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Zhao P, Hong S, Li Y, Chen H, Gao H, Wang C. From phyllosphere to insect cuticles: silkworms gather antifungal bacteria from mulberry leaves to battle fungal parasite attacks. MICROBIOME 2024; 12:40. [PMID: 38409012 PMCID: PMC10895815 DOI: 10.1186/s40168-024-01764-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/11/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Bacterial transfers from plants to insect herbivore guts have been well investigated. However, bacterial exchanges between plant phyllospheres and insect cuticles remain unclear, as does their related biological function. RESULTS Here, we report that the cuticular bacterial loads of silkworm larvae quickly increased after molting and feeding on the white mulberry (Morus alba) leaves. The isolation and examination of silkworm cuticular bacteria identified one bacterium Mammaliicoccus sciuri that could completely inhibit the spore germination of fungal entomopathogens Metarhizium robertsii and Beauveria bassiana. Interestingly, Ma. sciuri was evident originally from mulberry leaves, which could produce a secreted chitinolytic lysozyme (termed Msp1) to damage fungal cell walls. In consistency, the deletion of Msp1 substantially impaired bacterial antifungal activity. Pretreating silkworm larvae with Ma. sciuri cells followed by fungal topical infections revealed that this bacterium could help defend silkworms against fungal infections. Unsurprisingly, the protective efficacy of ΔMsp1 was considerably reduced when compared with that of wild-type bacterium. Administration of bacterium-treated diets had no negative effect on silkworm development; instead, bacterial supplementation could protect the artificial diet from Aspergillus contamination. CONCLUSIONS The results of this study evidence that the cross-kingdom transfer of bacteria from plant phyllospheres to insect herbivore cuticles can help protect insects against fungal parasite attacks. Video Abstract.
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Affiliation(s)
- Pengfei Zhao
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Song Hong
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yuekun Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haimin Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Hanchun Gao
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengshu Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Pentekhina I, Nedashkovskaya O, Seitkalieva A, Gorbach V, Slepchenko L, Kirichuk N, Podvolotskaya A, Son O, Tekutyeva L, Balabanova L. Chitinolytic and Fungicidal Potential of the Marine Bacterial Strains Habituating Pacific Ocean Regions. Microorganisms 2023; 11:2255. [PMID: 37764100 PMCID: PMC10535946 DOI: 10.3390/microorganisms11092255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Screening for chitinolytic activity in the bacterial strains from different Pacific Ocean regions revealed that the highly active representatives belong to the genera Microbulbifer, Vibrio, Aquimarina, and Pseudoalteromonas. The widely distributed chitinolytic species was Microbulbifer isolated from the sea urchin Strongylocentrotus intermedius. Among seventeen isolates with confirmed chitinolytic activity, only the type strain P. flavipulchra KMM 3630T and the strains of putatively new species Pseudoalteromonas sp. B530 and Vibrio sp. Sgm 5, isolated from sea water (Vietnam mollusc farm) and the sea urchin S. intermedius (Peter the Great Gulf, the Sea of Japan), significantly suppressed the hyphal growth of Aspergillus niger that is perspective for the biocontrol agents' development. The results on chitinolytic activities and whole-genome sequencing of the strains under study, including agarolytic type strain Z. galactanivorans DjiT, found the new functionally active chitinase structures and biotechnological potential.
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Affiliation(s)
- Iuliia Pentekhina
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Molecular Biology, Biotechnology and Bioinformatics Center, R&D, Arnika Ltd., Volno-Nadezhdinskoe, 692481 Vladivostok, Russia
| | - Olga Nedashkovskaya
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Aleksandra Seitkalieva
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Vladimir Gorbach
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Lubov Slepchenko
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Natalya Kirichuk
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
| | - Anna Podvolotskaya
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Molecular Biology, Biotechnology and Bioinformatics Center, R&D, Arnika Ltd., Volno-Nadezhdinskoe, 692481 Vladivostok, Russia
| | - Oksana Son
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Molecular Biology, Biotechnology and Bioinformatics Center, R&D, Arnika Ltd., Volno-Nadezhdinskoe, 692481 Vladivostok, Russia
| | - Liudmila Tekutyeva
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Molecular Biology, Biotechnology and Bioinformatics Center, R&D, Arnika Ltd., Volno-Nadezhdinskoe, 692481 Vladivostok, Russia
| | - Larissa Balabanova
- Institute of Biotechnology, Bioengineering and Food Systems, Advanced Engineering School, Far Eastern Federal University, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia; (A.S.); (L.S.); (A.P.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100-Letya Vladivostoka 152, 690022 Vladivostok, Russia; (O.N.); (V.G.); (N.K.)
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Molecular analysis of genes involved in chitin degradation from the chitinolytic bacterium Bacillus velezensis. Antonie van Leeuwenhoek 2022; 115:215-231. [PMID: 35001244 DOI: 10.1007/s10482-021-01697-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/29/2021] [Indexed: 12/30/2022]
Abstract
Bacillus velezensis RB.IBE29 is a potent biocontrol agent with high chitinase activity isolated from the rhizosphere of black pepper cultivated in the Central Highlands, Vietnam. Genome sequences revealed that this species possesses some GH18 chitinases and AA10 protein(s); however, these enzymes have not been experimentally characterized. In this work, three genes were identified from the genomic DNA of this bacterium and cloned in Escherichia coli. Sequence analysis exhibited that the ORF of chiA consists of 1,203 bp and encodes deduced 45.46 kDa-chitinase A of 400 aa. The domain structure of chitinase A is composed of a CBM 50 domain at the N-terminus and a catalytic domain at the C-terminus. The ORF of chiB includes 1,263 bp and encodes deduced 47.59 kDa-chitinase B of 420 aa. Chitinase B consists of two CBM50 domains at the N-terminus and a catalytic domain at the C-terminus. The ORF of lpmo10 is 621 bp and encodes a deduced 22.44 kDa-AA10 protein, BvLPMO10 of 206 aa. BvLPMO10 contains a signal peptide and an AA10 catalytic domain. Chitinases A and B were grouped into subfamily A of family 18 chitinases. Amino acid sequences in their catalytic domains lack aromatic residues (Trp, Phe, Tyr) probably involved in processivity and substrate binding compared with well-known bacterial GH18 chitinases. chiB was successfully expressed in E. coli. Purified rBvChiB degraded insoluble chitin and was responsible for inhibition of fungal spore-germination and egg hatching of plant-parasitic nematode. This is the first report describing the analysis of the chitinase system from B. velezensis.
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Chemical Proprieties of Biopolymers (Chitin/Chitosan) and Their Synergic Effects with Endophytic Bacillus Species: Unlimited Applications in Agriculture. Molecules 2021; 26:molecules26041117. [PMID: 33672446 PMCID: PMC7923285 DOI: 10.3390/molecules26041117] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/03/2021] [Accepted: 02/03/2021] [Indexed: 11/17/2022] Open
Abstract
Over the past decade, reckless usage of synthetic pesticides and fertilizers in agriculture has made the environment and human health progressively vulnerable. This setting leads to the pursuit of other environmentally friendly interventions. Amongst the suggested solutions, the use of chitin and chitosan came about, whether alone or in combination with endophytic bacterial strains. In the framework of this research, we reported an assortment of studies on the physico-chemical properties and potential applications in the agricultural field of two biopolymers extracted from shrimp shells (chitin and chitosan), in addition to their uses as biofertilizers and biostimulators in combination with bacterial strains of the genus Bacillus sp. (having biochemical and enzymatic properties).
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Singh RV, Sambyal K, Negi A, Sonwani S, Mahajan R. Chitinases production: A robust enzyme and its industrial applications. BIOCATAL BIOTRANSFOR 2021. [DOI: 10.1080/10242422.2021.1883004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - Krishika Sambyal
- University Institute of Biotechnology, Chandigarh University, Gharuan, India
| | - Anjali Negi
- University Institute of Biotechnology, Chandigarh University, Gharuan, India
| | - Shubham Sonwani
- Department of Biosciences, Christian Eminent College, Indore, India
| | - Ritika Mahajan
- Department of Microbiology, School of Sciences, JAIN (Deemed-to-be University), Bengaluru, India
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Ueda M, Nakadoi K, Tsukamoto K, Sakurai S. Effect of LPMO on the Hydrolysis of Crystalline Chitin by Chitinase A and β- N-Acetylglucosaminidase from Paenibacillus sp. Mol Biotechnol 2021. [DOI: 10.5772/intechopen.93761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We performed cloning and expression of chitinase A (Pb-ChiA), β-GlcNAcase (Pb-GlcNAcase), and lytic polysaccharide monooxygenase (Pb-LPMO) genes from Paenibacillus sp. The analysis of the hydrolysis products indicated Pb-ChiA to be an exo-type chitinase with 10-fold activity toward β-chitin as compared with α-chitin. The sequence of Pb-GlcNAcase was found to be similar to that of β-N-acetylhexosaminidase from P. barengoltzii (99%, WP_016313754.1). Pb-LPMO was expressed in the Brevibacillus expression system. Pb-ChiA was found to have affinity toward crystalline chitin higher than that of Pb-LPMO. Pb-LPMO boosted the activity of Pb-ChiA toward crystalline α-chitin but not toward crystalline β-chitin. When Pb-LPMO (3 μM) was added to the reaction mixture during the hydrolysis of crystalline α-chitin by Pb-ChiA, hydrolysis products at two-fold concentration were obtained. However, the hydrolysis products decreased upon addition of more than 3 μM Pb-LPMO to the reaction mixture.
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Yano S, Kanno H, Tsuhako H, Ogasawara S, Suyotha W, Konno H, Makabe K, Uechi K, Taira T. Cloning, expression, and characterization of a GH 19-type chitinase with antifungal activity from Lysobacter sp. MK9-1. J Biosci Bioeng 2020; 131:348-355. [PMID: 33281068 DOI: 10.1016/j.jbiosc.2020.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 11/24/2022]
Abstract
The chitin-assimilating gram-negative bacterium, Lysobacter sp. MK9-1, was isolated from soil and was the source of a glycoside hydrolase family 19-type chitinase (Chi19MK) gene that is 933-bp long and encodes a 311-residue protein. The deduced amino acid sequence of Chi19MK includes a signal peptide, an uncharacterized sequence, a carbohydrate-binding module family 12-type chitin binding domain, and a catalytic domain. The catalytic domain of Chi19MK is approximately 60% similar to those of ChiB from Burkholderia gladioli CHB101, chitinase N (ChiN) from Chitiniphilus shinanonensis SAY3T, ChiF from Streptomyces coelicolor A3(2), Chi30 from Streptomyces olivaceoviridisis, ChiA from Streptomyces cyaneus SP-27, and ChiC from Streptomyces griseus HUT6037. Chi19MK lacking the signal and uncharacterized sequences (Chi19MKΔNTerm) was expressed in Escherichia coli Rosetta-gami B(DE3), resulting in significant chitinase activity in the soluble fraction. Purified Chi19MKΔNTerm hydrolyzed colloidal chitin and released disaccharide. Furthermore, Chi19MKΔNTerm inhibited hyphal extension in Trichoderma reesei and Schizophyllum commune. Based on quantitative antifungal activity assays, Chi19MKΔNTerm inhibits the growth of Trichoderma viride with an IC50 value of 0.81 μM.
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Affiliation(s)
- Shigekazu Yano
- Department of Biochemical Engineering, Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan.
| | - Haruki Kanno
- Department of Biochemical Engineering, Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Haruna Tsuhako
- Department of Bioscience and Biotechnology, University of the Ryukyus, Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Sonoka Ogasawara
- Department of Biochemical Engineering, Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Wasana Suyotha
- Department of Industrial Biotechnology, Faculty of Agro-industry, Prince of Songkla University, Hat Yai 90112, Thailand
| | - Hiroyuki Konno
- Department of Biochemical Engineering, Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Koki Makabe
- Department of Biochemical Engineering, Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Keiko Uechi
- Department of Bioscience and Biotechnology, University of the Ryukyus, Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Toki Taira
- Department of Bioscience and Biotechnology, University of the Ryukyus, Senbaru, Nishihara, Okinawa 903-0213, Japan
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Chitinolytic actinobacteria isolated from an Algerian semi-arid soil: development of an antifungal chitinase-dependent assay and GH18 chitinase gene identification. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-018-1426-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Nishitani Y, Horiuchi A, Aslam M, Kanai T, Atomi H, Miki K. Crystal structures of an archaeal chitinase ChiD and its ligand complexes. Glycobiology 2018; 28:418-426. [PMID: 29800365 DOI: 10.1093/glycob/cwy024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 03/20/2018] [Indexed: 11/13/2022] Open
Abstract
Chitinase D (designated as Pc-ChiD) was found in a hyperthermophilic archaeon, Pyrococcus chitonophagus (previously described as Thermococcus chitonophagus), that was isolated from media containing only chitin as carbon source. Pc-ChiD displays chitinase activity and is thermostable at temperatures up to 95°C, suggesting its potential for industrial use. Pc-ChiD has a secretion signal peptide and two chitin-binding domains (ChBDs) in the N-terminal domain. However, the C-terminal domain shares no sequence similarity with previously identified saccharide-degrading enzymes and does not contain the DXDXE motif conserved in the glycoside hydrolase (GH) 18 family chitinases. To elucidate its overall structure and reaction mechanism, we determined the first crystal structures of Pc-ChiD, both in the ligand-free form and in complexes with substrates. Structure analyses revealed that the C-terminal domain of Pc-ChiD, Pc-ChiD(ΔBD), consists of a third putative substrate-binding domain, which cannot be predicted from the amino acid sequence, and a catalytic domain structurally similar to that found in not the GH18 family but the GH23 family. Based on the similarity with GH23 family chitinase, the catalytic residues of Pc-ChiD were predicted and confirmed by mutagenesis analyses. Moreover, the specific C-terminal 100 residues of Pc-ChiD are important to fix the putative substrate-binding domain next to the catalytic domain, contributing to the structure stability as well as the long chitin chain binding. Our findings reveal the structure of a unique archaeal chitinase that is distinct from previously known members of the GH23 family.
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Affiliation(s)
- Yuichi Nishitani
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ayumi Horiuchi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Mehwish Aslam
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.,JST, CREST, Gobancho 7, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.,JST, CREST, Gobancho 7, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.,JST, CREST, Gobancho 7, Chiyoda-ku, Tokyo 102-0076, Japan
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Ueda M, Shioyama T, Nakadoi K, Nakazawa M, Sakamoto T, Iwamoto T, Sakaguchi M. Cloning and expression of a chitinase gene from Eisenia fetida. Int J Biol Macromol 2017; 104:1648-1655. [DOI: 10.1016/j.ijbiomac.2017.03.140] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 02/22/2017] [Accepted: 03/25/2017] [Indexed: 11/17/2022]
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A Structurally Novel Chitinase from the Chitin-Degrading Hyperthermophilic Archaeon Thermococcus chitonophagus. Appl Environ Microbiol 2016; 82:3554-3562. [PMID: 27060120 DOI: 10.1128/aem.00319-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/03/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A structurally novel chitinase, Tc-ChiD, was identified from the hyperthermophilic archaeon Thermococcus chitonophagus, which can grow on chitin as the sole organic carbon source. The gene encoding Tc-ChiD contains regions corresponding to a signal sequence, two chitin-binding domains, and a putative catalytic domain. This catalytic domain shows no similarity with previously characterized chitinases but resembles an uncharacterized protein found in the mesophilic anaerobic bacterium Clostridium botulinum Two recombinant Tc-ChiD proteins were produced in Escherichia coli, one without the signal sequence [Tc-ChiD(ΔS)] and the other corresponding only to the putative catalytic domain [Tc-ChiD(ΔBD)]. Enzyme assays using N-acetylglucosamine (GlcNAc) oligomers indicated that both proteins hydrolyze GlcNAc oligomers longer than (GlcNAc)4 Chitinase assays using colloidal chitin suggested that Tc-ChiD is an exo-type chitinase that releases (GlcNAc)2 or (GlcNAc)3 Analysis with GlcNAc oligomers modified with p-nitrophenol suggested that Tc-ChiD recognizes the reducing end of chitin chains. While Tc-ChiD(ΔBD) displayed a higher initial velocity than that of Tc-ChiD(ΔS), we found that the presence of the two chitin-binding domains significantly enhanced the thermostability of the catalytic domain. In T. chitonophagus, another chitinase ortholog that is similar to the Thermococcus kodakarensis chitinase ChiA is present and can degrade chitin from the nonreducing ends. Therefore, the presence of multiple chitinases in T. chitonophagus with different modes of cleavage may contribute to its unique ability to efficiently degrade chitin. IMPORTANCE A structurally novel chitinase, Tc-ChiD, was identified from Thermococcus chitonophagus, a hyperthermophilic archaeon. The protein contains a signal peptide for secretion, two chitin-binding domains, and a catalytic domain that shows no similarity with previously characterized chitinases. Tc-ChiD thus represents a new family of chitinases. Tc-ChiD is an exo-type chitinase that recognizes the reducing end of chitin chains and releases (GlcNAc)2 or (GlcNAc)3 As a thermostable chitinase that recognizes the reducing end of chitin chains was not previously known, Tc-ChiD may be useful in a wide range of enzyme-based technologies to degrade and utilize chitin.
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Ohnuma T, Umemoto N, Taira T, Fukamizo T, Numata T. Crystallization and preliminary X-ray diffraction analysis of an active-site mutant of `loopless' family GH19 chitinase from Bryum coronatum in a complex with chitotetraose. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1360-2. [PMID: 24316830 DOI: 10.1107/s1744309113028935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 10/21/2013] [Indexed: 11/10/2022]
Abstract
The catalytic mechanism of family GH19 chitinases is not well understood owing to insufficient information regarding the three-dimensional structures of enzyme-substrate complexes. Here, the crystallization and preliminary X-ray diffraction analysis of a selenomethionine-labelled active-site mutant of `loopless' family GH19 chitinase from the moss Bryum coronatum in complex with chitotetraose, (GlcNAc)4, are reported. The crystals were grown using the vapour-diffusion method. They diffracted to 1.58 Å resolution using synchrotron radiation at the Photon Factory. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 74.5, b = 58.4, c = 48.1 Å, β = 115.6°. The asymmetric unit of the crystals is expected to contain one protein molecule, with a Matthews coefficient of 2.08 Å(3) Da(-1) and a solvent content of 41%.
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Affiliation(s)
- Takayuki Ohnuma
- Department of Advanced Bioscience, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan
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Adrangi S, Faramarzi MA. From bacteria to human: a journey into the world of chitinases. Biotechnol Adv 2013; 31:1786-95. [PMID: 24095741 DOI: 10.1016/j.biotechadv.2013.09.012] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/26/2013] [Accepted: 09/28/2013] [Indexed: 12/28/2022]
Abstract
Chitinases, the enzymes responsible for the biological degradation of chitin, are found in a wide range of organisms from bacteria to higher plants and animals. They participate in numerous physiological processes such as nutrition, parasitism, morphogenesis and immunity. Many organisms, in addition to chitinases, produce inactive chitinase-like lectins that despite lacking enzymatic activity are involved in several regulatory functions. Most known chitinases belong to families 18 and 19 of glycosyl hydrolases, however a few chitinases that belong to families 23 and 48 have also been identified in recent years. In this review, different aspects of chitinases and chi-lectins from bacteria, fungi, insects, plants and mammals are discussed.
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Affiliation(s)
- Sina Adrangi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Arimori T, Kawamoto N, Shinya S, Okazaki N, Nakazawa M, Miyatake K, Fukamizo T, Ueda M, Tamada T. Crystal structures of the catalytic domain of a novel glycohydrolase family 23 chitinase from Ralstonia sp. A-471 reveals a unique arrangement of the catalytic residues for inverting chitin hydrolysis. J Biol Chem 2013; 288:18696-706. [PMID: 23658014 DOI: 10.1074/jbc.m113.462135] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chitinase C from Ralstonia sp. A-471 (Ra-ChiC) has a catalytic domain sequence similar to goose-type (G-type) lysozymes and, unlike other chitinases, belongs to glycohydrolase (GH) family 23. Using NMR spectroscopy, however, Ra-ChiC was found to interact only with the chitin dimer but not with the peptidoglycan fragment. Here we report the crystal structures of wild-type, E141Q, and E162Q of the catalytic domain of Ra-ChiC with or without chitin oligosaccharides. Ra-ChiC has a substrate-binding site including a tunnel-shaped cavity, which determines the substrate specificity. Mutation analyses based on this structural information indicated that a highly conserved Glu-141 acts as a catalytic acid, and that Asp-226 located at the roof of the tunnel activates a water molecule as a catalytic base. The unique arrangement of the catalytic residues makes a clear contrast to the other GH23 members and also to inverting GH19 chitinases.
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Affiliation(s)
- Takao Arimori
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
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Chertkov OV, Chuprov-Netochin RN, Legotskiĭ SV, Sykilinda NN, Shneider MM, Ivanova MA, Pleteneva EA, Shaburova OV, Burkal'tseva MB, Kostriukova ES, Lazarev VN, Kliachko NL, Miroshnikov KA. Properties of the peptidoglycan-degrading enzyme of the Pseudomonas aeruginosa ϕPMG1 bacteriophage. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:807-14. [PMID: 22497079 DOI: 10.1134/s1068162011060057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Okazaki N, Arimori T, Nakazawa M, Miyatake K, Ueda M, Tamada T. Crystallization and preliminary X-ray diffraction studies of the catalytic domain of a novel chitinase, a member of GH family 23, from the moderately thermophilic bacterium Ralstonia sp. A-471. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:494-7. [PMID: 21505250 PMCID: PMC3080159 DOI: 10.1107/s1744309111004751] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 02/08/2011] [Indexed: 11/11/2022]
Abstract
Chitinase from the moderately thermophilic bacterium Ralstonia sp. A-471 (Ra-ChiC) is divided into two domains: a chitin-binding domain (residues 36-80) and a catalytic domain (residues 103-252). Although the catalytic domain of Ra-ChiC has homology to goose-type lysozyme, Ra-ChiC does not show lysozyme activity but does show chitinase activity. The catalytic domain with part of an interdomain loop (Ra-ChiC(89-252)) was crystallized under several different conditions using polyethylene glycol as a precipitant. The crystals diffracted to 1.85 Å resolution and belonged to space group P6(1)22 or P6(5)22, with unit-cell parameters a = b = 100, c = 243 Å. The calculated Matthews coefficient was approximately 3.2, 2.4 or 1.9 Å(3) Da(-1) assuming the presence of three, four or five Ra-ChiC(89-252) molecules in the asymmetric unit, respectively.
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Affiliation(s)
- Nobuo Okazaki
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Takao Arimori
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Masami Nakazawa
- Graduate School of Life Science and Environment, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, Osaka 599-8531, Japan
| | - Kazutaka Miyatake
- Graduate School of Life Science and Environment, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, Osaka 599-8531, Japan
| | - Mitsuhiro Ueda
- Graduate School of Life Science and Environment, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, Osaka 599-8531, Japan
| | - Taro Tamada
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
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Rhodes RG, Atoyan JA, Nelson DR. The chitobiose transporter, chbC, is required for chitin utilization in Borrelia burgdorferi. BMC Microbiol 2010; 10:21. [PMID: 20102636 PMCID: PMC2845121 DOI: 10.1186/1471-2180-10-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 01/26/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The bacterium Borrelia burgdorferi, the causative agent of Lyme disease, is a limited-genome organism that must obtain many of its biochemical building blocks, including N-acetylglucosamine (GlcNAc), from its tick or vertebrate host. GlcNAc can be imported into the cell as a monomer or dimer (chitobiose), and the annotation for several B. burgdorferi genes suggests that this organism may be able to degrade and utilize chitin, a polymer of GlcNAc. We investigated the ability of B. burgdorferi to utilize chitin in the absence of free GlcNAc, and we attempted to identify genes involved in the process. We also examined the role of RpoS, one of two alternative sigma factors present in B. burgdorferi, in the regulation of chitin utilization. RESULTS Using fluorescent chitinase substrates, we demonstrated an inherent chitinase activity in rabbit serum, a component of the B. burgdorferi growth medium (BSK-II). After inactivating this activity by boiling, we showed that wild-type cells can utilize chitotriose, chitohexose or coarse chitin flakes in the presence of boiled serum and in the absence of free GlcNAc. Further, we replaced the serum component of BSK-II with a lipid extract and still observed growth on chitin substrates without free GlcNAc. In an attempt to knockout B. burgdorferi chitinase activity, we generated mutations in two genes (bb0002 and bb0620) predicted to encode enzymes that could potentially cleave the beta-(1,4)-glycosidic linkages found in chitin. While these mutations had no effect on the ability to utilize chitin, a mutation in the gene encoding the chitobiose transporter (bbb04, chbC) did block utilization of chitin substrates by B. burgdorferi. Finally, we provide evidence that chitin utilization in an rpoS mutant is delayed compared to wild-type cells, indicating that RpoS may be involved in the regulation of chitin degradation by this organism. CONCLUSIONS The data collected in this study demonstrate that B. burgdorferi can utilize chitin as a source of GlcNAc in the absence of free GlcNAc, and suggest that chitin is cleaved into dimers before being imported across the cytoplasmic membrane via the chitobiose transporter. In addition, our data suggest that the enzyme(s) involved in chitin degradation are at least partially regulated by the alternative sigma factor RpoS.
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Affiliation(s)
- Ryan G Rhodes
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
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