Abstract
Dichloromethane (DCM) is efficiently utilized as a carbon and energy source by aerobic, Gram-negative, facultative methylotrophic bacteria. It also serves as a sole carbon and energy source for a nitrate-respiringHyphomicrobium sp. and for a strictly anaerobic co-culture of a DCM-fermenting bacterium and an acetogen. The first step of DCM utilization by methylotrophs is catalyzed by DCM dehalogenase which, in a glutathione-dependent substitution reaction, forms inorganic chloride and S-chloromethyl glutathione. This unstable intermediate decomposes to glutathione, inorganic chloride and formaldehyde, a central metabolite of methylotrophic growth. Genetic studies on DCM utilization are beginning to shed some light on questions pertaining to the evolution of DCM dehalogenases and on the regulation of DCM dehalogenase expression. DCM dehalogenase belongs to the glutathione S-transferase supergene family. Analysis of the amino acid sequences of two bacterial DCM dehalogenases reveals 56% identity, and comparison of these sequences to those of glutathione S-transferases indicates a closer relationship to class Theta eukaryotic glutathione S-transferases than to a number of bacterial glutathione S-transferases whose sequences have recently become available.dcmA, the structural gene of the highly substrate-inducible DCM dehalogenase, is carried in most DCM utilizing methylotrophs on large plasmids. InMethylobacterium sp. DM4 its expression is governed bydcmR, a regulatory gene located upstream ofdcmA. dcmR encodes atrans-acting factor which negatively controls DCM dehalogenase formation at the transcriptional level. Our working model thus assumes that thedcmR product is a repressor which, in the absence of DCM, binds to the promoter region ofdcmA and thereby inhibits initiation of transcription.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Anders MW & Pohl LR (1985) Halogenated alkanes. In: Anders MW (Ed) Bioactivation of Foreign Compounds (pp 284–341). Academic Press, New York
Anonymous (1993) Production by the U.S. Chemical Industry, C & EN, June:42
Bader R & Leisinger T (1993) Characterization ofdcmA inMethylophilus sp. DM11, the plasmid encoded structural gene of dichloromethane dehalogenase (Abstract). BioEngineering 9:58, P261
Bader R (1994) Das Strukturgen der Dichlormethan Dehalogenase/Glutathion S-Transferase ausMethylophilus sp. Stamm DM11. Ph.D. Thesis. Federal Institute of Technology, Zürich
Banger KK, Lock EA & Reed CJ (1993) The characterization of glutathione S-transferases from rat olfactory epithelium. Biochem. J. 290:199–204
Blocki FA, Ellis LBM & Wackett LP (1993) MIF proteins are theta class glutathione S-transferase homologs. Protein Science. 2:2095–2102
Braus-Stromeyer SA, Hermann R, Cook AM & Leisinger T (1993) Dichloromethane as carbon source for an acetogenic mixed culture and isolation of a fermentative, dichloromethane-degrading bacterium. Appl. Environ. Microbiol. 59:3790–3797
Brunner W, Staub D & Leisinger T (1980) Bacterial degradation of dichloromethane. Appl. Environ. Microbiol. 40:950–958
Class TH & Ballschmiter K (1988) Chemistry of organic traces in air. VIII: Sources and distribution of bromo- and bromochloromethanes in marine air and surfacewater of the Atlantic Ocean. J. At. Chem. 6:35–46
De Vries GE, Kües U & Stahl U (1990) Physiology and genetics of methylotrophic bacteria. FEMS Microbiol. Revs. 75:57–102
Di Ilio C, Aceto A, Piccolomini R, Allocati N, Faraone A, Cellini L, Ravagnan G & Federici G (1988) Purification and characterization of three forms of glutathione transferase fromProteus mirabilis. Biochem. J. 255:971–975
Diks RM & Ottengraf SP (1991) Verification studies of a simplified model for the removal of dichloromethane from waste gases using a biological trickling filter (part I). Bioprocess. Eng. 6:93–99
Doronina N & Trotsenko Y (1992) Personal Communication
Fahey RC & Sundquist AR (1991) Evolution of glutathione metabolism. In: Meister A (Ed) Advances in Enzymology, Vol 64 (pp 1–53). John Wiley & Sons, New York
Frank S (1993) Abbau von Dichlormethan durchHyphomicrobium DM2 unter denitrifizierenden Bedingungen. Diploma Thesis, Swiss Federal Institute of Technology, Zürich
Freedman DL & Gossett JM (1991) Biodegradation of dichloromethane and its utilization as a growth substrate under methanogenic conditions. Appl. Environ. Microbiol. 57:2847–2857
Gälli R, Stucki G & Leisinger T (1982) Mechanism of dehalogenation of dichloromethane by cell extract ofHyphomicrobium DM2. Experientia 38:1378
Gälli R & Leisinger T (1985) Specialized bacterial strains for the removal of dichloromethane from industrial waste. Conservation Recycling 8:91–100
Gälli R & Leisinger T (1988) Plasmid analysis and cloning of the dichloromethane-utilization genes ofMethylobacterium sp. DM4. J. Gen. Microbiol. 134:943–952
Gonnet GH (1992) A tutorial introduction to Computational Biochemistry using Darwin. Institut für Wissenschaftliches Rechnen, ETH Zürich, Zürich, Switzerland
Green PN (1993) Overview of the current state of methylotroph taxonomy. In: Murrell JC & Kelly DP (Eds) Microbial Growth on C1 Compounds (pp 253–265). Intercept Ltd, Andover, UK
Grove G, Zarlengo RP, Timmermann KP, Li N, Tam MF & Tu CPD (1988) Characterization and heterospecific expression of cDNA clones of genes in the maize GSH S-transferase multigene family. Nucleic Acids Res. 16:425–438
Hallier E, Langhof T, Dannapel D, Leutbecher M, Schröder K, Goergens HW, Müller A & Bolt HM (1993) Polymorphism of glutathione conjugation of methyl bromide, ethylene oxide and dichloromethane in human blood: influence on the induction of sister chromatid exchanges (SCE) in lymphocytes. Arch. Toxicol. 67:173–178
Hartmans S & Tramper J (1991) Dichloromethane removal from waste gases with a trickle-bed bioreactor. Bioprocess. Eng. 6:83–92
Henrysson, T & Mattiasson B (1993) A microbial biosensor system for dihalomethanes. Biodegradation 4:101–105
Hohenberg H, Mannweiler K & Müller M (1994) High pressure freezing of cell suspensions in cellulose capillary tubes. J. Microsc. In Press
Ji X, Zhang P, Armstrong RN & Gilliland GL (1992) The three-dimensional structure of a glutathione S-transferase from the mu gene class Structural analysis of the binary complex of isoenzyme 3-3 & glutathione at 2.2 Å resolution. Biochem. 31:10169–10184
Johnson WW, Liu S, Ji X, Gilliland GL & Armstrong RN (1993) Tyrosine 115 participates both in chemical & physical steps of the catalytic mechanism of a glutathione S-transferase. J. Biol. Chem. 268:11508–11511
Klecka, GM (1982) Fate and effects of methylene chloride in activated sludge. Appl. Environ. Microbiol. 44:701–707
Kohler-Staub D, Hartmans S, Gälli R, Suter F & Leisinger T (1986) Evidence for identical dichloromethane dehalogenases in different methylotrophic bacteria. J. Gen. Microbiol. 132:2837–2843
Kohler-Staub D & Leisinger T (1985) Dichloromethane dehalogenase ofHyphomicrobium sp. strain DM2. J. Bacteriol. 162:676–681
Kong K-H, Inoue H & Takahashi K (1993) Site-directed mutagenesis study on the roles of evolutionally conserved aspartic acid residues in human glutathione S-transferase P1-1. Protein Engineering 6:93–99
Lai HCJ, Grove G & Tu CPD (1986) Cloning and sequence analysis of a cDNA for a rat liver glutathione-S-transferase Yb subunit. Nucl. Acids Res. 14:6101–6114
La Pat-Polasko LT, McCarty PL & Zehnder AJB (1984) Secondary substrate utilization of methylene chloride by an isolated strain ofPseudomonas sp. Appl. Environ. Microbiol. 47:825–830
La Roche SD & Leisinger T (1990) Sequence analysis and expression of the bacterial dichloromethane dehalogenase structural gene, a member of the glutathione S-transferase supergene family. J. Bacteriol. 172:164–171
La Roche SD & Leisinger T (1991) Identification ofdcmR, the regulatory gene governing expression of dichloromethane dehalogenase inMethylobacterium sp. strain DM4. J. Bacteriol. 173:6714–6721
Leisinger T, La Roche S, Bader R, Schmid-Appert M, Braus-Stromeyer S & Cook AM (1993) Chlorinated methanes as carbon sources for aerobic and anaerobic bacteria. In: Murrell JC & Kelly DP (Eds) Microbial Growth on C1 Compounds (pp 351–363). Intercept Ltd, Andover, UK
Leisinger T & Bader R (1993) Microbial dehalogenation of synthetic organohalogen compounds: Hydrolytic dehalogenases. Chimia 47:116–121
Lidstrom ME & Sterling DI (1990) Methylotrophs: Genetics and commercial applications. Annu. Rev. Microbiol. 44:27–58
Liu S, Zhang P, Ji X, Johnson WW, Gilliland GL & Armstrong RN (1992) Contribution of tyrosine 6 to the catalytic mechanism of isoenzyme 3-3 of glutathione S-transferase. J. Biol. Chem. 267:4296–4299
Mabey W & Mill T (1978) Critical review of hydrolysis of organic compounds in water under environmental conditions. J. Phys. Chem. Ref. Data 7:383–415
Manoharan TH, Gulick AM, Reinemer P, Dirr HW, Huber R & Fahl WE (1992) Mutational substitution of residues implicated by crystal structure in binding of substrate glutathione to human glutathione S-transferase π. J. Mol. Biol. 226:319–322
Masai E, Katayama Y, Kubota S, Kawai S, Yamasaki M & Morohoshi N (1993) A bacterial enzyme degrading the model lignin compound β-etherase is a member of the glutathione S-transferase superfamily. FEBS Lett. 323:135–140
Meyer DJ, Coles B, Pemble SE, Gilmore KS, Fraser GM & Ketterer B (1991) Theta, a new class of glutathione transferases purified from rat and man. Biochem. J. 274:409–414
Meyer DJ, Xia C, Coles B, Chen H, Reinemer P, Huber R & Ketterer B (1993) Unusual reactivity of Tyr-7 of GSH transferase P1-1. Biochem. J. 293:351–356
Mignogna G, Allocati N, Aceto A, Piccolomini R, Di Ilio C, Barra D & Martini F (1993) The amino acid sequence of glutathione transferase fromProteus mirabilis a prototype of a new class of enzymes. Eur. J. Biochem. 211:421–425
Navas J, Leon J, Arroyo M & Garcia-Lobo JM (1990) Nucleotide sequence and intracellular location of the product of the fosfomycin resistance gene from transposon Tn 2921. Antimicrob. Agents Chemother. 34:2016–2018
Ogura K, Nishiyama T, Okada T, Kajita J, Narihata H, Watabe, T, Hiratsuka A & Watabe T (1991) Molecular cloning and amino acid sequencing of rat liver class theta glutathione S-transferase Yrs-Yrs inactivating reactive sulfate esters of carcinogenic arylmethanols. Biochem. Biophys. Res. Commun. 181:1294–1300
Orser CS, Dutton J, Lange C, Jablonski P, Xun L & Hargis M (1993) Characterization of aFlavobacterium glutathione S-transferase gene involved in reductive dechlorination. J. Bacteriol. 175:2640–2644
Pearson CR (1982) C1 and C2 halocarbons. In: Hutzinger O (Ed) The Handbook of Environmental Chemistry, Vol 3, Part B (pp 69–88). Springer Verlag, Berlin
Pemble SE & Taylor JB (1992) An evolutionary perspective on glutathione transferases inferred from class-theta glutathione transferase cDNA sequences. Biochem. J. 287:957–963
Piccolomini R, Di Ilio C, Aceto A, Ilocati N, Faraone A, Cellini L, Ravagnan G & Federici G (1989) Glutathione transferase in bacteria: subunit composition and antigenic characterization J. Gen. Microbiol. 135:3119–3125
Reinemer P, Dirr HW, Ladenstein R, Schäffer J, Gallay O & Huber R (1991) The three-dimensional structure of class π glutathione S-transferase in complex with glutathione sulfonate at 2.3 Å resolution. EMBO J. 10:1997–2005
Reinemer P, Dirr HW, Ladenstein R, Huber R, Lo Bello M, Federici G & Parker MW (1992) Three-dimensional structure of class π glutathione S-transferase from human placenta in complex with S-hexylglutathione at 2.8 Å resolution. J. Mol. Biol. 227:214–226
Scholtz R, Wackett LP, Egli C, Cook AM & Leisinger T (1988) Dichloromethane dehalogenase with improved catalytic activity isolated from a fast-growing dichloromethane-utilizing bacterium. J. Bacteriol. 170:5698–5704
Stenberg G, Board PG, Carlberg I & Mannervik B (1991) Effects of directed mutagenesis on conserved arginine residues in a human class alpha glutathione transferase. Biochem. J. 274:549–555
Stromeyer SA, Winkelbauer W, Kohler H, Cook AM & Leisinger T (1991) Dichloromethane utilized by an anaerobic mixed culture: acetogenesis and methanogenesis. Biodegradation 2:129–137
Stucki G, Gälli R, Ebersold HR & Leisinger T (1981) Dehalogenation of dichloromethane by cell extract ofHyphomicrobium DM2. Arch. Microbiol. 130:366–371
Stucki G (1990) Biological decomposition of dichloromethane from a chemical process effluent. Biodegradation 1:221–228
Sysoev OV, Govorukhina NI & Gruzman MB (1990) Glutathione S-transferase of methylotrophic bacteria: distribution and characterization. Appl. Biochem. Microbiol. 26:367–371
Telakowski-Hopkins CA, Rodkey JA, Bennett CD, Lu AYH & Pickett CB (1985) Rat liver glutathione S-transferases. Construction of a cDNA clone complementary to a Yc mRNA and prediction of the complete amino acid sequence of a Yc subunit. J. Biol. Chem. 260:5820–5825
Tew KD, Pickett CB, Mantle TJ, Mannervik B & Hayes J (1993) Structure and function of glutathione S-transferases. CRC Press, Boca Raton.
Tsuji K, Tsien HC, Hanson RS, De Palma, SR, Scholtz R & La Roche S (1990) 16S ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs. J. Gen. Microbiol. 136:1–10
Wackett LP, Logan MSP, Blocki FA & Bao-li C (1992) A mechanistic perspective on bacterial metabolism of chlorinated methanes. Biodegradation 3:19–36
Wever R (1993) Sources and sinks of halogenated methanes in nature. In: Murrell JC & Kelly DP (Eds) Microbial Growth on C1 Compounds (pp 35–45). Intercept Ltd, Andover, UK
Xia C, Meyer DJ, Chen H, Reinemer P, Huber R & Ketterer B (1993) Chemical modification of GSH transferase P1-1 confirms the presence of Arg-13, Lys-44 and one carboxylate group in the GSH-binding domain of the active site. Biochem. J. 293:357–362
Zhang P, Liu S, Shan S-O, Ji X, Gilliland GL & Armstrong RN (1992) Modular mutagenesis of exons 1,2 & 8 of a glutathione S-transferase from the mu class: mechanistic and structural consequences for chimeras of isoenzyme 3-3. Biochemistry 31:10185–10193
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Leisinger, T., Bader, R., Hermann, R. et al. Microbes, enzymes and genes involved in dichloromethane utilization. Biodegradation 5, 237–248 (1994). https://doi.org/10.1007/BF00696462
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00696462