1,203
Views
0
CrossRef citations to date
0
Altmetric
Article

Bioinformatics, bacterial expression and enzyme activity analyses of dichloromethane dehalogenase from Methylobacterium rhodesianum H13

, , , , & ORCID Icon
Pages 1065-1076 | Received 06 Jul 2020, Accepted 28 Aug 2020, Published online: 14 Sep 2020

References

  • Shestakova M, Sillanpaa M. Removal of dichloromethane from ground and wastewater: a review. Chemosphere. 2013;93(7):1258–1267.
  • Yu J, Cai W, Cheng Z, et al. Degradation of dichloromethane by an isolated strain Pandoraea pnomenusa and its performance in a biotrickling filter. J Environ Sci (China). 2014;26(5):1108–1117.
  • Hossaini R, Chipperfield MP, Montzka SA, et al. The increasing threat to stratospheric ozone from dichloromethane. Nat Commun. 2017;8:15962.
  • Park AS, Ritz B, Ling C, et al. Exposure to ambient dichloromethane in pregnancy and infancy from industrial sources and childhood cancers in California. Int J Hyg Environ Health. 2017;220(7):1133–1140.
  • Yu J, Song X, Wang J, et al. Bioelectrocatalytic dechlorination of trichloroacetic acid by hemoglobin modified graphite electrode in aqueous solutions of different pH and temperature. Int J Electrochem Sci. 2012;7:10519–10529.
  • Chen X, Yao X, Yu C, et al. Hydrodechlorination of polychlorinated biphenyls in contaminated soil from an e-waste recycling area, using nanoscale zerovalent iron and Pd/Fe bimetallic nanoparticles. Environ Sci Pollut Res Int. 2014;21(7):5201–5210.
  • Li YP, Cao HB, Zhang Y. Reductive dehalogenation of haloacetic acids by hemoglobin-loaded carbon nanotube electrode. Water Res. 2007;41(1):197–205.
  • Liu Q, Yu J, Xu Y, et al. Bioelectrocatalytic dechlorination of trichloroacetic acid at gel-immobilized hemoglobin on multiwalled carbon nanotubes modified graphite electrode: kinetic modeling and reaction pathways. Electrochim Acta. 2013;92:153–160.
  • Sun C, Baig SA, Lou Z, et al. Electrocatalytic dechlorination of 2,4-dichlorophenoxyacetic acid using nanosized titanium nitride doped palladium/nickel foam electrodes in aqueous solutions. Appl Catal B Environ. 2014;158–159:38–47.
  • Sun Z, Wei X, Han Y, et al. Complete dechlorination of 2,4-dichlorophenol in aqueous solution on palladium/polymeric pyrrole-cetyl trimethyl ammonium bromide/foam-nickel composite electrode. J Hazard Mater. 2013;244–245:287–294.
  • Wang H, Hu J, Xu K, et al. Biodegradation and chemotaxis of polychlorinated biphenyls, biphenyls, and their metabolites by Rhodococcus spp. Biodegradation. 2018;29(1):1–10.
  • Xu Y, Ding X, Ma H, et al. Selective hydrodechlorination of 3,5,6-trichloropicolinic acid at an activated silver cathode: synthesis of 3,5-dichloropicolinic acid. Electrochim Acta. 2015;151:284–288.
  • Matturro B, Di Lenola M, Ubaldi C, et al. First evidence on the occurrence and dynamics of Dehalococcoides mccartyi PCB-dechlorinase genes in marine sediment during Aroclor1254 reductive dechlorination. Mar Pollut Bull. 2016;112(1–2):189–194.
  • Wang S, Chng KR, Wilm A, et al. Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls. Proc Natl Acad Sci USA. 2014;111(33):12103–12108.
  • Wu S, Zhang H, Yu X, et al. Identification and cloning of a gene encoding dichloromethane dehalogenase from a methylotrophic bacterium, Bacillus circulans WZ-12 CCTCC M 207006. Bioprocess Biosyst Eng. 2009;32(6):845–852.
  • Muller EE, Hourcade E, Louhichi-Jelail Y, et al. Functional genomics of dichloromethane utilization in Methylobacterium extorquens DM4. Environ Microbiol. 2011;13(9):2518–2535.
  • Vuilleumier S, Chistoserdova L, Lee MC, et al. Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources. PLoS One. 2009;4(5):e5584.
  • Firsova JE, Doronina NV, Trotsenko YA. Analysis of the key functional genes in new aerobic degraders of dichloromethane. Microbiology. 2010;79(1):66–72.
  • Muller EE, Bringel F, Vuilleumier S. Dichloromethane-degrading bacteria in the genomic age. Res Microbiol. 2011;162(9):869–876.
  • Janssen DB, Oppentocht JE, Poelarends GJ. Microbial dehalogenation. Curr Opin Biotechnol. 2001;12(3):254–258.
  • Xue Y-P, Cao C-H, Zheng Y-G, et al. Enzymatic asymmetric synthesis of chiral amino acids. Chem Soc Rev. 2018;47(4):1516–1561.
  • Longkumer T, Parthasarathy S, Vemuri SG, et al. OxyR-dependent expression of a novel glutathione S-transferase (Abgst01) gene in Acinetobacter baumannii DS002 and its role in biotransformation of organophosphate insecticides. Microbiology (Reading). 2014;160(Pt 1):102–112.
  • Allocati N, Federici L, Masulli M, et al. Cysteine 10 is critical for the activity of Ochrobactrum anthropi glutathione transferase and its mutation to alanine causes the preferential binding of glutathione to the H-site. Proteins. 2008;71(1):16–23.
  • Stourman NV, Branch MC, Schaab MR, et al. Structure and function of YghU, a nu-class glutathione transferase related to YfcG from Escherichia coli. Biochemistry. 2011;50(7):1274–1281.
  • Tars K, Larsson AK, Shokeer A, et al. Structural basis of the suppressed catalytic activity of wild-type human glutathione transferase T1-1 compared to its W234R mutant. J Mol Biol. 2006;355(1):96–105.
  • Chen DZ, Ouyang DJ, Liu HX, et al. Effective utilization of dichloromethane by a newly isolated strain Methylobacterium rhodesianum H13. Environ Sci Pollut Res Int. 2014;21(2):1010–1019.
  • Yu J, Liu Q, Liu L, et al. Cloning and characterization of dichloromethane dehalogenase from Methylobacterium rhodesianum for dichloromethane degradation. Biorem J. 2017;21(2):71–80.
  • Wilkins MR, Gasteiger E, Bairoch A, et al. Protein identification and analysis tools in the ExPASy server. Methods Mol Biol. 1999;112:531–552.
  • Mohsenzadeh S, Saffari B, Mohabatkar H. A new member of Tau-class glutathione S-transferase from barley leaves. EXCLI J. 2009;8:190–194.
  • Arnold K, Bordoli L, Kopp J, et al. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics. 2006;22(2):195–201.
  • Bendl J, Stourac J, Sebestova E, et al. HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering. Nucleic Acids Res. 2016;44(W1):W479–W487.
  • Ballu S, Itteboina R, Sivan SK, et al. Rational design of methicillin resistance Staphylococcus aureus inhibitors through 3D-QSAR, molecular docking and molecular dynamics simulations. Comput Biol Chem. 2018;73:95–104.
  • Khosla C, Tang Y, Chen AY, et al. Structure and mechanism of the 6-deoxyerythronolide B synthase. Annu Rev Biochem. 2007;76:195–221.
  • Yu J, Shi J, Zhang Y, et al. Molecular docking and site-directed mutagenesis of dichloromethane dehalogenase to improve enzyme activity for dichloromethane degradation. Appl Biochem Biotechnol. 2020;190(2):487–505.
  • Farmani J, Safari M, Roohvand F, et al. Conjugated linoleic acid‐producing enzymes: a bioinformatics study. Eur J Lipid Sci Technol. 2010;112(10):1088–1100.
  • Bai Y, He S, Zhao G, et al. Toxoplasma gondii: bioinformatics analysis, cloning and expression of a novel protein TgIMP1. Exp Parasitol. 2012;132(4):458–464.
  • Lygina AS, Meyenberg K, Jahn R, et al. Transmembrane domain peptide/peptide nucleic acid hybrid as a model of a SNARE protein in vesicle fusion. Angew Chem Int Ed Engl. 2011;50(37):8597–8601.
  • Hohenberg H, Mannweiler K, Muller M. High-pressure freezing of cell suspensions in cellulose capillary tubes. J Microsc. 1994;175(Pt 1):34–43.
  • Micsonai A, Wien F, Kernya L, et al. Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy. Proc Natl Acad Sci USA. 2015;112(24):E3095–E3103.
  • Madero-Perez J, Fdez E, Fernandez B, et al. Parkinson disease-associated mutations in LRRK2 cause centrosomal defects via Rab8a phosphorylation. Mol Neurodegener. 2018;13(1):3.
  • Nitulescu II, Meyer SC, Wen QJ, et al. Mediator kinase phosphorylation of STAT1 S727 promotes growth of neoplasms with JAK-STAT activation. EBioMedicine. 2017;26:112–125.
  • Wiktelius E, Stenberg G. Novel class of glutathione transferases from cyanobacteria exhibit high catalytic activities towards naturally occurring isothiocyanates. Biochem J. 2007;406(1):115–123.
  • Li ZH, Tang ZX, Fang XJ, et al. Bioinformatics analysis of a non-specific nuclease from Yersinia enterocolitica subsp. palearctica. Comput Biol Chem. 2013;47:207–214.
  • Hao X, Zhang G, Zhou X. Guiding exploration in conformational feature space with Lipschitz underestimation for ab-initio protein structure prediction. Comput Biol Chem. 2018;73:105–119.
  • Scott TA, Heine D, Qin Z, et al. An L-threonine transaldolase is required for L-threo-β-hydroxy-α-amino acid assembly during obafluorin biosynthesis. Nat Commun. 2017;8:15935.
  • Wu SJ, Zhang LL, Wang JD, et al. Bacillus circulans WZ-12 - a newly discovered aerobic dichloromethane-degrading methylotrophic bacterium. Appl Microbiol Biotechnol. 2007;76(6):1289–1296.
  • Liu ZQ, Zhang XH, Xue YP, et al. Improvement of Alcaligenes faecalis nitrilase by gene site saturation mutagenesis and its application in stereospecific biosynthesis of (R)-(-)-mandelic acid. J Agric Food Chem. 2014;62(20):4685–4694.
  • de Jong RM, Dijkstra BW. Structure and mechanism of bacterial dehalogenases: different ways to cleave a carbon-halogen bond. Curr Opin Struct Biol. 2003;13(6):722–730.