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Wang B, Gao J, Xu J, Fu X, Han H, Li Z, Wang L, Zhang F, Tian Y, Peng R, Yao Q. Optimization and reconstruction of two new complete degradation pathways for 3-chlorocatechol and 4-chlorocatechol in Escherichia coli. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126428. [PMID: 34171665 DOI: 10.1016/j.jhazmat.2021.126428] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/11/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Chlorinated aromatic compounds are a serious environmental concern because of their widespread occurrence throughout the environment. Although several microorganisms have evolved to gain the ability to degrade chlorinated aromatic compounds and use them as carbon sources, they still cannot meet the diverse needs of pollution remediation. In this study, the degradation pathways for 3-chlorocatechol (3CC) and 4-chlorocatechol (4CC) were successfully reconstructed by the optimization, synthesis, and assembly of functional genes from different strains. The addition of a 13C-labeled substrate and functional analysis of different metabolic modules confirmed that the genetically engineered strains can metabolize chlorocatechol similar to naturally degrading strains. The strain containing either of these artificial pathways can degrade catechol, 3CC, and 4CC completely, although differences in the degradation efficiency may be noted. Proteomic analysis and scanning electron microscopy observation showed that 3CC and 4CC have toxic effects on Escherichia coli, but the engineered bacteria can significantly eliminate these inhibitory effects. As core metabolic pathways for the degradation of chloroaromatics, the two chlorocatechol degradation pathways constructed in this study can be used to construct pollution remediation-engineered bacteria, and the related technologies may be applied to construct complete degradation pathways for complex organic hazardous materials.
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Affiliation(s)
- Bo Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jianjie Gao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Jing Xu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Xiaoyan Fu
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Hongjuan Han
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Zhenjun Li
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Lijuan Wang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Fujian Zhang
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China
| | - Yongsheng Tian
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
| | - Rihe Peng
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
| | - Quanhong Yao
- Shanghai Key laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, PR China.
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Hsu DW, Wang TI, Huang DJ, Pao YJ, Lin YA, Cheng TW, Liang SH, Chen CY, Kao CM, Sheu YT, Chen CC. Copper promotes E. coli laccase-mediated TNT biotransformation and alters the toxicity of TNT metabolites toward Tigriopus japonicus. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 173:452-460. [PMID: 30798189 DOI: 10.1016/j.ecoenv.2019.02.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 06/09/2023]
Abstract
Although laccase is involved in the biotransformation of 2,4,6-trinitrotoluene (TNT), little is known regarding the effect of E. coli laccase on TNT biotransformation. In this study, E. coli K12 served as the parental strain to construct a laccase deletion strain and two laccase-overexpressing strains. These E. coli strains were used to investigate the effect of laccase together with copper ions on the efficiency of TNT biotransformation, the variety of TNT biotransformation products generated and the toxicity of the TNT metabolites. The results showed that the laccase level was not relevant to TNT biotransformation in the soluble fraction of the culture medium. Conversely, TNT metabolites varied in the insoluble fraction analyzed by thin-layer chromatography (TLC). The insoluble fraction from the laccase-null strain showed fewer and relatively fainter spots than those detected in the wild-type and laccase-overexpressing strains, indicating that laccase expression levels were interrelated determinants of the varieties and amounts of TNT metabolites produced. In addition, the aquatic invertebrate Tigriopus japonicus was used to assess the toxicity of the TNT metabolites. The toxicity of the TNT metabolite mixture increased when the intracellular laccase level in strains increased or when purified E. coli recombinant Laccase (rLaccase) was added to the culture medium. Thus, our results suggest that laccase activity must be considered when performing microbial TNT remediation.
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Affiliation(s)
- Duen-Wei Hsu
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Tzu-I Wang
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Da-Ji Huang
- Department of Environmental Resources Management, Chia Nan University of Pharmacy & Science, Tainan, Taiwan
| | - Yu-Jie Pao
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Yuya A Lin
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Ting-Wen Cheng
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Shih-Hsiung Liang
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Chien-Yen Chen
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Chih-Ming Kao
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yih-Terng Sheu
- Institute of Environmental Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chien-Cheng Chen
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan.
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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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Iman M, Sobati T, Panahi Y, Mobasheri M. Systems Biology Approach to Bioremediation of Nitroaromatics: Constraint-Based Analysis of 2,4,6-Trinitrotoluene Biotransformation by Escherichia coli. Molecules 2017; 22:E1242. [PMID: 28805729 PMCID: PMC6152126 DOI: 10.3390/molecules22081242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 01/02/2023] Open
Abstract
Microbial remediation of nitroaromatic compounds (NACs) is a promising environmentally friendly and cost-effective approach to the removal of these life-threating agents. Escherichia coli (E. coli) has shown remarkable capability for the biotransformation of 2,4,6-trinitro-toluene (TNT). Efforts to develop E. coli as an efficient TNT degrading biocatalyst will benefit from holistic flux-level description of interactions between multiple TNT transforming pathways operating in the strain. To gain such an insight, we extended the genome-scale constraint-based model of E. coli to account for a curated version of major TNT transformation pathways known or evidently hypothesized to be active in E. coli in present of TNT. Using constraint-based analysis (CBA) methods, we then performed several series of in silico experiments to elucidate the contribution of these pathways individually or in combination to the E. coli TNT transformation capacity. Results of our analyses were validated by replicating several experimentally observed TNT degradation phenotypes in E. coli cultures. We further used the extended model to explore the influence of process parameters, including aeration regime, TNT concentration, cell density, and carbon source on TNT degradation efficiency. We also conducted an in silico metabolic engineering study to design a series of E. coli mutants capable of degrading TNT at higher yield compared with the wild-type strain. Our study, therefore, extends the application of CBA to bioremediation of nitroaromatics and demonstrates the usefulness of this approach to inform bioremediation research.
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Affiliation(s)
- Maryam Iman
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran.
- Department of Pharmaceutics, School of Pharmacy, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran.
| | - Tabassom Sobati
- Young Researchers and Elite Club, Islamic Azad University, 46115655 Tehran, Iran.
| | - Yunes Panahi
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran.
| | - Meysam Mobasheri
- Young Researchers and Elite Club, Islamic Azad University, 46115655 Tehran, Iran.
- Department of Biotechnology, Faculty of Advanced Sciences & Technology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), 194193311 Tehran, Iran.
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Wijker RS, Zeyer J, Hofstetter TB. Isotope fractionation associated with the simultaneous biodegradation of multiple nitrophenol isomers by Pseudomonas putida B2. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2017; 19:775-784. [PMID: 28470308 DOI: 10.1039/c6em00668j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Quantifying the extent of biodegradation of nitroaromatic compounds (NACs) in contaminated soils and sediments is challenging because of competing oxidative and reductive reaction pathways. We have previously shown that the stable isotope fractionation of NACs reveals the routes of degradation even if it is simultaneously caused by different bacteria. However, it is unclear whether compound-specific isotope analysis (CSIA) can be applied in situations where multiple pollutants are biodegraded by only one microorganism under multi-substrate conditions. Here we examined the C and N isotope fractionation of 2-nitrophenol (2-NP) and 3-nitrophenol (3-NP) during biodegradation by Pseudomonas putida B2 through monooxygenation and partial reductive pathways, respectively, in the presence of single substrates vs. binary substrate mixtures. Laboratory experiments showed that the reduction of 3-NP by Pseudomonas putida B2 is associated with large N and minor C isotope fractionation with C and N isotope enrichment factors, εC and εN, of -0.3 ± 0.1‰ and -22 ± 0.2‰, respectively. The opposite isotope fractionation trends were found for 2-NP monooxygenation. In the simultaneous presence of 2-NP and 3-NP, 2-NP is biodegraded at identical rate constants and εC and εN values (-1.0 ± 0.1‰ and -1.3 ± 0.2‰) to those found for the monooxygenation of 2-NP in single substrate experiments. While the pathway and N isotope fractionation of 3-NP reduction (εN = -24 ± 1.1‰) are independent of the presence of 2-NP, intermediates of 2-NP monooxygenation interfere with 3-NP reduction. Because neither pH, substrate uptake, nor aromatic substituents affected the kinetic isotope effects of nitrophenol biodegradation, our study illustrates that CSIA provides robust scientific evidence for the assessment of natural attenuation processes.
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Affiliation(s)
- Reto S Wijker
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, Zürich, Switzerland.
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Sakil Munna M, Tahera J, Mohibul Hassan Afrad M, Nur IT, Noor R. Survival of Bacillus spp. SUBB01 at high temperatures and a preliminary assessment of its ability to protect heat-stressed Escherichia coli cells. BMC Res Notes 2015; 8:637. [PMID: 26526722 PMCID: PMC4630936 DOI: 10.1186/s13104-015-1631-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 10/26/2015] [Indexed: 12/18/2022] Open
Abstract
Background The bacterial stressed state upon temperature raise has widely been observed especially in Escherichia coli cells. The current study extended such physiological investigation on Bacillus spp. SUBB01 under aeration at 100 rpm on different culture media along with the high temperature exposure at 48, 50, 52, 53 and 54 °C. Bacterial growth was determined through the enumeration of the viable and culturable cells; i.e., cells capable of producing the colony forming units on Luria–Bertani and nutrient agar plates up to 24 h. Microscopic experiments were conducted to scrutinize the successive physiological changes. Suppression of bacterial growth due to the elevated heat was further confirmed by the observation of non-viability through spot tests. Results As expected, a quick drop in both cell turbidity and colony forming units (~104) along with spores were observed after 12–24 h of incubation period, when cells were grown at 54 °C in both Luria–Bertani and nutrient broth and agar. The critical temperature (the temperature above which it is no longer possible to survive) of Bacillus spp. SUBB01 was estimated to be 53 °C. Furthermore, a positive impact was observed on the inhibited E. coli SUBE01 growth at 45 and 47 °C, upon the supplementation of the extracellular fractions of Bacillus species into the growing culture. Conclusions Overall the present analysis revealed the conversion of the culturable cells into the viable and nonculturable (VBNC) state as a result of heat shock response in Bacillus spp. SUBB01 and the cellular adaptation at extremely high temperature.
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Affiliation(s)
- Md Sakil Munna
- Department of Microbiology, Stamford University, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
| | - Jannatun Tahera
- Department of Microbiology, Stamford University, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
| | - Md Mohibul Hassan Afrad
- Department of Microbiology, Stamford University, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
| | - Ifra Tun Nur
- Department of Microbiology, Stamford University, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
| | - Rashed Noor
- Department of Microbiology, Stamford University, 51 Siddeswari Road, Dhaka, 1217, Bangladesh.
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Wang L, Tang H, Yu H, Yao Y, Xu P. An unusual repressor controls the expression of a crucial nicotine-degrading gene cluster inPseudomonas putida S16. Mol Microbiol 2014; 91:1252-69. [DOI: 10.1111/mmi.12533] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Lijuan Wang
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Hao Yu
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Yuxiang Yao
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism; School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
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Singh D, Kumari A, Ramanathan G. 3-Nitrotoluene dioxygenase from Diaphorobacter sp. strains: cloning, sequencing and evolutionary studies. Biodegradation 2013; 25:479-92. [PMID: 24217981 DOI: 10.1007/s10532-013-9675-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 10/31/2013] [Indexed: 11/28/2022]
Abstract
The first step in the degradation of 3-nitrotoluene by Diaphorobacter sp. strain DS2 is the dihydroxylation of the benzene ring with the concomitant removal of nitro group. This is catalyzed by a dioxygenase enzyme system. We report here the cloning and sequencing of the complete dioxygenase gene with its putative regulatory sequence from the genomic DNA of Diaphorobacter sp. strains DS1, DS2 and DS3. Analysis of the 5 kb DNA stretch that was cloned, revealed five complete open reading frames (ORFs) encoding for a reductase, a ferredoxin and two dioxygenase subunits with predicted molecular weights (MW) of 35, 12, 50 and 23 kDa respectively. A regulatory protein was also divergently transcribed from the reductase subunit and has a predicated MW of 34 kDa. Presence of parts of two functional ORFs in between the reductase and the ferredoxin subunits reveals an evolutionary route from a naphthalene dioxygenase like system of Ralstonia sp. strain U2. Further a 100 % identity of its ferredoxin subunit reveals its evolution via dinitrotoluene dioxygenase like system present in Burkholderia cepacia strain R34. A modeled structure of oxygenase3NT from strain DS2 was generated using nitrobenzene dioxygenase as a template. The modeled structure only showed minor changes at its active site. Comparison of growth patterns of strains DS1, DS2 and DS3 revealed that Diaphorobacter sp. strain DS1 has been evolved to degrade 4-nitrotoluene better by an oxidative route amongst all three strains.
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Affiliation(s)
- Deepak Singh
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016, India
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Pérez-Pantoja D, Nikel PI, Chavarría M, de Lorenzo V. Endogenous stress caused by faulty oxidation reactions fosters evolution of 2,4-dinitrotoluene-degrading bacteria. PLoS Genet 2013; 9:e1003764. [PMID: 24009532 PMCID: PMC3757077 DOI: 10.1371/journal.pgen.1003764] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/16/2013] [Indexed: 01/13/2023] Open
Abstract
Environmental strain Burkholderia sp. DNT mineralizes the xenobiotic compound 2,4-dinitrotoluene (DNT) owing to the catabolic dnt genes borne by plasmid DNT, but the process fails to promote significant growth. To investigate this lack of physiological return of such an otherwise complete metabolic route, cells were exposed to DNT under various growth conditions and the endogenous formation of reactive oxygen species (ROS) monitored in single bacteria. These tests revealed the buildup of a strong oxidative stress in the population exposed to DNT. By either curing the DNT plasmid or by overproducing the second activity of the biodegradation route (DntB) we could trace a large share of ROS production to the first reaction of the route, which is executed by the multicomponent dioxygenase encoded by the dntA gene cluster. Naphthalene, the ancestral substrate of the dioxygenase from which DntA has evolved, also caused significant ROS formation. That both the old and the new substrate brought about a considerable cellular stress was indicative of a still-evolving DntA enzyme which is neither optimal any longer for naphthalene nor entirely advantageous yet for growth of the host strain on DNT. We could associate endogenous production of ROS with likely error-prone repair mechanisms of DNA damage, and the ensuing stress-induced mutagenesis in cells exposed to DNT. It is thus plausible that the evolutionary roadmap for biodegradation of xenobiotic compounds like DNT was largely elicited by mutagenic oxidative stress caused by faulty reactions of precursor enzymes with novel but structurally related substrates-to-be. Many bacteria have acquired the capacity of metabolizing chemical compounds that have never been in the Biosphere before the onset of contemporary synthetic chemistry. However, the factors that shape the new metabolic properties of such microorganisms remain obscure. We examined the performance of a still-evolving metabolic pathway for biodegradation of 2,4-dinitrotoluene (DNT, an archetypal xenobiotic compound) borne by a Burkholderia strain isolated from soil in an ammunition plant. The biodegradation pathway likely arose from a precursor set of genes for catabolism of naphthalene (although Burkholderia does not degrade this compound any longer), and is now advancing towards the new substrate, DNT. We found that the action of the first enzyme of the biodegradation pathway, a Rieske-type dioxygenase, on the still-suboptimal substrate (DNT) generates a high level of endogenous reactive oxygen species. This, in turn, damages DNA and increases mutagenesis, ultimately resulting in the creation of novelty that may foster evolution of xenobiotic-degrading variants of the strain hosting the biodegradation pathway. The very metabolic problem thus somehow seems to stimulate the exploration of the solution space. Our data is fully consistent with the notion that stress caused by faulty dioxygenation of DNT accelerates the rate of bacterial evolution.
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Affiliation(s)
- Danilo Pérez-Pantoja
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Max Chavarría
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Madrid, Spain
- * E-mail:
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Biomineralization of 3-nitrotoluene by Diaphorobacter species. Biodegradation 2012; 24:645-55. [DOI: 10.1007/s10532-012-9612-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 11/27/2012] [Indexed: 10/27/2022]
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The ecology of bacterial genes and the survival of the new. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:394026. [PMID: 22900231 PMCID: PMC3415099 DOI: 10.1155/2012/394026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 06/26/2012] [Indexed: 11/18/2022]
Abstract
Much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Genes can be considered semiautonomous entities that possess specific functional niches and evolutionary dynamics. The evolution of bacterial genes should respond both to selective pressures that favor competition, mostly among orthologs or paralogs that may occupy the same functional niches, and cooperation, with the majority of other genes coexisting in a given genome. The relative importance of either type of selection is likely to vary among different types of genes, based on the functional niches they cover and on the tightness of their association with specific organismal lineages. The frequent availability of new functional niches caused by environmental changes and biotic evolution should enable the constant diversification of gene families and the survival of new lineages of genes.
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