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Costa-Barbosa A, Ferreira D, Pacheco MI, Casal M, Duarte HO, Gomes C, Barbosa AM, Torrado E, Sampaio P, Collins T. Candida albicans chitinase 3 with potential as a vaccine antigen: production, purification, and characterisation. Biotechnol J 2024; 19:e2300219. [PMID: 37876300 DOI: 10.1002/biot.202300219] [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: 05/15/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 10/26/2023]
Abstract
Chitinases are widely studied enzymes that have already found widespread application. Their continued development and valorisation will be driven by the identification of new and improved variants and/or novel applications bringing benefits to industry and society. We previously identified a novel application for chitinases wherein the Candida albicans cell wall surface chitinase 3 (Cht3) was shown to have potential in vaccine applications as a subunit antigen against fungal infections. In the present study, this enzyme was investigated further, developing production and purification protocols, enriching our understanding of its properties, and advancing its application potential. Cht3 was heterologously expressed in Pichia pastoris and a 4-step purification protocol developed and optimised: this involves activated carbon treatment, hydrophobic interaction chromatography, ammonium sulphate precipitation, and gel filtration chromatography. The recombinant enzyme was shown to be mainly O-glycosylated and to retain the epitopes of the native protein. Functional studies showed it to be highly specific, displaying activity on chitin, chitosan, and chito-oligosaccharides larger than chitotriose only. Furthermore, it was shown to be a stable enzyme, exhibiting activity, and stability over broad pH and temperature ranges. This study represents an important step forward in our understanding of Cht3 and contributes to its development for application.
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Affiliation(s)
- Augusto Costa-Barbosa
- Centre of Molecular and Environmental Biology (CBMA)/Aquatic Research Network (ARNET), Department of Biology, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Diogo Ferreira
- Centre of Molecular and Environmental Biology (CBMA)/Aquatic Research Network (ARNET), Department of Biology, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Maria Inês Pacheco
- Centre of Molecular and Environmental Biology (CBMA)/Aquatic Research Network (ARNET), Department of Biology, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Margarida Casal
- Centre of Molecular and Environmental Biology (CBMA)/Aquatic Research Network (ARNET), Department of Biology, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Henrique Oliveira Duarte
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Catarina Gomes
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Ana Margarida Barbosa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Egídio Torrado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Paula Sampaio
- Centre of Molecular and Environmental Biology (CBMA)/Aquatic Research Network (ARNET), Department of Biology, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Tony Collins
- Centre of Molecular and Environmental Biology (CBMA)/Aquatic Research Network (ARNET), Department of Biology, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
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2
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Ran L, Wang X, He X, Guo R, Wu Y, Zhang P, Zhang XH. Genomic analysis and chitinase characterization of Vibrio harveyi WXL538: insight into its adaptation to the marine environment. Front Microbiol 2023; 14:1121720. [PMID: 37465025 PMCID: PMC10350509 DOI: 10.3389/fmicb.2023.1121720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/05/2023] [Indexed: 07/20/2023] Open
Abstract
Chitin, the most abundant bio-polymer in seawater, may be utilized by various microorganisms as a carbon source. Vibrios have been regarded as one of the main groups of chitin consumers in the marine carbon cycle and chitinase producers. The organisms are widely distributed in the aquatic environment. However, the co-working mechanism between their chitinases, and whether the chitinase's diversity contributes to their adaption to the environment, needs to be further elucidated. Here, we obtained a chitinolytic strain, Vibrio harveyi WXL538 with eight putative chitinase-coding genes. Five of the genes, i.e., Chi4733, Chi540, Chi4668, Chi5174, and Chi4963, were overexpressed and validated, in which Chi4668, Chi4733 and Chi540 were purified and characterized. The result of Chi4668 was described in our previous study. Endo-chitinase Chi4733 degraded colloidal chitin to produce (GlcNAc)2 and minor (GlcNAc)3. The enzymatic activity of Chi4733 was 175.5 U mg-1 and Kcat/Km was 54.9 s-1 M-1. Chi4733 had its maximum activity at 50°C and pH 4-6, activated by Sr2+, Co2+, Ca2+, and Mg2+ and inhibited by Al3+, Zn2+, Cu2+, Ni2+, and SDS. Exo-chitinase Chi540 degraded colloidal chitin to (GlcNAc)2. The enzymatic activity of Chi540 was 134.5 U mg-1 and Kcat/Km was 54.9 s-1 M-1. Chi540 had its maximum activity at 60°C and pH 6-8, was activated by Sr2+, Ca2+, and Mg2+ but inhibited by K+, Ba2+, Zn2+, Cu2+, Ni2+, SDS and urea. Whole genome analysis of V. harveyi WXL538 and characterization of its chitinase can provide a better understanding of its adaptability to the changing marine environment.
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Affiliation(s)
- Lingman Ran
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaolei Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xinxin He
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ruihong Guo
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yanhong Wu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Pingping Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
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3
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Zhang Q, Zhang X, He Y, Li Y. The synergistic action of two chitinases from Vibrio harveyi on chitin degradation. Carbohydr Polym 2023; 307:120640. [PMID: 36781282 DOI: 10.1016/j.carbpol.2023.120640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/16/2023] [Accepted: 01/27/2023] [Indexed: 02/02/2023]
Abstract
In this study, two chitinases (VhChit2 and VhChit6) from Vibrio harveyi possessed specific activity of 36.5 and 20.8 U/mg, respectively. Structure analysis indicates that their amino acid composition of active sites is similar, but the substrate binding cleft of VhChit2 is deeper than that of VhChit6. They were shown to have a synergistic effect on chitin degradation, and the optimized degree of synergy and the degradation ratio of chitin reached 1.75 and 23.6 %, respectively. The saturated adsorption capacity of VhChit2 and VhChit6 adsorbed in 1 g of chitin was 48.5 and 33.4 mg. It was found that VhChit2 and VhChit6 had different adsorption sites on chitin, making more enzymes absorbed by chitin. Furthermore, the combined use of VhChit2 and VhChit6 increased their binding force of chitinases with the substrate. The synergistic action of VhChit2 and VhChit6 may be attributed to their different adsorption sites on chitin and the increased binding force with chitin.
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Affiliation(s)
- Qiao Zhang
- College of Food Science and Engineering, Hainan University, Haikou 570228, China; College of Food and Biological Engineering, Hezhou University, Hezhou 542899, China
| | - Xueying Zhang
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Yuanchang He
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Yongcheng Li
- College of Food Science and Engineering, Hainan University, Haikou 570228, China; Hainan Provincial Research Center of Aquatic Resources Efficient Utilization in the South China Sea, Haikou 570228, China.
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4
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He X, Yu M, Wu Y, Ran L, Liu W, Zhang XH. Two Highly Similar Chitinases from Marine Vibrio Species have Different Enzymatic Properties. Mar Drugs 2020; 18:E139. [PMID: 32120805 PMCID: PMC7143101 DOI: 10.3390/md18030139] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 12/16/2022] Open
Abstract
Chitinase, as one of the most important extracellular enzymes in the marine environment, has great ecological and applied values. In this study, two chitinases (Chi1557 and Chi4668) with 97.33% amino acid sequences identity were individually found in Vibrio rotiferianus and Vibrio harveyi. They both were encoding by 561 amino acids, but differed in 15 amino acids and showed different enzymatic properties. The optimal temperature and pH ranges were 45-50 °C and pH 5.0-7.0 for Chi1557, while ~50 °C and pH 3.0-6.0 for Chi4668. K+, Mg2+, and EDTA increased the enzymatic activity of Chi4668 significantly, yet these factors were inhibitory to Chi1557. Moreover, Chi1557 degraded colloidal chitin to produce (GlcNAc)2 and minor GlcNAc, whereas Chi4668 produce (GlcNAc)2 with minor (GlcNAc)3 and (GlcNAc)4. The Kcat/Km of Chi4668 was ~4.7 times higher than that of Chi1557, indicating that Chi4668 had stronger catalytic activity than Chi1557. Furthermore, site-directed mutagenesis was performed on Chi1557 focusing on seven conserved amino acid residues of family GH18 chitinases. Chi1557 was almost completely inactive after Glu154, Gln219, Tyr221, or Trp312 was individually mutated, retained ~50% activity after Tyr37 was mutated, and increased two times activity after Asp152 was mutated, indicating that these six amino acids were key sites for Chi1557.
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Affiliation(s)
- Xinxin He
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Min Yu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Yanhong Wu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Lingman Ran
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Weizhi Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
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5
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Molecular engineering of chitinase from Bacillus sp. DAU101 for enzymatic production of chitooligosaccharides. Enzyme Microb Technol 2019; 124:54-62. [DOI: 10.1016/j.enzmictec.2019.01.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 01/21/2019] [Accepted: 01/29/2019] [Indexed: 01/20/2023]
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6
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Iino T, Sakurai M, Furuta T. A novel ring-shaped reaction pathway with interconvertible intermediates in chitinase A as revealed by QM/MM simulation combined with a one-dimensional projection technique. Phys Chem Chem Phys 2019; 21:24956-24966. [DOI: 10.1039/c9cp05163e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient sampling achieved by the use of a one-dimensional projection technique reveals the catalytic mechanism of chitinase A from Serratia marcescens.
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Affiliation(s)
- Tsubasa Iino
- Center for Biological Resources and Informatics
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics
- Tokyo Institute of Technology
- Yokohama
- Japan
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7
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Suginta W, Sritho N, Ranok A, Bulmer DM, Kitaoku Y, van den Berg B, Fukamizo T. Structure and function of a novel periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria. J Biol Chem 2018; 293:5150-5159. [PMID: 29444825 DOI: 10.1074/jbc.ra117.001012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 02/11/2018] [Indexed: 12/11/2022] Open
Abstract
Periplasmic solute-binding proteins in bacteria are involved in the active transport of nutrients into the cytoplasm. In marine bacteria of the genus Vibrio, a chitooligosaccharide-binding protein (CBP) is thought to be the major solute-binding protein controlling the rate of chitin uptake in these bacteria. However, the molecular mechanism of the CBP involvement in chitin metabolism has not been elucidated. Here, we report the structure and function of a recombinant chitooligosaccharide-binding protein from Vibrio harveyi, namely VhCBP, expressed in Escherichia coli Isothermal titration calorimetry revealed that VhCBP strongly binds shorter chitooligosaccharides ((GlcNAc) n , where n = 2, 3, and 4) with affinities that are considerably greater than those for glycoside hydrolase family 18 and 19 chitinases but does not bind longer ones, including insoluble chitin polysaccharides. We also found that VhCBP comprises two domains with flexible linkers and that the domain-domain interface forms the sugar-binding cleft, which is not long extended but forms a small cavity. (GlcNAc)2 bound to this cavity, apparently triggering a closed conformation of VhCBP. Trp-363 and Trp-513, which stack against the two individual GlcNAc rings, likely make a major contribution to the high affinity of VhCBP for (GlcNAc)2 The strong chitobiose binding, followed by the conformational change of VhCBP, may facilitate its interaction with an active-transport system in the inner membrane of Vibrio species.
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Affiliation(s)
- Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand,
| | - Natchanok Sritho
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Araya Ranok
- Rajamangala University of Technology Isan, Nakhon Ratchasima 30000, Thailand
| | - David Michael Bulmer
- the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom, and
| | - Yoshihito Kitaoku
- the Department of Advanced Bioscience, Kindai University, Nara 631-8505 Japan
| | - Bert van den Berg
- the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom, and
| | - Tamo Fukamizo
- From the Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.,the Department of Advanced Bioscience, Kindai University, Nara 631-8505 Japan
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8
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Meekrathok P, Kukic P, Nielsen JE, Suginta W. Investigation of Ionization Pattern of the Adjacent Acidic Residues in the DXDXE Motif of GH-18 Chitinases Using Theoretical pKa Calculations. J Chem Inf Model 2017; 57:572-583. [DOI: 10.1021/acs.jcim.6b00536] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Piyanat Meekrathok
- Biochemistry-Electrochemistry
Research Group and School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Predrag Kukic
- School
of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jens Erik Nielsen
- School
of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Wipa Suginta
- Biochemistry-Electrochemistry
Research Group and School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
- Centre
of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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9
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Chen J, An Y, Kumar A, Liu Z. Improvement of chitinase Pachi with nematicidal activities by random mutagenesis. Int J Biol Macromol 2016; 96:171-176. [PMID: 27989482 DOI: 10.1016/j.ijbiomac.2016.11.093] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 11/23/2016] [Accepted: 11/24/2016] [Indexed: 11/18/2022]
Abstract
Chitinase, an enzyme that can degrade the main compositions of insect intestine and cuticle, has been used in the bio-control field. Our previous work has reported the chitinase Pachi with nematicidal activity (Caenorhabditis elegans). In the present study, to improve the chitinolytic and nematicidal activities of Pachi, a random mutant library was constructed by error-prone PCR and screened by bacteriophage T7-based high-throughput screening system. One mutant, PachiN35D was obtained from about 10, 000 clones. The kinetics analysis revealed that PachiN35D exhibited a 63% decrease in Km value against chitosan, a 2.1-fold enhancement in kcat/Km value and a 1.2-fold increase in specific activity over the wild-type Pachi. Moreover, the mortality analysis against Caenorhabditis elegans showed that the 50% lethal concentration (LC50) of PachiN35D is 309.6±1.1μg/ml and a 20% increase in nematicidal activity over the wild-type Pachi (with a LC50 value of 387.3±31.7μg/ml). The structure modeling and superimposition indicated that the substitution N35D reduced the distance between substrate and substrate-binding site Asp141, finally resulting in an increase in substrate affinity, catalytic efficiency and specific activity. These results provide useful information for the study of structure-function relationship of Pachi and lay a foundation for its potential applications in agro-biotechnology.
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Affiliation(s)
- Junpeng Chen
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430 070, China
| | - Yangdongfang An
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430 070, China
| | - Ashok Kumar
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430 070, China
| | - Ziduo Liu
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430 070, China.
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10
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Suginta W, Sirimontree P, Sritho N, Ohnuma T, Fukamizo T. The chitin-binding domain of a GH-18 chitinase from Vibrio harveyi is crucial for chitin-chitinase interactions. Int J Biol Macromol 2016; 93:1111-1117. [DOI: 10.1016/j.ijbiomac.2016.09.066] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 09/06/2016] [Accepted: 09/18/2016] [Indexed: 11/26/2022]
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11
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Soysa HSM, Suginta W. Identification and Functional Characterization of a Novel OprD-like Chitin Uptake Channel in Non-chitinolytic Bacteria. J Biol Chem 2016; 291:13622-33. [PMID: 27226611 DOI: 10.1074/jbc.m116.728881] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 11/06/2022] Open
Abstract
Chitoporin from the chitinolytic marine Vibrio has been characterized as a trimeric OmpC-like channel responsible for effective chitin uptake. In this study we describe the identification and characterization of a novel OprD-like chitoporin (so-called EcChiP) from Escherichia coli The gene was identified, cloned, and functionally expressed in the Omp-deficient E. coli BL21 (Omp8) Rosetta strain. On size exclusion chromatography, EcChiP had an apparent native molecular mass of 50 kDa, as predicted by amino acid sequencing and mass analysis, confirming that the protein is a monomer. Black lipid membrane reconstitution demonstrated that EcChiP could readily form stable, monomeric channels in artificial phospholipid membranes, with an average single channel conductance of 0.55 ± 0.01 nanosiemens and a slight preference for cations. Single EcChiP channels showed strong specificity, interacting with long chain chitooligosaccharides but not with maltooligosaccharides. Liposome swelling assays indicated the bulk permeation of neutral monosaccharides and showed the size exclusion limit of EcChiP to be ∼200-300 Da for small permeants that pass through by general diffusion while allowing long chain chitooligosaccharides to pass through by a facilitated diffusion process. Taking E. coli as a model, we offer the first evidence that non-chitinolytic bacteria can activate a quiescent ChiP gene to express a functional chitoporin, enabling them to take up chitooligosaccharides for metabolism as an immediate source of energy.
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Affiliation(s)
- H Sasimali M Soysa
- From the Biochemistry-Electrochemistry Research Unit and School of Chemistry, Institute of Science and
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit and School of Chemistry, Institute of Science and Center of Excellence in Advanced Functional Materials, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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12
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Sirimontree P, Fukamizo T, Suginta W. Azide anions inhibit GH-18 endochitinase and GH-20 Exo β-N-acetylglucosaminidase from the marine bacterium Vibrio harveyi. J Biochem 2015; 159:191-200. [PMID: 26330565 DOI: 10.1093/jb/mvv087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 08/02/2015] [Indexed: 11/14/2022] Open
Abstract
Vibrio harveyi is a bioluminescent marine bacterium that utilizes chitin as its sole source of energy. In the course of chitin degradation, the bacterium primarily secretes an endochitinase A (VhChiA) to hydrolyze chitin, generating chitooligosaccharide fragments that are readily transported into the cell and broken down to GlcNAc monomers by an exo β-N-acetylglucosaminidase (VhGlcNAcase). Here we report that sodium salts, especially sodium azide, inhibit two classes of these chitin-degrading enzymes (VhChiA and VhGlcNAcase) with distinct modes of action. Kinetic analysis of the enzymatic hydrolysis of pNP-glycoside substrates reveals that sodium azide inhibition of VhChiA has a mixed-type mode, but that it inhibits VhGlcNAcase competitively. We propose that azide anions inhibit chitinase activity by acting as strong nucleophiles that attack Cγ of the catalytic Glu or Cβ of the neighbouring Asp residues. Azide anions may bind not only to the catalytic centre, but also to the other subsites in the substrate-binding cleft of VhChiA. In contrast, azide anions may merely occupy the small-binding pocket of VhGlcNAcase, thereby blocking the accessibility of its active site by short-chain substrates.
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Affiliation(s)
- Paknisa Sirimontree
- Biochemistry-Electrochemistry Research Unit, School of Biochemistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand and
| | - Tamo Fukamizo
- Department of Advanced Biosciences, Kinki University, Nara, Japan
| | - Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, School of Biochemistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand and
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13
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Fadel F, Zhao Y, Cachau R, Cousido-Siah A, Ruiz FX, Harlos K, Howard E, Mitschler A, Podjarny A. New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM. ACTA ACUST UNITED AC 2015; 71:1455-70. [PMID: 26143917 DOI: 10.1107/s139900471500783x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/21/2015] [Indexed: 11/10/2022]
Abstract
Chitotriosidase (CHIT1) is a human chitinase belonging to the highly conserved glycosyl hydrolase family 18 (GH18). GH18 enzymes hydrolyze chitin, an N-acetylglucosamine polymer synthesized by lower organisms for structural purposes. Recently, CHIT1 has attracted attention owing to its upregulation in immune-system disorders and as a marker of Gaucher disease. The 39 kDa catalytic domain shows a conserved cluster of three acidic residues, Glu140, Asp138 and Asp136, involved in the hydrolysis reaction. Under an excess concentration of substrate, CHIT1 and other homologues perform an additional activity, transglycosylation. To understand the catalytic mechanism of GH18 chitinases and the dual enzymatic activity, the structure and mechanism of CHIT1 were analyzed in detail. The resolution of the crystals of the catalytic domain was improved from 1.65 Å (PDB entry 1waw) to 0.95-1.10 Å for the apo and pseudo-apo forms and the complex with chitobiose, allowing the determination of the protonation states within the active site. This information was extended by hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. The results suggest a new mechanism involving changes in the conformation and protonation state of the catalytic triad, as well as a new role for Tyr27, providing new insights into the hydrolysis and transglycosylation activities.
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Affiliation(s)
- Firas Fadel
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Raul Cachau
- Leidos Biomedical Research Inc. Advanced Biomedical Computer Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alexandra Cousido-Siah
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Francesc X Ruiz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Eduardo Howard
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Andre Mitschler
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Alberto Podjarny
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
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14
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Sirimontree P, Suginta W, Sritho N, Kanda Y, Shinya S, Ohnuma T, Fukamizo T. Mutation strategies for obtaining chitooligosaccharides with longer chains by transglycosylation reaction of family GH18 chitinase. Biosci Biotechnol Biochem 2014; 78:2014-21. [DOI: 10.1080/09168451.2014.948373] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Abstract
Enhancing the transglycosylation (TG) activity of glycoside hydrolases does not always result in the production of oligosaccharides with longer chains, because the TG products are often decomposed into shorter oligosaccharides. Here, we investigated the mutation strategies for obtaining chitooligosaccharides with longer chains by means of TG reaction catalyzed by family GH18 chitinase A from Vibrio harveyi (VhChiA). HPLC analysis of the TG products from incubation of chitooligosaccharide substrates, GlcNAcn, with several mutant VhChiAs suggested that mutant W570G (mutation of Trp570 to Gly) and mutant D392N (mutation of Asp392 to Asn) significantly enhanced TG activity, but the TG products were immediately hydrolyzed into shorter GlcNAcn. On the other hand, the TG products obtained from mutants D313A and D313N (mutations of Asp313 to Ala and Asn, respectively) were not further hydrolyzed, leading to the accumulation of oligosaccharides with longer chains. The data obtained from the mutant VhChiAs suggested that mutations of Asp313, the middle aspartic acid residue of the DxDxE catalytic motif, to Ala and Asn are most effective for obtaining chitooligosaccharides with longer chains.
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Affiliation(s)
- Paknisa Sirimontree
- Biochemistry-Electrochemistry Research Unit, Schools of Chemistry and Biochemistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Wipa Suginta
- Biochemistry-Electrochemistry Research Unit, Schools of Chemistry and Biochemistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Natchanok Sritho
- Biochemistry-Electrochemistry Research Unit, Schools of Chemistry and Biochemistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Yuka Kanda
- Department of Advanced Biosciences, Kinki University, Nara, Japan
| | - Shoko Shinya
- Department of Advanced Biosciences, Kinki University, Nara, Japan
| | - Takayuki Ohnuma
- Department of Advanced Biosciences, Kinki University, Nara, Japan
| | - Tamo Fukamizo
- Department of Advanced Biosciences, Kinki University, Nara, Japan
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15
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Characterization and optimization of heterologous expression in Escherichia coli of the chitinase encoded by the chiA gene of Bacillus halodurans C-125. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.06.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Vaaje-Kolstad G, Horn SJ, Sørlie M, Eijsink VGH. The chitinolytic machinery ofSerratia marcescens- a model system for enzymatic degradation of recalcitrant polysaccharides. FEBS J 2013; 280:3028-49. [DOI: 10.1111/febs.12181] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 01/30/2013] [Accepted: 02/05/2013] [Indexed: 01/13/2023]
Affiliation(s)
- Gustav Vaaje-Kolstad
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
| | - Svein J. Horn
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
| | - Morten Sørlie
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
| | - Vincent G. H. Eijsink
- Department of Chemistry; Biotechnology and Food Science; Norwegian University of Life Sciences; Ås; Norway
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