Abstract
The wide use of malachite green (MG) as a dye has caused substantial concern owing to its toxicity. Bacillus cereus can against the toxic effect of MG and efficiently decolourise it. However, detailed information regarding its underlying adaptation and degradation mechanisms based on proteomic data is scarce. In this study, the isobaric tags for relative and absolute quantitation (iTRAQ)-facilitated quantitative method was applied to analyse the molecular mechanisms by which B. cereus degrades MG. Based on this analysis, 209 upregulated proteins and 198 downregulated proteins were identified with a false discovery rate of 1% or less during MG biodegradation. Gene ontology and KEGG analysis determined that the differentially expressed proteins were enriched in metabolic processes, catalytic activity, antioxidant activity, and responses to stimuli. Furthermore, real-time qPCR was utilised to further confirm the regulated proteins involved in benzoate degradation. The proteins BCE_4076 (Acetyl-CoA acetyltransferase), BCE_5143 (Acetyl-CoA acetyltransferase), BCE_5144 (3-hydroxyacyl-CoA dehydrogenase), BCE_4651 (Enoyl-CoA hydratase), and BCE_5474 (3-hydroxyacyl-CoA dehydrogenase) involved in the benzoate degradation pathway may play an important role in the biodegradation of MG by B. cereus. The results of this study not only provide a comprehensive view of proteomic changes in B. cereus upon MG loading but also shed light on the mechanism underlying MG biodegradation by B. cereus.
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References
Adav, S.S., Ng, C.S., and Sze, S.K. 2011. iTRAQ-based quantitative proteomic analysis of Thermobifida fusca reveals metabolic pathways of cellulose utilization. J. Proteomics 74, 2112–2122.
Amera, G.M., Khan, R.J., Pathak, A., Jha, R.K., Muthukumaran, J., and Singh, A.K. 2020. Computer aided ligand based screening for identification of promising molecules against enzymes involved in peptidoglycan biosynthetic pathway from Acinetobacter baumannii. Microb. Pathog. 147, 104205.
Cha, C.J., Doerge, D.R., and Cerniglia, C.E. 2001. Biotransformation of malachite green by the fungus Cunninghamella elegans. Appl. Environ. Microbiol. 67, 4358–4360.
Chang, J.S. and Kuo, T.S. 2000. Kinetics of bacterial decolorization of azo dye with Escherichia coli NO3. Bioresour. Technol. 75, 107–111.
Chen, C.Y., Kuo, J.T., Cheng, C.Y., Huang, Y.T., Ho, I.H., and Chung, Y.C. 2009. Biological decolorization of dye solution containing malachite green by Pandoraea pulmonicola YC32 using a batch and continuous system. J. Hazard. Mater. 172, 1439–1445.
Chen, K.C., Wu, J.Y., Liou, D.J., and Hwang, S.C.J. 2003. Decolorization of the textile dyes by newly isolated bacterial strains. J. Biotechnol. 101, 57–68.
Culp, S.J. and Beland, F.A. 1996. Malachite green: A toxicological review. J. Am. Coll. Toxicol. 15, 219–238.
Daneshvar, N., Ayazloo, M., Khataee, A.R., and Pourhassan, M. 2007a. Biological decolorization of dye solution containing malachite green by microalgae Cosmarium sp. Bioresour. Technol. 98, 1176–1182.
Daneshvar, N., Khataee, A.R., Rasoulifard, M.H., and Pourhassan, M. 2007b. Biodegradation of dye solution containing malachite green: optimization of effective parameters using taguchi method. J. Hazard. Mater. 143, 214–219.
Debnam, P., Glanville, S., and Clark, A.G. 1993. Inhibition of glutathione s-transferases from rat liver by basic triphenylmethane dyes. Biochem. Pharmacol. 45, 1227–1233.
Deng, D., Guo, J., Zeng, G., and Sun, G. 2008. Decolorization of anthraquinone, triphenylmethane and azo dyes by a new isolated Bacillus cereus strain DC11. Int. Biodeterior. Biodegradation 62, 263–269.
Du, L.N., Zhao, M., Li, G., Xu, F.C., Chen, W.H., and Zhao, Y.H. 2013. Biodegradation of malachite green by Micrococcus sp. strain BD15: Biodegradation pathway and enzyme analysis. Int. Biodeterior. Biodegradation 78, 108–116.
Fessard, V., Godard, T., Huet, S., Mourot, A., and Poul, J.M. 1999. Mutagenicity of malachite green and leucomalachite green in in vitro tests. J. Appl. Toxicol. 19, 421–430.
Ge, P., Ma, C., Wang, S., Gao, L., Li, X., Guo, G., Ma, W., and Yan, Y. 2012. Comparative proteomic analysis of grain development in two spring wheat varieties under drought stress. Anal. Bioanal. Chem. 402, 1297–1313.
Gopinathan, R., Kanhere, J., and Banerjee, J. 2015. Effect of malachite green toxicity on non target soil organisms. Chemosphere 120, 637–644.
Henderson, A.L., Schmitt, T.C., Heinze, T.M., and Cerniglia, C.E. 1997. Reduction of malachite green to leucomalachite green by intestinal bacteria. Appl. Environ. Microbiol. 63, 4099–4101.
Jia, D., Wang, B., Li, X., Peng, W., Zhou, J., Tan, H., Tang, J., Huang, Z., Tan, W., Gan, B., et al. 2017. Proteomic analysis revealed the fruiting-body protein profile of Auricularia polytricha. Curr. Microbiol. 74, 943–951.
Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., et al. 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480–D484.
Liu, S., Ma, Y., Zheng, Y., Zhao, W., Zhao, X., Luo, T., Zhang, J., and Yang, Z. 2020. Cold-stress response of probiotic Lactobacillus plantarum K25 by iTRAQ proteomic analysis. J. Microbiol. Biotechnol. 30, 187–195.
Mattevi, A., de Kok, A., and Perham, R.N. 1992. The pyruvate dehydrogenase multienzyme complex. Curr. Opin. Struct. Biol. 2, 877–887.
Mishra, P., Jain, A., Takabe, T., Tanaka, Y., Negi, M., Singh, N., Jain, N., Mishra, V., Maniraj, R., Krishnamurthy, S.L., et al. 2019. Heterologous expression of serine hydroxymethyltransferase-3 from rice confers tolerance to salinity stress in E. coli and arabidopsis. Front. Plant Sci. 10, 217.
Moumeni, O. and Hamdaoui, O. 2012. Intensification of sonochemical degradation of malachite green by Bromide ions. Ultrason. Sonochem. 19, 404–409.
Murugesan, K., Yang, I.H., Kim, Y.M., Jeon, J.R., and Chang, Y.S. 2009. Enhanced transformation of malachite green by laccase of Ganoderma lucidum in the presence of natural phenolic compounds. Appl. Microbiol. Biotechnol. 82, 341–350.
Musgrave, W.B., Yi, H., Kline, D., Cameron, J.C., Wignes, J., Dey, S., Pakrasi, H.B., and Jez, J.M. 2013. Probing the origins of glutathione biosynthesis through biochemical analysis of glutamate-cysteine ligase and glutathione synthetase from a model photosynthetic prokaryote. Biochem. J. 450, 63–72.
Ranish, J.A., Yi, E.C., Leslie, D.M., Purvine, S.O., Goodlett, D.R., Eng, J., and Aebersold, R. 2003. The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 33, 349–355.
Rasko, D.A., Ravel, J., Økstad, O.A., Helgason, E., Cer, R.Z., Jiang, L., Shores, K.A., Fouts, D.E., Tourasse, N.J., Angiuoli, S.V., et al. 2004. The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Res. 32, 977–988.
Rawat, D., Mishra, V., and Sharma, R.S. 2016. Detoxification of azo dyes in the context of environmental processes. Chemosphere 155, 591–605.
Reiter, L., Kolstø, A.B., and Piehler, A.P. 2011. Reference genes for quantitative, reverse-transcription PCR in Bacillus cereus group strains throughout the bacterial life cycle. J. Microbiol. Methods 86, 210–217.
Saha, S., Wang, J.M., and Pal, A. 2012. Nano silver impregnation on commercial TiO2 and a comparative photocatalytic account to degrade malachite green. Sep. Purif. Technol. 89, 147–159.
Srivastava, S., Sinha, R., and Roy, D. 2004. Toxicological effects of malachite green. Aquat. Toxicol. 66, 319–329.
Sun, S., Xie, S., Chen, H., Cheng, Y., Shi, Y., Qin, X., Dai, S.Y., Zhang, X., and Yuan, J.S. 2016. Genomic and molecular mechanisms for efficient biodegradation of aromatic dye. J. Hazard. Mater. 302, 286–295.
Szewczyk, R., Soboń, A., Słaba, M., and Dlugoński, J. 2015. Mechanism study of alachlor biodegradation by Paecilomyces marquandii with proteomic and metabolomic methods. J. Hazard. Mater. 291, 52–64.
Verma, P. and Madamwar, D. 2003. Decolourization of synthetic dyes by a newly isolated strain of Serratia marcescens. World J. Microbiol. Biotechnol. 19, 615–618.
Wang, B., Chen, Z., Meng, X., Li, M., Yang, X., and Zhang, C. 2017. iTRAQ quantitative proteomic study in patients with thoracic ossification of the ligamentum flavum. Biochem. Biophys. Res. Commun. 487, 834–839.
Wanyonyi, W.C., Onyari, J.M., Shiundu, P.M., and Mulaa, F.J. 2017. Biodegradation and detoxification of malachite green dye using novel enzymes from Bacillus cereus strain KM201428: kinetic and metabolite analysis. Energy Procedia 119, 38–51.
Xie, H., Yang, D.H., Yao, H., Bai, G., Zhang, Y.H., and Xiao, B.G. 2016. iTRAQ-based quantitative proteomic analysis reveals proteomic changes in leaves of cultivated tobacco (Nicotiana tabacum) in response to drought stress. Biochem. Biophys. Res. Commun. 469, 768–775.
Yang, X., Zhang, Z., Gu, T., Dong, M., Peng, Q., Bai, L., and Li, Y. 2016. Data for iTRAQ-based quantitative proteomics analysis of different biotypes in Echinochloa crus-galli with multi-herbicide treatment. Data Brief 9, 741–745.
Yatome, C., Yamada, S., Ogawa, T., and Matsui, M. 1993. Degradation of crystal violet by Nocardia corallina. Appl. Microbiol. Biotechnol. 38, 565–569.
Yi, W., Yang, K., Ye, J., Long, Y., Ke, J., and Ou, H. 2016. Triphenyltin degradation and proteomic response by an engineered Escherichia coli expressing cytochrome P450 enzyme. Ecotoxicol. Environ. Saf. 137, 29–34.
Yildirim, N.C., Tanyol, M., Yildirim, N., Serdar, O., and Tatar, S. 2018. Biochemical responses of Gammarus pulex to malachite green solutions decolorized by Coriolus versicolor as a biosorbent under batch adsorption conditions optimized with response surface methodology. Ecotoxicol. Environ. Saf. 156, 41–47.
Yu, Z. and Wen, X. 2005. Screening and identification of yeasts for decolorizing synthetic dyes in industrial wastewater. Int. Biodeterior. Biodegradation 56, 109–114.
Zhang, Q., Xie, X., Liu, Y., Zheng, X., Wang, Y., Cong, J., Yu, C., Liu, N., Sand, W., and Liu, J. 2020. Co-metabolic degradation of refractory dye: a metagenomic and metaproteomic study. Environ. Pollut. 256, 113456.
Zhang, C., Zhang, S., Diao, H., Zhao, H., Zhu, X., Lu, F., and Lu, Z. 2013. Purification and characterization of a temperature- and pH-stable laccase from the spores of Bacillus vallismortis fmb-103 and its application in the degradation of malachite green. J. Agric. Food Chem. 61, 5468–5473.
Zieske, L.R. 2006. A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies. J. Exp. Bot. 57, 1501–1508.
Acknowledgments
We thank the National Key Research and Development Program of China (2018YFD0800403), the National Natural Science Foundation of China (No. 21978287), and the Science and Technology Service Network Initiative Project of the Chinese Academy of Sciences (KFJ-STS-QYZX-112) for their financial support.
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Wang, B., Lu, J., Zheng, J. et al. iTRAQ-facilitated proteomic analysis of Bacillus cereus via degradation of malachite green. J Microbiol. 59, 142–150 (2021). https://doi.org/10.1007/s12275-021-0441-0
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DOI: https://doi.org/10.1007/s12275-021-0441-0