Identification of a Serine Hydrolase Which Cleaves the Alicyclic Ring of Tetralin

Hernáez, María José; Andújar, Eloísa; Rı́os, José-Luis; Kaschabek, Stefan R.; Reineke, Walter; Santero, Eduardo

doi:10.1128/jb.182.19.5448-5453.2000

Cited by 34 publications

(47 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, the gene encoding a third potential MCP hydrolase was cloned (2). DxnB2 has been reported to be more related to MCP hydrolases involved in the catabolism of monocyclic aromatic compounds than to enzymes such as BphD, which are involved in the degradation of bicyclic aromatics (15). This result, derived from amino acid sequence comparisons, is somewhat surprising as the substrates of DxnB and BphD differ by a single hydroxyl group on the phenyl ring.…”

mentioning

confidence: 40%

Characterization of a C—C Bond Hydrolase fromSphingomonas wittichiiRW1 with Novel Specificities towards Polychlorinated Biphenyl Metabolites

Seah

Denis

et al. 2007

J Bacteriol

View full text Add to dashboard Cite

Sphingomonas wittichii RW1 degrades chlorinated dibenzofurans and dibenzo-p-dioxins via meta cleavage. We used inverse PCR to amplify dxnB2, a gene encoding one of three meta-cleavage product (MCP) hydrolases identified in the organism that are homologues of BphD involved in biphenyl catabolism. Purified DxnB2 catalyzed the hydrolysis of 8-OH 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPDA) approximately six times faster than for HOPDA at saturating substrate concentrations. Moreover, the specificity of DxnB2 for HOPDA (k cat /K m ‫؍‬ 1.2 ؋ 10 7 M ؊1 s ؊1 ) was about half that of the BphDs of Burkholderia xenovorans LB400 and Rhodococcus globerulus P6, two potent polychlorinated biphenyl (PCB)-degrading strains. Interestingly, DxnB2 transformed 3-Cl and 4-OH HOPDAs, compounds that inhibit the BphDs and limit PCB degradation. DxnB2 had a higher specificity for 9-Cl HOPDA than for HOPDA but a lower specificity for 8-Cl HOPDA (k cat /K m ‫؍‬ 1.7 ؋ 10 6 M ؊1 s ؊1 ), the chlorinated analog of 8-OH HOPDA produced during dibenzofuran catabolism. Phylogenetic analyses based on structure-guided sequence alignment revealed that DxnB2 belongs to a previously unrecognized class of MCP hydrolases, evolutionarily divergent from the BphDs although the physiological substrates of both enzyme types are HOPDAs. However, both classes of enzymes have mainly small hydrophobic residues lining the subsite that binds the C-6 phenyl of HOPDA, in contrast to the bulky hydrophobic residues (Phe106, Phe135, Trp150, and Phe197) found in the class II enzymes that prefer substrates possessing a C-6 alkyl. Thr196 and/or Asn203 appears to be an important determinant of specificity for DxnB2, potentially forming hydrogen bonds with the 8-OH substituent. This study demonstrates that the substrate specificities of evolutionarily divergent hydrolases may be useful for degrading mixtures of pollutants, such as PCBs.Chlorinated aromatic compounds, such as polychlorinated biphenyls (PCBs) and dibenzofurans, are among the most widespread, toxic, and/or persistent environmental pollutants. The Bph and Dxn/Dbf pathways responsible for the aerobic bacterial catabolism of biphenyl and dibenzofuran, respectively, have been extensively studied, in part due to their potential for remediating environments contaminated with the polychlorinated compounds (2, 10). The pathways share three homologous enzymes ( Fig. 1): a multicomponent dioxygenase that catalyzes the initial step of ring hydroxylation, an extradiol dioxygenase that catalyzes oxygenolytic cleavage of the catecholic intermediate at the meta position to yield 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPDA) or ortho-substituted HOPDA, and a metacleavage product (MCP) hydrolase that catalyzes an unusual COC bond cleavage of the HOPDA.A general limitation of bacterial catabolic pathways for the degradation of complex industrial mixtures is that one or more pathway enzymes lack the requisite broad substrate specificity to degrade all man-made (xenobiotic) congeners of the naturally occurring compounds,...

show abstract

mentioning

confidence: 40%

Characterization of a C—C Bond Hydrolase fromSphingomonas wittichiiRW1 with Novel Specificities towards Polychlorinated Biphenyl Metabolites

Seah

Denis

et al. 2007

J Bacteriol

View full text Add to dashboard Cite

show abstract

“…The meta-cleavage product hydrolases belong to the ␣/␤-hydrolase family, and most of them are classified into two major groups, I and III, proposed by Hernáez et al (13). However, FlnE did not form a cluster with the group I proteins including BphD but formed a branch with the group IV proteins including OhpC and CmtE (data not shown).…”

mentioning

confidence: 90%

Characterization of the Upper Pathway Genes for Fluorene Metabolism in Terrabacter sp. Strain DBF63

et al. 2004

View full text Add to dashboard Cite

Genes involved in the degradation of fluorene to phthalate were characterized in the fluorene degrader Terrabacter sp. strain DBF63. The initial attack on both fluorene and 9-fluorenone was catalyzed by DbfA to yield 9-fluorenol and 1,1a-dihydroxy-1-hydro-9-fluorenone, respectively. The FlnB protein exhibited activities against both 9-fluorenol and 1,1a-dihydroxy-1-hydro-9-fluorenone to produce 9-fluorenone and 2-carboxy-2,3-dihydroxybiphenyl, respectively. FlnD is a heteromeric protein encoded by flnD1 and ORF16, being a member of the class III two-subunit extradiol dioxygenase. FlnE was identified as a serine hydrolase for the metacleavage products that yield phthalate.Polycyclic aromatic hydrocarbons (PAHs) have toxic, mutagenic, and carcinogenic properties, and therefore, their long persistence in the environment is of major concern. Among the PAHs, fluorene (FN) has been classified as one of 16 priority pollutants by the U.S. Environmental Protection Agency because of its toxicity to organisms and abundance in the environment (18). For the purpose of bioremediation, the bacterial degradation of FN has been studied for many years (2,3,8,9,10,11,19,26,27), and three major degradative pathways have been proposed (Fig. 1). Two of these pathways are initiated by a dioxygenation at the 1,2 (Fig. 1A) or 3,4 (Fig. 1B) position. The third route is initiated by monooxygenation at the C-9 position to give 9-fluorenol (VI), which is then dehydrogenated to 9-fluorenone (VII). Angular dioxygenation of 9-fluorenone then leads to 1,1a-dihydroxy-1-hydro-9-fluorenone (DHF, VIII) (6,7,23). Dehydrogenation of DHF produces a 2Ј-carboxy-2,3-dihydroxybiphenyl (CDB, IX; this metabolite is spontaneously transformed to 8-hydroxy-3,4-benzocoumarin [HBC, X]), which is metabolized by the reactions analogous to those of biphenyl degradation, leading to the formation of phthalate (XI) (2, 9, 26). However, although many FN-utilizing bacteria have been isolated and characterized, very little is known about the specific enzymes involved in the catabolism of FN and especially the genes coding for these enzymes.Terrabacter sp. strain DBF63 was originally isolated from a soil sample as a bacterium capable of utilizing dibenzofuran (DF) and FN as the sole source of carbon and energy (17,19). Recently, novel terminal oxygenase genes of angular dioxygenase (dbfA1 and dbfA2), whose products can catalyze the angular dioxygenation of DF with the complementation of the nonspecific electron transport system of Escherichia coli, were isolated by a PCR-based strategy (16). The facts that pht genes for phthalate to protocatechuate cluster together with the dbfA1A2 genes (12) and that both the dbfA1A2 and pht genes were expressed in suggested that the whole island could be involved in FN metabolism. The present report is the first on the characterization of the upper metabolic pathway genes for FN.Nucleotide sequencing of the downstream region of dbfA1A2 genes. We determined the nucleotide sequences of the 6,525-bp BamHI region (Fig. 2, shaded box) as de...

show abstract

“…Extensive sequence similarity has been detected between MhpC and other C-C bond hydrolases cleaving vinylogous 1,5-diketones from, for example, the meta-cleavage biphenyl (BphD and PcbD), xylene (XylF), toluene (TodF), and phenol (DmpD) biodegradative pathways (92). A dendrogram resulting from the comparison of amino acid sequences of hydrolases involved in meta-cleavage pathways of aromatic compounds revealed four different groups, with the MhpC protein being the only exception within group I of a hydrolase not involved in biodegradation of bicyclic molecules (136). All C-C bond hydrolases cleaving 1,5-diketones are members of the ␣/␤-hydrolase family (136), with residues Ser-114, Asp-239, and His-267 forming the putative catalytic triad of MhpC.…”

Section: Dhpp Meta Cleavage Hydrolytic Routementioning

confidence: 99%

Biodegradation of Aromatic Compounds by Escherichia coli

Dı́az

Ferrández

Prieto

et al. 2001

Microbiol Mol Biol Rev

324

235

View full text Add to dashboard Cite

Although Escherichia coli has long been recognized as the best-understood living organism, little was known about its abilities to use aromatic compounds as sole carbon and energy sources. This review gives an extensive overview of the current knowledge of the catabolism of aromatic compounds by E. coli. After giving a general overview of the aromatic compounds that E. coli strains encounter and mineralize in the different habitats that they colonize, we provide an up-to-date status report on the genes and proteins involved in the catabolism of such compounds, namely, several aromatic acids (phenylacetic acid, 3- and 4-hydroxyphenylacetic acid, phenylpropionic acid, 3-hydroxyphenylpropionic acid, and 3-hydroxycinnamic acid) and amines (phenylethylamine, tyramine, and dopamine). Other enzymatic activities acting on aromatic compounds in E. coli are also reviewed and evaluated. The review also reflects the present impact of genomic research and how the analysis of the whole E. coli genome reveals novel aromatic catabolic functions. Moreover, evolutionary considerations derived from sequence comparisons between the aromatic catabolic clusters of E. coli and homologous clusters from an increasing number of bacteria are also discussed. The recent progress in the understanding of the fundamentals that govern the degradation of aromatic compounds in E. coli makes this bacterium a very useful model system to decipher biochemical, genetic, evolutionary, and ecological aspects of the catabolism of such compounds. In the last part of the review, we discuss strategies and concepts to metabolically engineer E. coli to suit specific needs for biodegradation and biotransformation of aromatics and we provide several examples based on selected studies. Finally, conclusions derived from this review may serve as a lead for future research and applications

show abstract

Identification of a Serine Hydrolase Which Cleaves the Alicyclic Ring of Tetralin

Cited by 34 publications

References 36 publications

Characterization of a C—C Bond Hydrolase fromSphingomonas wittichiiRW1 with Novel Specificities towards Polychlorinated Biphenyl Metabolites

Characterization of a C—C Bond Hydrolase fromSphingomonas wittichiiRW1 with Novel Specificities towards Polychlorinated Biphenyl Metabolites

Characterization of the Upper Pathway Genes for Fluorene Metabolism in Terrabacter sp. Strain DBF63

Biodegradation of Aromatic Compounds by Escherichia coli

Contact Info

Product

Resources

About