Assimilation of aromatic compounds by Comamonas testosteroni: characterization and spreadability of protocatechuate 4,5-cleavage pathway in bacteria

Ni, Bin; Zhang, Yun; Chen, Dongwei; Wang, Baojun; Liu, Shuang‐Jiang

doi:10.1007/s00253-012-4402-8

Cited by 36 publications

(46 citation statements)

References 49 publications

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“…The molecular mass of the GalA, GalB, GalD, and LigJ CsE6 subunits, as determined by SDS-PAGE, was ϳ45, ϳ25, ϳ40, and ϳ40 kDa (data not shown), which is consistent with the predicted molecular mass values of 47.6, 27.5, 37.6, and 38.2 kDa, respectively, from previous reports (9,10,19,20).…”

Section: Methodssupporting

confidence: 77%

Structural and Kinetic Characterization of the 4-Carboxy-2-hydroxymuconate Hydratase from the Gallate and Protocatechuate 4,5-Cleavage Pathways of Pseudomonas putida KT2440

Mazurkewich

Brott

Kimber

et al. 2016

Journal of Biological Chemistry

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The bacterial catabolism of lignin and its breakdown products is of interest for applications in industrial processing of lignobiomass. The gallate degradation pathway of Pseudomonas putida KT2440 requires a 4-carboxy-2-hydroxymuconate (CHM) hydratase (GalB), which has a 12% sequence identity to a previously identified CHM hydratase (LigJ) from Sphingomonas sp. SYK-6. The structure of GalB was determined and found to be a member of the PIG-L N-acetylglucosamine deacetylase family; GalB is structurally distinct from the amidohydrolase fold of LigJ. LigJ has the same stereospecificity as GalB, providing an example of convergent evolution for catalytic conversion of a common metabolite in bacterial aromatic degradation pathways. Purified GalB contains a bound Zn 2؉ cofactor; however the enzyme is capable of using Fe 2؉ and Co 2؉ with similar efficiency. The general base aspartate in the PIG-L deacetylases is an alanine in GalB; replacement of the alanine with aspartate decreased the GalB catalytic efficiency for CHM by 9.5 ؋ 10 4 -fold, and the variant enzyme did not have any detectable hydrolase activity. Kinetic analyses and pH dependence studies of the wild type and variant enzymes suggested roles for Glu-48 and His-164 in the catalytic mechanism. A comparison with the PIG-L deacetylases led to a proposed mechanism for GalB wherein Glu-48 positions and activates the metal-ligated water for the hydration reaction and His-164 acts as a catalytic acid.

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Section: Methodssupporting

confidence: 77%

Structural and Kinetic Characterization of the 4-Carboxy-2-hydroxymuconate Hydratase from the Gallate and Protocatechuate 4,5-Cleavage Pathways of Pseudomonas putida KT2440

Mazurkewich

Brott

Kimber

et al. 2016

Journal of Biological Chemistry

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“…CNB-1 grows on benzoate, but how it degrades benzoate has not been investigated. Previous studies reported that gentisate 1,2-dioxygenase activity was induced when CNB-1 grew on benzoate (27). In the present study, we showed that CNB-1 degrades benzoate via a CoA-dependent epoxide pathway (Fig.…”

supporting

confidence: 65%

“…The present study demonstrated that CNB-1 degrades benzoate via a CoA-dependent epoxide pathway, although a previous investigation (27) and this study both observed that gentisate 1,2-dioxygenase and other enzymes of the gentisate pathway were induced when the CNB-1 strain was cultivated with benzoate as the carbon source. Rather et al (11) reported that 4 to 5% of the sequenced microbial genomes carry genes putatively encoding this CoA-dependent epoxide pathway.…”

Section: Discussioncontrasting

confidence: 38%

“…CNB-1 grows on benzoate as the sole carbon source. The only detectable aromatic ring cleavage dioxygenase activity from benzoate-grown cells was gentisate 1,2-dioxygenase activity (27), indicating that benzoate was metabolized via the gentisate 1,2-cleavage pathway (Fig. 1C).…”

Section: Resultsmentioning

confidence: 99%

“…In addition to 4-CNB, CNB-1 also uses benzoate and many other aromatic compounds as carbon sources for growth (26,27) and has been applied for rhizoremediation of CNB-polluted soil (28). Our previous investigations revealed that the CNB-1 strain metabolizes 4-CNB via a partial reductive pathway and metabolizes 3-hydroxybenzoate, 4-hydroxybenzoate, protocatechuate, and vanillate via the proto-catechuate 4,5-cleavage pathway.…”

mentioning

confidence: 99%

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Benzoate Metabolism Intermediate Benzoyl Coenzyme A Affects Gentisate Pathway Regulation in Comamonas testosteroni

Chen

Zhang

Jiang

et al. 2014

Appl Environ Microbiol

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A previous study showed that benzoate was catabolized via a coenzyme A (CoA)-dependent epoxide pathway in Azoarcus evansii (R. Niemetz, U. Altenschmidt, S. Brucker, and G. Fuchs, Eur. J. Biochem. 227:161-168, 1995), but gentisate 1,2-dioxygenase was induced. Similarly, we found that the Comamonas testosteroni strain CNB-1 degraded benzoate via a CoA-dependent epoxide pathway and that gentisate 1,2-dioxygenase (GenA) was also induced when benzoate or 3-hydroxybenzoate served as a carbon source for growth. Genes encoding the CoA-dependent epoxide (box genes) and gentisate (gen genes) pathways were identified. Genetic disruption revealed that the gen genes were not involved in benzoate and 3-hydroxybenzoate degradation. Hence, we investigated gen gene regulation in the CNB-1 strain. The P genA promoter, a MarR-type regulator (GenR), and the GenR binding site were identified. We found that GenR took gentisate, 3-hydroxybenzoate, and benzoyl-CoA as effectors and that binding of GenR to its target DNA sequence was prohibited when these effectors were present. In vivo studies showed that the CNB-1 mutant that lost benzoyl-CoA synthesis was not able to activate P genA promoter, while transcription of genA was upregulated in another CNB-1 mutant that lost the ability to degrade benzoyl-CoA. The finding that benzoyl-CoA (a metabolic intermediate of benzoate degradation) and 3-hydroxybenzoate function as GenR effectors explains why GenA was induced when CNB-1 grew on benzoate or 3-hydroxybenzoate. Regulation of gentisate pathways by MarR-, LysR-, and IclR-type regulators in diverse bacterial groups is discussed in detail.

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Assessment of Comamonas testosteroni strain PT9 as a rapid phthalic acid degrader for industrial wastewaters

2021

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In this study, characterization of industry-borne Comamonas testosteroni strain PT9 isolate was performed by determining degradation ability on phthalic acid (PA). High-performance liquid chromatography analyses showed that strain PT9 completely degraded 102.94 mg/L of PA within 6 h. Viability polymerase chain reaction (vPCR) was performed with propidium monoazide treatment. vPCR showed that the PA has positively stimulated the cell growth during degradation. To consider the fate of PA, the proposed catalytic genes (ophA2, iphA2, tphA2, tphA3, pmdA, and pmdB) for the degradation pathways of PA isomers for C. testosteroni were screened in strain PT9. All genes except iphA2 were detected in strain PT9, and expression levels of related genes were analyzed by Real-Time PCR (qPCR).

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Assimilation of aromatic compounds by Comamonas testosteroni: characterization and spreadability of protocatechuate 4,5-cleavage pathway in bacteria

Cited by 36 publications

References 49 publications

Structural and Kinetic Characterization of the 4-Carboxy-2-hydroxymuconate Hydratase from the Gallate and Protocatechuate 4,5-Cleavage Pathways of Pseudomonas putida KT2440

Structural and Kinetic Characterization of the 4-Carboxy-2-hydroxymuconate Hydratase from the Gallate and Protocatechuate 4,5-Cleavage Pathways of Pseudomonas putida KT2440

Benzoate Metabolism Intermediate Benzoyl Coenzyme A Affects Gentisate Pathway Regulation in Comamonas testosteroni

Assessment of Comamonas testosteroni strain PT9 as a rapid phthalic acid degrader for industrial wastewaters

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