1
|
Wang M, Cui H, Gu C, Li A, Qiao J, Schwaneberg U, Zhang L, Wei J, Li X, Huang H. Engineering All-Round Cellulase for Bioethanol Production. ACS Synth Biol 2023; 12:2187-2197. [PMID: 37403343 DOI: 10.1021/acssynbio.3c00289] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
One strategy to decrease both the consumption of crude oil and environmental damage is through the production of bioethanol from biomass. Cellulolytic enzyme stability and enzymatic hydrolysis play important roles in the bioethanol process. However, the gradually increased ethanol concentration often reduces enzyme activity and leads to inactivation, thereby limiting the final ethanol yield. Herein, we employed an optimized Two-Gene Recombination Process (2GenReP) approach to evolve the exemplary cellulase CBHI for practical bioethanol fermentation. Two all-round CBHI variants (named as R2 and R4) were obtained with simultaneously improved ethanol resistance, organic solvent inhibitor tolerance, and enzymolysis stability in simultaneous saccharification and fermentation (SSF). Notably, CBHI R4 had a 7.0- to 34.5-fold enhanced catalytic efficiency (kcat/KM) in the presence/absence of ethanol. Employing the evolved CBHI R2 and R4 in the 1G bioethanol process resulted in up to 10.27% (6.7 g/L) improved ethanol yield (ethanol concentration) than non-cellulase, which was far more beyond than other optimization strategies. Besides bioenergy fields, this transferable protein engineering routine holds the potential to generate all-round enzymes that meet the requirement in biotransformation and bioenergy fields.
Collapse
Affiliation(s)
- Minghui Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Chenlei Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Jie Qiao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Lihui Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Junnan Wei
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, China
| |
Collapse
|
2
|
Haataja T, Gado JE, Nutt A, Anderson NT, Nilsson M, Momeni MH, Isaksson R, Väljamäe P, Johansson G, Payne CM, Ståhlberg J. Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non-productive binding: insights from crystal structures and MD simulation. FEBS J 2023; 290:379-399. [PMID: 35997626 PMCID: PMC10087753 DOI: 10.1111/febs.16602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/30/2022] [Accepted: 08/17/2022] [Indexed: 02/05/2023]
Abstract
Cellobiohydrolases (CBHs) in the glycoside hydrolase family 7 (GH7) (EC3.2.1.176) are the major cellulose degrading enzymes both in industrial settings and in the context of carbon cycling in nature. Small carbohydrate conjugates such as p-nitrophenyl-β-d-cellobioside (pNPC), p-nitrophenyl-β-d-lactoside (pNPL) and methylumbelliferyl-β-d-cellobioside have commonly been used in colorimetric and fluorometric assays for analysing activity of these enzymes. Despite the similar nature of these compounds the kinetics of their enzymatic hydrolysis vary greatly between the different compounds as well as among different enzymes within the GH7 family. Through enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies using the closely related compound o-nitrophenyl-β-d-cellobioside (oNPC), in this work we examine the different hydrolysis characteristics of these compounds on two model enzymes of this class, TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium. Protein crystal structures of the E212Q mutant of TrCel7A with pNPC and pNPL, and the wildtype TrCel7A with oNPC, reveal that non-productive binding at the product site is the dominating binding mode for these compounds. Enzyme kinetics results suggest the strength of non-productive binding is a key determinant for the activity characteristics on these substrates, with PcCel7D consistently showing higher turnover rates (kcat ) than TrCel7A, but higher Michaelis-Menten (KM ) constants as well. Furthermore, oNPC turned out to be useful as an active-site probe for fluorometric determination of the dissociation constant for cellobiose on TrCel7A but could not be utilized for the same purpose on PcCel7D, likely due to strong binding to an unknown site outside the active site.
Collapse
Affiliation(s)
- Topi Haataja
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Japheth E Gado
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA.,Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Anu Nutt
- Department of Chemistry, Uppsala University, Sweden.,Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - Nolan T Anderson
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
| | - Mikael Nilsson
- Institute of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Majid Haddad Momeni
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Roland Isaksson
- Institute of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | | | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, USA
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
3
|
Beri D, Herring CD, Blahova S, Poudel S, Giannone RJ, Hettich RL, Lynd LR. Coculture with hemicellulose-fermenting microbes reverses inhibition of corn fiber solubilization by Clostridium thermocellum at elevated solids loadings. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:24. [PMID: 33461608 PMCID: PMC7814735 DOI: 10.1186/s13068-020-01867-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/24/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND The cellulolytic thermophile Clostridium thermocellum is an important biocatalyst due to its ability to solubilize lignocellulosic feedstocks without the need for pretreatment or exogenous enzyme addition. At low concentrations of substrate, C. thermocellum can solubilize corn fiber > 95% in 5 days, but solubilization declines markedly at substrate concentrations higher than 20 g/L. This differs for model cellulose like Avicel, on which the maximum solubilization rate increases in proportion to substrate concentration. The goal of this study was to examine fermentation at increasing corn fiber concentrations and investigate possible reasons for declining performance. RESULTS The rate of growth of C. thermocellum on corn fiber, inferred from CipA scaffoldin levels measured by LC-MS/MS, showed very little increase with increasing solids loading. To test for inhibition, we evaluated the effects of spent broth on growth and cellulase activity. The liquids remaining after corn fiber fermentation were found to be strongly inhibitory to growth on cellobiose, a substrate that does not require cellulose hydrolysis. Additionally, the hydrolytic activity of C. thermocellum cellulase was also reduced to less-than half by adding spent broth. Noting that > 15 g/L hemicellulose oligosaccharides accumulated in the spent broth of a 40 g/L corn fiber fermentation, we tested the effect of various model carbohydrates on growth on cellobiose and Avicel. Some compounds like xylooligosaccharides caused a decline in cellulolytic activity and a reduction in the maximum solubilization rate on Avicel. However, there were no relevant model compounds that could replicate the strong inhibition by spent broth on C. thermocellum growth on cellobiose. Cocultures of C. thermocellum with hemicellulose-consuming partners-Herbinix spp. strain LL1355 and Thermoanaerobacterium thermosaccharolyticum-exhibited lower levels of unfermented hemicellulose hydrolysis products, a doubling of the maximum solubilization rate, and final solubilization increased from 67 to 93%. CONCLUSIONS This study documents inhibition of C. thermocellum with increasing corn fiber concentration and demonstrates inhibition of cellulase activity by xylooligosaccharides, but further work is needed to understand why growth on cellobiose was inhibited by corn fiber fermentation broth. Our results support the importance of hemicellulose-utilizing coculture partners to augment C. thermocellum in the fermentation of lignocellulosic feedstocks at high solids loading.
Collapse
Affiliation(s)
- Dhananjay Beri
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Christopher D Herring
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA.
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
- Enchi Corporation, Lebanon, NH, 03766, USA.
| | - Sofie Blahova
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
| | - Suresh Poudel
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Richard J Giannone
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Robert L Hettich
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Enchi Corporation, Lebanon, NH, 03766, USA
| |
Collapse
|
4
|
Østby H, Hansen LD, Horn SJ, Eijsink VGH, Várnai A. Enzymatic processing of lignocellulosic biomass: principles, recent advances and perspectives. J Ind Microbiol Biotechnol 2020; 47:623-657. [PMID: 32840713 PMCID: PMC7658087 DOI: 10.1007/s10295-020-02301-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023]
Abstract
Efficient saccharification of lignocellulosic biomass requires concerted development of a pretreatment method, an enzyme cocktail and an enzymatic process, all of which are adapted to the feedstock. Recent years have shown great progress in most aspects of the overall process. In particular, increased insights into the contributions of a wide variety of cellulolytic and hemicellulolytic enzymes have improved the enzymatic processing step and brought down costs. Here, we review major pretreatment technologies and different enzyme process setups and present an in-depth discussion of the various enzyme types that are currently in use. We pay ample attention to the role of the recently discovered lytic polysaccharide monooxygenases (LPMOs), which have led to renewed interest in the role of redox enzyme systems in lignocellulose processing. Better understanding of the interplay between the various enzyme types, as they may occur in a commercial enzyme cocktail, is likely key to further process improvements.
Collapse
Affiliation(s)
- Heidi Østby
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Line Degn Hansen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway.
| |
Collapse
|
5
|
Giovannoni M, Gramegna G, Benedetti M, Mattei B. Industrial Use of Cell Wall Degrading Enzymes: The Fine Line Between Production Strategy and Economic Feasibility. Front Bioeng Biotechnol 2020; 8:356. [PMID: 32411686 PMCID: PMC7200985 DOI: 10.3389/fbioe.2020.00356] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Cell Wall Degrading Enzymes (CWDEs) are a heterogeneous group of enzymes including glycosyl-hydrolases, oxidoreductases, lyases, and esterases. Microbes with degrading activities toward plant cell wall polysaccharides are the most relevant source of CWDEs for industrial applications. These organisms secrete a wide array of CWDEs in amounts strictly necessary for their own sustenance, nonetheless the production of CWDEs from wild type microbes can be increased at large-scale by using optimized fermentation strategies. In the last decades, advances in genetic engineering allowed the expression of recombinant CWDEs also in lab-domesticated organisms such as E. coli, yeasts and plants, dramatically increasing the available options for the large-scale production of CWDEs. The optimization of a CWDE-producing biofactory is a hard challenge that biotechnologists tackle by testing different expression strategies and expression-hosts. Although both the yield and production costs are critical factors to produce biomolecules at industrial scale, these parameters are often disregarded in basic research. This review presents the main characteristics and industrial applications of CWDEs directed toward the cell wall of plants, bacteria, fungi and microalgae. Different biofactories for CWDE expression are compared in order to highlight strengths and weaknesses of each production system and how these aspects impact the final enzyme cost and, consequently, the economic feasibility of using CWDEs for industrial applications.
Collapse
Affiliation(s)
- Moira Giovannoni
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giovanna Gramegna
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Manuel Benedetti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| |
Collapse
|
6
|
Green Production and Biotechnological Applications of Cell Wall Lytic Enzymes. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9235012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
: Energy demand is constantly growing, and, nowadays, fossil fuels still play a dominant role in global energy production, despite their negative effects on air pollution and the emission of greenhouse gases, which are the main contributors to global warming. An alternative clean source of energy is represented by the lignocellulose fraction of plant cell walls, the most abundant carbon source on Earth. To obtain biofuels, lignocellulose must be efficiently converted into fermentable sugars. In this regard, the exploitation of cell wall lytic enzymes (CWLEs) produced by lignocellulolytic fungi and bacteria may be considered as an eco-friendly alternative. These organisms evolved to produce a variety of highly specific CWLEs, even if in low amounts. For an industrial use, both the identification of novel CWLEs and the optimization of sustainable CWLE-expressing biofactories are crucial. In this review, we focus on recently reported advances in the heterologous expression of CWLEs from microbial and plant expression systems as well as some of their industrial applications, including the production of biofuels from agricultural feedstock and of value-added compounds from waste materials. Moreover, since heterologous expression of CWLEs may be toxic to plant hosts, genetic strategies aimed in converting such a deleterious effect into a beneficial trait are discussed.
Collapse
|
7
|
Abstract
Cellulase enzymes deconstruct recalcitrant cellulose into soluble sugars, making them a biocatalyst of biotechnological interest for use in the nascent lignocellulosic bioeconomy. Cellobiohydrolases (CBHs) are cellulases capable of liberating many sugar molecules in a processive manner without dissociating from the substrate. Within the complete processive cycle of CBHs, dissociation from the cellulose substrate is rate limiting, but the molecular mechanism of this step is unknown. Here, we present a direct comparison of potential molecular mechanisms for dissociation via Hamiltonian replica exchange molecular dynamics of the model fungal CBH, Trichoderma reesei Cel7A. Computational rate estimates indicate that stepwise cellulose dethreading from the binding tunnel is 4 orders of magnitude faster than a clamshell mechanism, in which the substrate-enclosing loops open and release the substrate without reversing. We also present the crystal structure of a disulfide variant that covalently links substrate-enclosing loops on either side of the substrate-binding tunnel, which constitutes a CBH that can only dissociate via stepwise dethreading. Biochemical measurements indicate that this variant has a dissociation rate constant essentially equivalent to the wild type, implying that dethreading is likely the predominant mechanism for dissociation.
Collapse
|
8
|
Benedetti M, Vecchi V, Betterle N, Natali A, Bassi R, Dall'Osto L. Design of a highly thermostable hemicellulose-degrading blend from Thermotoga neapolitana for the treatment of lignocellulosic biomass. J Biotechnol 2019; 296:42-52. [PMID: 30885654 DOI: 10.1016/j.jbiotec.2019.03.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/07/2019] [Accepted: 03/12/2019] [Indexed: 01/06/2023]
Abstract
The biological conversion of lignocellulose into fermentable sugars is a key process for the sustainable production of biofuels from plant biomass. Polysaccharides in plant feedstock can be valorized using thermostable mixtures of enzymes that degrade the cell walls, thus avoiding harmful and expensive pre-treatments. (Hyper)thermophilic bacteria of the phylum Thermotogae provide a rich source of enzymes for such industrial applications. Here we selected T. neapolitana as a source of hyperthermophilic hemicellulases for the degradation of lignocellulosic biomass. Two genes encoding putative hemicellulases were cloned from T. neapolitana genomic DNA and expressed in Escherichia coli. Further characterization revealed that the genes encoded an endo-1,4-β-galactanase and an α-l-arabinofuranosidase with optimal temperatures of ˜90 °C and high turnover numbers during catalysis (kcat values of ˜177 and ˜133 s-1, respectively, on soluble substrates). These enzymes were combined with three additional T. neapolitana hyperthermophilic hemicellulases - endo-1,4-β-xylanase (XynA), endo-1,4-β-mannanase (ManB/Man5A) and β-glucosidase (GghA) - to form a highly thermostable hemicellulolytic blend. The treatment of barley straw and corn bran with this enzymatic cocktail resulted in the solubilization of multiple hemicelluloses and boosted the yield of fermentable sugars by up to 65% when the complex substrates were further degraded by cellulases.
Collapse
Affiliation(s)
- Manuel Benedetti
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Valeria Vecchi
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Nico Betterle
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Alberto Natali
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Roberto Bassi
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Luca Dall'Osto
- Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| |
Collapse
|
9
|
Abstract
Homology modeling is a very powerful tool in the absence of atomic structures for understanding the general fold of the enzyme, conserved residues, catalytic tunnel/pocket as well as substrate and product binding sites. This information is useful for structure-assisted enzyme design approach for the development of robust enzymes especially for industrial applications.
Collapse
|
10
|
Borisova AS, Eneyskaya EV, Jana S, Badino SF, Kari J, Amore A, Karlsson M, Hansson H, Sandgren M, Himmel ME, Westh P, Payne CM, Kulminskaya AA, Ståhlberg J. Correlation of structure, function and protein dynamics in GH7 cellobiohydrolases from Trichoderma atroviride, T. reesei and T. harzianum. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:5. [PMID: 29344086 PMCID: PMC5766984 DOI: 10.1186/s13068-017-1006-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/23/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND The ascomycete fungus Trichoderma reesei is the predominant source of enzymes for industrial conversion of lignocellulose. Its glycoside hydrolase family 7 cellobiohydrolase (GH7 CBH) TreCel7A constitutes nearly half of the enzyme cocktail by weight and is the major workhorse in the cellulose hydrolysis process. The orthologs from Trichoderma atroviride (TatCel7A) and Trichoderma harzianum (ThaCel7A) show high sequence identity with TreCel7A, ~ 80%, and represent naturally evolved combinations of cellulose-binding tunnel-enclosing loop motifs, which have been suggested to influence intrinsic cellobiohydrolase properties, such as endo-initiation, processivity, and off-rate. RESULTS The TatCel7A, ThaCel7A, and TreCel7A enzymes were characterized for comparison of function. The catalytic domain of TatCel7A was crystallized, and two structures were determined: without ligand and with thio-cellotriose in the active site. Initial hydrolysis of bacterial cellulose was faster with TatCel7A than either ThaCel7A or TreCel7A. In synergistic saccharification of pretreated corn stover, both TatCel7A and ThaCel7A were more efficient than TreCel7A, although TatCel7A was more sensitive to thermal inactivation. Structural analyses and molecular dynamics (MD) simulations were performed to elucidate important structure/function correlations. Moreover, reverse conservation analysis (RCA) of sequence diversity revealed divergent regions of interest located outside the cellulose-binding tunnel of Trichoderma spp. GH7 CBHs. CONCLUSIONS We hypothesize that the combination of loop motifs is the main determinant for the observed differences in Cel7A activity on cellulosic substrates. Fine-tuning of the loop flexibility appears to be an important evolutionary target in Trichoderma spp., a conclusion supported by the RCA data. Our results indicate that, for industrial use, it would be beneficial to combine loop motifs from TatCel7A with the thermostability features of TreCel7A. Furthermore, one region implicated in thermal unfolding is suggested as a primary target for protein engineering.
Collapse
Affiliation(s)
- Anna S. Borisova
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Centre “Kurchatov Institute”, Orlova Roscha, Gatchina, Leningrad Region 188300 Russia
| | - Elena V. Eneyskaya
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Centre “Kurchatov Institute”, Orlova Roscha, Gatchina, Leningrad Region 188300 Russia
| | - Suvamay Jana
- Department of Chemical and Materials Engineering, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, KY 40506-0046 USA
| | - Silke F. Badino
- Department of Science and Environment, Roskilde University, 1 Universitetsvej, 4000 Roskilde, Denmark
| | - Jeppe Kari
- Department of Science and Environment, Roskilde University, 1 Universitetsvej, 4000 Roskilde, Denmark
| | - Antonella Amore
- National Renewable Energy Laboratory, Biosciences Center, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, P.O. Box 7026, 750 07 Uppsala, Sweden
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
| | - Michael E. Himmel
- National Renewable Energy Laboratory, Biosciences Center, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Peter Westh
- Department of Science and Environment, Roskilde University, 1 Universitetsvej, 4000 Roskilde, Denmark
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, KY 40506-0046 USA
- Present Address: Division of Chemical, Bioengineering, Environmental, and Transport Systems, National Science Foundation, Alexandria, VA USA
| | - Anna A. Kulminskaya
- B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Centre “Kurchatov Institute”, Orlova Roscha, Gatchina, Leningrad Region 188300 Russia
- Department of Medical Physics, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
| |
Collapse
|
11
|
Joosten RP, Lütteke T. Carbohydrate 3D structure validation. Curr Opin Struct Biol 2016; 44:9-17. [PMID: 27816840 DOI: 10.1016/j.sbi.2016.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/07/2016] [Accepted: 10/13/2016] [Indexed: 12/11/2022]
Abstract
Glycoproteins and protein-carbohydrate complexes in the worldwide Protein Data Bank (wwPDB) can be an excellent source of information for glycoscientists. Unfortunately, a rather large number of errors and inconsistencies is found in the glycan moieties of these 3D structures. This review illustrates frequent problems of carbohydrate moieties in wwPDB entries, such as nomenclature issues, incorrect N-glycan core structures, missing or erroneous linkages, or poor glycan geometry, and describes the carbohydrate-specific validation tools that are designed to identify such problems. Recommendations how to avoid these issues or how to rectify incorrect structures are also given.
Collapse
Affiliation(s)
- Robbie P Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Frankfurter Str. 100, 35392 Giessen, Germany.
| |
Collapse
|
12
|
Baba Y, Sumitani JI, Tanaka K, Tani S, Kawaguchi T. Site-saturation mutagenesis for β-glucosidase 1 from Aspergillus aculeatus to accelerate the saccharification of alkaline-pretreated bagasse. Appl Microbiol Biotechnol 2016; 100:10495-10507. [DOI: 10.1007/s00253-016-7726-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/30/2016] [Accepted: 07/04/2016] [Indexed: 01/05/2023]
|
13
|
Biochemical and Structural Characterizations of Two Dictyostelium Cellobiohydrolases from the Amoebozoa Kingdom Reveal a High Level of Conservation between Distant Phylogenetic Trees of Life. Appl Environ Microbiol 2016; 82:3395-409. [PMID: 27037126 DOI: 10.1128/aem.00163-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 03/25/2016] [Indexed: 12/26/2022] Open
Abstract
UNLABELLED Glycoside hydrolase family 7 (GH7) cellobiohydrolases (CBHs) are enzymes commonly employed in plant cell wall degradation across eukaryotic kingdoms of life, as they provide significant hydrolytic potential in cellulose turnover. To date, many fungal GH7 CBHs have been examined, yet many questions regarding structure-activity relationships in these important natural and commercial enzymes remain. Here, we present the crystal structures and a biochemical analysis of two GH7 CBHs from social amoeba: Dictyostelium discoideum Cel7A (DdiCel7A) and Dictyostelium purpureum Cel7A (DpuCel7A). DdiCel7A and DpuCel7A natively consist of a catalytic domain and do not exhibit a carbohydrate-binding module (CBM). The structures of DdiCel7A and DpuCel7A, resolved to 2.1 Å and 2.7 Å, respectively, are homologous to those of other GH7 CBHs with an enclosed active-site tunnel. Two primary differences between the Dictyostelium CBHs and the archetypal model GH7 CBH, Trichoderma reesei Cel7A (TreCel7A), occur near the hydrolytic active site and the product-binding sites. To compare the activities of these enzymes with the activity of TreCel7A, the family 1 TreCel7A CBM and linker were added to the C terminus of each of the Dictyostelium enzymes, creating DdiCel7ACBM and DpuCel7ACBM, which were recombinantly expressed in T. reesei DdiCel7ACBM and DpuCel7ACBM hydrolyzed Avicel, pretreated corn stover, and phosphoric acid-swollen cellulose as efficiently as TreCel7A when hydrolysis was compared at their temperature optima. The Ki of cellobiose was significantly higher for DdiCel7ACBM and DpuCel7ACBM than for TreCel7A: 205, 130, and 29 μM, respectively. Taken together, the present study highlights the remarkable degree of conservation of the activity of these key natural and industrial enzymes across quite distant phylogenetic trees of life. IMPORTANCE GH7 CBHs are among the most important cellulolytic enzymes both in nature and for emerging industrial applications for cellulose breakdown. Understanding the diversity of these key industrial enzymes is critical to engineering them for higher levels of activity and greater stability. The present work demonstrates that two GH7 CBHs from social amoeba are surprisingly quite similar in structure and activity to the canonical GH7 CBH from the model biomass-degrading fungus T. reesei when tested under equivalent conditions (with added CBM-linker domains) on an industrially relevant substrate.
Collapse
|
14
|
Contrasted enzymatic cocktails reveal the importance of cellulases and hemicellulases activity ratios for the hydrolysis of cellulose in presence of xylans. AMB Express 2016; 6:24. [PMID: 27001439 PMCID: PMC4801825 DOI: 10.1186/s13568-016-0196-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/11/2016] [Indexed: 11/18/2022] Open
Abstract
Various enzymatic cocktails were produced from two Trichoderma reesei strains, a cellulase hyperproducer strain and a strain with β-glucosidase activity overexpression. By using various carbon sources (lactose, glucose, xylose, hemicellulosic hydrolysate) for strains growth, contrasted enzymatic activities were obtained. The enzymatic cocktails presented various levels of efficiency for the hydrolysis of cellulose Avicel into glucose, in presence of xylans, or not. These latter were also hydrolyzed with different extents according to cocktails. The most efficient cocktails (TR1 and TR3) on Avicel were richer in filter paper activity (FPU) and presented a low ratio FPU/β-glucosidase activity. Cocktails TR2 and TR5 which were produced on the higher amount of hemicellulosic hydrolysate, possess both high xylanase and β-xylosidase activities, and were the most efficient for xylans hydrolysis. When hydrolysis of Avicel was conducted in presence of xylans, a decrease of glucose release occurred for all cocktails compared to hydrolysis of Avicel alone. Mixing TR1 and TR5 cocktails with two different ratios of proteins (1/1 and 1/4) resulted in a gain of efficiency for glucose release during hydrolysis of Avicel in presence of xylans compared to TR5 alone. Our results demonstrate the importance of combining hemicellulase and cellulase activities to improve the yields of glucose release from Avicel in presence of xylans. In this context, strategies involving enzymes production with carbon sources comprising mixed C5 and C6 sugars or combining different cocktails produced on C5 or on C6 sugars are of interest for processes developed in the context of lignocellulosic biorefinery.
Collapse
|