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Qi Z, Lei B, Xiong M, Li W, Liao Y, Cai D, Ma X, Zhang R, Chen S. High-level production of chitinase by multi-strategy combination optimization in Bacillus licheniformis. World J Microbiol Biotechnol 2024; 40:181. [PMID: 38668833 DOI: 10.1007/s11274-024-03995-z] [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: 02/24/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
In view of the extensive potential applications of chitinase (ChiA) in various fields such as agriculture, environmental protection, medicine, and biotechnology, the development of a high-yielding strain capable of producing chitinase with enhanced activity holds significant importance. The objective of this study was to utilize the extracellular chitinase from Bacillus thuringiensis as the target, and Bacillus licheniformis as the expression host to achieve heterologous expression of ChiA with enhanced activity. Initially, through structural analysis and molecular dynamics simulation, we identified key amino acids to improve the enzymatic performance of chitinase, and the specific activity of chitinase mutant D116N/E118N was 48% higher than that of the natural enzyme, with concomitant enhancements in thermostability and pH stability. Subsequently, the expression elements of ChiA(D116N/E118N) were screened and modified in Bacillus licheniformis, resulting in extracellular ChiA activity reached 89.31 U/mL. Further efforts involved the successful knockout of extracellular protease genes aprE, bprA and epr, along with the gene clusters involved in the synthesis of by-products such as bacitracin and lichenin from Bacillus licheniformis. This led to the development of a recombinant strain, DW2△abelA, which exhibited a remarkable improvement in chitinase activity, reaching 145.56 U/mL. To further improve chitinase activity, a chitinase expression frame was integrated into the genome of DW2△abelA, resulting in a significant increas to 180.26 U/mL. Optimization of fermentation conditions and medium components further boosted shake flask enzyme activity shake flask enzyme activity, achieving 200.28 U/mL, while scale-up fermentation experiments yielded an impressive enzyme activity of 338.79 U/mL. Through host genetic modification, expression optimization and fermentation optimization, a high-yielding ChiA strain was successfully constructed, which will provide a solid foundation for the extracellular production of ChiA.
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Affiliation(s)
- Zhimin Qi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Bo Lei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Min Xiong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Weijia Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Yongqing Liao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Xin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Ruibin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China.
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China.
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Dohnálek J, Dušková J, Tishchenko G, Kolenko P, Skálová T, Novák P, Fejfarová K, Šimůnek J. Chitinase Chit62J4 Essential for Chitin Processing by Human Microbiome Bacterium Clostridium paraputrificum J4. Molecules 2021; 26:molecules26195978. [PMID: 34641521 PMCID: PMC8512545 DOI: 10.3390/molecules26195978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022] Open
Abstract
Commensal bacterium Clostridium paraputrificum J4 produces several extracellular chitinolytic enzymes including a 62 kDa chitinase Chit62J4 active toward 4-nitrophenyl N,N'-diacetyl-β-d-chitobioside (pNGG). We characterized the crude enzyme from bacterial culture fluid, recombinant enzyme rChit62J4, and its catalytic domain rChit62J4cat. This major chitinase, securing nutrition of the bacterium in the human intestinal tract when supplied with chitin, has a pH optimum of 5.5 and processes pNGG with Km = 0.24 mM and kcat = 30.0 s-1. Sequence comparison of the amino acid sequence of Chit62J4, determined during bacterial genome sequencing, characterizes the enzyme as a family 18 glycosyl hydrolase with a four-domain structure. The catalytic domain has the typical TIM barrel structure and the accessory domains-2x Fn3/Big3 and a carbohydrate binding module-that likely supports enzyme activity on chitin fibers. The catalytic domain is highly homologous to a single-domain chitinase of Bacillus cereus NCTU2. However, the catalytic profiles significantly differ between the two enzymes despite almost identical catalytic sites. The shift of pI and pH optimum of the commensal enzyme toward acidic values compared to the soil bacterium is the likely environmental adaptation that provides C. paraputrificum J4 a competitive advantage over other commensal bacteria.
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Affiliation(s)
- Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
- Correspondence: ; Tel.: +420-325-873-758; Fax: +420-325-873-710
| | - Jarmila Dušková
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
| | - Galina Tishchenko
- Department of Structural Analysis of Biomacromolecules, Institute of Macromolecular Chemistry of the Czech Academy of Sciences, v. v. i., Heyrovsky Sq. 2, 162 06 Prague, Czech Republic;
| | - Petr Kolenko
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
| | - Tereza Skálová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
| | - Petr Novák
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic;
| | - Karla Fejfarová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
| | - Jiří Šimůnek
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, v. v. i., Vídeňská 1083, 142 00 Prague, Czech Republic;
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Computational Analysis of Thermal Adaptation in Extremophilic Chitinases: The Achilles' Heel in Protein Structure and Industrial Utilization. Molecules 2021; 26:molecules26030707. [PMID: 33572971 PMCID: PMC7866400 DOI: 10.3390/molecules26030707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/24/2021] [Accepted: 01/24/2021] [Indexed: 11/28/2022] Open
Abstract
Understanding protein stability is critical for the application of enzymes in biotechnological processes. The structural basis for the stability of thermally adapted chitinases has not yet been examined. In this study, the amino acid sequences and X-ray structures of psychrophilic, mesophilic, and hyperthermophilic chitinases were analyzed using computational and molecular dynamics (MD) simulation methods. From the findings, the key features associated with higher stability in mesophilic and thermophilic chitinases were fewer and/or shorter loops, oligomerization, and less flexible surface regions. No consistent trends were observed between stability and amino acid composition, structural features, or electrostatic interactions. Instead, unique elements affecting stability were identified in different chitinases. Notably, hyperthermostable chitinase had a much shorter surface loop compared to psychrophilic and mesophilic homologs, implying that the extended floppy surface region in cold-adapted and mesophilic chitinases may have acted as a “weak link” from where unfolding was initiated. MD simulations confirmed that the prevalence and flexibility of the loops adjacent to the active site were greater in low-temperature-adapted chitinases and may have led to the occlusion of the active site at higher temperatures compared to their thermostable homologs. Following this, loop “hot spots” for stabilizing and destabilizing mutations were also identified. This information is not only useful for the elucidation of the structure–stability relationship, but will be crucial for designing and engineering chitinases to have enhanced thermoactivity and to withstand harsh industrial processing conditions
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Liu T, Zhu W, Wang J, Zhou Y, Duan Y, Qu M, Yang Q. The deduced role of a chitinase containing two nonsynergistic catalytic domains. Acta Crystallogr D Struct Biol 2018; 74:30-40. [PMID: 29372897 PMCID: PMC5786006 DOI: 10.1107/s2059798317018289] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/21/2017] [Indexed: 01/27/2023] Open
Abstract
The glycoside hydrolase family 18 chitinases degrade or alter chitin. Multiple catalytic domains in a glycoside hydrolase family 18 chitinase function synergistically during chitin degradation. Here, an insect group III chitinase from the agricultural pest Ostrinia furnacalis (OfChtIII) is revealed to be an arthropod-conserved chitinase that contains two nonsynergistic GH18 domains according to its catalytic properties. Both GH18 domains are active towards single-chained chitin substrates, but are inactive towards insoluble chitin substrates. The crystal structures of each unbound GH18 domain, as well as of GH18 domains complexed with hexa-N-acetyl-chitohexaose or penta-N-acetyl-chitopentaose, suggest that the two GH18 domains possess endo-specific activities. Physiological data indicated that the developmental stage-dependent gene-expression pattern of OfChtIII was the same as that of the chitin synthase OfChsA but significantly different from that of the chitinase OfChtI, which is indispensable for cuticular chitin degradation. Additionally, immunological staining indicated that OfChtIII was co-localized with OfChsA. Thus, OfChtIII is most likely to be involved in the chitin-synthesis pathway.
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Affiliation(s)
- Tian Liu
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Weixing Zhu
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Jing Wang
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Yong Zhou
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Yanwei Duan
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Mingbo Qu
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Qing Yang
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, People’s Republic of China
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Liu T, Chen L, Zhou Y, Jiang X, Duan Y, Yang Q. Structure, Catalysis, and Inhibition of OfChi-h, the Lepidoptera-exclusive Insect Chitinase. J Biol Chem 2017; 292:2080-2088. [PMID: 28053084 DOI: 10.1074/jbc.m116.755330] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/28/2016] [Indexed: 12/31/2022] Open
Abstract
Chitinase-h (Chi-h) is of special interest among insect chitinases due to its exclusive distribution in lepidopteran insects and high sequence identity with bacterial and baculovirus homologs. Here OfChi-h, a Chi-h from Ostrinia furnacalis, was investigated. Crystal structures of both OfChi-h and its complex with chitoheptaose ((GlcN)7) reveal that OfChi-h possesses a long and asymmetric substrate binding cleft, which is a typical characteristics of a processive exo-chitinase. The structural comparison between OfChi-h and its bacterial homolog SmChiA uncovered two phenylalanine-to-tryptophan site variants in OfChi-h at subsites +2 and possibly -7. The F232W/F396W double mutant endowed SmChiA with higher hydrolytic activities toward insoluble substrates, such as insect cuticle, α-chitin, and chitin nanowhisker. An enzymatic assay demonstrated that OfChi-h outperformed OfChtI, an insect endo-chitinase, toward the insoluble substrates, but showed lower activity toward the soluble substrate ethylene glycol chitin. Furthermore, OfChi-h was found to be inhibited by N,N',N″-trimethylglucosamine-N,N',N″,N″'-tetraacetylchitotetraose (TMG-(GlcNAc)4), a substrate analog which can be degraded into TMG-(GlcNAc)1-2 Injection of TMG-(GlcNAc)4 into 5th-instar O. furnacalis larvae led to severe defects in pupation. This work provides insights into a molting-indispensable insect chitinase that is phylogenetically closer to bacterial chitinases than insect chitinases.
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Affiliation(s)
- Tian Liu
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Lei Chen
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Yong Zhou
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Xi Jiang
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Yanwei Duan
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Qing Yang
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and .,Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 2 West Yuanmingyuan Road, Beijing 100193, China
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Itoh T, Hibi T, Suzuki F, Sugimoto I, Fujiwara A, Inaka K, Tanaka H, Ohta K, Fujii Y, Taketo A, Kimoto H. Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery. PLoS One 2016; 11:e0167310. [PMID: 27907169 PMCID: PMC5132251 DOI: 10.1371/journal.pone.0167310] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/13/2016] [Indexed: 12/03/2022] Open
Abstract
The Gram-positive bacterium Paenibacillus sp. str. FPU-7 effectively hydrolyzes chitin by using a number of chitinases. A unique chitinase with two catalytic domains, ChiW, is expressed on the cell surface of this bacterium and has high activity towards various chitins, even crystalline chitin. Here, the crystal structure of ChiW at 2.1 Å resolution is presented and describes how the enzyme degrades chitin on the bacterial cell surface. The crystal structure revealed a unique multi-modular architecture composed of six domains to function efficiently on the cell surface: a right-handed β-helix domain (carbohydrate-binding module family 54, CBM-54), a Gly-Ser-rich loop, 1st immunoglobulin-like (Ig-like) fold domain, 1st β/α-barrel catalytic domain (glycoside hydrolase family 18, GH-18), 2nd Ig-like fold domain and 2nd β/α-barrel catalytic domain (GH-18). The structure of the CBM-54, flexibly linked to the catalytic region of ChiW, is described here for the first time. It is similar to those of carbohydrate lyases but displayed no detectable carbohydrate degradation activities. The CBM-54 of ChiW bound to cell wall polysaccharides, such as chin, chitosan, β-1,3-glucan, xylan and cellulose. The structural and biochemical data obtained here also indicated that the enzyme has deep and short active site clefts with endo-acting character. The affinity of CBM-54 towards cell wall polysaccharides and the degradation pattern of the catalytic domains may help to efficiently decompose the cell wall chitin through the contact surface. Furthermore, we clarify that other Gram-positive bacteria possess similar cell-surface-expressed multi-modular enzymes for cell wall polysaccharide degradation.
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Affiliation(s)
- Takafumi Itoh
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
- * E-mail: (TI); (HK)
| | - Takao Hibi
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
| | - Fumiko Suzuki
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
| | - Ikumi Sugimoto
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
| | - Akihiro Fujiwara
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
| | - Koji Inaka
- Maruwa Foods and Biosciences Inc., Yamatokoriyama, Nara, Japan
| | | | - Kazunori Ohta
- Japan Aerospace Exploration Agency, Tsukuba, Ibaraki, Japan
| | - Yutaka Fujii
- Department of Molecular Biology and Chemistry, Faculty of Medicine, University of Fukui, Yoshida-gun, Fukui, Japan
| | - Akira Taketo
- Department of Environmental and Biotechnological Frontier Engineering, Fukui University of Technology, Fukui, Fukui, Japan
| | - Hisashi Kimoto
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
- * E-mail: (TI); (HK)
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de la Fuente-Salcido NM, Casados-Vázquez LE, García-Pérez AP, Barboza-Pérez UE, Bideshi DK, Salcedo-Hernández R, García-Almendarez BE, Barboza-Corona JE. The endochitinase ChiA Btt of Bacillus thuringiensis subsp. tenebrionis DSM-2803 and its potential use to control the phytopathogen Colletotrichum gloeosporioides. Microbiologyopen 2016; 5:819-829. [PMID: 27173732 PMCID: PMC5061718 DOI: 10.1002/mbo3.372] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/21/2016] [Accepted: 03/30/2016] [Indexed: 01/09/2023] Open
Abstract
Bacillus thuringiensis subsp. tenebrionis DSM‐2803 has been studied extensively and spore/crystal mixtures of this strain are used widely in commercial products to control coleopteran pests. The endochitinase chiA Btt gene of B. thuringiensis subsp. tenebrionis DSM‐2803 was cloned and expressed in Escherichia coli. The recombinant 6x‐histidine tagged protein (rChiA Btt, ~74 kDa), was purified by a HiTrap Ni affinity column. The Km of rChiA Btt was 0.847 μmol L−1 and its optimal activity occurred at pH 7 and ~40°C. Most divalent cations reduced endochitinase activity but only Hg+2 abolished activity of the enzyme. We report for the first time the characterization of a chitinase synthesized by B. thuringiensis subsp. tenebrionis DSM‐2803, and show that the purified rChiA74 Btt reduced the radial growth and increased the hyphal density of Colletotrichium gloeosporioides, the etiological agent of “anthracnose” in plants.
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Affiliation(s)
- Norma M de la Fuente-Salcido
- Aniversidad Autónoma de Coahuila, Escuela de Ciencias Biológicas, Torreón, Coahuila, 27104, México.,Posgrado en Biociencias, División de Ciencias de la Vida, Universidad de Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, 36500, México
| | - Luz E Casados-Vázquez
- Posgrado en Biociencias, División de Ciencias de la Vida, Universidad de Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, 36500, México.,Departamento de Alimentos, División de Ciencias de la Vida, Universidad de Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, 36500, México
| | - Ada P García-Pérez
- Aniversidad Autónoma de Coahuila, Escuela de Ciencias Biológicas, Torreón, Coahuila, 27104, México
| | - Uriel E Barboza-Pérez
- Tecnológico de Monterrey Campus Querétaro, Epigmenio González 500 Fracc, San Pablo, Querétaro, Qro, 76130, México
| | - Dennis K Bideshi
- Department of Natural and Mathematical Sciences, California Baptist University, 8432 Magnolia Avenue, Riverside, 92504, California.,Department of Entomology, University of California, Riverside, California, 92521
| | - Rubén Salcedo-Hernández
- Posgrado en Biociencias, División de Ciencias de la Vida, Universidad de Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, 36500, México.,Departamento de Alimentos, División de Ciencias de la Vida, Universidad de Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, 36500, México
| | | | - José E Barboza-Corona
- Posgrado en Biociencias, División de Ciencias de la Vida, Universidad de Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, 36500, México. .,Departamento de Alimentos, División de Ciencias de la Vida, Universidad de Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, 36500, México.
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Nakamura T, Niiyama M, Hashimoto W, Ida K, Abe M, Morita J, Uegaki K. Multiple crystal forms of N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus. Acta Crystallogr F Struct Biol Commun 2015; 71:657-62. [PMID: 26057790 PMCID: PMC4461325 DOI: 10.1107/s2053230x15005695] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/20/2015] [Indexed: 11/10/2022] Open
Abstract
Native N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus (Pf-Dac) and its selenomethionine derivative (Se-Pf-Dac) were crystallized and analyzed in the presence and absence of cadmium ion. The four crystal structures fell into three different crystal-packing groups, with the cadmium-free Pf-Dac and Se-Pf-Dac belonging to the same space group, with homologous unit-cell parameters. The crystal structures in the presence of cadmium contained distorted octahedral cadmium complexes coordinated by three chlorides, two O atoms and an S or Se atom from the N-terminal methionine or selenomethionine, respectively. The N-terminal cadmium complex was involved in crystal contacts between symmetry-related molecules through hydrogen bonding to the N-termini. While all six N-termini of Se-Pf-Dac were involved in cadmium-complex formation, only two of the Pf-Dac N-termini participated in complex formation in the Cd-containing crystal, resulting in different crystal forms. These differences are discussed in light of the higher stability of the Cd-Se bond than the Cd-S bond. This work provides an example of the contribution of cadmium towards determining protein crystal quality and packing depending on the use of the native protein or the selenomethionine derivative.
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Affiliation(s)
- Tsutomu Nakamura
- National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan
| | - Mayumi Niiyama
- National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan
| | - Wakana Hashimoto
- National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan
- Faculty of Human Life and Science, Doshisha Women’s College of Liberal Arts, Kyoto 602-0893, Japan
| | - Kurumi Ida
- National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan
- Faculty of Human Life and Science, Doshisha Women’s College of Liberal Arts, Kyoto 602-0893, Japan
| | - Manabu Abe
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Junji Morita
- Faculty of Human Life and Science, Doshisha Women’s College of Liberal Arts, Kyoto 602-0893, Japan
| | - Koichi Uegaki
- National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan
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Kim TK, Curran J, Mulenga A. Dual silencing of long and short Amblyomma americanum acidic chitinase forms weakens the tick cement cone stability. ACTA ACUST UNITED AC 2014; 217:3493-503. [PMID: 25189365 DOI: 10.1242/jeb.107979] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This study demonstrates that Amblyomma americanum (Aam) constitutively and ubiquitously expresses the long (L) and short (S) putative acidic chitinases (Ach) that are distinguished by a 210 base pair (bp) deletion in AamAch-S. Full-length AamAch-L and AamAch-S cDNA are 1959 and 1718 bp long, containing 1332 and 1104 bp open reading frames that code for 443 and 367 amino acid residues proteins with the former predicted to be extracellular and the latter intracellular. Both AamAch-L and AamAch-S mRNA are expressed in multiple organs as revealed by qualitative RT-PCR analysis. Furthermore, quantitative reverse transcription polymerase chain reaction analysis revealed that AamAch-L mRNA was downregulated in the mid-gut, but was unchanged in the salivary gland and in other organs in response to feeding. Of significant interest, AamAch-L and/or AamAch-S functions are probably associated with formation and/or maintenance of stability of A. americanum tick cement cone. Dual RNA interference silencing of AamAch-L and/or AamAch-S mRNA caused ticks to loosely attach onto host skin as suggested by bleeding around tick mouthparts and ticks detaching off host skin with a light touch. AamAch-L may apparently encode an inactive chitinase as indicated by Pichia pastoris-expressed recombinant AamAch-L failing to hydrolyse chitinase substrates. Unpublished related work in our laboratory, and published work by others that found AamAch-L in tick saliva, suggest that native AamAch-L is a non-specific immunoglobulin binding tick saliva protein in that rAamAch-L non-specifically bound rabbit, bovine and chicken non-immune sera. We discuss findings in this study with reference to advancing knowledge on tick feeding physiology.
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Affiliation(s)
- Tae K Kim
- Texas A&M University AgriLife Research, Department of Entomology, 2475 TAMU, College Station, TX 77843, USA
| | - Janet Curran
- Texas A&M University AgriLife Research, Department of Entomology, 2475 TAMU, College Station, TX 77843, USA
| | - Albert Mulenga
- Texas A&M University AgriLife Research, Department of Entomology, 2475 TAMU, College Station, TX 77843, USA
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Chen L, Liu T, Zhou Y, Chen Q, Shen X, Yang Q. Structural characteristics of an insect group I chitinase, an enzyme indispensable to moulting. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:932-42. [PMID: 24699639 PMCID: PMC3975886 DOI: 10.1107/s1399004713033841] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 12/13/2013] [Indexed: 11/23/2022]
Abstract
Insects possess a greater number of chitinases than any other organisms. This work is the first report of unliganded and oligosaccharide-complexed crystal structures of the insect chitinase OfChtI from Ostrinia furnacalis, which is essential to moulting. The obtained crystal structures were solved at resolutions between 1.7 and 2.2 Å. A structural comparison with other chitinases revealed that OfChtI contains a long substrate-binding cleft similar to the bacterial chitinase SmChiB from Serratia marcescens. However, unlike the exo-acting SmChiB, which has a blocked and tunnel-like cleft, OfChtI possesses an open and groove-like cleft. The complexed structure of the catalytic domain of OfChtI (OfChtI-CAD) with (GlcNAc)2/3 indicates that the reducing sugar at subsite -1 is in an energetically unfavoured `boat' conformation, a state that possibly exists just before the completion of catalysis. Because OfChtI is known to act from nonreducing ends, (GlcNAc)3 would be a hydrolysis product of (GlcNAc)6, suggesting that OfChtI possesses an endo enzymatic activity. Furthermore, a hydrophobic plane composed of four surface-exposed aromatic residues is adjacent to the entrance to the substrate-binding cleft. Mutations of these residues greatly impair the chitin-binding activity, indicating that this hydrophobic plane endows OfChtI-CAD with the ability to anchor chitin. This work reveals the unique structural characteristics of an insect chitinase.
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Affiliation(s)
- Lei Chen
- School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Tian Liu
- School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
- State Key Laboratory for Biocontrol, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Yong Zhou
- School of Software, Dalian University of Technology, 321 Tuqiang Street, Dalian, Liaoning 116620, People’s Republic of China
| | - Qi Chen
- School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Xu Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, People’s Republic of China
| | - Qing Yang
- School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
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Kreuzer M, Schmutzler K, Waege I, Thomm M, Hausner W. Genetic engineering of Pyrococcus furiosus to use chitin as a carbon source. BMC Biotechnol 2013; 13:9. [PMID: 23391022 PMCID: PMC3575233 DOI: 10.1186/1472-6750-13-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 02/04/2013] [Indexed: 01/14/2023] Open
Abstract
Background Bioinformatic analysis of the genes coding for the chitinase in Pyrococcus furiosus and Thermococcus kodakarensis revealed that most likely a one nucleotide insertion in Pyrococcus caused a frame shift in the chitinase gene. This splits the enzyme into two separate genes, PF1233 and PF1234, in comparison to Thermococcus kodakarensis. Furthermore, our attempts to grow the wild type strain of Pyrococcus furiosus on chitin were negative. From these data we assume that Pyrococcus furiosus is most likely unable to use chitin as a carbon source. The aim of this study was to analyze in vivo if the one nucleotide insertion is responsible for the inability to grow on chitin, using a recently described genetic system for Pyrococcus furiosus. Results A marker-less genetic system for Pyrococcus furiosus was developed using simvastatin for positive selection and 6-methylpurine for negative selection. Resistance against simvastatin was achieved by overexpression of the hydroxymethylglutaryl coenzyme A reductase gene. For the resistance to 6-methylpurine the hypoxanthine-guanine phosphoribosyltransferase gene was deleted. This system was used to delete the additional nucleotide at position 1006 in PF1234. The resulting chitinase in the mutant strain was a single subunit enzyme and aligns perfectly to the enzyme from Thermococcus kodakarensis. A detailed analysis of the wild type and the mutant using counted cell numbers as well as ATP and acetate production as growth indicators revealed that only the mutant is able to use chitin as a carbon source. An additional mutant strain containing a reduced chitinase version containing just one catalytic and one chitin-binding domain showed diminished growth on chitin in comparison to the mutant containing the single large enzyme. Conclusions Wild type Pyrococcus furiosus is most likely unable to grow on chitin in the natural biotope due to a nucleotide insertion which separates the chitinase gene into two ORFs, whereas a genetically engineered strain with the deleted nucleotide is able to grow on chitin. The overall high sequence identity of the two chitinases between P. furiosus and T. kodakarensis indicates that this mutation occurred very recently or there is still some kind of selection pressure for a functional enzyme using programmed +/−1 frameshifting.
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Affiliation(s)
- Martina Kreuzer
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, University of Regensburg, Regensburg, 93053, Germany.
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