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Sharma KK, Singh D, Mohite SV, Williamson PR, Kennedy JF. Metal manipulators and regulators in human pathogens: A comprehensive review on microbial redox copper metalloenzymes "multicopper oxidases and superoxide dismutases". Int J Biol Macromol 2023; 233:123534. [PMID: 36740121 DOI: 10.1016/j.ijbiomac.2023.123534] [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: 11/22/2022] [Revised: 01/17/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
The chemistry of metal ions with human pathogens is essential for their survival, energy generation, redox signaling, and niche dominance. To regulate and manipulate the metal ions, various enzymes and metal chelators are present in pathogenic bacteria. Metalloenzymes incorporate transition metal such as iron, zinc, cobalt, and copper in their reaction centers to perform essential metabolic functions; however, iron and copper have gained more importance. Multicopper oxidases have the ability to perform redox reaction on phenolic substrates with the help of copper ions. They have been reported from Enterobacteriaceae, namely Salmonella enterica, Escherichia coli, and Yersinia enterocolitica, but their role in virulence is still poorly understood. Similarly, superoxide dismutases participate in reducing oxidative stress and allow the survival of pathogens. Their role in virulence and survival is well established in Salmonella typhimurium and Mycobacterium tuberculosis. Further, to ensure survival against stress, like metal starvation or metal toxicity, redox metalloenzymes and metal transportation systems of pathogens actively participate in metal homeostasis. Recently, the omics and protein structure biology studies have helped to predict new targets for regulation the colonization potential of the pathogenic strains. The current review is focused on the major roles of redox metalloenzymes, especially MCOs and SODs of human pathogenic bacteria.
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Affiliation(s)
- Krishna Kant Sharma
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
| | - Deepti Singh
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Shreya Vishwas Mohite
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Peter R Williamson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John F Kennedy
- Chembiotech Laboratories, Advanced Science and Technology Institute, 5 the Croft, Buntsford Drive, Stoke Heath, Bromsgrove, Worcs B60 4JE, UK
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Mahuri M, Paul M, Sahu SK, Thatoi H. In silico homology modeling, docking and sequence analysis of some bacterial laccases to unravel enzymatic specificity towards lignin biodegradation. J Biomol Struct Dyn 2022:1-19. [PMID: 35838062 DOI: 10.1080/07391102.2022.2096117] [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: 10/17/2022]
Abstract
Laccase is a delignifying enzyme that belongs to the oxidoreductase family, and it has long been investigated as a pretreatment agent in biofuel production. In this study, amino acid sequences of five bacterial laccases from Bifidobacterium breve, Klebsiella pneumonia, Pseudodesulfovibrio hydrargyri, Pseudomonas aeruginosa and Veillonella rodentium have been retrieved from UniProtKB for sequence alignment, phylogenetic analysis using MEGA 7.0 and 3 D structure prediction by homology modeling in SWISS-MODEL. Multiple sequence alignment between all the bacterial laccase sequences revealed a similar structural fold, although the overall protein sequence varied greatly with the substrate binding sites. Further molecular docking in AutoDock Vina and MD stimulation (MDS) in GROMACS for those modelled enzymes were performed considering both apo and ligand bound structures considering both apo and its ligand bound form. Investigation of molecular interaction utilizing docking of five bacterial laccases with three substrates (ABTS, DMP and Guaiacol) revealed that ABTS with K. pneumoniae laccase had the highest binding energy of -7.00 kcal/mol. In the current MDS investigation, bacterial laccases demonstrated greater binding and substrate energy in the ligand bound complex than in the apo form for ABTS, DMP and Guaiacol. In most cases of bacterial laccase, MDS revealed that DMP bound complex was more stable within an average RMSD value lower than 0.5 nm throughout 100 ns time scale. Thus, in silico studies undertaken in this work will be useful in determining the stable enzyme-substrate complex which further might improve the enzymatic catalysis of bacterial laccases for lignin breakdown and biofuel generation.
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Affiliation(s)
- Monalisa Mahuri
- Department of Biotechnology, Maharaja Sriram Chandra BhanjaDeo University, Baripada, Odisha, India
| | - Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra BhanjaDeo University, Baripada, Odisha, India
| | - Sumanta Kumar Sahu
- Department of Bioinformatics, Central University of South Bihar, Gaya, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra BhanjaDeo University, Baripada, Odisha, India
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Ahlawat S, Singh AK, Shankar A, Yadav A, Sharma KK. Infected insect gut reveals differentially expressed proteins for cellular redox, metal resistance and secretion system in Yersinia enterocolitica-Helicoverpa armigera pathogenic model. Biotechnol Lett 2021; 43:1845-1867. [PMID: 34165641 DOI: 10.1007/s10529-021-03157-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Mouse infection models are frequently used to study the host-pathogen interaction studies. However, due to several constraints, there is an urgent need for a simple, rapid, easy to handle, inexpensive, and ethically acceptable in vivo model system for studying the virulence of enteropathogens. Thus, the present study was performed to develop the larvae of Helicoverpa armigera as a rapid-inexpensive in vivo model system to evaluate the effect of Yersinia enterocolitica strain 8081 on its midgut via a label-free proteomic approach. RESULTS Helicoverpa armigera larvae fed with Yersinia enterocolitica strain 8081 manifested significant reduction in body weight and damage in midgut. On performing label-free proteomic study, secretory systems, putative hemolysin, and two-component system emerged as the main pathogenic proteins. Further, proteome comparison between control and Yersinia added diet-fed (YADF) insects revealed altered cytoskeletal proteins in response to increased melanization (via a prophenoloxidase cascade) and free radical generation. In concurrence, FTIR-spectroscopy, and histopathological and biochemical analysis confirmed gut damage in YADF insects. Finally, the proteome data suggests that the mechanism of infection and the host response in Y. enterocolitica-H. armigera system mimics Yersinia-mammalian gut interactions. CONCLUSIONS All data from current study collectively suggest that H. armigera larva can be considered as a potential in vivo model system for studying the enteropathogenic infection by Y. enterocolitica strain 8081.
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Affiliation(s)
- Shruti Ahlawat
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Amarjeet Kumar Singh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Akshay Shankar
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Asha Yadav
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
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Muniraj I, Shameer S, Uthandi S. Tyrosinase and laccase-producing Bacillus aryabhattai TFG5 and its role in the polymerization of phenols. BMC Microbiol 2021; 21:187. [PMID: 34157975 PMCID: PMC8220707 DOI: 10.1186/s12866-021-02258-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/10/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Tyrosinases and laccases are oxidoreductase enzymes that are used widely in the food, feed, textile, and biofuel industries. The rapidly growing industrial demand for bacterial oxido-reductases has encouraged research on this enzyme worldwide. These enzymes also play a key role in the formation of humic substances (HS) that are involved in controlling the biogeochemical carbon cycle, providing nutrients and bio-stimulants for plant growth, and interacting with inorganic and organic pollutants besides increasing carbon sequestration and mitigating greenhouse gas emission in the environment. The present study aimed to screen and characterize extracellular tyrosinase and laccase-producing soil bacteria that could be utilized in the polymerization of phenols. RESULTS Twenty isolates from different soil samples collected from forest ecosystems were characterized through ARDRA using restriction digestion with AluI, HpaII, and HaeIII restriction enzymes. The results of Hierarchical Cluster Analysis (HCA) revealed a 60 % similarity coefficient among 13 out of 20 isolates, of which, the isolate TFG5 exhibited only 10 % similarity when compared to all the other isolates. The isolate TFG5 exhibited both tyrosinase (1.34 U.mL- 1) and laccase (2.01 U.mL- 1) activity and was identified as Bacillus aryabhattai. The increased polymerization activity was observed when B. aryabhattai TFG5 was treated with phenols. The monomers such as catechol, p-Hydroxy benzoic acid, ferulic acid, and salicylic acid were polymerized efficiently, as evidenced by their FT-IR spectra depicting increased functional groups compared to the standard mushroom tyrosinase. CONCLUSIONS The polymerization ability of B. aryabhattai TFG5 could be applied to phenol-rich wastewater treatment for efficient precipitation of phenols. Furthermore, tyrosinases can be used for enhancing the synthesis of HS in soil.
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Affiliation(s)
- Iniyakumar Muniraj
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641 003, India
- Present address: Department of Agricultural Microbiology, AMRITA School of Agricultural Sciences, Arasampalayam, Coimbatore, 642 109, India
| | - Syed Shameer
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641 003, India
| | - Sivakumar Uthandi
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641 003, India.
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Zhou Q, Guo M, Ni K, Kerton FM. Construction of supramolecular laccase enzymes and understanding of catalytic dye degradation using multispectral and molecular docking approaches. REACT CHEM ENG 2021. [DOI: 10.1039/d1re00111f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A non-covalent supramolecular enzyme system which was successfully constructed by non-covalent interaction of enzyme with substrates analogs can effectively recognize and degrade 13 kinds of dyes.
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Affiliation(s)
- Qingteng Zhou
- College of Engineering, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Ming Guo
- College of Engineering, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
- College of Science, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Kaijie Ni
- College of Science, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Francesca M. Kerton
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, Canada A1B 3X7
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Kumar A, Ahlawat S, Mohan H, Sharma KK. Stabilization-destabilization and redox properties of laccases from medicinal mushroom Ganoderma lucidum and human pathogen Yersinia enterocolitica. Int J Biol Macromol 2020; 167:369-381. [PMID: 33275974 DOI: 10.1016/j.ijbiomac.2020.11.169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 02/01/2023]
Abstract
Laccases or benzenediol oxygen oxidoreductases (EC 1.10.3.2) are polyphenol multicopper oxidases that are known for their structural and functional diversity in various life forms. In the present study, the molecular and physico-chemical properties (redox-potential and secondary structures) of fungal laccase isozymes (FLIs) isolated from a medicinal mushroom Ganoderma lucidum were analyzed and compared with those of the recombinant bacterial laccases (rLac) obtained from different Yersinia enterocolitica strains. It was revealed that the FLIs contained His-Cys-His as the most conserved residue in its domain I Cu site, while the fourth and fifth residues were variable (Ile, Leu, or Phe). Evidently, the cyclic voltammetric measurements of Glac L2 at Type 1 Cu site revealed greater E° for ABTS/ABTS+ (0.312 V) and ABTS+/ABTS2+ (0.773 V) compared to the E° of rLac. Furthermore, circular dichroism-based conformational analysis revealed structural stability of the FLIs at acidic pH (3.0) and low temperature (<30 °C), while the isozymes were destabilized at neutral pH (7.0) and high-temperature conditions (>70 °C). The zymographic studies further confirmed the functional inactivation of FLIs at high temperatures (≥70 °C), predominantly due to domain unfolding. These findings provide novel insight into the evolution of the catalytic efficiency and redox properties of the FLIs, contributing to the existing knowledge regarding stress responses, metabolite production, and the biotechnological utilization of metabolites.
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Affiliation(s)
- Amit Kumar
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Shruti Ahlawat
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Hari Mohan
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
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Proteomic analysis reveals the damaging role of low redox laccase from Yersinia enterocolitica strain 8081 in the midgut of Helicoverpa armigera. Biotechnol Lett 2020; 42:2189-2210. [PMID: 32472187 DOI: 10.1007/s10529-020-02925-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/25/2020] [Indexed: 01/25/2023]
Abstract
OBJECTIVE Earlier, we have found that the enteropathogenic Yersinia enterocolitica have evolved the survival mechanisms that regulate the expression of laccase-encoding genes in the gut. The present study aims to characterize the purified recombinant laccase from Y. enterocolitica strain 8081 biovar 1B and understand its effect on the midgut of cotton bollworm, Helicoverpa armigera (Hübner) larvae. RESULTS The recombinant laccase protein showed high purity fold and low molecular mass (~ 43 kDa). H. armigera larvae fed with laccase protein showed a significant decrease in body weight and damage in the midgut. Further, transmission electron microscopy (TEM) studies revealed the negative effect of laccase protein on trachea, malpighian tubules, and villi of the insect. The proteome comparison between control and laccase-fed larvae of cotton bollworm showed significant expression of proteolytic enzymes, oxidoreductases, cytoskeletal proteins, ribosomal proteins; and proteins for citrate (TCA cycle) cycle, glycolysis, stress response, cell redox homeostasis, xenobiotic degradation, and insect defence. Moreover, it also resulted in the reduction of antioxidants, increased melanization (insect innate immune response), and enhanced free radical generation. CONCLUSIONS All these data collectively suggest that H. armigera (Hübner) larvae can be used to study the effect of microbes and their metabolites on the host physiology, anatomy, and survival.
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Kwiatos N, Jędrzejczak-Krzepkowska M, Krzemińska A, Delavari A, Paneth P, Bielecki S. Evolved Fusarium oxysporum laccase expressed in Saccharomyces cerevisiae. Sci Rep 2020; 10:3244. [PMID: 32094483 PMCID: PMC7039978 DOI: 10.1038/s41598-020-60204-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/14/2020] [Indexed: 02/06/2023] Open
Abstract
Fusarium oxysporum laccase was functionally expressed in Saccharomyces cerevisiae and engineered towards higher expression levels and higher reactivity towards 2,6-dimethoxyphenol, that could be used as a mediator for lignin modification. A combination of classical culture optimization and protein engineering led to around 30 times higher activity in the culture supernatant. The winner mutant exhibited three times lower Km, four times higher kcat and ten times higher catalytic efficiency than the parental enzyme. The strategy for laccase engineering was composed of a combination of random methods with a rational approach based on QM/MM MD studies of the enzyme complex with 2,6-dimethoxyphenol. Laccase mediator system with 2,6-dimethoxyphenol caused fulvic acids release from biosolubilized coal.
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Affiliation(s)
- Natalia Kwiatos
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Marzena Jędrzejczak-Krzepkowska
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Agnieszka Krzemińska
- Institute of Physics, Lodz University of Technology, Wólczańska 219, 90-924, Lodz, Poland
| | | | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wróblewskiego 15, 93-590, Lodz, Poland
| | - Stanisław Bielecki
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland.
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Kumar A, Arora S, Jain KK, Sharma KK. Metabolic coupling in the co-cultured fungal-yeast suite of Trametes ljubarskyi and Rhodotorula mucilaginosa leads to hypersecretion of laccase isozymes. Fungal Biol 2019; 123:913-926. [DOI: 10.1016/j.funbio.2019.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 09/25/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022]
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Molecular modeling and docking of recombinant HAP-phytase of a thermophilic mould Sporotrichum thermophile reveals insights into molecular catalysis and biochemical properties. Int J Biol Macromol 2018; 115:501-508. [PMID: 29678789 DOI: 10.1016/j.ijbiomac.2018.04.086] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/16/2018] [Indexed: 11/23/2022]
Abstract
A thermostable and protease-resistant HAP-phytase of Sporotrichum thermophile was over-expressed in Pichia pastoris X-33. Purified recombinant phytase displayed all its biochemical properties similar to wild type. Molecular modeling and docking of phytase with various substrates showed differential binding patterns with GoldScore values ranging from 40.61 to 79.78. Docking with different substrates revealed strong binding affinity with ATP and phytic acid, while the lowest with AMP and phosphoenol pyruvate. This was further confirmed using biochemical assays, as the recombinant enzyme displayed broad substrate specificity. Docking with inhibitors also showed differential binding with GoldScore values ranging from 22.94 (2,3-butanedione) to 85.72 (myo-inositol hexasulphate). Validation using biochemical analysis revealed that both 2,3-butanedione and phenyl glyoxal inhibited the phytase activity significantly. Furthermore, presence of inorganic phosphate in the reaction mixture also inhibited the phytase activity, as there was no activity at and beyond 0.8 mM. Docking of phytase with metavanadate showed binding at the same atom in the active-site where the substrate i.e. phytic acid binds. Vanadium incorporation resulted in the catalytic conversion of phytase into a peroxidase with concomitant inhibition of phytase activity. Peroxidase activity was high in acidic range and the product formation showed correlation with reaction time. Furthermore, molecular modeling and docking of recombinant HAP-phytase of a thermophilic mould S. thermophile reveals insights into molecular catalysis that is validated by the biochemical properties.
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Sharma KK, Singh D, Rawat S. Molecular dynamics simulation studies suggests unconventional roles of non-secretary laccases from enteropathogenic gut bacteria and Cryptococcus neoformans serotype D. Comput Biol Chem 2018; 73:41-48. [PMID: 29425935 DOI: 10.1016/j.compbiolchem.2018.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/28/2017] [Accepted: 01/23/2018] [Indexed: 12/11/2022]
Abstract
Laccase in Cryptococcus neoformans is covalently linked to the carbohydrate moiety of the cell wall, which allows it to get access to the different substrates for catalyzing their oxidation and therefore plays a vital role in the virulence. The laccase gene (3.0 kb) from C. neoformans serotype D was amplified, cloned and sequenced for protein modeling, docking and simulation studies. The three dimensional homology models of laccase protein from C. neoformans and other pathogenic gut bacteria were docked with selected biomolecules like prostaglandins (PG), membrane phospholipids, neurotransmitters (serotonin) using GOLD software. The GOLDscore values of laccase from C. neoformans docked with prostaglandinH2 (59.76), prostaglandinG2 (59.45), prostaglandinE2 (60.99), phosphatidylinositol (54.95), phosphatidylcholine (46.26), phosphatidylserine (55.26), arachidonic acid (53.08) and serotonin (46.22) were similar to the laccase from enteropathogenic bacteria but showed a better binding affinity as compared to that of the non-pathogenic bacteria (e.g. Bacillus safensis, Bacillus pumilus and Bacillus subtilis). The RMSD of MD simulation study done for 25 ns using laccase protein from C. neoformans complexed with phosphatidylcholine was found to be highly stable, followed by the laccase-PGE2 and laccase-serotonin complexes. Furthermore, the binding free energy results were found to support the docking and MD simulation results. The present study implies that few candidate ligands can be intermediate substrate in the catalysis of microbial laccases, which can further play some crucial role in the cell signaling and pathogenesis of enteropathogenic gut micro flora and C. neoformans.
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Affiliation(s)
- Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India.
| | - Deepti Singh
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Surender Rawat
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
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Kameshwar AKS, Barber R, Qin W. Comparative modeling and molecular docking analysis of white, brown and soft rot fungal laccases using lignin model compounds for understanding the structural and functional properties of laccases. J Mol Graph Model 2017; 79:15-26. [PMID: 29127854 DOI: 10.1016/j.jmgm.2017.10.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 11/19/2022]
Abstract
Extrinsic catalytic properties of laccase enable it to oxidize a wide range of aromatic (phenolic and non-phenolic) compounds which makes it commercially an important enzyme. In this study, we have extensively compared and analyzed the physico-chemical, structural and functional properties of white, brown and soft rot fungal laccases using standard protein analysis software. We have computationally predicted the three-dimensional comparative models of these laccases and later performed the molecular docking studies using the lignin model compounds. We also report a customizable rapid and reliable protein modelling and docking pipeline for developing structurally and functionally stable protein structures. We have observed that soft rot fungal laccases exhibited comparatively higher structural variation (higher random coil) when compared to brown and white rot fungal laccases. White and brown rot fungal laccase sequences exhibited higher similarity for conserved domains of Trametes versicolor laccase, whereas soft rot fungal laccases shared higher similarity towards conserved domains of Melanocarpus albomyces laccase. Results obtained from molecular docking studies showed that aminoacids PRO, PHE, LEU, LYS and GLN were commonly found to interact with the ligands. We have also observed that white and brown rot fungal laccases showed similar docking patterns (topologically monomer, dimer and trimer bind at same pocket location and tetramer binds at another pocket location) when compared to soft rot fungal laccases. Finally, the binding efficiencies of white and brown rot fungal laccases with lignin model compounds were higher compared to the soft rot fungi. These findings can be further applied in developing genetically efficient laccases which can be applied in growing biofuel and bioremediation industries.
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Affiliation(s)
| | - Richard Barber
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario, P7 B 5E1, Canada
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario, P7 B 5E1, Canada.
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Investigation on electrochemical behavior and its catalytic effect on oxygen reduction reaction of 3-Ferrocenyl dihydropyrazole derivative as electron relay. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.09.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kumar A, Singh D, Sharma KK, Arora S, Singh AK, Gill SS, Singhal B. Gel-Based Purification and Biochemical Study of Laccase Isozymes from Ganoderma sp. and Its Role in Enhanced Cotton Callogenesis. Front Microbiol 2017; 8:674. [PMID: 28473815 PMCID: PMC5397484 DOI: 10.3389/fmicb.2017.00674] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 03/31/2017] [Indexed: 01/05/2023] Open
Abstract
Basidiomycetous fungi, Ganoderma lucidum MDU-7 and Ganoderma sp. kk-02 secreted multiple laccase isozymes under diverse growth condition. Aromatic compounds and metal salts were also found to regulate the differential expression of laccase isozymes from both the Ganoderma sp. Laccase isozymes induced in the presence of copper from G. lucidum MDU-7 were purified by gel-based (native-PAGE) purification method. The purity of laccase isozymes was checked by zymogram and SDS-PAGE. The SDS-PAGE of purified proteins confirmed the multimeric nature of laccase isozymes. The molecular mass of isozymes was found to be in the range of 40–66 kDa. Further, the purified laccase isozymes and their peptides were confirmed with the help of MALDI-TOF peptide fingerprinting. The biochemical characterization of laccase isozymes viz. Glac L2, Glac L3, Glac L4, and Glac L5 have shown the optimum temperature in the range of 30°–45°C and pH 3.0. The Km values of all the laccase isozymes determined for guaiacol were (96–281 μM), ABTS (15–83 μM) and O-tolidine (78–724 μM). Further, laccase isozymes from G. lucidum whole genome were studied using bioinformatics tools. The molecular modeling and docking of laccase isozymes with different substrates showed a significant binding affinity, which further validates our experimental results. Interestingly, copper induced laccase of 40 U/ml in culture medium was found to significantly induce cotton callogenesis. Interestingly, all the laccase isozymes were found to have an antioxidative role and therefore capable in free radicals scavenging during callogenesis. This is the first detailed study on the biochemical characterization of all the laccase isozymes purified by a gel-based novel method.
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Affiliation(s)
- Amit Kumar
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India.,School of Biotechnology, Gautam Buddha UniversityGreater Noida, India
| | - Deepti Singh
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
| | - Krishna K Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
| | - Sakshi Arora
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
| | - Amarjeet K Singh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South CampusNew Delhi, India
| | - Sarvajeet S Gill
- Stress Physiology and Molecular Biology Laboratory, Centre for Biotechnology, Maharshi Dayanand UniversityRohtak, India
| | - Barkha Singhal
- School of Biotechnology, Gautam Buddha UniversityGreater Noida, India
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Huo W, Zeng H, Yang Y, Zhang Y. Performance of glucose/O2 enzymatic fuel cell based on supporting electrodes over-coated by polymer-nanogold particle composite with entrapped enzymes. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Yang Y, Zeng H, Huo WS, Zhang YH. Direct Electrochemistry and Catalytic Function on Oxygen Reduction Reaction of Electrodes Based on Two Kinds of Magnetic Nano-particles with Immobilized Laccase Molecules. J Inorg Organomet Polym Mater 2016. [DOI: 10.1007/s10904-016-0464-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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17
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Tomar JS, Peddinti RK. Optimized method for TAG protein homology modeling: In silico and experimental structural characterization. Int J Biol Macromol 2016; 88:102-12. [DOI: 10.1016/j.ijbiomac.2016.03.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 01/03/2023]
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18
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Manas NHA, Bakar FDA, Illias RM. Computational docking, molecular dynamics simulation and subsite structure analysis of a maltogenic amylase from Bacillus lehensis G1 provide insights into substrate and product specificity. J Mol Graph Model 2016; 67:1-13. [DOI: 10.1016/j.jmgm.2016.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/14/2016] [Accepted: 04/18/2016] [Indexed: 10/21/2022]
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19
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Singh D, Rawat S, Waseem M, Gupta S, Lynn A, Nitin M, Ramchiary N, Sharma KK. Molecular modeling and simulation studies of recombinant laccase from Yersinia enterocolitica suggests significant role in the biotransformation of non-steroidal anti-inflammatory drugs. Biochem Biophys Res Commun 2016; 469:306-12. [DOI: 10.1016/j.bbrc.2015.11.096] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 11/22/2015] [Indexed: 01/30/2023]
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20
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Zhang J, Chen H, Chen M, Ren A, Huang J, Wang H, Zhao M, Feng Z. Cloning and functional analysis of a laccase gene during fruiting body formation in Hypsizygus marmoreus. Microbiol Res 2015; 179:54-63. [PMID: 26411895 DOI: 10.1016/j.micres.2015.06.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/27/2015] [Accepted: 06/19/2015] [Indexed: 10/23/2022]
Abstract
The Hypsizygus marmoreus laccase gene (lcc1) sequence was cloned and analyzed. The genomic DNA of lcc1 is 2336 bp, comprising 13 introns and 14 exons. The 1626-bp full-length cDNA encodes a mature laccase protein containing 542 amino acids, with a 21-amino acid signal peptide. Phylogenetic analysis showed that the lcc1 amino acid sequence is homologous to basidiomycete laccases and shares the highest similarity with Flammulina velutipes laccase. A 2021-bp promoter sequence containing a TATA box, CAAT box, and several putative cis-acting elements was also identified. To study the function of lcc1, we first overexpressed lcc1 in H. marmoreus and found that the transgenic fungus producing recombinant laccase displayed faster mycelial growth than the wild-type (wt) strain. Additionally, primordium initiation was induced 3-5 days earlier in the transgenic fungus, and fruiting body maturation was also promoted approximately five days earlier than in the wt strain. Furthermore, we detected that lcc1 was sustainably overexpressed and that laccase activity was also higher in the transgenic strains compared with the wt strain during development in H. marmoreus. These results indicate that the H. marmoreus lcc1 gene is involved in mycelial growth and fruiting body initiation by increasing laccase activity.
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Affiliation(s)
- Jinjing Zhang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People's Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, No. 1000, Jinqi Road, FengXian District, Shanghai 201403, China
| | - Hui Chen
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People's Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, No. 1000, Jinqi Road, FengXian District, Shanghai 201403, China
| | - Mingjie Chen
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People's Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, No. 1000, Jinqi Road, FengXian District, Shanghai 201403, China
| | - Ang Ren
- College of Life Science, Nanjing Agricultural University, No. 1, Weigang road, XuanWu District, Nanjing 210095, China
| | - Jianchun Huang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People's Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, No. 1000, Jinqi Road, FengXian District, Shanghai 201403, China
| | - Hong Wang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People's Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, No. 1000, Jinqi Road, FengXian District, Shanghai 201403, China
| | - Mingwen Zhao
- College of Life Science, Nanjing Agricultural University, No. 1, Weigang road, XuanWu District, Nanjing 210095, China
| | - Zhiyong Feng
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People's Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, No. 1000, Jinqi Road, FengXian District, Shanghai 201403, China; College of Life Science, Nanjing Agricultural University, No. 1, Weigang road, XuanWu District, Nanjing 210095, China.
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Kumar A, Sharma KK, Kumar P, Ramchiary N. Laccase isozymes from Ganoderma lucidum MDU-7: Isolation, characterization, catalytic properties and differential role during oxidative stress. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.01.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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