Polyaromatic Hydrocarbon Specific Ring Hydroxylating Dioxygenases:
Diversity, Structure, Function, and Protein Engineering

Tanjot      Kaur; Sudarshan   Singh   Lakhawat; Vikram      Kumar; Vinay      Sharma; Ravi Ranjan   Kumar   Neeraj; Pushpender   Kumar   Sharma
Abstract

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitously present in the environment. These compounds have demonstrated both mutagenic and carcinogenic properties. In the past few decades, scientists have constantly been looking for a possible route to their biological degradation. Bacterial ring hydroxylating dioxygenases (RHDs) implicated in the polycyclic aromatic hydrocarbon degradation comprise a large family of enzymes. RHD catalyzes the stereospecific oxidation of PAHs by incorporating molecular oxygen into inert aromatic nuclei. These biocatalysts hold the potential to completely transform and mineralize toxic forms of these compounds into non-toxic forms. RHDsmediated oxygenation produces cis-dihydrodiols, a chiral compound used in pharmaceutical industries. The Molecular investigation of 16S rRNA and key functional genes involved in pollutant degradation have revealed the dominant occurrence of phylum proteobacteria and actinobacteria in hydrocarbonpolluted environments. The present review is aimed at narrating the diversity, distribution, structural and functional characteristics of RHDs. The review further highlights key amino acids participating in RHDs catalysis. It also discusses the robustness of protein engineering methods in improving the structural and functional activity of the ring hydroxylating dioxygenases.
Graphical Abstract

[1]
Patel, A.B.; Shaikh, S.; Jain, K.R.; Desai, C.; Madamwar, D. Polycyclic aromatic hydrocarbons: Sources, toxicity, and remediation approaches. Front. Microbiol.,  2020, 11, 562813.
 [http://dx.doi.org/10.3389/fmicb.2020.562813] [PMID:  33224110]

[2]
Brzeszcz, J.; Kaszycki, P. Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: An undervalued strategy for metabolic diversity and flexibility. Biodegradation,  2018, 29(4), 359-407.
 [http://dx.doi.org/10.1007/s10532-018-9837-x] [PMID:  29948519]

[3]
Guermouche M’rassi, A.; Bensalah, F.; Gury, J.; Duran, R. Isolation and characterization of different bacterial strains for bioremediation of n-alkanes and polycyclic aromatic hydrocarbons. Environ. Sci. Pollut. Res. Int.,  2015, 22(20), 15332-15346.
 [http://dx.doi.org/10.1007/s11356-015-4343-8] [PMID:  25813636]

[4]
Ghosal, D.; Ghosh, S.; Dutta, T.K.; Ahn, Y. Current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (PAHs): A Review. Front. Microbiol.,  2016, 7, 1369.
 [http://dx.doi.org/10.3389/fmicb.2016.01369] [PMID:  27630626]

[5]
Imam, A.; Kumar Suman, S.; Kanaujia, P.K.; Ray, A. Biological machinery for polycyclic aromatic hydrocarbons degradation: A review. Bioresour. Technol.,  2022, 343, 126121.
 [http://dx.doi.org/10.1016/j.biortech.2021.126121] [PMID:  34653630]

[6]
Igiri, B.E.; Okoduwa, S.I.R.; Idoko, G.O.; Akabuogu, E.P.; Adeyi, A.O.; Ejiogu, I.K. Toxicity and bioremediation of heavy metals contaminated ecosystem from tannery wastewater: A review. J. Toxicol.,  2018, 2018, 1-16.
 [http://dx.doi.org/10.1155/2018/2568038] [PMID:  30363677]

[7]
Leong, Y.K.; Chang, J.S. Bioremediation of heavy metals using microalgae: Recent advances and mechanisms. Bioresour. Technol.,  2020, 303, 122886.
 [http://dx.doi.org/10.1016/j.biortech.2020.122886] [PMID:  32046940]

[8]
Rahman, Z.; Singh, V.P. Bioremediation of toxic heavy metals (THMs) contaminated sites: Concepts, applications and challenges. Environ. Sci. Pollut. Res. Int.,  2020, 27(22), 27563-27581.
 [http://dx.doi.org/10.1007/s11356-020-08903-0] [PMID:  32418096]

[9]
Sahoo, B.M.; Ravi Kumar, B.V.V.; Banik, B.K.; Borah, P. Polyaromatic Hydrocarbons (PAHs): Structures, synthesis and their biological profile. Curr. Org. Synth.,  2020, 17(8), 625-640.
 [http://dx.doi.org/10.2174/1570179417666200713182441] [PMID:  32660405]

[10]
Famiyeh, L.; Chen, K.; Xu, J.; Sun, Y.; Guo, Q.; Wang, C.; Lv, J.; Tang, Y.T.; Yu, H.; Snape, C.; He, J. A review on analysis methods, source identification, and cancer risk evaluation of atmospheric polycyclic aromatic hydrocarbons. Sci. Total Environ.,  2021, 789, 147741.
 [http://dx.doi.org/10.1016/j.scitotenv.2021.147741] [PMID:  34058584]

[11]
Greeley, M.A.; Van Winkle, L.S.; Edwards, P.C.; Plopper, C.G. Airway trefoil factor expression during naphthalene injury and repair. Toxicol. Sci.,  2010, 113(2), 453-467.
 [http://dx.doi.org/10.1093/toxsci/kfp268] [PMID:  19880587]

[12]
Kottuparambil, S.; Park, J. Anthracene phytotoxicity in the freshwater flagellate alga Euglena agilis Carter. Sci. Rep.,  2019, 9(1), 15323.
 [http://dx.doi.org/10.1038/s41598-019-51451-y] [PMID:  31653882]

[13]
Sun, Z.; Wang, X.; Liu, C.; Fang, G.; Chu, L.; Gu, C.; Gao, J. Persistent free radicals from low-molecular-weight organic compounds en-hance cross-coupling reactions and toxicity of anthracene on amorphous silica surfaces under light. Environ. Sci. Technol.,  2021, 55(6), 3716-3726.
 [http://dx.doi.org/10.1021/acs.est.0c07472] [PMID:  33635628]

[14]
Swaathy, S.; Kavitha, V.; Pravin, A.S.; Mandal, A.B.; Gnanamani, A. Microbial surfactant mediated degradation of anthracene in aqueous phase by marine Bacillus licheniformis MTCC 5514. Biotechnol. Rep. (Amst.),  2014, 4, 161-170.
 [http://dx.doi.org/10.1016/j.btre.2014.10.004] [PMID:  28626676]

[15]
Deng, S.; Deng, Q.; Hu, D.; Li, J.; Zhu, X.; Guo, H.; Wu, T. Association between urinary polycyclic aromatic hydrocarbon metabolites and elevated serum uric acid levels in coke oven workers. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi,  2014, 32(6), 406-410.
 [PMID:  25169220]

[16]
Saito, A.; Iwabuchi, T.; Harayama, S. A novel phenanthrene dioxygenase from Nocardioides sp. Strain KP7: Expression in Escherichia coli. J. Bacteriol.,  2000, 182(8), 2134-2141.
 [http://dx.doi.org/10.1128/JB.182.8.2134-2141.2000] [PMID:  10735855]

[17]
Hardonnière, K.; Saunier, E.; Lemarié, A.; Fernier, M.; Gallais, I.; Héliès-Toussaint, C.; Mograbi, B.; Antonio, S.; Bénit, P.; Rustin, P.; Janin, M.; Habarou, F.; Ottolenghi, C.; Lavault, M.T.; Benelli, C.; Sergent, O.; Huc, L.; Bortoli, S.; Lagadic-Gossmann, D. The environmental carcinogen benzo[a]pyrene induces a Warburg-like metabolic reprogramming dependent on NHE1 and associated with cell survival. Sci. Rep.,  2016, 6(1), 30776.
 [http://dx.doi.org/10.1038/srep30776] [PMID:  27488617]

[18]
Moody, J.D.; Freeman, J.P.; Fu, P.P.; Cerniglia, C.E. Degradation of Benzo[ a]pyrene by Mycobacterium vanbaalenii PYR-1. Appl. Environ. Microbiol.,  2004, 70(1), 340-345.
 [http://dx.doi.org/10.1128/AEM.70.1.340-345.2004] [PMID:  14711661]

[19]
Vaidya, S.; Devpura, N.; Jain, K.; Madamwar, D. Degradation of Chrysene by Enriched Bacterial Consortium. Front. Microbiol.,  2018, 9, 1333.
 [http://dx.doi.org/10.3389/fmicb.2018.01333] [PMID:  30013520]

[20]
 CID 9171- National Center for Biotechnology Information. Pub-Chem Compound Summary for CID 9171, Chrysene Available from: https://pubchem.ncbi.nlm.nih.gov/compound/Chrysene [Accessed on: March 11, 2022 ].

[21]
Hadibarata, T.; Tachibana, S.; Itoh, K. Biodegradation of chrysene, an aromatic hydrocarbon by Polyporus sp. S133 in liquid medium. J. Hazard. Mater.,  2009, 164(2-3), 911-917.
 [http://dx.doi.org/10.1016/j.jhazmat.2008.08.081] [PMID:  18835091]

[22]
Sun, N.; Liu, Q.; Wang, J.; He, F.; Jing, M.; Chu, S.; Zong, W.; Liu, R.; Gao, C. Probing the biological toxicity of pyrene to the earthworm Eisenia fetida and the toxicity pathways of oxidative damage: A systematic study at the animal and molecular levels. Environ. Pollut.,  2021, 289, 117936.
 [http://dx.doi.org/10.1016/j.envpol.2021.117936] [PMID:  34391044]

[23]
Wang, X.; Teng, Y.; Wang, X.; Li, X.; Luo, Y. Microbial diversity drives pyrene dissipation in soil. Sci. Total Environ.,  2022, 819, 153082.
 [http://dx.doi.org/10.1016/j.scitotenv.2022.153082] [PMID:  35038522]

[24]
 CID 5889- National Center for Biotechnology Information (2022). PubChem Compound Summary for CID 5889, Dibenz[a,h]anthracene. 2022. Available from: https://pubchem. ncbi.nlm.nih.gov/compound/Dibenz_a_h_anthracene [Accessed on: March 11, 2022].

[25]
 CID 5954 -National Center for Biotechnology Information. Pub-Chem Compound Summary for CID 5954, Benz[a]anthracene. Available from: https://pubchem.ncbi.nlm.nih.gov/compound/Benz_a_anthracene [Accessed on: March 11, 2022].

[26]
Saunders, C.R.; Shockley, D.C.; Knuckles, M.E. Fluoranthene-induced neurobehavioral toxicity in F-344 rats. Int. J. Toxicol.,  2003, 22(4), 263-276.
 [http://dx.doi.org/10.1080/10915810305114] [PMID:  12933321]

[27]
Jin, J.; Yao, J.; Liu, W.; Zhang, Q.; Liu, J. Fluoranthene degradation and binding mechanism study based on the active-site structure of ring-hydroxylating dioxygenase in Microbacterium paraoxydans JPM1. Environ. Sci. Pollut. Res. Int.,  2017, 24(1), 363-371.
 [http://dx.doi.org/10.1007/s11356-016-7809-4] [PMID:  27722881]

[28]
Guo, J.; Huang, J.; Zhang, L.; Li, C.; Qin, Y.; Liu, W.; Li, J.; Huang, G. Benzo[b]fluoranthene impairs mouse oocyte maturation via inducing the apoptosis. Front. Pharmacol.,  2020, 11, 1226.
 [http://dx.doi.org/10.3389/fphar.2020.01226] [PMID:  32982721]

[29]
Peiffer, J.; Grova, N.; Hidalgo, S.; Salquèbre, G.; Rychen, G.; Bisson, J.F.; Appenzeller, B.M.R.; Schroeder, H. Behavioral toxicity and physiological changes from repeated exposure to fluorene administered orally or intraperitoneally to adult male Wistar rats: A dose–response study. Neurotoxicology,  2016, 53, 321-333.
 [http://dx.doi.org/10.1016/j.neuro.2015.11.006] [PMID:  26616911]

[30]
Pinyakong, O.; Habe, H.; Kouzuma, A.; Nojiri, H.; Yamane, H.; Omori, T. Isolation and characterization of genes encoding polycyclic aromatic hydrocarbon dioxygenase from acenaphthene and acenaphthylene degrading Sphingomonas sp. strain A4. FEMS Microbiol. Lett.,  2004, 238(2), 297-305.
 [http://dx.doi.org/10.1016/j.femsle.2004.07.048] [PMID:  15358414]

[31]
Chaloupka, K.; Santostefano, M.; Goldfarb, I.S.; Liu, G.; Myers, M.J.; Tsyrolv, I.B.; Gelboin, H.V.; Krishnan, V.; Safe, S. Aryl hydrocar-bon (Ah) receptor-independent induction of Cypla2 gene expression by acenaphthylene and related compounds in B6C3F1 mice. Carcinogenesis,  1994, 15(12), 2835-2840.
 [http://dx.doi.org/10.1093/carcin/15.12.2835] [PMID:  8001243]

[32]
Miao, L.L.; Qu, J.; Liu, Z.P. Hydroxylation at multiple positions initiated the biodegradation of Indeno[1,2,3-cd]Pyrene in Rhodococcus aetherivorans IcdP1. Front. Microbiol.,  2020, 11, 568381.
 [http://dx.doi.org/10.3389/fmicb.2020.568381] [PMID:  33072027]

[33]
Pan, S.; Li, D.; Zhao, L.; Schenkman, J.B.; Rusling, J.F. Genotoxicity-related chemistry of human metabolites of benzo[ghi]perylene (B[ghi]P) investigated using electro-optical arrays and DNA/microsome biocolloid reactors with LC-MS/MS. Chem. Res. Toxicol.,  2013, 26(8), 1229-1239.
 [http://dx.doi.org/10.1021/tx400147c] [PMID:  23879290]

[34]
Jimoh, A.A.; Ikhimiukor, O.O.; Adeleke, R. Prospects in the bioremediation of petroleum hydrocarbon contaminants from hypersaline environments: A review. Environ. Sci. Pollut. Res. Int.,  2022, 29(24), 35615-35642.
 [http://dx.doi.org/10.1007/s11356-022-19299-4] [PMID:  35247173]

[35]
Borchert, E.; Hammerschmidt, K.; Hentschel, U.; Deines, P. Enhancing microbial pollutant degradation by integrating eco-evolutionary principles with environmental biotechnology. Trends Microbiol.,  2021, 29(10), 908-918.
 [http://dx.doi.org/10.1016/j.tim.2021.03.002] [PMID:  33812769]

[36]
Zhang, T.; Zhang, H. Microbial consortia are needed to degrade soil pollutants. Microorganisms,  2022, 10(2), 261.
 [http://dx.doi.org/10.3390/microorganisms10020261] [PMID:  35208716]

[37]
Dvořák, P.; Nikel, P.I.; Damborský, J.; de Lorenzo, V. Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of sys-temic biology. Biotechnol. Adv.,  2017, 35(7), 845-866.
 [http://dx.doi.org/10.1016/j.biotechadv.2017.08.001] [PMID:  28789939]

[38]
Laczi, K.; Erdeiné Kis, Á.; Szilágyi, Á.; Bounedjoum, N.; Bodor, A.; Vincze, G.E.; Kovács, T.; Rákhely, G.; Perei, K. New frontiers of anaerobic hydrocarbon biodegradation in the multi-omics era. Front. Microbiol.,  2020, 11, 590049.
 [http://dx.doi.org/10.3389/fmicb.2020.590049] [PMID:  33304336]

[39]
Rabus, R.; Boll, M.; Heider, J.; Meckenstock, R.U.; Buckel, W.; Einsle, O.; Ermler, U.; Golding, B.T.; Gunsalus, R.P.; Kroneck, P.M.; Krüger, M.; Lueders, T.; Martins, B.M.; Musat, F.; Richnow, H.H.; Schink, B.; Seifert, J.; Szaleniec, M.; Treude, T.; Ullmann, G.M.; Vogt, C.; von Bergen, M.; Wilkes, H. Anaerobic microbial degradation of hydrocarbons: From enzymatic reactions to the environment. J. Mol. Microbiol. Biotechnol.,  2016, 26(1-3), 5-28.
 [http://dx.doi.org/10.1159/000443997] [PMID:  26960061]

[40]
Hazen, T.C.; Prince, R.C.; Mahmoudi, N. Marine oil biodegradation. Environ. Sci. Technol.,  2016, 50(5), 2121-2129.
 [http://dx.doi.org/10.1021/acs.est.5b03333] [PMID:  26698270]

[41]
de Almeida, F.F.; Freitas, D.; Motteran, F.; Fernandes, B.S.; Gavazza, S. Bioremediation of polycyclic aromatic hydrocarbons in contami-nated mangroves: Understanding the historical and key parameter profiles. Mar. Pollut. Bull.,  2021, 169, 112553.
 [http://dx.doi.org/10.1016/j.marpolbul.2021.112553] [PMID:  34091245]

[42]
Zheng, M.; Zhao, Y.; Miao, L.; Gao, X.; Liu, Z. Advances in bioremediation of polycyclic aromatic hydrocarbons contaminated soil. Chin. J. Biotechnol.,  2021, 37(10), 3535-3548.
 [http://dx.doi.org/10.13345/j.cjb.210389] [PMID:  34708609]

[43]
Martin, F.; Malagnoux, L.; Violet, F.; Jakoncic, J.; Jouanneau, Y. Diversity and catalytic potential of PAH-specific ring-hydroxylating di-oxygenases from a hydrocarbon-contaminated soil. Appl. Microbiol. Biotechnol.,  2013, 97(11), 5125-5135.
 [http://dx.doi.org/10.1007/s00253-012-4335-2] [PMID:  22903320]

[44]
Mason, J.R.; Cammack, R. The electron-transport proteins of hydroxylating bacterial dioxygenases. Annu. Rev. Microbiol.,  1992, 46(1), 277-305.
 [http://dx.doi.org/10.1146/annurev.mi.46.100192.001425] [PMID:  1444257]

[45]
Jakoncic, J.; Jouanneau, Y.; Meyer, C.; Stojanoff, V. The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1. Biochem. Biophys. Res. Commun.,  2007, 352(4), 861-866.
 [http://dx.doi.org/10.1016/j.bbrc.2006.11.117] [PMID:  17157819]

[46]
Shetty, A.R.; de Gannes, V.; Obi, C.C.; Lucas, S.; Lapidus, A.; Cheng, J.F.; Goodwin, L.A.; Pitluck, S.; Peters, L.; Mikhailova, N.; Teshima, H.; Han, C.; Tapia, R.; Land, M.; Hauser, L.J.; Kyrpides, N.; Ivanova, N.; Pagani, I.; Chain, P.S.G.; Denef, V.J.; Woyke, T.; Hickey, W.J. Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4. Stand. Genomic Sci.,  2015, 10(1), 55.
 [http://dx.doi.org/10.1186/s40793-015-0041-x] [PMID:  26380642]

[47]
Kweon, O.; Kim, S.J.; Baek, S.; Chae, J.C.; Adjei, M.D.; Baek, D.H.; Kim, Y.C.; Cerniglia, C.E. A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases. BMC Biochem.,  2008, 9(1), 11.
 [http://dx.doi.org/10.1186/1471-2091-9-11] [PMID:  18387195]

[48]
Meynet, P.; Head, I.M.; Werner, D.; Davenport, R.J. Re-evaluation of dioxygenase gene phylogeny for the development and validation of a quantitative assay for environmental aromatic hydrocarbon degraders. FEMS Microbiol. Ecol.,  2015, 91(6), fiv049.
 [http://dx.doi.org/10.1093/femsec/fiv049] [PMID:  25944871]

[49]
Nam, J.W.; Nojiri, H.; Noguchi, H.; Uchimura, H.; Yoshida, T.; Habe, H.; Yamane, H.; Omori, T. Purification and characterization of car-bazole 1,9a-dioxygenase, a three-component dioxygenase system of Pseudomonas resinovorans strain CA10. Appl. Environ. Microbiol.,  2002, 68(12), 5882-5890.
 [http://dx.doi.org/10.1128/AEM.68.12.5882-5890.2002] [PMID:  12450807]

[50]
Kiyohara, H.; Nagao, K.; Kouno, K.; Yano, K. Phenanthrene-degrading phenotype of Alcaligenes faecalis AFK2. Appl. Environ. Microbiol.,  1982, 43(2), 458-461.
 [http://dx.doi.org/10.1128/aem.43.2.458-461.1982] [PMID:  7059173]

[51]
Jakoncic, J.; Jouanneau, Y.; Meyer, C.; Stojanoff, V. The crystal structure of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1. FEBS J.,  2007, 274(10), 2470-2481.
 [http://dx.doi.org/10.1111/j.1742-4658.2007.05783.x] [PMID:  17451434]

[52]
Jouanneau, Y.; Micoud, J.; Meyer, C. Purification and characterization of a three-component salicylate 1-hydroxylase from Sphingomonas sp. strain CHY-1. Appl Environ. Microbiol,  2007, 73(23), 7515-7521.
 [http://dx.doi.org/10.1128/AEM.01519-07]

[53]
Kauppi, B.; Lee, K.; Carredano, E.; Parales, R.E.; Gibson, D.T.; Eklund, H.; Ramaswamy, S. Structure of an aromatic-ring-hydroxylating dioxygenase–naphthalene 1,2-dioxygenase. Structure,  1998, 6(5), 571-586.
 [http://dx.doi.org/10.1016/S0969-2126(98)00059-8] [PMID:  9634695]

[54]
Boyd, C.; Larkin, M.J.; Reid, K.A.; Sharma, N.D.; Wilson, K. Metabolism of naphthalene, 1-Naphthol, indene, and indole by Rhodococcus sp. strain NCIMB 12038. Appl. Environ. Microbiol.,  1997, 63(1), 151-155.
 [http://dx.doi.org/10.1128/aem.63.1.151-155.1997] [PMID:  16535479]

[55]
Parales, R.E.; Emig, M.D.; Lynch, N.A.; Gibson, D.T. Substrate specificities of hybrid naphthalene and 2,4-dinitrotoluene dioxygenase enzyme systems. J. Bacteriol.,  1998, 180(9), 2337-2344.
 [http://dx.doi.org/10.1128/JB.180.9.2337-2344.1998] [PMID:  9573183]

[56]
Aukema, K.G.; Kasinkas, L.; Aksan, A.; Wackett, L.P. Use of silica-encapsulated Pseudomonas sp. strain NCIB 9816-4 in biodegradation of novel hydrocarbon ring structures found in hydraulic fracturing waters. Appl. Environ. Microbiol.,  2014, 80(16), 4968-4976.
 [http://dx.doi.org/10.1128/AEM.01100-14] [PMID:  24907321]

[57]
Nishino, S.F.; Spain, J.C. Oxidative pathway for the biodegradation of nitrobenzene by Comamonas sp. Strain JS765. Appl. Environ. Microbiol.,  1995, 61(6), 2308-2313.
 [http://dx.doi.org/10.1128/aem.61.6.2308-2313.1995] [PMID:  16535050]

[58]
Ju, K.S.; Parales, R.E. Control of substrate specificity by active-site residues in nitrobenzene dioxygenase. Appl. Environ. Microbiol.,  2006, 72(3), 1817-1824.
 [http://dx.doi.org/10.1128/AEM.72.3.1817-1824.2006] [PMID:  16517627]

[59]
Cao, H.; Zhang, X.; Wang, S.; Liu, J.; Han, D.; Zhao, B.; Wang, H. Insights Into mechanism of the naphthalene-enhanced biodegradation of phenanthrene by Pseudomonas sp. SL-6 Based on Omics Analysis. Front. Microbiol.,  2021, 12, 761216.
 [http://dx.doi.org/10.3389/fmicb.2021.761216] [PMID:  34867892]

[60]
He, C.; Li, Y.; Huang, C.; Chen, F.; Ma, Y. Genome sequence and metabolic analysis of a fluoranthene-degrading strain Pseudomonas aeruginosa DN1. Front. Microbiol.,  2018, 9, 2595.
 [http://dx.doi.org/10.3389/fmicb.2018.02595] [PMID:  30429835]

[61]
Griese, J.J.; P., Jakob R.; Schwarzinger, S.; Dobbek, H. Xenobiotic reductase A in the degradation of quinoline by Pseudomonas putida 86: Physiological function, structure and mechanism of 8-hydroxycoumarin reduction. J. Mol. Biol.,  2006, 361(1), 140-152.
 [http://dx.doi.org/10.1016/j.jmb.2006.06.007] [PMID:  16822524]

[62]
Ashikawa, Y.; Fujimoto, Z.; Noguchi, H.; Habe, H.; Omori, T.; Yamane, H.; Nojiri, H. Electron transfer complex formation between oxygenase and ferredoxin components in Rieske nonheme iron oxygenase system. Structure,  2006, 14(12), 1779-1789.
 [http://dx.doi.org/10.1016/j.str.2006.10.004] [PMID:  17161368]

[63]
Furusawa, Y.; Nagarajan, V.; Tanokura, M.; Masai, E.; Fukuda, M.; Senda, T. Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1. J. Mol. Biol.,  2004, 342(3), 1041-1052.
 [http://dx.doi.org/10.1016/j.jmb.2004.07.062] [PMID:  15342255]

[64]
McLeod, M.P.; Warren, R.L.; Hsiao, W.W.; Araki, N.; Myhre, M.; Fernandes, C.; Miyazawa, D.; Wong, W.; Lillquist, A.L.; Wang, D.; Dosanjh, M.; Hara, H.; Petrescu, A.; Morin, R.D.; Yang, G.; Stott, J.M.; Schein, J.E.; Shin, H.; Smailus, D.; Siddiqui, A.S.; Marra, M.A.; Jones, S.J.; Holt, R.; Brinkman, F.S.; Miyauchi, K.; Fukuda, M.; Davies, M. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. PNAS,  2006, 103(42), 1558215587.

[65]
Singh, D.; Kumari, A.; Ramanathan, G. 3-Nitrotoluene dioxygenase from Diaphorobacter sp. strains: Cloning, sequencing and evolution-ary studies. Biodegradation,  2014, 25(4), 479-492.
 [http://dx.doi.org/10.1007/s10532-013-9675-9] [PMID:  24217981]

[66]
Singh, D.; Kumari, A.; Ramaswamy, S.; Ramanathan, G. Expression, purification and substrate specificities of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2. Biochem. Biophys. Res. Commun.,  2014, 445(1), 36-42.
 [http://dx.doi.org/10.1016/j.bbrc.2014.01.113] [PMID:  24491551]

[67]
Gao, Y.Z.; Palatucci, M.L.; Waidner, L.A.; Li, T.; Guo, Y.; Spain, J.C.; Zhou, N.Y. A Nag‐like dioxygenase initiates 3,4‐dichloronitrobenzene degradation via 4,5‐dichlorocatechol in Diaphorobacter sp. strain JS3050. Environ. Microbiol.,  2021, 23(2), 1053-1065.
 [http://dx.doi.org/10.1111/1462-2920.15295] [PMID:  33103811]

[68]
Colbert, C.L.; Agar, N.Y.R.; Kumar, P.; Chakko, M.N.; Sinha, S.C.; Powlowski, J.B.; Eltis, L.D.; Bolin, J.T. Structural characterization of Pandoraea pnomenusa B-356 biphenyl dioxygenase reveals features of potent polychlorinated biphenyl-degrading enzymes. PLoS One,  2013, 8(1), e52550.
 [http://dx.doi.org/10.1371/journal.pone.0052550] [PMID:  23308114]

[69]
Ní Chadhain, S.M.; Moritz, E.M.; Kim, E.; Zylstra, G.J. Identification, cloning, and characterization of a multicomponent biphenyl dioxy-genase from Sphingobium yanoikuyae B1. J. Ind. Microbiol. Biotechnol.,  2007, 34(9), 605-613.
 [http://dx.doi.org/10.1007/s10295-007-0235-3] [PMID:  17647036]

[70]
Zubrova, A.; Michalikova, K.; Semerad, J.; Strejcek, M.; Cajthaml, T.; Suman, J.; Uhlik, O. Biphenyl 2,3-Dioxygenase in Pseudomonas alcaliphila JAB1 is both induced by phenolics and monoterpenes and involved in their transformation. Front. Microbiol.,  2021, 12, 657311.
 [http://dx.doi.org/10.3389/fmicb.2021.657311] [PMID:  33995321]

[71]
Mukerjee-Dhar, G.; Shimura, M.; Miyazawa, D.; Kimbara, K.; Hatta, T. bph genes of the thermophilic PCB degrader, Bacillus sp. JF8: Characterization of the divergent ring-hydroxylating dioxygenase and hydrolase genes upstream of the Mn-dependent BphC. Microbiology,  2005, 151(12), 4139-4151.
 [http://dx.doi.org/10.1099/mic.0.28437-0] [PMID:  16339959]

[72]
Moody, J.D.; Freeman, J.P.; Cerniglia, C.E. Degradation of benz[a]anthracene by Mycobacterium vanbaalenii strain PYR-1. Biodegradation,  2005, 16(6), 513-526.
 [http://dx.doi.org/10.1007/s10532-004-7217-1] [PMID:  15865344]

[73]
Xue, S.W.; Tian, Y.X.; Pan, J.C.; Liu, Y.N.; Ma, Y.L. Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseu-domonas aeruginosa DN1. Sci. Rep.,  2021, 11(1), 21317.
 [http://dx.doi.org/10.1038/s41598-021-00783-9] [PMID:  34716364]

[74]
Dong, W.; He, C.; Li, Y.; Huang, C.; Chen, F.; Ma, Y. Complete genome sequence of a versatile hydrocarbon degrader, Pseudomonas ae-ruginosa DN1 isolated from petroleum-contaminated soil. Gene Rep.,  2017, 7, 123-126.
 [http://dx.doi.org/10.1016/j.genrep.2017.04.001]

[75]
Hassa, J.; Maus, I.; Off, S.; Pühler, A.; Scherer, P.; Klocke, M.; Schlüter, A. Metagenome, metatranscriptome, and metaproteome ap-proaches unraveled compositions and functional relationships of microbial communities residing in biogas plants. Appl. Microbiol. Biotechnol.,  2018, 102(12), 5045-5063.
 [http://dx.doi.org/10.1007/s00253-018-8976-7] [PMID:  29713790]

[76]
Liang, C.; Huang, Y.; Wang, Y.; Ye, Q.; Zhang, Z.; Wang, H. Distribution of bacterial polycyclic aromatic hydrocarbon (PAH) ring-hydroxylating dioxygenases genes in oilfield soils and mangrove sediments explored by gene-targeted metagenomics. Appl. Microbiol. Biotechnol.,  2019, 103(5), 2427-2440.
 [http://dx.doi.org/10.1007/s00253-018-09613-x] [PMID:  30661109]

[77]
Iwai, S.; Chai, B.; Sul, W.J.; Cole, J.R.; Hashsham, S.A.; Tiedje, J.M. Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. ISME J.,  2010, 4(2), 279-285.
 [http://dx.doi.org/10.1038/ismej.2009.104] [PMID:  19776767]

[78]
Andreoni, V.; Cavalca, L.; Rao, M.A.; Nocerino, G.; Bernasconi, S.; Dell’Amico, E.; Colombo, M.; Gianfreda, L. Bacterial communities and enzyme activities of PAHs polluted soils. Chemosphere,  2004, 57(5), 401-412.
 [http://dx.doi.org/10.1016/j.chemosphere.2004.06.013] [PMID:  15331267]

[79]
Lafortune, I.; Juteau, P.; Déziel, E.; Lépine, F.; Beaudet, R.; Villemur, R. Bacterial diversity of a consortium degrading high-molecular-weight polycyclic aromatic hydrocarbons in a two-liquid phase biosystem. Microb. Ecol.,  2009, 57(3), 455-468.
 [http://dx.doi.org/10.1007/s00248-008-9417-4] [PMID:  18615233]

[80]
Lors, C.; Ryngaert, A.; Périé, F.; Diels, L.; Damidot, D. Evolution of bacterial community during bioremediation of PAHs in a coal tar contaminated soil. Chemosphere,  2010, 81(10), 1263-1271.
 [http://dx.doi.org/10.1016/j.chemosphere.2010.09.021] [PMID:  20943246]

[81]
Lu, C.; Hong, Y.; Liu, J.; Gao, Y.; Ma, Z.; Yang, B.; Ling, W.; Waigi, M.G. A PAH-degrading bacterial community enriched with contami-nated agricultural soil and its utility for microbial bioremediation. Environ. Pollut.,  2019, 251, 773-782.
 [http://dx.doi.org/10.1016/j.envpol.2019.05.044] [PMID:  31121542]

[82]
Molina, M.C.; González, N.; Bautista, L.F.; Sanz, R.; Simarro, R.; Sánchez, I.; Sanz, J.L. Isolation and genetic identification of PAH degrad-ing bacteria from a microbial consortium. Biodegradation,  2009, 20(6), 789-800.
 [http://dx.doi.org/10.1007/s10532-009-9267-x] [PMID:  19468841]

[83]
Sukhdhane, K.S.; Pandey, P.K.; Ajima, M.N.O.; Jayakumar, T.; Vennila, A.; Raut, S.M. Isolation and characterization of phenanthrene-degrading bacteria from PAHs contaminated mangrove sediment of Thane Creek in Mumbai, India. Polycycl. Aromat. Compd.,  2019, 39(1), 73-83.
 [http://dx.doi.org/10.1080/10406638.2016.1261911]

[84]
Rodgers-Vieira, E.A.; Zhang, Z.; Adrion, A.C.; Gold, A.; Aitken, M.D. Identification of anthraquinone-degrading bacteria in soil contami-nated with polycyclic aromatic hydrocarbons. Appl. Environ. Microbiol.,  2015, 81(11), 3775-3781.
 [http://dx.doi.org/10.1128/AEM.00033-15] [PMID:  25819957]

[85]
Moser, R.; Stahl, U. Insights into the genetic diversity of initial dioxygenases from PAH-degrading bacteria. Appl. Microbiol. Biotechnol.,  2001, 55(5), 609-618.
 [http://dx.doi.org/10.1007/s002530000489] [PMID:  11414329]

[86]
Kumar, M.; Khanna, S. Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremedi-ation. J. Appl. Microbiol.,  2010, 108(4), 1252-1262.
 [http://dx.doi.org/10.1111/j.1365-2672.2009.04523.x] [PMID:  19796097]

[87]
Chakraborty, J.; Ghosal, D.; Dutta, A.; Dutta, T.K. An insight into the origin and functional evolution of bacterial aromatic ring-hydroxylating oxygenases. J. Biomol. Struct. Dyn.,  2012, 30(4), 419-436.
 [http://dx.doi.org/10.1080/07391102.2012.682208] [PMID:  22694139]

[88]
Uyttebroek, M.; Spoden, A.; Ortega-Calvo, J.J.; Wouters, K.; Wattiau, P.; Bastiaens, L.; Springael, D. Differential responses of eubacterial, Mycobacterium, and Sphingomonas communities in polycyclic aromatic hydrocarbon (PAH)-contaminated soil to artificially induced changes in PAH profile. J. Environ. Qual.,  2007, 36(5), 1403-1411.
 [http://dx.doi.org/10.2134/jeq2006.0471] [PMID:  17766819]

[89]
Storey, S.; Ashaari, M.M.; Clipson, N.; Doyle, E.; de Menezes, A.B. Opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study. Front. Microbiol.,  2018, 9, 2815.
 [http://dx.doi.org/10.3389/fmicb.2018.02815] [PMID:  30519226]

[90]
Wu, P.; Wang, Y.S.; Sun, F.L.; Wu, M.L.; Peng, Y. Bacterial polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases in the sed-iments from the Pearl River estuary, China. Appl. Microbiol. Biotechnol.,  2014, 98(2), 875-884.
 [http://dx.doi.org/10.1007/s00253-013-4854-5] [PMID:  23558584]

[91]
Schuler, L.; Jouanneau, Y.; Ní Chadhain, S.M.; Meyer, C.; Pouli, M.; Zylstra, G.J.; Hols, P.; Agathos, S.N. Characterization of a ring-hydroxylating dioxygenase from phenanthrene-degrading Sphingomonas sp. strain LH128 able to oxidize benz[a]anthracene. Appl. Microbiol. Biotechnol.,  2009, 83(3), 465-475.
 [http://dx.doi.org/10.1007/s00253-009-1858-2] [PMID:  19172265]

[92]
Zhao, Q.; Bilal, M.; Yue, S.; Hu, H.; Wang, W.; Zhang, X. Identification of biphenyl 2, 3-dioxygenase and its catabolic role for phenazine degradation in Sphingobium yanoikuyae B1. J. Environ. Manage.,  2017, 204(Pt 1), 494-501.
 [http://dx.doi.org/10.1016/j.jenvman.2017.09.027] [PMID:  28930694]

[93]
Pinyakong, O.; Habe, H.; Omori, T. The unique aromatic catabolic genes in Sphingomonads degrading polycyclic aromatic hydrocar-bons(PAHs). J. Gen. Appl. Microbiol.,  2003, 49(1), 1-19.
 [http://dx.doi.org/10.2323/jgam.49.1] [PMID:  12682862]

[94]
Demanèche, S.; Meyer, C.; Micoud, J.; Louwagie, M.; Willison, J.C.; Jouanneau, Y. Identification and functional analysis of two aromatic-ring-hydroxylating dioxygenases from a Sphingomonas strain that degrades various polycyclic aromatic hydrocarbons. Appl. Environ. Microbiol.,  2004, 70(11), 6714-6725.
 [http://dx.doi.org/10.1128/AEM.70.11.6714-6725.2004] [PMID:  15528538]

[95]
Jouanneau, Y.; Meyer, C.; Duraffourg, N. Dihydroxylation of four- and five-ring aromatic hydrocarbons by the naphthalene dioxygenase from Sphingomonas CHY-1. Appl. Microbiol. Biotechnol.,  2016, 100(3), 1253-1263.
 [http://dx.doi.org/10.1007/s00253-015-7050-y] [PMID:  26476651]

[96]
Ferraro, D.J.; Brown, E.N.; Yu, C.L.; Parales, R.E.; Gibson, D.T.; Ramaswamy, S. Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1. BMC Struct. Biol.,  2007, 7(1), 10.
 [http://dx.doi.org/10.1186/1472-6807-7-10] [PMID:  17349044]

[97]
Khara, P.; Roy, M.; Chakraborty, J.; Dutta, A.; Dutta, T.K. Characterization of a topologically unique oxygenase from Sphingobium sp. PNB capable of catalyzing a broad spectrum of aromatics. Enzyme Microb. Technol.,  2018, 111, 74-80.
 [http://dx.doi.org/10.1016/j.enzmictec.2017.10.006] [PMID:  29421041]

[98]
Xiang, L.; Li, G.; Wen, L.; Su, C.; Liu, Y.; Tang, H.; Dai, J. Biodegradation of aromatic pollutants meets synthetic biology. Synth. Syst. Biotechnol.,  2021, 6(3), 153-162.
 [http://dx.doi.org/10.1016/j.synbio.2021.06.001] [PMID:  34278013]

[99]
Ferraro, D.J.; Gakhar, L.; Ramaswamy, S. Rieske business: Structure–function of Rieske non-heme oxygenases. Biochem. Biophys. Res. Commun.,  2005, 338(1), 175-190.
 [http://dx.doi.org/10.1016/j.bbrc.2005.08.222] [PMID:  16168954]

[100]
Yang, T.C.; Wolfe, M.D.; Neibergall, M.B.; Mekmouche, Y.; Lipscomb, J.D.; Hoffman, B.M. Substrate binding to NO-ferro-naphthalene 1,2-dioxygenase studied by high-resolution Q-band pulsed 2H-ENDOR spectroscopy. J. Am. Chem. Soc.,  2003, 125(23), 7056-7066.
 [http://dx.doi.org/10.1021/ja0214126] [PMID:  12783560]

[101]
Malik, Z.A.; Allen, C.C.; Gakhar, L.; Lipscomb, D.A.; Larkin, M.J.; Ramaswamy, S. Crystallization and preliminary X-ray diffraction analysis of naphthalene dioxygenase from Rhodococcus sp. strain NCIMB 12038. Acta Crystallogr D Biol Crystallogr,  2002, 58(Pt 12), 2173-4.
 [http://dx.doi.org/10.1107/S0907444902016803]

[102]
Gakhar, L.; Malik, Z.A.; Allen, C.C.R.; Lipscomb, D.A.; Larkin, M.J.; Ramaswamy, S. Structure and increased thermostability of Rhodo-coccus sp. naphthalene 1,2-dioxygenase. J. Bacteriol.,  2005, 187(21), 7222-7231.
 [http://dx.doi.org/10.1128/JB.187.21.7222-7231.2005] [PMID:  16237006]

[103]
Gómez-Gil, L.; Kumar, P.; Barriault, D.; Bolin, J.T.; Sylvestre, M.; Eltis, L.D. Characterization of biphenyl dioxygenase of Pandoraea pnomenusa B-356 as a potent polychlorinated biphenyl-degrading enzyme. J. Bacteriol.,  2007, 189(15), 5705-5715.
 [http://dx.doi.org/10.1128/JB.01476-06] [PMID:  17526697]

[104]
Kumari, A.; Singh, D.; Ramaswamy, S.; Ramanathan, G. Structural and functional studies of ferredoxin and oxygenase components of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2. PLoS One,  2017, 12(4), e0176398.
 [http://dx.doi.org/10.1371/journal.pone.0176398] [PMID:  28448625]

[105]
Friemann, R.; Ivkovic-Jensen, M.M.; Lessner, D.J.; Yu, C.L.; Gibson, D.T.; Parales, R.E.; Eklund, H.; Ramaswamy, S. Structural insight into the dioxygenation of nitroarene compounds: The crystal structure of nitrobenzene dioxygenase. J. Mol. Biol.,  2005, 348(5), 1139-1151.
 [http://dx.doi.org/10.1016/j.jmb.2005.03.052] [PMID:  15854650]

[106]
Peng, R.H.; Xiong, A.S.; Xue, Y.; Fu, X.Y.; Gao, F.; Zhao, W.; Tian, Y.S.; Yao, Q.H. A profile of ring-hydroxylating oxygenases that de-grade aromatic pollutants. Rev. Environ. Contam. Toxicol.,  2010, 206, 65-94.
 [http://dx.doi.org/10.1007/978-1-4419-6260-7_4] [PMID:  20652669]

[107]
Nojiri, H.; Ashikawa, Y.; Noguchi, H.; Nam, J.W.; Urata, M.; Fujimoto, Z.; Uchimura, H.; Terada, T.; Nakamura, S.; Shimizu, K.; Yoshida, T.; Habe, H.; Omori, T. Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase. J. Mol. Biol.,  2005, 351(2), 355-370.
 [http://dx.doi.org/10.1016/j.jmb.2005.05.059] [PMID:  16005887]

[108]
Denke, E.; Merbitz-Zahradnik, T.; Hatzfeld, O.M.; Snyder, C.H.; Link, T.A.; Trumpower, B.L. Alteration of the midpoint potential and catalytic activity of the rieske iron-sulfur protein by changes of amino acids forming hydrogen bonds to the iron-sulfur cluster. J. Biol. Chem.,  1998, 273(15), 9085-9093.
 [http://dx.doi.org/10.1074/jbc.273.15.9085] [PMID:  9535897]

[109]
Merbitz-Zahradnik, T.; Zwicker, K.; Nett, J.H.; Link, T.A.; Trumpower, B.L. Elimination of the disulfide bridge in the Rieske iron-sulfur protein allows assembly of the [2Fe-2S] cluster into the Rieske protein but damages the ubiquinol oxidation site in the cytochrome bc1 complex. Biochemistry,  2003, 42(46), 13637-13645.
 [http://dx.doi.org/10.1021/bi035344r] [PMID:  14622010]

[110]
Parales, R.E.; Resnick, S.M.; Yu, C.L.; Boyd, D.R.; Sharma, N.D.; Gibson, D.T. Regioselectivity and enantioselectivity of naphthalene dioxygenase during arene cis-dihydroxylation: control by phenylalanine 352 in the alpha subunit. J. Bacteriol.,  2000, 182(19), 5495-5504.
 [http://dx.doi.org/10.1128/JB.182.19.5495-5504.2000] [PMID:  10986254]

[111]
Xiong, A.S.; Peng, R.H.; Zhuang, J.; Liu, J.G.; Gao, F.; Xu, F.; Cai, B.; Yao, Q.H. A semi-rational design strategy of directed evolution combined with chemical synthesis of DNA sequences. bchm,  2007, 388(12), 1291-1300.
 [http://dx.doi.org/10.1515/BC.2007.153] [PMID: 18020945]

[112]
Bashton, M.; Chothia, C. The generation of new protein functions by the combination of domains. Structure,  2007, 15(1), 85-99.
 [http://dx.doi.org/10.1016/j.str.2006.11.009] [PMID:  17223535]

[113]
Furukawa, K.; Hirose, J.; Hayashida, S.; Nakamura, K. Efficient degradation of trichloroethylene by a hybrid aromatic ring dioxygenase. J. Bacteriol.,  1994, 176(7), 2121-2123.
 [http://dx.doi.org/10.1128/jb.176.7.2121-2123.1994] [PMID:  8144482]

[114]
Chemerys, A.; Pelletier, E.; Cruaud, C.; Martin, F.; Violet, F.; Jouanneau, Y. Characterization of novel polycyclic aromatic hydrocarbon dioxygenases from the bacterial metagenomic DNA of a contaminated soil. Appl. Environ. Microbiol.,  2014, 80(21), 6591-6600.
 [http://dx.doi.org/10.1128/AEM.01883-14] [PMID:  25128340]

[115]
Singleton, D.R.; Hu, J.; Aitken, M.D. Heterologous expression of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes from a novel pyrene-degrading betaproteobacterium. Appl. Environ. Microbiol.,  2012, 78(10), 3552-3559.
 [http://dx.doi.org/10.1128/AEM.00173-12] [PMID:  22427500]

[116]
Kumamaru, T.; Suenaga, H.; Mitsuoka, M.; Watanabe, T.; Furukawa, K. Enhanced degradation of polychlorinated biphenyls by directed evolution of biphenyl dioxygenase. Nat Biotechnol,  1998, 16(7), 663-6.
 [http://dx.doi.org/10.1038/nbt0798-663]

[117]
Brühlmann, F.; Chen, W. Tuning biphenyl dioxygenase for extended substrate specificity. Biotechnol. Bioeng.,  1999, 63(5), 544-551.
 [http://dx.doi.org/10.1002/(SICI)1097-0290(19990605)63:5<544:AID-BIT4>3.0.CO;2-6] [PMID:  10397810]

[118]
Vézina, J.; Barriault, D.; Sylvestre, M. Diversity of the C-terminal portion of the biphenyl dioxygenase large subunit. J. Mol. Microbiol. Biotechnol.,  2008, 15(2-3), 139-151.
 [http://dx.doi.org/10.1159/000121326] [PMID:  18685267]

[119]
Keenan, B.G.; Leungsakul, T.; Smets, B.F.; Mori, M.; Henderson, D.E.; Wood, T.K. Protein engineering of the archetypal nitroarene diox-ygenase of Ralstonia sp. strain U2 for activity on aminonitrotoluenes and dinitrotoluenes through alpha-subunit residues leucine 225, phenylalanine 350, and glycine 407. J. Bacteriol.,  2005, 187(10), 3302-3310.
 [http://dx.doi.org/10.1128/JB.187.10.3302-3310.2005] [PMID:  15866914]

[120]
Kimura, N.; Nishi, A.; Goto, M.; Furukawa, K. Functional analyses of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are similar structurally but different functionally. J. Bacteriol.,  1997, 179(12), 3936-3943.
 [http://dx.doi.org/10.1128/jb.179.12.3936-3943.1997] [PMID:  9190809]

[121]
Barriault, D.; Simard, C.; Chatel, H.; Sylvestre, M. Characterization of hybrid biphenyl dioxygenases obtained by recombining Burkhold-eria sp. strain LB400 bphA with the homologous gene of Comamonas testosteroni B-356. Can. J. Microbiol.,  2001, 47(11), 1025-1032.
 [http://dx.doi.org/10.1139/cjm-47-11-1025] [PMID:  11766051]

[122]
Chebrou, H.; Hurtubise, Y.; Barriault, D.; Sylvestre, M. Heterologous expression and characterization of the purified oxygenase compo-nent of Rhodococcus globerulus P6 biphenyl dioxygenase and of chimeras derived from it. J. Bacteriol.,  1999, 181(16), 4805-4811.
 [http://dx.doi.org/10.1128/JB.181.16.4805-4811.1999] [PMID:  10438748]

[123]
Jun, H.; Akiko, S.; Shinsaku, H.; Kensuke, F. Construction of hybrid biphenyl (bph) and toluene (tod) genes for functional analysis of aromatic ring dioxygenases. Gene,  1994, 138(1-2), 27-33.
 [http://dx.doi.org/10.1016/0378-1119(94)90779-X] [PMID:  8125315]

[124]
Standfuß-Gabisch, C.; Al-Halbouni, D.; Hofer, B. Characterization of biphenyl dioxygenase sequences and activities encoded by the meta-genomes of highly polychlorobiphenyl-contaminated soils. Appl. Environ. Microbiol.,  2012, 78(8), 2706-2715.
 [http://dx.doi.org/10.1128/AEM.07381-11] [PMID:  22327590]

[125]
Suyama, A.; Iwakiri, R.; Kimura, N.; Nishi, A.; Nakamura, K.; Furukawa, K. Engineering hybrid Pseudomonads capable of utilizing a wide range of aromatic hydrocarbons and of efficient degradation of trichloroethylene. J. Bacteriol.,  1996, 178(14), 4039-4046.
 [http://dx.doi.org/10.1128/jb.178.14.4039-4046.1996] [PMID:  8763929]

[126]
Keenan, B.G.; Wood, T.K. Orthric Rieske dioxygenases for degrading mixtures of 2,4-dinitrotoluene/naphthalene and 2-amino-4,6-dinitrotoluene/4-amino-2,6-dinitrotoluene. Appl. Microbiol. Biotechnol.,  2006, 73(4), 827-838.
 [http://dx.doi.org/10.1007/s00253-006-0538-8] [PMID:  16933133]

[127]
Dhindwal, S.; Gomez-Gil, L.; Neau, D.B.; Pham, T.T.M.; Sylvestre, M.; Eltis, L.D.; Bolin, J.T.; Kumar, P. Structural basis of the enhanced pollutant-degrading capabilities of an engineered biphenyl dioxygenase. J. Bacteriol.,  2016, 198(10), 1499-1512.
 [http://dx.doi.org/10.1128/JB.00952-15] [PMID:  26953337]

[128]
Parales, R.E. The role of active-site residues in naphthalene dioxygenase. J. Ind. Microbiol. Biotechnol.,  2003, 30(5), 271-278.
 [http://dx.doi.org/10.1007/s10295-003-0043-3] [PMID:  12695887]

[129]
Mondello, F.J.; Turcich, M.P.; Lobos, J.H.; Erickson, B.D. Identification and modification of biphenyl dioxygenase sequences that deter-mine the specificity of polychlorinated biphenyl degradation. Appl. Environ. Microbiol.,  1997, 63(8), 3096-3103.
 [http://dx.doi.org/10.1128/aem.63.8.3096-3103.1997] [PMID:  9251195]

[130]
Heinemann, P.M.; Armbruster, D.; Hauer, B. Active-site loop variations adjust activity and selectivity of the cumene dioxygenase. Nat. Commun.,  2021, 12(1), 1095.
 [http://dx.doi.org/10.1038/s41467-021-21328-8] [PMID:  33597523]

[131]
Peracchi, A. Enzyme catalysis: removing chemically ‘essential’ residues by site-directed mutagenesis. Trends Biochem. Sci.,  2001, 26(8), 497-503.
 [http://dx.doi.org/10.1016/S0968-0004(01)01911-9] [PMID:  11504626]

[132]
Cámara, B.; Seeger, M.; González, M.; Standfuß-Gabisch, C.; Kahl, S.; Hofer, B. Generation by a widely applicable approach of a hybrid dioxygenase showing improved oxidation of polychlorobiphenyls. Appl. Environ. Microbiol.,  2007, 73(8), 2682-2689.
 [http://dx.doi.org/10.1128/AEM.02523-06] [PMID:  17322323]

[133]
Carredano, E.; Karlsson, A.; Kauppi, B.; Choudhury, D.; Parales, R.E.; Parales, J.V.; Lee, K.; Gibson, D.T.; Eklund, H.; Ramaswamy, S. Substrate binding site of naphthalene 1,2-dioxygenase: Functional implications of indole binding 1 1Edited by D. C. Rees. J. Mol. Biol.,  2000, 296(2), 701-712.
 [http://dx.doi.org/10.1006/jmbi.1999.3462] [PMID:  10669618]

[134]
Fu, B.; Xu, T.; Cui, Z.; Ng, H.L.; Wang, K.; Li, J.; Li, Q.X. Mutation of Phenylalanine-223 to leucine enhances transformation of Ben-zo[a]pyrene by ring-hydroxylating dioxygenase of Sphingobium sp. FB3 by increasing accessibility of the catalytic site. J. Agric. Food Chem.,  2018, 66(5), 1206-1213.
 [http://dx.doi.org/10.1021/acs.jafc.7b05018]

[135]
Lee, K.S.; Parales, J.V.; Friemann, R.; Parales, R.E. Active site residues controlling substrate specificity in 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42. J. Ind. Microbiol. Biotechnol.,  2005, 32(10), 465-473.
 [http://dx.doi.org/10.1007/s10295-005-0021-z] [PMID:  16175409]
Cite As
Current Protein & Peptide Science

Polyaromatic Hydrocarbon Specific Ring Hydroxylating Dioxygenases: Diversity, Structure, Function, and Protein Engineering

Abstract

Graphical Abstract
