbiol Biotechnol 24(11):1559–1565
Xiao Z, Storms R, Tsang A (2004) Microplate-based filter paper assay to measure total cellulase activity. Biotechnol Bioeng 88(7):832–837
Li ZH, Du CM, Zhong YH, Wang TH (2010) Development of a highly efficient gene targeting system allowing rapid genetic manipulations in Penicillium decumbens. Appl Microbiol Biotechnol 87(3):1065–1076
Zhang G, Hartl L, Schuster A, Polak S, Schmoll M, Wang T, Seidl V, Seiboth B (2009) Gene targeting in a nonhomologous end joining deficient Hypocrea jecorina. J Biotechnol 139(2):146–151
Schuster A, Bruno KS, Collett JR, Baker SE, Seiboth B, Kubicek CP, Schmoll M (2012) A versatile toolkit for high throughput functional genomics with Trichoderma reesei. Biotechnol Biofuels 5:1
Steiger MG, Vitikainen M, Uskonen P, Brunner K, Adam G, Pakula T, Penttilä M, Saloheimo M, Mach RL, Mach-Aigner AR (2011) Transformation system for Hypocrea jecorina (Trichoderma reesei) that favors homologous integration and employs reusable bidirectionally selectable markers. Appl Environ Microbiol 77(1):114–121
Derntl C, Kiesenhofer DP, Mach RL, Mach-Aigner AR (2015) Novel strategies for genomic manipulation of Trichoderma reesei with the purpose of strain engineering. Appl Environ Microbiol 81(18):6314–6323
Magaña-Ortiz D, Coconi-Linares N, Ortiz-Vazquez E, Fernandez F, Loske AM, Gómez-Lim MA (2013) A novel and highly efficient method for genetic transformation of fungi employing shock waves. Fungal Genet Biol 56:9–16
He R, Guo W, Wang L, Zhang D (2015) Construction of an efficient RNAi system in the cellulolytic fungus Trichoderma reesei. J Microbiol Methods 108:70–73
Nødvig CS, Nielsen JB, Kogle ME, Mortensen UH (2015) A CRISPR-Cas9 system for genetic engineering of filamentous fungi. PLoS ONE 10(7):e0133085
Fuller KK, Chen S, Loros JJ, Dunlap JC (2015) Development of the CRISPR/Cas9 system for targeted gene disruption in Aspergillus fumigatus. Eukaryot Cell 14(11):1073–1080
Tripathi SA, Olson DG, Argyros DA, Miller BB, Barrett TF, Murphy DM, McCool JD, Warner AK, Rajgarhia VB, Lynd LR, Hogsett DA, Caiazza NC (2010) Development of pyrF-based genetic system for targeted gene deletion in Clostridium thermocellum and creation of a pta mutant. Appl Environ Microbiol 76(19):6591–6599
Olson DG, Tripathi SA, Giannone RJ, Lo J, Caiazza NC, Hogsett DA, Hettich RL, Guss AM, Dubrovsky G, Lynd LR (2010) Deletion of the Cel48S cellulase from Clostridium thermocellum. Proc Natl Acad Sci USA 107(41):17727–17732
Olson DG, Lynd LR (2012) Transformation of Clostridium thermocellum by electroporation. Methods Enzymol 510:317–330
Dashtban M, Qin W (2012) Overexpression of an exotic thermotolerant β-glucosidase in Trichoderma reesei and its significant increase in cellulolytic activity and saccharification of barley straw. Microb Cell Fact 11:63
Zhang J, Zhong Y, Zhao X, Wang T (2010) Development of the cellulolytic fungus Trichoderma reesei strain with enhanced β-glucosidase and filter paper activity using strong artificial cellobiohydrolase 1 promoter. Bioresour Technol 101(24):9815–9818
Hu Y, Xue H, Liu G, Song X, Qu Y (2015) Efficient production and evaluation of lignocellulolytic enzymes using a constitutive protein expression system in Penicillium oxalicum. J Ind Microbiol Biotechnol 42(6):877–887
Fang H, Xia L (2013) High activity cellulase production by recombinant Trichoderma reesei ZU-02 with the enhanced cellobiohydrolase production. Bioresour Technol 144:693–697
Lv X, Zheng F, Li C, Zhang W, Chen G, Liu W (2015) Characterization of a copper responsive promoter and its mediated overexpression of the xylanase regulator 1 results in an induction-independent production of cellulases in Trichoderma reesei. Biotechnol Biofuels 8:67
Derntl C, Gudynaite-Savitch L, Calixte S, White T, Mach RL, Mach-Aigner AR (2013) Mutation of the Xylanase regulator 1 causes a glucose blind hydrolase expressing phenotype in industrially used Trichoderma strains. Biotechnol Biofuels 6:62
Mello-de-Sousa TM, Gorsche R, Rassinger A, Poças-Fonseca MJ, Mach RL, Mach-Aigner AR (2014) A truncated form of the Carbon catabolite repressor 1 increases cellulase production in Trichoderma reesei. Biotechnol Biofuels 7(1):129
Fujii T, Inoue H, Ishikawa K (2013) Enhancing cellulase and hemicellulase production by genetic modification of the carbon catabolite repressor gene, creA, in Acremonium cellulolyticus. AMB Express 3(1):73
Zou G, Shi S, Jiang Y, van den Brink J, de Vries RP, Chen L, Zhang J, Ma L, Wang C, Zhou Z (2012) Construction of a cellulase hyper-expression system in Trichoderma reesei by promoter and enzyme engineering. Microb Cell Fact 11:21
Wang S, Liu G, Wang J, Yu J, Huang B, Xing M (2013) Enhancing cellulase production in Trichoderma reesei RUT C30 through combined manipulation of activating and repressing genes. J Ind Microbiol Biotechnol 40(6):633–641
Chen F, Chen XZ, Su XY, Qin LN, Huang ZB, Tao Y, Dong ZY (2015) An Ime2-like mitogen-activated protein kinase is involved in cellulase expression in the filamentous fungus Trichoderma reesei. Biotechnol Lett 37(10):2055–2062
Reilly MC, Qin L, Craig JP, Starr TL, Glass NL (2015) Deletion of homologs of the SREBP pathway results in hyper-production of cellulases in Neurospora crassa and Trichoderma reesei. Biotechnol Biofuels 8:121
Denton JA, Kelly JM (2011) Disruption of Trichoderma reesei cre2, encoding an ubiquitin C-terminal hydrolase, results in increased cellulase activity. BMC Biotechnol 11:103
Wei H, Wang W, Alahuhta M, Vander Wall T, Baker JO, Taylor LE 2nd, Decker SR, Himmel ME, Zhang M (2014) Engineering towards a complete heterologous cellulase secretome in Yarrowia lipolytica reveals its potential for consolidated bioprocessing. Biotechnol Biofuels 7(1):148
Hong J, Yang H, Zhang K, Liu C, Zou S, Zhang M (2014) Development of a cellulolytic Saccharomyces cerevisiae strain with enhanced cellobiohydrolase activity. World J Microbiol Biotechnol 30(11):2985–2993
Fitzpatrick J, Kricka W, James TC, Bond U (2014) Expression of three Trichoderma reesei cellulase genes in Saccharomyces pastorianus for the development of a two-step process of hydrolysis and fermentation of cellulose. J Appl Microbiol 117(1):96–108
Kim S, Baek SH, Lee K, Hahn JS (2013) Cellulosic ethanol production using a yeast consortium displaying a minicellulosome and β-glucosidase. Microb Cell Fact 12:14
Wang D, Qu Y, Gao P (1995) Regulation of cellulase synthesis in mycelial fungi: Participation of ATP and cyclic AMP. Biotechnol Lett 17:593–598
Baba Y, Sumitani J, Tani S, Kawaguchi T (2015) Characterization of Aspergillus aculeatus β-glucosidase 1 accelerating cellulose hydrolysis with Trichoderma cellulase system. AMB Exp 5(1):3
Gao L, Gao F, Zhang D, Zhang C, Wu G, Chen S (2013) Purification and characterization of a new β-glucosidase from Penicillium piceum and its application in enzymatic degradation of delignified corn stover. Bioresour Technol 147:658–661
Bunterngsook B, Eurwilaichitr L, Thamchaipenet A, Champreda V (2015) Binding characteristics and synergistic effects of bacterial expansins on cellulosic and hemicellulosic substrates. Bioresour Technol 176:129–135
Kang K, Wang S, Lai G, Liu G, Xing M (2013) Characterization of a novel swollenin from Penicillium oxalicum in facilitating enzymatic saccharification of cellulose. BMC Biotechnol 13:42
da Silva Delabona P, Cota J, Hoffmam ZB, Paixão DA, Farinas CS, Cairo JP, Lima DJ, Squina FM, Ruller R, Pradella JG (2013) Understanding the cellulolytic system of Trichoderma harzianum P49P11 and enhancing saccharification of pretreated sugarcane bagasse by supplementation with pectinase and α-l-arabinofuranosidase. Bioresour Technol 131:500–507
Berlin A, Maximenko V, Gilkes N, Saddler J (2007) Optimization of enzyme complexes for lignocellulose hydrolysis. Biotechnol Bioeng 97(2):287–296
Gonçalves GA, Takasugi Y, Jia L, Mori Y, Noda S, Tanaka T, Ichinose H, Kamiya N (2015) Synergistic effect and application of xylanases as accessory enzymes to enhance the hydrolysis of pretreated bagasse. Enzyme Microb Technol 72:16–24
Callow NV, Ju LK (2012) Promoting pellet growth of Trichoderma reesei Rut C30 by surfactants for easy separation and enhanced cellulase production. Enzyme Microb Technol 50(6–7):311–317
Sipos B, Szilagyi M, Sebestyen Z, Perazzini R, Dienes D, Jakab E, Crestini C, Reczey K (2011) Mechanism of the positive effect of poly(ethylene glycol) addition in enzymatic hydrolysis of steam pretreated lignocelluloses. C R Biol 334(11):812–823
Bilgin R, Yalcin MS, Yildirim D (2015) Optimization of covalent immobilization of Trichoderma reesei cellulase onto modified ReliZyme HA403 and Sepabeads EC-EP supports for cellulose hydrolysis, in buffer and ionic liquids/buffer media. Artif Cells Nanomed Biotechnol. doi:10.3109/21691401.2015.1024842
Abraham RE, Verma ML, Barrow CJ, Puri M (2014) Suitability of magnetic nanoparticle immobilised cellulases in enhancing enzymatic saccharification of pretreated hemp biomass. Biotechnol Biofuels 7:90
Cavka A, Alriksson B, Rose SH, van Zyl WH, Jonsson LJ (2014) Production of cellulosic ethanol and enzyme from waste fiber sludge using SSF, recycling of hydrolytic enzymes and yeast, and recombinant cellulase-producing Aspergillus niger. J Ind Microbiol Biotechnol 41(8):1191–1200
Maurya DP, Singh D, Pratap D, Maurya JP (2012) Optimization of solid state fermentation conditions for the production of cellulase by Trichoderma reesei. J Environ Biol 33(1):5–8
Ma L, Li C, Yang Z, Jia W, Zhang D, Chen S (2013) Kinetic studies on batch cultivation of Trichoderma reesei and application to enhance cellulase production by fed-batch fermentation. J Biotechnol 166(4):192–197
Wang M, Han L, Liu S, Zhao X, Yang J, Loh SK, Sun X, Zhang C, Fang X (2015) A Weibull statistics-based lignocellulose saccharification model and a built-in parameter accurately predict lignocellulose hydrolysis performance. Biotechnol J 10(9):1424–1433
Rana V, Eckard AD, Teller P, Ahring BK (2014) On-site enzymes produced from Trichoderma reesei RUT-C30 and Aspergillus saccharolyticus for hydrolysis of wet exploded corn stover and loblolly pine. Bioresour Technol 154:282–289
Huang GL, Anderson TD, Clubb RT (2014) Engineering microbial surfaces to degrade lignocellulosic biomass. Bioengineered 5(2):96–106
Hahn-Hagerdal B, Karhumaa K, Fonseca C, Spencer-Martins I, Gorwa-Grauslund MF (2007) Towards industrial pentose-fermenting yeast strains. Appl Microbiol Biotechnol 74(5):937–953
Jeffries TW (2006) Engineering yeasts for xylose metabolism. Curr Opin Biotechnol 17(3):320–326
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
Scalcinati G, Otero JM, van Vleet JR, Jeffries TW, Olsson L, Nielsen J (2012) Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption. FEMS Yeast Res 12(5):582–597
Walfridsson M, Anderlund M, Bao X, Hahn-Hagerdal B (1997) Expression of different levels of enzymes from the Pichia stipitisXYL1 and XYL2 genes in Saccharomyces cerevisiae and its effects on product formation during xylose utilisation. Appl Microbiol Biotechnol 48(2):218–224
Kuyper M, Harhangi HR, Stave AK, Winkler AA, Jetten MS, de Laat WT, den Ridder JJ, Op den Camp HJ, van Dijken JP, Pronk JT (2003) High-level functional expression of a fungal xylose isomerase: the key to efficient ethanolic fermentation of xylose by Saccharomyces cerevisiae? FEMS Yeast Res 4(1):69–78
van Maris AJ, Winkler AA, Kuyper M, de Laat WT, van Dijken JP, Pronk JT (2007) Development of efficient xylose fermentation in Saccharomyces cerevisiae: xylose isomerase as a key component. Adv Biochem Eng Biotechnol 108:179–204
Zhou H, Cheng JS, Wang BL, Fink GR, Stephanopoulos G (2012) Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae. Metab Eng 14(6):611–622
Eliasson A, Christensson C, Wahlbom CF, Hahn-Hagerdal B (2000) Anaerobic xylose fermentation by recombinant Saccharomyces cerevisiae carrying XYL1, XYL2, and XKS1 in mineral medium chemostat cultures. Appl Env Microbiol 66(8):3381–3386
Bengtsson O, Hahn-Hagerdal B, Gorwa-Grauslund MF (2009) Xylose reductase from Pichia stipitis with altered coenzyme preference improves ethanolic xylose fermentation by recombinant Saccharomyces cerevisiae. Biotechnol Biofuels 2:9
Hou J, Shen Y, Li XP, Bao XM (2007) Effect of the reversal of coenzyme specificity by expression of mutated Pichia stipitis xylitol dehydrogenase in recombinant Saccharomyces cerevisiae. Lett Appl Microbiol 45(2):184–189
Matsushika A, Watanabe S, Kodaki T, Makino K, Inoue H, Murakami K, Takimura O, Sawayama S (2008) Expression of protein engineered NADP+-dependent xylitol dehydrogenase increases ethanol production from xylose in recombinant Saccharomyces cerevisiae. Appl Microbiol Biotechnol 81(2):243–255
Verho R, Londesborough J, Penttilä M, Richard P (2003) Engineering redox cofactor regeneration for improved pentose fermentation in Saccharomyces cerevisiae. Appl Env Microbiol 69(10):5892–5897
Zhang GC, Liu JJ, Ding WT (2012) Decreased xylitol formation during xylose fermentation in Saccharomyces cerevisiae due to overexpression of water-forming NADH oxidase. Appl Env Microbiol 78(4):1081–1086
Bro C, Regenberg B, Forster J, Nielsen J (2006) In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab Eng 8(2):102–111
Grotkjaer T, Christakopoulos P, Nielsen J, Olsson L (2005) Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains. Metab Eng 7(5–6):437–444
Hou J, Vemuri GN, Bao X, Olsson L (2009) Impact of overexpressing NADH kinase on glucose and xylose metabolism in recombinant xylose-utilizing Saccharomyces cerevisiae. Appl Microbiol Biotechnol 82(5):909–919
Hou J, Shen Y, Jiao C, Ge R, Zhang X, Bao X (2015) Characterization and evolution of xylose isomerase screened from the bovine rumen metagenome in Saccharomyces cerevisiae. J Biosci Bioeng 121(2):160–165
Lee JY, Jang YS, Lee J, Papoutsakis ET, Lee SY (2009) Metabolic engineering of Clostridium acetobutylicum M5 for highly selective butanol production. Biotechnol J 4(10):1432–1440
Madhavan A, Tamalampudi S, Ushida K, Kanai D, Katahira S, Srivastava A, Fukuda H, Bisaria VS, Kondo A (2009) Xylose isomerase from polycentric fungus Orpinomyces: gene sequencing, cloning, and expression in Saccharomyces cerevisiae for bioconversion of xylose to ethanol. Appl Microbiol Biotechnol 82(6):1067–1078
Brat D, Boles E, Wiedemann B (2009) Functional expression of a bacterial xylose isomerase in Saccharomyces cerevisiae. Appl Env Microbiol 75(8):2304–2311
Hector R, Dien B, Cotta M, Mertens J (2013) Growth and fermentation of D-xylose by Saccharomyces cerevisiae expressing a novel d-xylose isomerase originating from the bacterium Prevotella ruminicola TC2-24. Biotechnol Biofuels 6:84
Peng B, Shen Y, Li X, Chen X, Hou J, Bao X (2012) Improvement of xylose fermentation in respiratory-deficient xylose-fermenting Saccharomyces cerevisiae. Metab Eng 14(1):9–18
Shen Y, Chen X, Peng B, Chen L, Hou J, Bao X (2012) An efficient xylose-fermenting recombinant Saccharomyces cerevisiae strain obtained through adaptive evolution and its global transcription profile. Appl Microbiol Biotechnol 96(4):1079–1091
Diao L, Liu Y, Qian F, Yang J, Jiang Y, Yang S (2013) Construction of fast xylose-fermenting yeast based on industrial ethanol-producing diploid Saccharomyces cerevisiae by rational design and adaptive evolution. BMC Biotechnol 13:110
Hahn-Hagerdal B, Karhumaa K, Jeppsson M, Gorwa-Grauslund MF (2007) Metabolic engineering for pentose utilization in Saccharomyces cerevisiae. Adv Biochem Eng Biotechnol 108:147–177
Schleif R (2000) Regulation of the l-arabinose operon of Escherichia coli. Trend Genet 16(12):559–565
Sedlak M, Ho NW (2001) Expression of E. coli araBAD operon encoding enzymes for metabolizing l-arabinose in Saccharomyces cerevisiae. Enzyme Microb Technol 28(1):16–24
Wang C, Shen Y, Zhang Y, Suo F, Hou J, Bao X (2013) Improvement of l-arabinose fermentation by modifying the metabolic pathway and transport in Saccharomyces cerevisiae. Biomed Res Int 2013:461204
Wright J, Bellissimi E, de Hulster E, Wagner A, Pronk JT, van Maris AJ (2011) Batch and continuous culture-based selection strategies for acetic acid tolerance in xylose-fermenting Saccharomyces cerevisiae. FEMS Yeast Res 11(3):299–306
Atsumi S, Liao JC (2008) Metabolic engineering for advanced biofuels production from Escherichia coli. Curr Opin Biotechnol 19(5):414–419
Ren C, Gu Y, Hu S, Wu Y, Wang P, Yang Y, Yang C, Yang S, Jiang W (2010) Identification and inactivation of pleiotropic regulator CcpA to eliminate glucose repression of xylose utilization in Clostridium acetobutylicum. Metab Eng 12(5):446–454
Xiao H, Gu Y, Ning Y, Yang Y, Mitchell WJ, Jiang W, Yang S (2011) 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 Env Microbiol 77(22):7886–7895
Jin L, Zhang H, Chen L, Yang C, Yang S, Jiang W, Gu Y (2014) Combined overexpression of genes involved in pentose phosphate pathway enables enhanced d-xylose utilization by Clostridium acetobutylicum. J Biotechnol 173:7–9
Baer SH, Blaschek HP, Smith TL (1987) Effect of butanol challenge and temperature on lipid composition and membrane fluidity of butanol-tolerant Clostridium acetobutylicum. Appl Env Microbiol 53(12):2854–2861
Jiang Y, Liu J, Jiang W, Yang Y, Yang S (2015) Current status and prospects of industrial bio-production of n-butanol in China. Biotechnol Adv 33(7):1493–1501
Hu S, Zheng H, Gu Y, Zhao J, Zhang W, Yang Y, Wang S, Zhao G, Yang S, Jiang W (2011) Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018. BMC Genom 12:93
Jiang Y, Xu C, Dong F, Yang Y, Jiang W, Yang S (2009) Disruption of the acetoacetate decarboxylase gene in solvent-producing Clostridium acetobutylicum increases the butanol ratio. Metab Eng 11(4–5):284–291
Jang YS, Malaviya A, Lee SY (2013) Acetone-butanol-ethanol production with high productivity using Clostridium acetobutylicum BKM19. Biotechnol Bioeng 110(6):1646–1653
Hong KK, Nielsen J (2012) Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries. Cell Mol Life Sci 69(16):2671–2690
Shen CR, Lan EI, Dekishima Y, Baez A, Cho KM, Liao JC (2011) Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli. Appl Environ Microbiol 77(9):2905–2915
Schirmer A, Rude MA, Li X, Popova E, del Cardayre SB (2010) Microbial biosynthesis of alkanes. Science 329(5991):559–562
Steen EJ, Kang Y, Bokinsky G, Hu Z, Schirmer A, McClure A, Del Cardayre SB, Keasling JD (2010) Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463(7280):559–562
Bruschi F, Dundar M, Gahan PB, Gartland K, Szente M, Viola-Magni MP, Akbarova Y (2011) Biotechnology worldwide and the ‘European Biotechnology Thematic Network’ Association (EBTNA). Curr Opin Biotechnol 22(Suppl 1):S7–S14
Chen Y, Nielsen J (2013) Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks. Curr Opin Biotechnol 24(6):965–972
Jantama K, Haupt MJ, Svoronos SA, Zhang X, Moore JC, Shanmugam KT, Ingram LO (2008) Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate. Biotechnol Bioeng 99(5):1140–1153
Henry CS, Broadbelt LJ, Hatzimanikatis V (2010) Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate. Biotechnol Bioeng 106(3):462–473
Rathnasingh C, Raj SM, Jo JE, Park S (2009) Development and evaluation of efficient recombinant Escherichia coli strains for the production of 3-hydroxypropionic acid from glycerol. Biotechnol Bioeng 104(4):729–739
Borodina I, Kildegaard KR, Jensen NB, Blicher TH, Maury J, Sherstyk S, Schneider K, Lamosa P, Herrgard MJ, Rosenstand I, Oberg F, Forster J, Nielsen J (2015) Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via beta-alanine. Metab Eng 27:57–64
Chen Y, Bao J, Kim IK, Siewers V, Nielsen J (2014) Coupled incremental precursor and co-factor supply improves 3-hydroxypropionic acid production in Saccharomyces cerevisiae. Metab Eng 22:104–109
Maury J, Asadollahi MA, Moller K, Clark A, Nielsen J (2005) Microbial isoprenoid production: an example of green chemistry through metabolic engineering. Adv Biochem Eng Biotechnol 100:19–51
Withers ST, Keasling JD (2007) Biosynthesis and engineering of isoprenoid small molecules. Appl Microbiol Biotechnol 73(5):980–990
Paddon CJ, Westfall PJ, Pitera DJ, Benjamin K, Fisher K, McPhee D, Leavell MD, Tai A, Main A, Eng D, Polichuk DR, Teoh KH, Reed DW, Treynor T, Lenihan J, Fleck M, Bajad S, Dang G, Dengrove D, Diola D, Dorin G, Ellens KW, Fickes S, Galazzo J, Gaucher SP, Geistlinger T, Henry R, Hepp M, Horning T, Iqbal T, Jiang H, Kizer L, Lieu B, Melis D, Moss N, Regentin R, Secrest S, Tsuruta H, Vazquez R, Westblade LF, Xu L, Yu M, Zhang Y, Zhao L, Lievense J, Covello PS, Keasling JD, Reiling KK, Renninger NS, Newman JD (2013) High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 496(7446):528–532
Westfall PJ, Pitera DJ, Lenihan JR, Eng D, Woolard FX, Regentin R, Horning T, Tsuruta H, Melis DJ, Owens A, Fickes S, Diola D, Benjamin KR, Keasling JD, Leavell MD, McPhee DJ, Renninger NS, Newman JD, Paddon CJ (2012) Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. Proc Natl Acad Sci USA 109(3):E111–E118
Richter H, Qureshi N, Heger S, Dien B, Cotta MA, Angenent LT (2012) Prolonged conversion of n-butyrate to n-butanol with Clostridium saccharoperbutylacetonicum in a two-stage continuous culture with in-situ product removal. Biotechnol Bioeng 109(4):913–921
Atsumi S, Wu TY, Eckl EM, Hawkins SD, Buelter T, Liao JC (2010) Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes. Appl Microbiol Biotechnol 85(3):651–657
Connor MR, Liao JC (2008) Engineering of an Escherichia coli strain for the production of 3-methyl-1-butanol. Appl Environ Microbiol 74(18):5769–5775
Atsumi S, Liao JC (2008) Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli. Appl Environ Microbiol 74(24):7802–7808
Zhang K, Sawaya MR, Eisenberg DS, Liao JC (2008) Expanding metabolism for biosynthesis of nonnatural alcohols. Proc Natl Acad Sci USA 105(52):20653–20658
Zhang F, Carothers JM, Keasling JD (2012) Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 30(4):354–359
Liu A, Tan X, Yao L, Lu X (2013) Fatty alcohol production in engineered E. coli expressing Marinobacter fatty acyl-CoA reductases. Appl Microbiol Biotechnol 97(15):7061–7071
Choi YJ, Lee SY (2013) Microbial production of short-chain alkanes. Nature 502(7472):571–574
Peralta-Yahya PP, Ouellet M, Chan R, Mukhopadhyay A, Keasling JD, Lee TS (2011) Identification and microbial production of a terpene-based advanced biofuel. Nat Comm 2:483
Hara KY, Araki M, Okai N, Wakai S, Hasunuma T, Kondo A (2014) Development of bio-based fine chemical production through synthetic bioengineering. Microb Cell Fact 13:173
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Wang, M., Hou, J. (2016). Biorefinery of Lignocellulosics for Biofuels and Biochemicals. In: C.K. Lau, P. (eds) Quality Living Through Chemurgy and Green Chemistry. Green Chemistry and Sustainable Technology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-53704-6_7
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