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1.
Chadhain SM Moritz EM Kim E Zylstra GJ 《Journal of industrial microbiology & biotechnology》2007,34(9):605-613
Sphingobium yanoikuyae B1 utilizes both polycyclic aromatic hydrocarbons (biphenyl, naphthalene, and phenanthrene) and monocyclic aromatic hydrocarbons
(toluene, m- and p-xylene) as its sole source of carbon and energy for growth. The majority of the genes for these intertwined monocyclic and
polycyclic aromatic pathways are grouped together on a 39 kb fragment of chromosomal DNA. However, this gene cluster is missing
several genes encoding essential enzymatic steps in the aromatic degradation pathway, most notably the genes encoding the
oxygenase component of the initial polycyclic aromatic hydrocarbon (PAH) dioxygenase. Transposon mutagenesis of strain B1
yielded a mutant blocked in the initial oxidation of PAHs. The transposon insertion point was sequenced and a partial gene
sequence encoding an oxygenase component of a putative PAH dioxygenase identified. A cosmid clone from a genomic library of
S. yanoikuyae B1 was identified which contains the complete putative PAH oxygenase gene sequence. Separate clones expressing the genes
encoding the electron transport components (ferredoxin and reductase) and the PAH dioxygenase were constructed. Incubation
of cells expressing the dioxygenase enzyme system with biphenyl or naphthalene resulted in production of the corresponding
cis-dihydrodiol confirming PAH dioxygenase activity. This demonstrates that a single multicomponent dioxygenase enzyme is involved
in the initial oxidation of both biphenyl and naphthalene in S. yanoikuyae B1. 相似文献
2.
Naphthalene and phenanthrene have long been used as model compounds to investigate the ability of bacteria to degrade polycyclic
aromatic hydrocarbons. The catabolic pathways have been determined, several of the enzymes have been purified to homogeneity,
and genes have been cloned and sequenced. However, the majority of this work has been performed with fast growing Pseudomonas strains related to the archetypal naphthalene-degrading P. putida strains G7 and NCIB 9816-4. Recently Comamonas testosteroni strains able to degrade naphthalene and phenanthrene have been isolated and shown to possess genes for polycyclic aromatic
hydrocarbon degradation that are different from the canonical genes found in Pseudomonas species. For instance, C. testosteroni GZ39 has genes for naphthalene and phenanthrene degradation which are not only different from those found in Pseudomonas species but are also arranged in a different configuration. C. testosteroni GZ42, on the other hand, has genes for naphthalene and phenanthrene degradation which are arranged almost the same as those
found in Pseudomonas species but show significant divergence in their sequences.
Received 10 August 1997/ Accepted in revised form 15 August 1997 相似文献
3.
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 相似文献
4.
5.
Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds 总被引:1,自引:0,他引:1
Lignins are the most abundant aromatic compounds in nature, and their decomposition is essential to the terrestrial carbon cycle. White rot fungi secreting phenol oxidases are assumed to be involved in the initial degradation of native lignin, whereas bacteria play a main role in the mineralization of lignin-derived low-molecular-weight compounds in soil. There are a number of reports on the degradation pathways for lignin-derived aromatic compounds, but their catabolism has not been enzymatically or genetically characterized. Sphingomonas paucimobilis SYK-6 is one of the best-characterized lignin-degrading bacteria. It can grow on a wide variety of lignin-related biaryls and monoaryls, including beta-aryl ether, biphenyl, diarylpropane, and phenylpropane. These compounds are degraded via the protocatechuate (PCA) 4,5-cleavage pathway or multiple 3-O-methylgallate (3MGA) catabolic pathways. In this review, the enzyme systems for beta-aryl ether and biphenyl degradation, O demethylation linked with one carbon metabolism, the PCA 4,5-cleavage pathway, and the multiple 3MGA catabolic pathways in SYK-6 are outlined. 相似文献
6.
Mycobacterium vanbaalenii PYR-1 is well known for its ability to degrade a wide range of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons
(PAHs). The genome of this bacterium has recently been sequenced, allowing us to gain insights into the molecular basis for
the degradation of PAHs. The 6.5 Mb genome of PYR-1 contains 194 chromosomally encoded genes likely associated with degradation
of aromatic compounds. The most distinctive feature of the genome is the presence of a 150 kb major catabolic region at positions
494 ~ 643 kb (region A), with an additional 31 kb region at positions 4,711 ~ 4,741 kb (region B), which is predicted to encode
most enzymes for the degradation of PAHs. Region A has an atypical mosaic structure made of several gene clusters in which
the genes for PAH degradation are complexly arranged and scattered around the clusters. Significant differences in the gene
structure and organization as compared to other well-known aromatic hydrocarbon degraders including Pseudomonas and Burkholderia were revealed. Many identified genes were enriched with multiple paralogs showing a remarkable range of diversity, which
could contribute to the wide variety of PAHs degraded by M. vanbaalenii PYR-1. The PYR-1 genome also revealed the presence of 28 genes involved in the TCA cycle. Based on the results, we proposed
a pathway in which HMW PAHs are degraded into the β-ketoadipate pathway through protocatechuate and then mineralized to CO2 via TCA cycle. We also identified 67 and 23 genes involved in PAH degradation and TCA cycle pathways, respectively, to be
expressed as proteins. 相似文献
7.
Sphingomonas yanoikuyae strain B1 is able to degrade a wider range of aromatic hydrocarbons than S. paucimobilis strain TNE12 can degrade. Various culture techniques were used to corroborate that B1 used m-xylene, biphenyl, toluene, naphthalene, and phenanthrene as sole carbon and energy sources. In contrast, TNE12 could not mineralize m-xylene, biphenyl, toluene, or naphthalene. However, fluoranthene served as carbon and energy source for TNE12 but not B1. Southern blots were performed using the cloned genomic region (approximately 23 kb) containing the degradative genes for the upstream pathways for biphenyl and m-xylene and a TOL plasmid-type meta operon from B1 as a probe against the Kpn I restriction-digested total DNA of TNE12. This 23 kb probe hybridized to three Kpn I-digested fragments of TNE12 DNA; thus significant homology existed between the aromatic hydrocarbon-degrading genes of B1 and TNE12. Further work with smaller probes revealed, however, that TNE12 DNA fragments did not hybridize with the probe containing the genes encoding for xylene monooxygenase and part of an aromatic dioxygenase. A recombinant plasmid, which contains only the genes for xylene monooxygenase, is able to complement TNE12 on m-xylene. These genes are, therefore, probably missing from TNE12. Hence, TNE12 cannot use monocylclic aromatics whereas B1 can. Pulsed field gel electrophoresis coupled with Southern blotting revealed that the aromatic degradative genes were on an approximately 240 kb plasmid of TNE12; the same genes in B1 are known to be chromosomal. 相似文献
8.
The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs) 总被引:17,自引:0,他引:17
Many members of the sphingomonad genus isolated from different geological areas can degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs) and related compounds. These sphingomonads such as Sphingobium yanoikuyae strain B1, Novosphingobium aromaticivorans strain F199, and Sphingobium sp. strain P2 have been found to possess a unique group of genes for aromatic degradation, which are distantly related with those in pseudomonads and other genera reported so far both in sequence homology and gene organization. Genes for aromatics degradation in these sphingomonads are complexly arranged; the genes necessary for one degradation pathway are scattered through several clusters. These aromatic catabolic gene clusters seem to be conserved among many other sphingomonads such as Sphingobium yanoikuyae strain Q1, Sphingomonas paucimobilis strain TNE12, S. paucimobilis strain EPA505, Sphingobium agrestis strain HV3, and Sphingomonas chungbukensis strain DJ77. Furthermore, some genes for naphthalenesulfonate degradation found in Sphingomonas xenophaga strain BN6 also share a high sequence homology with their homologues found in these sphingomonads. On the other hand, protocatechuic catabolic gene clusters found in fluorene-degrading Sphingomonas sp. strain LB126 appear to be more closely related with those previously found in lignin-degrading S. paucimobilis SYK-6 than the genes in this group of sphingomonads. This review summarizes the information on the distribution of these strains and relationships among their aromatic catabolic genes. 相似文献
9.
Kyung-Hwa Baek Byung-Dae Yoon Hee-Mock Oh Hee-Sik Kim In-Sook Lee 《Geomicrobiology journal》2013,30(5):253-259
We investigated the biodegradation of hydrocarbon components by Nocardia sp. H17-1 and the catabolic genes involved in the degradation pathways of both aliphatic and aromatic hydrocarbons. After 6 days of incubation, the aliphatic and aromatic fractions separated from Arabian light oil were degraded 99.0 ± 0.1% and 23.8 ± 0.8%, respectively. Detection of the catabolic genes involved in the hydrocarbon degradation indicated that H17-1 possessed the alkB genes for n-alkane biodegradation and catA gene for catechol 1,2-dioxygenase. However, H17-1 had neither the C23O gene for the degradation of aromatic hydrocarbons nor the catechol 2,3-dioxygenase activity. The investigation of the genes involved in the biodegradation of hydrocarbons supported the low degradation activity of H17-1 on the aromatic fractions. 相似文献
10.
Hirano S Haruki M Takano K Imanaka T Morikawa M Kanaya S 《Applied microbiology and biotechnology》2006,69(6):672-681
Xanthobacter polyaromaticivorans sp. nov. 127W is a bacterial strain that is capable of degrading a wide range of cyclic aromatic compounds such as dibenzothiophene,
biphenyl, naphthalene, anthracene, and phenanthrene even under extremely low oxygen [dissolved oxygen (DO)≤0.2 ppm] conditions
(Hirano et al., Biosci Biotechnol Biochem 68:557–564, 2004). A major protein fraction carrying dibenzothiophene degradation
activity was purified. Based on its partial amino acid sequences, dbdCa gene encoding alpha subunit terminal oxygenase (DbdCa) and its flanking region were cloned and sequenced. A phylogenetic
analysis based on the amino acid sequence demonstrates that DbdCa is a member of a terminal oxygenase component of group IV
ring-hydroxylating dioxygenases for biphenyls and monocyclic aromatic hydrocarbons, rather than group III dioxygenases for
polycyclic aromatic hydrocarbons. Gene disruption in dbdCa abolished almost of the degradation activity against biphenyl, dibenzothiophene, and anthracene. The gene disruption also
impaired degradation activity of the strain under extremely low oxygen conditions (DO≤0.2 ppm). These results indicate that
Dbd from 127W represents a group IV dioxygenase that is functional even under extremely low oxygen conditions. 相似文献
11.
Daniel J Ferraro Eric N Brown Chi-Li Yu Rebecca E Parales David T Gibson S Ramaswamy 《BMC structural biology》2007,7(1):10
Background
The initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism Sphingobium yanoikuyae strain B1 (B1), previously known as Sphingomonas yanoikuyae strain B1 and Beijerinckia sp. strain B1, is performed by a set of multiple terminal Rieske non-heme iron oxygenases. These enzymes share a single electron donor system consisting of a reductase and a ferredoxin (BPDO-FB1). One of the terminal Rieske oxygenases, biphenyl 2,3-dioxygenase (BPDO-OB1), is responsible for B1's ability to dihydroxylate large aromatic compounds, such as chrysene and benzo[a]pyrene. 相似文献12.
13.
J. W. Lengeler C. Merlin D. Springael M. Mergeay A. Toussaint 《Molecular & general genetics : MGG》1997,253(4):499-506
Tn4371 is a 55 kb transposon which encodes enzymes for the degradation of biphenyl and 4-chlorobiphenyl compounds into benzoate
and 4-chlorobenzo-ate derivatives. We constructed a cosmid library of Tn4371 DNA. The bph genes involved in biphenyl/4-chlorobiphenyl degradation were found to be clustered in the middle of the transposon. Sequencing
revealed an organisation of the bph genes similar to that previously found in Pseudomonas sp. KKS102, i.e. the bphEGF genes are located upstream of bphA1A2A3 and bphA4 is separated from bphA1A2A3 by bphBCD. Consensus sequences for σ54-associated RNA polymerase were found upstream of bphA1 and bphEGF. Plasmid RP4::Tn4371 was transferred into a mutant of Alcaligenes eutrophus H16 lacking σ54. In contrast to wild-type H16 exconjugants, the σ54 mutant exconjugants could not grow on biphenyl, indicating
the dependence of Tn4371bph gene expression on σ54. The Tn4371-encoded bph pathway was activated when biphenyl and various biphenyl-like compounds were present in the growth medium. Preliminary observations
indicate the presence of a region outside the catabolic genes downstream of bphA4 which is involved in mediating at least the basal expression of BphC.
Received: 13 May 1996 / Accepted: 16 September 1996 相似文献
14.
芳香族化合物生物降解的研究进展 总被引:1,自引:0,他引:1
本文综述了以苯、取代苯、联苯和多环芳烃为代表的芳香族化合物的生物降解途径,其共同之处在于经过两步双加氧酶作用,生成二醇和开环。两步双加氧酶分别为芳环羟基化双加氧酶和芳环断裂双加氧酶。以甲苯途径为代表讨论了芳香族化合物的分子生物学研究情况。代谢工程研究是九十年代兴起的芳香族化合物生物降解的研究内容,通过对甲苯途径的代谢工程研究明确了途径中的关键酶,并通过对关键酶的活性提高使整个途径的代谢流增加。 相似文献
15.
The Pseudomonas putida Crc global regulator controls the expression of genes from several chromosomal catabolic pathways for aromatic compounds 下载免费PDF全文
Morales G Linares JF Beloso A Albar JP Martínez JL Rojo F 《Journal of bacteriology》2004,186(5):1337-1344
The Crc protein is involved in the repression of several catabolic pathways for the assimilation of some sugars, nitrogenated compounds, and hydrocarbons in Pseudomonas putida and Pseudomonas aeruginosa when other preferred carbon sources are present in the culture medium (catabolic repression). Crc appears to be a component of a signal transduction pathway modulating carbon metabolism in pseudomonads, although its mode of action is unknown. To better understand the role of Crc, the proteome profile of two otherwise isogenic P. putida strains containing either a wild-type or an inactivated crc allele was compared. The results showed that Crc is involved in the catabolic repression of the hpd and hmgA genes from the homogentisate pathway, one of the central catabolic pathways for aromatic compounds that is used to assimilate intermediates derived from the oxidation of phenylalanine, tyrosine, and several aromatic hydrocarbons. This led us to analyze whether Crc also regulates the expression of the other central catabolic pathways for aromatic compounds present in P. putida. It was found that genes required to assimilate benzoate through the catechol pathway (benA and catBCA) and 4-OH-benzoate through the protocatechuate pathway (pobA and pcaHG) are also negatively modulated by Crc. However, the pathway for phenylacetate appeared to be unaffected by Crc. These results expand the influence of Crc to pathways used to assimilate several aromatic compounds, which highlights its importance as a master regulator of carbon metabolism in P. putida. 相似文献
16.
Pseudomonas fluorescens strain LP6a, isolated from petroleum condensate-contaminated soil, utilizes the polycyclic aromatic hydrocarbons (PAHs) naphthalene, phenanthrene, anthracene and 2-methylnaphthalene as sole carbon and energy sources. The isolate also co-metabolically transforms a suite of PAHs and heterocycles including fluorene, biphenyl, acenaphthene, 1-methylnaphthalene, indole, benzothiophene, dibenzothiophene and dibenzofuran, producing a variety of oxidized metabolites. A 63 kb plasmid (pLP6a) carries genes encoding enzymes necessary for the PAH-degrading phenotype of P. fluorescens LP6a. This plasmid hybridizes to the classical naphthalene degradative plasmids NAH7 and pWW60, but has different restriction endonuclease patterns. In contrast, plasmid pLP6a failed to hybridize to plasmids isolated from several phenanthrene-utilizing strains which cannot utilize naphthalene. Plasmid pLP6a exhibits reproducible spontaneous deletions of a 38 kb region containing the degradative genes. Two gene clusters corresponding to the archetypal naphthalene degradation upper and lower pathway operons, separated by a cryptic region of 18 kb, were defined by transposon mutagenesis. Gas chromatographic-mass spectrometric analysis of metabolites accumulated by selected transposon mutants indicates that the degradative enzymes encoded by genes on pLP6a have a broad substrate specificity permitting the oxidation of a suite of polycyclic aromatic and heterocyclic substrates. 相似文献
17.
E Masai Y Katayama S Nishikawa M Fukuda 《Journal of industrial microbiology & biotechnology》1999,23(4-5):364-373
Sphingomonas paucimobilis SYK-6 is able to grow on a wide variety of dimeric lignin compounds. These compounds are degraded via vanillate and syringate
by a unique enzymatic system, composed of etherases, O demethylases, ring cleavage oxygenases and side chain cleaving enzymes.
These unique and specific lignin modification enzymes are thought to be powerful tools for utilization of the most abundant
aromatic biomass, lignin. Here, we focus on the genes and enzymes involved in β-aryl ether cleavage and biphenyl degradation.
Two unique etherases are involved in the reductive cleavage of β-aryl ether. These two etherases have amino acid sequence
similarity with the glutathione S-transferases, and use glutathione as a hydrogen donor. It was found that 5,5′-dehydrodivanillate, which is a typical lignin-related
biphenyl structure, was transformed into 5-carboxyvanillate by the reaction sequence of O-demethylation, meta-ring cleavage, and hydrolysis, and the genes involved in the latter two reactions have been characterized. Vanillate and
syringate are the most common intermediate metabolites in lignin catabolism. These compounds are initially O-demethylated
and the resulting diol compounds, protocatechuate (PCA) and 3-O-methylgallate, respectively, are subjected to ring cleavage catalyzed by PCA 4,5-dioxygenase. The ring cleavage products
generated are further degraded through the PCA 4,5-cleavage pathway. We have isolated and characterized genes for enzymes
involved in this pathway. Disruption of a gene for 2-pyrone-4,6-dicarboxylate hydrolase (ligI) in this pathway suggested that an alternative route for 3-O-methylgallate degradation, in which ligI is not involved, would play a role in syringate catabolism. In this article, we describe the genetic and biochemical features
of the S. paucimobilis SYK-6 genes involved in degradation of lignin-related compounds. A possible application of the SYK-6 lignin degradation system
to produce a valuable chemical material is also described.
Received 01 May 1999/ Accepted in revised form 29 July 1999 相似文献
18.
Biodegradation of polycyclic aromatic hydrocarbons 总被引:67,自引:0,他引:67
Carl E. Cerniglia 《Biodegradation》1992,3(2-3):351-368
The intent of this review is to provide an outline of the microbial degradation of polycyclic aromatic hydrocarbons. A catabolically diverse microbial community, consisting of bacteria, fungi and algae, metabolizes aromatic compounds. Molecular oxygen is essential for the initial hydroxylation of polycyclic aromatic hydrocarbons by microorganisms. In contrast to bacteria, filamentous fungi use hydroxylation as a prelude to detoxification rather than to catabolism and assimilation. The biochemical principles underlying the degradation of polycyclic aromatic hydrocarbons are examined in some detail. The pathways of polycyclic aromatic hydrocarbon catabolism are discussed. Studies are presented on the relationship between the chemical structure of the polycyclic aromatic hydrocarbon and the rate of polycyclic aromatic hydrocarbon biodegradation in aquatic and terrestrial ecosystems. 相似文献
19.
Although aromatic compounds are most often present in the environment as components of complex mixtures, biodegradation studies
commonly focus on the degradation of individual compounds. The present study was performed to investigate the range of aromatic
substrates utilized by biphenyl- and naphthalene-degrading environmental isolates and to ascertain the effects of co-occurring
substrates during the degradation of mono-aromatic compounds. Bacterial strains were isolated on the basis of their ability
to utilize either biphenyl or naphthalene as a sole source of carbon. Growth and transformation assays were conducted on each
isolate to determine the range of substrates degraded. One isolate, Pseudomonas putida BP18, was tested for the ability to biodegrade benzene, toluene, ethylbenzene and xylene isomers (BTEX) individually and
as components of mixtures. Overall, the results indicate that organisms capable of growth on multi-ring aromatic compounds
may be particularly versatile in terms of aromatic hydrocarbon biodegradation. Furthermore, growth and transformation assays
performed with strain BP18 suggest that the biodegradation of BTEX and biphenyl by this strain is linked to a catabolic pathway
with overlapping specificities. The broad substrate specificity of these environmental isolates has important implications
for bioremediation efforts in the field.
Received: 4 August 1999 / Received revision: 25 October 1999 / Accepted: 5 November 1999 相似文献
20.
D T Gibson 《Journal of industrial microbiology & biotechnology》1999,23(4-5):284-293
Beijerinckia sp strain B1 grows with biphenyl as its sole source of carbon and energy. A mutant, strain B8/36, oxidized biphenyl to cis-(2S,3R)-dihydroxy-l-phenylcyclohexa-4,6-diene (cis-biphenyl dihydrodiol). Strain B8/36 oxidized anthracene, phenanthrene, benz[a]anthracene and benzo[a]pyrene to cis-dihydrodiols. Other substrates oxidized to cis-dihydrodiols were dibenzofuran, dibenzothiophene and dibenzo-p-dioxin. Biphenyl dioxygenase activity was observed in cells of Beijerinckia B1 and B8/36 after growth in the presence of biphenyl, m-, p-xylene and salicylate. Recent studies have led to the reclassification of Beijerinckia B1 as Sphingomonas yanoikuyae strain B1. Subsequent biotransformation studies showed that S. yanoikuyae B8/36 oxidized chrysene to a bis-cis-diol with hydroxyl substituents at the 3,4- and 9,10-positions. Dihydronaphthalene was oxidized to cis-1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene, naphthalene, cis-1,2-dihydroxy-1,2-dihydronaphthalene and 2-hydroxy-1,2-dihydronaphthalene. Anisole and phenetole were oxidized to phenol.
Thus the S. yanoikuyae biphenyl dioxygenase catalyzes cis-dihydroxylation, benzylic monohydroxylation, desaturation and dealkylation reactions. To date, the genes encoding biphenyl
dioxygenase have not been cloned. However, the nucleotide sequence of a S. yanoikuyaeB1 DNA fragment contains five different α subunits as determined by conserved amino acids coordinating iron in a Rieske [2Fe-2S]
center and mononuclear iron at the catalytic site. The specific role of the different putative oxygenases in biotransformation
reactions catalyzed by S. yanoikuyae is not known and presents an exciting challenge for future studies.
Received 29 May 1999/ Accepted in revised form 23 June 1999 相似文献