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Bopp CE, Bernet NM, Kohler HPE, Hofstetter TB. Elucidating the Role of O 2 Uncoupling in the Oxidative Biodegradation of Organic Contaminants by Rieske Non-heme Iron Dioxygenases. ACS ENVIRONMENTAL AU 2022; 2:428-440. [PMID: 36164353 PMCID: PMC9502038 DOI: 10.1021/acsenvironau.2c00023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Oxygenations of aromatic
soil and water contaminants with molecular
O2 catalyzed by Rieske dioxygenases are frequent initial
steps of biodegradation in natural and engineered environments. Many
of these non-heme ferrous iron enzymes are known to be involved in
contaminant metabolism, but the understanding of enzyme–substrate
interactions that lead to successful biodegradation is still elusive.
Here, we studied the mechanisms of O2 activation and substrate
hydroxylation of two nitroarene dioxygenases to evaluate enzyme- and
substrate-specific factors that determine the efficiency of oxygenated
product formation. Experiments in enzyme assays of 2-nitrotoluene
dioxygenase (2NTDO) and nitrobenzene dioxygenase (NBDO) with methyl-,
fluoro-, chloro-, and hydroxy-substituted nitroaromatic substrates
reveal that typically 20–100% of the enzyme’s activity
involves unproductive paths of O2 activation with generation
of reactive oxygen species through so-called O2 uncoupling.
The 18O and 13C kinetic isotope effects of O2 activation and nitroaromatic substrate hydroxylation, respectively,
suggest that O2 uncoupling occurs after generation of FeIII-(hydro)peroxo species in the catalytic cycle. While 2NTDO
hydroxylates ortho-substituted nitroaromatic substrates
more efficiently, NBDO favors meta-substituted, presumably
due to distinct active site residues of the two enzymes. Our data
implies, however, that the O2 uncoupling and hydroxylation
activity cannot be assessed from simple structure–reactivity
relationships. By quantifying O2 uncoupling by Rieske dioxygenases,
our work provides a mechanistic link between contaminant biodegradation,
the generation of reactive oxygen species, and possible adaptation
strategies of microorganisms to the exposure of new contaminants.
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Affiliation(s)
- Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Nora M. Bernet
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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Han SF, Jin W, Tu R, Ding B, Zhou X, Gao SH, Feng X, Yang Q, Wang Q. Screening and mutagenesis of high-efficient degrading bacteria of linear alkylbenzene sulfonates. CHEMOSPHERE 2020; 245:125559. [PMID: 31841794 DOI: 10.1016/j.chemosphere.2019.125559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/20/2019] [Accepted: 12/05/2019] [Indexed: 06/10/2023]
Abstract
As a widely used detergent, anionic surfactant linear alkylbenzene sulfonates (LAS) is a common toxic pollutant in wastewater. In this study, Pseudomonas sp. strain H6 was isolated from activated sludge and municipal wastewater, which had good degradation effect on LAS. The results showed that strain H6 could grow with LAS as the sole carbon source. When the concentration of LAS was less than 100 mg/L, strain H6 could degrade more than 80% of the LAS within 24 h. Meanwhile, the growth of strain H6 increased with the increase of LAS concentration, reaching the maximum growth at the presence of 100 mg/L LAS. When the concentration of LAS was over 100 mg/L, strain H6's cell growth and degradation of LAS showed a downward trend due to the strong toxicity of LAS, and the degradation rate of LAS almost tended to zero with 500 mg/L LAS. Further mutagenesis analysis of strain H6 showed that positive mutation occurred under ultraviolet and nitrite mutagenesis with using ampicillin to increase the screening pressure, and the degradation rate of LAS was 44.91% higher than that of original strain.
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Affiliation(s)
- Song-Fang Han
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China
| | - Wenbiao Jin
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China
| | - Renjie Tu
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China
| | - Binbin Ding
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China
| | - Xu Zhou
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China.
| | - Shu-Hong Gao
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Xiaochi Feng
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China
| | - Qinhui Yang
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China
| | - Qing Wang
- Shenzhen Engineering Laboratory of Microalgal Bioenergy, Harbin Institute of Technology (Shenzhen), 518055, Shenzhen, China
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Abstract
Pseudomonas putidais a fast-growing bacterium found mostly in temperate soil and water habitats. The metabolic versatility ofP. putidamakes this organism attractive for biotechnological applications such as biodegradation of environmental pollutants and synthesis of added-value chemicals (biocatalysis). This organism has been extensively studied in respect to various stress responses, mechanisms of genetic plasticity and transcriptional regulation of catabolic genes.P. putidais able to colonize the surface of living organisms, but is generally considered to be of low virulence. A number ofP. putidastrains are able to promote plant growth. The aim of this review is to give historical overview of the discovery of the speciesP. putidaand isolation and characterization ofP. putidastrains displaying potential for biotechnological applications. This review also discusses some major findings inP. putidaresearch encompassing regulation of catabolic operons, stress-tolerance mechanisms and mechanisms affecting evolvability of bacteria under conditions of environmental stress.
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Lazarini-Martínez A, Pérez-Valdespino A, Martínez FH, Ordaz NR, Galíndez-Mayer J, Juárez-Ramírez C, Curiel-Quesada E. Assembly of an atrazine catabolic operon and its introduction to Gram-negative hosts for robust and stable degradation of triazine herbicides. FEMS Microbiol Lett 2019; 366:5634263. [DOI: 10.1093/femsle/fnz233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/19/2019] [Indexed: 01/24/2023] Open
Abstract
ABSTRACTIn 1995, Pseudomonas sp. ADP, capable of metabolizing atrazine, was isolated from contaminated soil. Genes responsible for atrazine mineralization were found scattered in the 108.8 kb pADP-1 plasmid carried by this strain, some of them flanked by insertion sequences rendering them unstable. The goal of this work was to construct a transcriptional unit containing the atz operon in an easy to transfer manner, to be introduced and inherited stably by Gram-negative bacteria. atz genes were PCR amplified, joined into an operon and inserted onto the mobilizable plasmid pBAMD1–2. Primers were designed to add efficient transcription and translation signals. Plasmid bearing the atz operon was transferred to different Gram-negative strains by conjugation, which resulted in Tn5 transposase-mediated chromosomal insertion of the atz operon. To test the operon activity, atrazine degradation by transposants was assessed both colorimetrically and by high-performance liquid chromatography (HPLC). Transposants mineralized atrazine more efficiently than wild-type Pseudomonas sp. ADP and did not accumulate cyanuric acid. Atrazine degradation was not repressed by simple nitrogen sources. Genes conferring atrazine-mineralizing capacities were stable and had little or null effect on the fitness of different transposants. Introduction of catabolic operons in a stable fashion could be used to develop bacteria with better degrading capabilities useful in bioremediation.
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Affiliation(s)
- Alfredo Lazarini-Martínez
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás. CP11340 Mexico City, Mexico
| | - Abigail Pérez-Valdespino
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás. CP11340 Mexico City, Mexico
| | - Fernando Hernández Martínez
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás. CP11340 Mexico City, Mexico
| | - Nora Ruiz Ordaz
- Department of Biochemical Engineering, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. Av. Wilfrido Massieu 399, Unidad Adolfo López Mateos, CP07738 Mexico City, Mexico
| | - Juvencio Galíndez-Mayer
- Department of Biochemical Engineering, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. Av. Wilfrido Massieu 399, Unidad Adolfo López Mateos, CP07738 Mexico City, Mexico
| | - Cleotilde Juárez-Ramírez
- Department of Biochemical Engineering, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. Av. Wilfrido Massieu 399, Unidad Adolfo López Mateos, CP07738 Mexico City, Mexico
| | - Everardo Curiel-Quesada
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás. CP11340 Mexico City, Mexico
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Akkaya Ö, Nikel PI, Pérez-Pantoja D, de Lorenzo V. Evolving metabolism of 2,4-dinitrotoluene triggers SOS-independent diversification of host cells. Environ Microbiol 2018; 21:314-326. [DOI: 10.1111/1462-2920.14459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/12/2018] [Accepted: 10/21/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Özlem Akkaya
- Department of Molecular Biology and Genetics; Gebze Technical University; Kocaeli Turkey
- Centro Nacional de Biotecnología-CSIC; Campus de Cantoblanco; Madrid 28049 Spain
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 Kgs Lyngby Denmark
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación; Universidad Tecnológica Metropolitana; Ignacio Valdivieso 2409, San Joaquín, Santiago Chile
| | - Víctor de Lorenzo
- Centro Nacional de Biotecnología-CSIC; Campus de Cantoblanco; Madrid 28049 Spain
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Involvement of transcription-coupled repair factor Mfd and DNA helicase UvrD in mutational processes in Pseudomonas putida. DNA Repair (Amst) 2018; 72:18-27. [PMID: 30292721 DOI: 10.1016/j.dnarep.2018.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/19/2018] [Accepted: 09/22/2018] [Indexed: 11/20/2022]
Abstract
Stalled RNA polymerases (RNAPs) pose an obstacle for the replicating complexes, which could lead to transcription-replication conflicts and result in genetic instability. Stalled RNAPs and DNA lesions blocking RNAP elongation are removed by transcription-coupled repair (TCR), the process which in bacteria is mediated by TCR factor Mfd and helicase UvrD. Although the mechanism of TCR has been extensively studied, its role in mutagenesis is still obscure. In the current study we have investigated the role of Mfd and UvrD in mutational processes in soil bacterium Pseudomonas putida. Our results revealed that UvrD helicase is essential to prevent the emergence of mutations, as the loss of uvrD resulted in elevated mutant frequency both in exponential- and stationary-phase bacterial cultures. UvrD was also found to be necessary to survive DNA damage, but NER or MMR pathways are not completely abolished in UvrD-deficient P. putida. Mfd-deficiency had a moderate impact on surviving DNA damage and did not influence the frequency of mutations occurred in exponentially growing bacteria. However, the absence of Mfd caused approximately a two-fold decline in stationary-phase mutant frequency compared to the P. putida wild-type strain and suppressed the elevated mutant frequency observed in the ΔuvrD strain. Remarkably, the Mfd-deficient strain also formed less UV-induced mutants. These results suggest that in P. putida the Mfd-mediated TCR could be associated with UV- and stationary-phase mutagenesis.
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Akkaya Ö, Pérez-Pantoja DR, Calles B, Nikel PI, de Lorenzo V. The Metabolic Redox Regime of Pseudomonas putida Tunes Its Evolvability toward Novel Xenobiotic Substrates. mBio 2018; 9:e01512-18. [PMID: 30154264 PMCID: PMC6113623 DOI: 10.1128/mbio.01512-18] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 12/28/2022] Open
Abstract
During evolution of biodegradation pathways for xenobiotic compounds involving Rieske nonheme iron oxygenases, the transition toward novel substrates is frequently associated with faulty reactions. Such events release reactive oxygen species (ROS), which are endowed with high mutagenic potential. In this study, we evaluated how the operation of the background metabolic network by an environmental bacterium may either foster or curtail the still-evolving pathway for 2,4-dinitrotoluene (2,4-DNT) catabolism. To this end, the genetically tractable strain Pseudomonas putida EM173 was implanted with the whole genetic complement necessary for the complete biodegradation of 2,4-DNT (recruited from the environmental isolate Burkholderia sp. R34). By using reporter technology and direct measurements of ROS formation, we observed that the engineered P. putida strain experienced oxidative stress when catabolizing the nitroaromatic substrate. However, the formation of ROS was neither translated into significant activation of the SOS response to DNA damage nor did it result in a mutagenic regime (unlike what has been observed in Burkholderia sp. R34, the original host of the pathway). To inspect whether the tolerance of P. putida to oxidative challenges could be traced to its characteristic reductive redox regime, we artificially altered the NAD(P)H pool by means of a water-forming, NADH-specific oxidase. Under the resulting low-NAD(P)H status, catabolism of 2,4-DNT triggered a conspicuous mutagenic and genomic diversification scenario. These results indicate that the background biochemical network of environmental bacteria ultimately determines the evolvability of metabolic pathways. Moreover, the data explain the efficacy of some bacteria (e.g., pseudomonads) to host and evolve with new catabolic routes.IMPORTANCE Some environmental bacteria evolve with new capacities for the aerobic biodegradation of chemical pollutants by adapting preexisting redox reactions to novel compounds. The process typically starts by cooption of enzymes from an available route to act on the chemical structure of the substrate-to-be. The critical bottleneck is generally the first biochemical step, and most of the selective pressure operates on reshaping the initial reaction. The interim uncoupling of the novel substrate to preexisting Rieske nonheme iron oxygenases usually results in formation of highly mutagenic ROS. In this work, we demonstrate that the background metabolic regime of the bacterium that hosts an evolving catabolic pathway (e.g., biodegradation of the xenobiotic 2,4-DNT) determines whether the cells either adopt a genetic diversification regime or a robust ROS-tolerant status. Furthermore, our results offer new perspectives to the rational design of efficient whole-cell biocatalysts, which are pursued in contemporary metabolic engineering.
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Affiliation(s)
- Özlem Akkaya
- Department of Molecular Biology and Genetics, Faculty of Sciences, Gebze Technical University, Kocaeli, Turkey
| | - Danilo R Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago de Chile, Chile
| | - Belén Calles
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Madrid, Spain
| | - Pablo I Nikel
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Madrid, Spain
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