Characterization of a Protocatechuate Catabolic Gene Cluster from
            <i>Rhodococcus opacus</i>
            1CP: Evidence for a Merged Enzyme with 4-Carboxymuconolactone-Decarboxylating and 3-Oxoadipate Enol-Lactone-Hydrolyzing Activity

Eulberg, Dirk; Lakner, Silvia; Golovleva, L. A.; Schlömann, Michael

doi:10.1128/jb.180.5.1072-1081.1998

Cited by 118 publications

(38 citation statements)

References 61 publications

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“…However, YraC is much smaller than other annotated CMD family enzymes. CMD domain enzymes are involved in protocatechuate catabolism and in some bacteria a gene fusion event leads to expression of CMD with a hydrolase involved in the same pathway (Eulberg et al, 1998). In Methanosarcina acetivorans a CMD domain enzyme had protein disulphide reductase activity, which depends on a CxxC motif (Lessner and Ferry, 2007).…”

Section: Fa and Mg Induce Specific Aldehyde Detoxification Systems (Hmentioning

confidence: 99%

Genome‐wide responses to carbonyl electrophiles in Bacillus subtilis: control of the thiol‐dependent formaldehyde dehydrogenase AdhA and cysteine proteinase YraA by the MerR‐family regulator YraB (AdhR)

Huyen¹,

Eiamphungporn

Mäder³

et al. 2009

Molecular Microbiology

118

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SummaryQuinones and a,b-unsaturated carbonyls are naturally occurring electrophiles that target cysteine residues via thiol-(S)-alkylation. We analysed the global expression profile of Bacillus subtilis to the toxic carbonyls methylglyoxal (MG) and formaldehyde (FA). Both carbonyl compounds cause a stress response characteristic for thiol-reactive electrophiles as revealed by the induction of the Spx, CtsR, CymR, PerR, ArsR, CzrA, CsoR and SigmaD regulons. MG and FA triggered also a SOS response which indicates DNA damage. Protection against FA is mediated by both the hxlAB operon, encoding the ribulose monophosphate pathway for FA fixation, and a thioldependent formaldehyde dehydrogenase (AdhA) and DJ-1/PfpI-family cysteine proteinase (YraA). The adhA-yraA operon and the yraC gene, encoding a g-carboxymuconolactone decarboxylase, are positively regulated by the MerR-family regulator, YraB(AdhR). AdhR binds specifically to its target promoters which contain a 7-4-7 inverted repeat (CTTAAAG-N4-CTTTAAG) between the -35 and -10 elements. Activation of adhA-yraA transcription by AdhR requires the conserved Cys52 residue in vivo.We speculate that AdhR is redox-regulated via thiol-(S)-alkylation by aldehydes and that AdhA and YraA are specifically involved in reduction of aldehydes and degradation or repair of damaged thiolcontaining proteins respectively.

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Section: Fa and Mg Induce Specific Aldehyde Detoxification Systems (Hmentioning

confidence: 99%

Genome‐wide responses to carbonyl electrophiles in Bacillus subtilis: control of the thiol‐dependent formaldehyde dehydrogenase AdhA and cysteine proteinase YraA by the MerR‐family regulator YraB (AdhR)

Huyen¹,

Eiamphungporn

Mäder³

et al. 2009

Molecular Microbiology

118

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“…A similar arrangement of all pca genes in a single cluster was reported in Acinetobacter sp. ADP1 (Harwood and Parales, 1996), and it is also present in the α-proteobacteria Agrobacterium tumefaciens and Caulobacter crescentus, as well as in the Gram-positive nocardioform actinomycete Rhodococcus opacus (Eulberg et al, 1998) ( Fig. 2).…”

Section: Referencesmentioning

confidence: 99%

“…2). Moreover, pcaD is usually contiguous to the pcaC gene, or fused to the latter as a pcaL gene in some bacteria such as C. crescentus, R. metallidurans and R. opacus (Eulberg et al, 1998); however, in P. syringae, these two genes are located at different regions of the genome (Fig. 2).…”

Section: Referencesmentioning

confidence: 99%

“…L05770) (Parke et al, 2001); P. aeruginosa strain PAO1 (Pseudomonas Genome Project at http://www.pseudomonas.com) (Stover et al, 2000); R. opacus strain 1CP (accession no. AF003947) (Eulberg et al, 1998); B. pseudomallei, R. metallidurans strain CH34, P. putida strain KT2440, P. fluorescens strain Pf0-1 and P. syringae pv. tomato DC3000 (database of unfinished microbial genomes at the NCBI server: http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi).…”

Section: Referencesmentioning

confidence: 99%

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Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440

Jiménez

Miñambres

Garcı́a

et al. 2002

Environmental Microbiology

460

441

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Analysis of the catabolic potential of Pseudomonas putida KT2440 against a wide range of natural aromatic compounds and sequence comparisons with the entire genome of this microorganism predicted the existence of at least four main pathways for the catabolism of central aromatic intermediates, that is, the protocatechuate (pca genes) and catechol (cat genes) branches of the beta-ketoadipate pathway, the homogentisate pathway (hmg/fah/mai genes) and the phenylacetate pathway (pha genes). Two additional gene clusters that might be involved in the catabolism of N-heterocyclic aromatic compounds (nic cluster) and in a central meta-cleavage pathway (pcm genes) were also identified. Furthermore, the genes encoding the peripheral pathways for the catabolism of p-hydroxybenzoate (pob), benzoate (ben), quinate (qui), phenylpropenoid compounds (fcs, ech, vdh, cal, van, acd and acs), phenylalanine and tyrosine (phh, hpd) and n-phenylalkanoic acids (fad) were mapped in the chromosome of P. putida KT2440. Although a repetitive extragenic palindromic (REP) element is usually associated with the gene clusters, a supraoperonic clustering of catabolic genes that channel different aromatic compounds into a common central pathway (catabolic island) was not observed in P. putida KT2440. The global view on the mineralization of aromatic compounds by P. putida KT2440 will facilitate the rational manipulation of this strain for improving biodegradation/biotransformation processes, and reveals this bacterium as a useful model system for studying biochemical, genetic, evolutionary and ecological aspects of the catabolism of aromatic compounds.

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“…39 Then, the pca gene cluster, mainly pcaD (3-oxoadipate enol-lactonase) and pcaIJ (3-oxoadipate CoA-transferase), catalyzed the following steps to form 3-oxoadipyl CoA. 40 The pcaF (3-oxoadipyl CoA thiolase) was absent in strain JW, thus fadA (acetyl-CoA acyltransferase) should take the place to convert 3-oxoadipyl CoA to acetyl-CoA, which ended up in the citrate cycle (TCA cycle).…”

Section: Indole Biodegradation Characteristics Of Strain Jwmentioning

confidence: 99%

Biodegradation characteristics and genomic functional analysis of indole‐degrading bacterial strain Acinetobacter sp. JW

Zhang

Jing

Zhang

et al. 2018

J of Chemical Tech & Biotech

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BACKGROUND Indole, an important type of N‐heterocyclic aromatic compound, is considered a toxic and odorous pollutant in coking and municipal wastewater. For efficient bioremediation of indole‐containing wastewater, an indole‐degrading bacterial strain JW was isolated from activated sludge in this study. The indole biodegradation characteristics and the whole‐genome sequence of strain JW were also determined. RESULTS Strain JW, capable of utilizing indole as the sole carbon and nitrogen source, was identified as Acinetobacter sp. based on 16S rRNA gene sequence analysis. It was able to completely degrade 100 mg L−1 indole within 20 h, and transform organic nitrogen to ammonia (NH4+‐N) and nitrate (NO3−‐N). Meanwhile, strain JW also presented high capacity for indole degradation at a range of initial indole concentrations (25–200 mg L−1) and pH (6.0–8.0). The key metabolites during indole biodegradation were identified by liquid chromatography coupled to Q‐Exactive high resolution mass spectrometry, and included isatin, anthranilate, salicylate, catechol and indigo. The whole‐genome sequence of strain JW revealed the possible functional genes related to indole biodegradation, such as iif genes, ant genes and downstream metabolic genes. Thus, an indole biodegradation mechanism was proposed based on metabolites identification and genomic analysis. CONCLUSION The results suggested that Acinetobacter sp. JW could be a promising biological candidate for bioremediation of indole, and the useful genetic information might enrich our understanding of microbial degradation of indole. © 2018 Society of Chemical Industry

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Characterization of a Protocatechuate Catabolic Gene Cluster from Rhodococcus opacus 1CP: Evidence for a Merged Enzyme with 4-Carboxymuconolactone-Decarboxylating and 3-Oxoadipate Enol-Lactone-Hydrolyzing Activity

Cited by 118 publications

References 61 publications

Genome‐wide responses to carbonyl electrophiles in Bacillus subtilis: control of the thiol‐dependent formaldehyde dehydrogenase AdhA and cysteine proteinase YraA by the MerR‐family regulator YraB (AdhR)

Genome‐wide responses to carbonyl electrophiles in Bacillus subtilis: control of the thiol‐dependent formaldehyde dehydrogenase AdhA and cysteine proteinase YraA by the MerR‐family regulator YraB (AdhR)

Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440

Biodegradation characteristics and genomic functional analysis of indole‐degrading bacterial strain Acinetobacter sp. JW

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