The<i>bzd</i>Gene Cluster, Coding for Anaerobic Benzoate Catabolism, in<i>Azoarcus</i>sp. Strain CIB

Barragán, María J. López; Carmona, Manuel; Zamarro, Marı́a Teresa; Thiele, Bärbel; Boll, Matthias; Fuchs, Georg; Garcı́a, José Luis; Dı́az, Eduardo

doi:10.1128/jb.186.17.5762-5774.2004

Cited by 107 publications

(133 citation statements)

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“…However, there is a set of genes (Ferp_1184-1187) that encodes proteins with high homology to each of the four subunits of the class I bzd-type BCR complex (BzdNOPQ) (Supplementary Table 4) first described in Azoarcus spp. (Lopez Barragan et al, 2004). All four of these subunits are most similar to those found in A. aromaticum EbN1 (42-55% identity, 63-72% similarity).…”

Section: Resultsmentioning

confidence: 49%

“…One in R. palustris Gibson and Harwood, 2002) and an alternative pathway described in T. aromatica (Breese et al, 1998) and Azoarcus sp. (Lopez Barragan et al, 2004), which appears to be conserved in all previously described anaerobic benzoate-degrading heterotrophs (Carmona et al, 2009).…”

Section: Formation Of 3-hydroxypimeloyl-coamentioning

confidence: 99%

“…The best-studied class I BCRs include those from the facultative denitrifying species Thauera aromatica (Boll and Fuchs, 1995), Azoarcus spp. (Lopez Barragan et al, 2004) and the phototroph Rhodopseudomonas palustris (Egland et al, 1997).…”

Section: Introductionmentioning

confidence: 99%

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Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus

et al. 2011

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Insight into the mechanisms for the anaerobic metabolism of aromatic compounds by the hyperthermophilic archaeon Ferroglobus placidus is expected to improve understanding of the degradation of aromatics in hot (>80° C) environments and to identify enzymes that might have biotechnological applications. Analysis of the F. placidus genome revealed genes predicted to encode enzymes homologous to those previously identified as having a role in benzoate and phenol metabolism in mesophilic bacteria. Surprisingly, F. placidus lacks genes for an ATP-independent class II benzoyl-CoA (coenzyme A) reductase (BCR) found in all strictly anaerobic bacteria, but has instead genes coding for a bzd-type ATP-consuming class I BCR, similar to those found in facultative bacteria. The lower portion of the benzoate degradation pathway appears to be more similar to that found in the phototroph Rhodopseudomonas palustris, than the pathway reported for all heterotrophic anaerobic benzoate degraders. Many of the genes predicted to be involved in benzoate metabolism were found in one of two gene clusters. Genes for phenol carboxylation proceeding through a phenylphosphate intermediate were identified in a single gene cluster. Analysis of transcript abundance with a whole-genome microarray and quantitative reverse transcriptase polymerase chain reaction demonstrated that most of the genes predicted to be involved in benzoate or phenol metabolism had higher transcript abundance during growth on those substrates vs growth on acetate. These results suggest that the general strategies for benzoate and phenol metabolism are highly conserved between microorganisms living in moderate and hot environments, and that anaerobic metabolism of aromatic compounds might be analyzed in a wide range of environments with similar molecular targets.

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Section: Resultsmentioning

confidence: 49%

Section: Formation Of 3-hydroxypimeloyl-coamentioning

confidence: 99%

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Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus

et al. 2011

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“…Recently, we have characterized the bzd gene cluster involved in the anaerobic degradation of benzoate in Azoarcus sp. strain CIB, a denitrifying betaproteobacterium able to anaerobically degrade a large number of aromatic compounds via benzoyl-CoA (5). The bzd cluster is organized as a single catabolic operon (bzdNOPQM STUVWXYZA) and the bzdR regulatory gene (5).…”

mentioning

confidence: 99%

“…Benzoate has been used as a model compound to study the anaerobic catabolism of aromatic compounds in different microorganisms, such as Rhodopseudomonas palustris, Magnetospirillum magnetotacticum MS-1, Thauera aromatica, Azoarcus evansii, and Azoarcus sp. strain CIB (5,6,25). In all these bacteria, benzoate is first activated to benzoylcoenzyme A (benzoyl-CoA), which is further degraded to central intermediates by a series of reactions that involve aromatic-ring reduction, modified ␤ oxidation, and ring cleavage as critical steps (22,25).…”

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confidence: 99%

Oxygen-Dependent Regulation of the Central Pathway for the Anaerobic Catabolism of Aromatic Compounds inAzoarcussp. Strain CIB

et al. 2006

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The role of oxygen in the transcriptional regulation of the P N promoter that controls the bzd operon involved in the anaerobic catabolism of benzoate in the denitrifying Azoarcus sp. strain CIB has been investigated. In vivo experiments using P N ::lacZ translational fusions, in both Azoarcus sp. strain CIB and Escherichia coli cells, have shown an oxygen-dependent repression effect on the transcription of the bzd catabolic genes. E. coli Fnr was required for the anaerobic induction of the P N promoter, and the oxygen-dependent repression of the bzd genes could be bypassed by the expression of a constitutively active Fnr* protein. In vitro experiments revealed that Fnr binds to the P N promoter at a consensus sequence centered at position ؊41.5 from the transcription start site overlapping the ؊35 box, suggesting that P N belongs to the class II Fnr-dependent promoters. Fnr interacts with RNA polymerase (RNAP) and is strictly required for transcription initiation after formation of the RNAP-P N complex. An fnr ortholog, the acpR gene, was identified in the genome of Azoarcus sp. strain CIB. The Azoarcus sp. strain CIB acpR mutant was unable to grow anaerobically on aromatic compounds and it did not drive the expression of the P N ::lacZ fusion, suggesting that AcpR is the cognate transcriptional activator of the P N promoter. Since the lack of AcpR in Azoarcus sp. strain CIB did not affect growth on nonaromatic carbon sources, AcpR can be considered a transcriptional regulator of the Fnr/Crp superfamily that has evolved to specifically control the central pathway for the anaerobic catabolism of aromatic compounds in Azoarcus.

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Assessment of Microbial In Situ Activity in Contaminated Aquifers

Kästner

Fischer

Nijenhuis

et al. 2006

Engineering in Life Sciences

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Microbial ecologists and environmental engineers share the interest in identifying the key microorganisms responsible for compound turnover in the environment and in estimating the respective transformation rates. For the successful application of Natural Attenuation processes, a reliable assessment of the in situ turnover of a contaminant in an aquifer is essential. Here, we review and present new details of two recently developed approaches concerning the assessment of in situ biodegradation: (i) determination of biodegradation caused by microbial metabolism in a contamination plume by stable isotope fractionation analysis (SIFA) and (ii) determination of the actual degradation under the respective environmental conditions in the aquifer by using in situ microcosms (BACTRAPS®) amended with 13C‐labeled substrates as tracer compounds. Based on stable isotope fractionation analysis, the degradation occurring under anoxic biogeochemical conditions at a respective site can be calculated for the entire plume. This has been shown for benzene and toluene at the Zeitz site and partly for chlorobenzene at the Bitterfeld site. By use of the in situ microcosm approach with 13C‐labeled compounds, the microbial in situ degradation under strictly anaerobic conditions could be proven for benzene and toluene in Zeitz and for chlorobenzene in Bitterfeld. The transformation of 13C‐carbon of the labeled substrate into microbial fatty acids confirmed the assimilation of the pollutant resulting in the formation of biomass. In addition, metabolites such as benzylsuccinic acid were found in the toluene‐amended microcosms indicating anaerobic degradation of toluene. This result corresponds to the geochemical conditions found at the field site and therefore, the microcosm approach with 13C‐labeled compounds can be used to assign the predominant in situ degradation pathways in a contaminated aquifer. Since fatty acids profiles alone are often too unspecific for a community analysis at species level, the composition of the microbial communities was analyzed by genetic profiling and sequencing of partial 16S rRNA genes PCR‐amplified from total DNA extracted directly from the microcosms. Sequences retrieved from the microcosms indicated a dominance of not yet cultivated bacteria. Several sequences were phylogenetically closely related to sequences of bacteria known to be iron and sulfate reducers, typically found at sites polluted with BTEX and/or mineral oil. The results show that the current methods for monitoring microbial in situ activity at present stage are valuable tools for improving environmental control of compound turnover and will speed up engineering approaches.

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ThebzdGene Cluster, Coding for Anaerobic Benzoate Catabolism, inAzoarcussp. Strain CIB

Cited by 107 publications

References 59 publications

Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus

Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus

Oxygen-Dependent Regulation of the Central Pathway for the Anaerobic Catabolism of Aromatic Compounds inAzoarcussp. Strain CIB

Assessment of Microbial In Situ Activity in Contaminated Aquifers

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