[1]
Pauly, M.; Keegstra, K. Cell-wall carbohydrates and their modification as a resource for biofuels. Plant J., 2008, 54(4), 559-568. [http://dx.doi.org/10.1111/j.1365-313X.2008.03463.x]. [PMID: 18476863].
[2]
Sanderson, K. Lignocellulose: A chewy problem. Nature, 2011, 474(7352), S12-S14. [http://dx.doi.org/10.1038/474S012a]. [PMID: 21697834].
[3]
Purchase, D. Fungal applications in sustainable environmental biotechnology, 2016. [http://dx.doi.org/10.1007/978-3-319-42852-9].
[4]
Zhang, C.; Qi, W.; Wang, F.; Li, Q.; Su, R.; He, Z. Ethanol from corn stover using SSF: An economic assessment. Energy Sources B Econ. Plan. Policy, 2011, 6(2), 136-144. [http://dx.doi.org/10.1080/15567240903047640].
[5]
Goodell, B.; Qian, Y.; Jellison, J. Fungal decay of wood:
Soft Rot—Brown Rot—White Rot. ACS, 2009, 982, 9-31.
[6]
Blanchette, R.A.; Nilsson, T.; Daniel, G.; Abad, A. Biological
degradation of wood. ACS, 2009, 225, 141-174.
[7]
Brune, A. Symbiotic digestion of lignocellulose in termite guts. Nat. Rev. Microbiol., 2014, 12(3), 168-180. [http://dx.doi.org/10.1038/nrmicro3182]. [PMID: 24487819].
[8]
Zhu, L.; Wu, Q.; Dai, J.; Zhang, S.; Wei, F. Evidence of cellulose metabolism by the giant panda gut microbiome. Proc. Natl. Acad. Sci. USA, 2011, 108(43), 17714-17719. [http://dx.doi.org/10.1073/pnas.1017956108]. [PMID: 22006317].
[9]
Paddon, C.J.; Westfall, P.J.; Pitera, D.J.; Benjamin, K.; Fisher, K.; McPhee, D.; Leavell, M.D.; Tai, A.; Main, A.; Eng, D.; Polichuk, D.R.; Teoh, K.H.; Reed, D.W.; Treynor, T.; Lenihan, J.; Fleck, M.; Bajad, S.; Dang, G.; Dengrove, D.; Diola, D.; Dorin, G.; Ellens, K.W.; Fickes, S.; Galazzo, J.; Gaucher, S.P.; 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, L.F.; Xu, L.; Yu, M.; Zhang, Y.; Zhao, L.; Lievense, J.; Covello, P.S.; Keasling, J.D.; Reiling, K.K.; Renninger, N.S.; Newman, J.D. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature, 2013, 496(7446), 528-532. [http://dx.doi.org/10.1038/nature12051]. [PMID: 23575629].
[10]
Zhang, C.; Zou, R.; Chen, X.; Stephanopoulos, G.; Too, H.P. Experimental design-aided systematic pathway optimization of glucose uptake and deoxyxylulose phosphate pathway for improved amorphadiene production. Appl. Microbiol. Biotechnol., 2015, 99(9), 3825-3837. [http://dx.doi.org/10.1007/s00253-015-6463-y]. [PMID: 25715782].
[11]
Zhang, C.; Chen, X.; Stephanopoulos, G.; Too, H.P. Efflux transporter engineering markedly improves amorphadiene production in Escherichia coli. Biotechnol. Bioeng., 2016, 113(8), 1755-1763. [http://dx.doi.org/10.1002/bit.25943]. [PMID: 26804325].
[12]
Yuan, J.; Ching, C.B. Combinatorial engineering of mevalonate pathway for improved amorpha-4,11-diene production in budding yeast. Biotechnol. Bioeng., 2014, 111(3), 608-617. [http://dx.doi.org/10.1002/bit.25123]. [PMID: 24122315].
[13]
Ajikumar, P.K.; Xiao, W-H.; Tyo, K.E.; Wang, Y.; Simeon, F.; Leonard, E.; Mucha, O.; Phon, T.H.; Pfeifer, B.; Stephanopoulos, G. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science, 2010, 330(6000), 70-74. [http://dx.doi.org/10.1126/science.1191652]. [PMID: 20929806].
[14]
Zhou, K.; Qiao, K.; Edgar, S.; Stephanopoulos, G. Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nat. Biotechnol., 2015, 33(4), 377-383. [http://dx.doi.org/10.1038/nbt.3095]. [PMID: 25558867].
[15]
Thodey, K.; Galanie, S.; Smolke, C.D. A microbial biomanufacturing platform for natural and semisynthetic opioids. Nat. Chem. Biol., 2014, 10(10), 837-844. [http://dx.doi.org/10.1038/nchembio.1613]. [PMID: 25151135].
[16]
Nakagawa, A.; Matsumura, E.; Koyanagi, T.; Katayama, T.; Kawano, N.; Yoshimatsu, K.; Yamamoto, K.; Kumagai, H.; Sato, F.; Minami, H. Total biosynthesis of opiates by stepwise fermentation using engineered Escherichia coli. Nat. Commun., 2016, 7, 10390. [http://dx.doi.org/10.1038/ncomms10390]. [PMID: 26847395].
[17]
Galanie, S.; Thodey, K.; Trenchard, I.J.; Filsinger Interrante, M.; Smolke, C.D. Complete biosynthesis of opioids in yeast. Science, 2015, 349(6252), 1095-1100. [http://dx.doi.org/10.1126/science.aac9373]. [PMID: 26272907].
[18]
Salehi Jouzani, G.; Taherzadeh, M.J. Advances in consolidated bioprocessing systems for bioethanol and butanol production from biomass: a comprehensive review. Biofuel Res. J., 2015, 2(1), 152-195. [http://dx.doi.org/10.18331/BRJ2015.2.1.4].
[19]
Naik, S.N.; Goud, V.V.; Rout, P.K.; Dalai, A.K. Production of first and second generation biofuels: A comprehensive review. Renew. Sustain. Energy Rev., 2010, 14(2), 578-597. [http://dx.doi.org/10.1016/j.rser.2009.10.003].
[20]
Huang, R.; Su, R.; Qi, W.; He, Z. Bioconversion of lignocellulose into bioethanol: Process intensification and mechanism research. BioEnergy Res., 2011, 4(4), 225-245. [http://dx.doi.org/10.1007/s12155-011-9125-7].
[21]
Sanderson, K. Lignocellulose: A chewy problem. Nature, 2011, 474(7352), S12-S14. [http://dx.doi.org/10.1038/474S012a]. [PMID: 21697834].
[22]
Kim, J.S.; Lee, Y.Y.; Kim, T.H. A review on alkaline pretreatment technology for bioconversion of lignocellulosic biomass. Bioresour. Technol., 2016, 199, 42-48. [http://dx.doi.org/10.1016/j.biortech.2015.08.085]. [PMID: 26341010].
[23]
Cantarel, B.L.; Coutinho, P.M.; Rancurel, C.; Bernard, T.; Lombard, V.; Henrissat, B. The Carbohydrate-Active En-
Zymes database (CAZy): an ex-pert resource for Glycogenomics. Nucleic Acids Res., 2009, 37, (Datebase), D233-
D238.
[24]
Eastwood, D.C.; Floudas, D.; Binder, M.; Majcherczyk, A.; Schneider, P.; Aerts, A.; Asiegbu, F.O.; Baker, S.E.; Barry, K.; Bendiksby, M.; Blumentritt, M.; Coutinho, P.M.; Cullen, D.; de Vries, R.P.; Gathman, A.; Goodell, B.; Henrissat, B.; Ihrmark, K.; Kauserud, H.; Kohler, A.; LaButti, K.; Lapidus, A.; Lavin, J.L.; Lee, Y.H.; Lindquist, E.; Lilly, W.; Lucas, S.; Morin, E.; Murat, C.; Oguiza, J.A.; Park, J.; Pisabarro, A.G.; Riley, R.; Rosling, A.; Salamov, A.; Schmidt, O.; Schmutz, J.; Skrede, I.; Stenlid, J.; Wiebenga, A.; Xie, X.; Kües, U.; Hibbett, D.S.; Hoffmeister, D.; Högberg, N.; Martin, F.; Grigoriev, I.V.; Watkinson, S.C. The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science, 2011, 333(6043), 762-765. [http://dx.doi.org/10.1126/science.1205411]. [PMID: 21764756].
[25]
Kracher, D.; Scheiblbrandner, S.; Felice, A.K.; Breslmayr, E.; Preims, M.; Ludwicka, K.; Haltrich, D.; Eijsink, V.G.; Ludwig, R. Extracellular electron transfer systems fuel cellulose oxidative degradation. Science, 2016, 352(6289), 1098-1101. [http://dx.doi.org/10.1126/science.aaf3165]. [PMID: 27127235].
[26]
Floudas, D.; Binder, M.; Riley, R.; Barry, K.; Blanchette, R.A.; Henrissat, B.; Martínez, A.T.; Otillar, R.; Spatafora, J.W.; Yadav, J.S.; Aerts, A.; Benoit, I.; Boyd, A.; Carlson, A.; Copeland, A.; Coutinho, P.M.; de Vries, R.P.; Ferreira, P.; Findley, K.; Foster, B.; Gaskell, J.; Glotzer, D.; Górecki, P.; Heitman, J.; Hesse, C.; Hori, C.; Igarashi, K.; Jurgens, J.A.; Kallen, N.; Kersten, P.; Kohler, A.; Kües, U.; Kumar, T.K.; Kuo, A.; LaButti, K.; Larrondo, L.F.; Lindquist, E.; Ling, A.; Lombard, V.; Lucas, S.; Lundell, T.; Martin, R.; McLaughlin, D.J.; Morgenstern, I.; Morin, E.; Murat, C.; Nagy, L.G.; Nolan, M.; Ohm, R.A.; Patyshakuliyeva, A.; Rokas, A.; Ruiz-Dueñas, F.J.; Sabat, G.; Salamov, A.; Samejima, M.; Schmutz, J.; Slot, J.C.; St John, F.; Stenlid, J.; Sun, H.; Sun, S.; Syed, K.; Tsang, A.; Wiebenga, A.; Young, D.; Pisabarro, A.; Eastwood, D.C.; Martin, F.; Cullen, D.; Grigoriev, I.V.; Hibbett, D.S. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science, 2012, 336(6089), 1715-1719. [http://dx.doi.org/10.1126/science.1221748]. [PMID: 22745431].
[27]
Ohm, R.A.; de Jong, J.F.; Lugones, L.G.; Aerts, A.; Kothe, E.; Stajich, J.E.; de Vries, R.P.; Record, E.; Levasseur, A.; Baker, S.E.; Bartholomew, K.A.; Coutinho, P.M.; Erdmann, S.; Fowler, T.J.; Gathman, A.C.; Lombard, V.; Henrissat, B.; Knabe, N.; Kües, U.; Lilly, W.W.; Lindquist, E.; Lucas, S.; Magnuson, J.K.; Piumi, F.; Raudaskoski, M.; Salamov, A.; Schmutz, J.; Schwarze, F.W.; vanKuyk, P.A.; Horton, J.S.; Grigoriev, I.V.; Wösten, H.A. Genome sequence of the model mushroom Schizophyllum commune. Nat. Biotechnol., 2010, 28(9), 957-963. [http://dx.doi.org/10.1038/nbt.1643]. [PMID: 20622885].
[28]
Martinez, D.; Larrondo, L.F.; Putnam, N.; Gelpke, M.D.; Huang, K.; Chapman, J.; Helfenbein, K.G.; Ramaiya, P.; Detter, J.C.; Larimer, F.; Coutinho, P.M.; Henrissat, B.; Berka, R.; Cullen, D.; Rokhsar, D. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat. Biotechnol., 2004, 22(6), 695-700. [http://dx.doi.org/10.1038/nbt967]. [PMID: 15122302].
[29]
Martinez, D.; Challacombe, J.; Morgenstern, I.; Hibbett, D.; Schmoll, M.; Kubicek, C.P.; Ferreira, P.; Ruiz-Duenas, F.J.; Martinez, A.T.; Kersten, P.; Hammel, K.E.; Vanden Wymelenberg, A.; Gaskell, J.; Lindquist, E.; Sabat, G.; Bondurant, S.S.; Larrondo, L.F.; Canessa, P.; Vicuna, R.; Yadav, J.; Doddapaneni, H.; Subramanian, V.; Pisabarro, A.G.; Lavín, J.L.; Oguiza, J.A.; Master, E.; Henrissat, B.; Coutinho, P.M.; Harris, P.; Magnuson, J.K.; Baker, S.E.; Bruno, K.; Kenealy, W.; Hoegger, P.J.; Kües, U.; Ramaiya, P.; Lucas, S.; Salamov, A.; Shapiro, H.; Tu, H.; Chee, C.L.; Misra, M.; Xie, G.; Teter, S.; Yaver, D.; James, T.; Mokrejs, M.; Pospisek, M.; Grigoriev, I.V.; Brettin, T.; Rokhsar, D.; Berka, R.; Cullen, D. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc. Natl. Acad. Sci. USA, 2009, 106(6), 1954-1959. [http://dx.doi.org/10.1073/pnas.0809575106]. [PMID: 19193860].
[30]
Baldrian, P.; Valásková, V. Degradation of cellulose by basidiomycetous fungi. FEMS Microbiol. Rev., 2008, 32(3), 501-521. [http://dx.doi.org/10.1111/j.1574-6976.2008.00106.x]. [PMID: 18371173].
[31]
Kern, M.; McGeehan, J.E.; Streeter, S.D.; Martin, R.N.; Besser, K.; Elias, L.; Eborall, W.; Malyon, G.P.; Payne, C.M.; Himmel, M.E.; Schnorr, K.; Beckham, G.T.; Cragg, S.M.; Bruce, N.C.; McQueen-Mason, S.J. Structural characterization of a unique marine animal family 7 cellobiohydrolase suggests a mechanism of cellulase salt tolerance. Proc. Natl. Acad. Sci. USA, 2013, 110(25), 10189-10194. [http://dx.doi.org/10.1073/pnas.1301502110]. [PMID: 23733951].
[32]
Warnecke, F.; Luginbühl, P.; Ivanova, N.; Ghassemian, M.; Richardson, T.H.; Stege, J.T.; Cayouette, M.; McHardy, A.C.; Djordjevic, G.; Aboushadi, N.; Sorek, R.; Tringe, S.G.; Podar, M.; Martin, H.G.; Kunin, V.; Dalevi, D.; Madejska, J.; Kirton, E.; Platt, D.; Szeto, E.; Salamov, A.; Barry, K.; Mikhailova, N.; Kyrpides, N.C.; Matson, E.G.; Ottesen, E.A.; Zhang, X.; Hernández, M.; Murillo, C.; Acosta, L.G.; Rigoutsos, I.; Tamayo, G.; Green, B.D.; Chang, C.; Rubin, E.M.; Mathur, E.J.; Robertson, D.E.; Hugenholtz, P.; Leadbetter, J.R. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature, 2007, 450(7169), 560-565. [http://dx.doi.org/10.1038/nature06269]. [PMID: 18033299].
[33]
Watanabe, H.; Tokuda, G. Cellulolytic systems in insects. Annu. Rev. Entomol., 2010, 55, 609-632. [http://dx.doi.org/10.1146/annurev-ento-112408-085319]. [PMID: 19754245].
[34]
Ding, S-Y.; Liu, Y-S.; Zeng, Y.; Himmel, M.E.; Baker, J.O.; Bayer, E.A. How does plant cell wall nanoscale architecture correlate with enzymatic digestibility? Science, 2012, 338(6110), 1055-1060. [http://dx.doi.org/10.1126/science.1227491]. [PMID: 23180856].
[35]
Artzi, L.; Bayer, E.A.; Moraïs, S. Cellulosomes: bacterial nanomachines for dismantling plant polysaccharides. Nat. Rev. Microbiol., 2017, 15(2), 83-95. [http://dx.doi.org/10.1038/nrmicro.2016.164]. [PMID: 27941816].
[36]
Eriksson, T.; Karlsson, J.; Tjerneld, F. A model explaining declining rate in hydrolysis of lignocellulose substrates with cellobiohydrolase I (cel7A) and endoglucanase I (cel7B) of Trichoderma reesei. Appl. Biochem. Biotechnol., 2002, 101(1), 41-60. [http://dx.doi.org/10.1385/ABAB:101:1:41]. [PMID: 12008866].
[37]
You, C.; Zhang, Y-H. Self-assembly of synthetic metabolons through synthetic protein scaffolds: one-step purification, co-immobilization, and substrate channeling. ACS Synth. Biol., 2013, 2(2), 102-110. [http://dx.doi.org/10.1021/sb300068g]. [PMID: 23656373].
[38]
Cox, D.B.; Platt, R.J.; Zhang, F. Therapeutic genome editing: prospects and challenges. Nat. Med., 2015, 21(2), 121-131. [http://dx.doi.org/10.1038/nm.3793]. [PMID: 25654603].
[39]
Davidi, L.; Moraïs, S.; Artzi, L.; Knop, D.; Hadar, Y.; Arfi, Y.; Bayer, E.A. Toward combined delignification and saccharification of wheat straw by a laccase-containing designer cellulosome. Proc. Natl. Acad. Sci. USA, 2016, 113(39), 10854-10859. [http://dx.doi.org/10.1073/pnas.1608012113]. [PMID: 27621442].
[40]
Zhang, H.; Wang, X. Modular co-culture engineering, a new approach for metabolic engineering. Metab. Eng., 2016, 37, 114-121. [http://dx.doi.org/10.1016/j.ymben.2016.05.007]. [PMID: 27242132].
[41]
Gustavsson, M.; Lee, S.Y. Prospects of microbial cell factories developed through systems metabolic engineering. Microb. Biotechnol., 2016, 9(5), 610-617. [http://dx.doi.org/10.1111/1751-7915.12385]. [PMID: 27435545].
[42]
Newman, D.J.; Cragg, G.M. Natural products as sources of new drugs over the last 25 years. J. Nat. Prod., 2007, 70(3), 461-477. [http://dx.doi.org/10.1021/np068054v]. [PMID: 17309302].
[43]
Eichenberger, M.; Lehka, B.J.; Folly, C.; Fischer, D.; Martens, S.; Simón, E.; Naesby, M. Metabolic engineering of Saccharomyces cerevisiae for de novo production of dihydrochalcones with known antioxidant, antidiabetic, and sweet tasting properties. Metab. Eng., 2017, 39, 80-89. [http://dx.doi.org/10.1016/j.ymben.2016.10.019]. [PMID: 27810393].
[44]
Koopman, F.; Beekwilder, J.; Crimi, B.; van Houwelingen, A.; Hall, R.D.; Bosch, D.; van Maris, A.J.; Pronk, J.T.; Daran, J.M. De novo production of the flavonoid naringenin in engineered Saccharomyces cerevisiae. Microb. Cell Fact., 2012, 11, 155. [http://dx.doi.org/10.1186/1475-2859-11-155]. [PMID: 23216753].
[45]
Tu, Y. The discovery of artemisinin (qinghaosu) and gifts from Chinese medicine. Nat. Med., 2011, 17(10), 1217-1220. [http://dx.doi.org/10.1038/nm.2471]. [PMID: 21989013].
[46]
Ro, D-K.; Paradise, E.M.; Ouellet, M.; Fisher, K.J.; Newman, K.L.; Ndungu, J.M.; Ho, K.A.; Eachus, R.A.; Ham, T.S.; Kirby, J.; Chang, M.C.; Withers, S.T.; Shiba, Y.; Sarpong, R.; Keasling, J.D. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature, 2006, 440(7086), 940-943. [http://dx.doi.org/10.1038/nature04640]. [PMID: 16612385].
[47]
Zhang, C.; Chen, X.; Zou, R.; Zhou, K.; Stephanopoulos, G.; Too, H.P. Combining genotype improvement and statistical media optimization for isoprenoid production in E. coli. PLoS One, 2013, 8(10)e75164 [http://dx.doi.org/10.1371/journal.pone.0075164]. [PMID: 24124471].
[48]
Zou, R.; Zhou, K.; Stephanopoulos, G.; Too, H.P. Combinatorial engineering of 1-deoxy-D-xylulose 5-phosphate pathway using cross-lapping in vitro assembly (CLIVA) method. PLoS One, 2013, 8(11)e79557 [http://dx.doi.org/10.1371/journal.pone.0079557]. [PMID: 24223968].
[49]
Westfall, P.J.; Pitera, D.J.; Lenihan, J.R.; Eng, D.; Woolard, F.X.; Regentin, R.; Horning, T.; Tsuruta, H.; Melis, D.J.; Owens, A.; Fickes, S.; Diola, D.; Benjamin, K.R.; Keasling, J.D.; Leavell, M.D.; McPhee, D.J.; Renninger, N.S.; Newman, J.D.; Paddon, C.J. Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. Proc. Natl. Acad. Sci. USA, 2012, 109(3), E111-E118. [http://dx.doi.org/10.1073/pnas.1110740109]. [PMID: 22247290].
[50]
Yuan, J.; Ching, C.B. Dynamic control of ERG9 expression for improved amorpha-4,11-diene production in Saccharomyces cerevisiae. Microb. Cell Fact., 2015, 14, 38. [http://dx.doi.org/10.1186/s12934-015-0220-x]. [PMID: 25889168].
[51]
Zhou, K.; Zou, R.; Zhang, C.; Stephanopoulos, G.; Too, H.P. Optimization of amorphadiene synthesis in bacillus subtilis via transcriptional, translational, and media modulation. Biotechnol. Bioeng., 2013, 110(9), 2556-2561. [http://dx.doi.org/10.1002/bit.24900]. [PMID: 23483530].
[52]
Hao, X. Pan, J.; Zhu, X; Natural Products, 2013, pp. 2797-2812. [http://dx.doi.org/10.1007/978-3-642-22144-6_124]
[53]
Kusari, S.; Singh, S.; Jayabaskaran, C. Rethinking production of Taxol® (paclitaxel) using endophyte biotechnology. Trends Biotechnol., 2014, 32(6), 304-311. [http://dx.doi.org/10.1016/j.tibtech.2014.03.011]. [PMID: 24810040].
[54]
Peplow, M. Synthetic biology’s first malaria drug meets market resistance. Nature, 2016, 530(7591), 389-390. [http://dx.doi.org/10.1038/530390a]. [PMID: 26911755].
[55]
Minty, J.J.; Singer, M.E.; Scholz, S.A.; Bae, C.H.; Ahn, J.H.; Foster, C.E.; Liao, J.C.; Lin, X.N. Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc. Natl. Acad. Sci. USA, 2013, 110(36), 14592-14597. [http://dx.doi.org/10.1073/pnas.1218447110]. [PMID: 23959872].
[56]
Kothe, E. Mating-type genes for basidiomycete strain improvement in mushroom farming. Appl. Microbiol. Biotechnol., 2001, 56(5-6), 602-612. [http://dx.doi.org/10.1007/s002530100763]. [PMID: 11601606].
[57]
Song, H.; Ding, M.Z.; Jia, X.Q.; Ma, Q.; Yuan, Y.J. Synthetic microbial consortia: From systematic analysis to construction and applications. Chem. Soc. Rev., 2014, 43(20), 6954-6981. [http://dx.doi.org/10.1039/C4CS00114A]. [PMID: 25017039].
[58]
Li, Y.; Smolke, C.D. Engineering biosynthesis of the anticancer alkaloid noscapine in yeast. Nat. Commun., 2016, 7, 12137. [http://dx.doi.org/10.1038/ncomms12137]. [PMID: 27378283].