Homology Modeling of Laccase Enzyme of Filamentous Fungus Trichoderma sp. CNSC-2 and Its Role in Pyrene Degradation

References

• Abbas I, Badran G, Verdin A, Ledoux F, Roumié M, Courcot D, Garçon G. 2018. Polycyclic aromatic hydrocarbon derivatives in airborne particulate matter: sources, analysis and toxicity. Environ Chem Lett 16(2):439–475.
   Web of Science ®Google Scholar
• Abd El Monssef RA, Hassan EA, Ramadan EM. 2016. Production of laccase enzyme for their potential application to decolorize fungal pigments on aging paper and parchment. Ann Agric Sci 61(1):145–154.
   Google Scholar
• Agrawal N, Verma P, Shahi SK. 2018. Degradation of polycyclic aromatic hydrocarbons (phenanthrene and pyrene) by the ligninolytic fungi Ganoderma lucidum isolated from the hardwood stump. Bioresour Bioprocess. 5(1):1–9.
   Google Scholar
• Agrawal N, Shahi SK. 2017. Degradation of polycyclic aromatic hydrocarbon (pyrene) using novel fungal strain Coriolopsis byrsina strain APC5. Int Biodeterior Biodegrad 122:69–81.
   Web of Science ®Google Scholar
• Al Farraj DA, Hadibarata T, Elshikh MS, Al Khulaifi MM, Kristanti RA. 2020. Biotransformation and degradation pathway of pyrene by filamentous soil fungus Trichoderma sp. F03. Water Air Soil Pollut 231(4):1–9.
   Web of Science ®Google Scholar
• Al-Hawash AB, Alkooranee JT, Zhang X, Ma F. 2018. Fungal degradation of polycyclic aromatic hydrocarbons. Int J Pure App Biosci 6(2):8–24.
   Google Scholar
• Andriani A, Tachibana S, Itoh K. 2016. Effects of saline-alkaline stress on benzo [a] pyrene biotransformation and ligninolytic enzyme expression by Bjerkandera adusta SM46. World J Microbiol Biotechnol 32(3):1–16.
   PubMed Web of Science ®Google Scholar
• Arun A, Raja PP, Arthi R, Ananthi M, Kumar KS, Eyini M. 2008. Polycyclic aromatic hydrocarbons (PAHs) biodegradation by basidiomycetes fungi, Pseudomonas isolate, and their cocultures: comparative in vivo and in silico approach. Appl Biochem Biotechnol 151(2–3):132–142.
   PubMed Web of Science ®Google Scholar
• Awasthi M, Jaiswal N, Singh S, Pandey VP, Dwivedi UN. 2015. Molecular docking and dynamics simulation analyses unraveling the differential enzymatic catalysis by plant and fungal laccases with respect to lignin biosynthesis and degradation. J Biomol Struct Dyn 33(9):1835–1849.
   PubMed Web of Science ®Google Scholar
• Bankole PO, Semple KT, Jeon BH, Govindwar SP. 2020. Enhanced enzymatic removal of anthracene by the mangrove soil-derived fungus, Aspergillus sydowii BPOI. Front Environ Sci Eng 14(6):1–13.
   Web of Science ®Google Scholar
• Bishnoi K, Kumar R, Bishnoi NR. 2008. Biodegradation of polycyclic aromatic hydrocarbons by white rot fungi Phanerochaete chrysosporium in sterile and unsterile soil. J Sci Ind Res 67(7):538–542.
   Web of Science ®Google Scholar
• Chandra R, Chowdhary P. 2015. Properties of bacterial laccases and their application in bioremediation of industrial wastes. Environ Sci Process Impacts 17(2):326–342.
   PubMed Web of Science ®Google Scholar
• Chandra R, Kumar V, Yadav S. 2017. Extremophilic ligninolytic enzymes. In: Sani, R, Krishnaraj, R, editors. Extremophilic Enzymatic Processing of Lignocellulosic Feedstocks to Bioenergy. South Dakota: Springer International. p115–154.
   Google Scholar
• Chatterjee S, Kumari S, Rath S, Das S. 2022. Prospects and scope of microbial bioremediation for the restoration of the contaminated sites. In: Das, S, Dash, HR, editors. Microbial Biodegradation and Bioremediation. Amsterdam, The Netherlands: Elsevier. p3–31.
   Google Scholar
• Chauhan PS, Goradia B, Saxena A. 2017. Bacterial laccase: recent update on production, properties and industrial applications. 3 Biotech 7(5):323.
   PubMedGoogle Scholar
• Dai CC, Tian LS, Zhao YT, Chen Y, Xie H. 2010. Degradation of phenanthrene by the endophytic fungus Ceratobasidum stevensii found in Bischofia polycarpa. Biodegradation. 21(2):245–255.
   PubMed Web of Science ®Google Scholar
• Geourjon C, Deleage G. 1995. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci 11(6):681–684.
   PubMedGoogle Scholar
• Heo L, Park H, Seok C. 2013. GalaxyRefine: protein structure refinement driven by side-chain repacking. Nucleic Acids Res 41(Web Server issue):W384–W388.
   PubMed Web of Science ®Google Scholar
• Howell BW, Herz J. 2001. The LDL receptor gene family: signaling functions during development. Curr Opin Neurobiol 11(1):74–81.
   PubMed Web of Science ®Google Scholar
• Ijoma GN, Tekere M. 2017. Potential microbial applications of co-cultures involving ligninolytic fungi in the bioremediation of recalcitrant xenobiotic compounds. Int J Environ Sci Technol 14(8):1787–1806.
   Web of Science ®Google Scholar
• Jeon JR, Baldrian P, Murugesan K, Chang YS. 2012. Laccase‐catalysed oxidations of naturally occurring phenols: from in vivo biosynthetic pathways to green synthetic applications. Microb Biotechnol 5(3):318–332.
   PubMed Web of Science ®Google Scholar
• Jia SL, Chi Z, Liu GL, Hu Z, Chi ZM. 2020. Fungi in mangrove ecosystems and their potential applications. Crit Rev Biotechnol 40(6):852–864.
   PubMed Web of Science ®Google Scholar
• Kadri T, Rouissi T, Brar SK, Cledon M, Sarma S, Verma M. 2017. Biodegradation of polycyclic aromatic hydrocarbons (PAHs) by fungal enzymes: a review. J Environ Sci 51:52–74.
   Web of Science ®Google Scholar
• Kalra K, Chauhan R, Shavez M, Sachdeva S. 2013. Isolation of laccase producing Trichoderma spp. and effect of pH and temperature on its activity. Int J Environ Sci Technol 5(5):2229–2235.
   Google Scholar
• Kameshwar AKS, Barber R, Qin W. 2018. Comparative modelling 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 79:15–26.
   PubMed Web of Science ®Google Scholar
• Krishna MA, Reddy IB, Kumari MPM, Zaveri MK, Kaladhar DSVGK. 2013. Homology modelling and structural analysis of DNA binding response regulator of Bacillus anthracis. Bioinformatics 2(8):32–34.
   Google Scholar
• Kumari S, Gupta B, Das S. 2023. Functional amyloid of extracellular polymeric substances of marine bacterium Pseudomonas aeruginosa PFL-P1 in the binding of polycyclic aromatic hydrocarbons. Process Biochem 130:67–77.
   Web of Science ®Google Scholar
• Kumar M, Mishra A, Singh SS, Srivastava S, Thakur IS. 2018. Expression and characterization of novel laccase gene from Pandoraea sp. ISTKB and its application. Int J Biol Macromol 115:308–316.
   PubMed Web of Science ®Google Scholar
• Kumar S, Tsai CJ, Nussinov R. 2000. Factors enhancing protein thermostability. Protein Eng 13(3):179–191.
   PubMedGoogle Scholar
• Laskowski RA, Furnham N, Thornton JM. 2013. The Ramachandran plot and protein structure validation. In: Bansal, M, Srinivasan, N, editors. Biomolecular Forms and Functions: A Celebration of 50 Years of the Ramachandran Map. Bangalore, India: World Sci, p62–75.
   Google Scholar
• Liao L, Chen S, Peng H, Yin H, Ye J, Liu Z, Dang Z, Liu Z. 2015. Biosorption and biodegradation of pyrene by Brevibacillus brevis and cellular responses to pyrene treatment. Ecotoxicol Environ Saf 115:166–173.
   PubMed Web of Science ®Google Scholar
• Liu Y, Wei F, Xu R, Cheng T, Ma Y. 2023. Insights into the binding interaction of catechol 1, 2-dioxygenase with catechol in Achromobacter xylosoxidans DN002. Appl Biochem Biotechnol 195(1):298–313.
   PubMed Web of Science ®Google Scholar
• Lowenthal MS, Davis KS, Formolo T, Kilpatrick LE, Phinney KW. 2016. Identification of novel N-glycosylation sites at noncanonical protein consensus motifs. J Proteome Res 15(7):2087–2101.
   PubMed Web of Science ®Google Scholar
• Lüthy R, Bowie JU, Eisenberg D. 1992. Assessment of protein models with three-dimensional profiles. Nature 356(6364):83–85.
   PubMed Web of Science ®Google Scholar
• Mansouri N, Benslama O. 2022. Reprint of: Molecular docking exploration of the degradation activity of some synthetic hydrocarbons polymers by the laccase enzyme of Streptomyces. Mater Today Proc 53:A1–A4.
   Google Scholar
• Maurer-Stroh S, Eisenhaber F. 2004. Myristoylation of viral and bacterial proteins. Trends Microbiol 12(4):178–185.
   PubMed Web of Science ®Google Scholar
• Mohamed SS, Tamer AR, Bensaber SM, Jaeda MI, Ermeli NB, Allafi AA, Mrema IA, Erhuma M, Hermann A, Gbaj AM. 2013. Design, synthesis, molecular modelling, and biological evaluation of sulfanilamide-imines derivatives as potential anticancer agents. Naunyn Schmiedebergs Arch Pharmacol 386(9):813–822.
   PubMed Web of Science ®Google Scholar
• Patel H, Gupta A. 2016. Optimization of different culture conditions for enhanced laccase production and its purification from Tricholoma giganteum AGHP. Bioresour Bioprocess 3(1):1–10.
   Google Scholar
• Patel AB, Shaikh S, Jain KR, Desai C, Madamwar D. 2020. Polycyclic aromatic hydrocarbons: sources, toxicity, and remediation approaches. Front Microbiol 11:562813.
   PubMed Web of Science ®Google Scholar
• Pawar SS, Rohane SH. 2021. Review on discovery studio: an important tool for molecular docking. Asian J Res Chem 14(1):86–88.
   Google Scholar
• Pinheiro AAF, Taranto AG, Duarte AA, Neto AG, da Hora Júnior BT, Pereira GAG, dos Santos Júnior MC, de Assis SA. 2012. Homology modeling studies of beta (1, 3)‐D‐glucan synthase of Moniliophthora perniciosa. Int J Quantum Chem 112(20):3356–3363.
   Web of Science ®Google Scholar
• Saoudi O, Ghaouar N, Othman T. 2017. Fluorescence study of laccase from Trametes versicolor under the effects of pH, chemical denaturants and ionic liquids. J Mol Liq 225:56–63.
   Web of Science ®Google Scholar
• Sarkar S, Banerjee A, Chakraborty N, Soren K, Chakraborty P, Bandopadhyay R. 2020. Structural-functional analyses of textile dye degrading azoreductase, laccase and peroxidase: a comparative in silico study. Electron J Biotechnol 43:48–54.
   Web of Science ®Google Scholar
• Senthivelan T, Kanagaraj J, Panda RC, Narayani T. 2019. Screening and production of a potential extracellular fungal laccase from Penicillium chrysogenum: media optimization by response surface methodology (RSM) and central composite rotatable design (CCRD). Biotechnol Rep 23:e00344.
   Google Scholar
• Singh S, Ashesh A, Devi NL, Yadav IC. 2022. A comprehensive review on occurrence, source, effect, and measurement techniques of polycyclic aromatic hydrocarbons in India. Microchem J 183:108005.
   Web of Science ®Google Scholar
• Singh D, Gupta N. 2020. Microbial laccase: a robust enzyme and its industrial applications. Biologia 75(8):1183–1193.
   Web of Science ®Google Scholar
• Tamboli AS, Rane NR, Patil SM, Biradar SP, Pawar PK, Govindwar SP. 2015. Physicochemical characterization, structural analysis and homology modeling of bacterial and fungal laccases using in silico methods. Netw Model Anal Health Inform Bioinforma. 4(17):1–12.
   Google Scholar
• Tiwary BN, Das R, Paul V. 2022. Bioremediation technology: a cumulative study on microbial bioremediation of heavy metals, aromatic hydrocarbons, acrylamide, and polyacrylamide. In: Verma, P, editor. Industrial Microbiology and Biotechnology. Singapore: Springer Singapore, p589–623.
   Google Scholar
• Vani V, Jayashree DJ, Navya KS, Zaman ST. 2020. Homology modelling and in silico characterization of laccase from Lentinula edodes. IJPI 10(3):273–278.
   Google Scholar
• Varanasi, JL, Das D. 2018. Bioremediation and power generation from organic wastes using microbial fuel cell. In: Das, D, editor. Microbial Fuel Cell: A Bioelectrochemical System That Converts Waste to Watts. New Delhi: Springer International Publishing in addition with Capital Publishing Company. p285–306.
   Google Scholar
• Vasconcelos MR, Vieira GA, Otero IV, Bonugli-Santos RC, Rodrigues MV, Rehder VL, Ferro M, Boaventura S, Bacci M, Sette LD. 2019. Pyrene degradation by marine-derived ascomycete: process optimization, toxicity, and metabolic analyses. Environ Sci Pollut Res Int 26(12):12412–12424.
   PubMed Web of Science ®Google Scholar
• Wingfield P. 2001. Protein precipitation using ammonium sulfate. Curr Protocol Protein Sci 13(1):3FA.
   Google Scholar
• Xiang Z. 2006. Advances in homology protein structure modeling. Curr Protein Pept Sci. 7(3):217–227.
   PubMed Web of Science ®Google Scholar
• Zafra G, Absalón AE, Cortés-Espinosa DV. 2015. Morphological changes and growth of filamentous fungi in the presence of high concentrations of PAHs. Braz J Microbiol 46(3):937–941.
   PubMed Web of Science ®Google Scholar
• Zhang S, Ning Y, Zhang X, Zhao Y, Yang X, Wu K, Yang S, La G, Sun X, Li X. 2015. Contrasting characteristics of anthracene and pyrene degradation by wood rot fungus Pycnoporus sanguineus H1. Int Biodeterior Biodegrad 105:228–232.
   Web of Science ®Google Scholar
• Zhang S, Wu Z, Chen G, Wang Z. 2018. An improved method to encapsulate laccase from Trametes versicolor with enhanced stability and catalytic activity. Catalysts 8(7):286.
   Web of Science ®Google Scholar