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Characterization of a Marine Diatom Chitin Synthase Using a Combination of Meta-Omics, Genomics, and Heterologous Expression Approaches. mSystems 2023; 8:e0113122. [PMID: 36790195 PMCID: PMC10134812 DOI: 10.1128/msystems.01131-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
β-Chitin has important ecological and physiological roles and potential for widespread applications, but the characterization of chitin-related enzymes from β-chitin producers was rarely reported. Querying against the Tara Oceans Gene Atlas, 4,939 chitin-related unique sequences from 12 Pfam accessions were found in Bacillariophyta metatranscriptomes. Putative chitin synthase (CHS) sequences are decreasingly present in Crustacea (39%), Stramenopiles (16%) and Insecta (14%) from the Marine Atlas of Tara Oceans Unigenes version 1 Metatranscriptomes (MATOUv1+T) database. A CHS gene from the model diatom Thalassiosira pseudonana (Thaps3_J4413, designated TpCHS1) was identified. Homology analysis of TpCHS1 in Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP), PhycoCosm, and the PLAZA diatom omics data set showed that Mediophyceae and Thalassionemales species were potential new β-chitin producers besides Thalassiosirales. TpCHS1 was overexpressed in Saccharomyces cerevisiae and Phaeodactylum tricornutum. In transgenic P. tricornutum lines, TpCHS1-eGFP localizes to the Golgi apparatus and plasma membrane and predominantly accumulates in the cleavage furrow during cell division. Enhanced TpCHS1 expression could induce abnormal cell morphology and reduce growth rates in P. tricornutum, which might be ascribed to the inhibition of the G2/M phase. S. cerevisiae was proved to be a better system for expressing large amounts of active TpCHS1, which effectively incorporates UDP-N-acetylglucosamine in radiometric in vitro assays. Our study expands the knowledge on chitin synthase taxonomic distribution in marine eukaryotic microbes, and is the first to collectively characterize an active marine diatom CHS which may play an important role during cell division. IMPORTANCE As the most abundant biopolymer in the oceans, the significance of chitin and its biosynthesis is rarely demonstrated in diatoms, which are the main contributors to the primary productivity of the oceans, ascribed to their huge biomass and efficient photosynthesis. We retrieved genes involved in chitin-based metabolism against the Tara Oceans Gene Atlas to expand our knowledge about their diversity and distribution in the marine environment. Potential new producers of chitin were found from the analysis of various algal transcriptome and genome databases. Heterologous expression confirms that Thalassiosira pseudonana contains an active chitin synthase (CHS) which may play an important role in the cell division process of diatoms. This study provides new insight into CHS geographic and taxonomic distribution in marine eukaryotic microbes, as well as into a new CHS functioning in the biosynthesis of β-chitin in diatoms.
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2
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Bacterial chitinases: genetics, engineering and applications. World J Microbiol Biotechnol 2022; 38:252. [DOI: 10.1007/s11274-022-03444-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022]
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Li J, Wang S, Liu C, Li Y, Wei Y, Fu G, Liu P, Ma H, Huang D, Lin J, Zhang D. Going Beyond the Local Catalytic Activity Space of Chitinase Using a Simulation-Based Iterative Saturation Mutagenesis Strategy. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jinlong Li
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Sijia Wang
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Cui Liu
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Yixin Li
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Yu Wei
- College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, P. R. China
| | - Gang Fu
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Pi Liu
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Hongwu Ma
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Dawei Huang
- College of Life Sciences, Nankai University, Tianjin 300071, P. R. China
| | - Jianping Lin
- College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, P. R. China
| | - Dawei Zhang
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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4
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Otsuka Y, Sasaki K, Suyotha W, Furusawa H, Miyazawa K, Konno H, Yano S. Construction of a fusion protein consisting of α-1,3-glucan-binding domains and tetrameric red fluorescent protein, which is involved in the aggregation of α-1,3-glucan and inhibition of fungal biofilm formation. J Biosci Bioeng 2022; 133:524-532. [PMID: 35314116 DOI: 10.1016/j.jbiosc.2022.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 11/24/2022]
Abstract
Agl-KA, an α-1,3-glucan-hydrolyzing enzyme from Bacillus circulans KA-304, has three α-1,3-glucan-binding domains DS1, CB6, and DS2 (DCD). While their individual binding activities toward insoluble α-1,3-glucan and fungal cell-wall are weak, the three domains in combination bind strongly to the α-1,3-glucan and the cell-wall. In this study, we constructed DCD-tetraRFP by fusing DCD with DsRed-Express2, a tetrameric red fluorescent protein. DCD-tetraRFP forms a tetramer in an aqueous solution and contains twelve substrate-binding domains in one complex. We also constructed DCD-monoGFP by fusing DCD with AcGFP1, a monomeric green fluorescent protein. The molecular weight of DCD-tetraRFP and DCD-monoGFP were compared. The results of gel filtration chromatography and dynamic light scattering indicated that DCD-tetraRFP was larger than DCD-monoGFP, suggesting that DCD-tetraRFP had a tetrameric structure. In addition, DCD-tetraRFP bound to insoluble α-1,3-glucan strongly, and the amount of DCD-tetraRFP binding to 0.01% α-1,3-glucan was about twice of DCD-monoGFP. The Kd values of DCD-tetraRFP (measurements per subunit) and DCD-monoGFP were 0.16 and 0.84 μM, respectively. Adding DCD-tetraRFP to a suspension of α-1,3-glucan caused glucan aggregation; however, adding DCD-monoGFP did not. These data suggested that DCD-tetraRFP had four DCDs sterically arranged in different directions so that DCD-tetraRFP cross-linked with the substrate, causing aggregation. Lastly, the aggregates of DCD-tetraRFP and α-1,3-glucan captured Aspergillus oryzae conidia and decreased their biofilm formation by 80% in a 24-well dish.
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Affiliation(s)
- Yuitsu Otsuka
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Kai Sasaki
- 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 Furusawa
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Ken Miyazawa
- Laboratory of Filamentous Mycoses, Department of Fungal Infection, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Hiroyuki Konno
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Shigekazu Yano
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata 992-8510, Japan.
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Eigenfeld M, Kerpes R, Becker T. Recombinant protein linker production as a basis for non-invasive determination of single-cell yeast age in heterogeneous yeast populations. RSC Adv 2021; 11:31923-31932. [PMID: 35495491 PMCID: PMC9041608 DOI: 10.1039/d1ra05276d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/16/2021] [Indexed: 11/30/2022] Open
Abstract
The physiological and metabolic diversity of a yeast culture is the sum of individual cell phenotypes. As well as environmental conditions, genetics, and numbers of cell divisions, a major factor influencing cell characteristics is cell age. A postcytokinesis bud scar on the mother cell, a benchmark in the replicative life span, is a quantifiable indicator of cell age, characterized by significant amounts of chitin. We developed a binding process for visualizing the bud scars of Saccharomyces pastorianus var. carlsbergensis using a protein linker containing a polyhistidine tag, a superfolder green fluorescent protein (sfGFP), and a chitin-binding domain (His6-SUMO-sfGFP-ChBD). The binding did not affect yeast viability; thus, our method provides the basis for non-invasive cell age determination using flow cytometry. The His6-SUMO-sfGFP-ChBD protein was synthesized in Escherichia coli, purified using two-stage chromatography, and checked for monodispersity and purity. Linker-cell binding and the characteristics of the bound complex were determined using flow cytometry and confocal laser scanning microscopy (CLSM). Flow cytometry showed that protein binding increased to 60 455 ± 2706 fluorescence units per cell. The specific coupling of the linker to yeast cells was additionally verified by CLSM and adsorption isotherms using yeast cells, E. coli cells, and chitin resin. We found a relationship between the median bud scar number, the median of the fluorescence units, and the chitin content of yeast cells. A fast measurement of yeast population dynamics by flow cytometry is possible, using this protein binding technique. Rapid qualitative determination of yeast cell age distribution can therefore be performed.
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Affiliation(s)
- Marco Eigenfeld
- Technical University of Munich, Chair of Brewing and Beverage Technology, Research Group Beverage and Cereal Biotechnology Weihenstephaner Steig 20 85354 Freising Germany
| | - Roland Kerpes
- Technical University of Munich, Chair of Brewing and Beverage Technology, Research Group Beverage and Cereal Biotechnology Weihenstephaner Steig 20 85354 Freising Germany
| | - Thomas Becker
- Technical University of Munich, Chair of Brewing and Beverage Technology, Research Group Beverage and Cereal Biotechnology Weihenstephaner Steig 20 85354 Freising Germany
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6
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Cheng H, Bowler C, Xing X, Bulone V, Shao Z, Duan D. Full-Length Transcriptome of Thalassiosira weissflogii as a Reference Resource and Mining of Chitin-Related Genes. Mar Drugs 2021; 19:392. [PMID: 34356817 PMCID: PMC8307304 DOI: 10.3390/md19070392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 11/17/2022] Open
Abstract
β-Chitin produced by diatoms is expected to have significant economic and ecological value due to its structure, which consists of parallel chains of chitin, its properties and the high abundance of diatoms. Nevertheless, few studies have functionally characterised chitin-related genes in diatoms owing to the lack of omics-based information. In this study, we first compared the chitin content of three representative Thalassiosira species. Cell wall glycosidic linkage analysis and chitin/chitosan staining assays showed that Thalassiosira weissflogii was an appropriate candidate chitin producer. A full-length (FL) transcriptome of T. weissflogii was obtained via PacBio sequencing. In total, the FL transcriptome comprised 23,362 annotated unigenes, 710 long non-coding RNAs (lncRNAs), 363 transcription factors (TFs), 3113 alternative splicing (AS) events and 3295 simple sequence repeats (SSRs). More specifically, 234 genes related to chitin metabolism were identified and the complete biosynthetic pathways of chitin and chitosan were explored. The information presented here will facilitate T. weissflogii molecular research and the exploitation of β-chitin-derived high-value enzymes and products.
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Affiliation(s)
- Haomiao Cheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chris Bowler
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France;
| | - Xiaohui Xing
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 10691 Stockholm, Sweden; (X.X.); (V.B.)
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, Australia
- Adelaide Glycomics, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, Australia
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 10691 Stockholm, Sweden; (X.X.); (V.B.)
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, Australia
- Adelaide Glycomics, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae 5064, Australia
| | - Zhanru Shao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Bright Moon Seaweed Group Co., Ltd., Qingdao 266400, China
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7
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Zhang T, Na JH, Li S, Chen Z, Zhang G, Pang S, Daniyan AF, Li Y, Shi L, Du YCN. Functional impact of cancer patient-associated Bcl-xL mutations. MedComm (Beijing) 2020; 1:328-337. [PMID: 34308416 PMCID: PMC8302207 DOI: 10.1002/mco2.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Bcl-xL, an antiapoptotic protein, is frequently overexpressed in cancer to promote survival of tumor cells. However, we have previously shown that Bcl-xL promotes migration, invasion, and metastasis independent of its antiapoptotic function in mitochondria. The pro-metastatic function of Bcl-xL may require its translocation into the nucleus. Besides overexpression, patient-associated mutations of Bcl-xL have been identified in large-scale cancer genomics projects. Understanding the functions of these mutations will guide the development of precision medicine. Here, we selected four patient-associated Bcl-xL mutations, R132W, N136K, R165W, and A201T, to investigate their impacts on antiapoptosis, migration, and nuclear translocation. We found that all four mutation proteins could be detected in both the nucleus and cytosol. Although all four mutations disrupted the antiapoptosis function, one of these mutants, N136K, significantly improved the ability to promote cell migration. These data suggest the importance of developing novel Bcl-xL inhibitors to ablate both antiapoptotic and pro-metastatic functions of Bcl-xL in cancer.
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Affiliation(s)
- Tiantian Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Joseph HyungJoon Na
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Samantha Li
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, New York, New York
| | - George Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Sharon Pang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Anthony F Daniyan
- Department of Medicine, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yi Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Yi-Chieh Nancy Du
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
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Mathew GM, Madhavan A, Arun KB, Sindhu R, Binod P, Singhania RR, Sukumaran RK, Pandey A. Thermophilic Chitinases: Structural, Functional and Engineering Attributes for Industrial Applications. Appl Biochem Biotechnol 2020; 193:142-164. [PMID: 32827066 DOI: 10.1007/s12010-020-03416-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
Chitin is the second most widely found natural polymer next to cellulose. Chitinases degrade the insoluble chitin to bioactive chitooligomers and monomers for various industrial applications. Based on their function, these enzymes act as biocontrol agents against pathogenic fungi and invasive pests compared with conventional chemical fungicides and insecticides. They have other functional roles in shellfish waste management, fungal protoplast generation, and Single-Cell Protein production. Among the chitinases, thermophilic and thermostable chitinases are gaining popularity in recent years, as they can withstand high temperatures and maintain the enzyme stability for longer periods. Not all chitinases are thermostable; hence, tailor-made thermophilic chitinases are designed to enhance their thermostability by direct evolution, genetic engineering involving mutagenesis, and proteomics approach. Although research has been done extensively on cloning and expression of thermophilic chitinase genes, there are only few papers discussing on the mechanism of chitin degradation using thermophiles. The current review discusses the sources of thermophilic chitinases, improvement of protein stability by gene manipulation, metagenomics approaches, chitin degradation mechanism in thermophiles, and their prospective applications for industrial, agricultural, and pharmaceutical purposes.
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Affiliation(s)
- Gincy M Mathew
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Aravind Madhavan
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - K B Arun
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | | | - Rajeev K Sukumaran
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR - Indian Institute of Toxicology Research, Lucknow, 226 001, India.
- Frontier Research Lab, Yonsei University, Seoul, South Korea.
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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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Inubushi Y, Tachibana A. Uniform spheroid formation on a laboratory-made, low cell attachment surface consisting of a chitin sheet. Biosci Biotechnol Biochem 2020; 84:997-1000. [PMID: 31928142 DOI: 10.1080/09168451.2020.1714423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We utilized the reaction of chitosan with acetic anhydride to form a chitin gel. This gel was then dried, which formed a chitin sheet. The procedure was extremely easy for a biologist unfamiliar with materials engineering. Spheroids derived from HEK293T cells were formed on the chitin sheet, because the spheroids slightly attached and slowly moved on the chitin sheet.
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Affiliation(s)
- Yusaku Inubushi
- Department of Bioengineering, Graduate School of Engineering, Osaka City University, Osaka, Japan
| | - Akira Tachibana
- Department of Bioengineering, Graduate School of Engineering, Osaka City University, Osaka, Japan
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Bartholomew ES, Black K, Feng Z, Liu W, Shan N, Zhang X, Wu L, Bailey L, Zhu N, Qi C, Ren H, Liu X. Comprehensive Analysis of the Chitinase Gene Family in Cucumber ( Cucumis sativus L.): From Gene Identification and Evolution to Expression in Response to Fusarium oxysporum. Int J Mol Sci 2019; 20:E5309. [PMID: 31731414 PMCID: PMC6861899 DOI: 10.3390/ijms20215309] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 12/25/2022] Open
Abstract
Chitinases, a subgroup of pathogenesis-related proteins, are responsible for catalyzing the hydrolysis of chitin. Accumulating reports indicate that chitinases play a key role in plant defense against chitin-containing pathogens and are therefore good targets for defense response studies. Here, we undertook an integrated bioinformatic and expression analysis of the cucumber chitinases gene family to identify its role in defense against Fusarium oxysporum f. sp. cucumerinum. A total of 28 putative chitinase genes were identified in the cucumber genome and classified into five classes based on their conserved catalytic and binding domains. The expansion of the chitinase gene family was due mainly to tandem duplication events. The expression pattern of chitinase genes was organ-specific and 14 genes were differentially expressed in response to F. oxysporum challenge of fusarium wilt-susceptible and resistant lines. Furthermore, a class I chitinase, CsChi23, was constitutively expressed at high levels in the resistant line and may play a crucial role in building a basal defense and activating a rapid immune response against F. oxysporum. Whole-genome re-sequencing of both lines provided clues for the diverse expression patterns observed. Collectively, these results provide useful genetic resource and offer insights into the role of chitinases in cucumber-F. oxysporum interaction.
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Affiliation(s)
- Ezra S. Bartholomew
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Kezia Black
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Zhongxuan Feng
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Wan Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Nan Shan
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Xiao Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Licai Wu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Latoya Bailey
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Ning Zhu
- Changping Agricultural Technology Service Center, Beijing 102200, China; (N.Z.); (C.Q.)
| | - Changhong Qi
- Changping Agricultural Technology Service Center, Beijing 102200, China; (N.Z.); (C.Q.)
| | - Huazhong Ren
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
| | - Xingwang Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, China; (E.S.B.); (K.B.); (Z.F.); (W.L.); (N.S.); (X.Z.); (L.W.); (L.B.); (H.R.)
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12
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Tachibana A, Yasuma D, Takahashi R, Tanabe T. Chitin degradation enzyme-responsive system for controlled release of fibroblast growth factor-2. J Biosci Bioeng 2019; 129:116-120. [PMID: 31492610 DOI: 10.1016/j.jbiosc.2019.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 06/07/2019] [Accepted: 07/19/2019] [Indexed: 11/19/2022]
Abstract
Chitin is widely found in fungal cell walls and arthropod exoskeletons, and is used as a biomedical material. However, chitin is not water-soluble, restricting its use for controlled release materials. We found that water-soluble chitosan can be acetylated to produce a chitin equivalent, or chitin gel. Chitin gel, produced by mixing chitosan solution with acetic anhydride, can be degraded by lysozyme and fetal bovine serum, so could provide an ideal means for controlled release in biological systems. We tested a combination of chitin gel with a chitin binding domain (CBD) fusion protein as a controlled release system regulated by chitin degradation. A fusion protein consisting of fibroblast growth factor 2 (FGF-2) fused to CBD bound the chitin gel, and was released time-dependently rather than as an initial burst during lysozyme degradation, suggesting that this system could provide a means for controlled drug release in biological systems. Contrastingly, the trinitrophenyl residue (TNP-X) covalently bound to chitin gel, and was released by lysozyme degradation with an initial burst. If release of CBD-FGF-2 were simply dependent on lysozyme degradation of the chitin gel, the release behavior of CBD-FGF-2 would be similar to that of TNP-X, with an initial burst. Therefore, we propose that CBD-FGF-2 repeats the cycle of binding, release, and re-binding to the chitin gel during degradation. This system allows for a time-dependent, controlled release of CBD-FGF-2 without an initial burst.
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Affiliation(s)
- Akira Tachibana
- Department of Bioengineering, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan.
| | - Dai Yasuma
- Department of Bioengineering, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Ryo Takahashi
- Department of Bioengineering, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Toshizumi Tanabe
- Department of Bioengineering, Graduate School of Engineering, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
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13
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Shao Z, Thomas Y, Hembach L, Xing X, Duan D, Moerschbacher BM, Bulone V, Tirichine L, Bowler C. Comparative characterization of putative chitin deacetylases from Phaeodactylum tricornutum and Thalassiosira pseudonana highlights the potential for distinct chitin-based metabolic processes in diatoms. THE NEW PHYTOLOGIST 2019; 221:1890-1905. [PMID: 30288745 DOI: 10.1111/nph.15510] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/23/2018] [Indexed: 06/08/2023]
Abstract
Chitin is generally considered to be present in centric diatoms but not in pennate species. Many aspects of chitin biosynthetic pathways have not been explored in diatoms. We retrieved chitin metabolic genes from pennate (Phaeodactylum tricornutum) and centric (Thalassiosira pseudonana) diatom genomes. Chitin deacetylase (CDA) genes from each genome (PtCDA and TpCDA) were overexpressed in P. tricornutum. We performed comparative analysis of their sequence structure, phylogeny, transcriptional profiles, localization and enzymatic activities. The chitin relevant proteins show complex subcellular compartmentation. PtCDA was likely acquired by horizontal gene transfer from prokaryotes, whereas TpCDA has closer relationships with sequences in Opisthokonta. Using transgenic P. tricornutum lines expressing CDA-green fluorescent protein (GFP) fusion proteins, PtCDA predominantly localizes to Golgi apparatus whereas TpCDA localizes to endoplasmic reticulum/chloroplast endoplasmic reticulum membrane. CDA-GFP overexpression upregulated the transcription of chitin synthases and potentially enhanced the ability of chitin synthesis. Although both CDAs are active on GlcNAc5 , TpCDA is more active on the highly acetylated chitin polymer DA60. We have addressed the ambiguous characters of CDAs from P. tricornutum and T. pseudonana. Differences in localization, evolution, expression and activities provide explanations underlying the greater potential of centric diatoms for chitin biosynthesis. This study paves the way for in vitro applications of novel CDAs.
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Affiliation(s)
- Zhanru Shao
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 266071, Qingdao, China
| | - Yann Thomas
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
| | - Lea Hembach
- Institute of Plant Biology and Biotechnology, Westphalian Wilhelm's-University Münster, 48143, Münster, Germany
| | - Xiaohui Xing
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
- Adelaide Glycomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, SE10691, Sweden
| | - Delin Duan
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 266071, Qingdao, China
| | - Bruno M Moerschbacher
- Institute of Plant Biology and Biotechnology, Westphalian Wilhelm's-University Münster, 48143, Münster, Germany
| | - Vincent Bulone
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
- Adelaide Glycomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, SE10691, Sweden
| | - Leila Tirichine
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
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14
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Tanaka H, Akutsu H, Yabuta I, Hara M, Sugimoto H, Ikegami T, Watanabe T, Fujiwara T. A novel chitin‐binding mode of the chitin‐binding domain of chitinase A1 from
Bacillus circulans
WL
‐12 revealed by solid‐state
NMR. FEBS Lett 2018; 592:3173-3182. [DOI: 10.1002/1873-3468.13226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Hiroki Tanaka
- Institute for Protein Research Osaka University Suita Japan
| | - Hideo Akutsu
- Institute for Protein Research Osaka University Suita Japan
- Graduate School of Medical Life Science Yokohama City University Tsurumi‐ku Yokohama Japan
| | - Izumi Yabuta
- Institute for Protein Research Osaka University Suita Japan
| | - Masashi Hara
- Department of Applied Biological Chemistry Faculty of Agriculture Niigata University Niigata Japan
| | - Hayuki Sugimoto
- Department of Applied Biological Chemistry Faculty of Agriculture Niigata University Niigata Japan
| | - Takahisa Ikegami
- Institute for Protein Research Osaka University Suita Japan
- Graduate School of Medical Life Science Yokohama City University Tsurumi‐ku Yokohama Japan
| | - Takeshi Watanabe
- Department of Applied Biological Chemistry Faculty of Agriculture Niigata University Niigata Japan
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15
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Zhao J, Yuan S, Gao B, Zhu S. Molecular diversity of fungal inhibitor cystine knot peptides evolved by domain repeat and fusion. FEMS Microbiol Lett 2018; 365:5046422. [PMID: 29961831 DOI: 10.1093/femsle/fny158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 06/26/2018] [Indexed: 12/23/2022] Open
Affiliation(s)
- Jingru Zhao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Shouli Yuan
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
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16
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Casteleijn MG, Richardson D, Parkkila P, Granqvist N, Urtti A, Viitala T. Spin coated chitin films for biosensors and its analysis are dependent on chitin-surface interactions. Colloids Surf A Physicochem Eng Asp 2018. [DOI: 10.1016/j.colsurfa.2017.12.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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17
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Vogt S, Kelkenberg M, Nöll T, Steinhoff B, Schönherr H, Merzendorfer H, Nöll G. Rapid determination of binding parameters of chitin binding domains using chitin-coated quartz crystal microbalance sensor chips. Analyst 2018; 143:5255-5263. [DOI: 10.1039/c8an01453a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Chitin present in fungal cell walls has been considered as a diagnostic polymer for the detection of fungal infections.
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Affiliation(s)
- Stephan Vogt
- Organic Chemistry
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
| | - Marco Kelkenberg
- Molecular Biology
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
| | - Tanja Nöll
- Organic Chemistry
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
| | - Benedikt Steinhoff
- Physical Chemistry I and Research Center of Micro and Nanochemistry and Engineering (Cμ)
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
| | - Holger Schönherr
- Physical Chemistry I and Research Center of Micro and Nanochemistry and Engineering (Cμ)
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
| | - Hans Merzendorfer
- Molecular Biology
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
| | - Gilbert Nöll
- Organic Chemistry
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
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18
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P. Katare D, Malik S, J. Mani R, Ranjpour M, Jain SK. Novel mutations in transthyretin gene associated with hepatocellular carcinoma. Mol Carcinog 2017; 57:70-77. [DOI: 10.1002/mc.22732] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/08/2017] [Accepted: 09/05/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Deepshikha P. Katare
- Proteomics and Translational Research Lab; Centre for Medical Biotechnology; Amity Institute of Biotechnology; Amity University; Noida Uttar Pradesh India
| | - Shabnam Malik
- Faculty of Chemical and Life Sciences; Department of Biotechnology; Hamdard Institute of Medical Sciences and Research; Hamdard University; New Delhi India
| | - Ruchi J. Mani
- Proteomics and Translational Research Lab; Centre for Medical Biotechnology; Amity Institute of Biotechnology; Amity University; Noida Uttar Pradesh India
| | - Maryam Ranjpour
- Faculty of Chemical and Life Sciences; Department of Biotechnology; Hamdard Institute of Medical Sciences and Research; Hamdard University; New Delhi India
| | - Swatantra K. Jain
- Faculty of Chemical and Life Sciences; Department of Biotechnology; Hamdard Institute of Medical Sciences and Research; Hamdard University; New Delhi India
- Department of Medical Biochemistry; Hamdard Institute of Medical Sciences and Research; Hamdard University; New Delhi India
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19
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Weli SC, Dale OB, Hansen H, Gjessing MC, Rønneberg LB, Falk K. A case study of Desmozoon lepeophtherii infection in farmed Atlantic salmon associated with gill disease, peritonitis, intestinal infection, stunted growth, and increased mortality. Parasit Vectors 2017; 10:370. [PMID: 28764744 PMCID: PMC5540559 DOI: 10.1186/s13071-017-2303-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 07/20/2017] [Indexed: 11/25/2022] Open
Abstract
Background In September 2008, a disease outbreak characterized by acute, severe gill pathology and peritonitis, involving the gastrointestinal tract, was observed in an Atlantic salmon (Salmo salar L.) farm in north-western Norway. During subsequent sampling in November 2008 and January 2009, chronic proliferative gill inflammation and peritonitis was observed. Cumulative mortalities of 5.6–12.8% and severe growth retardation were observed. Routine diagnostic analysis revealed no diseases known to salmon at the time, but microsporidian infection of tissues was observed. Methods To characterize the disease outbreak, a combination of histopathology, in situ hybridization (ISH), chitin, calcofluor-white (CFW) staining, and real-time PCR were used to describe the disease progression with visualization of the D. lepeophtherii stages in situ. Results The presence of the microsporidian Desmozoon lepeophtherii was confirmed with real-time PCR, DNA sequencing and ISH, and the parasite was detected in association with acute lesions in the gills and peritoneum. ISH using a probe specific to small subunit 16S rRNA gene provided an effective tool for demonstrating the distribution of D. lepeophtherii in the tissue. Infection in the peritoneum seemed localized in and around pre-existing vaccine granulomas, and in the gastrointestinal walls. In the heart, kidney and spleen, the infection was most often associated with mononuclear leucocytes and macrophages, including melanomacrophages. Desmozoon lepeophtherii exospores were found in the nuclei of the gastrointestinal epithelium for the first time, suggesting a role of the gastrointestinal tract in the spread of spores to the environment. Conclusions This study describes the progression of D. lepeophtherii disease outbreak in an Atlantic salmon farm without any other known diseases present. Using different methods to examine the disease outbreak, new insight into the pathology of D. lepeophtherii was obtained. The parasite was localized in situ in association with severe tissue damage and inflammation in the gills, peritoneal cavity and in the gastrointestinal (GI) tract that links the parasite directly to the observed pathology.
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Affiliation(s)
- Simon Chioma Weli
- Norwegian Veterinary Institute, P.O.Box 750 Dep., N-0106, Oslo, Norway
| | - Ole Bendik Dale
- Norwegian Veterinary Institute, P.O.Box 750 Dep., N-0106, Oslo, Norway.
| | - Haakon Hansen
- Norwegian Veterinary Institute, P.O.Box 750 Dep., N-0106, Oslo, Norway
| | | | - Liv Birte Rønneberg
- Present address: Fiske-liv AS, Marine Harvest Apotekergt. 9A, 6004, Ålesund, Norway
| | - Knut Falk
- Norwegian Veterinary Institute, P.O.Box 750 Dep., N-0106, Oslo, Norway
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20
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Xie Z, Lin W, Luo J. Comparative Phenotype and Genome Analysis of Cellvibrio sp. PR1, a Xylanolytic and Agarolytic Bacterium from the Pearl River. BIOMED RESEARCH INTERNATIONAL 2017; 2017:6304248. [PMID: 28798934 PMCID: PMC5536142 DOI: 10.1155/2017/6304248] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/03/2017] [Accepted: 06/18/2017] [Indexed: 12/29/2022]
Abstract
Cellvibrio sp. PR1 is a xylanolytic and agarolytic bacterium isolated from the Pearl River. Strain PR1 is closely related to Cellvibrio fibrivorans and C. ostraviensis (identity > 98%). The xylanase and agarase contents of strain PR1 reach up to 15.4 and 25.9 U/mL, respectively. The major cellular fatty acids consisted of C16:0 (36.7%), C18:0 (8.8%), C20:0 (6.8%), C15:0 iso 2-OH or/and C16:1ω7c (17.4%), and C18:1ω7c or/and C18:1ω6c (6.7%). A total of 251 CAZyme modules (63 CBMs, 20 CEs, 128 GHs, 38 GTs, and 2 PLs) were identified from 3,730 predicted proteins. Genomic analysis suggested that strain PR1 has a complete xylan-hydrolyzing (5 β-xylanases, 16 β-xylosidases, 17 α-arabinofuranosidases, 9 acetyl xylan esterases, 4 α-glucuronidases, and 2 ferulic acid esterases) and agar-hydrolyzing enzyme system (2 β-agarases and 2 α-neoagarooligosaccharide hydrolases). In addition, the main metabolic pathways of xylose, arabinose, and galactose are established in the genome-wide analysis. This study shows that strain PR1 contains a large number of glycoside hydrolases.
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Affiliation(s)
- Zhangzhang Xie
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, College of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Weitie Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, College of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Jianfei Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, College of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
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21
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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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22
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Identification of Deleterious Mutations in Myostatin Gene of Rohu Carp (Labeo rohita) Using Modeling and Molecular Dynamic Simulation Approaches. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7562368. [PMID: 27019850 PMCID: PMC4785247 DOI: 10.1155/2016/7562368] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 01/13/2016] [Accepted: 01/27/2016] [Indexed: 11/18/2022]
Abstract
The myostatin (MSTN) is a known negative growth regulator of skeletal muscle. The mutated myostatin showed a double-muscular phenotype having a positive significance for the farmed animals. Consequently, adequate information is not available in the teleosts, including farmed rohu carp, Labeo rohita. In the absence of experimental evidence, computational algorithms were utilized in predicting the impact of point mutation of rohu myostatin, especially its structural and functional relationships. The four mutations were generated at different positions (p.D76A, p.Q204P, p.C312Y, and p.D313A) of MSTN protein of rohu. The impacts of each mutant were analyzed using SIFT, I-Mutant 2.0, PANTHER, and PROVEAN, wherein two substitutions (p.D76A and p.Q204P) were predicted as deleterious. The comparative structural analysis of each mutant protein with the native was explored using 3D modeling as well as molecular-dynamic simulation techniques. The simulation showed altered dynamic behaviors concerning RMSD and RMSF, for either p.D76A or p.Q204P substitution, when compared with the native counterpart. Interestingly, incorporated two mutations imposed a significant negative impact on protein structure and stability. The present study provided the first-hand information in identifying possible amino acids, where mutations could be incorporated into MSTN gene of rohu carp including other carps for undertaking further in vivo studies.
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Enhanced resistance to Sclerotinia sclerotiorum in Brassica napus by co-expression of defensin and chimeric chitinase genes. J Appl Genet 2016; 57:417-425. [PMID: 26862081 DOI: 10.1007/s13353-016-0340-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 01/19/2023]
Abstract
Sclerotinia stem rot caused by Sclerotinia sclerotiorum is one of the major fungal diseases of Brassica napus L. To develop resistance against this fungal disease, the defensin gene from Raphanus sativus and chimeric chit42 from Trichoderma atroviride with a C-terminal fused chitin-binding domain from Serratia marcescens were co-expressed in canola via Agrobacterium-mediated transformation. Twenty transformants were confirmed to carry the two transgenes as detected by polymerase chain reaction (PCR), with 4.8 % transformation efficiency. The chitinase activity of PCR-positive transgenic plants were measured in the presence of colloidal chitin, and five transgenic lines showing the highest chitinase activity were selected for checking the copy number of the transgenes through Southern blot hybridisation. Two plants carried a single copy of the transgenes, while the remainder carried either two or three copies of the transgenes. The antifungal activity of two transgenic lines that carried a single copy of the transgenes (T4 and T10) was studied by a radial diffusion assay. It was observed that the constitutive expression of these transgenes in the T4 and T10 transgenic lines suppressed the growth of S. sclerotiorum by 49 % and 47 %, respectively. The two transgenic lines were then let to self-pollinate to produce the T2 generation. Greenhouse bioassays were performed on the transgenic T2 young leaves by challenging with S. sclerotiorum and the results revealed that the expression of defensin and chimeric chitinase from a heterologous source in canola demonstrated enhanced resistance against sclerotinia stem rot disease.
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RASAL KD, CHAKRAPANI V, PATRA SK, JENA S, MOHAPATRA SD, NAYAK S, SUNDARAY JK, JAYASANKAR P, BARMAN HK. Identification and prediction of the consequences of nonsynonymous SNPs in glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene of zebrafish Danio rerio. Turk J Biol 2016. [DOI: 10.3906/biy-1501-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Zhu Y, Ye XH, Liu Y, Yan ZC, Stanley D, Ye GY, Fang Q. A Venom Gland Extracellular Chitin-Binding-Like Protein from Pupal Endoparasitoid Wasps, Pteromalus Puparum, Selectively Binds Chitin. Toxins (Basel) 2015; 7:5098-113. [PMID: 26633500 PMCID: PMC4690117 DOI: 10.3390/toxins7124867] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/12/2015] [Accepted: 11/17/2015] [Indexed: 11/16/2022] Open
Abstract
Chitin-binding proteins (CBPs) are present in many species and they act in a variety of biological processes. We analyzed a Pteromalus puparum venom apparatus proteome and transcriptome and identified a partial gene encoding a possible CBP. Here, we report cloning a full-length cDNA of a sequence encoding a chitin-binding-like protein (PpCBP) from P. puparum, a pupal endoparasitoid of Pieris rapae. The cDNA encoded a 96-amino-acid protein, including a secretory signal peptide and a chitin-binding peritrophin-A domain. Phylogenetic analysis of chitin binding domains (CBDs) of cuticle proteins and peritrophic matrix proteins in selected insects revealed that the CBD of PpCBP clustered with the CBD of Nasonia vitripennis. The PpCBP is specifically expressed in the venom apparatus of P. puparum, mostly in the venom gland. PpCBP expression was highest at day one after adult eclosion and much lower for the following five days. We produced a recombinant PpCBP and binding assays showed the recombinant protein selectively binds chitin but not cellulose in vitro. We infer that PpCBP serves a structural role in the venom reservoir, or may be injected into the host to help wound healing of the host exoskeleton.
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Affiliation(s)
- Yu Zhu
- State Key Laboratory of Rice Biology & Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Xin-Hai Ye
- The College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Yang Liu
- State Key Laboratory of Rice Biology & Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Zhi-Chao Yan
- State Key Laboratory of Rice Biology & Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
| | - David Stanley
- Biological Control of Insects Research Laboratory, USDA/Agricultural Research Service, Columbia, MO 65203, USA.
| | - Gong-Yin Ye
- State Key Laboratory of Rice Biology & Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Qi Fang
- State Key Laboratory of Rice Biology & Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
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Parasuraman P, Murugan V, Selvin JFA, Gromiha MM, Fukui K, Veluraja K. Theoretical investigation on the glycan-binding specificity ofAgrocybe cylindraceagalectin using molecular modeling and molecular dynamics simulation studies. J Mol Recognit 2015; 28:528-38. [DOI: 10.1002/jmr.2468] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/23/2015] [Accepted: 01/23/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Ponnusamy Parasuraman
- Department of Physics; Manonmaniam Sundaranar University; Tirunelveli Tamil Nadu 627012 India
| | - Veeramani Murugan
- Department of Physics; Manonmaniam Sundaranar University; Tirunelveli Tamil Nadu 627012 India
| | | | - M Michael Gromiha
- Department of Biotechnology; Indian Institute of Technology Madras; Chennai Tamil Nadu 600036 India
| | - Kazuhiko Fukui
- Molecular Profiling Research Center for Drug Discovery (molprof); National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7 Aomi Koto-ku Tokyo 135-0064 Japan
| | - Kasinadar Veluraja
- School of Advanced Sciences; VIT University; Vellore Tamil Nadu 632014 India
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Parasuraman P, Murugan V, Selvin JFA, Gromiha MM, Fukui K, Veluraja K. Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2-3)Gal: a study by in silico mutations and molecular dynamics simulations. J Mol Recognit 2015; 27:482-92. [PMID: 24984865 DOI: 10.1002/jmr.2369] [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: 10/23/2013] [Revised: 02/02/2014] [Accepted: 02/02/2014] [Indexed: 02/06/2023]
Abstract
Wheat germ agglutinin (WGA) is a plant lectin, which specifically recognizes the sugars NeuNAc and GlcNAc. Mutated WGA with enhanced binding specificity can be used as biomarkers for cancer. In silico mutations are performed at the active site of WGA to enhance the binding specificity towards sialylglycans, and molecular dynamics simulations of 20 ns are carried out for wild type and mutated WGAs (WGA1, WGA2, and WGA3) in complex with sialylgalactose to examine the change in binding specificity. MD simulations reveal the change in binding specificity of wild type and mutated WGAs towards sialylgalactose and bound conformational flexibility of sialylgalactose. The mutated polar amino acid residues Asn114 (S114N), Lys118 (G118K), and Arg118 (G118R) make direct and water mediated hydrogen bonds and hydrophobic interactions with sialylgalactose. An analysis of possible hydrogen bonds, hydrophobic interactions, total pair wise interaction energy between active site residues and sialylgalactose and MM-PBSA free energy calculation reveals the plausible binding modes and the role of water in stabilizing different binding modes. An interesting observation is that the binding specificity of mutated WGAs (cyborg lectin) towards sialylgalactose is found to be higher in double point mutation (WGA3). One of the substituted residues Arg118 plays a crucial role in sugar binding. Based on the interactions and energy calculations, it is concluded that the order of binding specificity of WGAs towards sialylgalactose is WGA3 > WGA1 > WGA2 > WGA. On comparing with the wild type, double point mutated WGA (WGA3) exhibits increased specificity towards sialylgalactose, and thus, it can be effectively used in targeted drug delivery and as biological cell marker in cancer therapeutics.
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Affiliation(s)
- Ponnusamy Parasuraman
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, 627 012, India
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Computational Approaches and Resources in Single Amino Acid Substitutions Analysis Toward Clinical Research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 94:365-423. [DOI: 10.1016/b978-0-12-800168-4.00010-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Kowsari M, Motallebi M, Zamani M. Protein engineering of chit42 towards improvement of chitinase and antifungal activities. Curr Microbiol 2013; 68:495-502. [PMID: 24322404 DOI: 10.1007/s00284-013-0494-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 10/15/2013] [Indexed: 01/29/2023]
Abstract
The antagonism of Trichoderma strains usually correlates with the secretion of fungal cell wall degrading enzymes such as chitinases. Chitinase Chit42 is believed to play an important role in the biocontrol activity of Trichoderma strains as a biocontrol agent against phytopathogenic fungi. Chit42 lacks a chitin-binding domain (ChBD) which is involved in its binding activity to insoluble chitin. In this study, a chimeric chitinase with improved enzyme activity was produced by fusing a ChBD from T. atroviride chitinase 18-10 to Chit42. The improved chitinase containing a ChBD displayed a 1.7-fold higher specific activity than chit42. This increase suggests that the ChBD provides a strong binding capacity to insoluble chitin. Moreover, Chit42-ChBD transformants showed higher antifungal activity towards seven phytopathogenic fungal species.
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Affiliation(s)
- Mojegan Kowsari
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, km 15, Tehran - Karaj Highway, P.O. Box 14965-161, Tehran, Iran,
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Wang C, Kittle JD, Qian C, Roman M, Esker AR. Chitinase Activity on Amorphous Chitin Thin Films: A Quartz Crystal Microbalance with Dissipation Monitoring and Atomic Force Microscopy Study. Biomacromolecules 2013; 14:2622-8. [DOI: 10.1021/bm4004833] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chao Wang
- Department
of Chemistry and ‡Department of Sustainable Biomaterials, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Joshua D. Kittle
- Department
of Chemistry and ‡Department of Sustainable Biomaterials, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Chen Qian
- Department
of Chemistry and ‡Department of Sustainable Biomaterials, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Maren Roman
- Department
of Chemistry and ‡Department of Sustainable Biomaterials, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Alan R. Esker
- Department
of Chemistry and ‡Department of Sustainable Biomaterials, Virginia Tech, Blacksburg, Virginia 24061, United States
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Lobo MDP, Silva FDA, Landim PGDC, da Cruz PR, de Brito TL, de Medeiros SC, Oliveira JTA, Vasconcelos IM, Pereira HD, Grangeiro TB. Expression and efficient secretion of a functional chitinase from Chromobacterium violaceum in Escherichia coli. BMC Biotechnol 2013; 13:46. [PMID: 23725035 PMCID: PMC3701571 DOI: 10.1186/1472-6750-13-46] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 05/17/2013] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Chromobacterium violaceum is a free-living β-proteobacterium found in tropical and subtropical regions. The genomic sequencing of C. violaceum ATCC 12472 has revealed many genes that underpin its adaptability to diverse ecosystems. Moreover, C. violaceum genes with potential applications in industry, medicine and agriculture have also been identified, such as those encoding chitinases. However, none of the chitinase genes of the ATCC 12472 strain have been subjected to experimental validation. Chitinases (EC 3.2.1.14) hydrolyze the β-(1,4) linkages in chitin, an abundant biopolymer found in arthropods, mollusks and fungi. These enzymes are of great biotechnological interest as potential biocontrol agents against pests and pathogens. This work aimed to experimentally validate one of the chitinases from C. violaceum. RESULTS The open reading frame (ORF) CV2935 of C. violaceum ATCC 12472 encodes a protein (439 residues) that is composed of a signal peptide, a chitin-binding domain, a linker region, and a C-terminal catalytic domain belonging to family 18 of the glycoside hydrolases. The ORF was amplified by PCR and cloned into the expression vector pET303/CT-His. High levels of chitinolytic activity were detected in the cell-free culture supernatant of E. coli BL21(DE3) cells harboring the recombinant plasmid and induced with IPTG. The secreted recombinant protein was purified by affinity chromatography on a chitin matrix and showed an apparent molecular mass of 43.8 kDa, as estimated by denaturing polyacrylamide gel electrophoresis. N-terminal sequencing confirmed the proper removal of the native signal peptide during the secretion of the recombinant product. The enzyme was able to hydrolyze colloidal chitin and the synthetic substrates p-nitrophenyl-β-D-N,N'-diacetylchitobiose and p-nitrophenyl-β-D-N,N',N"-triacetylchitotriose. The optimum pH for its activity was 5.0, and the enzyme retained ~32% of its activity when heated to 60°C for 30 min. CONCLUSIONS A C. violaceum chitinase was expressed in E. coli and purified by affinity chromatography on a chitin matrix. The secretion of the recombinant protein into the culture medium was directed by its native signal peptide. The mature enzyme was able to hydrolyze colloidal chitin and synthetic substrates. This newly identified signal peptide is a promising secretion factor that should be further investigated in future studies, aiming to demonstrate its usefulness as an alternative tool for the extracellular production of recombinant proteins in E. coli.
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Affiliation(s)
- Marina Duarte Pinto Lobo
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE CEP 60.455-970, Brazil
| | - Fredy Davi Albuquerque Silva
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE CEP 60.455-970, Brazil
| | | | | | - Thaís Lima de Brito
- Departamento de Biologia, UFC, Laboratório de Genética Molecular, Fortaleza, CE, Brazil
| | | | - José Tadeu Abreu Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE CEP 60.455-970, Brazil
| | - Ilka Maria Vasconcelos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE CEP 60.455-970, Brazil
| | - Humberto D’Muniz Pereira
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Sãocarlense, 400, São Carlos, SP CEP 13.566-590, Brazil
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Hara M, Sugimoto H, Uemura M, Akagi KI, Suzuki K, Ikegami T, Watanabe T. Involvement of Gln679, in addition to Trp687, in chitin-binding activity of the chitin-binding domain of chitinase A1 from Bacillus circulans WL-12. J Biochem 2013; 154:185-93. [DOI: 10.1093/jb/mvt043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Designing a new chitinase with more chitin binding and antifungal activity. World J Microbiol Biotechnol 2013; 29:1517-23. [DOI: 10.1007/s11274-013-1318-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 03/12/2013] [Indexed: 10/27/2022]
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Abraham A, Narayanan SP, Philip S, Nair DG, Chandrasekharan A, Kochupurackal J. In silico characterization of a novel β-1,3-glucanase gene from Bacillus amyloliquefaciens--a bacterial endophyte of Hevea brasiliensis antagonistic to Phytophthora meadii. J Mol Model 2012; 19:999-1007. [PMID: 23108702 DOI: 10.1007/s00894-012-1645-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/11/2012] [Indexed: 11/25/2022]
Abstract
We report the molecular characterization of β-1,3-glucanase-producing Bacillus amyloliquefaciens-an endophyte of Hevea brasiliensis antagonistic to Phytophthora meadii. After cloning and sequencing, the β-1,3-glucanase gene was found to be 747 bp in length. A homology model of the β-1,3-glucanase protein was built from the amino acid sequence obtained upon translation of the gene. The target β-1,3-glucanase protein and the template protein, endo β-1,3-1,4-glucanase protein (PDB ID: 3o5s), were found to share 94% sequence identity and to have similar secondary and tertiary structures. In the modeled structure, three residues in the active site region of the template-Asn52, Ile157 and Val158-were substituted with Asp, Leu and Ala, respectively. Computer-aided docking studies of the substrate disaccharide (β-1, 3-glucan) with the target as well as with the template proteins showed that the two protein-substrate complexes were stabilized by three hydrogen bonds and by many van der Waals interactions. Although the binding energies and the number of hydrogen bonds were the same in both complexes, the orientations of the substrate in the active sites of the two proteins were different. These variations might be due to the change in the three amino acids in the active site region of the two proteins. The difference in substrate orientation in the active site could also affect the catalytic potential of the β-1,3 glucanase enzyme.
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Affiliation(s)
- Amith Abraham
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, India
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Synthesis of long-chain chitooligosaccharides by a hypertransglycosylating processive endochitinase of Serratia proteamaculans 568. J Bacteriol 2012; 194:4260-71. [PMID: 22685288 DOI: 10.1128/jb.06473-11] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe the heterologous expression and characterization of a 407-residue single-domain glycosyl hydrolase family 18 chitinase (SpChiD) from Gram-negative Serratia proteamaculans 568 that has unprecedented catalytic properties. SpChiD was optimally active at pH 6.0 and 40 °C, where it showed a K(m) of 83 mg ml(-1), a k(cat) of 3.9 × 10(2) h(-1), and a k(cat)/K(m) of 4.7 h mg(-1) ml(-1) on colloidal chitin. On chitobiose, the K(m), k(cat), and k(cat)/K(m) were 203 μM, 1.3 × 10(2) h(-1), and 0.62 h(-1) μM(-1), respectively. Hydrolytic activity on chitooligosaccharides (CHOS) and colloidal chitin indicated that SpChiD was an endo-acting processive enzyme, with the unique ability to convert released chitobiose to N-acetylglucosamine, the major end product. SpChiD showed hyper transglycosylation (TG) with trimer-hexamer CHOS substrates, generating considerable amounts of long-chain CHOS. The TG activity of SpChiD was dependent on both the length and concentration of the oligomeric substrate and also on the enzyme concentration. The length and amount of accumulated TG products increased with increases in the length of the substrate and its concentration and decreased with increases in the enzyme concentration. The SpChiD bound to insoluble and soluble chitin substrates despite the absence of accessory domains. Sequence alignments and structural modeling indicated that SpChiD would have a deep substrate-binding groove lined with aromatic residues, which is characteristic of processive enzymes. SpChiD shows a combination of properties that seems rare among family 18 chitinases and that may resemble the properties of human chitotriosidase.
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Park JK, Choi DJ, Kim SM, Choi HN, Park JW, Jang SJ, Choo YK, Lee CG, Park YI. Purification and characterization of a polysialic acid-specific sialidase from Pseudomonas fluorescens JK-0412. BIOTECHNOL BIOPROC E 2012. [DOI: 10.1007/s12257-011-0495-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Purushotham P, Arun PVPS, Prakash JSS, Podile AR. Chitin binding proteins act synergistically with chitinases in Serratia proteamaculans 568. PLoS One 2012; 7:e36714. [PMID: 22590591 PMCID: PMC3348882 DOI: 10.1371/journal.pone.0036714] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 04/12/2012] [Indexed: 12/02/2022] Open
Abstract
Genome sequence of Serratia proteamaculans 568 revealed the presence of three family 33 chitin binding proteins (CBPs). The three Sp CBPs (Sp CBP21, Sp CBP28 and Sp CBP50) were heterologously expressed and purified. Sp CBP21 and Sp CBP50 showed binding preference to β-chitin, while Sp CBP28 did not bind to chitin and cellulose substrates. Both Sp CBP21 and Sp CBP50 were synergistic with four chitinases from S. proteamaculans 568 (Sp ChiA, Sp ChiB, Sp ChiC and Sp ChiD) in degradation of α- and β-chitin, especially in the presence of external electron donor (reduced glutathione). Sp ChiD benefited most from Sp CBP21 or Sp CBP50 on α-chitin, while Sp ChiB and Sp ChiD had major advantage with these Sp CBPs on β-chitin. Dose responsive studies indicated that both the Sp CBPs exhibit synergism ≥0.2 µM. The addition of both Sp CBP21 and Sp CBP50 in different ratios to a synergistic mixture did not significantly increase the activity. Highly conserved polar residues, important in binding and activity of CBP21 from S. marcescens (Sm CBP21), were present in Sp CBP21 and Sp CBP50, while Sp CBP28 had only one such polar residue. The inability of Sp CBP28 to bind to the test substrates could be attributed to the absence of important polar residues.
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Affiliation(s)
- Pallinti Purushotham
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - P. V. Parvati Sai Arun
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Jogadhenu S. S. Prakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Appa Rao Podile
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
- * E-mail:
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Purushotham P, Sarma PVSRN, Podile AR. Multiple chitinases of an endophytic Serratia proteamaculans 568 generate chitin oligomers. BIORESOURCE TECHNOLOGY 2012; 112:261-269. [PMID: 22406064 DOI: 10.1016/j.biortech.2012.02.062] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 02/10/2012] [Accepted: 02/13/2012] [Indexed: 05/31/2023]
Abstract
Serratia proteamaculans 568 genome revealed the presence of four family 18 chitinases (Sp ChiA, Sp ChiB, Sp ChiC, and Sp ChiD). Heterologous expression and characterization of Sp ChiA, Sp ChiB, and Sp ChiC showed that these enzymes were optimally active at pH 6.0-7.0, and 40°C. The three Sp chitinases displayed highest activity/binding to β-chitin and showed broad range of substrate specificities, and released dimer as major end product from oligomeric and polymeric substrates. Longer incubation was required for hydrolysis of trimer for the three Sp chitinases. The three Sp chitinases released up to tetramers from colloidal chitin substrate. Sp ChiA and Sp ChiB were processive chitinases, while Sp ChiC was a non-processive chitinase. Based on the known structures of ChiA and ChiB from S. marcescens, 3D models of Sp ChiA and Sp ChiB were generated.
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Affiliation(s)
- Pallinti Purushotham
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad-500 046, India
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Analyzing effects of naturally occurring missense mutations. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2012; 2012:805827. [PMID: 22577471 PMCID: PMC3346971 DOI: 10.1155/2012/805827] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/01/2012] [Accepted: 02/01/2012] [Indexed: 11/17/2022]
Abstract
Single-point mutation in genome, for example, single-nucleotide polymorphism (SNP) or rare genetic mutation, is the change of a single nucleotide for another in the genome sequence. Some of them will produce an amino acid substitution in the corresponding protein sequence (missense mutations); others will not. This paper focuses on genetic mutations resulting in a change in the amino acid sequence of the corresponding protein and how to assess their effects on protein wild-type characteristics. The existing methods and approaches for predicting the effects of mutation on protein stability, structure, and dynamics are outlined and discussed with respect to their underlying principles. Available resources, either as stand-alone applications or webservers, are pointed out as well. It is emphasized that understanding the molecular mechanisms behind these effects due to these missense mutations is of critical importance for detecting disease-causing mutations. The paper provides several examples of the application of 3D structure-based methods to model the effects of protein stability and protein-protein interactions caused by missense mutations as well.
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Fusion of a novel genetically engineered chitosan affinity protein and green fluorescent protein for specific detection of chitosan in vitro and in situ. Appl Environ Microbiol 2012; 78:3114-9. [PMID: 22367086 DOI: 10.1128/aem.07506-11] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chitin is the second most abundant polysaccharide, present, e.g., in insect and arthropod exoskeletons and fungal cell walls. In some species or under specific conditions, chitin appears to be enzymatically de-N-acetylated to chitosan-e.g., when pathogenic fungi invade their host tissues. Here, the deacetylation of chitin is assumed to represent a pathogenicity mechanism protecting the fungus from the host's chitin-driven immune response. While highly specific chitin binding lectins are well known and easily available, this is not the case for chitosan-specific probes. This is partly due to the poor antigenicity of chitosan so that producing high-affinity, specific antibodies is difficult. Also, lectins with specificity to chitosan have been described but are not commercially available, and our attempts to reproduce the findings were not successful. We have, therefore, generated a fusion protein between a chitosanase inactivated by site-directed mutagenesis, the green fluorescent protein (GFP), and StrepII, as well as His(6) tags for purification and detection. The recombinant chitosan affinity protein (CAP) expressed in Escherichia coli was shown to specifically bind to chitosan, but not to chitin, and the affinity increased with decreasing degree of acetylation. In vitro, CAP detection was possible either based on GFP fluorescence or using Strep-Tactin conjugates or anti-His(5) antibodies. CAP fluorescence microscopy revealed binding to the chitosan exposing endophytic infection structures of the wheat stem rust fungus, but not the chitin exposing ectophytic infection structures, verifying its suitability for in situ chitosan staining.
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41
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Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res 2011; 39:e118. [PMID: 21727090 PMCID: PMC3177186 DOI: 10.1093/nar/gkr407] [Citation(s) in RCA: 1414] [Impact Index Per Article: 108.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
As large-scale re-sequencing of genomes reveals many protein mutations, especially in human cancer tissues, prediction of their likely functional impact becomes important practical goal. Here, we introduce a new functional impact score (FIS) for amino acid residue changes using evolutionary conservation patterns. The information in these patterns is derived from aligned families and sub-families of sequence homologs within and between species using combinatorial entropy formalism. The score performs well on a large set of human protein mutations in separating disease-associated variants (∼19 200), assumed to be strongly functional, from common polymorphisms (∼35 600), assumed to be weakly functional (area under the receiver operating characteristic curve of ∼0.86). In cancer, using recurrence, multiplicity and annotation for ∼10 000 mutations in the COSMIC database, the method does well in assigning higher scores to more likely functional mutations ('drivers'). To guide experimental prioritization, we report a list of about 1000 top human cancer genes frequently mutated in one or more cancer types ranked by likely functional impact; and, an additional 1000 candidate cancer genes with rare but likely functional mutations. In addition, we estimate that at least 5% of cancer-relevant mutations involve switch of function, rather than simply loss or gain of function.
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Affiliation(s)
- Boris Reva
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, NY 10065, USA
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42
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Heath-Heckman EAC, McFall-Ngai MJ. The occurrence of chitin in the hemocytes of invertebrates. ZOOLOGY 2011; 114:191-8. [PMID: 21723107 DOI: 10.1016/j.zool.2011.02.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 02/10/2011] [Accepted: 02/11/2011] [Indexed: 10/18/2022]
Abstract
The light-organ symbiosis of Euprymna scolopes, the Hawaiian bobtail squid, is a useful model for the study of animal-microbe interactions. Recent analyses have demonstrated that chitin breakdown products play a role in communication between E. scolopes and its bacterial symbiont Vibrio fischeri. In this study, we sought to determine the source of chitin in the symbiotic organ. We used a commercially available chitin-binding protein (CBP) conjugated to fluorescein to label the polymeric chitin in host tissues. Confocal microscopy revealed that the only cells in contact with the symbionts that labeled with the probe were the macrophage-like hemocytes, which traffic into the light-organ crypts where the bacteria reside. Labeling of extracted hemocytes by CBP was markedly decreased following treatment with purified chitinase, providing further evidence that the labeled molecule is polymeric chitin. Further, CBP-positive areas co-localized with both a halide peroxidase antibody and Lysotracker, a lysosomal marker, suggesting that the chitin-like biomolecule occurs in the lysosome or acidic vacuoles. Reverse transcriptase polymerase chain reaction (PCR) of hemocytes revealed mRNA coding for a chitin synthase, suggesting that the hemocytes synthesize chitin de novo. Finally, upon surveying blood cells from other invertebrate species, we observed CBP-positive regions in all granular blood cells examined, suggesting that this feature is a shared character among the invertebrates; the vertebrate blood cells that we sampled did not label with CBP. Although the function of the chitin-like material remains undetermined, its presence and subcellular location in invertebrate hemocytes suggests a conserved role for this polysaccharide in the immune system of diverse animals.
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Neeraja C, Anil K, Purushotham P, Suma K, Sarma P, Moerschbacher BM, Podile AR. Biotechnological approaches to develop bacterial chitinases as a bioshield against fungal diseases of plants. Crit Rev Biotechnol 2010; 30:231-41. [PMID: 20572789 DOI: 10.3109/07388551.2010.487258] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Fungal diseases of plants continue to contribute to heavy crop losses in spite of the best control efforts of plant pathologists. Breeding for disease-resistant varieties and the application of synthetic chemical fungicides are the most widely accepted approaches in plant disease management. An alternative approach to avoid the undesired effects of chemical control could be biological control using antifungal bacteria that exhibit a direct action against fungal pathogens. Several biocontrol agents, with specific fungal targets, have been registered and released in the commercial market with different fungal pathogens as targets. However, these have not yet achieved their full commercial potential due to the inherent limitations in the use of living organisms, such as relatively short shelf life of the products and inconsistent performance in the field. Different mechanisms of action have been identified in microbial biocontrol of fungal plant diseases including competition for space or nutrients, production of antifungal metabolites, and secretion of hydrolytic enzymes such as chitinases and glucanases. This review focuses on the bacterial chitinases that hydrolyze the chitinous fungal cell wall, which is the most important targeted structural component of fungal pathogens. The application of the hydrolytic enzyme preparations, devoid of live bacteria, could be more efficacious in fungal control strategies. This approach, however, is still in its infancy, due to prohibitive production costs. Here, we critically examine available sources of bacterial chitinases and the approaches to improve enzymatic properties using biotechnological tools. We project that the combination of microbial and recombinant DNA technologies will yield more effective environment-friendly products of bacterial chitinases to control fungal diseases of crops.
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Affiliation(s)
- Chilukoti Neeraja
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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44
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Khoushab F, Yamabhai M. Chitin research revisited. Mar Drugs 2010; 8:1988-2012. [PMID: 20714419 PMCID: PMC2920538 DOI: 10.3390/md8071988] [Citation(s) in RCA: 216] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2010] [Revised: 05/24/2010] [Accepted: 05/08/2010] [Indexed: 12/22/2022] Open
Abstract
Two centuries after the discovery of chitin, it is widely accepted that this biopolymer is an important biomaterial in many aspects. Numerous studies on chitin have focused on its biomedical applications. In this review, various aspects of chitin research including sources, structure, biosynthesis, chitinolytic enzyme, chitin binding protein, genetic engineering approach to produce chitin, chitin and evolution, and a wide range of applications in bio- and nanotechnology will be dealt with.
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Affiliation(s)
- Feisal Khoushab
- School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand; E-Mail:
| | - Montarop Yamabhai
- School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand; E-Mail:
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Molecular characterization of an endochitinase from Bacillus thuringiensis subsp. konkukian. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0401-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Iizasa E, Mitsutomi M, Nagano Y. Direct binding of a plant LysM receptor-like kinase, LysM RLK1/CERK1, to chitin in vitro. J Biol Chem 2010; 285:2996-3004. [PMID: 19951949 PMCID: PMC2823440 DOI: 10.1074/jbc.m109.027540] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 11/19/2009] [Indexed: 11/06/2022] Open
Abstract
Plants induce immune responses against fungal pathogens by recognition of chitin, which is a component of the fungal cell wall. Recent studies have revealed that LysM receptor-like kinase 1/chitin elicitor receptor kinase 1 (LysM RLK1/CERK1) is a critical component for the immune responses to chitin in Arabidopsis thaliana. However, the molecular mechanism of the chitin recognition by LysM RLK1 still remains unknown. Here, we present the first evidence for direct binding of LysM RLK1 to chitin. We expressed LysM RLK1 fused with yeast-enhanced green fluorescent protein (LysM RLK1-yEGFP) in yeast cells. Binding studies using the solubilized LysM RLK1-yEGFP and several insoluble polysaccharides having similar structures showed that LysM RLK1-yEGFP specifically binds to chitin. Subsequently, the fluorescence microscopic observation of the solubilized LysM RLK1-yEGFP binding to chitin beads revealed that the binding was saturable and had a high affinity, with a K(d) of approximately 82 nm. This binding was competed by the addition of soluble glycol chitin or high concentration of chitin oligosaccharides having 4-8 residues of N-acetyl glucosamine. However, the competition of these chitin oligosaccharides is weaker than that of glycol chitin. These data suggest that LysM RLK1 has a higher affinity for chitin having a longer residue of N-acetyl glucosamine. We also found that LysM RLK1-yEGFP was autophosphorylated in vitro and that chitin does not affect the phosphorylation of LysM RLK1-yEGFP. Our results provide a new dimension to chitin elicitor perception in plants.
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Affiliation(s)
- Ei'ichi Iizasa
- From the Analytical Research Center for Experimental Sciences and
- the United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
| | - Masaru Mitsutomi
- the Department of Applied Biochemistry and Food Science, Saga University, 1 Honjo-machi, Saga 840-8502 and
- the United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
| | - Yukio Nagano
- From the Analytical Research Center for Experimental Sciences and
- the United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
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Mehmood MA, Xiao X, Hafeez FY, Gai Y, Wang F. Purification and characterization of a chitinase from Serratia proteamaculans. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0094-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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48
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Kurek DV, Lopatin SA, Varlamov VP. Prospects of application of the chitin-binding domains to isolation and purification of recombinant proteins by affinity chromatography. APPL BIOCHEM MICRO+ 2009. [DOI: 10.1134/s0003683809010013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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49
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Molecular and Biochemical Characterization of an Endochitinase (ChiA-HD73) from Bacillus thuringiensis subsp. kurstaki HD-73. Mol Biotechnol 2007; 39:29-37. [DOI: 10.1007/s12033-007-9025-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Accepted: 11/21/2007] [Indexed: 10/22/2022]
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50
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Fazelinia H, Cirino PC, Maranas CD. Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity. Biophys J 2007; 92:2120-30. [PMID: 17208966 PMCID: PMC1861794 DOI: 10.1529/biophysj.106.096016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this article we extend the Iterative Protein Redesign and Optimization (IPRO) framework for the design of protein libraries with targeted ligand specificity. Mutations that minimize the binding energy with the desired ligand are identified. At the same time explicit constraints are introduced that maintain the binding energy for all decoy ligands above a threshold necessary for successful binding. The proposed framework is demonstrated by computationally altering the effector binding specificity of the bacterial transcriptional regulatory protein AraC, belonging to the AraC/XylS family of transcriptional regulators for different unnatural ligands. The obtained results demonstrate the importance of systematically suppressing the binding energy for competing ligands. Pinpointing a small set of mutations within the binding pocket greatly improves the difference in binding energies between targeted and decoy ligands, even when they are very similar.
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Affiliation(s)
- Hossein Fazelinia
- Department of Chemical Engineering, 112A Fenske Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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