Improving lignocellulolytic enzyme production with Penicillium: from strain screening to systems biology

• Merino ST, Cherry J. Progress and challenges in enzyme development for biomass utilization. Adv. Biochem. Eng. Biotech.108,95–120 (2007).
   PubMed Web of Science ®Google Scholar
• Liu G, Qin Y, Li Z, Qu Y. Development of highly efficient, low-cost lignocellulolytic enzyme systems in the post-genomic era. Biotechnol. Adv. doi:10.1016/j.biotechadv.2013.03.001 (2013) (Epub ahead of print).
   Web of Science ®Google Scholar
• Klein-Marcuschamer D, Oleskowicz-Popiel P, Simmons BA, Blanch HW. The challenge of enzyme cost in the production of lignocellulosic biofuels. Biotechnol. Bioeng.109(4),1083–1087 (2011).
   PubMed Web of Science ®Google Scholar
• Seidl V, Seiboth B. Trichoderma reesei: genetic approaches to improving strain efficiency.Biofuels1(2),343–354 (2010).
   Google Scholar
• Kubicek CP, Mikus M, Schuster A, Schmoll M, Seiboth B. Metabolic engineering strategies for the improvement of cellulase production by Hypocrea jecorina. Biotechnol. Biofuels2,19 (2009).
   PubMed Web of Science ®Google Scholar
• Gusakov AV, Sinitsyn AP. Cellulases from Penicillium species for producing fuels from biomass. Biofuels3(4),463–477 (2012).
   Google Scholar
• Marjamaa K, Toth K, Bromann PA, Szakacs G, Kruus K. Novel Penicillium cellulases for total hydrolysis of lignocellulosics. Enzyme Microb. Tech.52(6–7),358–369 (2013).
   PubMed Web of Science ®Google Scholar
• Chekushina A, Dotsenko G, Sinitsyn A. Comparing the efficiency of plant material bioconversion processes using biocatalysts based on Trichoderma and Penicillium verruculosum enzyme preparations. Catal. Ind.5(1),98–104 (2013).
   Google Scholar
• Sahare P, Singh R, Laxman RS, Rao M. Effect of alkali pretreatment on the structural properties and enzymatic hydrolysis of corn cob. Appl. Biochem. Biotech.168(7),1806–1819 (2012).
   PubMed Web of Science ®Google Scholar
• Guais O, Borderies G, Pichereaux C et al. Proteomics analysis of ‘Rovabiot Excel’, a secreted protein cocktail from the filamentous fungus Penicillium funiculosum grown under industrial process fermentation. J. Ind. Microbiol. Biotech.35(12),1659–1668 (2008).
   PubMed Web of Science ®Google Scholar
• Larkin MA, Blackshields G, Brown NP et al. Clustal W and Clustal X version 2.0. Bioinformatics23(21),2947–2948 (2007).
   PubMed Web of Science ®Google Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol.28(10),2731–2739 (2011).
   PubMed Web of Science ®Google Scholar
• Qu Y, Gao P, Wang Z. Screening of catabolite repression-resistant mutants of cellulase producing Penicillium spp. Acta. Mycol. Sin.3,238–243 (1984).
   Google Scholar
• Qu Y, Zhao X, Gao P, Wang Z. Cellulase production from spent sulfite liquor and paper-mill waste fiber. Appl. Biochem. Biotech.28–29,363–368 (1991).
   PubMed Web of Science ®Google Scholar
• Zhao X, Qu Y, Gao P. The discussion on the selection of a cellulase-production strain in black liquor. J. Cellulose Sci. Technol.1(2),28–32 (1993).
   Google Scholar
• Cheng Y, Song X, Qin Y, Qu Y. Genome shuffling improves production of cellulase by Penicillium decumbens JU-A10. J. Appl. Microbiol.107(6),1837–1846 (2009).
   PubMed Web of Science ®Google Scholar
• Liu K, Lin X, Yue J et al. High concentration ethanol production from corncob residues by fed-batch strategy. Bioresource Technol.101(13),4952–4958 (2010).
   PubMed Web of Science ®Google Scholar
• Yao L, Yue J, Zhao J, Dong J, Li X, Qu Y. Application of acidic wastewater from monosodium glutamate process in pretreatment and cellulase production for bioconversion of corn stover – feasibility evaluation. Bioresource Technol.101(22),8755–8761 (2010).
   PubMed Web of Science ®Google Scholar
• Liu G, Zhang L, Qin Y et al. Long-term strain improvements accumulate mutations in regulatory elements responsible for hyper-production of cellulolytic enzymes. Sci. Rep.3,1569 (2013).
   PubMed Web of Science ®Google Scholar
• Liu G, Zhang L, Wei X et al. Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens. PLoS ONE8(2),e55185 (2013).
   PubMed Web of Science ®Google Scholar
• Tian C, Beeson WT, Iavarone AT et al. Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa. Proc. Natl Acad. Sci. USA106(52),22157–22162 (2009).
   PubMed Web of Science ®Google Scholar
• Zhang Y, Zhang J, Xiao P, Wang T, Qu Y. Improved cellulase production via disruption of PDE01641 in cellulolytic fungus Penicillium decumbens. Bioresource Technol.123,733–737 (2012).
   PubMed Web of Science ®Google Scholar
• Chen M, Qin Y, Cao Q et al. Promotion of extracellular lignocellulolytic enzymes production by restraining the intracellular β-glucosidase in Penicillium decumbens. Bioresource Technol.137,33–40 (2013).
   PubMed Web of Science ®Google Scholar
• Li Z, Du C, Zhong Y, Wang T. Development of a highly efficient gene targeting system allowing rapid genetic manipulations in Penicillium decumbens. Appl. Microbiol. Biotech.87(3),1065–1076 (2010).
   PubMed Web of Science ®Google Scholar
• Qin Y, Zheng K, Liu G, Chen M, Qu Y. Improved cellulolytic efficacy in Penicilium decumbens via heterologous expression of Hypocrea jecorina endoglucanase II. Arch. Biol. Sci. Belgrade65(1),305–314 (2013).
   Web of Science ®Google Scholar
• Steiger MG, Vitikainen M, Uskonen P et al. Transformation system for Hypocrea jecorina (Trichoderma reesei) that favors homologous integration and employs reusable bidirectionally selectable markers. Appl. Environ. Microbiol.77(1),114–121 (2011).
   PubMed Web of Science ®Google Scholar
• Qu Y, Gao P, Wang Z. Studies on the cellulase system of Penicillium decumbens I. The conditions of enzyme production and reaction of mutant JU1. J. Shandong Univ.21(1),140–143 (1986).
   Google Scholar
• De Castro AM, De Albuquerque De Carvalho ML, Leite SG, Pereira N Jr. Cellulases from Penicillium funiculosum: production, properties and application to cellulose hydrolysis. J. Ind. Microbiol. Biotech.37(2),151–158 (2010).
   PubMed Web of Science ®Google Scholar
• Castellanos O, Sinitsyn A, Vlasenko EY. Comparative evaluation of hydrolytic efficiency toward microcrystalline cellulose of Penicillium and Trichoderma cellulases. Bioresource Technol.52(2),119–124 (1995).
   Web of Science ®Google Scholar
• Busto M, Ortega N, Perez-Mateos M. Location, kinetics and stability of cellulases induced in Trichoderma reesei cultures. Bioresource Technol.57(2),187–192 (1996).
   Web of Science ®Google Scholar
• Wang M, Mu Z, Wang J et al. The identification of and relief from Fe3+ inhibition for both cellulose and cellulase in cellulose saccharification catalyzed by cellulases from Penicillium decumbens. Bioresource Technol.133,507–512 (2013).
   PubMed Web of Science ®Google Scholar
• Zhang YH, Lynd LR. Toward an aggregated understanding of enzymatic hydrolysis of cellulose: noncomplexed cellulase systems. Biotechnol. Bioeng.88(7),797–824 (2004).
   PubMed Web of Science ®Google Scholar
• Sun X, Liu Z, Zheng K, Song X, Qu Y. The composition of basal and induced cellulase systems in Penicillium decumbens under induction or repression conditions. Enzyme Microb. Technol.42(7),560–567 (2008).
   Web of Science ®Google Scholar
• Qu Y, Gao P, Wang Z. Studies on cellulase system from Penicillium decumbens. Acta Microbiol. Sin.28(2),121–130 (1988).
   Google Scholar
• Gao L, Gao F, Wang L et al. N-glycoform diversity of cellobiohydrolase I from Penicillium decumbens and the synergism of a nonhydrolytic glycoform in cellulose degradation. J. Biol. Chem.287(19),15906–15915 (2012).
   PubMed Web of Science ®Google Scholar
• Gao L, Wang F, Gao F, Wang L, Zhao J, Qu Y. Purification and characterization of a novel cellobiohydrolase (PdCel6A) from Penicillium decumbens JU-A10 for bioethanol production. Bioresource Technol.102(17),8339–8342 (2011).
   PubMed Web of Science ®Google Scholar
• Liu Z, Sun X, Qu Y. Cloning cellobiohydrolase I from Penicillium decumbens 114–2 with TAIL-PCR and comparing with its derepressed mutant JU-A10. Acta. Microbiol. Sin.48(5),667–671 (2008).
   PubMedGoogle Scholar
• Liu G, Wei X, Qin Y, Qu Y. Characterization of the endoglucanase and glucomannanase activities of a glycoside hydrolase family 45 protein from Penicillium decumbens 114–2. J. Gen. Appl. Microbiol.56(3),223–229 (2010).
   PubMed Web of Science ®Google Scholar
• Wei X, Qin Y, Qu Y. Molecular cloning and characterization of two major endoglucanases from Penicillium decumbens. J. Microbiol. Biotechnol.20(2),265–270 (2010).
   PubMed Web of Science ®Google Scholar
• Gruno M, Valjamae P, Pettersson G, Johansson G. Inhibition of the Trichoderma reesei cellulases by cellobiose is strongly dependent on the nature of the substrate. Biotechnol. Bioeng.86(5),503–511 (2004).
   PubMed Web of Science ®Google Scholar
• Shen Y, Zhang Y, Ma T et al. Simultaneous saccharification and fermentation of acid-pretreated corncobs with a recombinant Saccharomyces cerevisiae expressing β-glucosidase. Bioresource Technol.99(11),5099–5103 (2008).
   PubMed Web of Science ®Google Scholar
• Chen M, Qin Y, Liu Z, Liu K, Wang F, Qu Y. 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 (2010).
   PubMed Web of Science ®Google Scholar
• Ma L, Zhang J, Zou G, Wang C, Zhou Z. 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 (2011).
   PubMed Web of Science ®Google Scholar
• Phillips CM, Beeson WT, Cate JH, Marletta MA. Cellobiose dehydrogenase and a copper-dependent polysaccharide monooxygenase potentiate cellulose degradation by Neurospora crassa. ACS Chem. Biol.6(12),1399–1406 (2011).
   PubMed Web of Science ®Google Scholar
• Punta M, Coggill PC, Eberhardt RY et al. The Pfam protein families database. Nucleic Acids Res.40,D290–D301 (2012).
   PubMed Web of Science ®Google Scholar
• Liu G, Qin Y, Hu Y, Gao M, Peng S, Qu Y. An endo-1,4-β-glucanase PdCel5C from cellulolytic fungus Penicillium decumbens with distinctive domain composition and hydrolysis product profile. Enzyme Microb. Technol.52(3),190–195 (2013).
   PubMed Web of Science ®Google Scholar
• Herpoel-Gimbert I, Margeot A, Dolla A et al. Comparative secretome analyses of two Trichoderma reesei RUT-C30 and CL847 hypersecretory strains. Biotechnol. Biofuels1(1),18 (2008).
   PubMedGoogle Scholar
• Chundawat SP, Lipton MS, Purvine SO et al. Proteomics-based compositional analysis of complex cellulase–hemicellulase mixtures. J. Proteome Res.10(10),4365–4372 (2011).
   PubMed Web of Science ®Google Scholar
• Martinez D, Berka RM, Henrissat B et al. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat. Biotechnol.26(5),553–560 (2008).
   PubMed Web of Science ®Google Scholar
• Krogh K, Kastberg H, Jørgensen C, Berlin A, Harris P, Olsson L. Cloning of a GH5 endoglucanase from genus Penicillium and its binding to different lignins. Enzyme Microb. Technol.44(6),359–367 (2009).
   Web of Science ®Google Scholar
• Bouws H, Wattenberg A, Zorn H. Fungal secretomes – nature’s toolbox for white biotechnology. Appl. Microbiol. Biotechnol.80(3),381–388 (2008).
   PubMed Web of Science ®Google Scholar
• Aro N, Pakula T, Penttila M. Transcriptional regulation of plant cell wall degradation by filamentous fungi. FEMS Microbiol. Rev.29(4),719–739 (2005).
   PubMed Web of Science ®Google Scholar
• Qu Y, Gao P, Wang Z. Studies on the cellulase system of Penicillium decumbens II. Physiological characters of the mutant JU1 and regulation of its enzymes synthesis. J. Shandong Univ.22(13),97–104 (1987).
   Google Scholar
• Wei X, Zheng K, Chen M et al. Transcription analysis of lignocellulolytic enzymes of Penicillium decumbens 114–2 and its catabolite-repression-resistant mutant. C. R. Biol.334(11),806–811 (2011).
   PubMed Web of Science ®Google Scholar
• Warzywoda M, Ferre V, Pourquie J. Development of a culture medium for large-scale production of cellulolytic enzymes by Trichoderma reesei. Biotechnol. Bioeng.25(12),3005–3011 (1983).
   PubMed Web of Science ®Google Scholar
• Sternberg D, Mandels GR. Induction of cellulolytic enzymes in Trichoderma reesei by sophorose. J. Bacteriol.139(3),761–769 (1979).
   PubMed Web of Science ®Google Scholar
• Wang D, Qu Y, Gao P. Regulation of cellulase synthesis in mycelial fungi: participation of ATP and cyclic AMP. Biotechnol. Lett.17(6),593–598 (1995).
   Web of Science ®Google Scholar
• Znameroski EA, Coradetti ST, Roche CM et al. Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins. Proc. Natl Acad. Sci. USA109(16),6012–6017 (2012).
   PubMed Web of Science ®Google Scholar
• Schmoll M, Kubicek CP. Regulation of Trichoderma cellulase formation: lessons in molecular biology from an industrial fungus. A review. Acta Microbiol. Immunol. Hung.50(2–3),125–145 (2003).
   PubMedGoogle Scholar
• Sun X, Liu Z, Qu Y, Li X. The effects of wheat bran composition on the production of biomass-hydrolyzing enzymes by Penicillium decumbens. Appl. Biochem. Biotechnol.146(1–3),119–128 (2008).
   PubMed Web of Science ®Google Scholar
• Vaheri M, Leisola M, Kauppinen V. Transglycosylation products of cellulase system of Trichoderma reesei. Biotechnol. Lett.1(1),41–46 (1979).
   Web of Science ®Google Scholar
• Kurasawa T, Yachi M, Suto M, Kamagata Y, Takao S, Tomita F. Induction of cellulase by gentiobiose and its sulfur-containing analog in Penicillium purpurogenum. Appl. Environ. Microbiol.58(1),106–110 (1992).
   PubMed Web of Science ®Google Scholar
• Schmoll M, Schuster A, Silva Rdo N, Kubicek CP. The G-alpha protein GNA3 of Hypocrea jecorina (anamorph Trichoderma reesei) regulates cellulase gene expression in the presence of light. Eukaryot. Cell8(3),410–420 (2009).
   PubMedGoogle Scholar
• Zhang J, Zhang Y, Zhong Y, Qu Y, Wang T. Ras GTPases modulate morphogenesis, sporulation and cellulase gene expression in the cellulolytic fungus Trichoderma reesei. PLoS ONE7(11),e48786 (2012).
   PubMedGoogle Scholar
• Zhou G, Lv J, Li Z et al. Enhanced cellulase production of Penicillium decumbens by knocking out creB encoding a deubiquitination enzyme. Chin. J. Biotech.28(8),959–972 (2012).
   Google Scholar
• Aro N, Ilmen M, Saloheimo A, Penttila M. ACEI of Trichoderma reesei is a repressor of cellulase and xylanase expression. Appl. Environ. Microbiol.69(1),56–65 (2003).
   PubMed Web of Science ®Google Scholar
• Coradetti ST, Craig JP, Xiong Y, Shock T, Tian C, Glass NL. Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi. Proc. Natl Acad. Sci. USA109(19),7397–7402 (2012).
   PubMed Web of Science ®Google Scholar
• Van Peij NN, Visser J, De Graaff LH. Isolation and analysis of xlnR, encoding a transcriptional activator co-ordinating xylanolytic expression in Aspergillus niger. Mol. Microbiol.27(1),131–142 (1998).
   PubMed Web of Science ®Google Scholar
• Bailey JE, Sburlati A, Hatzimanikatis V, Lee K, Renner WA, Tsai PS. Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol. Bioeng.52(1),109–121 (1996).
   PubMed Web of Science ®Google Scholar
• Petersen KL, Lehmbeck J, Christensen T. A new transcriptional activator for amylase genes in Aspergillus. Mol. Gen. Genet.262(4–5),668–676 (1999).
   PubMedGoogle Scholar
• Mo H, Zhang X, Li Z. Control of gas phase for enhanced cellulase production by Penicillium decumbens in solid-state culture. Process Biochem.39(10),1293–1297 (2004).
   Web of Science ®Google Scholar
• Xu F, Chen H, Li Z. Effect of periodically dynamic changes of air on cellulase production in solid-state fermentation. Enzyme Microb. Technol.30(1),45–48 (2002).
   Web of Science ®Google Scholar
• Zhang X, Mo H, Zhang J, Li Z. A solid-state bioreactor coupled with forced aeration and pressure oscillation. Biotechnol. Lett.25(5),417–420 (2003).
   PubMed Web of Science ®Google Scholar
• Fang X, Shen Y, Zhao J, Bao X, Qu Y. Status and prospect of lignocellulosic bioethanol production in China. Bioresource Technol.101(13),4814–4819 (2010).
   PubMed Web of Science ®Google Scholar
• Zhao J, Li X, Qu Y. Application of enzymes in producing bleached pulp from wheat straw. Bioresource Technol.97(13),1470–1476 (2006).
   PubMed Web of Science ®Google Scholar
• Chen S, Xing X, Huang J, Xu M. Enzyme-assisted extraction of flavonoids from Ginkgo biloba leaves: improvement effect of flavonol transglycosylation catalyzed by Penicillium decumbens cellulase. Enzyme Microb. Technol.48(1),100–105 (2011).
   PubMed Web of Science ®Google Scholar
• Qu Y, Zhu M, Liu K, Bao X, Lin J. Studies on cellulosic ethanol production for sustainable supply of liquid fuel in China. Biotechnol. J.1(11),1235–1240 (2006).
   PubMedGoogle Scholar
• Zhao X, Qu Y, Gao P. Acceleration of ethanol production from paper mill waste fiber by supplementation with β-glucosidase. Enzyme Microb. Technol.15(1),62–65 (1993).
   Web of Science ®Google Scholar
• Visser H, Joosten V, Punt PJ et al. Development of a mature fungal technology and production platform for industrial enzymes based on a Myceliophthora thermophila isolate, previously known as Chrysosporium lucknowense C1. Ind. Biotechnol.7(3),214–223 (2011).
   Google Scholar

▪ Website

• TEGreen Prospects Asia. Shandong longlive bio-technology delivers first batch of fuel ethanol from corncobs. XTwww.greenprospectsasia.com/content/shandong-longlive-bio-technology-delivers-first-batch-fuel-ethanol-corncobs
   Google Scholar