Abstract
Ethylbenzene dehydrogenase initiates the anaerobic bacterial degradation of ethylbenzene and propylbenzene. Although the enzyme is currently only known from a few closely related denitrifying bacterial strains affiliated to the Rhodocyclaceae, it clearly marks a universally occurring mechanism used for attacking recalcitrant substrates in the absence of oxygen. Ethylbenzene dehydrogenase belongs to subfamily 2 of the DMSO reductase-type molybdenum enzymes together with paralogous enzymes involved in the oxygen-independent hydroxylation of p-cymene, the isoprenoid side chains of sterols and even possibly n-alkanes; the subfamily also extends to dimethylsulfide dehydrogenases, selenite, chlorate and perchlorate reductases and, most significantly, dissimilatory nitrate reductases. The biochemical, spectroscopic and structural properties of the oxygen-independent hydroxylases among these enzymes are summarized and compared. All of them consist of three subunits, contain a molybdenum-bis-molybdopterin guanine dinucleotide cofactor, five Fe-S clusters and a heme b cofactor of unusual ligation, and are localized in the periplasmic space as soluble enzymes. In the case of ethylbenzene dehydrogenase, it has been determined that the heme b cofactor has a rather high redox potential, which may also be inferred for the paralogous hydroxylases. The known structure of ethylbenzene dehydrogenase allowed the calculation of detailed models of the reaction mechanism based on the density function theory as well as QM-MM (quantum mechanics - molecular mechanics) methods, which yield predictions of mechanistic properties such as kinetic isotope effects that appeared consistent with experimental data.
References
1.
Aeckersberg F, Bak F, Widdel F: Anaerobic oxidation of saturated hydrocarbons to CO2 by a new type of sulfate-reducing bacterium. Arch Microbiol 1991;156:5-14.
2.
Aeckersberg F, Rainey FA, Widdel F: Growth, natural relationships, cellular fatty acids and metabolic adaptation of sulfate-reducing bacteria that utilize long-chain alkanes under anoxic conditions. Arch Microbiol 1998;170:361-369.
3.
Afshar S, Johnson E, de Vries S, Schröder I: Properties of a thermostable nitrate reductase from the hyperthermophilic archaeon Pyrobaculum aerophilum. J Bacteriol 2001;183:5491-5495.
4.
Ball HA, Johnson HA, Reinhard M, Spormann AM: Initial reactions in anaerobic ethylbenzene oxidation by a denitrifying bacterium, strain EB1. J Bacteriol 1996;178:5755-5761.
5.
Bender KS, Shang C, Chakraborty R, Belchik SM, Coates JD, Achenbach LA: Identification, characterization, and classification of genes encoding perchlorate reductase. J Bacteriol 2005;187:5090-5096.
6.
Bertero MG, Rothery RA, Palak M, Hou C, Lim D, Blasco F, Weiner JH, Strynadka NCJ: Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A. Nat Struct Biol 2003;10:681-687.
7.
Blasco F, Guigliarelli B, Magalon A, Asso M, Giordano G, Rothery RA: The coordination and function of the redox centres of the membrane-bound nitrate reductases. Cell Mol Life Sci 2001;58:179-193.
8.
Borowski T, Quesne M, Szaleniec M: QM and QM/MM methods compared: case studies on reaction mechanisms of metalloenzymes. Adv Protein Chem and Struct Biol 2015;100:187-224.
9.
Brodkorb D, Gottschall M, Marmulla R, Luddeke F, Harder J: Linalool dehydratase-isomerase, a bifunctional enzyme in the anaerobic degradation of monoterpenes. J Biol Chem 2010;285:30436-30442.
10.
Callaghan AV, Davidova IA, Savage-Ashlock K, Parisi VA, Gieg LM, Suflita JM, Kukor JJ, Wawrik B: Diversity of benzyl- and alkylsuccinate synthase genes in hydrocarbon-impacted environments and enrichment cultures. Environ Sci Technol 2010;44:7287-7294.
11.
Chemical Market Associates: World Light Olefins Analysis. Houston, Chemical Market Associates, 2004, vol I, II.
12.
Chiang YR, Ismail W, Gallien S, Heintz D, Van Dorsselaer A, Fuchs G: Cholest-4-en-3-one-Δ1-dehydrogenase, a flavoprotein catalyzing the second step in anoxic cholesterol metabolism. Appl Environ Microbiol 2008;74:107-113.
13.
Chiang YR, Ismail W, Müller M, Fuchs G: Initial steps in the anoxic metabolism of cholesterol by the denitrifying Sterolibacterium denitrificans. J Biol Chem 2007;282:13240-13249.
14.
Corkery DM, Oconnor KE, Buckley CM, Dobson ADW: Ethylbenzene degradation by Pseudomonas fluorescens strain Ca-4. FEMS Microbiol Lett 1994;124:23-27.
15.
Creevey NL, McEwan AG, Hanson GR, Bernhardt PV: Thermodynamic characterization of the redox centers within dimethylsulfide dehydrogenase. Biochemistry 2008;47:3770-3776.
16.
Dangel W, Tschech A, Fuchs G: Enzyme-reactions involved in anaerobic cyclohexanol metabolism by a denitrifying Pseudomonas species. Arch Microbiol 1989;152:273-279.
17.
Dean JA: Lange's Handbook of Chemistry. New York, McGraw Hill, 1992.
18.
Dermer J, Fuchs G: Molybdoenzyme that catalyzes the anaerobic hydroxylation of a tertiary carbon atom in the side chain of cholesterol. J Biol Chem 2012;287:36905-36916.
19.
Dridge E, Watts C, Jepson B, Line K, Santini J, Richardson D, Butler C: Investigation of the redox centres of periplasmic selenate reductase from Thauera selenatis by EPR spectroscopy. Biochem J 2007;408:19-28.
20.
Dudzik A, Kozik B, Tataruch M, Wojcik A, Knack D, Borowski T, Heider J, Witko M, Szaleniec M: The reaction mechanism of chiral hydroxylation of p-OH and p-NH2 substituted compounds by ethylbenzene dehydrogenase. Can J Chem 2013;91:775-786.
21.
Fahrbach M, Krauss M, Preiss A, Kohler HP, Hollender J: Anaerobic testosterone degradation in Steroidobacter denitrificans - identification of transformation products. Environ Pollut 2010;158:2572-2581.
22.
Fahrbach M, Kuever J, Meinke R, Kampfer P, Hollender J: Denitratisoma oestradiolicum gen. nov., sp. nov., a 17β-oestradiol-degrading, denitrifying betaproteobacterium. Int J Syst Evol Microbiol 2006;56:1547-1552.
23.
Fahrbach M, Kuever J, Remesch M, Huber BE, Kampfer P, Dott W, Hollender J: Steroidobacter denitrificans gen. nov., sp. nov., a steroidal hormone-degrading gammaproteobacterium. Int J Syst Evol Microbiol 2008;58:2215-2223.
24.
Filipovic D, Paulsen MD, Loida PJ, Sligar SG, Ornstein RL: Ethylbenzene hydroxylation by cytochrome-P450cam. Biochem Biophys Res Commun 1992;189:488-495.
25.
Fuchs G, Boll M, Heider J: Microbial degradation of aromatic compounds - from one strategy to four. Nature Rev Microbiol 2011;9:803-816.
26.
Gibson DT, Gschwend.B, Yeh WK, Kobal VM: Initial reactions in oxidation of ethylbenzene by Pseudomonas putida. Biochemistry 1973;12:1520-1528.
27.
Guigliarelli B, Asso M, More C, Augier V, Blasco F, Pommier J, Giordano G, Bertrand P: EPR and redox characterization of iron-sulfur centers in nitrate reductases A and Z from Escherichia coli. Eur J Biochem 1992;207:61-68.
28.
Hamid H, Eskicioglu C: Fate of estrogenic hormones in wastewater and sludge treatment: a review of properties and analytical detection techniques in sludge matrix. Water Res 2012;46:5813-5833.
29.
Harder J, Probian C: Anaerobic mineralization of cholesterol by a novel type of denitrifying bacterium. Arch Microbiol 1997;167:269-274.
30.
Harms G, Rabus R, Widdel F: Anaerobic oxidation of the aromatic plant hydrocarbon p-cymene by newly isolated denitrifying bacteria. Arch Microbiol 1999;172:303-312.
31.
Heider J, Schühle K: Anaerobic biodegradation of hydrocarbons including methane; in Rosenberg E, DeLong EF, Thompson F, Lory S, Stackebrandt E (eds): The Prokaryotes: Prokaryotic Physiology and Biochemistry. New York, Springer, 2013, pp 601-630.
32.
Hille R: The molybdenum oxotransferases and related enzymes. Dalton Trans 2013;42:3029-3042.
33.
Hille R, Hall J, Basu P: The mononuclear molybdenum enzymes. Chem Rev 2014;114:3963-4038.
34.
Höffken HW, Duong M, Friedrich T, Breuer M, Hauer B, Reinhardt R, Rabus R, Heider J: Crystal structure and enzyme kinetics of the (S)-specific 1-phenylethanol dehydrogenase of the denitrifying bacterium strain EbN1. Biochemistry 2006;45:82-93.
35.
Jindrova E, Chocova M, Demnerova K, Brenner V: Bacterial aerobic degradation of benzene, toluene, ethylbenzene and xylene. Folia Microbiol 2002;47:83-93.
36.
Jobst B, Schühle K, Linne U, Heider J: ATP-dependent carboxylation of acetophenone by a novel type of carboxylase. J Bacteriol 2010;192:1387-1394.
37.
Johnson HA, Pelletier DA, Spormann AM: Isolation and characterization of anaerobic ethylbenzene dehydrogenase, a novel Mo-Fe-S enzyme. J Bacteriol 2001;183:4536-4542.
38.
Jormakka M, Richardson D, Byrne B, Iwata S: Architecture of NarGH reveals a structural classification of Mo-bis-MGD enzymes. Structure 2004;12:95-104.
39.
Kalimuthu P, Heider J, Knack D, Bernhardt PV: Electrocatalytic hydrocarbon hydroxylation by ethylbenzene dehydrogenase from Aromatoleum aromaticum. J Phys Chem B 2015;119:3456-3463.
40.
Kengen SWM, Rikken GB, Hagen WR, van Ginkel CG, Stams AJM: Purification and characterization of (per)chlorate reductase from the chlorate-respiring strain GR-1. J Bacteriol 1999;181:6706-6711.
41.
Kieslich K: Microbial side-chain degradation of sterols. J Basic Microbiol 1985;25:461-474.
42.
Kloer DP, Hagel C, Heider J, Schulz GE: Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum. Structure 2006;14:1377-1388.
43.
Knack D, Hagel C, Szaleniec M, Dudzik A, Salwinski A, Heider J: Substrate and inhibitor spectrum of ethylbenzene dehydrogenase: perspectives on application potential and catalytic mechanism. Appl Environ Microbiol 2012;78:6475-6482.
44.
Knack D, Marshall JL, Harlow GP, Dudzik A, Szaleniec M, Liu SY, Heider J: BN/CC isosteric compounds as enzyme inhibitors: N- and B-ethyl-1,2-azaborine inhibit ethylbenzene hydroxylation as nonconvertible substrate analogues. Angew Chem Int Edit 2013;52:2599-2601.
45.
Kniemeyer O, Fischer T, Wilkes H, Glockner FO, Widdel F: Anaerobic degradation of ethylbenzene by a new type of marine sulfate-reducing bacterium. Appl Environ Microbiol 2003;69:760-768.
46.
Kniemeyer O, Heider J: Ethylbenzene dehydrogenase, a novel hydrocarbon-oxidizing molybdenum/iron-sulfur/heme enzyme. J Biol Chem 2001a;276:21381-21386.
47.
Kniemeyer O, Heider J: (S)-1-Phenylethanol dehydrogenase of Azoarcus sp. strain EbN1, an enzyme of anaerobic ethylbenzene catabolism. Arch Microbiol 2001b;176:129-135.
48.
Kniemeyer O, Musat F, Sievert SM, Knittel K, Wilkes H, Blumenberg M, Michaelis W, Classen A, Bolm C, Joye SB, Widdel F: Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria. Nature 2007;449:898-901.
49.
Krafft T, Bowen A, Theis F, Macy JM: Cloning and sequencing of the genes encoding the periplasmic-cytochrome b-containing selenate reductase of Thauera selenati s. DNA Seq 2000;10:365-377.
50.
Kropp KG, Davidova IA, Suflita JM: Anaerobic oxidation of n-dodecane by an addition reaction in a sulfate-reducing bacterial enrichment culture. Appl Environ Microb 2000;66:5393-5398.
51.
Lee K, Gibson DT: Toluene and ethylbenzene oxidation by purified naphthalene dioxygenase from Pseudomonas sp strain NCIB 9816-4. Appl Environ Microbiol 1996;62:3101-3106.
52.
Leu YL, Wang PH, Shiao MS, Ismail W, Chiang YR: A novel testosterone catabolic pathway in bacteria. J Bacteriol 2011;193:4447-4455.
53.
Lin CW, Wang PH, Ismail W, Tsai YW, El Nayal A, Yang CY, Yang FC, Wang CH, Chiang YR: Substrate uptake and subcellular compartmentation of anoxic cholesterol catabolism in Sterolibacterium denitrificans. J Biol Chem 2015;290:1155-1169.
54.
Lledo B, Martinez-Espinosa RM, Marhuenda-Egea FC, Bonete MJ: Respiratory nitrate reductase from haloarchaeon Haloferaxmediterranei: biochemical and genetic analysis. Biochim Biophys Acta 2004;1674:50-59.
55.
Magalon A, Lemesle-Meunier D, Rothery RA, Frixon C, Weiner JH, Blasco F: Heme axial ligation by the highly conserved His residues in helix ii of cytochrome b (NarI) of Escherichia coli nitrate reductase a (NarGHI). J Biol Chem 1997;272:25652-25658.
56.
Maillard J, Spronk CA, Buchanan G, Lyall V, Richardson DJ, Palmer T, Vuister GW, Sargent F: Structural diversity in twin-arginine signal peptide-binding proteins. Proc Natl Acad Sci USA 2007;104:15641-15646.
57.
McDevitt CA, Hanson GR, Noble CJ, Cheesman MR, McEwan AG: Characterization of the redox centers in dimethyl sulfide dehydrogenase from Rhodovulum sulfidophilum. Biochemistry 2002a;41:15234-15244.
58.
McDevitt CA, Hugenholtz P, Hanson GR, McEwan AG: Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes. Mol Microbiol 2002b;44:1575-1587.
59.
Montgomery JA, Frisch MJ, Ochterski JW, Petersson GA: A complete basis set model chemistry. VI. Use of density functional geometries and frequencies. J Chem Phys 1999;110:2822-2827.
60.
Montgomery JA, Frisch MJ, Ochterski JW, Petersson GA: A complete basis set model chemistry. VII. Use of the minimum population localization method. J Chem Phys 2000;112:6532-6542.
61.
Moser CC, Page CC, Farid R, Dutton PL: Biological electron transfer. J Bioenerg Biomembr 1995;27:263-274.
62.
Nes WD: Biosynthesis of cholesterol and other sterols. Chem Rev 2011;111:6423-6451.
63.
Page CC, Moser CC, Chen XX, Dutton PL: Natural engineering principles of electron tunnelling in biological oxidation-reduction. Nature 1999;402:47-52.
64.
Rabus R, Heider J: Initial reactions of anaerobic metabolism of alkylbenzenes in denitrifying and sulfate reducing bacteria. Arch Microbiol 1998;170:377-384.
65.
Rabus R, Kube M, Beck A, Widdel F, Reinhardt R: Genes involved in the anaerobic degradation of ethylbenzene in a denitrifying bacterium, strain EbN1. Arch Microbiol 2002;178:506-516.
66.
Rabus R, Kube M, Heider J, Beck A, Heitmann K, Widdel F, Reinhardt R: The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Arch Microbiol 2005;183:27-36.
67.
Rabus R, Widdel F: Anaerobic degradation of ethylbenzene and other aromatic-hydrocarbons by new denitrifying bacteria. Arch Microbiol 1995;163:96-103.
68.
Rabus R, Wilkes H, Behrends A, Armstroff A, Fischer T, Pierik AJ, Widdel F: Anaerobic initial reaction of n-alkanes in a denitrifying bacterium: Evidence for (1-methylpentyl)succinate as initial product and for involvement of an organic radical in n-hexane metabolism. J Bacteriol 2001;183:1707-1715.
69.
Rothery RA, Bertero MG, Cammack R, Palak M, Blasco F, Strynadka NCJ, Weiner JH: The catalytic subunit of Escherichia coli nitrate reductase a contains a novel [4Fe-4S] cluster with a high-spin ground state. Biochemistry 2004;43:5324-5333.
70.
Rugor A, Bojarski A, Szaleniec M: A unique bacterial molybdoenzyme - from structural insights to industrial application; in: Chmielewski MC (ed): Annual Report. Warsaw, Polish Academy of Sciences, 2015, pp 46-48.
71.
Sakaki T, Sugimoto H, Hayashi K, Yasuda K, Munetsuna E, Kamakura M, Ikushiro S, Shiro Y: Bioconversion of vitamin D to its active form by bacterial or mammalian cytochrome P450. Biochem Biophys Acta 2011;1814:249-256.
72.
Schröder I, Rech S, Krafft T, Macy JM: Purification and characterization of the selenate reductase from Thauera selenatis. J Biol Chem 1997;272:23765-23768.
73.
Schühle K, Heider J: Acetone and butanone metabolism of the denitrifying bacterium ‘Aromatoleum aromaticum' demonstrates novel biochemical properties of an ATP-dependent aliphatic ketone carboxylase. J Bacteriol 2012;194:131-141.
74.
Sluis MK, Larsen RA, Krum JG, Anderson R, Metcalf WW, Ensign SA: Biochemical, molecular, and genetic analyses of the acetone carboxylases from Xanthobacter autotrophicus strain Py2 and Rhodobacter capsulatus strain B10. J Bacteriol 2002;184:2969-2977.
75.
So CM, Phelps CD, Young LY: Anaerobic transformation of alkanes to fatty acids by a sulfate-reducing bacterium, strain Hxd3. Appl Environ Microb 2003;69:3892-3900.
76.
Soffker M, Tyler CR: Endocrine disrupting chemicals and sexual behaviors in fish - a critical review on effects and possible consequences. Crit Rev Toxicol 2012;42:653-668.
77.
Strijkstra A, Trautwein K, Jarling R, Wöhlbrand L, Dorries M, Reinhardt R, Drozdowska M, Golding BT, Wilkes H, Rabus R: Anaerobic activation of p-cymene in denitrifying betaproteobacteria: methyl group hydroxylation versus addition to fumarate. Appl Environ Microbiol 2014;80:7592-7603.
78.
Szaleniec J, Wiatr M, Szaleniec M, Skladzien J, Tomik J, Oles K, Tadeusiewicz R: Artificial neural network modelling of the results of tympanoplasty in chronic suppurative otitis media patients. Comput Biol Med 2013;43:16-22.
79.
Szaleniec M, Borowski T, Schühle K, Witko M, Heider J: Ab initio modeling of ethylbenzene dehydrogenase reaction mechanism. J Am Chem Soc 2010;132:6014-6024.
80.
Szaleniec M, Dudzik A, Kozik B, Borowski T, Heider J, Witko M: Mechanistic basis for the enantioselectivity of the anaerobic hydroxylation of alkylaromatic compounds by ethylbenzene dehydrogenase. J Inorg Biochem 2014;139:9-20.
81.
Szaleniec M, Hagel C, Menke M, Nowak P, Witko M, Heider J: Kinetics and mechanism of oxygen-independent hydrocarbon hydroxylation by ethylbenzene dehydrogenase. Biochemistry 2007;46:7637-7646.
82.
Szaleniec M, Jobst B, Heider J: Ethylbenzene dehydrogenase: oxidation of hydrocarbons without oxygen. Ann Pol Chem Soc 2003:240-245.
83.
Szaleniec M, Salwinski A, Borowski T, Heider J, Witko M: Quantum chemical modeling studies of ethylbenzene dehydrogenase activity. Intl J Quantum Chem 2012;112:1990-1999.
84.
Szaleniec M, Witko M, Heider J: Quantum chemical modelling of the C-H cleavage mechanism in oxidation of ethylbenzene and its derivates by ethylbenzene dehydrogenase. J Mol Catal A Chem 2008;286:128-136.
85.
Szaleniec M, Witko M, Tadeusiewicz R, Goclon J: Application of artificial neural networks and DFT-based parameters for prediction of reaction kinetics of ethylbenzene dehydrogenase. J Comput Aid Mol Des 2006;20:145-157.
86.
Szaleniec M, Rugor A, Dudzik A, Tataruch M, Szymańska K, Jarzębski A: Method of obtaining 25-hydroxylated sterol derivatives, including 25-hydroxy-7-dehydrocholesterol. Polish Patent Application, P.411750.
87.
Tarlera S, Denner EBM: Sterolibacterium denitrificans gen. nov., sp nov., a novel cholesterol-oxidizing, denitrifying member of the β-Proteobacteria. Int J Syst Evol Microbiol 2003;53:1085-1091.
88.
Tataruch M, Heider J, Bryjak J, Nowak P, Knack D, Czerniak A, Liesiene J, Szaleniec M: Suitability of the hydrocarbon-hydroxylating molybdenum-enzyme ethylbenzene dehydrogenase for industrial chiral alcohol production. J Biotechnol 2014;192:400-409.
89.
Thorell HD, Stenklo K, Karlsson J, Nilsson T: A gene cluster for chlorate metabolism in Ideonella dechloratans. Appl Environ Microbiol 2003;69:5585-5592.
90.
Wang PH, Lee TH, Ismail W, Tsai CY, Lin CW, Tsai YW, Chiang YR: An oxygenase-independent cholesterol catabolic pathway operates under oxic conditions. PLoS One 2013a;8:e66675.
91.
Wang PH, Leu YL, Ismail W, Tang SL, Tsai CY, Chen HJ, Kao AT, Chiang YR: Anaerobic and aerobic cleavage of the steroid core ring structure by Steroidobacter denitrificans. J Lipid Res 2013b;54:1493-1504.
92.
Warnke M, Dermer J, Hipp K, Jehmlich N, Bergen M, Ferlaino S, Fries A, Müller M, Boll M: 25-Hydroxyvitamin D3 synthesis by enzymatic steroid side chain hydroxylation with water. Angew Chem Int Ed Engl 2016, DOI: 10.1002/anie.201510331R1.
93.
Wöhlbrandt L, Rabus R: Development of a genetic system for the denitrifying bacterium ‘Aromatoleum aromaticum' strain EbN1. J Mol Microbiol Biotechnol 2009;17:41-52.
94.
Yasutake Y, Nishioka T, Imoto N, Tamura T: A single mutation at the ferredoxin binding site of P450 VDH enables efficient biocatalytic production of 25-hydroxyvitamin D3. Chembiochem 2013;14:2284-2291.
95.
Yoshimatsu K, Araya O, Fujiwara T: Haloarcula marismortui cytochrome b-561 is encoded by the narC gene in the dissimilatory nitrate reductase operon. Extremophiles 2007;11:41-47.
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