Delineation of the Caffeine C-8 Oxidation Pathway in Pseudomonas sp. Strain CBB1 via Characterization of a New Trimethyluric Acid Monooxygenase and Genes Involved in Trimethyluric Acid Metabolism

Mohanty, Sujit K.; Yu, Chung Huang; Das, Shuvendu; Louie, Tai Man; Gakhar, Lokesh; Subramanian, Mani

doi:10.1128/jb.00597-12

Cited by 37 publications

(41 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This pathway has been observed in both mixed cultures (Madyastha and Sridhar, ) and pure bacterial isolates (Mohapatra et al ., ; Yu et al ., ; Mohanty et al ., ). 1,3,7‐trimethyluric acid is further metabolized to sequentially form 1,3,7‐trimethyl‐5‐hydroxyisouric acid (TM‐HIU), 3,6,8‐trimethyl‐2‐oxo‐4‐hydroxy‐4‐carboxy‐5‐ureidoimidazoline (TM‐OHCU) and 3,6,8‐trimethylallantoin (TMA) (Mohanty et al ., ). Further degradation of TMA has not yet been fully characterized.…”

Section: Caffeine Metabolismmentioning

confidence: 99%

“…Two other genes in this cluster, tmuH and tmuD (Fig. inset), are proposed to encode putative enzymes (TM‐HIU hydroxylase and TM‐OHCU decarboxylase, respectively) of the C‐8 oxidation pathway (Mohanty et al ., ) based on their homology to enzymes of the uric acid metabolic pathway in K. pneumoniae (French and Ealick, 2010; 2011; Mohanty, ). The presence of these putative enzymes in CBB1 suggests enzymatic formation of S‐(+)‐TMA from TM‐HIU via TM‐OHCU in the C‐8 oxidation pathway (Mohanty et al ., ).…”

Section: Genetic Basis For Caffeine Degradationmentioning

confidence: 99%

See 1 more Smart Citation

Genetic characterization of caffeine degradation by bacteria and its potential applications

Summers

Mohanty

Gopishetty

et al. 2015

Microbial Biotechnology

Self Cite

View full text Add to dashboard Cite

The ability of bacteria to grow on caffeine as sole carbon and nitrogen source has been known for over 40 years. Extensive research into this subject has revealed two distinct pathways, N-demethylation and C-8 oxidation, for bacterial caffeine degradation. However, the enzymological and genetic basis for bacterial caffeine degradation has only recently been discovered. This review article discusses the recent discoveries of the genes responsible for both N-demethylation and C-8 oxidation. All of the genes for the N-demethylation pathway, encoding enzymes in the Rieske oxygenase family, reside on 13.2-kb genomic DNA fragment found in Pseudomonas putida CBB5. A nearly identical DNA fragment, with homologous genes in similar orientation, is found in Pseudomonas sp. CES. Similarly, genes for C-8 oxidation of caffeine have been located on a 25.2-kb genomic DNA fragment of Pseudomonas sp. CBB1. The C-8 oxidation genes encode enzymes similar to those found in the uric acid metabolic pathway of Klebsiella pneumoniae. Various biotechnological applications of these genes responsible for bacterial caffeine degradation, including bio-decaffeination, remediation of caffeine-contaminated environments, production of chemical and fuels and development of diagnostic tests have also been demonstrated.

show abstract

Section: Caffeine Metabolismmentioning

confidence: 99%

Section: Genetic Basis For Caffeine Degradationmentioning

confidence: 99%

Genetic characterization of caffeine degradation by bacteria and its potential applications

Summers

Mohanty

Gopishetty

et al. 2015

Microbial Biotechnology

Self Cite

View full text Add to dashboard Cite

show abstract

“…strain KK5 genome with Ն50% amino acid identity to the previously reported ndmABCDE genes. Caffeine degradation can also occur via the C-8 oxidation pathway (31). One of the key enzymes for the C-8 oxidation pathway is caffeine dehydrogenase (cdh), which contains three subunits (cdhABC) (32).…”

Section: Figmentioning

confidence: 99%

Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem

Wang

Hatt

Tsementzi

et al. 2017

Appl Environ Microbiol

View full text Add to dashboard Cite

A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (Ͻ0.1%), the so-called "rare biosphere." How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species.IMPORTANCE A single liter of water or gram of soil contains hundreds of lowabundance bacterial and archaeal species, the so called rare biosphere. The value of this astonishing biodiversity for ecosystem functioning remains poorly understood, primarily due to the fact that microbial community analysis frequently focuses on abundant organisms. Using a combination of culture-dependent and culture-independent (metagenomics) techniques, we showed that rare taxa and genes commonly contribute to the microbial community response to organic pollutants. Our findings should have implications for future studies that aim to study the role of rare species in environmental processes, including environmental bioremediation efforts of oil spills or other contaminants.

show abstract

“…A flavin-dependent monooxygenase similar to HpxO, but involved in the metabolism of caffeine by Pseudomonas sp. strain CBB1 was recently identified; this enzyme catalyzes the conversion of 1,3,7-trimethyluric acid to 1,3,7-trimethyl-5-hydroxyisouric acid but differs in its substrate binding pocket and does not catalyze monooxygenation of uric acid (37). …”

Section: Discussionmentioning

confidence: 99%

Structural and Mechanistic Studies of HpxO, a Novel Flavin Adenine Dinucleotide-Dependent Urate Oxidase from Klebsiella pneumoniae

et al. 2013

View full text Add to dashboard Cite

HpxO is a flavin-dependent urate oxidase that catalyzes the hydroxylation of uric acid to 5-hydroxyisourate and functions in a novel pathway for purine catabolism found in Klebsiella pneumoniae. We have determined the structures of HpxO with and without uric acid at 2.0 Å and 2.2 Å, respectively. We have also determined the structure of the R204Q variant at 2.0 Å resolution in the absence of uric acid. The variant structure is very similar to wild type HpxO except for the conformation of Arg103, which interacts with FAD in the variant but not in the wild type structure. Interestingly, the R204Q variant results in the uncoupling of NADH oxidation from uric acid hydroxylation. This suggests that Arg204 facilitates the deprotonation of uric acid activating it for the oxygen transfer. Based on these data, a mechanism for this reaction is proposed consisting of a nucleophilic attack of the urate anion on the flavin hydroperoxide resulting in the formation of 5-hydroxyisourate.

show abstract

Delineation of the Caffeine C-8 Oxidation Pathway in Pseudomonas sp. Strain CBB1 via Characterization of a New Trimethyluric Acid Monooxygenase and Genes Involved in Trimethyluric Acid Metabolism

Cited by 37 publications

References 37 publications

Genetic characterization of caffeine degradation by bacteria and its potential applications

Genetic characterization of caffeine degradation by bacteria and its potential applications

Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem

Structural and Mechanistic Studies of HpxO, a Novel Flavin Adenine Dinucleotide-Dependent Urate Oxidase from Klebsiella pneumoniae

Contact Info

Product

Resources

About