The bphC gene-encoded 2,3-dihydroxybiphenyl-1,2-dioxygenase is involved in complete degradation of dibenzofuran by the biphenyl-degrading bacterium Ralstonia sp. SBUG 290

AIMS: Biphenyl-degrading bacteria are able to metabolize dibenzofuran via lateral dioxygenation and meta-cleavage of the dihydroxylated dibenzofuran produced. This degradation was considered to be incomplete because accumulation of a yellow-orange ring-cleavage product was observed. In this study, we want to characterize the 1,2-dihydroxydibenzofuran cleaving enzyme which is involved in dibenzofuran degradation in the bacterium Ralstonia sp. SBUG 290. METHODS AND RESULTS: In this strain, complete degradation of dibenzofuran was observed after cultivation on biphenyl. The enzyme shows a wide substrate utilization spectrum, including 1,2-dihydroxydibenzofuran, 2,3-dihydroxybiphenyl, 1,2-dihydroxynaphthalene, 3- and 4-methylcatechol and catechol. MALDI-TOF analysis of the protein revealed a strong homology to the bphC gene products. We therefore cloned a 3.2 kb DNA fragment containing the bphC gene of Ralstonia sp. SBUG 290. The deduced amino acid sequence of bphC is identical to that of the corresponding gene in Pseudomonas sp. KKS102. The bphC gene was expressed in Escherichia coli and the meta-fission activity was detected using either 2,3-dihydroxybiphenyl or 1,2-dihydroxydibenzofuran as substrate. CONCLUSIONS: These results demonstrate that complete degradation of dibenzofuran by biphenyl degraders can occur after initial oxidation steps catalysed by gene products encoded by the bph-operon. The ring fission of 1,2-dihydroxydibenzofuran is catalysed by BphC. Differences found in the metabolism of the ring fission product of dibenzofuran among biphenyl degrading bacteria are assumed to be caused by different substrate specificities of BphD. SIGNIFICANCE AND IMPACT OF THE STUDY: This study shows for the first time that the gene products of the bph-operon are involved in the mineralization of dibenzofuran in biphenyl degrading bacteria.     

Expression in Escherichia coli of Biphenyl 2,3-Dioxygenase Genes from a Gram-Positive Polychlorinated Biphenyl Degrader,Rhodococcus jostii RHA1

Rhodococcus jostii RHA1 is a polychlorinated biphenyl degrader. Multi-component biphenyl 2,3-dioxygenase (BphA) genes of RHA1 encode large and small subunits of oxygenase component and ferredoxin and reductase components. They did not express enzyme activity in Escherichia coli. To obtain BphA activity in E. coli, hybrid BphA gene derivatives were constructed by replacing ferredoxin and/or reductase component genes of RHA1 with those of Pseudomonas pseudoalcaligenes KF707. The results obtained indicate a lack of catalytic activity of the RHA1 ferredoxin component gene, bphAc in E. coli. To determine the cause of inability of RHA1 bphAc to express in E. coli, the bphAc gene was introduced into Rosetta (DE3) pLacI, which has extra tRNA genes for rare codons in E. coli. The resulting strain abundantly produced the bphAc product, and showed activity. These results suggest that codon usage bias is involved in inability of RHA1 bphAc to express its catalytic activity in E. coli.     

5-Chloropicolinic acid is produced by specific degradation of 4-chlorobenzoic acid by Sphingomonas paucimobilis BPSI-3

We have previously shown that the bacterium Sphingomonas paucimobilis BPSI-3, isolated from PCB-contaminated soil, can degrade halogenated biphenyls, naphthalenes, catechols and benzoic acids. However, before such an organism can be used in bioremediation, it is important to characterise the degradation products and determine the degradation pathways to ensure that compounds more toxic or mobile than the original contaminants are not produced. In the degradation of 4-chlorobiphenyl, S. paucimobilis BPSI-3 produces a novel chlorinated picolinic acid. In this paper, we show that 4-chlorobenzoate is an intermediate in this degradation and, through ¹⁵N-labelling, that 5-chloropicolinate is the only nitrogenous metabolite isolated under the extraction conditions used. The position of the chlorine indicates that degradation of 4-chlorocatechol occurs exclusively via a 2,3-extradiol cleavage. These data allow us to postulate a more definitive catabolic pathway for the biodegradation of 4-chlorobiphenyl to 5-chloro-2-hydroxymuconic acid semialdehyde via 4-chlorobenzoate in S. paucimobilis BPSI-3. Received 19 April 1999/ Accepted in revised form 23 July 1999     

Nucleotide sequence of the gene encoding cis-biphenyl dihydrodiol dehydrogenase (bphB) and the expression of an active recombinant His-tagged bphB gene product from a PCB degrading bacterium, Pseudomonas putida OU83

The nucleotide sequence of the bphB gene of Pseudomonas putida strain OU83 was determined. The bphB gene, which encodes cis-biphenyl dihydrodiol dehydrogenase (BDDH), was composed of 834 base pairs with an ATG initiation codon and a TGA termination codon. It can encode a polypeptide of 28.91 kDa, containing 277 amino acids. Promoter-like and ribosome-binding sequences were identified upstream of the bphB gene. The bphB nucleotide sequence was used to produce His-tagged BDDH, in Escherichia coli. The His-tagged BDDH construction, carrying a single 6×His tail on the N-terminal portion, was active. The molecular mass of the native enzyme was 128 kDa and on SDS-PAGE analysis the molecular mass was 31 kDa. This enzyme requires NAD⁺ for its activity and its optimum pH is 8.5. Nucleotide and the deduced amino acid sequence analyses revealed a high degree of homology between the bphB gene from Pseudomonas putida OU83 and the bphB genes from P. cepacia LB400 and P. pseudoalcaligenes KF707.     

Involvement of naphthalene dioxygenase in indole-3-acetic acid biosynthesis by Pseudomonas putida

Two variants of plant growth-promoting strain Pseudomonas putida BS1380 harboring the naphthalene degradative plasmid pBS2 and the recombinant plasmid pNAU64 that contains the genes encoding for naphthalene dioxygenase were constructed by conjugation. The ability of this strain to produce phytohormone indole-3-acetic acid from different carbon sources was studied. Indole-3-acetic acid synthesis by these transconjugants was 15-30 times as much in contrast to a wild-type strain with glucose as the sole carbon source. No difference was observed in other carbon or nitrogen sources. It is suggested that naphthalene dioxygenase is involved in the conversion of indole-3-pyruvic acid to indole-3-acetic acid.     

Metabolism of fensulfothion by a soil bacterium, Pseudomonas alcaligenes C1

Fensulfothion (O,O-diethyl O-[4-(methylsulfinyl)phenyl]phosphorothioate), an organophosphorus pesticide used to control the golden nematode Heterodera rostochiensis, is used as a source of carbon by microorganisms isolated from soils treated with the pesticide. Two of the microbial isolates, Pseudomonas alcaligenes C1 and Alcaligenes sp. strain NC3, used more than 80% of the pesticide in 120 h in culture when supplemented as a source of carbon. P. alcaligenes C1, which showed maximal growth on fensulfothion, degraded the compound to p-methylsulfinyl phenol and diethyl phosphorothioic acid. The phenolic metabolite could be identified by conventional spectral analysis, whereas the spectral patterns of the phosphorus-containing metabolite suggested that the compound was complexed with some cellular molecules. However, utilization of the phosphoric acid ester and ethanol by P. alcaligenes C1 suggested that the microbe attacks fensulfothion by an initial hydrolysis of the compound and subsequent utilization of the phosphoric acid ester. The pathway of degradation of fensulfothion by P. alcaligenes is of great value in the detoxification of the pesticide residues and also in the environmentally stable phosphoric acid esters.     

Biodegradation of 4-chlorobiphenyl by using induced cells and cell extract of Burkholderia xenovorans

This study aimed to evaluate the efficiency of Burkholderia xenovorans LB400 cells and their cell extract to remediate 4-chlorobiphenyl (4-CB). The bacterium previously induced with 4-CB was able to degrade up to 98% of initial 50 mg L^?1 of 4-CB from mineral medium within 96 h of incubation. The degradation of 4-CB occurred through the formation of meta-cleavage product 2-hydroxy-6-oxo-6phenylhexa-2,4-dienoic acid (HOPDA), as revealed through enzymatic assay of 2,3-dihydroxybiphenyl 1,2-dioxygenase (2,3-DHBD). A derivative of 1,2-benzenedicarboxylic acid was observed as one of the major intermediate metabolites of 4-CB degradation. Time course production of 2,3-DHBD during growth corresponds with the degradation pattern of 4-CB by the bacterium. In vitro degradation of 4-CB using cell extract of B. xenovorans showed complete degradation of initial 25 mg L^?1 of 4-CB within 6 h of incubation. To the best of the authors' knowledge, this is the first report in which in vitro degradation of 4-CB using cell extract of Burkholderia xenovorans is presented.     

Metabolism of fensulfothion by a soil bacterium, Pseudomonas alcaligenes C1.

Fensulfothion (O,O-diethyl O-[4-(methylsulfinyl)phenyl]phosphorothioate), an organophosphorus pesticide used to control the golden nematode Heterodera rostochiensis, is used as a source of carbon by microorganisms isolated from soils treated with the pesticide. Two of the microbial isolates, Pseudomonas alcaligenes C1 and Alcaligenes sp. strain NC3, used more than 80% of the pesticide in 120 h in culture when supplemented as a source of carbon. P. alcaligenes C1, which showed maximal growth on fensulfothion, degraded the compound to p-methylsulfinyl phenol and diethyl phosphorothioic acid. The phenolic metabolite could be identified by conventional spectral analysis, whereas the spectral patterns of the phosphorus-containing metabolite suggested that the compound was complexed with some cellular molecules. However, utilization of the phosphoric acid ester and ethanol by P. alcaligenes C1 suggested that the microbe attacks fensulfothion by an initial hydrolysis of the compound and subsequent utilization of the phosphoric acid ester. The pathway of degradation of fensulfothion by P. alcaligenes is of great value in the detoxification of the pesticide residues and also in the environmentally stable phosphoric acid esters.     

Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1

Biphenyl dioxygenase is the enzyme that catalyzes the stereospecific dioxygenation of the aromatic ring. This enzyme has attracted the attention of researchers due to its ability to oxidize polychlorinated biphenyls, which is one of the serious environmental contaminants. We determined the crystal structure of the terminal oxygenase component of the biphenyl dioxygenase (BphA1A2) derived from Rhodococcus strain sp. RHA1 in substrate-free and complex forms. These crystal structures revealed that the substrate-binding pocket makes significant conformational changes upon substrate binding to accommodate the substrate into the pocket. Our analysis of the crystal structures suggested that the residues in the substrate-binding pocket can be classified into three groups, which, respectively, seem to be responsible for the catalytic reaction, the orientation/conformation of the substrate, and the conformational changes of the substrate-binding pocket. The cooperative actions of residues in the three groups seem to determine the substrate specificity of the enzyme.     

Transformation of polychlorinated biphenyls by a novel BphA variant through the meta-cleavage pathway

The transformation of 20 polychlorinated biphenyls (PCBs) through the meta-cleavage pathway by recombinant Escherichia coli cells expressing the bphEFGBC locus from Burkholderia cepacia LB400 and the bphA genes from different sources was compared. The analysis of PCB congeners for which hydroxylation was observed but no formation of the corresponding yellow meta-cleavage product demonstrated that only lightly chlorinated congeners including one tetrachlorobiphenyl (2,2',4,4'-CB) were transformed into their corresponding yellow meta-cleavage products. Although many other tetrachlorobiphenyls (2, 2',5,5'-CB, 2,2',3,5'-CB, 2,4,4',5-CB, 2,3',4',5-CB, 2,3',4,4'-CB) and one pentachlorobiphenyl (2,2',4,5,5'-CB) tested were depleted from resting cell suspensions, no yellow meta-cleavage products were observed. For most of these congeners, dihydrodiol compounds accumulated as the endproducts, indicating that the bphB-encoded biphenyl-2,3-dihydrodiol-2,3-dehydrogenase is a key limiting step for further degradation of highly chlorinated congeners. These results suggest that engineering the biphenyl dioxygenase alone is insufficient for an improved removal of PCB. Rather, improved degradation of PCBs is more likely to be achieved with recombinant strains containing metabolic pathways not only specifically engineered for expanding the initial dioxygenation but also for the mineralization of PCBs.     

Degradation of diphenylether by Pseudomonas cepacia Et4: enzymatic release of phenol from 2,3-dihydroxydiphenylether

2,3-Dihydroxybiphenyl dioxygenase from Pseudomonas cepacia Et 4 was found to catalyze the ring fission of 2,3-dihydroxydiphenylether in the course of diphenylether degradation. The enzyme was purified and characterized. It had a molecular mass of 240 kDa and is dissociated by SDS into eight subunits of equal mass (31 kDa). The purified enzyme was found to be most active with 2,3-dihydroxybiphenyl as substrate and showed moderate activity with 2,3-dihydroxydiphenylether, catechol and some 3-substituted catechols. The K _m-value of 1 M for 2,3-dihydroxydiphenylether indicated a high affinity of the enzyme towards this substrate. The cleavage of 2,3-dihydroxydiphenylether by 2,3-dihydroxybiphenyl dioxygenase lead to the formation of phenol and 2-pyrone-6-carboxylate as products of ring fission and ether cleavage without participation of free intermediates. Isotope labeling experiments carried out with ¹⁸O₂ and H₂ ¹⁸O indicated the incorporation of ¹⁸O from the atmosphere into the carboxyl residue as well as into the carbonyl oxygen of the lactone moiety of 2-pyrone-6-carboxylate. Based on these experimental findings the reaction mechanism for the formation of phenol and 2-pyrone-6-carboxylate is proposed in accordance with the mechanism suggested by Kersten et al. (1982).Non-standard abbreviations DPE diphenylether - 2,3-dihydroxy-DPE 2,3-dihydroxydiphenylether - PCA 2-pyrone-6-carboxylic acid - 2,3-dihydroxy-BP dioxygenase 2,3-dihydroxybiphenyl dioxygenase - GC gas chromatography     

Metabolism of monofluoro- and monochlorobenzoates by a denitrifying bacterium

Monofluoro- and monochlorobenzoates did not support the growth of Pseudomonas PN-1, either aerobically or anaerobically (nitrate respiration), when supplied as sole sources of carbon and energy. Anaerobic growth yields on nonfluorinated substrates were increased by p-fluorobenzoate (pFBz) with a utilization of pFBz and release of F^-. Cell suspensions grown on p-hydroxybenzoate (pOHBz), either aerobically or anaerobically, only degraded o-fluorobenzoate (oFBz) and pFBz of the monohalogenated benzoates tested. Both compounds were catabolized anaerobically, but not aerobically, with a release of F^-. oFBz was immediately attacked, by cells grown anaerobically on pOHBz, whereas pFBz was only degraded after a lag phase; chloramphenicol inhibited the breakdown of pFBz, but not oFBz, thereby indicating the need for additional enzyme(s) to attack pFBz. o-Chlorobenzoate (oClBz) inhibited the anaerobic, but not aerobic, oxidation of pOHBz and stopped anaerobic growth on pOHBz. A mutant was isolated which metabolized pOHBz in the presence of oClBz but it was defective in its anaerobic metabolism of benzoate (Bz). Comparative studies, of the mutant and Pseudomonas PN-1, indicated that the mutation involved a metabolic site common to Bz, oClBz and the monofluorobenzoates. The dependence of the oxidation rate of Bz and oFBz on their concentrations at a millimolar level, in the mutant but not Pseudomonas PN-1, suggested a defect at the permease level: the uptake of ¹⁴C-labelled Bz by the mutant was also concentration-dependent. The response of the organism to the inhibitory effect of oClBz on pOHBz catabolism is discussed with respect to its significance in the perturbation of natural degradative processes by unnatural chemicals in the environment.Non-common abbreviations Bz benzoate - pOHBz p-hydroxybenzoate - oFBz o-fluorobenzoate - mFBz m-fluorobenzoate - pFBz p-fluorobenzoate - oClBz o-chlorobenzoate     

The reductase component of the chromosomally encoded benzoate dioxygenase from Pseudomonas putida C-1 is immunologically homologous with a product of the plasmid encoded xyl D gene (toluate dioxygenase) from Pseudomonas putida mt-2

Vibrio vulnificus, an autochthonous inhabitant of the estuarine environment, was detected in water and oysters from the Great Bay Estuary System of New Hampshire and Maine. Previously, it had not been detected north of Boston Harbor on the east coast of the United States. V. vulnificus was detected in water and shellfish samples at five out of ten sites, and only in areas that were not open to recreational shellfishing. Although samples were collected from May into December, V. vulnificus was only detected in shellfish in July and August. Water sampling began in August, and V. vulnificus persisted at one site into October.     

双加氧酶活力对细菌降解菲的指示作用

在液体培养基中选用两种石油降解细菌进行菲降解实验,研究了菲降解率和双加氧酶活力的变化。结果表明,菲降解率受其浓度的影响,当菲浓度为100mg·L-1时,其降解率为最高。而菲浓度高于100mg·L-1时,其降解率下降。实验发现在菲浓度为50～250mg·L-1条件下,细菌的双加氧酶活力与其菲的降解率存在较好的相关性,对细菌降解菲具有指示作用,可将双加氧酶活力作为菲降解率变化的评价指标。     

施氏假单胞菌YC-YH1的萘降解特性及产物分析

【目的】萘是一种重要的环境污染物,它在环境中的积累会对人类健康造成危害,生物降解是解决这一问题的有效方法。本实验室保存的施氏假单胞菌YC-YH1对萘具有较强的降解能力,在此基础上,研究和分析菌株对萘的降解特性、环境因素对萘降解率的影响以及代谢产物。【方法】本文首先采用单因素实验法研究pH、温度、接种量、萘初始浓度对萘降解率的影响;并在单因素实验结果的基础上,利用Design-Expert 8.0.5软件和Box-Behnken设计对pH、温度、接种量3个影响因素进行响应面优化分析,建立环境因素对萘降解率影响的优化模型。利用LC-MS检测萘降解过程中产生的重要代谢产物,从而推测菌株对萘的代谢途径。【结果】响应面分析结果表明,优化模型极显著(P<0.001),拟合度良好,预测结果可信度高。降解实验证明,在培养温度为32.4 °C、pH为7.10、接种量5.74% (体积比)的优化条件下培养3 d即可将浓度为100 mg/L的萘100%降解。LC-MS分析表明,菌株降解萘的过程中,能够被检测到的主要代谢产物有1,2-二羟基萘、水杨酸、邻苯二酚等。【结论】施氏假单胞菌YC-YH1对萘有高的降解效率,pH、温度、接种量3个因素对菌株的降解率有较大影响。利用响应面法优化菌株对萘的降解条件,能够提高YC-YH1菌株对萘的生物降解性能。初步推测菌株YC-YH1对萘的降解是通过水杨酸途径,萘首先被其代谢为1,2-二羟基萘,而后被转化为水杨酸和邻苯二酚,最后进入三羧酸循环被彻底降解。     

Functional analysis of genes involved in biphenyl, naphthalene, phenanthrene, and m-xylene degradation by Sphingomonas yanoikuyae B1

Sphingomonas yanoikuyae B1 is able to utilize toluene, m-xylene, p-xylene, biphenyl, naphthalene, phenanthrene, and anthracene as sole sources of carbon and energy for growth. A forty kilobase region of DNA containing most of the genes for the degradation of these aromatic compounds was previously cloned and sequenced. Insertional inactivation of bphC results in the inability of B1 to grow on both polycyclic and monocyclic compounds. Complementation experiments indicate that the metabolic block is actually due to a polar effect on the expression of bphA3, coding for a ferredoxin component of a dioxygenase. Lack of the ferredoxin results in a nonfunctional polycyclic aromatic hydrocarbon dioxygenase and a nonfunctional toluate dioxygenase indicating that the electron transfer components are capable of interacting with multiple oxygenase components. Insertional inactivation of a gene for a dioxygenase oxygenase component downstream of bphA3 had no apparent effect on growth besides a polar effect on nahD which is only needed for growth of B1 on naphthalene. Insertional inactivation of either xylE or xylG in the meta-cleavage operon results in a polar effect on bphB, the last gene in the operon. However, insertional inactivation of xylX at the beginning of this cluster of genes does not result in a polar effect suggesting that the genes for the meta-cleavage pathway, although colinear, are organized in at least two operons. These experiments confirm the biological role of several genes involved in metabolism of aromatic compounds by S. yanoikuyae B1 and demonstrate the interdependency of the metabolic pathways for polycyclic and monocyclic aromatic hydrocarbon degradation. Received 13 May 1999/ Accepted in revised form 05 July 1999     

Biodegradation of BTEX at high salinity by an enrichment culture from hypersaline sediments of Rozel Point at Great Salt Lake

Aims: The primary goal of this research was to assess the biodegradation of benzene, toluene, ethylbenzene and xylenes in sediment from Great Salt Lake, near Rozel Point, UT. Methods and Results: An enrichment culture that degraded benzene or toluene as the sole carbon source at high salinity was developed from a sediment sample obtained from Rozel Point. The enrichment degraded benzene or toluene within 1, 2 and 5 weeks in the presence of 14%, 23% and 29% NaCl respectively. PCR studies using degenerate primers revealed that degradation occurred primarily via catechol and the meta‐cleavage pathway. Molecular analysis showed that the Gammaproteobacteria were the dominant members of the enrichment and that shifts in community composition occurred during benzene metabolism. Conclusions: This study demonstrated that micro‐organisms at Rozel Point have the ability to degrade hydrocarbons over a broad range of salinities (1–5 mol l^?1 NaCl) and that the members of the Gammaproteobacteria class play an important role in the degradation process. Significance and Impact of the Study: These results are significant as little is known about the fate of petroleum seeps at Rozel Point. Also, the identity of microbes and the key enzymes involved in the degradation steps are important for understanding natural attenuation potential of hydrocarbons.     

Enantioselective transformation of alpha-hexachlorocyclohexane by the dehydrochlorinases LinA1 and LinA2 from the soil bacterium Sphingomonas paucimobilis B90A

Sphingomonas paucimobilis B90A contains two variants, LinA1 and LinA2, of a dehydrochlorinase that catalyzes the first and second steps in the metabolism of hexachlorocyclohexanes (R. Kumari, S. Subudhi, M. Suar, G. Dhingra, V. Raina, C. Dogra, S. Lal, J. R. van der Meer, C. Holliger, and R. Lal, Appl. Environ. Microbiol. 68:6021-6028, 2002). On the amino acid level, LinA1 and LinA2 were 88% identical to each other, and LinA2 was 100% identical to LinA of S. paucimobilis UT26. Incubation of chiral alpha-hexachlorocyclohexane (alpha-HCH) with Escherichia coli BL21 expressing functional LinA1 and LinA2 S-glutathione transferase fusion proteins showed that LinA1 preferentially converted the (+) enantiomer, whereas LinA2 preferred the (-) enantiomer. Concurrent formation and subsequent dissipation of beta-pentachlorocyclohexene enantiomers was also observed in these experiments, indicating that there was enantioselective formation and/or dissipation of these enantiomers. LinA1 preferentially formed (3S,4S,5R,6R)-1,3,4,5,6-pentachlorocyclohexene, and LinA2 preferentially formed (3R,4R,5S,6S)-1,3,4,5,6-pentachlorocyclohexene. Because enantioselectivity was not observed in incubations with whole cells of S. paucimobilis B90A, we concluded that LinA1 and LinA2 are equally active in this organism. The enantioselective transformation of chiral alpha-HCH by LinA1 and LinA2 provides the first evidence of the molecular basis for the changed enantiomer composition of alpha-HCH in many natural environments. Enantioselective degradation may be one of the key processes determining enantiomer composition, especially when strains that contain only one of the linA genes, such as S. paucimobilis UT26, prevail.