Differential Expression of Two Catechol 1,2-Dioxygenases in
            <i>Burkholderia</i>
            sp. Strain TH2

Suzuki, Katsuhisa; Ichimura, Atsushi; Ogawa, Naoto; Hasebe, Akira; Miyashita, Kiyotaka

doi:10.1128/jb.184.20.5714-5722.2002

Cited by 33 publications

(25 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In the CCDs from gram-negative bacteria and catechol 1,2-dioxygenases from gram-positive bacteria, the amino acid at position 52 or the corresponding position is Val, except in TcbC (Ala-52). However, the amino acid at the corresponding position of catechol 1,2-dioxygenases of gram-negative bacteria is His or Lys (18,58) and that of ClcA from R. opacus 1CP is Ala (13).…”

Section: Discussionmentioning

confidence: 99%

Amino Acids in Positions 48, 52, and 73 Differentiate the Substrate Specificities of the Highly Homologous Chlorocatechol 1,2-Dioxygenases CbnA and TcbC

et al. 2005

Self Cite

View full text Add to dashboard Cite

Chlorocatechols are the central metabolites in the bacterial degradation processes of many chlorinated aromatic compounds (reviewed in references 50 and 60). The degradation processes via chlorocatechols have been studied intensively with simple chlorinated aromatics such as chlorobenzoates (7, 10, 18, 23, 25, 26), chlorobenzenes (21, 47, 51, 53, 54, 56, 57, 62), and 2,4-dichlorophenoxyacetic acid (2,4-D) (4,9,14). In the degradation of chlorocatechols, the chlorocatechol orthocleavage pathway (modified ortho-cleavage pathway) plays a central role, converting chlorocatechols into 3-oxoadipate (reviewed in references 24, 42, and 50), although several examples of degradation of chlorocatechols via the meta-cleavage pathway have been documented (1, 34).The genes encoding enzymes of the chlorocatechol orthocleavage pathway have been found as a cluster and mostly on large plasmids, which are often transmissible (3,6,7,8,32,39,62,67; for a review, see reference 38). Some of the chlorocatechol gene clusters have been found to be carried on transposons (30,40,45,63) or a phage-like element (49,55). Recent reports on the entire sequencing of two 2,4-D degradative plasmids, pJP4 and pEST4011, illustrated their genetic features of basic plasmid functions such as replication, maintenance, and transfer, shared with other broad-host-range IncP1 plasmids (59, 63). These findings have revealed some of the reasons underlying the wide distribution of the gene clusters of the chlorocatechol ortho-cleavage pathway.In the first step of the chlorocatechol ortho-cleavage pathway, chlorocatechol 1,2-dioxygenase (CCD) cleaves the aromatic ring, converting chlorocatechols into chloro-cis,cis-muconates, and thus has been a subject of intensive study from an enzymatic viewpoint. The CCDs of several strains have been characterized, and some of them have been purified (2,5,10,27,31,33,35,43,44,46,61). The early enzymatic studies of the CCD from the 3-chlorobenzoate (3-CB)-degradative Pseudomonas sp. strain B13 revealed that the CCD is adapted for the conversion of chlorocatechols such as 3-chlorocatechol, unlike catechol 1,2-dioxygenase, which cannot process chlorocatechols efficiently (10, 11). Several studies have revealed a tendency such that CCDs responsible for the conversion of 3,5-dichlorocatechol (3,5-DC) produced as an intermediate of 2,4-D degradation are adapted for the preferential conversion of 3,5-DC (2, 43). CCDs engaged in degradative pathways for other compounds could show different substrate specificities towards congeners of chlorocatechols: one example is TcbC from the 1,2,4-trichlorobenzene-degrading Pseudomonas sp. strain P51, which favors 3,4-dichlorocatechol (3,4-DC) (61). Recently, the crystal structure of the 4-chlorocatechol 1,2-dioxygenase from Rhodococcus opacus strain 1CP has been solved (15, 17), and another CCD from the strain 1CP has been

show abstract

Section: Discussionmentioning

confidence: 99%

Amino Acids in Positions 48, 52, and 73 Differentiate the Substrate Specificities of the Highly Homologous Chlorocatechol 1,2-Dioxygenases CbnA and TcbC

et al. 2005

Self Cite

View full text Add to dashboard Cite

show abstract

“…The resulting phylogenetic tree shows that the benA genes from the isolates are closely related to the nonfunctional benA gene in Burkholderia sp. strain TH2 (43), as well as chlorobenzoate dioxygenase genes from Burkholderia sp. strain NK8 (13), Burkholderia sp.…”

Section: Resultsmentioning

confidence: 99%

Field-Based Stable Isotope Probing Reveals the Identities of Benzoic Acid-Metabolizing Microorganisms and Their In Situ Growth in Agricultural Soil

Pumphrey

Madsen

2008

Appl Environ Microbiol

View full text Add to dashboard Cite

We used a combination of stable isotope probing (SIP), gas chromatography-mass spectrometry-based respiration, isolation/cultivation, and quantitative PCR procedures to discover the identity and in situ growth of soil microorganisms that metabolize benzoic acid. We added [13 C]benzoic acid or [ 12 C]benzoic acid (100 g) once, four times, or five times at 2-day intervals to agricultural field plots. After monitoring 13 CO 2 evolution from the benzoic acid-dosed soil, field soils were harvested and used for nucleic acid extraction and for cultivation of benzoate-degrading bacteria. Exposure of soil to benzoate increased the number of culturable benzoate degraders compared to unamended soil, and exposure to benzoate shifted the dominant culturable benzoate degraders from Pseudomonas species to Burkholderia species. Isopycnic separation of heavy [13 C]DNA from the unlabeled fraction allowed terminal restriction fragment length polymorphism (T-RFLP) analyses to confirm that distinct 16S rRNA genes were localized in the heavy fraction. Phylogenetic analysis of sequenced 16S rRNA genes revealed a predominance (15 of 58 clones) of Burkholderia species in the heavy fraction. Burkholderia sp. strain EBA09 shared 99.5% 16S rRNA sequence similarity with a group of clones representing the dominant RFLP pattern, and the T-RFLP fragment for strain EBA09 and a clone from that cluster matched the fragment enriched in the [ 13 C]DNA fraction. Growth of the population represented by EBA09 during the field-dosing experiment was demonstrated by using most-probable-number-PCR and primers targeting EBA09 and the closely related species Burkholderia hospita. Thus, the target population identified by SIP not only actively metabolized benzoic acid but reproduced in the field upon the addition of the substrate.Soil environments are commonly carbon limited (1), and carbon input through decomposition, industrial spills, or other disturbances can lead to an increase in microbial activity (36). In order to understand the population dynamics of bacteria in soils, it is necessary to understand which organisms respond to increases in carbon availability and how the population changes. Investigations using stable isotope probing (SIP) are particularly suited to identifying bacteria that metabolize a specific carbon compound because cellular biomarkers used to identify organisms become 13 C labeled when organisms metabolize and incorporate 13

show abstract

“…The unique Mpe_B0528 and Mpe_B0529 transposases (part of a predicted composite transposon consisting of genes Mpe_B0527 to Mpe_B0529 and located just upstream of the main MTBE gene cluster) are similar to a transposase associated with catechol 1,2-dioxygenase in Burkholderia sp. strain TH2 (51). Finally, a transposase associated with the p-toluenesulfonate degradation transposon of pTSA in Comamonas testosteroni T-2 is similar to the ISmp8 transposase.…”

mentioning

confidence: 97%

Comparative Transcriptome Analysis of Methylibium petroleiphilum PM1 Exposed to the Fuel Oxygenates Methyl tert -Butyl Ether and Ethanol

Schmidt

Chakicherla

Legler

et al. 2007

Appl Environ Microbiol

View full text Add to dashboard Cite

High-density whole-genome cDNA microarrays were used to investigate substrate-dependent gene expression of Methylibium petroleiphilum PM1, one of the best-characterized aerobic methyl tert-butyl ether (MTBE)-degrading bacteria. Differential gene expression profiling was conducted with PM1 grown on MTBE and ethanol as sole carbon sources. Based on microarray high scores and protein similarity analysis, an MTBE regulon located on the megaplasmid was identified for further investigation. Putative functions for enzymes encoded in this regulon are described with relevance to the predicted MTBE degradation pathway. A new unique dioxygenase enzyme system that carries out the hydroxylation of tert-butyl alcohol to 2-methyl-2-hydroxy-1-propanol in M. petroleiphilum PM1 was discovered. Hypotheses regarding the acquisition and evolution of MTBE genes as well as the involvement of IS elements in these complex processes were formulated. The pathways for toluene, phenol, and alkane oxidation via toluene monooxygenase, phenol hydroxylase, and propane monooxygenase, respectively, were upregulated in MTBE-grown cells compared to ethanol-grown cells. Four out of nine putative cyclohexanone monooxygenases were also upregulated in MTBE-grown cells. The expression data allowed prediction of several hitherto-unknown enzymes of the upper MTBE degradation pathway in M. petroleiphilum PM1 and aided our understanding of the regulation of metabolic processes that may occur in response to pollutant mixtures and perturbations in the environment.Petroleum releases are among the most ubiquitous sources of composite organic contaminants in groundwater. The majority of petroleum-associated contaminants reach aquifers via spills or leaks from underground storage tanks at service stations (49). Over 300,000 releases from underground storage tanks have been confirmed, with more than 150,000 remediation efforts completed in the United States (32). Fuel oxygenates, such as methyl tertiary butyl ether (MTBE), often form extensive, unattenuated "plumes" in groundwater because of their high water solubility and low biodegradation rates under oxygen-limited conditions (24,28,34). MTBE was one of the major oxygenates incorporated into reformulated gasoline to increase the fuel's oxygen content and decrease carbon monoxide and ozone emissions. MTBE and its primary metabolite tert-butyl alcohol (TBA) are suspected and known carcinogens, respectively (1, 7, 31, 57). Recently, alternative oxygenates, such as ethanol, have been substituted for MTBE, but because of the very slow depletion of contaminant mass from spill areas under anoxic conditions, the impacts of MTBE on the subsurface will be felt for many years and likely decades to come (8,29).Methylibium petroleiphilum PM1 is one of the best-characterized aerobic MTBE degraders known to date, and PM1-like bacteria have been shown to be present in several MTBEcontaminated aquifers in California (19,20,25) and Europe (12,33,42). M. petroleiphilum PM1 uses MTBE as a sole carbon source, oxidizing it complete...

show abstract

Differential Expression of Two Catechol 1,2-Dioxygenases in Burkholderia sp. Strain TH2

Cited by 33 publications

References 43 publications

Amino Acids in Positions 48, 52, and 73 Differentiate the Substrate Specificities of the Highly Homologous Chlorocatechol 1,2-Dioxygenases CbnA and TcbC

Amino Acids in Positions 48, 52, and 73 Differentiate the Substrate Specificities of the Highly Homologous Chlorocatechol 1,2-Dioxygenases CbnA and TcbC

Field-Based Stable Isotope Probing Reveals the Identities of Benzoic Acid-Metabolizing Microorganisms and Their In Situ Growth in Agricultural Soil

Comparative Transcriptome Analysis of Methylibium petroleiphilum PM1 Exposed to the Fuel Oxygenates Methyl tert -Butyl Ether and Ethanol

Contact Info

Product

Resources

About