Switchgrass Biomass Content, Synthesis, and Biochemical Conversion to Biofuels

Compendium of Bioenergy Plants: Switchgrass

Volumn , Issue , 2014, Pages 109-169

  Bartley, Laura ^a   Xu, Tao ^a   Zhang, Chengcheng ^a   Nguyen, Hoang ^a   Zhou, Jizhong ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85042812910     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/b16681-10     Document Type: Chapter

References (275)

1. Abdulrazzak, N., B. Pollet, J. Ehlting, K. Larsen, C. Asnaghi, S. Ronseau, C. Proux, M. Erhardt, V. Seltzer, J.P. Renou, P. Ullmann, M. Pauly, C. Lapierre and D. Werck-Reichhart. 2006. A coumaroyl-ester-3-hydroxylase insertion mutant reveals the existence of nonredundant meta-hydroxylation pathways and essential roles for phenolic precursors in cell expansion and plant growth. Plant Physiol. 140: 30-48.
2. Abramson, M., O. Shoseyov and Z. Shani. 2010. Plant cell wall reconstruction toward improved lignocellulosic production and processability. Plant Science 178: 61-72.
3. Adlakha, N., R. Rajagopal, S. Kumar, V.S. Reddy and S.S. Yazdani. 2011. Synthesis and characterization of chimeric proteins based on cellulase and xylanase from an insect gut bacterium. Appl. Environ. Microbiol. 77: 4859-4866.
4. Agbor, V.B., N. Cicek, R. Sparling, A. Berlin and D.B. Levin. 2011. Biomass pretreatment: Fundamentals toward application. Biotechnol. Adv. 29: 675-685.
5. Akin, D.E., L.L. Rigsby, A. Sethuraman, W.H. Morrison, G.R. Gamble and K.E. Eriksson. 1995. Alterations in structure, chemistry, and biodegradability of grass lignocellulose treated with the white rot fungi Ceriporiopsis subvermispora and Cyathus stercoreus. Appl. Environ. Microbiol. 61: 1591-1598.
6. Alexander, J.K. 1968. Purification and specificity of cellobiose phosphorylase from Clostridium thermocellum. J. Biol. Chem. 243: 2899-2904.
7. Alvira, P., A.D. Moreno, D. Ibarra, F. Sáez and M. Ballesteros. 2013. Improving the fermentation performance of Saccharomyces cerevisiae by laccase during ethanol production from steamexploded wheat straw at high-substrate loadings. Biotechnol. Progress 29: 74-82.
8. Ambavaram, M.M., A. Krishnan, K.R. Trijatmiko and A. Pereira. 2012. Coordinated activation of cellulose and repression of lignin biosynthesis pathways in rice. Plant Physiol. 155: 916-931.
9. Anders, N., M.D. Wilkinson, A. Lovegrove, J. Freeman, T. Tryfona, T.K. Pellny, T. Weimar, J.C. Mortimer, K. Stott, J.M. Baker, M. Defoin-Platel, P.R. Shewry, P. Dupree and R.A. Mitchell. 2012. Glycosyl transferases in family 61 mediate arabinofuranosyl transfer onto xylan in grasses. Proc. Natl. Acad. Sci. USA 109: 989-993.
10. Appenzeller, L., M. Doblin, R. Barreiro, H.Y. Wang, X.M. Niu, K. Kollipara, L. Carrigan, D. Tomes, M. Chapman and K.S. Dhugga. 2004. Cellulose synthesis in maize: isolation and expression analysis of the cellulose synthase (CesA) gene family. Cellulose 11: 287-299.
11. Arioli, T., L. Peng, A.S. Betzner, J. Burn, W. Wittke, W. Herth, C. Camilleri, H. Hofte, J. Plazinski, R. Birch, A. Cork, J. Glover, J. Redmond and R.E. Williamson. 1998. Molecular analysis of cellulose biosynthesis in Arabidopsis. Science 279: 717-720.
12. Arora, D.S. and R.K. Sharma. 2010. Ligninolytic fungal laccases and their biotechnological applications. Appl. Biochem. Biotechnol. 160: 1760-1788.
13. Balan, V., B. Bals, S.S. Chundawat, D. Marshall and B. Dale. 2009. Lignocellulosic biomass pretreatment using AFEX. Biofuels. J. R. Mielenz, Humana Press. 581: 61-77.
14. Bartley, L.E., M.L. Peck, S.R. Kim, B. Ebert, C. Maniseri, D.M. Chiniquy, R. Sykes, L. Gao, C. Rautengarten, P. Benke, P. Canlas, P. Cao, X. Zhang, F. Lin, M.E. Vega-Sanchez, R. Jentoff, J. Zhou, A. Ziebell, G. An, H.V. Scheller and P.C. Ronald. 2013a. Over expression of OsAT10, a member of a grass-expanded clade of BAHD acyltransferases, alters rice cell wall polysaccharide hydroxycinnamic acids and saccharification. Plant Physiol. 161: 1615-1633.
15. Bartley, L.E., Y. Wu, A.J. Saathoff and G. Sarath. 2013b. Switchgrass genetics and breeding challenges. Biomass Crops: Breeding and Genetics. M. Saha, Wiley-Blackwell (in press).
16. Baucher, M., C. Halpin, M. Petit-Conil and W. Boerjan. 2003. Lignin: genetic engineering and impact on pulping. Crit. Rev. Biochem. Mol. Biol. 38: 305-350.
17. Bayer, E.A. and R. Lamed. 1986. Ultrastructure of the cell surface cellulosome of Clostridium thermocellum and its interaction with cellulose. J. Bacteriol. 167: 828-836.
18. Bayer, E.A., L.J. Shimon, Y. Shoham and R. Lamed. 1998. Cellulosomes-structure and ultrastructure. J. Struct. Biol. 124: 221-234.
19. Beloqui, A., M. Pita, J. Polaina, A. Martinez-Arias, O.V. Golyshina, M. Zumarraga, M.M. Yakimov, H. Garcia-Arellano, M. Alcalde, V.M. Fernandez, K. Elborough, J.M. Andreu, A. Ballesteros, F.J. Plou, K.N. Timmis, M. Ferrer and P.N. Golyshin. 2006. Novel polyphenol oxidase mined from a metagenome expression library of bovine rumen: biochemical properties, structural analysis, and phylogenetic relationships. J. Biol. Chem. 281: 22933-22942.
20. Berg Miller, M.E., D.A. Antonopoulos, M.T. Rincon, M. Band, A. Bari, T. Akraiko, A. Hernandez, J. Thimmapuram, B. Henrissat, P.M. Coutinho, I. Borovok, S. Jindou, R. Lamed, H.J. Flint, E.A. Bayer and B.A. White. 2009. Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. PLoS One 4: e6650.
21. Besseau, S., L. Hoffmann, P. Geoffroy, C. Lapierre, B. Pollet and M. Legrand. 2007. Flavonoid accumulation in Arabidopsis repressed in lignin synthesis affects auxin transport and plant growth. Plant Cell 19: 148-162.
22. Betancur, L., B. Singh, R.A. Rapp, J.F. Wendel, M.D. Marks, A.W. Roberts and C.H. Haigler. 2010. Phylogenetically distinct cellulose synthase genes support secondary wall thickening in arabidopsis shoot trichomes and cotton fiber. J. Integr. Plant Biol. 52: 205-220.
23. Brachypodium Genome Initiative. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768.
24. Bhargava, A., S.D. Mansfield, H.C. Hall, C.J. Douglas and B.E. Ellis. 2010. MYB75 functions in regulation of secondary cell wall formation in the Arabidopsis inflorescence stem. Plant Physiol. 154: 1428-1438.
25. Blouzard, J.C., P.M. Coutinho, H.P. Fierobe, B. Henrissat, S. Lignon, C. Tardif, S. Pages and P. de Philip. 2010. Modulation of cellulosome composition in Clostridium cellulolyticum: adaptation to the polysaccharide environment revealed by proteomic and carbohydrateactive enzyme analyses. Proteomics 10: 541-554.
26. Boateng, A.A., K.B. Hicks and K.P. Vogel. 2006. Pyrolysis of switchgrass (Panicum virgatum) harvested at several stages of maturity. J. of Anal. Applied Pyrolysis 75: 55-64.
27. Boerjan, W., J. Ralph and M. Baucher. 2003. Lignin biosynthesis. Annu. Rev. Plant Biol. 54: 519-546.
28. Bokinsky, G., P.P. Peralta-Yahya, A. George, B.M. Holmes, E.J. Steen, J. Dietrich, T. Soon Lee, D. Tullman-Ercek, C.A. Voigt, B.A. Simmons and J.D. Keasling. 2011. Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. Proc. Natl. Acad. Sci. USA 108: 19949-19954.
29. Bonawitz, N.D. and C. Chapple. 2013. Can genetic engineering of lignin deposition be accomplished without an unacceptable yield penalty? Curr. Opin. Biotechnol. 24: 336-343.
30. Borkhardt, B., J. Harholt, P. Ulvskov, B.K. Ahring, B. Jørgensen and H. Brinch-Pedersen. 2010. Autohydrolysis of plant xylans by apoplastic expression of thermophilic bacterial endoxylanases. Plant Biotechnol. J. 8: 363-374.
31. Bourbonnais, R., M.G. Paice, I.D. Reid, P. Lanthier and M. Yaguchi. 1995. Lignin oxidation by laccase isozymes from Trametes versicolor and role of the mediator 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonate) in kraft lignin depolymerization. Appl. Environ. Microbiol. 61: 1876-1880.
32. Brown, D., R. Wightman, Z. Zhang, L.D. Gomez, I. Atanassov, J.P. Bukowski, T. Tryfona, S.J. McQueen-Mason, P. Dupree and S. Turner. 2011. Arabidopsis genes IRREGULAR XYLEM (IRX15) and IRX15L encode DUF579-containing proteins that are essential for normal xylan deposition in the secondary cell wall. Plant J. 66: 401-413.
33. Brown, D.M., F. Goubet, V. W. Wong, R. Goodacre, E. Stephens, P. Dupree and S.R. Turner. 2007. Comparison of five xylan synthesis mutants reveals new insight into the mechanisms of xylan synthesis. Plant J. 52: 1154-1168.
34. Brown, D.M., Z. Zhang, E. Stephens, P. Dupree and S.R. Turner. 2009. Characterization of IRX10 and IRX10-like reveals an essential role in glucuronoxylan biosynthesis in Arabidopsis. Plant J. 57: 732-746.
35. Brunecky, R., M.J. Selig, T.B. Vinzant, M.E. Himmel, D. Lee, M.J. Blaylock and S.R. Decker. 2011. In planta expression of A. cellulolyticus Cel5A endocellulase reduces cell wall recalcitrance in tobacco and maize. Biotechnol. Biofuels 4: 1.
36. Buanafina, M.M. 2009. Feruloylation in grasses: Current and future perspectives. Mol. Plant 2: 861-872.
37. Buanafina, M.M., T. Langdon, B. Hauck, S.J. Dalton and P. Morris. 2006. Manipulating the phenolic acid content and digestibility of italian ryegrass (Lolium multiflorum) by vacuolartargeted expression of a fungal ferulic acid esterase. Appl. Biochem. Biotechnol. 129-132: 416-426.
38. Buanafina, M.M.d.O., T. Langdon, B. Hauck, S. Dalton and P. Morris. 2008. Expression of a fungal ferulic acid esterase increases cell wall digestibility of tall fescue (Festuca arundinacea). Plant Biotechnol. J. 6: 264-280.
39. Buanafina, M.M.d.O., T. Langdon, B. Hauck, S. Dalton, E. Timms-Taravella and P. Morris. 2010. Targeting expression of a fungal ferulic acid esterase to the apoplast, endoplasmic reticulum or golgi can disrupt feruloylation of the growing cell wall and increase the biodegradability of tall fescue (Festuca arundinacea). Plant Biotechnol. J. 8: 316-331.
40. Bugg, T.D., M. Ahmad, E.M. Hardiman and R. Singh. 2011. The emerging role for bacteria in lignin degradation and bio-product formation. Curr. Opin. Biotechnol. 22: 394-400.
41. Bunzel, M., J. Ralph, F. Lu, R.D. Hatfield and H. Steinhart. 2004. Lignins and ferulate-coniferyl alcohol cross-coupling products in cereal grains. J. Agric. Food Chem. 52: 6496-6502.
42. Cano-Delgado, A., S. Penfield, C. Smith, M. Catley and M. Bevan. 2003. Reduced cellulose synthesis invokes lignification and defense responses in Arabidopsis thaliana. Plant J. 34: 351-362.
43. Cantarel, B.L., P.M. Coutinho, C. Rancurel, T. Bernard, V. Lombard and B. Henrissat. 2009. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic. Acids Res. 37: D233-238.
44. Carpita, N.C. 2011. Update on mechanisms of plant cell wall biosynthesis: how plants make cellulose and other (1->4)-beta-D-glycans. Plant Physiol. 155: 171-184.
45. Carpita, N.C. 2012. Progress in the biological synthesis of the plant cell wall: new ideas for improving biomass for bioenergy. Curr. Opin. Biotechnol. 23: 330-337.
46. Casler, M.D. and H.-J.G. Jung. 2006. Relationships of fibre, lignin, and phenolics to in vitro fibre digestibility in three perennial grasses. Animal Feed Science and Technology 125: 151-161.
47. Casler, M.D., C.M. Tobias, S.M. Kaeppler, C.R. Buell, Z.-Y. Wang, P. Cao, J. Schmutz and P. Ronald. 2011. The switchgrass genome: Tools and strategies. Plant Genome 4: 273-282.
48. Chang, V.S. and M.T. Holtzapple. 2000. Fundamental factors affecting biomass enzymatic reactivity. Appl. Biochem. Biotechnol. 84-86: 5-37.
49. Chen, F., M.S. Srinivasa Reddy, S. Temple, L. Jackson, G. Shadle and R.A. Dixon. 2006. Multisite genetic modulation of monolignol biosynthesis suggests new routes for formation of syringyl lignin and wall-bound ferulic acid in alfalfa (Medicago sativa L.). Plant J. 48: 113-124.
50. Chen, X., M.E. Vega-Sánchez, Y. Verhertbruggen, D. Chiniquy, P.E. Canlas, A. Fagerström, L. Prak, U. Christensen, A. Oikawa, M. Chern, S. Zuo, F. Lin, M. Auer, W.G.T. Willats, L. Bartley, J. Harholt, H.V. Scheller and P.C. Ronald. 2013. Inactivation of OsIRX10 leads to decreased xylan content in rice culm cell walls and improved biomass saccharification. Mol. Plant. 6: 570-573.
51. Chiniquy, D., V. Sharma, A. Schultink, E.E. Baidoo, C. Rautengarten, K. Cheng, A. Carroll, P. Ulvskov, J. Harholt, J.D. Keasling, M. Pauly, H.V. Scheller and P.C. Ronald. 2012. XAX1from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan. Proc. Natl. Acad. Sci. USA 109: 17117-17122.
52. Chou, H.L., Z. Dai, C.W. Hsieh and M.S. Ku. 2011. High level expression of Acidothermus cellulolyticus β-1, 4-endoglucanase in transgenic rice enhances the hydrolysis of its straw by cultured cow gastric fluid. Biotechnol. Biofuels 4: 58.
53. Chuck, G.S., C. Tobias, L. Sun, F. Kraemer, C. Li, D. Dibble, R. Arora, J.N. Bragg, J.P. Vogel, S. Singh, B.A. Simmons, M. Pauly and S. Hake. 2011. Overexpression of the maize Corngrass1 microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass. Proc. Natl. Acad. Sci. USA 108: 17550-17555.
54. Coco, W.M., W.E. Levinson, M.J. Crist, H.J. Hektor, A. Darzins, P.T. Pienkos, C.H. Squires and D.J. Monticello. 2001. DNA shuffling method for generating highly recombined genes and evolved enzymes. Nat. Biotechnol. 19: 354-359.
55. Cortese, L., J. Honig, C. Miller and S. Bonos. 2010. Genetic diversity of twelve switchgrass populations using molecular and morphological markers. BioEnergy Res. 3: 262-271.
56. Cosgrove, D.J. 1999. Enzymes and other agents that enhance cell wall extensibility. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 391-417.
57. Cosgrove, D.J. 2005. Growth of the plant cell wall. Nat. Rev. Mol. Cell Biol. 6: 850-861.
58. Crowell, E.F., M. Gonneau, Y.D. Stierhof, H. Hofte and S. Vernhettes. 2010. Regulated trafficking of cellulose synthases. Curr. Opin. Plant Biol. 13: 700-705.
59. Dai, Z., B.S. Hooker, R.D. Quesenberry and J. Gao. 1999. Expression of Trichoderma reesei exocellobiohydrolase I in transgenic tobacco leaves and calli. Appl. Biochem. Biotechnol. 77-79: 689-699.
60. Devos, K.M. 2005. Updating the ‘crop circle’. Curr. Opin. Plant Biol. 8: 155-162.
61. Ding, S.Y., E.A. Bayer, D. Steiner, Y. Shoham and R. Lamed. 2000. A scaffoldin of the Bacteroides cellulosolvens cellulosome that contains 11 type II cohesins. J. Bacteriol. 182: 4915-4925.
62. Doblin, M.S., I. Kurek, D. Jacob-Wilk and D.P. Delmer. 2002. Cellulose biosynthesis in plants: from genes to rosettes. Plant Cell Physiol. 43: 1407-1420.
63. Doi, R.H. 2008. Cellulases of mesophilic microorganisms: cellulosome and noncellulosome producers. Ann. N. Y. Acad. Sci. 1125: 267-279.
64. Doi, R.H. and A. Kosugi. 2004. Cellulosomes: plant-cell-wall-degrading enzyme complexes. Nat. Rev. Microbiol. 2: 541-551.
65. Domon, J.M., L. Baldwin, S. Acket, E. Caudeville, S. Arnoult, H. Zub, F. Gillet, I. Lejeune-Henaut, M. Brancourt-Hulmel, J. Pelloux and C. Rayon. 2012. Cell wall compositional modifications of Miscanthus ecotypes in response to cold acclimation. Phytochemistry.
66. Eggert, C., U. Temp and K.E. Eriksson. 1997. Laccase is essential for lignin degradation by the white-rot fungus Pycnoporus cinnabarinus. FEBS Lett. 407: 89-92.
67. Ellis, C., I. Karafyllidis, C. Wasternack and J.G. Turner. 2002. The Arabidopsis mutant cev1 links cell wall signaling to jasmonate and ethylene responses. Plant Cell 14: 1557-1566.
68. Ellis, C. and J.G. Turner. 2001. The Arabidopsis mutant cev1 has constitutively active jasmonate and ethylene signal pathways and enhanced resistance to pathogens. Plant Cell 13: 1025-1033.
69. Endler, A. and S. Persson. 2011. Cellulose synthases and synthesis in Arabidopsis. Mol. Plant 4: 199-211.
70. Escamilla-Trevino, L.L., H. Shen, S.R. Uppalapati, T. Ray, Y.H. Tang, T. Hernandez, Y.B. Yin, Y. Xu and R.A. Dixon. 2010. Switchgrass (Panicum virgatum) possesses a divergent family of cinnamoyl CoA reductases with distinct biochemical properties. New Phytol. 185: 143-155.
71. Fagard, M., T. Desnos, T. Desprez, F. Goubet, G. Refregier, G. Mouille, M. McCann, C. Rayon, S. Vernhettes and H. Hofte. 2000. PROCUSTE1 encodes a cellulose synthase required for normal cell elongation specifically in roots and dark-grown hypocotyls of Arabidopsis. Plant Cell 12: 2409-2424.
72. Faik, A. 2010. Xylan biosynthesis: news from the grass. Plant Physiol. 153: 396-402.
73. Fan, L.H., Z.J. Zhang, X.Y. Yu, Y.X. Xue and T.W. Tan. 2012. Self-surface assembly of cellulosomes with two miniscaffoldins on Saccharomyces cerevisiae for cellulosic ethanol production. Proc Natl Acad. Sci. USA 109: 13260-13265.
74. Fargione, J., J. Hill, D. Tilman, S. Polasky and P. Hawthorne. 2008. Land clearing and the biofuel carbon debt. Science 319: 1235-1238.
75. Farrell, A.E., R.J. Plevin, B. T. Turner, A. D. Jones, M. O’Hare and D.M. Kammen. 2006. Ethanol can contribute to energy and environmental goals. Science 311: 506-508.
76. Fenel, F., M. Leisola, J. Janis and O. Turunen. 2004. A de novo designed N-terminal disulphide bridge stabilizes the Trichoderma reesei endo-1,4-beta-xylanase II. J. Biotechnol. 108: 137-143.
77. Filho, E.X., M.G. Tuohy, J. Puls and M.P. Coughlan. 1991. The xylan-degrading enzyme systems of Penicillium capsulatum and Talaromyces emersonii. Biochem. Soc. Trans 19: 25S.
78. Floudas, D., M. Binder, R. Riley, K. Barry, R.A. Blanchette, B. Henrissat, A.T. Martinez, R. Otillar, J.W. Spatafora, J. S. Yadav, A. Aerts, I. Benoit, A. Boyd, A. Carlson, A. Copeland, P.M. Coutinho, R.P. de Vries, P. Ferreira, K. Findley, B. Foster, J. Gaskell, D. Glotzer, P. Gorecki, J. Heitman, C. Hesse, C. Hori, K. Igarashi, J.A. Jurgens, N. Kallen, P. Kersten, A. Kohler, U. Kues, T.K. Kumar, A. Kuo, K. LaButti, L. F. Larrondo, E. Lindquist, A. Ling, V. Lombard, S. Lucas, T. Lundell, R. Martin, D.J. McLaughlin, I. Morgenstern, E. Morin, C. Murat, L.G. Nagy, M. Nolan, R.A. Ohm, A. Patyshakuliyeva, A. Rokas, F. J. Ruiz-Duenas, G. Sabat, A. Salamov, M. Samejima, J. Schmutz, J. C. Slot, F. St John, J. Stenlid, H. Sun, S. Sun, K. Syed, A. Tsang, A. Wiebenga, D. Young, A. Pisabarro, D.C. Eastwood, F. Martin, D. Cullen, I.V. Grigoriev and D.S. Hibbett. 2012. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336: 1715-1719.
79. Fontes, C.M. and H.J. Gilbert. 2010. Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates. Annu. Rev. Biochem. 79: 655-681.
80. Fornale, S., X. Shi, C. Chai, A. Encina, S. Irar, M. Capellades, E. Fuguet, J.L. Torres, P. Rovira, P. Puigdomenech, J. Rigau, E. Grotewold, J. Gray and D. Caparros-Ruiz. 2010. ZmMYB31 directly represses maize lignin genes and redirects the phenylpropanoid metabolic flux. Plant J. 64: 633-644.
81. Fu, C., J.R. Mielenz, X. Xiao, Y. Ge, C.Y. Hamilton, M. Rodriguez, Jr., F. Chen, M. Foston, A. Ragauskas, J. Bouton, R.A. Dixon and Z.Y. Wang. 2011. Genetic manipulation of lignin reduces recalcitrance and improves ethanol production from switchgrass. Proc. Natl. Acad. Sci. USA 108: 3803-3808.
82. Fu, C., X. Xiao, Y. Xi, Y. Ge, F. Chen, J. Bouton, R.A. Dixon and Z.-Y. Wang. 2011. Downregulation of cinnamyl alcohol dehydrogenase (CAD) leads to improved saccharification efficiency in switchgrass. BioEnergy Res. 4: 153-164.
83. Galbe, M. and G. Zacchi. 2007. Pretreatment of lignocellulosic materials for efficient bioethanol production. Biofuels. L. Olsson, Springer Berlin Heidelberg. 108: 41-65.
84. Gan, J., W. Yuan, L. Johnson, D. Wang, R. Nelson and K. Zhang. 2012. Hydrothermal conversion of big bluestem for bio-oil production: The effect of ecotype and planting location. Bioresour. Technol. 116: 413-420.
85. Gilbert, H.J. 2010. The biochemistry and structural biology of plant cell wall deconstruction. Plant Physiol. 153: 444-455.
86. Gilbert, H.J., H. Stalbrand and H. Brumer. 2008. How the walls come crumbling down: recent structural biochemistry of plant polysaccharide degradation. Curr. Opin. Plant Biol. 11: 338-348.
87. Girio, F.M., C. Fonseca, F. Carvalheiro, L.C. Duarte, S. Marques and R. Bogel-Lukasik. 2010. Hemicelluloses for fuel ethanol: A review. Bioresour. Technol. 101: 4775-4800.
88. Gold, M.H. and M. Alic. 1993. Molecular biology of the lignin-degrading basidiomycete Phanerochaete chrysosporium. Microbiol. Rev. 57: 605-622.
89. Goyal, G., S.L. Tsai, B. Madan, N.A. DaSilva and W. Chen. 2011. Simultaneous cell growth and ethanol production from cellulose by an engineered yeast consortium displaying a functional mini-cellulosome. Microb. Cell Fact. 10: 89.
90. Gray, B.N., O. Bougri, A.R. Carlson, J. Meissner, S. Pan, M.H. Parker, D. Zhang, V. Samoylov, N.A. Ekborg and R. Michael Raab. 2011. Global and grain-specific accumulation of glycoside hydrolase family 10 xylanases in transgenic maize (Zea mays). Plant Biotechnol. J. 9: 1100-1108.
91. Gray, J., D. Caparrós-Ruiz and E. Grotewold. 2012. Grass phenylpropanoids: Regulate before using! Plant Science 184: 112-120.
92. Gruno, M., P. Valjamae, G. Pettersson and G. Johansson. 2004. Inhibition of the Trichoderma reesei cellulases by cellobiose is strongly dependent on the nature of the substrate. Biotechnol. Bioeng. 86: 503-511.
93. Handakumbura, P.P. and S.P. Hazen. 2012. Transcriptional regulation of grass secondary cell wall biosynthesis: Playing catch-up with Arabidopsis thaliana. Front Plant Sci. 3: 74.
94. Harholt, J., I.C. Bach, S. Lind-Bouquin, K.J. Nunan, S.M. Madrid, H. Brinch-Pedersen, P. B. Holm and H.V. Scheller. 2010. Generation of transgenic wheat (Triticum aestivum L.) accumulating heterologous endo-xylanase or ferulic acid esterase in the endosperm. Plant Biotechnol. J. 8: 351-362.
95. Harrington, M.J., M. Mutwil, Y. Barrière, R. Sibout, L. Jouanin and C. Lapierre. 2012. Molecular biology of lignification in grasses. Adv. Botan. Res. 61: 77-112.
96. Harris, D.M., K. Corbin, T. Wang, R. Gutierrez, A.L. Bertolo, C. Petti, D.-M. Smilgies, J.M. Estevez, D. Bonetta, B.R. Urbanowicz, D.W. Ehrhardt, C.R. Somerville, J.K.C. Rose, M. Hong and S. DeBolt. 2012. Cellulose microfibril crystallinity is reduced by mutating C-terminal transmembrane region residues CESA1A903V and CESA3T942I of cellulose synthase. Proceedings of the National Academy of Sciences 109: 4098-4103.
97. Hartati, S., E. Sudarmonowati, Y.W. Park, T. Kaku, R. Kaida, K. Baba and T. Hayashi. 2008. Overexpression of poplar cellulase accelerates growth and disturbs the closing movements of leaves in sengon. Plant Physiol. 147: 552-561.
98. Harvey, P.J., R. Floris, T. Lundell, J.M. Palmer, H.E. Schoemaker and R. Wever. 1992. Catalytic mechanisms and regulation of lignin peroxidase. Biochem. Soc. Trans 20: 345-349.
99. Hatfield, R.D., J.M. Marita, K. Frost, J. Grabber, J. Ralph, F.C. Lu and H. Kim. 2009. Grass lignin acylation: p-coumaroyl transferase activity and cell wall characteristics of C3 and C4 grasses. Planta 229: 1253-1267.
100. Heinzelman, P., C.D. Snow, I. Wu, C. Nguyen, A. Villalobos, S. Govindarajan, J. Minshull and F.H. Arnold. 2009. A family of thermostable fungal cellulases created by structure-guided recombination. Proc. Natl. Acad. Sci. USA 106: 5610-5615.
101. Hendriks, A.T. W.M. and G. Zeeman. 2009. Pretreatments to enhance the digestibility of lignocellulosic biomass. Bioresour. Technol. 100: 10-18.
102. Henriksson, G., G. Johansson and G. Pettersson. 2000. A critical review of cellobiose dehydrogenases. J. Biotechnol. 78: 93-113.
103. Hess, M., A. Sczyrba, R. Egan, T.W. Kim, H. Chokhawala, G. Schroth, S. Luo, D.S. Clark, F. Chen, T. Zhang, R.I. Mackie, L.A. Pennacchio, S.G. Tringe, A. Visel, T. Woyke, Z. Wang and E.M. Rubin. 2011. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331: 463-467.
104. Higashide, W., Y. Li, Y. Yang and J.C. Liao. 2011. Metabolic engineering of Clostridium cellulolyticum for production of isobutanol from cellulose. Appl. Environ. Microbiol. 77: 2727-2733.
105. Hood, E.E., R. Love, J. Lane, J. Bray, R. Clough, K. Pappu, C. Drees, K.R. Hood, S. Yoon, A. Ahmad and J.A. Howard. 2007. Subcellular targeting is a key condition for highlevel accumulation of cellulase protein in transgenic maize seed. Plant Biotechnol. J. 5: 709-719.
106. Hopkins, A.A., K.P. Vogel and K.J. Moore. 1993. Predicted and realized gains from selection for in vitro dry matter digestibility and forage yield in switchgrass. Crop Sci. 33: 253-258.
107. Hughes, S.R., S.B. Riedmuller, J.A. Mertens, X.L. Li, K.M. Bischoff, N. Qureshi, M.A. Cotta and P.J. Farrelly. 2006. High-throughput screening of cellulase F mutants from multiplexed plasmid sets using an automated plate assay on a functional proteomic robotic workcell. Proteome Sci. 4: 10.
108. Humphrey, T.V., D.T. Bonetta and D.R. Goring. 2007. Sentinels at the wall: cell wall receptors and sensors. New Phytologist. 176: 7-21.
109. Jeffries, T.W. and Y.S. Jin. 2004. Metabolic engineering for improved fermentation of pentoses by yeasts. Appl. Microbiol. Biotechnol. 63: 495-509.
110. Johansson, T. and P.O. Nyman. 1996. A cluster of genes encoding major isozymes of lignin peroxidase and manganese peroxidase from the white-rot fungus Trametes versicolor. Gene 170: 31-38.
111. Jung, S., S. Kim, H. Bae, H.S. Lim and H.J. Bae. 2010. Expression of thermostable bacterial betaglucosidase (BglB) in transgenic tobacco plants. Bioresour. Technol. 101: 7144-7150.
112. Jung, S.-K., V. Parisutham, S.H. Jeong and S.K. Lee. 2012. Heterologous expression of plant cell wall degrading enzymes for effective production of cellulosic biofuels. J. Biomed. Biotechnol. 2012: 10.
113. Kaida, R., T. Kaku, K. Baba, S. Hartati, E. Sudarmonowati and T. Hayashi. 2009. Enhancement of saccharification by overexpression of poplar cellulase in sengon. J. Wood Sci. 55: 435-440.
114. Kaida, R., T. Kaku, K. Baba, M. Oyadomari, T. Watanabe, K. Nishida, T. Kanaya, Z. Shani, O. Shoseyov and T. Hayashi. 2009. Loosening xyloglucan accelerates the enzymatic degradation of cellulose in wood. Mol. Plant 2: 904-909.
115. Kaku, T., R. Kaida, K. Baba, S. Hartati, E. Sudarmonowati and T. Hayashi. 2011. Improvement of fermentable sugar yields of mangium through transgenic overexpression of xyloglucanase. J. Wood Sci. 57: 545-548.
116. Kim, Y., N.S. Mosier, M.R. Ladisch, V. Ramesh Pallapolu, Y.Y. Lee, R. Garlock, V. Balan, B.E. Dale, B.S. Donohoe, T.B. Vinzant, R.T. Elander, M. Falls, R. Sierra, M.T. Holtzapple, J. Shi, M. A. Ebrik, T. Redmond, B. Yang, C.E. Wyman and R.E. Warner. 2011. Comparative study on enzymatic digestibility of switchgrass varieties and harvests processed by leading pretreatment technologies. Bioresour. Technol. 102: 11089-11096.
117. King, B.C., K.D. Waxman, N.V. Nenni, L.P. Walker, G.C. Bergstrom and D.M. Gibson. 2011. Arsenal of plant cell wall degrading enzymes reflects host preference among plant pathogenic fungi. Biotechnol. Biofuels 4: 4.
118. Kleman-Leyer, K.M., M. Siika-Aho, T.T. Teeri and T.K. Kirk. 1996. The cellulases endoglucanase I and cellobiohydrolase II of Trichoderma reesei act synergistically to solubilize native cotton cellulose but not to decrease its molecular size. Appl. Environ. Microbiol. 62: 2883-2887.
119. Konishi, T., T. Aohara, T. Igasaki, N. Hayashi, Y. Miyazaki, A. Takahashi, H. Hirochika, H. Iwai, S. Satoh and T. Ishii. 2011. Down-regulation of UDP-arabinopyranose mutase reduces the proportion of arabinofuranose present in rice cell walls. Phytochemistry 72: 1962-1968.
120. Konishi, T., T. Takeda, Y. Miyazaki, M. Ohnishi-Kameyama, T. Hayashi, M.A. O’Neill and T. Ishii. 2007. A plant mutase that interconverts UDP-arabinofuranose and UDParabinopyranose. Glycobiology 17: 345-354.
121. Koua, D., L. Cerutti, L. Falquet, C.J.A. Sigrist, G. Theiler, N. Hulo and C. Dunand. 2009. PeroxiBase: a database with new tools for peroxidase family classification. Nucleic Acids Res. 37: D261-D266.
122. Kubo, M., M. Udagawa, N. Nishikubo, G. Horiguchi, M. Yamaguchi, J. Ito, T. Mimura, H. Fukuda and T. Demura. 2005. Transcription switches for protoxylem and metaxylem vessel formation. Genes Dev. 19: 1855-1860.
123. Kuhad, R.C., R. Gupta and A. Singh. 2011. Microbial cellulases and their industrial applications. Enzyme Res. 2011: 280696.
124. Lee, C., R. Zhong, E.A. Richardson, D.S. Himmelsbach, B.T. McPhail and Z.H. Ye. 2007. The PARVUS gene is expressed in cells undergoing secondary wall thickening and is essential for glucuronoxylan biosynthesis. Plant Cell Physiol. 48: 1659-1672.
125. Lee, J., Y.S. Jang, S.J. Choi, J.A. Im, H. Song, J.H. Cho, Y. Seung do, E.T. Papoutsakis, G.N. Bennett and S. Y. Lee. 2012. Metabolic engineering of Clostridium acetobutylicum ATCC 824 for isopropanol-butanol-ethanol fermentation. Appl. Environ. Microbiol. 78: 1416-1423.
126. Lei, L., S. Li and Y. Gu. 2012. Cellulose synthase complexes: composition and regulation. Front. Plant Sci 3: 75.
127. Lemus, R., E.C. Brummer, K.J. Moore, N.E. Molstad, C.L. Burras and M.F. Barker. 2002. Biomass yield and quality of 20 switchgrass populations in southern Iowa, USA. Biomass Bioenergy 23: 433-442.
128. Leonowicz, A., N.S. Cho, J. Luterek, A. Wilkolazka, M. Wojtas-Wasilewska, A. Matuszewska, M. Hofrichter, D. Wesenberg and J. Rogalski. 2001. Fungal laccase: properties and activity on lignin. J. Basic. Microbiol. 41: 185-227.
129. Leple, J.C., R. Dauwe, K. Morreel, V. Storme, C. Lapierre, B. Pollet, A. Naumann, K.Y. Kang, H. Kim, K. Ruel, A. Lefebvre, J.P. Joseleau, J. Grima-Pettenati, R. De Rycke, S. Andersson-Gunneras, A. Erban, I. Fehrle, M. Petit-Conil, J. Kopka, A. Polle, E. Messens, B. Sundberg, S.D. Mansfield, J. Ralph, G. Pilate and W. Boerjan. 2007. Downregulation of cinnamoylcoenzyme A reductase in poplar: multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure. Plant Cell 19: 3669-3691.
130. Li, C., B. Knierim, C. Manisseri, R. Arora, H.V. Scheller, M. Auer, K.P. Vogel, B.A. Simmons and S. Singh. 2010. Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification. Bioresour. Technol. 101: 4900-4906.
131. Li, E., S. Wang, Y. Liu, J.G. Chen and C.J. Douglas. 2011. OVATE FAMILY PROTEIN4 (OFP4) interaction with KNAT7 regulates secondary cell wall formation in Arabidopsis thaliana. Plant J. 67: 328-341.
132. Li, X., E. Ximenes, Y. Kim, M. Slininger, R. Meilan, M. Ladisch and C. Chapple. 2010. Lignin monomer composition affects Arabidopsis cell-wall degradability after liquid hot water pretreatment. Biotechnol. Biofuels 3: 27.
133. Lois, R., A. Dietrich, K. Hahlbrock and W. Schulz. 1989. A phenylalanine ammonia-lyase gene from parsley: structure, regulation and identification of elicitor and light responsive cisacting elements. EMBO J. 8: 1641-1648.
134. Lundell, T.K., M.R. Makela and K. Hilden. 2010. Lignin-modifying enzymes in filamentous basidiomycetes-ecological, functional and phylogenetic review. J. Basic. Microbiol. 50: 5-20.
135. Lutke-Eversloh, T. and H. Bahl. 2011. Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production. Curr. Opin. Biotechnol. 22: 634-647.
136. Lynd, L.R., M.S. Laser, D. Bransby, B.E. Dale, B. Davison, R. Hamilton, M. Himmel, M. Keller, J.D. McMillan, J. Sheehan and C.E. Wyman. 2008. How biotech can transform biofuels. Nat. Biotechnol. 26: 169-172.
137. Lynd, L.R., W.H. van Zyl, J.E. McBride and M. Laser. 2005. Consolidated bioprocessing of cellulosic biomass: an update. Curr. Opin. Biotechnol. 16: 577-583.
138. Lynd, L.R., P.J. Weimer, W.H. van Zyl and I.S. Pretorius. 2002. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol. Mol. Biol. Rev. 66: 506-577.
139. Mahadevan, S.A., S.G. Wi, Y.O. Kim, K.H. Lee and H.J. Bae. 2011. In planta differential targeting analysis of Thermotoga maritima Cel5A and CBM6-engineered Cel5A for autohydrolysis. Transgenic Res. 20: 877-886.
140. Mahadevan, S.A., S.G. Wi, D.S. Lee and H.J. Bae. 2008. Site-directed mutagenesis and CBM engineering of Cel5A (Thermotoga maritima). FEMS Microbiol. Lett. 287: 205-211.
141. Masai, E., Y. Katayama, S. Nishikawa and M. Fukuda. 1999. Characterization of Sphingomonas paucimobilis SYK-6 genes involved in degradation of lignin-related compounds. J. Ind. Microbiol. Biotechnol. 23: 364-373.
142. Masset, J., M. Calusinska, C. Hamilton, S. Hiligsmann, B. Joris, A. Wilmotte and P. Thonart. 2012. Fermentative hydrogen production from glucose and starch using pure strains and artificial co-cultures of Clostridium spp. Biotechnol. Biofuels 5: 35.
143. McMillan, J.D., M.M. Newman, D.W. Templeton and A. Mohagheghi. 1999. Simultaneous saccharification and cofermentation of dilute-acid pretreated yellow poplar hardwood to ethanol using xylose-fermenting Zymomonas mobilis. Appl. Biochem. Biotechnol. 77-79: 649-665.
144. Mendu, V., J.S. Griffiths, S. Persson, J. Stork, A.B. Downie, C. Voiniciuc, G.W. Haughn and S. DeBolt. 2011. Subfunctionalization of cellulose synthases in seed coat epidermal cells mediates secondary radial wall synthesis and mucilage attachment. Plant Physiol. 157: 441-453.
145. Mir Derikvand, M., J.B. Sierra, K. Ruel, B. Pollet, C.T. Do, J. Thevenin, D. Buffard, L. Jouanin and C. Lapierre. 2008. Redirection of the phenylpropanoid pathway to feruloyl malate in Arabidopsis mutants deficient for cinnamoyl-CoA reductase 1. Planta 227: 943-956.
146. Mitsuda, N., A. Iwase, H. Yamamoto, M. Yoshia, M. Seki, K. Shinozaki, M. Ohme-Takagi. 2007. NAC transcription factors, NST1 and NST3, are key regulators of the formation of secondary walls in woody tissues of Arabidopsis. Plant Cell 19: 270-280.
147. Mitchell, R., J. Fritz, K. Moore, L. Moser, K. Vogel, D. Redfearn and D. Wester. 2001. Predicting forage quality in switchgrass and big bluestem. Agron. J. 93: 118-124.
148. Mitchell, R.A., P. Dupree and P.R. Shewry. 2007. A novel bioinformatics approach identifies candidate genes for the synthesis and feruloylation of arabinoxylan. Plant Physiol. 144: 43-53.
149. Mitchell, R.B., K.J. Moore, L.E. Moser, J.O. Fritz and D.D. Redfearn. 1997. Predicting developmental morphology in switchgrass and big bluestem. Agron. J. 89: 827-832.
150. Mohammadi, M., G.D. Najafpour, H. Younesi, P. Lahijani, M.H. Uzir and A.R. Mohamed. 2011. Bioconversion of synthesis gas to second generation biofuels: A review. Renewable and Sustainable Energy Reviews 15: 4255-4273.
151. Moreira, P.R., C. Duez, D. Dehareng, A. Antunes, E. Almeida-Vara, J.M. Frere, F.X. Malcata and J.C. Duarte. 2005. Molecular characterisation of a versatile peroxidase from a Bjerkandera strain. J. Biotechnol. 118: 339-352.
152. Mortimer, J.C., G.P. Miles, D.M. Brown, Z. Zhang, M.P. Segura, T. Weimar, X. Yu, K.A. Seffen, E. Stephens, S.R. Turner and P. Dupree. 2010. Absence of branches from xylan in Arabidopsis gux mutants reveals potential for simplification of lignocellulosic biomass. Proc. Natl. Acad. Sci. USA 107: 17409-17414.
153. Naumoff, D.G. 2011. Hierarchical classification of glycoside hydrolases. Biochemistry (Mosc.) 76: 622-635.
154. Nemeth, A., S. Kamondi, A. Szilagyi, C. Magyar, Z. Kovari and P. Zavodszky. 2002. Increasing the thermal stability of cellulase C using rules learned from thermophilic proteins: a pilot study. Biophys. Chem. 96: 229-241.
155. NSF 2008. Breaking the Chemical and Engineering Barriers to Lignocellulosic Biofuels: Next Generation Hydrocarbon Biorefineries. G.W. Huber. Washington, D.C., University of Massachusetts, Amherst 180.
156. Oelgeschläger, E. and M. Rother. 2008. Carbon monoxide-dependent energy metabolism in anaerobic bacteria and archaea. Archives of Microbiology 190: 257-269.
157. Oey, M., M. Lohse, B. Kreikemeyer and R. Bock. 2009. Exhaustion of the chloroplast protein synthesis capacity by massive expression of a highly stable protein antibiotic. Plant J. 57: 436-445.
158. Oh, K.K., S.W. Kim, Y.S. Jeong and S.I. Hong. 2000. Bioconversion of cellulose into ethanol by nonisothermal simultaneous saccharification and fermentation. Appl. Biochem. Biotechnol. 89: 15-30.
159. Olofsson, K., M. Bertilsson and G. Liden. 2008. A short review on SSF-an interesting process option for ethanol production from lignocellulosic feedstocks. Biotechnol. Biofuels 1: 7.
160. Olofsson, K., B. Palmqvist and G. Liden. 2010. Improving simultaneous saccharification and co-fermentation of pretreated wheat straw using both enzyme and substrate feeding. Biotechnol. Biofuels 3: 17.
161. Olsson, L., H.R. Soerensen, B.P. Dam, H. Christensen, K.M. Krogh and A.S. Meyer. 2006. Separate and simultaneous enzymatic hydrolysis and fermentation of wheat hemicellulose with recombinant xylose utilizing Saccharomyces cerevisiae. Appl. Biochem. Biotechnol. 129-132: 117-129.
162. Oraby, H., B. Venkatesh, B. Dale, R. Ahmad, C. Ransom, J. Oehmke and M. Sticklen. 2007. Enhanced conversion of plant biomass into glucose using transgenic rice-produced endoglucanase for cellulosic ethanol. Transgenic Res. 16: 739-749.
163. Park, E.Y., K. Naruse and T. Kato. 2012. One-pot bioethanol production from cellulose by co-culture of Acremonium cellulolyticus and Saccharomyces cerevisiae. Biotechnol. Biofuels 5: 64.
164. Park, Y.W., K. Baba, Y. Furuta, I. Iida, K. Sameshima, M. Arai and T. Hayashi. 2004. Enhancement of growth and cellulose accumulation by overexpression of xyloglucanase in poplar. FEBS Lett. 564: 183-187.
165. Park, Y.W., R. Tominaga, J. Sugiyama, Y. Furuta, E. Tanimoto, M. Samejima, F. Sakai and T. Hayashi. 2003. Enhancement of growth by expression of poplar cellulase in Arabidopsis thaliana. Plant J. 33: 1099-1106.
166. Pauly, M. and K. Keegstra. 2008. Cell-wall carbohydrates and their modification as a resource for biofuels. Plant J. 54: 559-568.
167. Pena, M.J., R. Zhong, G.K. Zhou, E.A. Richardson, M.A. O’Neill, A.G. Darvill, W.S. York and Z.H. Ye. 2007. Arabidopsis irregular xylem8 and irregular xylem9: implications for the complexity of glucuronoxylan biosynthesis. Plant Cell 19: 549-563.
168. Penning, B.W., C.T. Hunter, 3rd, R. Tayengwa, A.L. Eveland, C.K. Dugard, A.T. Olek, W. Vermerris, K.E. Koch, D.R. McCarty, M.F. Davis, S.R. Thomas, M.C. McCann and N. C. Carpita. 2009. Genetic resources for maize cell wall biology. Plant Physiol. 151: 1703-1728.
169. Peralta-Yahya, P.P. and J.D. Keasling. 2010. Advanced biofuel production in microbes. Biotechnol. J. 5: 147-162.
170. Perez, J., J. Munoz-Dorado, T. de la Rubia and J. Martinez. 2002. Biodegradation and biological treatments of cellulose, hemicellulose and lignin: an overview. Int. Microbiol. 5: 53-63.
171. Perret, S., H. Maamar, J.P. Belaich and C. Tardif. 2004. Use of antisense RNA to modify the composition of cellulosomes produced by Clostridium cellulolyticum. Mol. Microbiol. 51: 599-607.
172. Petersen, K. and R. Bock. 2011. High-level expression of a suite of thermostable cell walldegrading enzymes from the chloroplast genome. Plant Mol. Biol. 76: 311-321.
173. Philippidis, G.P., T.K. Smith and C.E. Wyman. 1993. Study of the enzymatic hydrolysis of cellulose for production of fuel ethanol by the simultaneous saccharification and fermentation process. Biotechnol. Bioeng. 41: 846-853.
174. Phillips, C.M., W.T. Beeson, J.H. Cate and M.A. Marletta. 2011. Cellobiose dehydrogenase and a copper-dependent polysaccharide monooxygenase potentiate cellulose degradation by Neurospora crassa. ACS Chem. Biol. 6: 1399-1406.
175. Piston, F., C. Uauy, L. Fu, J. Langston, J. Labavitch and J. Dubcovsky. 2010. Down-regulation of four putative arabinoxylan feruloyl transferase genes from family PF02458 reduces ester-linked ferulate content in rice cell walls. Planta 231: 677-691.
176. Podkaminer, K.K., W.R. Kenealy, C.D. Herring, D.A. Hogsett and L.R. Lynd. 2012. Ethanol and anaerobic conditions reversibly inhibit commercial cellulase activity in thermophilic simultaneous saccharification and fermentation (tSSF). Biotechnol. Biofuels 5: 43.
177. Ralph, J. 2010. Hydroxycinnamates in lignification. Phytochem. Rev. 9: 65-83.
178. Ralph, J., S. Quideau, J.H. Grabber and R.D. Hatfield. 1994. Identification and synthesis of new ferulic acid dehydrodimers present in grass cell walls. J. Chemical. Soc., Perkin Transact. 1: 3485-3498.
179. Raman, B., C. Pan, G.B. Hurst, M. Rodriguez, Jr., C.K. McKeown, P.K. Lankford, N.F. Samatova and J.R. Mielenz. 2009. Impact of pretreated switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: a quantitative proteomic analysis. PLoS One 4: e5271.
180. Ramasamy, K., R.L. Kelley and C.A. Reddy. 1985. Lack of lignin degradation by glucose oxidase-negative mutants of Phanerochaete chrysosporium. Biochem. Biophys. Res. Commun. 131: 436-441.
181. Rautengarten, C., B. Ebert, T. Herter, C.J. Petzold, T. Ishii, A. Mukhopadhyay, B. Usadel and H.V. Scheller. 2011. The interconversion of UDP-arabinopyranose and UDParabinofuranose is indispensable for plant development in Arabidopsis. Plant Cell 23: 1373-1390.
182. Reichenbecher, M., F. Lottspeich and K. Bronnenmeier. 1997. Purification and properties of a cellobiose phosphorylase (CepA) and a cellodextrin phosphorylase (CepB) from the cellulolytic thermophile Clostridium stercorarium. Eur. J. Biochem. 247: 262-267.
183. Rennie, E.A., S.F. Hansen, E.E. Baidoo, M.Z. Hadi, J.D. Keasling and H.V. Scheller. 2012. Three members of the Arabidopsis glycosyltransferase family 8 are xylan glucuronosyltransferases. Plant Physiol. 159: 1408-1417.
184. Rodriguez Couto, S. and J.L. Toca Herrera. 2006. Industrial and biotechnological applications of laccases: a review. Biotechnol. Adv. 24: 500-513.
185. Ruiz-Duenas, F.J., M. Morales, M. Perez-Boada, T. Choinowski, M.J. Martinez, K. Piontek and A.T. Martinez. 2007. Manganese oxidation site in Pleurotus eryngii versatile peroxidase: a site-directed mutagenesis, kinetic, and crystallographic study. Biochemistry 46: 66-77.
186. Ruprect, C. and S. Persson. 2012. Co-expression of cell wall related genes: new tools and insights. Front. Plant Sci. 3: 83.
187. Saathoff, A.J., M.S. Hargrove, E.J. Haas, C.M. Tobias, P. Twigg, S. Sattler and G. Sarath. 2012. Switchgrass PviCAD1: Understanding residues important for substrate preferences and activity. Appl. Biochem. Biotechnol. 168: 1086-1100.
188. Saathoff, A.J., G. Sarath, E.K. Chow, B.S. Dien and C.M. Tobias. 2011. Downregulation of cinnamyl-alcohol dehydrogenase in switchgrass by RNA silencing results in enhanced glucose release after cellulase treatment. PLoS ONE 6: e16416.
189. Saathoff, A.J., C.M. Tobias, S.E. Sattler, E.J. Haas, P. Twigg and G. Sarath. 2011. Switchgrass contains two cinnamyl alcohol dehydrogenases involved in lignin formation. BioEnergy Res. 4: 120-133.
190. Saha, B.C., N.N. Nichols, N. Qureshi and M.A. Cotta. 2011. Comparison of separate hydrolysis and fermentation and simultaneous saccharification and fermentation processes for ethanol production from wheat straw by recombinant Escherichia coli strain FBR5. Appl. Microbiol. Biotechnol. 92: 865-874.
191. Sainz, M.B. 2009. Commercial cellulosic ethanol: The role of plant-expressed enzymes. In vitro Cell Development Biol-Plant 45: 314-329.
192. Sarath, G., D.E. Akin, R.B. Mitchell and K.P. Vogel. 2008. Cell-wall composition and accessibility to hydrolytic enzymes is differentially altered in divergently bred switchgrass (Panicum virgatum L.) genotypes. Appl. Biochem. Biotechnol. 150: 1-14.
193. Sarath, G., L.M. Baird, K.P. Vogel and R.B. Mitchell. 2007. Internode structure and cell wall composition in maturing tillers of switchgrass (Panicum virgatum L.). Bioresour. Technol. 98: 2985-2992.
194. Sarath, G., B. Dien, A.J. Saathoff, K.P. Vogel, R.B. Mitchell and H. Chen. 2011. Ethanol yields and cell wall properties in divergently bred switchgrass genotypes. Bioresour. Technol. 102: 9579-9585.
195. Saxena, I.M. and R.M. Brown, Jr. 2005. Cellulose biosynthesis: Current views and evolving concepts. Ann. Bot. 96: 9-21.
196. Scheible, W.R., R. Eshed, T. Richmond, D. Delmer and C. Somerville. 2001. Modifications of cellulose synthase confer resistance to isoxaben and thiazolidinone herbicides in Arabidopsis Ixr1 mutants. Proc. Natl. Acad. Sci. USA 98: 10079-10084.
197. Scheller, H.V. and P. Ulvskov. 2010. Hemicelluloses. Annu. Rev. Plant. Biol. 61: 263-289.
198. Schmer, M.R., K.P. Vogel, R.B. Mitchell, B.S. Dien, H.G. Jung and M.D. Casler. 2012. Temporal and spatial variation in switchgrass biomass composition and theoretical ethanol yield. Agron. J. 104: 54-64.
199. Schmer, M.R., K.P. Vogel, R.B. Mitchell and R.K. Perrin. 2008. Net energy of cellulosic ethanol from switchgrass. Proc. Natl. Acad. Sci. USA 105: 464-469.
200. Schwarz, W.H. 2001. The cellulosome and cellulose degradation by anaerobic bacteria. Appl. Microbiol. Biotechnol. 56: 634-649.
201. Shadle, G., F. Chen, M.S. Srinivasa Reddy, L. Jackson, J. Nakashima and R.A. Dixon. 2007. Down-regulation of hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase in transgenic alfalfa affects lignification, development and forage quality. Phytochemistry 68: 1521-1529.
202. Sharma, S.S., S. Chong and S.W. Harcum. 2006. Intein-mediated protein purification of fusion proteins expressed under high-cell density conditions in E. coli. J. Biotechnol. 125: 48-56.
203. Shen, B., X. Sun, X. Zuo, T. Shilling, J. Apgar, M. Ross, O. Bougri, V. Samoylov, M. Parker, E. Hancock, H. Lucero, B. Gray, N.A. Ekborg, D. Zhang, J.C. Johnson, G. Lazar and R.M. Raab. 2012. Engineering a thermoregulated intein-modified xylanase into maize for consolidated lignocellulosic biomass processing. Nat. Biotechnol. 30:1131-1136.
204. Shen, H., C. Fu, X. Xiao, T. Ray, Y. Tang, Z. Wang and F. Chen. 2009. Developmental control of lignification in stems of lowland switchgrass variety Alamo and the effects on saccharification efficiency. BioEnergy Res. 2: 233-245.
205. Shen, H., X. He, C.R. Poovaiah, W.A. Wuddineh, J. Ma, D.G. Mann, H. Wang, L. Jackson, Y. Tang, C.N. Stewart, Jr., F. Chen and R.A. Dixon. 2012. Functional characterization of the switchgrass (Panicum virgatum) R2R3-MYB transcription factor PvMYB4 for improvement of lignocellulosic feedstocks. New Phytol. 193: 121-136.
206. Sibout, R., A. Eudes, G. Mouille, B. Pollet, C. Lapierre, L. Jouanin and A. Seguin. 2005. CINNAMYL ALCOHOL DEHYDROGENASE-C and-D are the primary genes involved in lignin biosynthesis in the floral stem of Arabidopsis. Plant Cell 17: 2059-2076.
207. Sirim, D., F. Wagner, L. Wang, R.D. Schmid and J. Pleiss. 2011. The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases. Database (Oxford) 2011: bar006.
208. Skjot, M., M. Pauly, M.S. Bush, B. Borkhardt, M.C. McCann and P. Ulvskov. 2002. Direct interference with rhamnogalacturonan I biosynthesis in Golgi vesicles. Plant Physiol. 129: 95-102.
209. Skretas, G. and D.W. Wood. 2005. Regulation of protein activity with small-molecule-controlled inteins. Protein Sci. 14: 523-532.
210. Sladden, S., D. Bransby and G. Aiken. 1991. Biomass yield, composition and production costs for eight switchgrass varieties in Alabama. Biomass Bioenergy 1: 119-122.
211. Somerville, C. 2006. Cellulose synthesis in higher plants. Annu. Rev. Cell Dev. Biol. 22: 53-78.
212. Sommer, M.O., G.M. Church and G. Dantas. 2010. A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion. Mol. Syst. Biol. 6: 360.
213. Sonbol, F.M., S. Fornale, M. Capellades, A. Encina, S. Tourino, J.L. Torres, P. Rovira, K. Ruel, P. Puigdomenech, J. Rigau and D. Caparros-Ruiz. 2009. The maize ZmMYB42 represses the phenylpropanoid pathway and affects the cell wall structure, composition and degradability in Arabidopsis thaliana. Plant Mol. Biol. 70: 283-296.
214. Soyano, T., S. Thitamadee, Y. Machida and N.H. Chua. 2008. ASYMMETRIC LEAVES2-LIKE19/LATERAL ORGAN BOUNDARIES DOMAIN30 and ASL20/LBD18 regulate tracheary element differentiation in Arabidopsis. Plant Cell 20: 3359-3373.
215. Steen, E. J., Y. Kang, G. Bokinsky, Z. Hu, A. Schirmer, A. McClure, S.B. Del Cardayre and J. D. Keasling. 2010. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463: 559-562.
216. Stewart, J.J., T. Akiyama, C. Chapple, J. Ralph and S. D. Mansfield. 2009. The effects on lignin structure of overexpression of ferulate 5-hydroxylase in hybrid poplar. Plant Physiol. 150: 621-635.
217. Sticklen, M. 2006. Plant genetic engineering to improve biomass characteristics for biofuels. Curr. Opin. Biotechnol. 17: 315-319.
218. Stork, J., D. Harris, J. Griffiths, B. Williams, F. Beisson, Y. Li-Beisson, V. Mendu, G. Haughn and S. Debolt. 2010. CELLULOSE SYNTHASE9 serves a nonredundant role in secondary cell wall synthesis in Arabidopsis epidermal testa cells. Plant Physiol. 153: 580-589.
219. Sullivan, S., M.C. Ralet, A. Berger, E. Diatloff, V. Bischoff, M. Gonneau, A. Marion-Poll and H. M. North. 2011. CESA5 is required for the synthesis of cellulose with a role in structuring the adherent mucilage of Arabidopsis seeds. Plant Physiol. 156: 1725-1739.
220. Sygmund, C., D. Kracher, S. Scheiblbrandner, K. Zahma, A.K. Felice, W. Harreither, R. Kittl and R. Ludwig. 2012. Characterization of the two Neurospora crassa cellobiose dehydrogenases and their connection to oxidative cellulose degradation. Appl. Environ. Microbiol. 78: 6161-6171.
221. Takahama, U. and T. Oniki. 1994. Effects of ascorbate on the oxidation of derivatives of hydroxycinnamic acid and the mechanism of oxidation of sinapic acid by cell wall-bound peroxidases. Plant Cell Physiol. 35: 593-600.
222. Tanaka, K., K. Murata, M. Yamazaki, K. Onosato, A. Miyao and H. Hirochika. 2003. Three distinct rice cellulose synthase catalytic subunit genes required for cellulose synthesis in the secondary wall. Plant Physiol. 133: 73-83.
223. Tang, Y., D. Zhao, C. Cristhian and J. Jiang. 2011. Simultaneous saccharification and cofermentation of lignocellulosic residues from commercial furfural production and corn kernels using different nutrient media. Biotechnol. Biofuels 4: 22.
224. Taylor, L.E., Z. Dai, S.R. Decker, R. Brunecky, W.S. Adney, S.-Y. Ding and M.E. Himmel. 2008. Heterologous expression of glycosyl hydrolases in planta: a new departure for biofuels. Trends Biotechnol. 26: 413-424.
225. Taylor, N.G., R.M. Howells, A.K. Huttly, K. Vickers and S.R. Turner. 2003. Interactions among three distinct CesA proteins essential for cellulose synthesis. Proc. Natl. Acad. Sci. USA 100: 1450-1455.
226. Ten Have, R. and P.J. Teunissen. 2001. Oxidative mechanisms involved in lignin degradation by white-rot fungi. Chem. Rev. 101: 3397-3413.
227. Terashima, N., T. Awano, K. Takabe and M. Yoshida. 2004. Formation of macromolecular lignin in ginkgo xylem cell walls as observed by field emission scanning electron microscopy. Comptes Rendus Biologies 327: 903-910.
228. Thomason, W.E., W.R. Ruan, G.V. Johnson, C. Taliaferro, K.W. Freeman, K.J. Wynn and R.W. Mullen. 2004. Switchgrass response to harvest frequency and time and rate of applied nitrogen. J. Plant Nutrition 27: 1199-1226.
229. Tobias, C.M., G. Sarath, P. Twigg, E. Lindquist, J. Pangilinan, B.W. Penning, K. Barry, M.C. McCann, N.C. Carpita and G.R. Lazo. 2008. Comparative genomics in switchgrass using 61,585 high-quality expressed sequence tags. Plant Genome 1: 111-124.
230. Tolonen, A.C., W. Haas, A.C. Chilaka, J. Aach, S.P. Gygi and G.M. Church. 2011. Proteome-wide systems analysis of a cellulosic biofuel-producing microbe. Mol. Syst. Biol. 7: 461.
231. Truntzler, M., Y. Barrière, M. Sawkins, D. Lespinasse, J. Betran, A. Charcosset and L. Moreau. 2010. Meta-analysis of QTL involved in silage quality of maize and comparison with the position of candidate genes. Theoretical Appl. Genetics 121: 1465-1482.
232. Tucker, M.P., A. Mohagheghi, K. Grohmann and M.E. Himmel. 1989. Ultra-thermostable cellulases from Acidothermus cellulolyticus: Comparison of temperature optima with previously reported cellulases. Nat. Biotech. 7: 817-820.
233. US-DOE 2011. U.S. Billion-Ton Update: Biomass Supply for a Bioenergy and Bioproducts Industry. R.D. Perlack and B.J. Stokes. Oak Ridge, TN, Oak Ridge National Labs.
234. Vanholme, R., B. Demedts, K. Morreel, J. Ralph and W. Boerjan. 2010. Lignin biosynthesis and structure. Plant Physiol. 153: 895-905.
235. Vanholme, R., K. Morreel, C. Darrah, P. Oyarce, J.H. Grabber, J. Ralph and W. Boerjan. 2012. Metabolic engineering of novel lignin in biomass crops. New Phytol. 196: 978-1000.
236. Vanholme, R., K. Morreel, J. Ralph and W. Boerjan. 2008. Lignin engineering. Curr. Opin. Plant Biol. 11: 278-285.
237. Vega-Sanchez, M.E., Y. Verhertbruggen, U. Christensen, X. Chen, V. Sharma, P. Varanasi, S.A. Jobling, M. Talbot, R.G. White, M. Joo, S. Singh, M. Auer, H.V. Scheller and P.C. Ronald. 2012. Loss of Cellulose synthase-like F6 function affects mixed-linkage glucan deposition, cell wall mechanical properties, and defense responses in vegetative tissues of rice. Plant Physiol. 159: 56-69.
238. Verma, D., A. Kanagaraj, S.X. Jin, N.D. Singh, P.E. Kolattukudy and H. Daniell. 2010. Chloroplast-derived enzyme cocktails hydrolyse lignocellulosic biomass and release fermentable sugars. Plant Biotechnol. J. 8: 332-350.
239. Vidal, B., Jr., B. Dien, K.C. Ting and V. Singh. 2011. Influence of feedstock particle size on lignocellulose conversion-a review. Appl. Biochem. Biotechnol. 164: 1405-1421.
240. Vogel, J. 2008. Unique aspects of the grass cell wall. Curr. Opin. Plant Biol. 11: 301-307.
241. Vogel, K.P., B.S. Dien, H.G. Jung, M.D. Casler, S.D. Masterson and R.B. Mitchell. 2010. Quantifying actual and theoretical ethanol yields for switchgrass strains using NIRS analyses. BioEnergy Res. 4: 96-110.
242. Wang, H., U. Avci, J. Nakashima, M.G. Hahn, F. Chen and R.A. Dixon. 2010. Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants. Proc. Natl. Acad. Sci. USA 107: 22338-22343.
243. Wang, Q., D. Tull, A. Meinke, N.R. Gilkes, R. A. Warren, R. Aebersold and S.G. Withers. 1993. Glu280 is the nucleophile in the active site of Clostridium thermocellum CelC, a family A endo-beta-1,4-glucanase. J. Biol. Chem. 268: 14096-14102.
244. Wang, T., X. Liu, Q. Yu, X. Zhang, Y. Qu and P. Gao. 2005. Directed evolution for engineering pH profile of endoglucanase III from Trichoderma reesei. Biomol. Eng. 22: 89-94.
245. Wariishi, H., K. Valli and M.H. Gold. 1992. Manganese(II) oxidation by manganese peroxidase from the basidiomycete Phanerochaete chrysosporium. Kinetic mechanism and role of chelators. J. Biol. Chem. 267: 23688-23695.
246. Warnecke, F., P. Luginbuhl, N. Ivanova, M. Ghassemian, T.H. Richardson, J.T. Stege, M. Cayouette, A. C. McHardy, G. Djordjevic, N. Aboushadi, R. Sorek, S.G. Tringe, M. Podar, H.G. Martin, V. Kunin, D. Dalevi, J. Madejska, E. Kirton, D. Platt, E. Szeto, A. Salamov, K. Barry, N. Mikhailova, N.C. Kyrpides, E.G. Matson, E.A. Ottesen, X. Zhang, M. Hernandez, C. Murillo, L.G. Acosta, I. Rigoutsos, G. Tamayo, B.D. Green, C. Chang, E.M. Rubin, E.J. Mathur, D.E. Robertson, P. Hugenholtz and J. R. Leadbetter. 2007. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450: 560-565.
247. Wegrzyn, J.L., A.J. Eckert, M. Choi, J.M. Lee, B.J. Stanton, R. Sykes, M.F. Davis, C.J. Tsai and D.B. Neale. 2010. Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem. New Phytol. 188: 515-532.
248. Wen, F., J. Sun and H. Zhao. 2010. Yeast surface display of trifunctional minicellulosomes for simultaneous saccharification and fermentation of cellulose to ethanol. Appl. Environ. Microbiol. 76: 1251-1260.
249. Weng, J.K., X. Li, N.D. Bonawitz and C. Chapple. 2008. Emerging strategies of lignin engineering and degradation for cellulosic biofuel production. Curr. Opin. Biotechnol. 19: 166-172.
250. Withers, S., F. Lu, H. Kim, Y. Zhu, J. Ralph and C.G. Wilkerson. 2012. Identification of grass-specific enzyme that acylates monolignols with p-coumarate. J. Biol. Chem. 287: 8347-8355.
251. Wohlfahrt, G., T. Pellikka, H. Boer, T.T. Teeri and A. Koivula. 2003. Probing pH-dependent functional elements in proteins: modification of carboxylic acid pairs in Trichoderma reesei cellobiohydrolase Cel6A. Biochemistry 42: 10095-10103.
252. Wolf, S., K. Hematy and H. Hofte. 2012. Growth control and cell wall signaling in plants. Annu. Rev. Plant Biol. 63: 381-407.
253. Wong, D.W. 2009. Structure and action mechanism of ligninolytic enzymes. Appl. Biochem. Biotechnol. 157: 174-209.
254. Wu, Z. and Y.Y. Lee. 1998. Nonisothermal simultaneous saccharification and fermentation for direct conversion of lignocellulosic biomass to ethanol. Appl. Biochem. Biotechnol. 70-72: 479-492.
255. Xu, B., L.L. Escamilla-Trevino, N. Sathitsuksanoh, Z. Shen, H. Shen, Y.H. Zhang, R.A. Dixon and B. Zhao. 2011. Silencing of 4-coumarate:coenzyme A ligase in switchgrass leads to reduced lignin content and improved fermentable sugar yields for biofuel production. New Phytol. 192: 611-625.
256. Xu, Q., E.A. Bayer, M. Goldman, R. Kenig, Y. Shoham and R. Lamed. 2004. Architecture of the Bacteroides cellulosolvens cellulosome: description of a cell surface-anchoring scaffoldin and a family 48 cellulase. J. Bacteriol. 186: 968-977.
257. Yamaguchi, M., M. Ohtani, N. Mitsuda, M. Kubo, M. Ohme-Takagi, H. Fukuda and T. Demura. 2010. VND-INTERACTING2, a NAC domain transcription factor, negatively regulates xylem vessel formation in Arabidopsis. Plant Cell 22: 1249-1263.
258. Yan, J., Z. Hu, Y. Pu, E. Charles Brummer and A.J. Ragauskas. 2010. Chemical compositions of four switchgrass populations. Biomass Bioenergy 34: 48-53.
259. Yang, P., Y. Wang, Y. Bai, K. Meng, H. Luo, T. Yuan, Y. Fan and B. Yao. 2007. Expression of xylanase with high specific activity from Streptomyces olivaceoviridis A1 in transgenic potato plants (Solanum tuberosum L.). Biotechnol. Letters 29: 659-667.
260. Yeh, Y.F., S.C. Chang, H.W. Kuo, C.G. Tong, S.M. Yu and T.H. Ho. 2012. A metagenomic approach for the identification and cloning of an endoglucanase from rice straw compost. Gene.
261. York, W.S. and M.A. O’Neill. 2008. Biochemical control of xylan biosynthesis-which end is up? Curr. Opin. Plant Biol. 11: 258-265.
262. You, C., X.Z. Zhang and Y.H.P. Zhang. 2012. Mini-scaffoldin enhanced mini-cellulosome hydrolysis performance on low-accessibility cellulose (Avicel) more than on highaccessibility amorphous cellulose. Biochem. Engineering J. 63: 57-65.
263. Youngs, H. and C. Somerville. 2012. Development of feedstocks for cellulosic biofuels. F1000 Biol. Rep. 4: 10.
264. Yue, Z., W. Bin, Y. Baixu and G. Peiji. 2004. Mechanism of cellobiose inhibition in cellulose hydrolysis by cellobiohydrolase. Sci. China C. Life Sci. 47: 18-24.
265. Zeng, W., N. Jiang, R. Nadella, T.L. Killen, V. Nadella and A. Faik. 2010. A glucurono(arabino) xylan synthase complex from wheat contains members of the GT43, GT47, and GT75 families and functions cooperatively. Plant Physiol. 154: 78-97.
266. Zhao, Q. and R.A. Dixon. 2011. Transcriptional networks for lignin biosynthesis: more complex than we thought? Trends Plant Sci. 16: 227-233.
267. Zhong, R., T. Demura and Z.H. Ye. 2006. SND1, a NAC domain transcription factor, is a key regulator of secondary wall synthesis in fibers of Arabidopsis. Plant Cell 18: 3158-3170.
268. Zhong, R., C. Lee, Z.H. Ye. 2010. Global analysis of direct targets of secondary wall NAC mwaster switches in Arabidopsis. Mol. Plant 3: 1087-1103.
269. Zhong, R., C. Lee, R.L. McCarthy, C.K. Reeves, E.G. Jones and Z.H. Ye. 2011. Transcriptional activation of secondary wall biosynthesis by rice and maize NAC and MYB transcription factors. Plant Cell Physiol. 52: 1856-1871.
270. Zhong, R., W.H. Morrison III, G.D. Freshour, M.G. Hahn and Z.H. Ye. 2003. Expression of a mutant form of cellulose synthase AtCesA7 causes dominant negative effect on cellulose biosynthesis. Plant Physiol. 132: 786-795.
271. Zhong, R., E.A. Richardson and Z.H. Ye. 2007. The MYB46 transcription factor is a direct target of SND1 and regulates secondary wall biosynthesis in Arabidopsis. Plant Cell 19: 2776-2792.
272. Zhong, R. and Z.H. Ye. 2012. MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes. Plant Cell Physiol. 53: 368-380.
273. Zhu, M., P. Li, X. Gong and J. Wang. 2012. A comparison of the production of ethanol between simultaneous saccharification and fermentation and separate hydrolysis and fermentation using unpretreated cassava pulp and enzyme cocktail. Biosci. Biotechnol. Biochem. 76: 671-678.
274. Zhu, Y., Y.Y. Lee and R.T. Elander. 2007. Conversion of aqueous ammonia-treated corn stover to lactic acid by simultaneous saccharification and cofermentation. Appl. Biochem. Biotechnol. 137-140: 721-738.
275. Ziegelhoffer, T., J.A. Raasch and S. Austin-Phillips. 2001. Dramatic effects of truncation and sub-cellular targeting on the accumulation of recombinant microbial cellulase in tobacco. Mol. Breeding 8: 147-158.