System biology analysis of endosulfan biodegradation in bacteria and its effect in other living systems: modeling and simulation studies

References

• Autiero, I., Costantini, S., & Colonna, G. (2009). Modeling of the bacterial mechanism of methicillin-resistance by a systems biology approach. PLoS One, 4(7), e6226. https://doi.org/10.1371/journal.pone.0006226
   PubMed Web of Science ®Google Scholar
• Bajaj, A., Pathak, A., Mudiam, M. R., Mayilraj, S., & Manickam, N. (2010). Isolation and characterization of a Pseudomonas sp. strain IITR01 capable of degrading α-endosulfan and endosulfan sulfate. Journal of Applied Microbiology, 109(6), 2135–2143. https://doi.org/10.1111/j.1365-2672.2010.04845.x
   PubMed Web of Science ®Google Scholar
• Barabási, A. L. (2009). Scale-free networks: A decade and beyond. Science (New York, N.Y.), 325(5939), 412–413. https://doi.org/10.1126/science.1173299
   PubMed Web of Science ®Google Scholar
• Barabasi, A. L., & Oltvai, Z. N. (2004). Network biology: Understanding the cell's functional organization. Nature Reviews. Genetics, 5(2), 101–113. 2004
   PubMed Web of Science ®Google Scholar
• Bhalerao, T. S. (2012). Bioremediation of endosulfan-contaminated soil by using bioaugmentation treatment of fungal inoculants Aspergillus niger. Turk J. Biol, 36, 561–567.
   Web of Science ®Google Scholar
• Bhatt, P., Joshi, T., Bhatt, K., Zhang, W., Huang, Y., & Chen, S. (2021). Binding interaction of glyphosate with glyphosate oxidoreductase and C-P lyase: Molecular docking and molecular dynamics simulation studies. Journal of Hazardous Materials, 409, 124927. https://doi.org/10.1016/j.jhazmat.2020.12492733450511
   PubMed Web of Science ®Google Scholar
• Bhatt, P., Rene, E. R., Kumar, A. J., Zhang, W., & Chen, S. (2020c). Binding interaction of allethrin with esterase: Bioremediation potential and mechanism. Bioresource Technology, 315, 123845https://doi.org/10.1016/j.biortech.2020.12384532707504
   PubMed Web of Science ®Google Scholar
• Bhatt, P., Gangola, S., Bhandari, G., Zhang, W., Maithani, D., Mishra, S., & Chen, S. (2020a). New insights into the degradation of synthetic pollutants in contaminated environments. Chemosphere. Chemosphere, 268, 128827. https://doi.org/10.1016/j.chemosphere.2020.128827
   PubMed Web of Science ®Google Scholar
• Bhatt, P., Gangola, S., Chaudhary, P., Khati, P., Kumar, G., Sharma, A., & Srivastava, A. (2019c). Pesticide induced up-regulation of esterase and aldehyde dehydrogenase in indigenous Bacillus spp. Bioremediation Journal, 23(1), 42–52. https://doi.org/10.1080/10889868.2019.1569586
   Web of Science ®Google Scholar
• Bhatt, P., Pal, K., Bhandari, G., & Barh, A. (2019a). Modelling of the methyl halide biodegradation in bacteria and its effect on environmental systems. Pesticide Biochemistry and Physiology, 158, 88–100. https://doi.org/10.1016/j.pestbp.2019.04.015
   PubMed Web of Science ®Google Scholar
• Bhatt, P., Pathak, R., & Bhatt, K. (2019b). System biology, simulation, and network analysis of enzymes in waste removal from the environment. In Smart bioremediation techniques (pp. 347–358). Academic Press.
   Google Scholar
• Bhatt, P., Sethi, K., Gangola, S., Bhandari, G., Verma, A., Adnan, M., Singh, Y., & Chaube, S. (2020b). Modeling and simulation of atrazine biodegradation in bacteria and its effect in other living systems. Journal of Biomolecular Structure & Dynamics, 12, 1–11. https://doi.org/10.1080/07391102.2020.1846623
   Google Scholar
• Bonnet, J., Yin, P., Ortiz, M. E., Subsoontorn, P., & Endy, D. (2013). Amplifying genetic logic gates. Science (New York, N.Y.), 340(6132), 599–603. https://doi.org/10.1126/science.1232758
   PubMed Web of Science ®Google Scholar
• Caride, A., Lafuente, A., & Cabaleiro, T. (2010). Endosulfan effects on pituitary hormone and both nitrosative and oxidative stress in pubertal male rats. Toxicology Letters, 197(2), 106–112. https://doi.org/10.1016/j.toxlet.2010.05.006
   PubMed Web of Science ®Google Scholar
• Doncheva, N. T., Assenov, Y., Domingues, F. S., & Albrecht, M. (2012). Topological analysis and interactive visualization of biological networks and protein structures. Nature Protocols, 7(4), 670–685. https://doi.org/10.1038/nprot.2012.004
   PubMed Web of Science ®Google Scholar
• Drager, A., & Palsson, B. O. (2014). Improving collaboration by standardization efforts in systems biology. Frontiers in Bioengineering and Biotechnology, 2, 61 https://doi.org/10.3389/fbioe.2014.00061
   PubMedGoogle Scholar
• Drager, A., Zielinski, D. C., Keller, R., Rall, M., Eichner, J., Palsson, B. O., & Zell, A. (2015). SBMLsqueezer 2: Context-sensitive creation of kinetic equations in biochemical networks. BMC Syst Biol, 9(1), 68 https://doi.org/10.1186/s12918-015-0212-9
   PubMedGoogle Scholar
• El Bakouri, H., Ouassini, A., Morillo, J., & Usero, J. (2007). Endosulfan sulfate mobility in soil columns and pesticide pollution of groundwater in Northwest Morocco. Water Environ Res, 79(13), 2578–2584. https://doi.org/10.2175/106143007x184528
   PubMed Web of Science ®Google Scholar
• Fang, Y., Nie, Z., Yang, J., Die, Q., Tian, Y., Liu, F., He, J., Wang, J., & Huang, Q. (2018). Spatial distribution of and seasonal variations in endosulfan concentrations in soil, air, and biota around a contaminated site. Ecotoxicology and Environment Safety., 161, 402–408. https://doi.org/10.1016/j.ecoenv.2018.06.013
   PubMed Web of Science ®Google Scholar
• Funahashi, A., Matsuoka, Y., Jouraku, A., Morohashi, M., Kikuchi, N., & Kitano, H. (2008). CellDesigner 3.5: A versatile modeling tool for biochemical networks. Proceedings of the IEEE, 96(8), 1254–1265. https://doi.org/10.1109/JPROC.2008.925458
   Web of Science ®Google Scholar
• Funahashi, A., Morohashi, M., Kitano, H., & Tanimura, N. (2003). Cell Designer: A process diagram editor for gene-regulatory and biochemical networks. BIOSILICO, 1(5), 159–162. 5382(03)02370-9 https://doi.org/10.1016/S1478-
   Google Scholar
• Gao, Y., Zheng, H., Xia, Y., & Cai, M. (2020). Global scale distribution, seasonal changes and long-range transport potentiality of endosulfan in the surface seawater and air. Chemosphere. Chemosphere, 260, 127634. https://doi.org/10.1016/j.chemosphere.2020.127634
   PubMed Web of Science ®Google Scholar
• Hernández-Ramos, A. C., Hernández, S., & Ortíz, I. (2019). Study on endosulfan-degrading capability of Paecilomycesvariotii, Paecilomyceslilacinus and Sphingobacterium sp. in liquid cultures. Bioremedication Journal, 23(4), 251-258. https://doi.org/10.1080/10889868.2019.1671794
   Google Scholar
• Hinojosa-Garro, D., Chan, A. M. B., & Osten, JR-v. (2016). Organochlorine pesticides (OCPs) in sediment and fish of two tropical water bodies under different land use. Bulletin of Environmental Contamination and Toxicology, 97 (1), 105–111. https://doi.org/10.1007/s00128-016-1828-1
   PubMed Web of Science ®Google Scholar
• Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., & Kummer, U. (2006). COPASI-a COmplex Pathway SImulator. Bioinformatics (Oxford, England), 22(24), 3067–3074. https://doi.org/10.1093/bioinformatics/btl485
   PubMed Web of Science ®Google Scholar
• Hu, J. X., Thomas, C. E., & Brunak, S. (2016). Network biology concepts in complex disease comorbidities. Nat Rev Genet, 17(10), 615–629. https://doi.org/10.1038/nrg.2016.87
   PubMed Web of Science ®Google Scholar
• Ito, K., Kawashima, F., Takagi, K., Kataoka, R., Kotake, M., Kiyota, H., Yamazaki, K., Sakakibara, F., & Okada, S. (2016). Isolation of endosulfan sulfate-degrading Rhodococcus koreensis strain S1-1 from endosulfan contaminated soil and identification of a novel metabolite, endosulfan diol monosulfate. Biochemical and Biophysical Research Communications, 473(4), 1094–1099. https://doi.org/10.1016/j.bbrc.2016.04.021
   PubMed Web of Science ®Google Scholar
• Jaiswal, S., Singh, D., K., & Shukla, P. (2019). Gene editing and systems biology tools for pesticide bioremediation: A review. Frontiers in Microbiology, 10, 87. https://doi.org/10.3389/fmicb.2019.00087
   PubMed Web of Science ®Google Scholar
• Jesitha, K., Nimisha, K. M., Manjusha, C. M., & Harikumar, P. S. (2015). Biodegradation of endosulfan by Pseudomonas fluorescens. Environmental Processes, 2(1), 225–240. https://doi.org/10.1007/s40710-015-0059-5
   Google Scholar
• Joosten, V., & Van Berkel, W. J. H. (2007). Flavoenzymes. Current Opinion in Chemical Biology, 11(2), 195–202. https://doi.org/10.1016/j.cbpa.2007.01.010
   PubMed Web of Science ®Google Scholar
• Kamei, I., Takagi, K., & Kondo, R. (2011). Degradation of endosulfan and endosulfansulfate by white-rot fungus Trameteshirsuta. Journal of Wood Science, 57(4), 317–322. https://doi.org/10.1007/s10086-011-1176-z
   Web of Science ®Google Scholar
• Kataoka, R., & Takagi, K. (2013). Biodegradability and biodegradation pathways of endosulfan and endosulfan sulfate. Applied Microbiology and Biotechnology, 97(8), 3285–3292. https://doi.org/10.1007/s00253-013-4774-4
   PubMed Web of Science ®Google Scholar
• Keller, R., Dorr, A., Tabira, A., Funahashi, A., Ziller, M. J., Adams, R., Rodriguez, N., Le Novere, N., Hiroi, N., Planatscher, H., Zell, A., & Drager, A. (2013). The systems biology simulation core algorithm. BMC Systems Biology, 7(1), 55 https://doi.org/10.1186/1752-0509-7-55
   PubMedGoogle Scholar
• Kohl, M., Wiese, S., & Warscheid, B. (2011). Cytoscape: software for visualization and analysis of biological networks. In Michael Hamacher, Martin Eisenacher and Christian Stephan (Eds.), Data mining in proteomics (pp. 291–303). Humana Press.
   Google Scholar
• Kumar, A., Bhoot, N., Soni, I., & John, P. J. (2014). Isolation and characterization of a Bacillus subtilis strain that degrades endosulfan and endosulfan sulfate. 3 Biotech, 4(5), 467–475. https://doi.org/10.1007/s13205-013-0176-7
   PubMedGoogle Scholar
• Kumari, M., Ghosh, P., & Swati Thakur, I. S. (2014). Microcosmic study of endosulfan degradation by Paenibacillussp ISTP10 and its toxicological evaluation using mammalian cell line. International Biodeterioration and Biodegradation, 96, 33–40. https://doi.org/10.1016/j.ibiod.2014.08.003
   Web of Science ®Google Scholar
• Liebermeister, W., Uhlendorf, J., & Klipp, E. (2010). Modular rate laws for enzymatic reactions: Thermodynamics, elasticities and implementation. Bioinformatics (Oxford, England), 26(12), 1528–1534. https://doi.org/10.1093/bioinformatics/btq141
   PubMed Web of Science ®Google Scholar
• Lu, X., Jain, V. V., Finn, P. W., & Perkins, D. L. (2007). Hubs in biological interaction networks exhibit low changes in expression in experimental asthma. Molecular Systems Biology, 3, 1–6.
   Web of Science ®Google Scholar
• Machne, R., Finney, A., M€Uller, S., Lu, J., Widder, S., & Flamm, C. (2006). The SBML ODE Solver Library: A native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics (Oxford, England), 22(11), 1406–1407. https://doi.org/10.1093/bioinformatics/btl086
   PubMed Web of Science ®Google Scholar
• Maier-Bode, H. (1968). Properties, effect, residues and analytics of the insecticide endosulfan. Residue Reviews, 22, 1–44.
   PubMedGoogle Scholar
• Milesi, M. M., Varayoud, J., Ramos, J. G., & Luque, E. H. (2017). Uterine ERα epigenetic modifications are induced by the endocrine disruptor endosulfan in female rats with impaired fertility. Molecular and Cellular Endocrinology, 454, 1–11. https://doi.org/10.1016/j.mce.2017.05.028
   PubMed Web of Science ®Google Scholar
• Mir, Z. A., Ali, S., Tyagi, A., Ali, A., Bhat, J. A., Jaiswal, P., Qari, H. A., & Oves, M. (2017). Degradation and conversion of endosulfan by newly isolated Pseudomonas mendocina ZAM1 strain. 3 Biotech, 7(3), 211 https://doi.org/10.1007/s13205-017-0823-5
   PubMedGoogle Scholar
• Mishra, S., Zhang, W., Lin, Z., Pang, S., Huang, Y., Bhatt, P., & Chen, S. (2020). Carbofuran toxicity and its microbial degradation in contaminated environments. Chemosphere, 259, 127419 https://doi.org/10.1016/j.chemosphere.2020.127419
   PubMed Web of Science ®Google Scholar
• Nawaz, A., Razpotnik, A., Rouimi, P., De Sousa, G., Cravedi, J. P., & Rahmani, R. (2014). Cellular impact of combinations of endosulfan, atrazine, and chlorpyrifos on human primary hepatocytes and HepaRG cells after short and chronic exposures. Cell Biology and Toxicology, 30(1), 17–29. https://doi.org/10.1007/s10565-013-9266-x
   PubMed Web of Science ®Google Scholar
• Newman, M. E. J., Barabási, A. L., & Watts, D. J. (2006). The Structure and Dynamics of Networks. Princeton University Press.
   Google Scholar
• OSPAR. (2002). OSPAR—Background Document on Endosulphan. Hazardous Substance Series. OSPAR Commission. Oslo–Paris Convention for the North–East Atlantic0946956987; p. 1–42.
   Google Scholar
• Pathak, R. K., Baunthiyal, M., Pandey, N., Pandey, D., & Kumar, A. (2017). Modeling of the jasmonatesignaling pathway in Arabidopsis thaliana with respect to pathophysiology of Alternaria blight in Brassica. Scientific Reports, 7(1), 1–12. https://doi.org/10.1038/s41598-017-16884-3
   PubMedGoogle Scholar
• Rodríguez, A., Castrejón-Godínez, M. L., Salazar-Bustamante, E., Gama-Martínez, Y., Sánchez-Salinas, E., Mussali-Galante, P., Tovar-Sánchez, E., & Ortiz-Hernández, M. L. (2020). Omics approaches to pesticide biodegradation. Current Microbiology, 77(4), 545-563. https://doi.org/10.1007/s00284-020-01916-5
   Google Scholar
• Saito, R., Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P. L., Lotia, S., Pico, A. R., G. D., Bader, G. D., & Ideker, T. (2012). A travel guide to Cytoscape plugins. Nature Methods, 9(11), 1069–1076. https://doi.org/10.1038/nmeth.2212
   PubMed Web of Science ®Google Scholar
• Seralathan, M. V., Sivanesan, S., Nargunanathan, S., Bafana, A., Kannan, K., & Chakrabarti, T. (2015). Chemotaxis-based endosulfan biotransformation: enrichment and isolation of endosulfan-degrading bacteria. Environmental Technology, 36(1–4), 60–67. https://doi.org/10.1080/09593330.2014.937464
   PubMed Web of Science ®Google Scholar
• Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498–2504. https://doi.org/10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Singh, D. K., & Sarat Singh, N. (2017). Endosulfan a Cyclodiene Organochlorine Pesticide: Possible Pathways of Its Biodegradation. In: Singh S. (eds.), Microbe-Induced Degradation of Pesticides. Environmental Science and Engineering. Springer. https://doi.org/10.1007/978-3-319-45156-5_5
   Google Scholar
• Sutherland, T. D., Horne, I., Lacey, M. J., Harcourt, R. L., Russell, R. J., & Oakeshott, J. G. (2002). Isolation and characterization of a Mycobacterium strain that metabolizes the insecticide endosulfan. Journal of Applied Microbiology, 93(3), 380–389. https://doi.org/10.1046/j.1365-2672.2002.01728.x
   PubMed Web of Science ®Google Scholar
• Syed, J. H., Alamdar, A., Mohammad, A., Ahad, K., Shabir, Z., Ahmed, H., Ali, S. M., Sani, S. G. A. S., Bokhari, H., Gallagher, K. D., Ahmad, I., & Eqani, S. A. M. A. S. (2014). Pesticide residues in fruits and vegetables from Pakistan: A review of the occurrence and associated human health risks. Environmental Science and Pollution Research International, 21(23), 13367–13393. doi:10.1007/s11356-014-3117-z.
   PubMed Web of Science ®Google Scholar
• Thangadurai, P., & Suresh, S. (2014). Biodegradation of endosulfan by soil bacterial cultures. International Biodeterioration & Biodegradation, 94, 38–47. https://doi.org/10.1016/j.ibiod.2014.06.017
   Web of Science ®Google Scholar
• Touré, V., Le Novère, N., Waltemath, D., & Wolkenhauer, O. (2018). Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PLoS Computational Biology, 14(2), e1005740 https://doi.org/10.1371/journal.pcbi.1005740
   PubMed Web of Science ®Google Scholar
• Ulčnik, A., Kralj Cigić, I., & Pohleven, F. (2013). Degradation of lindane and endosulfan by fungi, fungal and bacterial laccases. World Journal of Microbiology & Biotechnology , 29(12), 2239–2247. https://doi.org/10.1007/s11274-013-1389-y
   PubMed Web of Science ®Google Scholar
• Vivekanandhan, N., & Duraisamy, A. (2012). Ecological impact of pesticides principally organochlorine insecticide endosulfan: A review. Universal Journal of Environmental Research and Technology, 2 (5), 369–376.
   Google Scholar
• Wang, P., Lu, J., & Yu, X. (2014). Identification of important nodes in directed biological networks: a network motif approach. PLoS One, 9(8), e106132. https://doi.org/10.1371/journal.pone.0106132
   PubMed Web of Science ®Google Scholar
• Yoon, J., Blumer, A., & Lee, K. (2006). An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality. Bioinformatics (Oxford, England), 22(24), 3106–3108. https://doi.org/10.1093/bioinformatics/btl533
   PubMed Web of Science ®Google Scholar
• Zaffar, H., Sabir, S. R., Pervez, A., & Naqvi, T. A. (2018). Kinetics of endosulfan biodegradation by Stenotrophomonas maltophilia EN-1 isolated from pesticide-contaminated soil. Soil and Sediment Contamination: An International Journal, 27(4), 267–279. https://doi.org/10.1080/15320383.2018.1470605
   Web of Science ®Google Scholar
• Zinovyev, A., Viara, E., Calzone, L., & Barillot, E. (2008). BiNoM: A Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics (Oxford, England), 24(6), 876–877. https://doi.org/10.1093/bioinformatics/btm553
   PubMed Web of Science ®Google Scholar