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Rwere F, Cartee NMP, Yang Y, Waskell L. A flexible linker of 8-amino acids between the membrane binding segment and the FMN domain of cytochrome P450 reductase is necessary for optimal activity. J Inorg Biochem 2024; 259:112667. [PMID: 39032346 PMCID: PMC11298297 DOI: 10.1016/j.jinorgbio.2024.112667] [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: 04/02/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
The diflavin NADPH-cytochrome P450 reductase (CYPOR) plays a critical role in human cytochrome P450 (CYP) activity by sequentially delivering two electrons from NADPH to CYP enzymes during catalysis. Although electron transfer to forty-eight human CYP enzymes by the FMN hydroquinone of CYPOR is well-known, the role of the linker between the NH2-terminus membrane-binding domain (MBD) and FMN domain in supporting the activity of P450 enzymes remains poorly understood. Here we demonstrate that a linker with at least eight residues is required to form a functional CYPOR-CYP2B4 complex. The linker has been shortened in two amino-acid increments from Phe44 to Ile57 using site directed mutagenesis. The ability of the deletion mutants to support cytochrome P450 2B4 (CYP2B4) catalysis and reduce ferric CYP2B4 was determined using an in vitro assay and stopped-flow spectrophotometry. Steady-state enzyme kinetics showed that shortening the linker by 8-14 amino acids inhibited (63-99%) the ability of CYPOR to support CYP2B4 activity and significantly increased the Km of CYPOR for CYP2B4. In addition, the reductase mutants decreased the rate of reduction of ferric CYP2B4 (46-95%) compared to wildtype when the linker was shortened by 8-14 residues. These results indicate that a linker with a minimum length of eight residues is necessary to enable the FMN domain of reductase to interact with CYP2B4 to form a catalytically competent complex. Our study provides evidence that the length of the MBD-FMN domain linker is a major determinant of the ability of CYPOR to support CYP catalysis and drug metabolism by P450 enzymes. PREAMBLE: This manuscript is dedicated in memory of Dr. James R. Kincaid who was the doctoral advisor to Dr. Freeborn Rwere and a longtime collaborator and friend of Dr. Lucy Waskell. Dr. James R. Kincaid was a distinguished professor of chemistry specializing in resonance Raman (rR) studies of heme proteins. He inspired Dr. Rwere (a Zimbabwean native) and three other Zimbabweans (Dr. Remigio Usai, Dr. Daniel Kaluka and Ms. Munyaradzi E. Manyumwa) to use lasers to document subtle changes occurring at heme active site of globin proteins (myoglobin and hemoglobin) and cytochrome P450 enzymes. Dr. Rwere appreciate his contributions to the development of talented Black scientists from Africa.
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Affiliation(s)
- Freeborn Rwere
- Department of Anesthesiology, University of Michigan and VAMC, 2215 Fuller Road, Ann Arbor, MI, USA; Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, 3174 Porter Dr, Palo Alto, CA, USA.
| | - Naw May P Cartee
- Department of Anesthesiology, University of Michigan and VAMC, 2215 Fuller Road, Ann Arbor, MI, USA
| | - Yuting Yang
- Department of Anesthesiology, University of Michigan and VAMC, 2215 Fuller Road, Ann Arbor, MI, USA
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan and VAMC, 2215 Fuller Road, Ann Arbor, MI, USA
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2
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Forsberg Z, Stepnov AA, Tesei G, Wang Y, Buchinger E, Kristiansen SK, Aachmann FL, Arleth L, Eijsink VGH, Lindorff-Larsen K, Courtade G. The effect of linker conformation on performance and stability of a two-domain lytic polysaccharide monooxygenase. J Biol Chem 2023; 299:105262. [PMID: 37734553 PMCID: PMC10598543 DOI: 10.1016/j.jbc.2023.105262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/05/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
A considerable number of lytic polysaccharide monooxygenases (LPMOs) and other carbohydrate-active enzymes are modular, with catalytic domains being tethered to additional domains, such as carbohydrate-binding modules, by flexible linkers. While such linkers may affect the structure, function, and stability of the enzyme, their roles remain largely enigmatic, as do the reasons for natural variation in length and sequence. Here, we have explored linker functionality using the two-domain cellulose-active ScLPMO10C from Streptomyces coelicolor as a model system. In addition to investigating the WT enzyme, we engineered three linker variants to address the impact of both length and sequence and characterized these using small-angle X-ray scattering, NMR, molecular dynamics simulations, and functional assays. The resulting data revealed that, in the case of ScLPMO10C, linker length is the main determinant of linker conformation and enzyme performance. Both the WT and a serine-rich variant, which have the same linker length, demonstrated better performance compared with those with either a shorter linker or a longer linker. A highlight of our findings was the substantial thermostability observed in the serine-rich variant. Importantly, the linker affects thermal unfolding behavior and enzyme stability. In particular, unfolding studies show that the two domains unfold independently when mixed, whereas the full-length enzyme shows one cooperative unfolding transition, meaning that the impact of linkers in biomass-processing enzymes is more complex than mere structural tethering.
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Affiliation(s)
- Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Giulio Tesei
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Yong Wang
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark; College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Edith Buchinger
- Vectron Biosolutions AS, Trondheim, Norway; Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Sandra K Kristiansen
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Finn L Aachmann
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Lise Arleth
- X-ray and Neutron Science, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Gaston Courtade
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway.
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Iglesias Rando MR, Gorojovsky N, Zylberman V, Goldbaum FA, Craig PO. Improvement of Cellulomonas fimi endoglucanase CenA by multienzymatic display on a decameric structural scaffold. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12581-6. [PMID: 37212884 DOI: 10.1007/s00253-023-12581-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/27/2023] [Accepted: 05/06/2023] [Indexed: 05/23/2023]
Abstract
The development of multifunctional particles using polymeric scaffolds is an emerging technology for many nanobiotechnological applications. Here we present a system for the production of multifunctional complexes, based on the high affinity non-covalent interaction of cohesin and dockerin modules complementary fused to decameric Brucella abortus lumazine synthase (BLS) subunits, and selected target proteins, respectively. The cohesin-BLS scaffold was solubly expressed in high yield in Escherichia coli, and revealed a high thermostability. The production of multienzymatic particles using this system was evaluated using the catalytic domain of Cellulomonas fimi endoglucanase CenA recombinantly fused to a dockerin module. Coupling of the enzyme to the scaffold was highly efficient and occurred with the expected stoichiometry. The decavalent enzymatic complexes obtained showed higher cellulolytic activity and association to the substrate compared to equivalent amounts of the free enzyme. This phenomenon was dependent on the multiplicity and proximity of the enzymes coupled to the scaffold, and was attributed to an avidity effect in the polyvalent enzyme interaction with the substrate. Our results highlight the usefulness of the scaffold presented in this work for the development of multifunctional particles, and the improvement of lignocellulose degradation among other applications. KEY POINTS: • New system for multifunctional particle production using the BLS scaffold • Higher cellulolytic activity of polyvalent endoglucanase compared to the free enzyme • Amount of enzyme associated to cellulose is higher for the polyvalent endoglucanase.
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Affiliation(s)
- Matías R Iglesias Rando
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
| | - Natalia Gorojovsky
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
| | - Vanesa Zylberman
- Inmunova SA, Gral. San Martín, 25 de Mayo 1021 (CP 1650), Villa Lynch, Buenos Aires, Argentina
| | - Fernando A Goldbaum
- Inmunova SA, Gral. San Martín, 25 de Mayo 1021 (CP 1650), Villa Lynch, Buenos Aires, Argentina
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (CP 1405), Buenos Aires, Argentina
- Centro de Rediseño e Ingeniería de Proteínas (CRIP), UNSAM Campus Miguelete, 25 de Mayo y Francia (CP 1650), Gral. San Martín, Buenos Aires, Argentina
| | - Patricio O Craig
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina.
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina.
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Kittler S, Ebner J, Besleaga M, Larsbrink J, Darnhofer B, Birner-Gruenberger R, Schobesberger S, Akhgar CK, Schwaighofer A, Lendl B, Spadiut O. Recombinant Protein L: Production, Purification and Characterization of a Universal Binding Ligand. J Biotechnol 2022; 359:108-115. [DOI: 10.1016/j.jbiotec.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/28/2022] [Accepted: 10/01/2022] [Indexed: 11/26/2022]
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5
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Gräwe A, Merkx M, Stein V. iFLinkC-X: A Scalable Framework to Assemble Bespoke Genetically Encoded Co-polymeric Linkers of Variable Lengths and Amino Acid Composition. Bioconjug Chem 2022; 33:1415-1421. [PMID: 35815527 DOI: 10.1021/acs.bioconjchem.2c00250] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Linker engineering is rapidly gaining prominence as protein engineers and synthetic biologists construct increasingly sophisticated protein assemblies capable of executing complex molecular functions in the context of biosensing, biocatalysis, or biotherapeutics. Depending on the application, the structural and functional requirements imposed on the underlying linkers can differ vastly. At the same time, there is a distinct lack of methods to effectively code linkers at the level of DNA and tailor them to the functional requirements of different fusion proteins. Addressing these limitations, a scalable framework is presented to compose co-polymeric linkers of variable lengths and amino acid composition based on a limited number of linker fragments stored in sequence-verified entry plasmids. The assembly process is exemplified for Pro-rich linkers in the context of a Zn2+-responsive dual-readout BRET/FRET sensor while examining how linker composition impacts key functional properties such as ligand affinity, dynamic range, and their ability to separate structurally distinct domains.
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Affiliation(s)
- Alexander Gräwe
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany.,Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology (TU/e), 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology (TU/e), 5600 MB Eindhoven, The Netherlands
| | - Viktor Stein
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany.,Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
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Research progress and the biotechnological applications of multienzyme complex. Appl Microbiol Biotechnol 2021; 105:1759-1777. [PMID: 33564922 DOI: 10.1007/s00253-021-11121-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/07/2021] [Accepted: 01/16/2021] [Indexed: 11/26/2022]
Abstract
The multienzyme complex system has become a research focus in synthetic biology due to its highly efficient overall catalytic ability and has been applied to various fields. Multienzyme complexes are formed by cascading complexes, which are multiple functionally related enzymes that continuously and efficiently catalyze the production of substrates. Compared with current mainstream microbial cell catalytic systems, in vitro multienzyme molecular machines have many advantages, such as fewer side reactions, a high product yield, a fast reaction speed, easy product separation, a tolerable toxic environment, and robust system operability, showing increasing competitiveness in the field of biomanufacturing. In this review, the research progress of multienzyme complexes in nature and multienzyme cascades in vivo or in vitro will be introduced, and the discovered enzyme cascades concerning scaffolding proteins will also be discussed. This review is expected to provide a more theoretical basis for the modification of multienzyme complexes and broaden their application in the field of synthetic biology. KEY POINTS: • The cascade reactions of some natural multienzyme complexes are reviewed. • The main approaches of constructing artificial multienzyme complexes are summarized. • The structure and application of cellulosomes are discussed and prospected.
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8
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A linker of the proline-threonine repeating motif sequence is bimodal. J Mol Model 2020; 26:178. [PMID: 32562031 DOI: 10.1007/s00894-020-04434-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 06/02/2020] [Indexed: 10/24/2022]
Abstract
The linker of the endoglucanase from Xanthomonas campestris pv. campestris ((PT)12) has a specific sequence, a repeating proline-threonine motif. In order to understand its role, it has been compared to a regular sequence linker, in this work-the cellobiohydrolase 2 from Trichoderma reesei (CBH2). Elastic properties of the two linkers have been estimated by calculating free energy profile along the linker length from an enhanced sampling molecular dynamics simulation. The (PT)12 exhibits more pronounced elastic behaviour than CBH2. The PT repeating motif results in a two-mode energy profile which could be very useful in the enzyme motions along the substrate during hydrolytic catalysis.
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9
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Meng D, Wang J, You C. The properties of the linker in a mini-scaffoldin influence the catalytic efficiency of scaffoldin-mediated enzyme complexes. Enzyme Microb Technol 2020; 133:109460. [DOI: 10.1016/j.enzmictec.2019.109460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 10/25/2022]
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10
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Gonçalves F, Ribeiro A, Silva C, Cavaco-Paulo A. Release of Fragrances from Cotton Functionalized with Carbohydrate-Binding Module Proteins. ACS APPLIED MATERIALS & INTERFACES 2019; 11:28499-28506. [PMID: 31283162 DOI: 10.1021/acsami.9b08191] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Perspiration as a response to daily activity and physical exercise results in unpleasant odors that cause social unrest and embarrassment. To tackle it, functional textiles incorporating fragrances could be an effective clothing deodorizing product. This work presents two strategies for the release of β-citronellol from functionalized cotton with carbohydrate-binding module (CBM)-based complexes (OBP::GQ20::CBM/β-citronellol-approach 1 and CBM::GQ20::SP-DS3-liposome/β-citronellol-approach 2). CBM from Cellulomonas fimi was fused with the odorant-binding protein (OBP::GQ20::CBM) and with an anchor peptide with affinity to the liposome membrane (CBM::GQ20::SP-DS3). In approach 1, OBP fusion protein served as a fragrance container, whereas in approach 2, the fragrance was loaded into liposomes with a higher cargo capacity. The two strategies showed a differentiated β-citronellol release profile triggered by an acidic sweat solution. OBP::GQ20::CBM complex revealed a fast release (31.9% and 25.8% of the initial amount, after 1.5 and 24 h of exposure with acidic sweat solution, respectively), while the CBM::GQ20::SP-DS3-liposome complex demonstrated a slower and controlled release (5.9% and 10.5% of the initial amount, after 1.5 and 24 h of exposure with acidic sweat solution, respectively). Both strategies revealed high potential for textile functionalization aimed at controlled release of fragrances. The OBP::GQ20::CBM/β-citronellol complex is ideal for applications requiring fast release of a high amount of fragrance, whereas the CBM::GQ20::SP-DS3-liposome/β-citronellol complex is more suitable for prolonged and controlled release of a lower amount of β-citronellol.
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Affiliation(s)
- Filipa Gonçalves
- Centre of Biological Engineering , University of Minho , Campus de Gualtar, 4710-057 , Braga , Portugal
| | - Artur Ribeiro
- Centre of Biological Engineering , University of Minho , Campus de Gualtar, 4710-057 , Braga , Portugal
| | - Carla Silva
- Centre of Biological Engineering , University of Minho , Campus de Gualtar, 4710-057 , Braga , Portugal
| | - Artur Cavaco-Paulo
- Centre of Biological Engineering , University of Minho , Campus de Gualtar, 4710-057 , Braga , Portugal
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11
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Wang Y, Jian Y, Wu Y, Sun H, Zhang G, Zhang W, Gao Z. Organometallic titanocene complex as highly efficient bifunctional catalyst for intramolecular Mannich reaction. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.4925] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yunyun Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, MOE, School of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710062 China
- College of Chemistry and Chemical EngineeringNingxia Normal University Guyuan 756000 People's Republic of China
| | - Yajun Jian
- Key Laboratory of Applied Surface and Colloid Chemistry, MOE, School of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710062 China
| | - Ya Wu
- College of Chemistry and Chemical EngineeringXi'an Shiyou University Xi'an 710065 People's Republic of China
| | - Huaming Sun
- Key Laboratory of Applied Surface and Colloid Chemistry, MOE, School of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710062 China
| | - Guofang Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, MOE, School of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710062 China
| | - Weiqiang Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, MOE, School of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710062 China
| | - Ziwei Gao
- Key Laboratory of Applied Surface and Colloid Chemistry, MOE, School of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710062 China
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12
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Yano S, Suyotha W, Zanma S, Konno H, Cherdvorapong V, Wakayama M. Deletion of uncharacterized domain from α-1,3-glucanase of Bacillus circulans KA-304 enhances heterologous enzyme production in Escherichia coli. J GEN APPL MICROBIOL 2018; 64:212-220. [PMID: 29743460 DOI: 10.2323/jgam.2017.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
α-1,3-Glucanase (Agl-KA) of Bacillus circulans KA-304 consists of an N-terminal discoidin domain (DS1), a carbohydrate binding module family 6 (CBM6), threonine and proline repeats (TP), a second discoidin domain (DS2), an uncharacterized conserved domain (UCD), and a C-terminal catalytic domain. Previously, we reported that DS1, CBM6, and DS2 have α-1,3-glucan-binding activity and contribute to α-1,3-glucan hydrolysis. In this study, UCD deletion mutant (AglΔUCD) was constructed, and its properties were compared with those of Agl-KA. α-1,3-Glucan hydrolyzing, α-1,3-glucan binding, and protoplast-forming activities of AglΔUCD were almost the same as those of Agl-KA. kcat/Km values of AgΔUCD and Agl-KA were 11.4 and 11.1 s-1 mg-1 mL, respectively. AglΔUCD and Agl-KA exhibited similar characteristics, such as optimal pH, pH stability, optimal temperature, and thermostability. These results suggest that UCD is not α-1,3-glucan-binding and flexible linker domain, and that deletion of UCD does not affect the affinity of N-terminal binding domains and the catalytic action of the C-terminal domain. Subsequently, heterologous UCenzyme productivity of AglΔD in Escherichia coli was compared with that of Agl-KA. The productivity of AglΔUCD was about 4-fold larger than that of Agl-KA after an 8-h induction at 30°C. In the case of induction at 20°C, the productivity of AglΔUCD was also larger than that of Agl-KA. These findings indicate that deletion of only UCD enhances the enzyme productivity in E. coli.
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Affiliation(s)
- Shigekazu Yano
- Department of Biochemical Engineering, Graduate School of Sciences and Engineering, Yamagata University
| | - Wasana Suyotha
- Department of Industrial Biotechnology, Faculty of Agro-industry, Prince of Songkla University
| | - Sumika Zanma
- Department of Biochemical Engineering, Graduate School of Sciences and Engineering, Yamagata University
| | - Hiroyuki Konno
- Department of Biochemical Engineering, Graduate School of Sciences and Engineering, Yamagata University
| | | | - Mamoru Wakayama
- Department of Biotechnology, Faculty of Life Sciences, Ritsumeikan University
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The PT/S-Box of Modular Cellulase AcCel12B Plays a Key Role in the Hydrolysis of Insoluble Cellulose. Catalysts 2018. [DOI: 10.3390/catal8030123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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14
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Badino SF, Bathke JK, Sørensen TH, Windahl MS, Jensen K, Peters GHJ, Borch K, Westh P. The influence of different linker modifications on the catalytic activity and cellulose affinity of cellobiohydrolase Cel7A from Hypocrea jecorina. Protein Eng Des Sel 2017; 30:495-501. [PMID: 28873985 DOI: 10.1093/protein/gzx036] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/04/2017] [Indexed: 12/13/2022] Open
Abstract
Various cellulases consist of a catalytic domain connected to a carbohydrate-binding module (CBM) by a flexible linker peptide. The linker if often strongly O-glycosylated and typically has a length of 20-50 amino acid residues. Functional roles, other than connecting the two folded domains, of the linker and its glycans, have been widely discussed, but experimental evidence remains sparse. One of the most studied cellulose degrading enzymes is the multi-domain cellobiohydrolase Cel7A from Hypocrea jecorina. Here, we designed variants of Cel7A with mutations in the linker region to elucidate the role of the linker. We found that moderate modification of the linker could result in significant changes in substrate affinity and catalytic efficacy. These changes were quite different for different linker variants. Thus, deletion of six residues near the catalytic domain had essentially no effects on enzyme function. Conversely, a substitution of four glycosylation sites near the middle of the linker reduced substrate affinity and increased maximal turnover. The observation of weaker binding provides some support of recent suggestions that linker glycans may be directly involved in substrate interactions. However, a variant with several inserted glycosylation sites near the CBM also showed lower affinity for the substrate compared to the wild-type, and we suggest that substrate interactions of the glycans depend on their exact location as well as other factors such as changes in structure and dynamics of the linker peptide.
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Affiliation(s)
- Silke Flindt Badino
- Research Unit for Functional Biomaterials, Department of Science and Environment, INM, Roskilde University, 1 Universitetsvej, Build. 28 C, DK-4000, Roskilde, Denmark
| | - Jenny Kim Bathke
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Build. 207, DK-2800 Kgs. Lyngby, Denmark
| | - Trine Holst Sørensen
- Research Unit for Functional Biomaterials, Department of Science and Environment, INM, Roskilde University, 1 Universitetsvej, Build. 28 C, DK-4000, Roskilde, Denmark
| | - Michael Skovbo Windahl
- Research Unit for Functional Biomaterials, Department of Science and Environment, INM, Roskilde University, 1 Universitetsvej, Build. 28 C, DK-4000, Roskilde, Denmark
| | - Kenneth Jensen
- Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Build. 207, DK-2800 Kgs. Lyngby, Denmark
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880, Bagsværd, Denmark
| | - Peter Westh
- Research Unit for Functional Biomaterials, Department of Science and Environment, INM, Roskilde University, 1 Universitetsvej, Build. 28 C, DK-4000, Roskilde, Denmark
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15
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Maddock DJ, Gerth ML, Patrick WM. An Engineered Glycerol Dehydratase With Improved Activity for the Conversion ofmeso-2,3-butanediol to Butanone. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700480] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 08/30/2017] [Indexed: 11/09/2022]
Affiliation(s)
| | - Monica L. Gerth
- Department of Biochemistry; University of Otago; Dunedin 9054 New Zealand
| | - Wayne M. Patrick
- Department of Biochemistry; University of Otago; Dunedin 9054 New Zealand
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17
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Chung D, Young J, Bomble YJ, Vander Wall TA, Groom J, Himmel ME, Westpheling J. Homologous expression of the Caldicellulosiruptor bescii CelA reveals that the extracellular protein is glycosylated. PLoS One 2015; 10:e0119508. [PMID: 25799047 PMCID: PMC4370642 DOI: 10.1371/journal.pone.0119508] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/14/2015] [Indexed: 12/19/2022] Open
Abstract
Members of the bacterial genus Caldicellulosiruptor are the most thermophilic cellulolytic microbes described with ability to digest lignocellulosic biomass without conventional pretreatment. The cellulolytic ability of different species varies dramatically and correlates with the presence of the multimodular cellulase CelA, which contains both a glycoside hydrolase family 9 endoglucanase and a glycoside hydrolase family 48 exoglucanase known to be synergistic in their activity, connected by three cellulose-binding domains via linker peptides. This architecture exploits the cellulose surface ablation driven by its general cellulase processivity as well as excavates cavities into the surface of the substrate, revealing a novel paradigm for cellulase activity. We recently reported that a deletion of celA in C. bescii had a significant effect on its ability to utilize complex biomass. To analyze the structure and function of CelA and its role in biomass deconstruction, we constructed a new expression vector for C. bescii and were able, for the first time, to express significant quantities of full-length protein in vivo in the native host. The protein, which contains a Histidine tag, was active and excreted from the cell. Expression of CelA protein with and without its signal sequence allowed comparison of protein retained intracellularly to protein transported extracellularly. Analysis of protein in culture supernatants revealed that the extracellular CelA protein is glycosylated whereas the intracellular CelA is not, suggesting that either protein transport is required for this post-translational modification or that glycosylation is required for protein export. The mechanism and role of protein glycosylation in bacteria is poorly understood and the ability to express CelA in vivo in C. bescii will allow the study of the mechanism of protein glycosylation in this thermophile. It will also allow the study of glycosylation of CelA itself and its role in the structure and function of this important enzyme in biomass deconstruction.
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Affiliation(s)
- Daehwan Chung
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jenna Young
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Todd A. Vander Wall
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Joseph Groom
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Janet Westpheling
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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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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20
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Payne CM, Resch MG, Chen L, Crowley MF, Himmel ME, Taylor LE, Sandgren M, Ståhlberg J, Stals I, Tan Z, Beckham GT. Glycosylated linkers in multimodular lignocellulose-degrading enzymes dynamically bind to cellulose. Proc Natl Acad Sci U S A 2013; 110:14646-51. [PMID: 23959893 PMCID: PMC3767562 DOI: 10.1073/pnas.1309106110] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plant cell-wall polysaccharides represent a vast source of food in nature. To depolymerize polysaccharides to soluble sugars, many organisms use multifunctional enzyme mixtures consisting of glycoside hydrolases, lytic polysaccharide mono-oxygenases, polysaccharide lyases, and carbohydrate esterases, as well as accessory, redox-active enzymes for lignin depolymerization. Many of these enzymes that degrade lignocellulose are multimodular with carbohydrate-binding modules (CBMs) and catalytic domains connected by flexible, glycosylated linkers. These linkers have long been thought to simply serve as a tether between structured domains or to act in an inchworm-like fashion during catalytic action. To examine linker function, we performed molecular dynamics (MD) simulations of the Trichoderma reesei Family 6 and Family 7 cellobiohydrolases (TrCel6A and TrCel7A, respectively) bound to cellulose. During these simulations, the glycosylated linkers bind directly to cellulose, suggesting a previously unknown role in enzyme action. The prediction from the MD simulations was examined experimentally by measuring the binding affinity of the Cel7A CBM and the natively glycosylated Cel7A CBM-linker. On crystalline cellulose, the glycosylated linker enhances the binding affinity over the CBM alone by an order of magnitude. The MD simulations before and after binding of the linker also suggest that the bound linker may affect enzyme action due to significant damping in the enzyme fluctuations. Together, these results suggest that glycosylated linkers in carbohydrate-active enzymes, which are intrinsically disordered proteins in solution, aid in dynamic binding during the enzymatic deconstruction of plant cell walls.
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Affiliation(s)
- Christina M. Payne
- Biosciences Center and
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506
| | | | - Liqun Chen
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | | | | | | | - Mats Sandgren
- Department of Molecular Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Ingeborg Stals
- Faculty of Applied Bioscience Engineering, University College Ghent, 9000 Ghent, Belgium
- Department of Biochemistry and Molecular Biology, Ghent University, 9000 Ghent, Belgium; and
| | - Zhongping Tan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | - Gregg T. Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401
- Department of Chemical Engineering, Colorado School of Mines, Golden, CO 80401
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21
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Wilson RH, Morton SK, Deiderick H, Gerth ML, Paul HA, Gerber I, Patel A, Ellington AD, Hunicke-Smith SP, Patrick WM. Engineered DNA ligases with improved activities in vitro. Protein Eng Des Sel 2013; 26:471-8. [DOI: 10.1093/protein/gzt024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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22
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Domain structure and function of α-1,3-glucanase from Bacillus circulans KA-304, an enzyme essential for degrading basidiomycete cell walls. Biosci Biotechnol Biochem 2013; 77:639-47. [PMID: 23470772 DOI: 10.1271/bbb.120900] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Bacillus circulans KA-304 α-1,3-glucanase (Agl-KA) includes an N-terminal discoidin domain (DS1), a carbohydrate binding module family 6 (CB6), threonine and proline repeats (TPs), a second discoidin domain (DS2), an uncharacterized conserved domain (UCD), and a C-terminal catalytic domain. Domain deletion enzymes lacking DS1, CB6, and DS2 exhibited lower α-1,3-glucan-hydrolyzing and -binding activities than the wild type, Agl-KA. An α-1,3-glucan binding assay with fluorescent protein fusion proteins indicated that DS1, CB6, and DS2 bound to α-1,3-glucan and fungal cell walls, and that binding efficiency was increased by their combined action. In contrast, UCD did not exhibit any α-1,3-glucan-binding activity. A dramatic decrease in protoplast formation in the Schizophyllum commune mycelium was observed given only a DS1 deletion. An Agl-KA with deletion DS1, CB6, and DS2 produced no protoplasts. These results indicate that the combined actions of DS1, CB6, and DS2 contributed to increased cell-wall binding and were indispensable for efficient Agl-KA cell-wall degradation.
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23
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Sammond DW, Payne CM, Brunecky R, Himmel ME, Crowley MF, Beckham GT. Cellulase linkers are optimized based on domain type and function: insights from sequence analysis, biophysical measurements, and molecular simulation. PLoS One 2012; 7:e48615. [PMID: 23139804 PMCID: PMC3490864 DOI: 10.1371/journal.pone.0048615] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 09/27/2012] [Indexed: 01/02/2023] Open
Abstract
Cellulase enzymes deconstruct cellulose to glucose, and are often comprised of glycosylated linkers connecting glycoside hydrolases (GHs) to carbohydrate-binding modules (CBMs). Although linker modifications can alter cellulase activity, the functional role of linkers beyond domain connectivity remains unknown. Here we investigate cellulase linkers connecting GH Family 6 or 7 catalytic domains to Family 1 or 2 CBMs, from both bacterial and eukaryotic cellulases to identify conserved characteristics potentially related to function. Sequence analysis suggests that the linker lengths between structured domains are optimized based on the GH domain and CBM type, such that linker length may be important for activity. Longer linkers are observed in eukaryotic GH Family 6 cellulases compared to GH Family 7 cellulases. Bacterial GH Family 6 cellulases are found with structured domains in either N to C terminal order, and similar linker lengths suggest there is no effect of domain order on length. O-glycosylation is uniformly distributed across linkers, suggesting that glycans are required along entire linker lengths for proteolysis protection and, as suggested by simulation, for extension. Sequence comparisons show that proline content for bacterial linkers is more than double that observed in eukaryotic linkers, but with fewer putative O-glycan sites, suggesting alternative methods for extension. Conversely, near linker termini where linkers connect to structured domains, O-glycosylation sites are observed less frequently, whereas glycines are more prevalent, suggesting the need for flexibility to achieve proper domain orientations. Putative N-glycosylation sites are quite rare in cellulase linkers, while an N-P motif, which strongly disfavors the attachment of N-glycans, is commonly observed. These results suggest that linkers exhibit features that are likely tailored for optimal function, despite possessing low sequence identity. This study suggests that cellulase linkers may exhibit function in enzyme action, and highlights the need for additional studies to elucidate cellulase linker functions.
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Affiliation(s)
- Deanne W. Sammond
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
| | - Christina M. Payne
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
| | - Michael F. Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
| | - Gregg T. Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
- Department of Chemical Engineering, Colorado School of Mines, Golden, Colorado, United States of America
- * E-mail:
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Rizk M, Antranikian G, Elleuche S. End-to-end gene fusions and their impact on the production of multifunctional biomass degrading enzymes. Biochem Biophys Res Commun 2012; 428:1-5. [DOI: 10.1016/j.bbrc.2012.09.142] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 09/30/2012] [Indexed: 11/29/2022]
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25
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Gokhale AA, Lee I. Cellulase Immobilized Nanostructured Supports for Efficient Saccharification of Cellulosic Substrates. Top Catal 2012. [DOI: 10.1007/s11244-012-9891-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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26
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Li XH, Zhang P, Liang S, Zhou F, Wang MX, Bhaskar R, Malik FA, Niu YS, Miao YG. Molecular Cloning and Characterization of a Putative cDNA Encoding Endoglucanase IV from Trichoderma Viride and its Expression in Bombyx Mori. Appl Biochem Biotechnol 2011; 166:309-20. [DOI: 10.1007/s12010-011-9426-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 10/19/2011] [Indexed: 10/15/2022]
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27
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Colussi F, Garcia W, Rosseto FR, de Mello BLS, de Oliveira Neto M, Polikarpov I. Effect of pH and temperature on the global compactness, structure, and activity of cellobiohydrolase Cel7A from Trichoderma harzianum. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:89-98. [PMID: 22048567 DOI: 10.1007/s00249-011-0762-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 10/03/2011] [Accepted: 10/11/2011] [Indexed: 11/29/2022]
Abstract
Due to its elevated cellulolytic activity, the filamentous fungus Trichoderma harzianum (T. harzianum) has considerable potential in biomass hydrolysis application. Cellulases from Trichoderma reesei have been widely used in studies of cellulose breakdown. However, cellulases from T. harzianum are less-studied enzymes that have not been characterized biophysically and biochemically as yet. Here, we examined the effects of pH and temperature on the secondary and tertiary structures, compactness, and enzymatic activity of cellobiohydrolase Cel7A from T. harzianum (Th Cel7A) using a number of biophysical and biochemical techniques. Our results show that pH and temperature perturbations affect Th Cel7A stability by two different mechanisms. Variations in pH modify protonation of the enzyme residues, directly affecting its activity, while leading to structural destabilization only at extreme pH limits. Temperature, on the other hand, has direct influence on mobility, fold, and compactness of the enzyme, causing unfolding of Th Cel7A just above the optimum temperature limit. Finally, we demonstrated that incubation with cellobiose, the product of the reaction and a competitive inhibitor, significantly increased the thermal stability of Th Cel7A. Our studies might provide insights into understanding, at a molecular level, the interplay between structure and activity of Th Cel7A at different pH and temperature conditions.
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Affiliation(s)
- Francieli Colussi
- Grupo de Cristalografia, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Sao Carlense 400, São Carlos, SP, Brazil
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Watanabe H, Kanazaki K, Nakanishi T, Shiotsuka H, Hatakeyama S, Kaieda M, Imamura T, Umetsu M, Kumagai I. Biomimetic engineering of modular bispecific antibodies for biomolecule immobilization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:9656-9661. [PMID: 21736316 DOI: 10.1021/la2006259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Modular bispecific antibodies (BsAb's) that interact directly with a gold surface were engineered for immobilization on biosensing devices. The BsAb's consist of the variable fragments of antigold and antilysozyme antibodies connected via one of three linkers derived from naturally occurring proteins. The BsAb's were bound tightly to both the gold surface and to lysozyme, thus functioning as interface molecules between lysozyme and the gold surface without a substantial loss of antigen-binding activity. The antigen-binding capacity (the ratio of the amount of immobilized lysozyme to the amount of immobilized BsAb) on the gold surface reached 82%. An analysis of the correlation between binding capacity and linker characteristics indicated that the presence of a long, rigid linker sequence derived from a cellulase resulted in a higher antigen-binding capacity than did the presence of a long but relatively flexible glycine-rich linker. This result suggests a strategy for designing linkers suitable for BsAb-based biomolecular immobilization.
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Affiliation(s)
- Hideki Watanabe
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-11, Aramaki-aza, Aoba-ku, Sendai 980-8579, Japan
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29
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Chu CY, Tseng CW, Yueh PY, Duan CH, Liu JR. Molecular cloning and characterization of a β-glucanase from Piromyces rhizinflatus. J Biosci Bioeng 2011; 111:541-6. [DOI: 10.1016/j.jbiosc.2011.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Revised: 01/11/2011] [Accepted: 01/12/2011] [Indexed: 10/18/2022]
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30
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Beckham GT, Bomble YJ, Matthews JF, Taylor CB, Resch MG, Yarbrough JM, Decker SR, Bu L, Zhao X, McCabe C, Wohlert J, Bergenstråhle M, Brady JW, Adney WS, Himmel ME, Crowley MF. The O-glycosylated linker from the Trichoderma reesei Family 7 cellulase is a flexible, disordered protein. Biophys J 2011; 99:3773-81. [PMID: 21112302 DOI: 10.1016/j.bpj.2010.10.032] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 10/19/2010] [Accepted: 10/20/2010] [Indexed: 10/18/2022] Open
Abstract
Fungi and bacteria secrete glycoprotein cocktails to deconstruct cellulose. Cellulose-degrading enzymes (cellulases) are often modular, with catalytic domains for cellulose hydrolysis and carbohydrate-binding modules connected by linkers rich in serine and threonine with O-glycosylation. Few studies have probed the role that the linker and O-glycans play in catalysis. Since different expression and growth conditions produce different glycosylation patterns that affect enzyme activity, the structure-function relationships that glycosylation imparts to linkers are relevant for understanding cellulase mechanisms. Here, the linker of the Trichoderma reesei Family 7 cellobiohydrolase (Cel7A) is examined by simulation. Our results suggest that the Cel7A linker is an intrinsically disordered protein with and without glycosylation. Contrary to the predominant view, the O-glycosylation does not change the stiffness of the linker, as measured by the relative fluctuations in the end-to-end distance; rather, it provides a 16 Å extension, thus expanding the operating range of Cel7A. We explain observations from previous biochemical experiments in the light of results obtained here, and compare the Cel7A linker with linkers from other cellulases with sequence-based tools to predict disorder. This preliminary screen indicates that linkers from Family 7 enzymes from other genera and other cellulases within T. reesei may not be as disordered, warranting further study.
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Affiliation(s)
- Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado, USA
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Cockburn DW, Clarke AJ. Modulating the pH-activity profile of cellulase A from Cellulomonas fimi by replacement of surface residues. Protein Eng Des Sel 2011; 24:429-37. [DOI: 10.1093/protein/gzr004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Characterization of Thermobifida fusca cutinase-carbohydrate-binding module fusion proteins and their potential application in bioscouring. Appl Environ Microbiol 2010; 76:6870-6. [PMID: 20729325 DOI: 10.1128/aem.00896-10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cutinase from Thermobifida fusca is thermally stable and has potential application in the bioscouring of cotton in the textile industry. In the present study, the carbohydrate-binding modules (CBMs) from T. fusca cellulase Cel6A (CBM(Cel6A)) and Cellulomonas fimi cellulase CenA (CBM(CenA)) were fused, separately, to the carboxyl terminus of T. fusca cutinase. Both fusion enzymes, cutinase-CBM(Cel6A) and cutinase-CBM(CenA), were expressed in Escherichia coli and purified to homogeneity. Enzyme characterization showed that both displayed similar catalytic properties and pH stabilities in response to T. fusca cutinase. In addition, both fusion proteins displayed an activity half-life of 53 h at their optimal temperature of 50°C. Compared to T. fusca cutinase, in the absence of pectinase, the binding activity on cotton fiber was enhanced by 2% for cutinase-CBM(Cel6A) and by 28% for cutinase-CBM(CenA), whereas in the presence of pectinase, the binding activity was enhanced by 40% for the former and 45% for the latter. Notably, a dramatic increase of up to 3-fold was observed in the amount of released fatty acids from cotton fiber by both cutinase-CBM fusion proteins when acting in concert with pectinase. This is the first report of improving the scouring efficiency of cutinase by fusing it with CBM. The improvement in activity and the strong synergistic effect between the fusion proteins and pectinase suggest that they may have better applications in textile bioscouring than the native cutinase.
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Quirk A, Lipkowski J, Vandenende C, Cockburn D, Clarke AJ, Dutcher JR, Roscoe SG. Direct visualization of the enzymatic digestion of a single fiber of native cellulose in an aqueous environment by atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:5007-13. [PMID: 20170174 DOI: 10.1021/la9037028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Atomic force microscopy (AFM) was used to study native cellulose films prepared from a bacterial cellulose source, Acetobacter xylinum, using a novel application of the Langmuir-Blodgett technique. These films allowed high-resolution AFM images of single fibers and their microfibril structure to be obtained. Two types of experiments were performed. First, the fibers were characterized using samples that were dried after LB deposition. Next, novel protocols that allowed us to image single fibers of cellulose in films that were never dried were developed. This procedure allowed us to perform in situ AFM imaging studies of the enzymatic hydrolysis of single cellulose fibers in solution using cellulolytic enzymes. The in situ degradation of cellulose fibers was monitored over a 9 h period using AFM. These studies provided the first direct, real-time images of the enzymatic degradation of a single cellulose fiber. We have demonstrated the tremendous potential of AFM to study the mechanism of the enzymatic digestion of cellulose and to identify the most effective enzymes for the digestion of various cellulose structures or isomorphs.
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Affiliation(s)
- Amanda Quirk
- Department of Chemistry, University of Guelph, Guelph, Ontario, N1G 2W1 Canada
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Niu D, Zhou XX, Yuan TY, Lin ZW, Ruan H, Li WF. Effect of the C-terminal domains and terminal residues of catalytic domain on enzymatic activity and thermostability of lichenase from Clostridium thermocellum. Biotechnol Lett 2010; 32:963-7. [DOI: 10.1007/s10529-010-0241-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 02/19/2010] [Indexed: 11/29/2022]
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36
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Cockburn DW, Vandenende C, Clarke AJ. Modulating the pH−Activity Profile of Cellulase by Substitution: Replacing the General Base Catalyst Aspartate with Cysteinesulfinate in Cellulase A from Cellulomonas fimi. Biochemistry 2010; 49:2042-50. [DOI: 10.1021/bi1000596] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Darrell W. Cockburn
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Chris Vandenende
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Anthony J. Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Matamá T, Araújo R, Gübitz GM, Casal M, Cavaco-Paulo A. Functionalization of cellulose acetate fibers with engineered cutinases. Biotechnol Prog 2009; 26:636-43. [DOI: 10.1002/btpr.364] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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38
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Scaglione D, Acquadro A, Portis E, Taylor CA, Lanteri S, Knapp SJ. Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database. BMC Genomics 2009; 10:454. [PMID: 19785740 PMCID: PMC2760586 DOI: 10.1186/1471-2164-10-454] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 09/28/2009] [Indexed: 12/02/2022] Open
Abstract
Background The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genomic analysis, and we have exploited recently acquired EST (expressed sequence tag) sequence data (Composite Genome Project - CGP) to develop an extensive set of microsatellite markers. Results A unigene assembly was created from over 36,000 globe artichoke EST sequences, containing 6,621 contigs and 12,434 singletons. Over 12,000 of these unigenes were functionally assigned on the basis of homology with Arabidopsis thaliana reference proteins. A total of 4,219 perfect repeats, located within 3,308 unigenes was identified and the gene ontology (GO) analysis highlighted some GO term's enrichments among different classes of microsatellites with respect to their position. Sufficient flanking sequence was available to enable the design of primers to amplify 2,311 of these microsatellites, and a set of 300 was tested against a DNA panel derived from 28 C. cardunculus genotypes. Consistent amplification and polymorphism was obtained from 236 of these assays. Their polymorphic information content (PIC) ranged from 0.04 to 0.90 (mean 0.66). Between 176 and 198 of the assays were informative in at least one of the three available mapping populations. Conclusion EST-based microsatellites have provided a large set of de novo genetic markers, which show significant amounts of polymorphism both between and within the three taxa of C. cardunculus. They are thus well suited as assays for phylogenetic analysis, the construction of genetic maps, marker-assisted breeding, transcript mapping and other genomic applications in the species.
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Affiliation(s)
- Davide Scaglione
- DiVaPRA Plant Genetics and Breeding, University of Torino, via L, da Vinci 44, 10095 Grugliasco, Torino, Italy.
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Eldridge B, Cooley RN, Odegrip R, McGregor DP, FitzGerald KJ, Ullman CG. An in vitro selection strategy for conferring protease resistance to ligand binding peptides. Protein Eng Des Sel 2009; 22:691-8. [DOI: 10.1093/protein/gzp052] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Production and purification of the isolated family 2a carbohydrate-binding module from Cellulomonas fimi. Protein Expr Purif 2009; 64:63-8. [DOI: 10.1016/j.pep.2008.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 10/16/2008] [Accepted: 10/17/2008] [Indexed: 11/23/2022]
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41
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Cloning of a rumen fungal xylanase gene and purification of the recombinant enzyme via artificial oil bodies. Appl Microbiol Biotechnol 2008; 79:225-33. [PMID: 18415096 DOI: 10.1007/s00253-008-1418-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Revised: 02/14/2008] [Accepted: 02/15/2008] [Indexed: 10/22/2022]
Abstract
A gene encoding a xylanase, named xynS20, was cloned from the ruminal fungus Neocallimastix patriciarum. The DNA sequence of xynS20 revealed that the gene was 1,008 bp in size and encoded amino acid sequences with a predicted molecular weight of 36 kDa. The amino acid sequence alignment showed that the highest sequence identity (28.4%) is with insect gut xylanase XYL6805. According to the sequence-based classification, a putative conserved domain of glycosyl hydrolase family 11 was detected at the N-terminus of XynS20 and a putative conserved domain of family 1 carbohydrate-binding module (CBM) was observed at the C-terminus of XynS20. An Asn-rich linker sequence was found between the N-terminal catalytic domain and the C-terminal CBM of XynS20. To examine the activity of the gene product, xynS20 gene was cloned as an oleosin-fused protein, expressed in Escherichia coli, affinity-purified by formation of artificial oil bodies, released from oleosin by intein-mediated peptide cleavage, and finally harvested by concentration of the supernatant. The specific activity of purified XynS20 toward oat spelt xylan was 1,982.8 U mg(-1). The recombinant XynS20 was stable in the mild acid pH range from 5.0 to 6.0, and the optimum pH was 6.0. The optimal reaction temperature of XynS20 was 45 degrees C; at temperatures below 30 and above 55 degrees C, enzyme activity was less than 50% of that at the optimal temperature.
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42
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Jørgensen AD, Nøhr J, Kastrup JS, Gajhede M, Sigurskjold BW, Sauer J, Svergun DI, Svensson B, Vestergaard B. Small Angle X-ray Studies Reveal That Aspergillus niger Glucoamylase Has a Defined Extended Conformation and Can Form Dimers in Solution. J Biol Chem 2008; 283:14772-80. [DOI: 10.1074/jbc.m801709200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Qi M, O'Brien JP, Yang J. A recombinant triblock protein polymer with dispersant and binding properties for digital printing. Biopolymers 2008; 90:28-36. [PMID: 17972282 DOI: 10.1002/bip.20878] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A structured triblock protein was designed to explore the potential of engineered peptides to function as high-performance ink dispersants and binders. The protein consists of three functional elements, including a pigment binding domain, a hydrophilic linker, and a printing surface binding domain. To construct such a chimeric protein, a carbon black binding peptide, FHENWPS, and a cellulose binding peptide, THKTSTQRLLAA, were identified from phage display libraries through biopanning, based on their strong and specific binding affinities to carbon black and cellulose. They were used as carbon black and cellulose binding domains, respectively, in a recombinant triblock protein. A linker sequence, PTPTPTPTPTPTPTPTPTPTPTP, was adapted from endoglucanase A of the bacterium Cellulomonas fimi, as a small, rigid, and hydrophilic interdomain linker. When incorporated into the triblock structure between the carbon black and cellulose binding sequences, the linker sufficiently isolates these two elements and allows dual binding activity. The structured triblock protein was shown to disperse carbon black particles and attach it to paper surfaces. Thus, the utility of structured proteins having useful dispersant and binding properties for digital printing inks was demonstrated.
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Affiliation(s)
- Min Qi
- DuPont Central Research and Development, Experimental Station, Wilmington, DE 19880-0402, USA
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Biochemical and molecular characterization of a novel type of Mutanase from Paenibacillus sp. strain RM1: identification of its mutan-binding domain, essential for degradation of Streptococcus mutans biofilms. Appl Environ Microbiol 2008; 74:2759-65. [PMID: 18326674 DOI: 10.1128/aem.02332-07] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel type of mutanase (termed mutanase RM1) was isolated from Paenibacillus sp. strain RM1. The purified enzyme specifically hydrolyzed alpha-1,3-glucan (mutan) and effectively degraded biofilms formed by Streptococcus mutans, a major etiologic agent in the progression of dental caries, even following brief incubation. The nucleotide sequence of the gene for this protein contains a 3,873-bp open reading frame encoding 1,291 amino acids with a calculated molecular mass of 135 kDa. The protein contains two major domains, the N-terminal domain (277 residues) and the C-terminal domain (937 residues), separated by a characteristic sequence composed of proline and threonine repeats. The characterization of the recombinant proteins for each domain which were expressed in Escherichia coli demonstrated that the N-terminal domain had strong mutan-binding activity but no mutanase activity whereas the C-terminal domain was responsible for mutanase activity but had mutan-binding activity significantly lower than that of the intact protein. Importantly, the biofilm-degrading activity observed with the intact protein was not exhibited by either domain alone or in combination with the other. Therefore, these results indicate that the structural integrity of mutanase RM1 containing the N-terminal mutan-binding domain is required for the biofilm-degrading activity.
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45
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Cho KM, Math RK, Hong SY, Asraful Islam SM, Kim JO, Hong SJ, Kim H, Yun HD. Changes in the activity of the multifunctional β-glycosyl hydrolase (Cel44C-Man26A) from Paenibacillus polymyxa by removal of the C-terminal region to minimum size. Biotechnol Lett 2008; 30:1061-8. [DOI: 10.1007/s10529-008-9640-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 01/07/2008] [Accepted: 01/07/2008] [Indexed: 11/27/2022]
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46
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Sonan G, Receveur-Brechot V, Duez C, Aghajari N, Czjzek M, Haser R, Gerday C. The linker region plays a key role in the adaptation to cold of the cellulase from an Antarctic bacterium. Biochem J 2008; 407:293-302. [PMID: 17635108 PMCID: PMC2049020 DOI: 10.1042/bj20070640] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The psychrophilic cellulase, Cel5G, from the Antarctic bacterium Pseudoalteromonas haloplanktis is composed of a catalytic module (CM) joined to a carbohydrate-binding module (CBM) by an unusually long, extended and flexible linker region (LR) containing three loops closed by three disulfide bridges. To evaluate the possible role of this region in cold adaptation, the LR was sequentially shortened by protein engineering, successively deleting one and two loops of this module, whereas the last disulfide bridge was also suppressed by replacing the last two cysteine residue by two alanine residues. The kinetic and thermodynamic properties of the mutants were compared with those of the full-length enzyme, and also with those of the cold-adapted CM alone and with those of the homologous mesophilic enzyme, Cel5A, from Erwinia chrysanthemi. The thermostability of the mutated enzymes as well as their relative flexibility were evaluated by differential scanning calorimetry and fluorescence quenching respectively. The topology of the structure of the shortest mutant was determined by SAXS (small-angle X-ray scattering). The data indicate that the sequential shortening of the LR induces a regular decrease of the specific activity towards macromolecular substrates, reduces the relative flexibility and concomitantly increases the thermostability of the shortened enzymes. This demonstrates that the long LR of the full-length enzyme favours the catalytic efficiency at low and moderate temperatures by rendering the structure not only less compact, but also less stable, and plays a crucial role in the adaptation to cold of this cellulolytic enzyme.
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Affiliation(s)
- Guillaume K. Sonan
- *Laboratoire de Biochimie et Centre d'Ingénierie des Protéines, Institut de Chimie B6, Université de Liège, B-4000 Liège Sart-Tilman, Belgium
| | - Véronique Receveur-Brechot
- †Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS et Universités d'Aix-Marseille I et II, 163 avenue de Luminy, F-13488 Marseille cedex, France
| | - Colette Duez
- *Laboratoire de Biochimie et Centre d'Ingénierie des Protéines, Institut de Chimie B6, Université de Liège, B-4000 Liège Sart-Tilman, Belgium
| | - Nushin Aghajari
- ‡Laboratoire de Bio Cristallographie, Institut de Biologie et Chimie des Protéines, CNRS et Université Claude Bernard Lyon 1, UMR 5086, IFR 128 “Biosciences Lyon-Gerland”, 7 Passage du Vercors, F-69367 Lyon Cedex 07 France
| | - Mirjam Czjzek
- §Station Biologique de Roscoff, Végétaux Marins et Biomolécules, UMR 7139, Place George Teissier, BP 74, F-29682 Roscoff cedex, France
| | - Richard Haser
- ‡Laboratoire de Bio Cristallographie, Institut de Biologie et Chimie des Protéines, CNRS et Université Claude Bernard Lyon 1, UMR 5086, IFR 128 “Biosciences Lyon-Gerland”, 7 Passage du Vercors, F-69367 Lyon Cedex 07 France
| | - Charles Gerday
- *Laboratoire de Biochimie et Centre d'Ingénierie des Protéines, Institut de Chimie B6, Université de Liège, B-4000 Liège Sart-Tilman, Belgium
- To whom correspondence should be addressed (email )
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Jin Y, Wang M, Fu J, Xuan N, Zhu Y, Lian Y, Jia Z, Zheng J, Wang G. Phylogenetic and expression analysis of ZnF-AN1 genes in plants. Genomics 2007; 90:265-75. [PMID: 17524611 DOI: 10.1016/j.ygeno.2007.03.019] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2007] [Revised: 03/23/2007] [Accepted: 03/27/2007] [Indexed: 11/24/2022]
Abstract
In plants, ZnF-AN1 genes are part of a multigene family with 13 members in Arabidopsis thaliana, 19 members in Populus trichocarpa, 17 members in Oryza sativa, at least 11 members in Zea mays, and 2 members in Chlamydomonas reinhardtii. All ZnF-AN1 genes contain the ZnF-AN1 domain. According to the phylogenetic analysis of the ZnF-AN1 domain, we divided plant ZnF-AN1 genes into two types. The coding sequences of most type I members do not possess any introns, while most type II members do possess intron(s). Through Northern blot analysis of maize members and digital Northern analysis of Arabidopsis members, we found that most ZnF-AN1 genes are involved in responses to abiotic stresses. The evolutionary analysis indicated that the expansion rate of type I was higher than that of type II. After expansion, some ZnF-AN1 genes may have gained new functions, some may have lost their functions, and some were specialized to perform their functions in stress-specific or tissue-specific modes. In addition, we propose an evolutionary model of type II ZnF-AN1 genes in plants.
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Affiliation(s)
- Ying Jin
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100094, China
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48
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Kavoosi M, Creagh AL, Kilburn DG, Haynes CA. Strategy for selecting and characterizing linker peptides for CBM9-tagged fusion proteins expressed inEscherichia coli. Biotechnol Bioeng 2007; 98:599-610. [PMID: 17394253 DOI: 10.1002/bit.21396] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The influence of linker design on fusion protein production and performance was evaluated when a family 9 carbohydrate-binding module (CBM9) serves as the affinity tag for recombinant proteins expressed in Escherichia coli. Two bioinformatic strategies for linker design were applied: the first identifies naturally occurring linkers within the proteome of the host organism, the second involves screening peptidases and their known specificities using the bioinformatics software MEROPS to design an artificial linker resistant to proteolysis within the host. Linkers designed using these strategies were compared against traditional poly-glycine linkers. Although widely used, glycine-rich linkers were found by tandem MS data to be susceptible to hydrolysis by E. coli peptidases. The natural (PT)(x)P and MEROPS-designed S(3)N(10) linkers were significantly more stable, indicating both strategies provide a useful approach to linker design. Factor X(a) processing of the fusion proteins depended strongly on linker chemistry, with poly(G) and S(3)N(10) linkers showing the fastest cleavage rates. Luminescence resonance energy transfer studies, used to measure average distance of separation between GFP and Tb(III) bound to a strong calcium-binding site of CBM9, revealed that, for a given linker chemistry, the separation distance increases with increasing linker length. This increase was particularly large for poly(G) linkers, suggesting that this linker chemistry adopts a hydrated, extended configuration that makes it particularly susceptible to proteolysis. Differential scanning calorimetry studies on the PT linker series showed that fusion of CBM9 to GFP did not alter the T(m) of GFP but did result in a destabilization, as seen by both a decrease in T(m) and DeltaH(cal), of CBM9. The degree of destabilization increased with decreasing length of the (PT)(x)P linker such that DeltaT(m) = -8.4 degrees C for the single P linker.
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Affiliation(s)
- Mojgan Kavoosi
- Michael Smith Laboratories and Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3
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49
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Poon DKY, Withers SG, McIntosh LP. Direct demonstration of the flexibility of the glycosylated proline-threonine linker in the Cellulomonas fimi Xylanase Cex through NMR spectroscopic analysis. J Biol Chem 2006; 282:2091-100. [PMID: 17121820 DOI: 10.1074/jbc.m609670200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The modular xylanase Cex (or CfXyn10A) from Cellulomonas fimi consists of an N-terminal catalytic domain and a C-terminal cellulose-binding domain, joined by a glycosylated proline-threonine (PT) linker. To characterize the conformation and dynamics of the Cex linker and the consequences of its modification, we have used NMR spectroscopy to study full-length Cex in its nonglycosylated ( approximately 47 kDa) and glycosylated ( approximately 51 kDa) forms. The PT linker lacks any predominant structure in either form as indicated by random coil amide chemical shifts. Furthermore, heteronuclear (1)H-(15)N nuclear Overhauser effect relaxation measurements demonstrate that the linker is flexible on the ns-to-ps time scale and that glycosylation partially dampens this flexibility. The catalytic and cellulose-binding domains also exhibit identical amide chemical shifts whether in isolation or in the context of either unmodified or glycosylated full-length Cex. Therefore, there are no noncovalent interactions between the two domains of Cex or between either domain and the linker. This conclusion is supported by the distinct (15)N relaxation properties of the two domains, as well as their differential alignment within a magnetic field by Pf1 phage particles. These data demonstrate that the PT linker is a flexible tether, joining the structurally independent catalytic and cellulose-binding domains of Cex in an ensemble of conformations; however, more extended forms may predominate because of restrictions imparted by the alternating proline residues. This supports the postulate that the binding-domain anchors Cex to the surface of cellulose, whereas the linker provides flexibility for the catalytic domain to hydrolyze nearby hemicellulose (xylan) chains.
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Affiliation(s)
- David K Y Poon
- Department of Biochemistry and Molecular Biology, The Protein Engineering Network of Centres of Excellence, and The Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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50
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Mulakala C, Reilly PJ. Hypocrea jecorina (Trichoderma reesei) Cel7A as a molecular machine: A docking study. Proteins 2005; 60:598-605. [PMID: 16001418 DOI: 10.1002/prot.20547] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hypocrea jecorina (formerly Trichoderma reesei) Cel7A has a catalytic domain (CD) and a cellulose-binding domain (CBD) separated by a highly glycosylated linker. Very little is known of how the 2 domains interact to degrade crystalline cellulose. Based on the interaction energies and forces on cello-oligosaccharides computationally docked to the CD and CBD, we propose a molecular machine model, where the CBD wedges itself under a free chain end on the crystalline cellulose surface and feeds it to the CD active site tunnel. Enzyme-substrate interactions produce the forces required to pull cellulose chains from the surface and also to help the enzyme move on the cellulose chain for processive hydrolysis. The energy to generate these forces is ultimately derived from the chemical energy of glycosidic bond breakage.
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Affiliation(s)
- Chandrika Mulakala
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011-2230, USA
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