Evidence That <i>pcpA</i> Encodes 2,6-Dichlorohydroquinone Dioxygenase, the Ring Cleavage Enzyme Required for Pentachlorophenol Degradation in <i>Sphingomonas chlorophenolica </i>Strain ATCC 39723

Xu, Ling; Resing, Katheryn A.; Lawson, Sherry L.; Babbitt, Patricia C.; Copley, Shelley D.

doi:10.1021/bi990103y

Cited by 73 publications

(33 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…2). A similar feature was described for extradiol dioxygenases (68,80). For comparison, intradiol dioxygenases display a maximum in the visible region around 450 nm (41,50) due to tyrosine ligandation (54).…”

Section: Resultssupporting

confidence: 65%

Hydroquinone Dioxygenase from Pseudomonas fluorescens ACB: a Novel Member of the Family of Nonheme-Iron(II)-Dependent Dioxygenases

et al. 2008

View full text Add to dashboard Cite

Several aerobic microorganisms are capable of utilizing acetophenones for their growth (16,17,(30)(31)(32). However, relatively little is known about the oxidative enzymes involved in acetophenone mineralization (45,47). The catabolism of 4-hydroxyacetophenone in Pseudomonas fluorescens ACB proceeds through the initial formation of 4-hydroxyphenyl acetate and hydroquinone (31,37,47). The latter compound is further degraded via 4-hydroxymuconic semialdehyde and maleylacetate to ␤-ketoadipate (46). We have purified HapA, the enzyme responsible for the Baeyer-Villiger oxidation of 4-hydroxyacetophenone, and expressed its gene in Escherichia coli (37). Moreover, we established that this flavin adenine dinucleotide-containing monooxygenase is useful for the production of phenols and catechols, which are valuable intermediates in the synthesis of pharmaceuticals, agricultural chemicals, and material products (36,38,48).In the accompanying paper (46), we showed that the genes encoding 4-hydroxyacetophenone monooxygenase (hapA), 4-hydroxyphenylacetate esterase (hapB), 4-hydroxymuconic semialdehyde dehydrogenase (hapE), and maleylacetate reductase (hapF) belong to a gene cluster (hapCDEFGHIBA) involved in 4-hydroxyacetophenone utilization. Based on biochemical data and sequence analysis, we proposed that the function of the hapC and hapD genes is linked to the conversion of hydroquinone to 4-hydroxymuconic semialdehyde.Several ring cleavage enzymes acting on substituted hydroquinones have been described. These include intradiol dioxygenases acting on hydroxyhydroquinone (4,20,22,35,39,42,55,66) and extradiol dioxygenases that are active with (homo-)gentisate (3, 28) or chlorohydroquinone (10,44,51). However, enzymes that use hydroquinone as the physiological ring cleavage substrate have not been characterized. Here we report on the purification and properties of hydroquinone dioxygenase (HQDO) from P. fluorescens ACB. It is shown that the heterotetrameric enzyme, encoded by the hapC and hapD genes, is a novel member of the family of nonheme-iron(II)-dependent dioxygenases. The present results confirm that the hapG gene, encoding an intradiol dioxygenase (46), is not involved in 4-hydroxyacetophenone degradation. This finding has important implications for the function of related genes involved in the catabolism of other aromatic compounds.

show abstract

Section: Resultssupporting

confidence: 65%

Hydroquinone Dioxygenase from Pseudomonas fluorescens ACB: a Novel Member of the Family of Nonheme-Iron(II)-Dependent Dioxygenases

et al. 2008

View full text Add to dashboard Cite

show abstract

“…This reaction presumably is catalyzed by an iron(II)-dependent extradiol dioxygenase (93). These enzymes generally contain a His 2 -carboxylate triad involved in binding the iron atom (49,75,78,79,82,89).…”

Section: Discussionmentioning

confidence: 99%

Elucidation of the 4-Hydroxyacetophenone Catabolic Pathway in Pseudomonas fluorescens ACB

et al. 2008

View full text Add to dashboard Cite

The catabolism of 4-hydroxyacetophenone in Pseudomonas fluorescens ACB is known to proceed through the intermediate formation of hydroquinone. Here, we provide evidence that hydroquinone is further degraded through 4-hydroxymuconic semialdehyde and maleylacetate to ␤-ketoadipate. The P. fluorescens ACB genes involved in 4-hydroxyacetophenone utilization were cloned and characterized. Sequence analysis of a 15-kb DNA fragment showed the presence of 14 open reading frames containing a gene cluster (hapCDEFGHIBA) of which at least four encoded enzymes are involved in 4-hydroxyacetophenone degradation: 4-hydroxyacetophenone monooxygenase (hapA), 4-hydroxyphenyl acetate hydrolase (hapB), 4-hydroxymuconic semialdehyde dehydrogenase (hapE), and maleylacetate reductase (hapF). In between hapF and hapB, three genes encoding a putative intradiol dioxygenase (hapG), a protein of the Yci1 family (hapH), and a [2Fe-2S] ferredoxin (hapI) were found. Downstream of the hap genes, five open reading frames are situated encoding three putative regulatory proteins (orf10, orf12, and orf13) and two proteins possibly involved in a membrane efflux pump (orf11 and orf14). Upstream of hapE, two genes (hapC and hapD) were present that showed weak similarity with several iron(II)-dependent extradiol dioxygenases. Based on these findings and additional biochemical evidence, it is proposed that the hapC and hapD gene products are involved in the ring cleavage of hydroquinone.

show abstract

“…This idea has been applied successfully using the original implementation of the Shotgun program to the problem of deducing function of proteins when only remote homologs of those proteins are present in the data bases (39). In those studies (43)(44)(45), however, Shotgun analysis used full-length proteins as queries rather than short sequence fragments such as described in this study.…”

Section: Identification Of Possible Homologs From Searchesmentioning

confidence: 99%

Functional Assignment of the 20 S Proteasome from Trypanosoma brucei Using Mass Spectrometry and New Bioinformatics Approaches

Huang¹,

Jacob²,

Pegg³

et al. 2001

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

As experimental technologies for characterization of proteomes emerge, bioinformatic analysis of the data becomes essential. Separation and identification technologies currently based on two-dimensional gels/mass spectrometry provide the inherent analytical power required. This strategy involves protein spot digestion and accurate mass mapping together with computational interrogation of available data bases for protein functional identification. When either no exact match is found or when the possible matches only partially account for molecular weights actually observed, peptide sequencing by tandem mass spectrometry has emerged as the methodology of choice to provide the basic additional information required. To evaluate the capabilities of bioinformatics methods employed for identifying homologs of a protein of interest, we attempted to identify the major proteins from the 20 S proteasome of Trypanosoma brucei using sequence information determined using mass spectrometry. The results suggest that neither the traditional query engines, BLAST and FASTA, nor specialized software developed for analysis of sequence information obtained by mass spectrometry are able to identify even closely related sequences at statistically significant scores. To address this deficit, new bioinformatics approaches were developed for concomitant use of the multiple fragments of short sequence typically available from methods of tandem mass spectrometry. These approaches rely on the occurrence of congruence across searches of multiple fragments from a single protein. This method resulted in sharply better statistical significance values for correct hits in the data base output relative to that achieved for independent searches using single sequence fragments.Fueled by the genome projects, encyclopedic increases in the banking of newly obtained, comprehensive biological data are transforming studies of biology and medicine (1). As the postgenomic era moves into high gear, new "high throughput" technologies are allowing characterization of gene expression profiles, comparisons of genomic complements, and identification of the genetic markers associated with normal, pathological, or environmentally triggered states. Yet information derived from full analysis of genomics alone is clearly inadequate to explain the complexities of cell biology. Recent studies showing differences between the genome and the proteome suggest that the profound understanding we seek will require the complete and direct characterization of the proteome as well (2, 3).Peptide mass mapping by MALDI-TOF 1 MS (4) or liquid chromatography-electrospray ionization MS (5, 6), combined with interrogation of sequence data bases (7-12), currently is the most widely employed strategy for the identification of expressed proteins. This methodology involves electrophoretic separation of proteins at sub-picomole levels, digestion with trypsin, and measurement of the molecular weights of the resulting peptide mixture by mass spectrometry. This strategy can routinely identify p...

show abstract

Evidence That pcpA Encodes 2,6-Dichlorohydroquinone Dioxygenase, the Ring Cleavage Enzyme Required for Pentachlorophenol Degradation in Sphingomonas chlorophenolica Strain ATCC 39723

Cited by 73 publications

References 38 publications

Hydroquinone Dioxygenase from Pseudomonas fluorescens ACB: a Novel Member of the Family of Nonheme-Iron(II)-Dependent Dioxygenases

Hydroquinone Dioxygenase from Pseudomonas fluorescens ACB: a Novel Member of the Family of Nonheme-Iron(II)-Dependent Dioxygenases

Elucidation of the 4-Hydroxyacetophenone Catabolic Pathway in Pseudomonas fluorescens ACB

Functional Assignment of the 20 S Proteasome from Trypanosoma brucei Using Mass Spectrometry and New Bioinformatics Approaches

Contact Info

Product

Resources

About