TheBordetella bronchiseptica niclocus encodes a nicotinic acid degradation pathway and the 6-hydroxynicotinate-responsive regulator BpsR

ABSTRACT Phenoxyalkanoic compounds are used worldwide as herbicides. Cupriavidus necator JMP134(pJP4) catabolizes 2,4-dichlorophenoxyacetate (2,4-D) and 4-chloro-2-methylphenoxyacetate (MCPA), using tfd functions carried on plasmid pJP4. TfdA cleaves the ether bonds of these herbicides to produce 2,4-dichlorophenol (2,4-DCP) and 4-chloro-2-methylphenol (MCP), respectively. These intermediates can be degraded by two chlorophenol hydroxylases encoded by the tfdB I and tfdB II genes to produce the respective chlorocatechols. We studied the specific contribution of each of the TfdB enzymes to the 2,4-D/MCPA degradation pathway. To accomplish this, the tfdB I and tfdB II genes were independently inactivated, and growth on each chlorophenoxyacetate and total chlorophenol hydroxylase activity were measured for the mutant strains. The phenotype of these mutants shows that both TfdB enzymes are used for growth on 2,4-D or MCPA but that TfdBI contributes to a significantly higher extent than TfdBII. Both enzymes showed similar specificity profiles, with 2,4-DCP, MCP, and 4-chlorophenol being the best substrates. An accumulation of chlorophenol was found to inhibit chlorophenoxyacetate degradation, and inactivation of the tfdB genes enhanced the toxic effect of 2,4-DCP on C. necator cells. Furthermore, increased chlorophenol production by overexpression of TfdA also had a negative effect on 2,4-D degradation by C. necator JMP134 and by a different host, Burkholderia xenovorans LB400, harboring plasmid pJP4. The results of this work indicate that codification and expression of the two tfdB genes in pJP4 are important to avoid toxic accumulations of chlorophenols during phenoxyacetic acid degradation and that a balance between chlorophenol-producing and chlorophenol-consuming reactions is necessary for growth on these compounds.

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Analysis of Hydroxycinnamic Acid Degradation in Agrobacterium fabrum Reveals a Coenzyme A-Dependent, Beta-Oxidative Deacetylation Pathway

Applied and Environmental Microbiology ◽

10.1128/aem.00475-14 ◽

2014 ◽

Vol 80 (11) ◽

pp. 3341-3349 ◽

Cited By ~ 26

Author(s):

Tony Campillo ◽

Sébastien Renoud ◽

Isabelle Kerzaon ◽

Ludovic Vial ◽

Jessica Baude ◽

...

Keyword(s):

Ferulic Acid ◽

Protocatechuic Acid ◽

Coenzyme A ◽

Degradation Pathway ◽

Hydroxycinnamic Acid ◽

Plant Materials ◽

Toxic Compounds ◽

Content Type ◽

Acid Degradation ◽

Species Specific

ABSTRACTThe soil- and rhizosphere-inhabiting bacteriumAgrobacterium fabrum(genomospecies G8 of theAgrobacterium tumefaciensspecies complex) is known to have species-specific genes involved in ferulic acid degradation. Here, we characterized, by genetic and analytical means, intermediates of degradation as feruloyl coenzyme A (feruloyl-CoA), 4-hydroxy-3-methoxyphenyl-β-hydroxypropionyl–CoA, 4-hydroxy-3-methoxyphenyl-β-ketopropionyl–CoA, vanillic acid, and protocatechuic acid. The genesatu1416,atu1417, andatu1420have been experimentally shown to be necessary for the degradation of ferulic acid. Moreover, the genesatu1415andatu1421have been experimentally demonstrated to be essential for this degradation and are proposed to encode a phenylhydroxypropionyl-CoA dehydrogenase and a 4-hydroxy-3-methoxyphenyl-β-ketopropionic acid (HMPKP)–CoA β-keto-thiolase, respectively. We thus demonstrated that theA. fabrumhydroxycinnamic degradation pathway is an original coenzyme A-dependent β-oxidative deacetylation that could also transformp-coumaric and caffeic acids. Finally, we showed that this pathway enables the metabolism of toxic compounds from plants and their use for growth, likely providing the species an ecological advantage in hydroxycinnamic-rich environments, such as plant roots or decaying plant materials.

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Faculty Opinions recommendation of Completing the uric acid degradation pathway through phylogenetic comparison of whole genomes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.11495.468975 ◽

2006 ◽

Author(s):

Robert Terkeltaub

Keyword(s):

Uric Acid ◽

Degradation Pathway ◽

Acid Degradation ◽

Phylogenetic Comparison ◽

Whole Genomes

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Mechanism of 6-Hydroxynicotinate 3-Monooxygenase, a Flavin-Dependent Decarboxylative Hydroxylase Involved in Bacterial Nicotinic Acid Degradation

Biochemistry ◽

10.1021/acs.biochem.8b00969 ◽

2019 ◽

Vol 58 (13) ◽

pp. 1751-1763 ◽

Cited By ~ 1

Author(s):

Kent D. Nakamoto ◽

Scott W. Perkins ◽

Ryan G. Campbell ◽

Matthew R. Bauerle ◽

Tyler J. Gerwig ◽

...

Keyword(s):

Nicotinic Acid ◽

Acid Degradation

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Cyanuric Acid Biodegradation via Biuret: Physiology, Taxonomy, and Geospatial Distribution

Applied and Environmental Microbiology ◽

10.1128/aem.01964-19 ◽

2019 ◽

Vol 86 (2) ◽

Author(s):

Kelly G. Aukema ◽

Lambros J. Tassoulas ◽

Serina L. Robinson ◽

Jessica F. Konopatski ◽

Madison D. Bygd ◽

...

Keyword(s):

Cyanuric Acid ◽

Current Knowledge ◽

Model Organism ◽

The United States ◽

Degradation Pathway ◽

Acid Hydrolase ◽

Single Model ◽

Acid Degradation ◽

Degrading Bacteria

ABSTRACT Cyanuric acid is an industrial chemical produced during the biodegradation of s-triazine pesticides. The biodegradation of cyanuric acid has been elucidated using a single model system, Pseudomonas sp. strain ADP, in which cyanuric acid hydrolase (AtzD) opens the s-triazine ring and AtzEG deaminates the ring-opened product. A significant question remains as to whether the metabolic pathway found in Pseudomonas sp. ADP is the exception or the rule in bacterial genomes globally. Here, we show that most bacteria utilize a different pathway, metabolizing cyanuric acid via biuret. The new pathway was determined by reconstituting the pathway in vitro with purified enzymes and by mining more than 250,000 genomes and metagenomes. We isolated soil bacteria that grow on cyanuric acid as a sole nitrogen source and showed that the genome from a Herbaspirillum strain had a canonical cyanuric acid hydrolase gene but different flanking genes. The flanking gene trtB encoded an enzyme that we show catalyzed the decarboxylation of the cyanuric acid hydrolase product, carboxybiuret. The reaction generated biuret, a pathway intermediate further transformed by biuret hydrolase (BiuH). The prevalence of the newly defined pathway was determined by cooccurrence analysis of cyanuric acid hydrolase genes and flanking genes. Here, we show the biuret pathway was more than 1 order of magnitude more prevalent than the original Pseudomonas sp. ADP pathway. Mining a database of over 40,000 bacterial isolates with precise geospatial metadata showed that bacteria with concurrent cyanuric acid and biuret hydrolase genes were distributed throughout the United States. IMPORTANCE Cyanuric acid is produced naturally as a contaminant in urea fertilizer, and it is used as a chlorine stabilizer in swimming pools. Cyanuric acid-degrading bacteria are used commercially in removing cyanuric acid from pool water when it exceeds desired levels. The total volume of cyanuric acid produced annually exceeds 200 million kilograms, most of which enters the natural environment. In this context, it is important to have a global understanding of cyanuric acid biodegradation by microbial communities in natural and engineered systems. Current knowledge of cyanuric acid metabolism largely derives from studies on the enzymes from a single model organism, Pseudomonas sp. ADP. In this study, we obtained and studied new microbes and discovered a previously unknown cyanuric acid degradation pathway. The new pathway identified here was found to be much more prevalent than the pathway previously established for Pseudomonas sp. ADP. In addition, the types of environment, taxonomic prevalences, and geospatial distributions of the different cyanuric acid degradation pathways are described here.

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Biochemical and structural characterization ofKlebsiella pneumoniaeoxamate amidohydrolase in the uric acid degradation pathway

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798316007099 ◽

2016 ◽

Vol 72 (6) ◽

pp. 808-816 ◽

Cited By ~ 2

Author(s):

Katherine A. Hicks ◽

Steven E. Ealick

Keyword(s):

Uric Acid ◽

Active Site ◽

Degradation Pathway ◽

Α Subunit ◽

Acid Degradation ◽

Substrate Complex ◽

Steady State Kinetics ◽

Biochemical Studies ◽

Kinetics Of ◽

Insight Into

HpxW from the ubiquitous pathogenKlebsiella pneumoniaeis involved in a novel uric acid degradation pathway downstream from the formation of oxalurate. Specifically, HpxW is an oxamate amidohydrolase which catalyzes the conversion of oxamate to oxalate and is a member of the Ntn-hydrolase superfamily. HpxW is autoprocessed from an inactive precursor to form a heterodimer, resulting in a 35.5 kDa α subunit and a 20 kDa β subunit. Here, the structure of HpxW is presented and the substrate complex is modeled. In addition, the steady-state kinetics of this enzyme and two active-site variants were characterized. These structural and biochemical studies provide further insight into this class of enzymes and allow a mechanism for catalysis consistent with other members of the Ntn-hydrolase superfamily to be proposed.

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