Co-evolution of β-glucosidase activity and product tolerance for increasing cellulosic ethanol yield.
Directed evolution
Enzyme activity
Molecular dynamics simulation
Product tolerance
β-Glucosidase
Journal
Biotechnology letters
ISSN: 1573-6776
Titre abrégé: Biotechnol Lett
Pays: Netherlands
ID NLM: 8008051
Informations de publication
Date de publication:
Nov 2020
Nov 2020
Historique:
received:
22
03
2020
accepted:
30
05
2020
pubmed:
26
6
2020
medline:
6
7
2021
entrez:
26
6
2020
Statut:
ppublish
Résumé
β-Glucosidase (BGL) plays a key role in cellulose hydrolysis. However, it is still a great challenge to enhance product tolerance and enzyme activity of BGL simultaneously. Here, we utilized one round error-prone PCR to engineer the Penicillium oxalicum 16 BGL (16BGL) for improving the cellulosic ethanol yield. We identified a new variant (L-6C), a triple mutant (M280T/V484L/D589E), with enhanced catalytic efficiency ([Formula: see text]) for hydrolyzing pNPG and reduced strength of inhibition ([Formula: see text]) by glucose. To be specific, L-6C achieved a [Formula: see text] of 0.35 at a glucose concentration of 20 mM, which was 3.63 times lower than that attained by 16BGL. The catalytic efficiency for L-6C to hydrolyze pNPG was determined to be 983.68 mM
Identifiants
pubmed: 32583369
doi: 10.1007/s10529-020-02935-9
pii: 10.1007/s10529-020-02935-9
doi:
Substances chimiques
Fungal Proteins
0
Nitrophenylgalactosides
28347-45-7
4-nitrophenylgalactoside
3150-24-1
beta-Glucosidase
EC 3.2.1.21
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2239-2250Subventions
Organisme : National Natural Science Foundation of China
ID : 21666010
Organisme : National Natural Science Foundation of China
ID : 31360217
Organisme : Doctoral Starting up Foundation of Jiangxi Normal University
ID : 5451
Références
Abraham MJ, Murtola T, Schulz R et al (2015) GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1:19–25
Agirre J, Ariza A, Offen WA et al (2016) Three-dimensional structures of two heavily N-glycosylated Aspergillus sp. family GH3 β-d-glucosidases. Acta Crystallogr D 72:254–265
Arnold FH (1998) Design by directed evolution. Acc Chem Res 31:125–131
Basit A, Tajwar R, Sadaf S et al (2019) Improvement in activity of cellulase Cel12A of Thermotoga neapolitana by error prone PCR. J Biotechnol 306:118–124
pubmed: 31550489
Best RB, Zhu X, Shim J et al (2012) Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone ϕ, ψ and side-chain χ1 and χ2 dihedral angles. J Chem Theory Comput 8:3257–3273
pubmed: 23341755
pmcid: 3549273
Biasini M, Bienert S, Waterhouse A et al (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 42:W252–W258
pubmed: 24782522
pmcid: 4086089
Bruice TC (2002) A view at the millennium: the efficiency of enzymatic catalysis. Acc Chem Res 35:139–148
pubmed: 11900517
Bruice TC, Benkovic SJ (2000) Chemical basis for enzyme catalysis. Biochemistry 39:6267–6274
pubmed: 10828939
Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J Chem Phys 126:014101
pubmed: 17212484
Czjzek M, Cicek M, Zamboni V et al (2000) The mechanism of substrate (aglycone) specificity in β-glucosidases is revealed by crystal structures of mutant maize β-glucosidase-DIMBOA, -DIMBOAGlc, and -dhurrin complexes. Proc Natl Acad Sci 97:13555–13560
pubmed: 11106394
Davies G, Henrissat B (1995) Structures and mechanisms of glycosyl hydrolases. Structure 3:853–859
pubmed: 8535779
Essmann U, Perera L, Berkowitz ML et al (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593
Gudmundsson M, Hansson H, Karkehabadi S et al (2016) Structural and functional studies of the glycoside hydrolase family 3 β-glucosidase Cel3A from the moderately thermophilic fungus Rasamsonia emersonii. Acta Crystallogr D 72:860–870
He J, Huang X, Xue J et al (2018) Computational redesign of penicillin acylase for cephradine synthesis with high kinetic selectivity. Green Chem 20:5484–5490
Hess B, Bekker H, Berendsen HJ et al (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463–1472
Huang X, Han K, Zhu Y (2013a) Systematic optimization model and algorithm for binding sequence selection in computational enzyme design. Protein Sci 22:929–941
pubmed: 23649589
pmcid: 3719087
Huang X, Yang J, Zhu Y (2013b) A solvated ligand rotamer approach and its application in computational protein design. J Mol Model 19:1355–1367
pubmed: 23192355
Huang X, Xue J, Zhu Y (2017) Computational design of cephradine synthase in a new scaffold identified from structural databases. Chem Commun 53:7604–7607
Huang X, Xue J, Lin M et al (2016) Use of an improved matching algorithm to select scaffolds for enzyme design based on a complex active site model. PLoS ONE 11:e0156559
pubmed: 27243223
pmcid: 4887040
Jimenez-Oses G, Osuna S, Gao X et al (2014) The role of distant mutations and allosteric regulation on LovD active site dynamics. Nat Chem Biol 10:431–436
pubmed: 24727900
pmcid: 4028369
Jing X, Zhang X, Bao J (2009) Inhibition performance of lignocellulose degradation products on industrial cellulase enzymes during cellulose hydrolysis. Appl Biochem Biotechnol 159:696
pubmed: 19184544
Jorgensen WL, Chandrasekhar J, Madura JD et al (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935
Kan SJ, Lewis RD, Chen K et al (2016) Directed evolution of cytochrome c for carbon–silicon bond formation: bringing silicon to life. Science 354:1048–1051
pubmed: 27885032
pmcid: 5243118
Khalil HA, Bhat A, Yusra AI (2012) Green composites from sustainable cellulose nanofibrils: a review. Carbohydr Polym 87:963–979
Kiss G, Celebi-Olcum N, Moretti R et al (2013) Computational enzyme design. Angew Chem Int Ed Engl 52:5700–5725
pubmed: 23526810
Kumari R, Kumar R, Consortium OSDD et al (2014) g_mmpbsa—a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model 54:1951–1962
pubmed: 24850022
Li Q, Huang X, Zhu Y (2014) Evaluation of active designs of cephalosporin C acylase by molecular dynamics simulation and molecular docking. J Mol Model 20:2314
pubmed: 24935111
Li H, Yi S, Bell EW et al (2019) Recombinant Penicillium oxalicum 16 β-glucosidase 1 displays comprehensive inhibitory resistance to several lignocellulose pretreatment products, ethanol, and salt. Appl Biochem Biotechnol. https://doi.org/10.1007/s12010-019-03183-y
doi: 10.1007/s12010-019-03183-y
pubmed: 31863349
pmcid: 6882806
Liu L, Li X, Wang J et al (2017) Two distant catalytic sites are responsible for C2c2 RNase activities. Cell 168:121–134
pubmed: 28086085
Mascal M, Nikitin EB (2008) Direct, high-yield conversion of cellulose into biofuel. Angew Chem Int Ed 47:7924–7926
Miller GL, Blum R, Glennon WE et al (1960) Measurement of carboxymethylcellulase activity. Anal Biochem 1:127–132
Morris GM, Huey R, Lindstrom W et al (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785–2791
pubmed: 2760638
pmcid: 2760638
Parrinello M, Rahman A (1981) Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys 52:7182–7190
Qu G, Li A, Sun Z et al (2020) The crucial role of methodology development in directed evolution of selective enzymes. Angew Chem Int Ed 59:2–30
Sterling T, Irwin JJ (2015) ZINC 15—ligand discovery for everyone. J Chem Inf Model 55:2324–2337
pubmed: 4658288
pmcid: 4658288
Sterner R, Merkl R, Raushel FM (2008) Computational design of enzymes. Chem Biol 15:421–423
pubmed: 18482694
Tian Y, Huang X, Li Q et al (2017a) Computational design of variants for cephalosporin C acylase from Pseudomonas strain N176 with improved stability and activity. Appl Microbiol Biotechnol 101:621–632
pubmed: 27557716
Tian Y, Xu Z, Huang X et al (2017b) Computational design to improve catalytic activity of cephalosporin C acylase from Pseudomonas strain N176. RSC Adv 7:30370–30375
Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461
pubmed: 19499576
pmcid: 19499576
Vanommeslaeghe K, Hatcher E, Acharya C et al (2010) CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem 31:671–690
pubmed: 19575467
pmcid: 2888302
Wang Y, Zhou Y, Shi S et al (2020) A rational design for improving the pepsin resistance of cellulase E4 isolated from T. fusca based on the evaluation of the transition complex and molecular structure. Biochem Eng J 153:107417
Xue J, Huang X, Lin M et al (2016) A fast loop-closure algorithm to accelerate residue matching in computational enzyme design. J Mol Model 22:49
pubmed: 26825974
Xue J, Huang X, Zhu Y (2019) Using molecular dynamics simulations to evaluate active designs of cephradine hydrolase by molecular mechanics/Poisson–Boltzmann surface area and molecular mechanics/generalized Born surface area methods. RSC Adv 9:13868–13877
Yang J, Roy A, Zhang Y (2013) Protein–ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics 29:2588–2595
pubmed: 23975762
pmcid: 3789548
Yang Y, Zhang X, Yin Q et al (2015) A mechanism of glucose tolerance and stimulation of GH1 β-glucosidases. Sci Rep 5:1–12
Yi S, Zhang X, Li H et al (2018) Screening and mutation of Saccharomyces cerevisiae UV-20 with a high yield of second generation bioethanol and high tolerance of temperature, glucose and ethanol. Indian J Microbiol 58:440–447
pubmed: 30262954
pmcid: 6141394
Yin Q, Zhou G, Peng C et al (2019) The first fungal laccase with an alkaline pH optimum obtained by directed evolution and its application in indigo dye decolorization. AMB Express 9:151
pubmed: 31535295
pmcid: 6751238
Yu W, He X, Vanommeslaeghe K et al (2012) Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations. J Comput Chem 33:2451–2468
pubmed: 22821581
pmcid: 3477297
Zhang Y-HP, Himmel ME, Mielenz JR (2006) Outlook for cellulase improvement: screening and selection strategies. Biotechnol Adv 24:452–481
Zhao X, Wang W, Wang F et al (2012) A comparative study of β-1, 4-endoglucanase (possessing β-1, 4-exoglucanase activity) from Bacillus subtilis LH expressed in Pichia pastoris GS115 and Escherichia coli Rosetta (DE3). Bioresour Technol 110:539–545
pubmed: 22336741
Zhao X, Wang W, Tong B et al (2016) A newly isolated Penicillium oxalicum 16 cellulase with high efficient synergism and high tolerance of monosaccharide. Appl Biochem Biotechnol 178:173–183
pubmed: 26410224
Zhao X, Yi S, Li H (2019) The optimized co-cultivation system of Penicillium oxalicum 16 and Trichoderma reesei RUT-C30 achieved a high yield of hydrolase applied in second-generation bioethanol production. Renew Energy 136:1028–1035