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DeChellis A, Nemmaru B, Sammond D, Douglass J, Patil N, Reste O, Chundawat SPS. Supercharging carbohydrate-binding module alone enhances endocellulase thermostability, binding, and activity on cellulosic biomass. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.557007. [PMID: 37745483 PMCID: PMC10515785 DOI: 10.1101/2023.09.09.557007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Lignocellulosic biomass recalcitrance to enzymatic degradation necessitates high enzyme loadings incurring large processing costs for industrial-scale biofuels or biochemicals production. Manipulating surface charge interactions to minimize non-productive interactions between cellulolytic enzymes and plant cell wall components (e.g., lignin or cellulose) via protein supercharging has been hypothesized to improve biomass biodegradability, but with limited demonstrated success to date. Here we characterize the effect of introducing non-natural enzyme surface mutations and net charge on cellulosic biomass hydrolysis activity by designing a library of supercharged family-5 endoglucanase Cel5A and its native family-2a carbohydrate binding module (CBM) originally belonging to an industrially relevant thermophilic microbe Thermobifida fusca . A combinatorial library of 33 mutant constructs containing different CBM and Cel5A designs spanning a net charge range of -52 to 37 was computationally designed using Rosetta macromolecular modelling software. Activity for all mutants was rapidly characterized as soluble cell lysates and promising mutants (containing mutations either on the CBM, Cel5A catalytic domain, or both CBM and Cel5A domains) were then purified and systematically characterized. Surprisingly, often endocellulases with mutations on the CBM domain alone resulted in improved activity on cellulosic biomass, with three top-performing supercharged CBM mutants exhibiting between 2-5-fold increase in activity, compared to native enzyme, on both pretreated biomass enriched in lignin (i.e., corn stover) and isolated crystalline/amorphous cellulose. Furthermore, we were able to clearly demonstrate that endocellulase net charge can be selectively fine-tuned using protein supercharging protocol for targeting distinct substrates and maximizing biocatalytic activity. Additionally, several supercharged CBM containing endocellulases exhibited a 5-10 °C increase in optimal hydrolysis temperature, compared to native enzyme, which enabled further increase in hydrolytic yield at higher operational reaction temperatures. This study demonstrates the first successful implementation of enzyme supercharging of cellulolytic enzymes to increase hydrolytic activity towards complex lignocellulosic biomass derived substrates.
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Chaudhari YB, Várnai A, Sørlie M, Horn SJ, Eijsink VGH. Engineering cellulases for conversion of lignocellulosic biomass. Protein Eng Des Sel 2023; 36:gzad002. [PMID: 36892404 PMCID: PMC10394125 DOI: 10.1093/protein/gzad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/13/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023] Open
Abstract
Lignocellulosic biomass is a renewable source of energy, chemicals and materials. Many applications of this resource require the depolymerization of one or more of its polymeric constituents. Efficient enzymatic depolymerization of cellulose to glucose by cellulases and accessory enzymes such as lytic polysaccharide monooxygenases is a prerequisite for economically viable exploitation of this biomass. Microbes produce a remarkably diverse range of cellulases, which consist of glycoside hydrolase (GH) catalytic domains and, although not in all cases, substrate-binding carbohydrate-binding modules (CBMs). As enzymes are a considerable cost factor, there is great interest in finding or engineering improved and robust cellulases, with higher activity and stability, easy expression, and minimal product inhibition. This review addresses relevant engineering targets for cellulases, discusses a few notable cellulase engineering studies of the past decades and provides an overview of recent work in the field.
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Affiliation(s)
- Yogesh B Chaudhari
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
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3
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Navvabi A, Homaei A, Pletschke BI, Navvabi N, Kim SK. Marine Cellulases and their Biotechnological Significance from Industrial Perspectives. Curr Pharm Des 2022; 28:3325-3336. [PMID: 35388747 DOI: 10.2174/1381612828666220406125132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/03/2021] [Accepted: 01/18/2022] [Indexed: 01/28/2023]
Abstract
Marine microorganisms represent virtually unlimited sources of novel biological compounds and can survive extreme conditions. Cellulases, a group of enzymes that are able to degrade cellulosic materials, are in high demand in various industrial and biotechnological applications, such as in the medical and pharmaceutical industries, food, fuel, agriculture, and single-cell protein, and as probiotics in aquaculture. The cellulosic biopolymer is a renewable resource and is a linearly arranged polysaccharide of glucose, with repeating units of disaccharide connected via β-1,4-glycosidic bonds, which are broken down by cellulase. A great deal of biodiversity resides in the ocean, and marine systems produce a wide range of distinct, new bioactive compounds that remain available but dormant for many years. The marine environment is filled with biomass from known and unknown vertebrates and invertebrate microorganisms, with much potential for use in medicine and biotechnology. Hence, complex polysaccharides derived from marine sources are a rich resource of microorganisms equipped with enzymes for polysaccharides degradation. Marine cellulases' extracts from the isolates are tested for their functional role in degrading seaweed and modifying wastes to low molecular fragments. They purify and renew environments by eliminating possible feedstocks of pollution. This review aims to examine the various types of marine cellulase producers and assess the ability of these microorganisms to produce these enzymes and their subsequent biotechnological applications.
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Affiliation(s)
- Azita Navvabi
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Brett I Pletschke
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Nazila Navvabi
- Department of Tumor Biology and Immunotherapy, Molecular Biology of Cancer, Institute of Experimental Medicine, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Prague, Czech Republic
| | - Se-Kwon Kim
- Department of Marine Sciences and Convergent Technology, Hanyang University, Ansan, Seoul 426-791, Republic of Korea
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Zajki-Zechmeister K, Eibinger M, Nidetzky B. Enzyme Synergy in Transient Clusters of Endo- and Exocellulase Enables a Multilayer Mode of Processive Depolymerization of Cellulose. ACS Catal 2022; 12:10984-10994. [PMID: 36082050 PMCID: PMC9442579 DOI: 10.1021/acscatal.2c02377] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/12/2022] [Indexed: 11/29/2022]
Abstract
Biological degradation of cellulosic materials relies on the molecular-mechanistic principle that internally chain-cleaving endocellulases work synergistically with chain end-cleaving exocellulases in polysaccharide chain depolymerization. How endo-exo synergy becomes effective in the deconstruction of a solid substrate that presents cellulose chains assembled into crystalline material is an open question of the mechanism, with immediate implications on the bioconversion efficiency of cellulases. Here, based on single-molecule evidence from real-time atomic force microscopy, we discover that endo- and exocellulases engage in the formation of transient clusters of typically three to four enzymes at the cellulose surface. The clusters form specifically at regular domains of crystalline cellulose microfibrils that feature molecular defects in the polysaccharide chain organization. The dynamics of cluster formation correlates with substrate degradation through a multilayer-processive mode of chain depolymerization, overall leading to the directed ablation of single microfibrils from the cellulose surface. Each multilayer-processive step involves the spatiotemporally coordinated and mechanistically concerted activity of the endo- and exocellulases in close proximity. Mechanistically, the cooperativity with the endocellulase enables the exocellulase to pass through its processive cycles ∼100-fold faster than when acting alone. Our results suggest an advanced paradigm of efficient multienzymatic degradation of structurally organized polymer materials by endo-exo synergetic chain depolymerization.
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Affiliation(s)
- Krisztina Zajki-Zechmeister
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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5
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Sinitsyn AP, Sinitsyna OA. Bioconversion of Renewable Plant Biomass. Second-Generation Biofuels: Raw Materials, Biomass Pretreatment, Enzymes, Processes, and Cost Analysis. BIOCHEMISTRY (MOSCOW) 2021; 86:S166-S195. [PMID: 33827407 DOI: 10.1134/s0006297921140121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review discusses various aspects of renewable plant biomass conversion and production of the second-generation biofuels, including the types of plant biomass, its composition and reaction ability in the enzymatic hydrolysis, and various pretreatment methods for increasing the biomass reactivity. Conversion of plant biomass into sugars requires the use of a complex of enzymes, the composition of which should be adapted to the biomass type and the pretreatment method. The efficiency of enzymatic hydrolysis can be increased by optimizing the composition of the enzymatic complex and by increasing the catalytic activity and operational stability of its constituent enzymes. The availability of active enzyme producers also plays an important role. Examples of practical implementation and scaling of processes for the production of second-generation biofuels are presented together with the cost analysis of bioethanol production.
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Affiliation(s)
- Arkadij P Sinitsyn
- Bakh Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia. .,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Olga A Sinitsyna
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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6
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The contribution of specific subsites to catalytic activities in active site architecture of a GH11 xylanase. Appl Microbiol Biotechnol 2020; 104:8735-8745. [DOI: 10.1007/s00253-020-10865-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/11/2020] [Accepted: 08/26/2020] [Indexed: 12/14/2022]
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Fu L, Zhang J, Si T. Recent advances in high-throughput mass spectrometry that accelerates enzyme engineering for biofuel research. ACTA ACUST UNITED AC 2020. [DOI: 10.1186/s42500-020-0011-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractEnzymes play indispensable roles in producing biofuels, a sustainable and renewable source of transportation fuels. Lacking rational design rules, the development of industrially relevant enzyme catalysts relies heavily on high-throughput screening. However, few universal methods exist to rapidly characterize large-scale enzyme libraries. Therefore, assay development is necessary on an ad hoc basis to link enzyme properties to spectrophotometric signals and often requires the use of surrogate, optically active substrates. On the other hand, mass spectrometry (MS) performs label-free enzyme assays that utilize native substrates and is therefore generally applicable. But the analytical speed of MS is considered rate limiting, mainly due to the use of time-consuming chromatographic separation in traditional MS analysis. Thanks to new instrumentation and sample preparation methods, direct analyte introduction into a mass spectrometer without a prior chromatographic step can be achieved by laser, microfluidics, and acoustics, so that each sample can be analyzed within seconds. Here we review recent advances in MS platforms that improve the throughput of enzyme library screening and discuss how these advances can potentially facilitate biofuel research by providing high sensitivity, selectivity and quantitation that are difficult to obtain using traditional assays. We also highlight the limitations of current MS assays in studying biofuel-related enzymes and propose possible solutions.
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Acharyya A, DiGiuseppi D, Stinger BL, Schweitzer-Stenner R, Vaden TD. Structural Destabilization of Azurin by Imidazolium Chloride Ionic Liquids in Aqueous Solution. J Phys Chem B 2019; 123:6933-6945. [DOI: 10.1021/acs.jpcb.9b04113] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, Pennsylvania 19104, United States
| | - David DiGiuseppi
- Department of Chemistry, Drexel University, 32 S. 32nd Street, Philadelphia, Pennsylvania 19104, United States
| | - Brittany L. Stinger
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 32 S. 32nd Street, Philadelphia, Pennsylvania 19104, United States
| | - Timothy D. Vaden
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
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de Paula RG, Antoniêto ACC, Ribeiro LFC, Srivastava N, O'Donovan A, Mishra PK, Gupta VK, Silva RN. Engineered microbial host selection for value-added bioproducts from lignocellulose. Biotechnol Adv 2019; 37:107347. [PMID: 30771467 DOI: 10.1016/j.biotechadv.2019.02.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/27/2019] [Accepted: 02/08/2019] [Indexed: 12/12/2022]
Abstract
Lignocellulose is a rich and sustainable globally available carbon source and is considered a prominent alternative raw material for producing biofuels and valuable chemical compounds. Enzymatic hydrolysis is one of the crucial steps of lignocellulose degradation. Cellulolytic and hemicellulolytic enzyme mixes produced by different microorganisms including filamentous fungi, yeasts and bacteria, are used to degrade the biomass to liberate monosaccharides and other compounds for fermentation or conversion to value-added products. During biomass pretreatment and degradation, toxic compounds are produced, and undesirable carbon catabolic repression (CCR) can occur. In order to solve this problem, microbial metabolic pathways and transcription factors involved have been investigated along with the application of protein engineering to optimize the biorefinery platform. Engineered Microorganisms have been used to produce specific enzymes to breakdown biomass polymers and metabolize sugars to produce ethanol as well other biochemical compounds. Protein engineering strategies have been used for modifying lignocellulolytic enzymes to overcome enzymatic limitations and improving both their production and functionality. Furthermore, promoters and transcription factors, which are key proteins in this process, are modified to promote microbial gene expression that allows a maximum performance of the hydrolytic enzymes for lignocellulosic degradation. The present review will present a critical discussion and highlight the aspects of the use of microorganisms to convert lignocellulose into value-added bioproduct as well combat the bottlenecks to make the biorefinery platform from lignocellulose attractive to the market.
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Affiliation(s)
- Renato Graciano de Paula
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Liliane Fraga Costa Ribeiro
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Neha Srivastava
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Anthonia O'Donovan
- School of Science and Computing, Galway-Mayo Institute of Technology, Galway, Ireland
| | - P K Mishra
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Vijai K Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia.
| | - Roberto N Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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10
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Zhang H, Dong S, Lou T, Wang S. Complete genome sequence unveiled cellulose degradation enzymes and secondary metabolic potentials in Streptomyces sp. CC0208. J Basic Microbiol 2018; 59:267-276. [PMID: 30589093 DOI: 10.1002/jobm.201800563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/19/2018] [Accepted: 11/30/2018] [Indexed: 11/10/2022]
Abstract
Marine Streptomyces sp. CC0208 isolated from the Bohai Bay showed high efficiency of cellulose degradation under optimized fermentation parameters. Also, as one of the bioinformatics-based approaches for the discovery of novel natural product and enzyme effectively, genome mining has been developed and applied widely. Herein, we reported the complete genome sequence of Streptomyces sp. CC0208.Whole-genome sequencing analysis revealed a genome size of 9,325,981 bp with a linear chromosome, GC content of 70.59% and 8487 protein-coding genes. Abundant genes have predicted functions in antibiotic metabolism and enzymes. A 20 enzymes closely associated with cellulose degradation were discovered. A total of 25 biosynthetic gene clusters (BGCs) of secondary metabolites were identified, including diverse classes of natural products. The availability of genome sequence of Streptomyces sp. CC0208 not only will assist in cracking the mechanism of cellulose degradation but also will provide the insights into the significant secondary metabolic potentials for the production of diverse compound classes based on rational strategies.
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Affiliation(s)
- Hongyu Zhang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shirui Dong
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Tingting Lou
- Tianjin Entry and Exit Inspection and Quarantine Bureau, Tianjin, China
| | - Suying Wang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
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11
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Xue D, Zeng X, Gong C, Lin D, Yao S. A cold adapt and ethanol tolerant endoglucanase from a marine Bacillus subtilis. Chin J Chem Eng 2018. [DOI: 10.1016/j.cjche.2018.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Oleson KR, Sprenger KG, Pfaendtner J, Schwartz DT. Inhibition of the Exoglucanase Cel7A by a Douglas-Fir-Condensed Tannin. J Phys Chem B 2018; 122:8665-8674. [PMID: 30111095 DOI: 10.1021/acs.jpcb.8b05850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Douglas-fir forestry residues are a potential feedstock for saccharification-based biofuels, and condensed tannins are expected to make up ∼3% of the dry mass of this feedstock. Condensed tannins are well-known for their ability to interact with proteins and can bind and inhibit cellulase enzymes used in saccharification. In this study, we use molecular docking and classical molecular dynamics simulations to investigate how a characterized condensed tannin from Douglas-fir bark binds to the exoglucanase Cel7A from Trichoderma reesei. Through looking at the "occupancy" and "residency" of specific amino acid residue-tannin interactions, we find that the binding sites are characterized by many simultaneous tannin-enzyme interactions with the strongest occurring on the catalytic module as opposed to the carbohydrate-binding module. The simulations indicate that tannin inhibition can result from binding at or near the catalytic tunnel's entrance and exit. The analyzed tannin further prefers to bind to loops around the catalytic region and has affinity for aromatic and charged amino acid residues. These insights provide direction for the rational design of tannin-resistant cellulases.
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Affiliation(s)
- Karl R Oleson
- Dept. of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98198-1750 , United States
| | - Kayla G Sprenger
- Dept. of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98198-1750 , United States.,Institute for Medical Engineering and Science , Massachusetts Institute of Technology , E25-352, Cambridge , Massachusetts 02139 , United States
| | - Jim Pfaendtner
- Dept. of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98198-1750 , United States
| | - Daniel T Schwartz
- Dept. of Chemical Engineering , University of Washington , Box 351750, Seattle , Washington 98198-1750 , United States
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13
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Dotsenko A, Gusakov A, Rozhkova A, Sinitsyna O, Shashkov I, Sinitsyn A. Enzymatic hydrolysis of cellulosic materials using synthetic mixtures of purified cellulases bioengineered at N-glycosylation sites. 3 Biotech 2018; 8:396. [PMID: 30221109 DOI: 10.1007/s13205-018-1419-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/01/2018] [Indexed: 01/18/2023] Open
Abstract
Mutant forms of recombinant endoglucanase II (EG II, N194A), cellobiohydrolase I (CBH I, N45A) and cellobiohydrolase II (CBH II, N219A) from Penicillium verruculosum with enhanced cellulase activities, achieved by engineering of enzyme N-glycosylation sites in our previous studies, were used as components of the binary and ternary mixtures of cellulases in hydrolysis of Avicel and milled aspen wood. Using the engineered forms of the enzymes at a dosage of 10 mg/g substrate resulted in significant boosting of the glucose release from cellulose in the presence of excess β-glucosidase relative to the performance of the corresponding wild-type mixtures at the same loading. The boosting effects reached 11-40% depending on the reaction time and substrate type. In hydrolysis of both cellulosic substrates by the binary mixtures of cellulases, all the enzyme pairs exhibited synergism. The magnitude of the synergistic effects (Ks) did not depend notably upon the induced mutations in the enzymes, and they were in the range of 1.3-1.8 for the combinations of EG II with CBH I (or CBH II), and 2.3-2.9 for the CBH I-CBH II pair. The results of this study should provide a basis for the development of a more effective fungal strain capable of producing cellulase cocktails with enhanced hydrolytic performance against lignocellulosic materials.
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Affiliation(s)
- Anna Dotsenko
- 1Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Pr. 33/2, Moscow, 119071 Russia
| | - Alexander Gusakov
- 1Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Pr. 33/2, Moscow, 119071 Russia
- 2Department of Chemistry, M.V. Lomonosov Moscow State University, Vorobyovy Gory 1/11, Moscow, 119991 Russia
| | - Aleksandra Rozhkova
- 1Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Pr. 33/2, Moscow, 119071 Russia
- 2Department of Chemistry, M.V. Lomonosov Moscow State University, Vorobyovy Gory 1/11, Moscow, 119991 Russia
| | - Olga Sinitsyna
- 1Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Pr. 33/2, Moscow, 119071 Russia
- 2Department of Chemistry, M.V. Lomonosov Moscow State University, Vorobyovy Gory 1/11, Moscow, 119991 Russia
| | - Igor Shashkov
- 1Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Pr. 33/2, Moscow, 119071 Russia
| | - Arkady Sinitsyn
- 1Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Pr. 33/2, Moscow, 119071 Russia
- 2Department of Chemistry, M.V. Lomonosov Moscow State University, Vorobyovy Gory 1/11, Moscow, 119991 Russia
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14
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Leis B, Held C, Andreeßen B, Liebl W, Graubner S, Schulte LP, Schwarz WH, Zverlov VV. Optimizing the composition of a synthetic cellulosome complex for the hydrolysis of softwood pulp: identification of the enzymatic core functions and biochemical complex characterization. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:220. [PMID: 30116297 PMCID: PMC6083626 DOI: 10.1186/s13068-018-1220-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/31/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND The development of efficient cellulase blends is a key factor for cost-effectively valorizing biomass in a new bio-economy. Today, the enzymatic hydrolysis of plant-derived polysaccharides is mainly accomplished with fungal cellulases, whereas potentially equally effective cellulose-degrading systems from bacteria have not been developed. Particularly, a thermostable multi-enzyme cellulase complex, the cellulosome from the anaerobic cellulolytic bacterium Clostridium thermocellum is promising of being applied as cellulolytic nano-machinery for the production of fermentable sugars from cellulosic biomass. RESULTS In this study, 60 cellulosomal components were recombinantly produced in E. coli and systematically permuted in synthetic complexes to study the function-activity relationship of all available enzymes on Kraft pulp from pine wood as the substrate. Starting from a basic exo/endoglucanase complex, we were able to identify additional functional classes such as mannanase and xylanase for optimal activity on the substrate. Based on these results, we predicted a synthetic cellulosome complex consisting of seven single components (including the scaffoldin protein and a β-glucosidase) and characterized it biochemically. We obtained a highly thermostable complex with optimal activity around 60-65 °C and an optimal pH in agreement with the optimum of the native cellulosome (pH 5.8). Remarkably, a fully synthetic complex containing 47 single cellulosomal components showed comparable activity with a commercially available fungal enzyme cocktail on the softwood pulp substrate. CONCLUSIONS Our results show that synthetic bacterial multi-enzyme complexes based on the cellulosome of C. thermocellum can be applied as a versatile platform for the quick adaptation and efficient degradation of a substrate of interest.
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Affiliation(s)
- Benedikt Leis
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
- Present Address: Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Winchester Str. 2, 35394 Gießen, Germany
| | - Claudia Held
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Björn Andreeßen
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Wolfgang Liebl
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Sigrid Graubner
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Louis-Philipp Schulte
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Wolfgang H. Schwarz
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, Moscow, 123182 Russia
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15
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Single-molecule study of oxidative enzymatic deconstruction of cellulose. Nat Commun 2017; 8:894. [PMID: 29026070 PMCID: PMC5638905 DOI: 10.1038/s41467-017-01028-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 08/02/2017] [Indexed: 01/29/2023] Open
Abstract
LPMO (lytic polysaccharide monooxygenase) represents a unique paradigm of cellulosic biomass degradation by an oxidative mechanism. Understanding the role of LPMO in deconstructing crystalline cellulose is fundamental to the enzyme’s biological function and will help to specify the use of LPMO in biorefinery applications. Here we show with real-time atomic force microscopy that C1 and C4 oxidizing types of LPMO from Neurospora crassa (NcLPMO9F, NcLPMO9C) bind to nanocrystalline cellulose with high preference for the very same substrate surfaces that are also used by a processive cellulase (Trichoderma reesei CBH I) to move along during hydrolytic cellulose degradation. The bound LPMOs, however, are immobile during their adsorbed residence time ( ~ 1.0 min for NcLPMO9F) on cellulose. Treatment with LPMO resulted in fibrillation of crystalline cellulose and strongly ( ≥ 2-fold) enhanced the cellulase adsorption. It also increased enzyme turnover on the cellulose surface, thus boosting the hydrolytic conversion. Understanding the role of enzymes in biomass depolymerization is essential for the development of more efficient biorefineries. Here, the authors show by atomic force microscopy the real-time mechanism of cellulose deconstruction by lytic polysaccharide monooxygenases.
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16
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Pensupa N, Leu SY, Hu Y, Du C, Liu H, Jing H, Wang H, Lin CSK. Recent Trends in Sustainable Textile Waste Recycling Methods: Current Situation and Future Prospects. Top Curr Chem (Cham) 2017; 375:76. [DOI: 10.1007/s41061-017-0165-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/27/2017] [Indexed: 10/19/2022]
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17
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Jiang X, Li W, Chen G, Wang L. Dynamic Perturbation of the Active Site Determines Reversible Thermal Inactivation in Glycoside Hydrolase Family 12. J Chem Inf Model 2017; 57:288-297. [DOI: 10.1021/acs.jcim.6b00692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xukai Jiang
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Wen Li
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Guanjun Chen
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
| | - Lushan Wang
- State Key Laboratory
of Microbial
Technology, Shandong University, Jinan 250100, China
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18
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Gusakov AV, Dotsenko AS, Rozhkova AM, Sinitsyn AP. N-Linked glycans are an important component of the processive machinery of cellobiohydrolases. Biochimie 2017; 132:102-108. [DOI: 10.1016/j.biochi.2016.11.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/10/2016] [Indexed: 02/02/2023]
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19
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Rizk M, Antranikian G, Elleuche S. Influence of Linker Length Variations on the Biomass-Degrading Performance of Heat-Active Enzyme Chimeras. Mol Biotechnol 2016; 58:268-79. [PMID: 26921187 DOI: 10.1007/s12033-016-9925-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Plant cell walls are composed of complex polysaccharides such as cellulose and hemicellulose. In order to efficiently hydrolyze cellulose, the synergistic action of several cellulases is required. Some anaerobic cellulolytic bacteria form multienzyme complexes, namely cellulosomes, while other microorganisms produce a portfolio of diverse enzymes that work in synergistic fashion. Molecular biological methods can mimic such effects through the generation of artificial bi- or multifunctional fusion enzymes. Endoglucanase and β-glucosidase from extremely thermophilic anaerobic bacteria Fervidobacterium gondwanense and Fervidobacterium islandicum, respectively, were fused end-to-end in an approach to optimize polysaccharide degradation. Both enzymes are optimally active at 90 °C and pH 6.0-7.0 representing excellent candidates for fusion experiments. The direct linkage of both enzymes led to an increased activity toward the substrate specific for β-glucosidase, but to a decreased activity of endoglucanase. However, these enzyme chimeras were superior over 1:1 mixtures of individual enzymes, because combined activities resulted in a higher final product yield. Therefore, such fusion enzymes exhibit promising features for application in industrial bioethanol production processes.
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Affiliation(s)
- Mazen Rizk
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, 21073, Hamburg, Germany
| | - Garabed Antranikian
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, 21073, Hamburg, Germany
| | - Skander Elleuche
- Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, 21073, Hamburg, Germany.
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20
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Abstract
Complex carbohydrates are ubiquitous in all kingdoms of life. As major components of the plant cell wall they constitute both a rich renewable carbon source for biotechnological transformation into fuels, chemicals and materials, and also form an important energy source as part of a healthy human diet. In both contexts, there has been significant, sustained interest in understanding how microbes transform these substrates. Classical perspectives of microbial polysaccharide degradation are currently being augmented by recent advances in the discovery of lytic polysaccharide monooxygenases (LPMOs) and polysaccharide utilization loci (PULs). Fundamental discoveries in carbohydrate enzymology are both advancing biological understanding, as well as informing applications in industrial biomass conversion and modulation of the human gut microbiota to mediate health benefits.
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21
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Extra carbohydrate binding module contributes to the processivity and catalytic activity of a non-modular hydrolase family 5 endoglucanase from Fomitiporia mediterranea MF3/22. Enzyme Microb Technol 2016; 91:42-51. [DOI: 10.1016/j.enzmictec.2016.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/12/2016] [Accepted: 06/01/2016] [Indexed: 11/23/2022]
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22
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Mattam AJ, Kuila A, Suralikerimath N, Choudary N, Rao PVC, Velankar HR. Cellulolytic enzyme expression and simultaneous conversion of lignocellulosic sugars into ethanol and xylitol by a new Candida tropicalis strain. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:157. [PMID: 27462368 PMCID: PMC4960679 DOI: 10.1186/s13068-016-0575-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/14/2016] [Indexed: 05/31/2023]
Abstract
BACKGROUND Lignocellulosic ethanol production involves major steps such as thermochemical pretreatment of biomass, enzymatic hydrolysis of pre-treated biomass and the fermentation of released sugars into ethanol. At least two different organisms are conventionally utilized for producing cellulolytic enzymes and for ethanol production through fermentation, whereas in the present study a single yeast isolate with the capacity to simultaneously produce cellulases and xylanases and ferment the released sugars into ethanol and xylitol has been described. RESULTS A yeast strain isolated from soil samples and identified as Candida tropicalis MTCC 25057 expressed cellulases and xylanases over a wide range of temperatures (32 and 42 °C) and in the presence of different cellulosic substrates [carboxymethylcellulose and wheat straw (WS)]. The studies indicated that the cultivation of yeast at 42 °C in pre-treated hydrolysate containing 0.5 % WS resulted in proportional expression of cellulases (exoglucanases and endoglucanases) at concentrations of 114.1 and 97.8 U g(-1) ds, respectively. A high xylanase activity (689.3 U g(-1) ds) was also exhibited by the yeast under similar growth conditions. Maximum expression of cellulolytic enzymes by the yeast occurred within 24 h of incubation. Of the sugars released from biomass after pretreatment, 49 g L(-1) xylose was aerobically converted into 15.8 g L(-1) of xylitol. In addition, 25.4 g L(-1) glucose released after the enzymatic hydrolysis of biomass was fermented by the same yeast to obtain an ethanol titer of 7.3 g L(-1). CONCLUSIONS During the present study, a new strain of C. tropicalis was isolated and found to have potential for consolidated bioprocessing (CBP) applications. The strain could grow in a wide range of process conditions (temperature, pH) and in the presence of lignocellulosic inhibitors such as furfural, HMF and acetic acid. The new yeast produced cellulolytic enzymes over a wide temperature range and in the presence of various cellulosic substrates. The cellulolytic enzymes produced by the yeast were effectively used for the hydrolysis of pretreated biomass. The released sugars, xylose and glucose were, respectively, converted into xylitol and ethanol. The potential shown by the new inhibitor tolerant cellulolytic C. tropicalis to produce ethanol or xylitol is of great industrial significance.
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Affiliation(s)
- Anu Jose Mattam
- Bioprocess Group, Hindustan Petroleum Corporation Limited, HP Green R&D Centre, KIADB Industrial Area, Tarabahalli, Devanagundi, Hoskote, Bengaluru, 560067 India
| | - Arindam Kuila
- Bioprocess Group, Hindustan Petroleum Corporation Limited, HP Green R&D Centre, KIADB Industrial Area, Tarabahalli, Devanagundi, Hoskote, Bengaluru, 560067 India
| | - Niranjan Suralikerimath
- Bioprocess Group, Hindustan Petroleum Corporation Limited, HP Green R&D Centre, KIADB Industrial Area, Tarabahalli, Devanagundi, Hoskote, Bengaluru, 560067 India
| | - Nettem Choudary
- Bioprocess Group, Hindustan Petroleum Corporation Limited, HP Green R&D Centre, KIADB Industrial Area, Tarabahalli, Devanagundi, Hoskote, Bengaluru, 560067 India
| | - Peddy V. C. Rao
- Bioprocess Group, Hindustan Petroleum Corporation Limited, HP Green R&D Centre, KIADB Industrial Area, Tarabahalli, Devanagundi, Hoskote, Bengaluru, 560067 India
| | - Harshad Ravindra Velankar
- Bioprocess Group, Hindustan Petroleum Corporation Limited, HP Green R&D Centre, KIADB Industrial Area, Tarabahalli, Devanagundi, Hoskote, Bengaluru, 560067 India
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23
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Dotsenko AS, Gusakov AV, Rozhkova AM, Sinitsyna OA, Nemashkalov VA, Sinitsyn AP. Effect of
N
-linked glycosylation on the activity and other properties of recombinant endoglucanase IIa (Cel5A) from
Penicillium verruculosum. Protein Eng Des Sel 2016; 29:495-502. [DOI: 10.1093/protein/gzw030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/17/2016] [Accepted: 06/20/2016] [Indexed: 12/14/2022] Open
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24
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Influence of surface charge, binding site residues and glycosylation on Thielavia terrestris cutinase biochemical characteristics. Appl Microbiol Biotechnol 2016; 100:4435-46. [PMID: 26758295 DOI: 10.1007/s00253-015-7254-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 09/13/2015] [Accepted: 12/12/2015] [Indexed: 02/06/2023]
Abstract
Cutinases are esterases of industrial importance for applications in recycling and surface modification of polyesters. The cutinase from Thielavia terrestris (TtC) is distinct in terms of its ability to retain its stability and activity in acidic pH. Stability and activity in acidic pHs are desirable for esterases as the pH of the reaction tends to go down with the generation of acid. The pH stability and activity are governed by the charged state of the residues involved in catalysis or in substrate binding. In this study, we performed the detailed structural and biochemical characterization of TtC coupled with surface charge analysis to understand its acidic tolerance. The stability of TtC in acidic pH was rationalized by evaluating the contribution of charge interactions to the Gibbs free energy of unfolding at varying pHs. The activity of TtC was found to be limited by substrate binding affinity, which is a function of the surface charge. Additionally, the presence of glycosylation affects the biochemical characteristics of TtC owing to steric interactions with residues involved in substrate binding.
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25
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Druzhinina IS, Kubicek CP. Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes. ADVANCES IN APPLIED MICROBIOLOGY 2016; 95:69-147. [PMID: 27261782 DOI: 10.1016/bs.aambs.2016.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) has properties of an efficient cell factory for protein production that is exploited by the enzyme industry, particularly with respect to cellulase and hemicellulase formation. Under conditions of industrial fermentations it yields more than 100g secreted protein L(-1). Consequently, T. reesei has been intensively studied in the 20th century. Most of these investigations focused on the biochemical characteristics of its cellulases and hemicellulases, on the improvement of their properties by protein engineering, and on enhanced enzyme production by recombinant strategies. However, as the fungus is rare in nature, its ecology remained unknown. The breakthrough in the understanding of the fundamental biology of T. reesei only happened during 2000s-2010s. In this review, we compile the current knowledge on T. reesei ecology, physiology, and genomics to present a holistic view on the natural behavior of the organism. This is not only critical for science-driven further improvement of the biotechnological applications of this fungus, but also renders T. reesei as an attractive model of filamentous fungi with superior saprotrophic abilities.
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Affiliation(s)
- I S Druzhinina
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - C P Kubicek
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
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26
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Jiang X, Chen G, Wang L. Structural and dynamic evolution of the amphipathic N-terminus diversifies enzyme thermostability in the glycoside hydrolase family 12. Phys Chem Chem Phys 2016; 18:21340-50. [DOI: 10.1039/c6cp02998a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The N-terminus diversifies enzyme thermostability in the GH12 family, which was investigated by MD simulations, and provides potential applications in protein engineering.
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Affiliation(s)
- Xukai Jiang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan 250100
- China
- State Key Laboratory of Biochemical Engineering
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27
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Zhang X, Wang S, Wu X, Liu S, Li D, Xu H, Gao P, Chen G, Wang L. Subsite-specific contributions of different aromatic residues in the active site architecture of glycoside hydrolase family 12. Sci Rep 2015; 5:18357. [PMID: 26670009 PMCID: PMC4680936 DOI: 10.1038/srep18357] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/16/2015] [Indexed: 01/22/2023] Open
Abstract
The active site architecture of glycoside hydrolase (GH) is a contiguous subregion of the enzyme constituted by residues clustered in the three-dimensional space, recognizing the monomeric unit of ligand through hydrogen bonds and hydrophobic interactions. Mutations of the key residues in the active site architecture of the GH12 family exerted different impacts on catalytic efficiency. Binding affinities between the aromatic amino acids and carbohydrate rings were quantitatively determined by isothermal titration calorimetry (ITC) and the quantum mechanical (QM) method, showing that the binding capacity order of Tyr>Trp>His (and Phe) was determined by their side-chain properties. The results also revealed that the binding constant of a certain residue remained unchanged when altering its location, while the catalytic efficiency changed dramatically. Increased binding affinity at a relatively distant subsite, such as the mutant of W7Y at the -4 subsite, resulted in a marked increase in the intermediate product of cellotetraose and enhanced the reactivity of endoglucanase by 144%; while tighter binding near the catalytic center, i.e. W22Y at the -2 subsite, enabled the enzyme to bind and hydrolyze smaller oligosaccharides. Clarification of the specific roles of the aromatics at different subsites may pave the way for a more rational design of GHs.
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Affiliation(s)
- Xiaomei Zhang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Shuai Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Xiuyun Wu
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Shijia Liu
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Dandan Li
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Hao Xu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P.R. China
| | - Peiji Gao
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Guanjun Chen
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
| | - Lushan Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, P.R. China
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28
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Lytic Polysaccharide Monooxygenases in Biomass Conversion. Trends Biotechnol 2015; 33:747-761. [DOI: 10.1016/j.tibtech.2015.09.006] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/28/2015] [Accepted: 09/08/2015] [Indexed: 01/02/2023]
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29
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Structural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module. PLoS One 2015; 10:e0142107. [PMID: 26562160 PMCID: PMC4643050 DOI: 10.1371/journal.pone.0142107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 10/16/2015] [Indexed: 01/08/2023] Open
Abstract
Cellulases are the key enzymes used in the biofuel industry. A typical cellulase contains a catalytic domain connected to a carbohydrate-binding module (CBM) through a flexible linker. Here we report the structure of an atypical trimodular cellulase which harbors a catalytic domain, a CBM46 domain and a rigid CBM_X domain between them. The catalytic domain shows the features of GH5 family, while the CBM46 domain has a sandwich-like structure. The catalytic domain and the CBM46 domain form an extended substrate binding cleft, within which several tryptophan residues are well exposed. Mutagenesis assays indicate that these residues are essential for the enzymatic activities. Gel affinity electrophoresis shows that these tryptophan residues are involved in the polysaccharide substrate binding. Also, electrostatic potential analysis indicates that almost the entire solvent accessible surface of CelB is negatively charged, which is consistent with the halophilic nature of this enzyme.
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30
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Dotsenko AS, Gusakov AV, Volkov PV, Rozhkova AM, Sinitsyn AP. N-linked glycosylation of recombinant cellobiohydrolase I (Cel7A) fromPenicillium verruculosumand its effect on the enzyme activity. Biotechnol Bioeng 2015; 113:283-91. [DOI: 10.1002/bit.25812] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/07/2015] [Accepted: 08/16/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Anna S. Dotsenko
- Department of Chemistry; M. V. Lomonosov Moscow State University; Vorobyovy Gory 1/11 Moscow 119899 Russia
| | - Alexander V. Gusakov
- Department of Chemistry; M. V. Lomonosov Moscow State University; Vorobyovy Gory 1/11 Moscow 119899 Russia
- A. N. Bach Institute of Biochemistry; Russian Academy of Sciences; Leninsky Pr. 33 Moscow 119991 Russia
| | - Pavel V. Volkov
- A. N. Bach Institute of Biochemistry; Russian Academy of Sciences; Leninsky Pr. 33 Moscow 119991 Russia
| | - Aleksandra M. Rozhkova
- Department of Chemistry; M. V. Lomonosov Moscow State University; Vorobyovy Gory 1/11 Moscow 119899 Russia
- A. N. Bach Institute of Biochemistry; Russian Academy of Sciences; Leninsky Pr. 33 Moscow 119991 Russia
| | - Arkady P. Sinitsyn
- Department of Chemistry; M. V. Lomonosov Moscow State University; Vorobyovy Gory 1/11 Moscow 119899 Russia
- A. N. Bach Institute of Biochemistry; Russian Academy of Sciences; Leninsky Pr. 33 Moscow 119991 Russia
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31
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Computational design, functional analysis and antigenic epitope estimation of a novel hybrid of 12 peptides of hirudin and reteplase. J Mol Model 2015; 21:229. [PMID: 26267298 DOI: 10.1007/s00894-015-2774-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/20/2015] [Indexed: 10/23/2022]
Abstract
Cardiovascular and cerebrovascular diseases are leading causes of morbidity and mortality for human beings, and thrombosis is the major risk factor. Thrombolytic therapy has been testified to be the most effective approach to cure thrombosis-related diseases. In clinical treatment, we often adopt a combination therapeutic regimen of both thrombolytic and anticoagulant agents to prevent the recurrence of thrombosis. Thus, a novel hybrid (HV12p-rPA) comprised of the C-terminal 12 residues of hirudin-PA (HV12p) and reteplase (rPA) was designed. The three-dimensional structure of this hybrid was mimicked based on homology modeling and refined with dynamics simulation by utilizing Amber12.0 software. The function of the hybrid was analyzed by structure comparison and the root mean square deviation (RMSD) of Cα atoms between the hybrid and native rPA was calculated. The results showed that HV12p, which was located in the N-terminus of the hybrid, was far from the rPA segment of the hybrid and had no influence on the conformational stability of the rPA domain. The RMSD of Cα atoms of these superimposed proteins was about 40Å, implying that the hybrid had a similar spatial conformation to that of native rPA. Additionally, the antigenic epitopes of the hybrid were predicted by estimations of Hopp-Wood hydrophilicity, Janin accessibility, Zimmermane-Simha polarity, Bhaskaran-Ponnuswamy flexibility, as well as secondary structure analysis and Kolaskar-Tongaonkar antigenicity prediction. The results showed that the most likely antigenic determinants were located at or near regions 148-152, 257-262 and 321-330.
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32
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Guerriero G, Hausman JF, Strauss J, Ertan H, Siddiqui KS. Destructuring plant biomass: focus on fungal and extremophilic cell wall hydrolases. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 234:180-93. [PMID: 25804821 PMCID: PMC4937988 DOI: 10.1016/j.plantsci.2015.02.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 05/05/2023]
Abstract
The use of plant biomass as feedstock for biomaterial and biofuel production is relevant in the current bio-based economy scenario of valorizing renewable resources. Fungi, which degrade complex and recalcitrant plant polymers, secrete different enzymes that hydrolyze plant cell wall polysaccharides. The present review discusses the current research trends on fungal, as well as extremophilic cell wall hydrolases that can withstand extreme physico-chemical conditions required in efficient industrial processes. Secretomes of fungi from the phyla Ascomycota, Basidiomycota, Zygomycota and Neocallimastigomycota are presented along with metabolic cues (nutrient sensing, coordination of carbon and nitrogen metabolism) affecting their composition. We conclude the review by suggesting further research avenues focused on the one hand on a comprehensive analysis of the physiology and epigenetics underlying cell wall degrading enzyme production in fungi and on the other hand on the analysis of proteins with unknown function and metagenomics of extremophilic consortia. The current advances in consolidated bioprocessing, altered secretory pathways and creation of designer plants are also examined. Furthermore, recent developments in enhancing the activity, stability and reusability of enzymes based on synergistic, proximity and entropic effects, fusion enzymes, structure-guided recombination between homologous enzymes and magnetic enzymes are considered with a view to improving saccharification.
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Affiliation(s)
- Gea Guerriero
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, Luxembourg.
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, Luxembourg
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, Fungal Genetics and Genomics Unit, University of Natural Resources and Life Sciences Vienna (BOKU), University and Research Center Campus Tulln-Technopol, Tulln/Donau, Austria; Health and Environment Department, Austrian Institute of Technology GmbH - AIT, University and Research Center Campus Tulln-Technopol, Tulln/Donau, Austria
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Department of Molecular Biology and Genetics, Istanbul University, Turkey
| | - Khawar Sohail Siddiqui
- Biology Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran, Saudi Arabia.
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33
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Nieves LM, Panyon LA, Wang X. Engineering Sugar Utilization and Microbial Tolerance toward Lignocellulose Conversion. Front Bioeng Biotechnol 2015; 3:17. [PMID: 25741507 PMCID: PMC4332379 DOI: 10.3389/fbioe.2015.00017] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/04/2015] [Indexed: 12/22/2022] Open
Abstract
Production of fuels and chemicals through a fermentation-based manufacturing process that uses renewable feedstock such as lignocellulosic biomass is a desirable alternative to petrochemicals. Although it is still in its infancy, synthetic biology offers great potential to overcome the challenges associated with lignocellulose conversion. In this review, we will summarize the identification and optimization of synthetic biological parts used to enhance the utilization of lignocellulose-derived sugars and to increase the biocatalyst tolerance for lignocellulose-derived fermentation inhibitors. We will also discuss the ongoing efforts and future applications of synthetic integrated biological systems used to improve lignocellulose conversion.
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Affiliation(s)
- Lizbeth M Nieves
- School of Life Sciences, Arizona State University , Tempe, AZ , USA
| | - Larry A Panyon
- School of Life Sciences, Arizona State University , Tempe, AZ , USA
| | - Xuan Wang
- School of Life Sciences, Arizona State University , Tempe, AZ , USA
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34
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Colussi F, Sørensen TH, Alasepp K, Kari J, Cruys-Bagger N, Windahl MS, Olsen JP, Borch K, Westh P. Probing substrate interactions in the active tunnel of a catalytically deficient cellobiohydrolase (Cel7). J Biol Chem 2014; 290:2444-54. [PMID: 25477511 DOI: 10.1074/jbc.m114.624163] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolases break down cellulose sequentially by sliding along the crystal surface with a single cellulose strand threaded through the catalytic tunnel of the enzyme. This so-called processive mechanism relies on a complex pattern of enzyme-substrate interactions, which need to be addressed in molecular descriptions of processivity and its driving forces. Here, we have used titration calorimetry to study interactions of cellooligosaccharides (COS) and a catalytically deficient variant (E212Q) of the enzyme Cel7A from Trichoderma reesei. This enzyme has ∼10 glucopyranose subsites in the catalytic tunnel, and using COS ligands with a degree of polymerization (DP) from 2 to 8, different regions of the tunnel could be probed. For COS ligands with a DP of 2-3 the binding constants were around 10(5) m(-1), and for longer ligands (DP 5-8) this value was ∼10(7) m(-1). Within each of these groups we did not find increased affinity as the ligands got longer and potentially filled more subsites. On the contrary, we found a small but consistent affinity loss as DP rose from 6 to 8, particularly at the higher investigated temperatures. Other thermodynamic functions (ΔH, ΔS, and ΔCp) decreased monotonously with both temperature and DP. Combined interpretation of these thermodynamic results and previously published structural data allowed assessment of an affinity profile along the length axis of the active tunnel.
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Affiliation(s)
- Francieli Colussi
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Trine H Sørensen
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Kadri Alasepp
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Jeppe Kari
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Nicolaj Cruys-Bagger
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Michael S Windahl
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Johan P Olsen
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Peter Westh
- From the Roskilde University, NSM, Research Unit for Functional Biomaterials, 1 Universitetsvej, Building 28, DK-4000 Denmark and
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35
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Lambertz C, Garvey M, Klinger J, Heesel D, Klose H, Fischer R, Commandeur U. Challenges and advances in the heterologous expression of cellulolytic enzymes: a review. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:135. [PMID: 25356086 PMCID: PMC4212100 DOI: 10.1186/s13068-014-0135-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/03/2014] [Indexed: 05/03/2023]
Abstract
Second generation biofuel development is increasingly reliant on the recombinant expression of cellulases. Designing or identifying successful expression systems is thus of preeminent importance to industrial progress in the field. Recombinant production of cellulases has been performed using a wide range of expression systems in bacteria, yeasts and plants. In a number of these systems, particularly when using bacteria and plants, significant challenges have been experienced in expressing full-length proteins or proteins at high yield. Further difficulties have been encountered in designing recombinant systems for surface-display of cellulases and for use in consolidated bioprocessing in bacteria and yeast. For establishing cellulase expression in plants, various strategies are utilized to overcome problems, such as the auto-hydrolysis of developing plant cell walls. In this review, we investigate the major challenges, as well as the major advances made to date in the recombinant expression of cellulases across the commonly used bacterial, plant and yeast systems. We review some of the critical aspects to be considered for industrial-scale cellulase production.
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Affiliation(s)
- Camilla Lambertz
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Megan Garvey
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- />Present address: School of Medicine, Deakin University, CSIRO Australian Animal Health Laboratory, 5 Portarlington Rd, Newcomb, VIC 3219 Australia
| | - Johannes Klinger
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Dirk Heesel
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Holger Klose
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- />Present address: Institute for Botany and Molecular Genetics, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Rainer Fischer
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- />Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074 Aachen, Germany
| | - Ulrich Commandeur
- />Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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