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Shobade SO, Zabotina OA, Nilsen-Hamilton M. Plant root associated chitinases: structures and functions. FRONTIERS IN PLANT SCIENCE 2024; 15:1344142. [PMID: 38362446 PMCID: PMC10867124 DOI: 10.3389/fpls.2024.1344142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024]
Abstract
Chitinases degrade chitin, a linear homopolymer of β-1,4-linked N-acetyl-D-glucosamine (GlcNAc) residues found in the cell walls of fungi and the exoskeletons of arthropods. They are secreted by the roots into the rhizosphere, a complex and dynamic environment where intense nutrient exchange occurs between plants and microbes. Here we modeled, expressed, purified, and characterized Zea mays and Oryza sativa root chitinases, and the chitinase of a symbiotic bacterium, Chitinophaga oryzae 1303 for their activities with chitin, di-, tri-, and tetra-saccharides and Aspergillus niger, with the goal of determining their role(s) in the rhizosphere and better understanding the molecular mechanisms underlying plant-microbe interactions. We show that Zea mays basic endochitinase (ZmChi19A) and Oryza sativa chitinase (OsChi19A) are from the GH19 chitinase family. The Chitinophaga oryzae 1303 chitinase (CspCh18A) belongs to the GH18 family. The three enzymes have similar apparent K M values of (20-40 µM) for the substrate 4-MU-GlcNAc3. They vary in their pH and temperature optima with OsChi19A activity optimal between pH 5-7 and 30-40°C while ZmChi19A and CspCh18A activities were optimal at pH 7-9 and 50-60°C. Modeling and site-directed mutation of ZmChi19A identified the catalytic cleft and the active residues E147 and E169 strategically positioned at ~8.6Å from each other in the folded protein. Cleavage of 4-MU-GlcNAc3 was unaffected by the absence of the CBD but diminished in the absence of the flexible C-terminal domain. However, unlike for the soluble substrate, the CBD and the newly identified flexible C-terminal domain were vital for inhibiting Aspergillus niger growth. The results are consistent with the involvement of the plant chitinases in defense against pathogens like fungi that have chitin exoskeletons. In summary, we have characterized the functional features and structural domains necessary for the activity of two plant root chitinases that are believed to be involved in plant defense and a bacterial chitinase that, along with the plant chitinases, may participate in nutrient recycling in the rhizosphere.
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Affiliation(s)
- Samuel O. Shobade
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Olga A. Zabotina
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Marit Nilsen-Hamilton
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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Liu X, Liu X, Deng Z, He X, Jiang Y. Xanthomonas chitinilytica sp. nov., a novel chitinolytic bacterium isolated from a microbial fermentation bed material. Antonie Van Leeuwenhoek 2024; 117:17. [PMID: 38189878 DOI: 10.1007/s10482-023-01904-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 10/27/2023] [Indexed: 01/09/2024]
Abstract
A Gram-stain-negative bacterium, H13-6T, was isolated from a microbial fermentation bed material collected from a pig farm located in Yan'an, Shaanxi, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H13-6T was affiliated with the genus Xanthomonas and showed highest similarity to strain Xanthomonas maliensis M97T (98.38%), Xanthomonas prunicola CFBP 8353T (98.26%) and Xanthomonas oryzae ATCC 35933T (98.11%). The pairwise ortho Average Nucleotide Identity values and the digital DNA-DNA hybridization values between strain H13-6T and the other Xanthomonas species were all below their respective cut-offs. Two genes encoding for chitinase were found and the strain showed a strong chitin-degrading activity. The major fatty acids were Iso-C15:0 (55.9%), Antesio-C15:0 (7.4%) and Iso-C11:0 (5.5%) and the major polar lipids were diphosphatidylglycerol, phosphatidyglycerol and phosphatidylethanolamine. Based on the phenotypic properties and phylogenetic distinctiveness, Xanthomonas chitinilytica was proposed as a novel species of the genus Xanthomonas, with strain H13-6T (= CGMCC 1.61317T = NBRC 115641T) as type strain.
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Affiliation(s)
- Xiaodong Liu
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
- Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China
| | - Xin Liu
- Research and Development Department, Shandong Xianglong Pharmaceutical Research Institute Co., Ltd, Yantai, 264003, China
| | - Zhenshan Deng
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
- Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China
| | - Xiaolong He
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
- Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China
| | - Yingying Jiang
- College of Life Sciences, Yan'an University, Yan'an, 716000, China.
- Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China.
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China.
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Son DJ, Kim GG, Choo HY, Chung NJ, Choo YM. Functional Comparison of Three Chitinases from Symbiotic Bacteria of Entomopathogenic Nematodes. Toxins (Basel) 2024; 16:26. [PMID: 38251242 PMCID: PMC10821219 DOI: 10.3390/toxins16010026] [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: 11/20/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Xenorhabdus and Photorhabdus, bacterial symbionts of entomopathogenic nematodes Steinernema and Heterorhabditis, respectively, have several biological activities including insecticidal and antimicrobial activities. Thus, XnChi, XhChi, and PtChi, chitinases of X. nematophila, X. hominickii, and P. temperata isolated from Korean indigenous EPNs S. carpocapsae GJ1-2, S. monticolum GJ11-1, and H. megidis GJ1-2 were cloned and expressed in Escherichia coli BL21 to compare their biological activities. Chitinase proteins of these bacterial symbionts purified using the Ni-NTA system showed different chitobiosidase and endochitinase activities, but N-acetylglucosamidinase activities were not shown in the measuring of chitinolytic activity through N-acetyl-D-glucosarmine oligomers. In addition, the proteins showed different insecticidal and antifungal activities. XnChi showed the highest insecticidal activity against Galleria mellonella, followed by PtChi and XhChi. In antifungal activity, XhChi showed the highest half-maximal inhibitory concentration (IC50) against Fusarium oxysporum with 0.031 mg/mL, followed by PtChi with 0.046 mg/mL, and XnChi with 0.072 mg/mL. XhChi also showed the highest IC50 against F. graminearum with 0.040 mg/mL, but XnChi was more toxic than PtChi with 0.055 mg/mL and 0.133 mg/mL, respectively. This study provides an innovative approach to the biological control of insect pests and fungal diseases of plants with the biological activity of symbiotic bacterial chitinases of entomopathogenic nematodes.
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Affiliation(s)
- Da-Jeong Son
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea;
- Division of Research and Development, Jinju Bioindustry Foundation, Jinju 52839, Republic of Korea
| | - Geun-Gon Kim
- Division of Research and Development, Nambo Co., Ltd., Jinju 52840, Republic of Korea; (G.-G.K.); (H.-Y.C.)
| | - Ho-Yul Choo
- Division of Research and Development, Nambo Co., Ltd., Jinju 52840, Republic of Korea; (G.-G.K.); (H.-Y.C.)
| | - Nam-Jun Chung
- Division of Research and Development, Nambo Co., Ltd., Jinju 52840, Republic of Korea; (G.-G.K.); (H.-Y.C.)
| | - Young-Moo Choo
- Division of Research and Development, Jinju Bioindustry Foundation, Jinju 52839, Republic of Korea
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