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Hu R, Liu S, Huang W, Nan Q, Strong PJ, Saleem M, Zhou Z, Luo Z, Shu F, Yan Q, He Z, Wang C. Evidence for Assimilatory Nitrate Reduction as a Previously Overlooked Pathway of Reactive Nitrogen Transformation in Estuarine Suspended Particulate Matter. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14852-14866. [PMID: 36098560 DOI: 10.1021/acs.est.2c04390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Suspended particulate matter (SPM) contributes to the loss of reactive nitrogen (Nr) in estuarine ecosystems. Although denitrification and anaerobic ammonium oxidation in SPM compensate for the current imbalance of global nitrogen (N) inputs and sinks, it is largely unclear whether other pathways for Nr transformation exist in SPM. Here, we combined stable isotope measurements with metagenomics and metatranscriptomics to verify the occurrence of dissimilatory nitrate reduction to ammonium (DNRA) in the SPM of the Pearl River Estuary (PRE). Surprisingly, the conventional functional genes of DNRA (nirBD) were abundant and highly expressed in SPM, which was inconsistent with a low potential rate. Through taxonomic and comparative genomic analyses, we demonstrated that nitrite reductase (NirBD) in conjunction with assimilatory nitrate reductase (NasA) performed assimilatory nitrate reduction (ANR) in SPM, and diverse alpha- and gamma-proteobacterial lineages were identified as key active heterotrophic ANR bacteria. Moreover, ANR was predicted to have a relative higher occurrence than denitrification and DNRA in a survey of Nr transformation pathways in SPM across the PRE spanning 65 km. Collectively, this study characterizes a previously overlooked pathway of Nr transformation mediated by heterotrophic ANR bacteria in SPM and has important implications for our understanding of N cycling in estuaries.
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Affiliation(s)
- Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510006, China
| | - Songfeng Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510006, China
| | - Weiming Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510006, China
| | - Qiong Nan
- Max Planck Institute for Marine Microbiology, 28359Bremen, Germany
- Institute of Environmental Science and Technology, College of Environment and Resource Science, Zhejiang University, Hangzhou310029, PR China
| | - P J Strong
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy.Queensland University of Technology, BrisbaneQLD 4001, Australia
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, Alabama36104, United States
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510006, China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510006, China
| | - Fangqi Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510006, China
- College of Agronomy, Hunan Agricultural University, Changsha410128, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510006, China
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Guerra V, Tiago I, Aires A, Coelho C, Nunes J, Martins LO, Veríssimo A. The gastrointestinal microbiome of browsing goats (Capra hircus). PLoS One 2022; 17:e0276262. [PMID: 36251671 PMCID: PMC9576075 DOI: 10.1371/journal.pone.0276262] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/04/2022] [Indexed: 11/25/2022] Open
Abstract
Despite the growing interest in the ruminants' gastrointestinal tract (GIT) microbiomes' ability to degrade plant materials by animal husbandry and industrial sectors, only a few studies addressed browsing ruminants. The present work describes the taxonomic and functional profile of the bacterial and archaeal communities from five different gastrointestinal sections (rumen, omasum-abomasum, jejunum, cecum and colon) of browsing Capra hircus, by metabarcoding using 16S rRNA genes hypervariable regions. The bacterial communities across the GITs are mainly composed of Bacillota and Bacteroidota. Prevotella was the leading bacterial group found in the stomachs, Romboutsia in the jejuna, and Rikenellaceae_RC9_gut_group, Bacteroides, UCG-010_ge, UCG-005, and Alistipes in large intestines. The archaeal communities in the stomachs and jejuna revealed to be mainly composed of Methanobrevibacter, while in the large intestines its dominance is shared with Methanocorpusculum. Across the GITs, the main metabolic functions were related to carbohydrate, amino acid, and energy metabolisms. Significant differences in the composition and potential biological functions of the bacterial communities were observed among stomachs, jejuna and large intestines. In contrast, significant differences were observed among stomachs and jejuna verse large intestines for archaeal communities. Overall different regions of the GIT are occupied by different microbial communities performing distinct biological functions. A high variety of glycoside hydrolases (GHs) indispensable for degrading plant cell wall materials were predicted to be present in all the GIT sections.
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Affiliation(s)
- Vera Guerra
- Department of Life Sciences, Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Centre Bio R&D Unit, Association BLC3—Technology and Innovation Campus, Lagares da Beira, Oliveira do Hospital, Portugal
| | - Igor Tiago
- Department of Life Sciences, Centre for Functional Ecology–Science for People and the Planet, University of Coimbra, Coimbra, Portugal
| | - Aitana Aires
- Department of Life Sciences, Centre for Functional Ecology–Science for People and the Planet, University of Coimbra, Coimbra, Portugal
- FitoLab, Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra, Portugal
| | - Catarina Coelho
- Department of Life Sciences, Centre for Functional Ecology–Science for People and the Planet, University of Coimbra, Coimbra, Portugal
| | - João Nunes
- Centre Bio R&D Unit, Association BLC3—Technology and Innovation Campus, Lagares da Beira, Oliveira do Hospital, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia e Química Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - António Veríssimo
- Department of Life Sciences, Centre for Functional Ecology–Science for People and the Planet, University of Coimbra, Coimbra, Portugal
- * E-mail:
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Chemo-Enzymatic Production of 4-Nitrophenyl-2-acetamido-2-deoxy-α-D-galactopyranoside Using Immobilized β-N-Acetylhexosaminidase. Catalysts 2022. [DOI: 10.3390/catal12050474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
α-Nitrophenyl derivatives of glycosides are convenient substrates used to detect and characterize α-N-acetylgalactosaminidase. A new procedure combining chemical and biocatalytic steps was developed to prepare 4-nitrophenyl-2-acetamido-2-deoxy-α-D-galactopyranoside (4NP-α-GalNAc). The α-anomer was prepared through chemical synthesis of an anomeric mixture followed by selective removal of the β-anomer using specific enzymatic hydrolysis. Fungal β-N-acetylhexosaminidase (Hex) from Penicillium oxalicum CCF 1959 served this purpose owing to its high chemo-and regioselectivity towards the β-anomeric N-acetylgalactosamine (GalNAc) derivative. The kinetic measurements of the hydrolytic reaction showed that the enzyme was not inhibited by the substrate or reaction products. The immobilization of Hex in lens-shaped polyvinyl alcohol hydrogel capsules provided a biocatalyst with very good storage and operational stability. The immobilized Hex retained 97% of the initial activity after ten repeated uses and 90% of the initial activity after 18 months of storage at 4 °C. Immobilization inactivated 65% of the enzyme activity. However, the effectiveness factor and kinetic and mass transfer phenomena approached unity indicating negligible mass transfer limitations.
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Peat-Inhabiting Verrucomicrobia of the Order Methylacidiphilales Do Not Possess Methanotrophic Capabilities. Microorganisms 2021; 9:microorganisms9122566. [PMID: 34946166 PMCID: PMC8706344 DOI: 10.3390/microorganisms9122566] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 01/04/2023] Open
Abstract
Methanotrophic verrucomicrobia of the order Methylacidiphilales are known as extremely acidophilic, thermophilic or mesophilic bacteria that inhabit acidic geothermal ecosystems. The occurrence of verrucomicrobial methanotrophs in other types of acidic environments remains an open question. Notably, Methylacidiphilales-affiliated 16S rRNA gene sequences are commonly retrieved from acidic (pH 3.5–5.5) peatlands. In this study, we compared the patterns of verrucomicrobial diversity in four acidic raised bogs and six neutral fens located in European North Russia. Methylacidiphilales-like 16S rRNA gene reads displaying 83–86% similarity to 16S rRNA gene sequences of currently described verrucomicrobial methanotrophs were recovered exclusively from raised bogs. Laboratory incubation of peat samples with 10% methane for 3 weeks resulted in the pronounced increase of a relative abundance of alphaproteobacterial methanotrophs, while no response was detected for Methylacidiphilales-affiliated bacteria. Three metagenome-assembled genomes (MAGs) of peat-inhabiting Methylacidiphilales bacteria were reconstructed and examined for the presence of genes encoding methane monooxygenase enzymes and autotrophic carbon fixation pathways. None of these genomic determinants were detected in assembled MAGs. Metabolic reconstructions predicted a heterotrophic metabolism, with a potential to hydrolyze several plant-derived polysaccharides. As suggested by our analysis, peat-inhabiting representatives of the Methylacidiphilales are acidophilic aerobic heterotrophs, which comprise a sister family of the methanotrophic Methylacidiphilaceae.
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Muccee F, Ejaz S, Riaz N, Iqbal J. Molecular and functional analysis of naphthalene-degrading bacteria isolated from the effluents of indigenous tanneries. J Basic Microbiol 2021; 61:627-641. [PMID: 34197651 DOI: 10.1002/jobm.202100123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/10/2021] [Accepted: 05/23/2021] [Indexed: 11/06/2022]
Abstract
During present study, four naphthalene- metabolizing bacteria were isolated from tanneries effluents through enrichment on naphthalene as sole carbon source in minimal salt medium. The bacteria were analyzed to document growth pattern, naphthalene removal efficiency, biochemical and molecular characteristics, antibiotic sensitivity, and metabolic profile. The 16S ribosomal RNA gene sequences were compared through BLAST (basic local alignment search tool) similarity search tool and three isolates were found homologous to Brevibacillus agri strain NBRC 15538 and one similar to Burkholderia lata strain 383. The naphthalene removal efficiencies ranged from 1.16 ± 0.056 mg/h (IUBN1) to 1.379 ± 0.021 mg/h (IUBN26). All isolates were positive for p-nitrophenyl phosphate (PO4 ), esculin, and inulin fermentation tests. Majority were positive for glucosaminidase (IUBN3, 17, and 26) and a few for mannitol and sorbitol fermentation (IUBN1). Identification of metabolites through gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry analysis allowed tracing pathways associated with naphthalene degradation. Intermediates such as cis-dihydrodiolnaphthalene, 2-hydroxychromene-2-carboxylate, 6-hydroxyhexanoic acid, acetyl-CoA confirmed that the present study bacteria can metabolize naphthalene through a pathway which differs from the pathways reported in earlier known bacteria. Due to fast growth rates, high naphthalene removal potentials, and multiple degradation pathways, these bacteria can be exploited for bioremediation of naphthalene.
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Affiliation(s)
- Fatima Muccee
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Samina Ejaz
- Department of Biochemistry, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Naheed Riaz
- Institute of Chemistry, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Jamshed Iqbal
- Department of Pharmacy, Comsats University, Abbottabad, Pakistan
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Calzoni E, Cesaretti A, Montegiove N, Di Michele A, Emiliani C. Enhanced Stability of Long-Living Immobilized Recombinant β-d- N-Acetyl-Hexosaminidase A on Polylactic Acid (PLA) Films for Potential Biomedical Applications. J Funct Biomater 2021; 12:jfb12020032. [PMID: 34064736 PMCID: PMC8162980 DOI: 10.3390/jfb12020032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 05/06/2021] [Indexed: 01/24/2023] Open
Abstract
β-d-N-acetyl-hexosaminidase (Hex, EC 3.2.1.52) is an acid hydrolase that catalyzes the cleavage of the β-1,4 bond in N-acetyl-d-galactosamine (Gal-NAc) and N-acetyl-d-glucosamine (Glc-NAc) from the non-reducing end of oligosaccharides and glycoconjugates. It is widely expressed in both the prokaryotic and eukaryotic world, where it performs multiple and important functions. Hex has antifungal activity in plants, is capable of degrading many biological substrates, and can play an important role in the biomedical field for the treatment of Tay-Sachs and Sandhoff diseases. With the aim being able to obtain a device with a stable enzyme, a method of covalent immobilization on polylactic acid (PLA) films was developed for the A isoform of the β-d-N-acetyl-hexosaminidase enzyme (HexA), produced in a recombinant way from Human Embryonic Kidney-293 (HEK-293) cells and suitably purified. An in-depth biochemical characterization of the immobilized enzyme was carried out, evaluating the optimal temperature, thermal stability, pH parameters, and Km value. Moreover, the stability of the enzymatic activity over time was assessed. The results obtained showed an improvement in terms of kinetic parameters and stability to heat for the enzyme following immobilization and the presence of HexA in two distinct immobilized forms, with an unexpected ability for one of them to maintain its functionality for a long period of time (over a year). The stability and functionality of the enzyme in its immobilized form are therefore extremely promising for potential biotechnological and biomedical applications.
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Affiliation(s)
- Eleonora Calzoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy; (E.C.); (N.M.); (C.E.)
| | - Alessio Cesaretti
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy; (E.C.); (N.M.); (C.E.)
- Center of Excellence on Innovative Nanostructured Materials—CEMIN, University of Perugia, 06123 Perugia, Italy
- Correspondence: ; Tel.: +39-075-585-7436
| | - Nicolò Montegiove
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy; (E.C.); (N.M.); (C.E.)
| | | | - Carla Emiliani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy; (E.C.); (N.M.); (C.E.)
- Center of Excellence on Innovative Nanostructured Materials—CEMIN, University of Perugia, 06123 Perugia, Italy
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Giovannoni M, Gramegna G, Benedetti M, Mattei B. Industrial Use of Cell Wall Degrading Enzymes: The Fine Line Between Production Strategy and Economic Feasibility. Front Bioeng Biotechnol 2020; 8:356. [PMID: 32411686 PMCID: PMC7200985 DOI: 10.3389/fbioe.2020.00356] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Cell Wall Degrading Enzymes (CWDEs) are a heterogeneous group of enzymes including glycosyl-hydrolases, oxidoreductases, lyases, and esterases. Microbes with degrading activities toward plant cell wall polysaccharides are the most relevant source of CWDEs for industrial applications. These organisms secrete a wide array of CWDEs in amounts strictly necessary for their own sustenance, nonetheless the production of CWDEs from wild type microbes can be increased at large-scale by using optimized fermentation strategies. In the last decades, advances in genetic engineering allowed the expression of recombinant CWDEs also in lab-domesticated organisms such as E. coli, yeasts and plants, dramatically increasing the available options for the large-scale production of CWDEs. The optimization of a CWDE-producing biofactory is a hard challenge that biotechnologists tackle by testing different expression strategies and expression-hosts. Although both the yield and production costs are critical factors to produce biomolecules at industrial scale, these parameters are often disregarded in basic research. This review presents the main characteristics and industrial applications of CWDEs directed toward the cell wall of plants, bacteria, fungi and microalgae. Different biofactories for CWDE expression are compared in order to highlight strengths and weaknesses of each production system and how these aspects impact the final enzyme cost and, consequently, the economic feasibility of using CWDEs for industrial applications.
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Affiliation(s)
- Moira Giovannoni
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giovanna Gramegna
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Manuel Benedetti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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Konada RSR, Krishnapati LS, Ashapogu V, Lin CH, Nadimpalli SK. Comparative analysis of β-hexosaminidase and acid phosphatase from Hydra vulgaris Ind-Pune, H. vulgaris Naukuchiatal and H. magnipapillata sf-1: Localization studies of acid phosphatase and β-hexosaminidase from H. vulgaris Ind-Pune. Comp Biochem Physiol B Biochem Mol Biol 2019; 239:110365. [PMID: 31629812 DOI: 10.1016/j.cbpb.2019.110365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/08/2019] [Accepted: 09/18/2019] [Indexed: 11/25/2022]
Abstract
The present report describes a comprehensive study on comparative biochemical characterization of two lysosomal enzymes, acid phosphatase and β-hexosaminidase in three different strains of Hydra; Hydra vulgaris Ind-Pune, H. vulgaris Naukuchiatal and H. magnipapillata sf-1 (self-feeder-1). Since morphology and habitat of Hydra effect lysosomal enzymes and their response to environmental pollutants, it would be interesting to identify them in different Hydra strains so as to use them as toxicity testing. Preliminary studies revealed a differential expression of acid phosphatase, β-hexosaminidase and β-glucuronidase in three Hydra strains. Expression of all three lysosomal enzymes in H. vulgaris Ind-Pune was low in comparison to H. vulgaris Naukuchiatal and H. magnipapillata sf-1, while their expression is comparable in H. vulgaris Naukuchiatal and H. magnipapillata sf-1. The Michaelis-Menten (KM) values for lysosomal β-hexosaminidase using 4-nitrophenyl N-acetyl-β-D-glucosaminide as substrate were found to be 1.3 mM, 1.1 mM and 0.8 mM, respectively for H. vulgaris Ind-Pune, H. vulgaris Naukuchiatal and H. magnipapillata sf-1. For acid phosphatase using 4-nitrophenyl-phosphate as substrate, the KM values were 0.38 mM, 1.2 mM and 0.52 mM respectively, for H. vulgaris Ind-Pune, H. vulgaris Naukuchiatal and sf-1 strains. The optimum temperature for β-hexosaminidase was 60 °C for H. vulgaris Ind-Pune, while 50 °C was observed for H. vulgaris Naukuchiatal and sf-1 strains. The optimum pH for β-hexosaminidase was found to be 6.0 for H. vulgaris Ind-Pune and H. vulgaris Naukuchiatal, and 5.0 for sf-1. The optimum temperature and pH of acid phosphatase was similar in all three strains, viz., 40 °C and 3.0, respectively. Preliminary localization studies using whole mount in situ hybridization revealed predominant endodermal expression of three enzymes in H. vulgaris Ind-Pune. Our results thus support the conservation of lysosomal hydrolases in Hydra.
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Affiliation(s)
- Rohit Sai Reddy Konada
- Protein Biochemistry and Glycobiology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Lakshmi Surekha Krishnapati
- Protein Biochemistry and Glycobiology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Venugopal Ashapogu
- Protein Biochemistry and Glycobiology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Chung-Hung Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Siva Kumar Nadimpalli
- Protein Biochemistry and Glycobiology Laboratory, Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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Muccee F, Ejaz S. An Investigation of Petrol Metabolizing Bacteria Isolated from Contaminated Soil Samples Collected from Various Fuel Stations. Pol J Microbiol 2019; 68:193-201. [PMID: 31250589 PMCID: PMC7256828 DOI: 10.33073/pjm-2019-019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/11/2022] Open
Abstract
The present study aimed to isolate the high-efficiency petrol metabolizing thermophilic bacteria from petrol contaminated soil samples. Isolation was carried out through enrichment culture, serial dilution and pour plate methods using the petrol supplemented minimal salt media. The isolated bacteria were analyzed to document growth behavior, petrol removal efficiencies, antibiotic resistance profile, and biochemical characteristics. The 16S rRNA based phylogenetic analysis helped to reveal the identity of isolated bacterial species and construct the phylogenetic trees. Total nine bacteria were isolated, out of which three (IUBP2, IUBP3, IUBP5) were identified as Brevibacillus formosus, one (IUBP1) was found similar to Brevibacillus agri, four (IUBP7, IUBP8, IUBP13, and IUBP14) shared homology with Burkholderia lata, and one (IUBP15) with Burkholderia pyrrocinia. All the isolates were fast growing and exhibited considerable petrol degradation potential. The highest petrol removal efficiency (69.5% ± 13.44/6 days) was recorded for the strain IUBP15 at a petrol concentration of 0.1% (v/v). All bacteria studied (100%) were positive for esculinase and phosphatase. Many strains exhibited positive responses for arginine dehydrolase (22%), β-naphthylamidase (11%), β-D-glucosaminide (33%), mannitol (55%), sorbitol (66%) and inulin (88%) fermentation test. While all were sensitive to the antibiotics, some of them were found resistant against chloramphenicol and oxacillin. The remarkable biochemical characteristics and considerable petrol removal potential (40–70%) highlights utilization of the bacteria isolated for petrol bioremediation, mineralization of organophosphates, dairy and food industry, and also as biofertilizers and biocontrol agents.
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Affiliation(s)
- Fatima Muccee
- Department of Biochemistry and Biotechnology , The Islamia University of Bahawalpur , Bahawalpur , Pakistan
| | - Samina Ejaz
- Department of Biochemistry and Biotechnology , The Islamia University of Bahawalpur , Bahawalpur , Pakistan
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Phylogeny and physiology of candidate phylum BRC1 inferred from the first complete metagenome-assembled genome obtained from deep subsurface aquifer. Syst Appl Microbiol 2019; 42:67-76. [DOI: 10.1016/j.syapm.2018.08.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/21/2018] [Accepted: 08/29/2018] [Indexed: 11/24/2022]
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Genome of the candidate phylum Aminicenantes bacterium from a deep subsurface thermal aquifer revealed its fermentative saccharolytic lifestyle. Extremophiles 2019; 23:189-200. [DOI: 10.1007/s00792-018-01073-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/17/2018] [Indexed: 10/27/2022]
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Genome Analysis of Fimbriiglobus ruber SP5 T, a Planctomycete with Confirmed Chitinolytic Capability. Appl Environ Microbiol 2018; 84:AEM.02645-17. [PMID: 29374042 DOI: 10.1128/aem.02645-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 01/21/2018] [Indexed: 11/20/2022] Open
Abstract
Members of the bacterial order Planctomycetales have often been observed in associations with Crustacea. The ability to degrade chitin, however, has never been reported for any of the cultured planctomycetes although utilization of N-acetylglucosamine (GlcNAc) as a sole carbon and nitrogen source is well recognized for these bacteria. Here, we demonstrate the chitinolytic capability of a member of the family Gemmataceae, Fimbriiglobus ruber SP5T, which was isolated from a peat bog. As revealed by metatranscriptomic analysis of chitin-amended peat, the pool of 16S rRNA reads from F. ruber increased in response to chitin availability. Strain SP5T displayed only weak growth on amorphous chitin as a sole source of carbon but grew well with chitin as a source of nitrogen. The genome of F. ruber SP5T is 12.364 Mb in size and is the largest among all currently determined planctomycete genomes. It encodes several enzymes putatively involved in chitin degradation, including two chitinases affiliated with the glycoside hydrolase (GH) family GH18, GH20 family β-N-acetylglucosaminidase, and the complete set of enzymes required for utilization of GlcNAc. The gene encoding one of the predicted chitinases was expressed in Escherichia coli, and the endochitinase activity of the recombinant enzyme was confirmed. The genome also contains genes required for the assembly of type IV pili, which may be used to adhere to chitin and possibly other biopolymers. The ability to use chitin as a source of nitrogen is of special importance for planctomycetes that inhabit N-depleted ombrotrophic wetlands.IMPORTANCE Planctomycetes represent an important part of the microbial community in Sphagnum-dominated peatlands, but their potential functions in these ecosystems remain poorly understood. This study reports the presence of chitinolytic potential in one of the recently described peat-inhabiting members of the family Gemmataceae, Fimbriiglobus ruber SP5T This planctomycete uses chitin, a major constituent of fungal cell walls and exoskeletons of peat-inhabiting arthropods, as a source of nitrogen in N-depleted ombrotrophic Sphagnum-dominated peatlands. This study reports the chitin-degrading capability of representatives of the order Planctomycetales.
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Uehara A, Takahashi N, Moriyama M, Hirano T, Hakamata W, Nishio T. Synthesis of Chitin Oligosaccharides Using Dried Stenotrophomonas maltophilia Cells Containing a Transglycosylation Reaction-Catalyzing β-N-Acetylhexosaminidase as a Whole-Cell Catalyst. Appl Biochem Biotechnol 2017; 184:673-684. [DOI: 10.1007/s12010-017-2585-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/16/2017] [Indexed: 10/19/2022]
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A Novel Multifunctional β-N-Acetylhexosaminidase Revealed through Metagenomics of an Oil-Spilled Mangrove. Bioengineering (Basel) 2017; 4:bioengineering4030062. [PMID: 28952541 PMCID: PMC5615308 DOI: 10.3390/bioengineering4030062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 06/25/2017] [Accepted: 07/06/2017] [Indexed: 11/22/2022] Open
Abstract
The use of culture-independent approaches, such as metagenomics, provides complementary access to environmental microbial diversity. Mangrove environments represent a highly complex system with plenty of opportunities for finding singular functions. In this study we performed a functional screening of fosmid libraries obtained from an oil contaminated mangrove site, with the purpose of identifying clones expressing hydrolytic activities. A novel gene coding for a β-N-acetylhexosaminidase with 355 amino acids and 43KDa was retrieved and characterized. The translated sequence showed only 38% similarity to a β-N-acetylhexosaminidase gene in the genome of Veillonella sp. CAG:933, suggesting that it might constitute a novel enzyme. The enzyme was expressed, purified, and characterized for its enzymatic activity on carboxymethyl cellulose, p-Nitrophenyl-2acetamide-2deoxy-β-d-glucopyranoside, p-Nitrophenyl-2acetamide-2deoxy-β-d-galactopyranoside, and 4-Nitrophenyl β-d-glucopyranoside, presenting β-N-acetylglucosaminidase, β-glucosidase, and β-1,4-endoglucanase activities. The enzyme showed optimum activity at 30 °C and pH 5.5. The characterization of the putative novel β-N-acetylglucosaminidase enzyme reflects similarities to characteristics of the environment explored, which differs from milder conditions environments. This work exemplifies the application of cultivation-independent molecular techniques to the mangrove microbiome for obtaining a novel biotechnological product.
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Naqvi S, Moerschbacher BM. The cell factory approach toward biotechnological production of high-value chitosan oligomers and their derivatives: an update. Crit Rev Biotechnol 2015; 37:11-25. [DOI: 10.3109/07388551.2015.1104289] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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16
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Elevated temperature altered photosynthetic products in wheat seedlings and organic compounds and biological activity in rhizopshere soil under cadmium stress. Sci Rep 2015; 5:14426. [PMID: 26395070 PMCID: PMC4585777 DOI: 10.1038/srep14426] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/28/2015] [Indexed: 11/13/2022] Open
Abstract
The objective of this study was to investigate the effects of slightly elevated atmospheric temperature in the spring on photosynthetic products in wheat seedlings and on organic compounds and biological activity in rhizosphere soil under cadmium (Cd) stress. Elevated temperature was associated with increased soluble sugars, reducing sugars, starch, and total sugars, and with decreased amino acids in wheat seedlings under Cd stress. Elevated temperature improved total soluble sugars, free amino acids, soluble phenolic acids, and organic acids in rhizosphere soil under Cd stress. The activity of amylase, phenol oxidase, invertase, β-glucosidase, and l-asparaginase in rhizosphere soil was significantly improved by elevated temperature under Cd stress; while cellulase, neutral phosphatase, and urease activity significantly decreased. Elevated temperature significantly improved bacteria, fungi, actinomycetes, and total microorganisms abundance and fluorescein diacetate activity under Cd stress. In conclusion, slightly elevated atmospheric temperature in the spring improved the carbohydrate levels in wheat seedlings and organic compounds and biological activity in rhizosphere soil under Cd stress in the short term. In addition, elevated atmospheric temperature in the spring stimulated available Cd by affecting pH, DOC, phenolic acids, and organic acids in rhizosphere soil, which resulted in the improvement of the Cd uptake by wheat seedlings.
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Slámová K, Kulik N, Fiala M, Krejzová-Hofmeisterová J, Ettrich R, Křen V. Expression, characterization and homology modeling of a novel eukaryotic GH84 β-N-acetylglucosaminidase from Penicillium chrysogenum. Protein Expr Purif 2014; 95:204-10. [DOI: 10.1016/j.pep.2014.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/03/2014] [Accepted: 01/06/2014] [Indexed: 01/09/2023]
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18
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Bakunina I, Nedashkovskaya O, Balabanova L, Zvyagintseva T, Rasskasov V, Mikhailov V. Comparative analysis of glycoside hydrolases activities from phylogenetically diverse marine bacteria of the genus Arenibacter. Mar Drugs 2013; 11:1977-98. [PMID: 23752354 PMCID: PMC3721217 DOI: 10.3390/md11061977] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/22/2013] [Accepted: 05/27/2013] [Indexed: 11/16/2022] Open
Abstract
A total of 16 marine strains belonging to the genus Arenibacter, recovered from diverse microbial communities associated with various marine habitats and collected from different locations, were evaluated in degradation of natural polysaccharides and chromogenic glycosides. Most strains were affiliated with five recognized species, and some presented three new species within the genus Arenibacter. No strains contained enzymes depolymerizing polysaccharides, but synthesized a wide spectrum of glycosidases. Highly active β-N-acetylglucosaminidases and α-N-acetylgalactosaminidases were the main glycosidases for all Arenibacter. The genes, encoding two new members of glycoside hydrolyses (GH) families, 20 and 109, were isolated and characterized from the genomes of Arenibacter latericius. Molecular genetic analysis using glycosidase-specific primers shows the absence of GH27 and GH36 genes. A sequence comparison with functionally-characterized GH20 and GH109 enzymes shows that both sequences are closest to the enzymes of chitinolytic bacteria Vibrio furnissii and Cellulomonas fimi of marine and terrestrial origin, as well as human pathogen Elisabethkingia meningoseptica and simbionts Akkermansia muciniphila, gut and non-gut Bacteroides, respectively. These results revealed that the genus Arenibacter is a highly taxonomic diverse group of microorganisms, which can participate in degradation of natural polymers in marine environments depending on their niche and habitat adaptations. They are new prospective candidates for biotechnological applications due to their production of unique glycosidases.
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Affiliation(s)
- Irina Bakunina
- Laboratory of Enzyme Chemistry, Laboratory of Microbiology and Laboratory of Molecular Biology of G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690022, Russia; E-Mails: (O.N.); (L.B.); (T.Z.); (V.R.); (V.M.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +7-432-231-07-05-3; Fax: +7-432-231-07-05-7
| | - Olga Nedashkovskaya
- Laboratory of Enzyme Chemistry, Laboratory of Microbiology and Laboratory of Molecular Biology of G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690022, Russia; E-Mails: (O.N.); (L.B.); (T.Z.); (V.R.); (V.M.)
| | - Larissa Balabanova
- Laboratory of Enzyme Chemistry, Laboratory of Microbiology and Laboratory of Molecular Biology of G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690022, Russia; E-Mails: (O.N.); (L.B.); (T.Z.); (V.R.); (V.M.)
| | - Tatyana Zvyagintseva
- Laboratory of Enzyme Chemistry, Laboratory of Microbiology and Laboratory of Molecular Biology of G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690022, Russia; E-Mails: (O.N.); (L.B.); (T.Z.); (V.R.); (V.M.)
| | - Valery Rasskasov
- Laboratory of Enzyme Chemistry, Laboratory of Microbiology and Laboratory of Molecular Biology of G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690022, Russia; E-Mails: (O.N.); (L.B.); (T.Z.); (V.R.); (V.M.)
| | - Valery Mikhailov
- Laboratory of Enzyme Chemistry, Laboratory of Microbiology and Laboratory of Molecular Biology of G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690022, Russia; E-Mails: (O.N.); (L.B.); (T.Z.); (V.R.); (V.M.)
- School of Natural Sciences, Far Eastern Federal University, Vladivostok 690091, Russia
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Xie XL, Zhou HT, Huang QS, Wei XQ, Wang Y, Yan JH, Chen QX. Inhibitory kinetics of betaine on beta-N-acetyl-D-glucosaminidase from prawn (Litopenaeus vannamei). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:3820-3824. [PMID: 20158206 DOI: 10.1021/jf9039952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The effects of betaine on prawn beta-N-acetyl-D-glucosaminidase (NAGase) activity for the hydrolysis of p-nitrophenyl-N-acetyl- beta-D-glucosaminide (pNP-NAG) have been studied. The results showed that appropriate concentrations of betaine could lead to reversible inhibition against NAGase, and the IC(50) value was estimated to be 15.00 +/- 0.30 mM. The inhibitory kinetics assay showed that betaine was a mixed type inhibitor with a K(I) value of 9.17 +/- 0.85 mM and a K(IS) value of 45.58 +/- 2.52 mM. The inhibitory model was set, and the microscopic rate constants were determined using the kinetic method of the substrate reaction. The time course of the hydrolysis of pNP-NAG catalyzed by NAGase in the presence of different betaine concentrations showed that at each betaine concentration, the rate decreased with an increase in time until a straight line was approached, indicating that the inhibition of NAGase by betaine is a slow, reversible reaction with fractional residual activity. The fact that k(+0) is much larger than k(+0)(') indicated that the free enzyme molecule is more fragile than the enzyme-substrate complex against betaine. It is suggested that the presence of the substrate offers marked protection of NAGase against inhibition by betaine.
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Affiliation(s)
- Xiao-Lan Xie
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, China
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20
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Xie XL, Huang QS, Wang Y, Ke CH, Chen QX. Modification and modificatory kinetics of the active center of prawn beta-N-acetyl-D-glucosaminidase. J Biomol Struct Dyn 2009; 26:781-6. [PMID: 19385706 DOI: 10.1080/07391102.2009.10507290] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Beta-N-acetyl-D-glucosaminidase (NAGase, EC3.2.1.52) plays important role in molting, digestion of chitinous foods, and defense systems against parasites in prawn (Litopenaeus vannamei). However, study on functional groups and catalytic mechanism of NAGase are yet limited. The modification of the active center of NAGase from prawn has been first studied. The results demonstrate that the disulfide bonds and the carbamidine groups of arginine residues are not essential to the enzyme's activity. The modification of indole group of tryptophan of the enzyme by N-bromosuccinimide (NBS) can lead to the complete inactivation, accompanying the absorption decreasing at 276 nm, indicating that tryptophan is essential residue to the enzyme. The modificatory kinetics of NAGase in the appropriate concentrations of NBS solution has been studied and the numbers of essential tryptophan residues have been determined using the kinetic method of the substrate reaction. The result shows that only one tryptophan residue is essential for enzyme activity. And the modifications of histidine, lysine residue, and the carboxyl groups also inactivate the enzyme completely or incompletely. The results showed that the carboxyl groups of acidic amino acid, imidazole groups of histidine residue, amino groups of lysine residue, and indole group of tryptophan were essential for the activity of enzyme.
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Affiliation(s)
- Xiao-Lan Xie
- Department of Oceanography, School of Oceanography and Environmental Sciences, Xiamen University, Xiamen 361005, China
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21
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An orthologue of Bacteroides fragilis NanH is the principal sialidase in Tannerella forsythia. J Bacteriol 2009; 191:3623-8. [PMID: 19304852 DOI: 10.1128/jb.01618-08] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sialidase activity is a putative virulence factor of the anaerobic periodontal pathogen Tannerella forsythia, but it is uncertain which genes encode this activity. Characterization of a putative sialidase, SiaHI, by others, indicated that this protein alone may not be responsible for all of the sialidase activity. We describe a second sialidase in T. forsythia (TF0035), an orthologue of Bacteroides fragilis NanH, and its expression in Escherichia coli. Sialidase activity of the expressed NanH was confirmed by using 2'-(4-methylumbelliferyl)-alpha-D-N-acetylneuraminic acid as a substrate. Biochemical characterization of the recombinant T. forsythia NanH indicated that it was active over a broad pH range, with optimum activity at pH 5.5. This enzyme has high affinity for 2'-(4-methylumbelliferyl)-alpha-D-N-acetylneuraminic acid (K(m) of 32.9 +/- 10.3 microM) and rapidly releases 4-methylumbelliferone (V(max) of 170.8 +/- 11.8 nmol of 4-methylumbelliferone min(-1) mg of protein(-1)). E. coli lysates containing recombinant T. forsythia NanH cleave sialic acid from a range of substrates, with a preference for alpha2-3 glycosidic linkages. The genes adjacent to nanH encode proteins apparently involved in the metabolism of sialic acid, indicating that the NanH sialidase is likely to be involved in nutrient acquisition.
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22
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Xie XL, Huang QS, Gong M, Du J, Yang Y, Chen QX. Inhibitory kinetics ofβ-N-acetyl-D-glucosaminidase from prawn (Litopenaeus vannamei) by zinc ion. IUBMB Life 2009; 61:163-70. [DOI: 10.1002/iub.140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Kadokura K, Sakamoto Y, Rokutani A, Ikegami T, Hirano T, Yamamoto M, Saito K, Hakamata W, Itoi S, Sugita H, Oku T, Nishio T. Purification, Characterization and Cloning of Vibrio parahaemolyticus Chitinolytic Enzymes and Application to Oligosaccharide Production. J Appl Glycosci (1999) 2008. [DOI: 10.5458/jag.55.157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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24
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Xie XL, Du J, Huang QS, Shi Y, Chen QX. Inhibitory kinetics of bromacetic acid on beta-N-acetyl-D-glucosaminidase from prawn (Penaeus vannamei). Int J Biol Macromol 2007; 41:308-13. [PMID: 17531314 DOI: 10.1016/j.ijbiomac.2007.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 03/30/2007] [Accepted: 03/30/2007] [Indexed: 10/23/2022]
Abstract
beta-N-Acetyl-D-glucosaminidase (NAGase, EC.3.2.1.52), a composition of chitinases, cooperates with endo-chitinase and exo-chitinase to disintegrate chitin into N-acetylglucosamine (NAG). NAGase from prawn (Penaeus vannamei) is involved in digestion and molting processes. The investigation of enzymatic properties, functional groups and catalytic mechanism is an essential mission to its commercial application. Bromacetic acid (BrAc) is a specific modifier for the histidine residue in specific condition. In this paper, the effect of BrAc on prawn NAGase activity for the hydrolysis of pNP-NAG has been investigated. The results showed that BrAc can reversibly and non-competitively inhibit the enzyme activity at appropriate concentrations and the value of IC(50) was estimated to be 17.05+/-0.65 mM. The inhibition kinetics of the enzyme by BrAc has been studied using the kinetic method of the substrate reaction. And the inhibition model was set up and the microscopic rate constants for the reaction of the inhibitor with free enzyme and the enzyme-substrate complexes were determined for inactivation and reactivation. The rate constant of the forward inactivation (k(+0)), which is 1.25 x 10(-3)s(-1), is about eight times as much as that of the reverse reactivation (k(-0)), which is 1.64 x 10(-4)s(-1). Therefore, when the BrAc concentration is sufficiently large, the enzyme is completely inactivated.
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Affiliation(s)
- Xiao-Lan Xie
- Key Laboratory of Ministry of Education for Cell Biology and Tumor Cell Engineering, Xiamen University, Xiamen 361005, China
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25
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Kadokura K, Rokutani A, Yamamoto M, Ikegami T, Sugita H, Itoi S, Hakamata W, Oku T, Nishio T. Purification and characterization of Vibrio parahaemolyticus extracellular chitinase and chitin oligosaccharide deacetylase involved in the production of heterodisaccharide from chitin. Appl Microbiol Biotechnol 2007; 75:357-65. [PMID: 17334758 DOI: 10.1007/s00253-006-0831-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 12/20/2006] [Accepted: 12/24/2006] [Indexed: 11/30/2022]
Abstract
A chitin-degrading bacterial strain, KN1699, isolated from Yatsu dry beach (Narashino, Chiba Prefecture, Japan), was identified as Vibrio parahaemolyticus. Treatment of powdered chitin with crude enzyme solution prepared from the supernatant of KN1699 cultures yielded a disaccharide, beta-D-N-acetylglucosaminyl-(1,4)-D-glucosamine (GlcNAc-GlcN), as the primary chitin degradation product. The extracellular enzymes involved in the production of this heterodisaccharide, chitinase (Pa-Chi; molecular mass, 92 kDa) and chitin oligosaccharide deacetylase (Pa-COD; molecular mass, 46 kDa), were isolated from the crude enzyme solution, and their hydrolysis specificities were elucidated. These studies confirmed that (1) Pa-Chi hydrolyzes chitin to produce (GlcNAc)(2) and (2) Pa-COD hydrolyzes the acetamide group of reducing end GlcNAc residue of (GlcNAc)(2). These findings indicate that GlcNAc-GlcN is produced from chitin by the cooperative hydrolytic reactions of both Pa-Chi and Pa-COD.
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Affiliation(s)
- K Kadokura
- Department of Biological Chemistry, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-8510, Japan
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Shi Y, Jiang Z, Han P, Zheng GX, Song KK, Chen QX. Purification and some properties of β-N-acetyl-d-glucosaminidase from the cabbage butterfly (Pieris rapae). Biochimie 2007; 89:347-54. [PMID: 17258376 DOI: 10.1016/j.biochi.2006.06.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Accepted: 06/12/2006] [Indexed: 11/28/2022]
Abstract
A beta-N-acetyl-D-glucosaminidase (NAGase) from the cabbage butterfly (Pieris rapae) was purified. The purified enzyme was a single band on polyacrylamide gel electrophoresis and the specific activity was determined to be 8715 U/mg. The molecular weight of whole enzyme was determined to be 106 kDa by gel filtration, and the result of SDS-PAGE showed that the enzyme was a heterodimer, which contained two subunits with different mass of 59.5 and 57.2 kDa. The optimum pH and optimum temperature of the enzyme for the hydrolysis of p-nitrophenyl-N-acetyl-beta-D-glucosaminide (pNP-NAG) were investigated to be at pH 6.2 and at 42 degrees C, respectively, and the Michaelis-Menten constant (K(m)) was determined to be 0.285 mM at pH 6.2 and 37 degrees C. The stability of the enzyme was investigated and the results showed that the enzyme was stable at the pH range from 4.0 to 9.0 and at the temperature below 45 degrees C. The activation energy was 83.86 kJ/mol. The reaction of this enzyme with pNP-NAG was judged to be Ordered Bi-Bi mechanism according to the inhibitory behaviors of the products. The ionization constant, pK(e), of ionizing group at the active site of the enzyme was found to be 5.20 at 39.0 degrees C, and the standard dissociation enthalpy (DeltaH(o)) was determined to be 2.18 kcal/mol. These results showed that the ionizing group of the enzyme active center was the carboxyl group. The results of chemical modification also suggested that carboxyl group was essential to the enzyme activity. Moreover, Zn(2+), Hg(2+), Cu(2+) had strongly inhibitory effects on the enzyme activity.
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Affiliation(s)
- Yan Shi
- Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen 361005, People's Republic of China
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27
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Giordano A, Andreotti G, Tramice A, Trincone A. Marine glycosyl hydrolases in the hydrolysis and synthesis of oligosaccharides. Biotechnol J 2006; 1:511-30. [PMID: 16892287 DOI: 10.1002/biot.200500036] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The marine ecosystem can be considered a rather unexplored source of biological material (e.g. natural substances with therapeutic activity) and can also be a surprising source of enzymes carrying new and interesting catalytic activities to be applied in biocatalysis. The use of glycosyl hydrolases from marine environments dates back to the end of the 1960s and was mainly focused on the development of sensitive and reliable hydrolytic methods for the analysis of sugar chains. As a result not all the benefits of a particular enzymatic activity have been investigated, especially regarding the transglycosylation potential of these enzymes for the synthesis of glycosidic bonds. In this review, the potential of marine sources will be demonstrated reporting on the few examples found in literature for the synthesis and hydrolysis of biologically relevant oligosaccharides catalyzed by glycosyl hydrolases of marine origin. Particular emphasis is given to the synthesis of glycosidic bonds, which is easy by the use of glycosyl hydrolases. Further aspects considered in this review are applications of these biocatalysts for vegetal waste treatment in recovering useful materials, for structural identification and for preparation of target materials from new purified polysaccharides, for the synthesis or modification of food-related compounds and for glycobiology related studies.
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Ogawa M, Kitagawa M, Tanaka H, Ueda K, Watsuji TO, Beppu T, Kondo A, Kawachi R, Oku T, Nishio T. A β-N-acetylhexosaminidase from Symbiobacterium thermophilum; gene cloning, overexpression, purification and characterization. Enzyme Microb Technol 2006. [DOI: 10.1016/j.enzmictec.2005.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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29
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Kuk JH, Jung WJ, Jo GH, Kim KY, Park RD. Production of N,N′-diacetylchitobiose from chitin using temperature-sensitive chitinolytic enzyme preparations of Aeromonas sp. GJ-18. World J Microbiol Biotechnol 2005. [DOI: 10.1007/s11274-005-9009-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Xie XL, Chen QX. Inactivation kinetics of ?-N-acetyl-D-glucosaminidase from prawn (Penaeus vannamei) in dioxane solution. BIOCHEMISTRY (MOSCOW) 2004; 69:1365-71. [PMID: 15627392 DOI: 10.1007/s10541-005-0082-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
beta-N-Acetyl-D-glucosaminidase (NAGase, EC 3.2.1.52) catalyzes the cleavage of N-acetylglucosamine polymers. It is in the composition of the chitinases and cooperates with endo-chitinase and exo-chitinase to disintegrate chitin into N-acetylglucosamine. In this work, the effects of dioxane on the enzyme activity for the hydrolysis of p-nitrophenyl-N-acetyl-beta-D-glucosaminide from the prawn (Penaeus vannamei) have been studied. The results show that appropriate concentrations of dioxane can lead to reversible inactivation of the enzyme, and the IC(50) is estimated to be 1.1 M. The kinetics of inactivation of NAGase in the appropriate concentrations of dioxane solution has been studied using the kinetic method of the substrate reaction. The rate constants of inactivation have been determined. The results show that the free enzyme molecule is more fragile than the enzyme-substrate complex in the dioxane solution. It is suggested that the presence of the substrate offers marked protection of this enzyme against inactivation by dioxane.
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Affiliation(s)
- Xiao-Lan Xie
- Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen 361005, People's Republic of China
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Hydrolytic and transglycosylation reactions of N-acyl modified substrates catalysed by β-N-acetylhexosaminidases. Tetrahedron 2004. [DOI: 10.1016/j.tet.2003.10.111] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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33
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Vrba J. Comment to Sherr and Sherr (1999): "Is there any appropriate way to distinguish different beta-N-acetylhexosaminidase activities in aquatic environments?". FEMS Microbiol Ecol 2000; 33:81-84. [PMID: 10922506 DOI: 10.1111/j.1574-6941.2000.tb00729.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The recent paper of Sherr and Sherr on detecting low-affinity beta-glucosaminidase activity in several marine microbes extends current knowledge about hydrolytic enzyme activities in natural aquatic systems. However, their conclusions regarding the whole-cell assay with MUF-N-acetyl-beta-D-glucosaminide (MUF-[GlcNAc]) cannot be accepted. First, we explicitly demonstrate a strong correlation between extracellular activities of the high-affinity enzymes and grazing rates of bacterivorous protists. Therefore, the assay can still be recommended for the estimation of total protistan grazing on prokaryotic picoplankton. Second, the ability of many aquatic organisms to produce enzymes which cleave fluorogenic substrates, such as MUF-[GlcNAc] and/or MUF-beta-D-N,N',N"-triacetylchitotriose (MUF-[GlcNAc](3)), has been well-documented during the last decade. Thus, neither of the two substrates may be considered as exclusively specific for targeting either lysozymes or beta-N-acetylhexosaminidases.
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Affiliation(s)
- J Vrba
- Hydrobiological Institute AS CR, Na sádkách 7, CZ-37005, Ceské Budejovice, Czech Republic
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34
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Vocadlo DJ, Mayer C, He S, Withers SG. Mechanism of action and identification of Asp242 as the catalytic nucleophile of Vibrio furnisii N-acetyl-beta-D-glucosaminidase using 2-acetamido-2-deoxy-5-fluoro-alpha-L-idopyranosyl fluoride. Biochemistry 2000; 39:117-26. [PMID: 10625486 DOI: 10.1021/bi991958d] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The novel mechanism-based reagent 2-acetamido-2-deoxy-5-fluoro-alpha-L-idopyranosykl fluoride has been synthesized, and the kinetic parameters K(M) = 0.23 mM and K(CAT)= 0.55 min(-1) for its hydrolysis by vibrio furnisi beta-N-acetylglucosaminidase (ExoII) HAVE been determined. Investigation of mixtures of enzyme with this slow substrate by electrospray mass spectrometry revealed a high steady-state population of the 2-acetamido-2-deoxy-5-fluoro-beta-L-idopyranosyl-enzyme, indicating that the hydrolytic mechanism of ExoII involves the formation and rate-determining hydrolysis of a glycosyl-enzyme intermediate. Analysis of a peptic digest of the glycosyl-enzyme by HPLC/ESMS/MS in the netural-loss mode permitted identification of a peptide bearing the 5-fluoro-sugar moiety. Tandem MS sequencing of the labeled peptide, in conjuction with multiple sequence alignmentsS of family 3 members, allowed the identification of ASP242 as the catalytic nucleophile within the sequence IVFSDDLSM.
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Affiliation(s)
- D J Vocadlo
- Protein Engineering Network of Centres of Excellence of Canada, Department of Chemistry, University of British Columbia, Vancouver
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Abstract
Tremendous advances in biocatalytic approaches to oligosaccharide synthesis have taken place in the past two years. The use of isolated enzymes, both glycosyltransferases and glycosidases, or engineered whole cells allows the preparation of natural oligosaccharides and analogs required for glycobiology research.
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Affiliation(s)
- M M Palcic
- Department of Chemistry, University of Alberta, Edmonton, T6C 2G2, Canada.
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