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Camacho J, Mesén-Porras E, Rojas-Gätjens D, Pérez-Pantoja D, Puente-Sánchez F, Chavarría M. Draft genome sequence of three hydrocarbon-degrading Pseudomonadota strains isolated from an abandoned century-old oil exploration well. Microbiol Resour Announc 2024; 13:e0107623. [PMID: 38289048 PMCID: PMC10868222 DOI: 10.1128/mra.01076-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/17/2024] [Indexed: 02/16/2024] Open
Abstract
We present genome sequences of three Pseudomonadota strains isolated from an abandoned century-old oil exploration well. A Pseudomonas sp. genome showed a size of 5,378,420 bp, while Acinetobacter genomes sized 3,522,593 and 3,864,311 bp. Genomes included catabolic genes for benzoate, 4-hydroxybenzoate, salicylate, vanillate, indoleacetate, anthranilate, n-alkanes, 4-hydroxyphenylacetate, phenylacetate, among others.
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Affiliation(s)
- Jefferson Camacho
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
| | - Esteve Mesén-Porras
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Danilo Pérez-Pantoja
- Instituto Universitario de Investigación y Desarrollo Tecnológico, Universidad Tecnológica Metropolitana, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Fernando Puente-Sánchez
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Lennart Hjelms väg, Uppsala, Sweden
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
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Salvà-Serra F, Pérez-Pantoja D, Donoso RA, Jaén-Luchoro D, Fernández-Juárez V, Engström-Jakobsson H, Moore ERB, Lalucat J, Bennasar-Figueras A. Comparative genomics of Stutzerimonas balearica ( Pseudomonas balearica): diversity, habitats, and biodegradation of aromatic compounds. Front Microbiol 2023; 14:1159176. [PMID: 37275147 PMCID: PMC10234333 DOI: 10.3389/fmicb.2023.1159176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
Stutzerimonas balearica (Pseudomonas balearica) has been found principally in oil-polluted environments. The capability of S. balearica to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of S. balearica. In this study, genome sequences of S. balearica strains from different origins were analyzed, revealing that it is a diverse species with an open pan-genome that will continue revealing new genes and functionalities as the genomes of more strains are sequenced. The nucleotide signatures and intra- and inter-species variation of the 16S rRNA genes of S. balearica were reevaluated. A strategy of screening 16S rRNA gene sequences in public databases enabled the detection of 158 additional strains, of which only 23% were described as S. balearica. The species was detected from a wide range of environments, although mostly from aquatic and polluted environments, predominantly related to petroleum oil. Genomic and phenotypic analyses confirmed that S. balearica possesses varied inherent capabilities for aromatic compounds degradation. This study increases the knowledge of the biology and diversity of S. balearica and will serve as a basis for future work with the species.
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Affiliation(s)
- Francisco Salvà-Serra
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Raúl A. Donoso
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Víctor Fernández-Juárez
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Hedvig Engström-Jakobsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Antoni Bennasar-Figueras
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
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Rojas-Gätjens D, Fuentes-Schweizer P, Rojas-Jiménez K, Pérez-Pantoja D, Avendaño R, Alpízar R, Coronado-Ruíz C, Chavarría M. Methylotrophs and Hydrocarbon-Degrading Bacteria Are Key Players in the Microbial Community of an Abandoned Century-Old Oil Exploration Well. Microb Ecol 2022; 83:83-99. [PMID: 33864491 DOI: 10.1007/s00248-021-01748-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
In this work, we studied the microbial community and the physicochemical conditions prevailing in an exploratory oil well, abandoned a century ago, located in the Cahuita National Park (Costa Rica). According to our analysis, Cahuita well is characterized by a continuous efflux of methane and the presence of a mixture of hydrocarbons including phenanthrene/anthracene, fluoranthene, pyrene, dibenzothiophene, tricyclic terpanes, pyrene, sesquiterpenes, sterane, and n-alkanes. Based on the analysis of 16S rRNA gene amplicons, we detected a significant abundance of methylotrophic bacteria such as Methylobacillus (6.3-26.0% of total reads) and Methylococcus (4.1-30.6%) and the presence of common genera associated with hydrocarbon degradation, such as Comamonas (0.8-4.6%), Hydrogenophaga (1.5-3.3%) Rhodobacter (1.0-4.9%), and Flavobacterium (1.1-6.5%). The importance of C1 metabolism in this niche was confirmed by amplifying the methane monooxygenase (MMO)-encoding gene (pmo) from environmental DNA and the isolation of two strains closely related to Methylorubrum rhodesianum and Paracoccus communis with the ability to growth using methanol and formate as sole carbon source respectively. In addition, we were able to isolated 20 bacterial strains from the genera Pseudomonas, Acinetobacter, and Microbacterium which showed the capability to grow using the hydrocarbons detected in the oil well as sole carbon source. This work describes the physicochemical properties and microbiota of an environment exposed to hydrocarbons for 100 years, and it not only represents a contribution to the understanding of microbial communities in environments with permanently high concentrations of these compounds but also has biotechnological implications for bioremediation of petroleum-polluted sites.
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Affiliation(s)
- Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Paola Fuentes-Schweizer
- Centro de Investigación en Electroquímica y Energía Química (CELEQ), Universidad de Costa Rica, San José, 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica
| | - Keilor Rojas-Jiménez
- Escuela de Biología, Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Randall Alpízar
- Hidroambiente Consultores, 45, Goicoechea, San José, Costa Rica
| | - Carolina Coronado-Ruíz
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica.
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica.
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica.
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Donoso RA, Ruiz D, Gárate-Castro C, Villegas P, González-Pastor JE, de Lorenzo V, González B, Pérez-Pantoja D. Identification of a self-sufficient cytochrome P450 monooxygenase from Cupriavidus pinatubonensis JMP134 involved in 2-hydroxyphenylacetic acid catabolism, via homogentisate pathway. Microb Biotechnol 2021; 14:1944-1960. [PMID: 34156761 PMCID: PMC8449657 DOI: 10.1111/1751-7915.13865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 11/28/2022] Open
Abstract
The self-sufficient cytochrome P450 RhF and its homologues belonging to the CYP116B subfamily have attracted considerable attention due to the potential for biotechnological applications based in their ability to catalyse an array of challenging oxidative reactions without requiring additional protein partners. In this work, we showed for the first time that a CYP116B self-sufficient cytochrome P450 encoded by the ohpA gene harboured by Cupriavidus pinatubonensis JMP134, a β-proteobacterium model for biodegradative pathways, catalyses the conversion of 2-hydroxyphenylacetic acid (2-HPA) into homogentisate. Mutational analysis and HPLC metabolite detection in strain JMP134 showed that 2-HPA is degraded through the well-known homogentisate pathway requiring a 2-HPA 5-hydroxylase activity provided by OhpA, which was additionally supported by heterologous expression and enzyme assays. The ohpA gene belongs to an operon including also ohpT, coding for a substrate-binding subunit of a putative transporter, whose expression is driven by an inducible promoter responsive to 2-HPA in presence of a predicted OhpR transcriptional regulator. OhpA homologues can be found in several genera belonging to Actinobacteria and α-, β- and γ-proteobacteria lineages indicating a widespread distribution of 2-HPA catabolism via homogentisate route. These results provide first time evidence for the natural function of members of the CYP116B self-sufficient oxygenases and represent a significant input to support novel kinetic and structural studies to develop cytochrome P450-based biocatalytic processes.
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Affiliation(s)
- Raúl A Donoso
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile.,Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Daniela Ruiz
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.,Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Carla Gárate-Castro
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile.,Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Pamela Villegas
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile
| | - José Eduardo González-Pastor
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Bernardo González
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.,Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile
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Donoso RA, González-Toro F, Pérez-Pantoja D. Widespread distribution of hmf genes in Proteobacteria reveals key enzymes for 5-hydroxymethylfurfural conversion. Comput Struct Biotechnol J 2021; 19:2160-2169. [PMID: 33995910 PMCID: PMC8091172 DOI: 10.1016/j.csbj.2021.04.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 04/05/2021] [Accepted: 04/05/2021] [Indexed: 11/25/2022] Open
Abstract
Furans represent a class of promising chemicals, since they constitute valuable intermediates in conversion of biomass into sustainable products intended to replace petroleum-derivatives. Conversely, generation of furfural and 5-hydroxymethylfurfural (HMF) as by-products in lignocellulosic hydrolysates is undesirable due its inhibitory effect over fermentative microorganisms. Therefore, the search for furans-metabolizing bacteria has gained increasing attention since they are valuable tools to solve these challenging issues. A few bacterial species have been described at genetic level, leading to a proposed HMF pathway encoded by a set of genes termed hmf/psf, although some enzymatic functions are still elusive. In this work we performed a genomic analysis of major subunits of furoyl-CoA dehydrogenase orthologues, revealing that the furoic acid catabolic route, key intermediate in HMF biodegradation, is widespread in proteobacterial species. Additionally, presence/absence profiles of hmf/psf genes in selected proteobacterial strains suggest parallel and/or complementary roles of enzymes with previously unclear function that could be key in HMF conversion. The furans utilization pattern of selected strains harboring different hmf/psf gene sets provided additional support for bioinformatic predictions of the relevance of some enzymes. On the other hand, at least three different types of transporter systems are clustered with hmf/psf genes, whose presence is mutually exclusive, suggesting a core and parallel role in furans transport in Proteobacteria. This study expands the number of bacteria that could be recruited in biotechnological processes for furans biodetoxification and predicts a core set of genes required to establish a functional HMF pathway in heterologous hosts for metabolic engineering endeavors.
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Affiliation(s)
- Raúl A. Donoso
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Fabián González-Toro
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile
- Corresponding author.
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Pérez-Pantoja D, Nikel PI, Chavarría M, de Lorenzo V. Transcriptional control of 2,4-dinitrotoluene degradation in Burkholderia sp. R34 bears a regulatory patch that eases pathway evolution. Environ Microbiol 2021; 23:2522-2531. [PMID: 33734558 DOI: 10.1111/1462-2920.15472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/27/2021] [Accepted: 03/16/2021] [Indexed: 11/26/2022]
Abstract
The dnt pathway of Burkholderia sp. R34 is in the midst of an evolutionary journey from its ancestral, natural substrate (naphthalene) towards a new xenobiotic one [2,4-dinitrotoluene (DNT)]. The gene cluster encoding the leading multicomponent ring dioxygenase (DntA) has activity on the old and the new substrate, but it is induced by neither. Instead, the transcriptional factor encoded by the adjacent gene (dntR) activates expression of the dnt cluster upon addition of salicylate, one degradation intermediate of the ancestral naphthalene route but not any longer a substrate/product of the evolved DntA enzyme. Fluorescence of cells bearing dntA-gfp fusions revealed that induction of the dnt genes by salicylate was enhanced upon exposure to bona fide DntA substrates, i.e., naphthalene or DNT. Such amplification was dependent on effective dioxygenation of these pathway-specific head compounds, which thereby fostered expression of the cognate catabolic operon. The phenomenon seems to happen not through direct binding to a cognate transcriptional factor but through the interplay of a non-specific regulator with a substrate-specific enzyme. This regulatory scenario may ease transition of complete catabolic operons (i.e. enzymes plus regulatory devices) from one substrate to another without loss of fitness during the evolutionary roadmap between two optimal specificities.
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Affiliation(s)
- Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, 8940577, Chile
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, 2800, Denmark
| | - Max Chavarría
- Escuela de Química and CIPRONA, Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
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Akkaya Ö, Aparicio T, Pérez-Pantoja D, de Lorenzo V. The faulty SOS response of Pseudomonas putida KT2440 stems from an inefficient RecA-LexA interplay. Environ Microbiol 2021; 23:1608-1619. [PMID: 33393180 DOI: 10.1111/1462-2920.15384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 11/29/2022]
Abstract
Despite its environmental robustness Pseudomonas putida strain KT2440 is very sensitive to DNA damage and displays poor homologous recombination efficiencies. To gain an insight into this deficiency isogenic ∆recA and ∆lexA1 derivatives of prophage-free strain P. putida EM173 were generated and responses of the recA and lexA1 promoters to DNA damage tested with GFP reporter technology. Basal expression of recA and lexA1 of P. putida were high in the absence of DNA damage and only moderately induced by norfloxacin. A similar behaviour was observed when equivalent GFP fusions to the recA and lexA promoters of E. coli were placed in P. putida EM173. In contrast, all SOS promoters were subject to strong repression in E. coli, which was released only when cells were treated with the antibiotic. Replacement of P. putida's native LexA1 and RecA by E. coli homologues did not improve the responsiveness of the indigenous functions to DNA damage. Taken together, it seems that P. putida fails to mount a strong SOS response due to the inefficacy of the crucial RecA-LexA interplay largely tractable to the weakness of the corresponding promoters and the inability of the repressor to shut them down entirely in the absence of DNA damage.
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Affiliation(s)
- Özlem Akkaya
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, 28049, Spain.,Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
| | - Tomás Aparicio
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, 28049, Spain
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, 28049, Spain
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Lamprecht-Grandío M, Cortesão M, Mirete S, de la Cámara MB, de Figueras CG, Pérez-Pantoja D, White JJ, Farías ME, Rosselló-Móra R, González-Pastor JE. Novel Genes Involved in Resistance to Both Ultraviolet Radiation and Perchlorate From the Metagenomes of Hypersaline Environments. Front Microbiol 2020; 11:453. [PMID: 32292392 PMCID: PMC7135895 DOI: 10.3389/fmicb.2020.00453] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/03/2020] [Indexed: 12/25/2022] Open
Abstract
Microorganisms that thrive in hypersaline environments on the surface of our planet are exposed to the harmful effects of ultraviolet radiation. Therefore, for their protection, they have sunscreen pigments and highly efficient DNA repair and protection systems. The present study aimed to identify new genes involved in UV radiation resistance from these microorganisms, many of which cannot be cultured in the laboratory. Thus, a functional metagenomic approach was used and for this, small-insert libraries were constructed with DNA isolated from microorganisms of high-altitude Andean hypersaline lakes in Argentina (Diamante and Ojo Seco lakes, 4,589 and 3,200 m, respectively) and from the Es Trenc solar saltern in Spain. The libraries were hosted in a UV radiation-sensitive strain of Escherichia coli (recA mutant) and they were exposed to UVB. The resistant colonies were analyzed and as a result, four clones were identified with environmental DNA fragments containing five genes that conferred resistance to UV radiation in E. coli. One gene encoded a RecA-like protein, complementing the mutation in recA that makes the E. coli host strain more sensitive to UV radiation. Two other genes from the same DNA fragment encoded a TATA-box binding protein and an unknown protein, both responsible for UV resistance. Interestingly, two other genes from different and remote environments, the Ojo Seco Andean lake and the Es Trenc saltern, encoded two hypothetical proteins that can be considered homologous based on their significant amino acid similarity (49%). All of these genes also conferred resistance to 4-nitroquinoline 1-oxide (4-NQO), a compound that mimics the effect of UV radiation on DNA, and also to perchlorate, a powerful oxidant that can induce DNA damage. Furthermore, the hypothetical protein from the Es Trenc salterns was localized as discrete foci possibly associated with damaged sites in the DNA in cells treated with 4-NQO, so it could be involved in the repair of damaged DNA. In summary, novel genes involved in resistance to UV radiation, 4-NQO and perchlorate have been identified in this work and two of them encoding hypothetical proteins that could be involved in DNA damage repair activities not previously described.
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Affiliation(s)
| | - Marta Cortesão
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Salvador Mirete
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | | | | | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Joseph John White
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), Centro Científico Tecnológico, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán, Argentina
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Fuentes-Valdés JJ, Soto-Liebe K, Pérez-Pantoja D, Tamames J, Belmar L, Pedrós-Alió C, Garrido D, Vásquez M. Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay. Stand Genomic Sci 2018; 13:26. [PMID: 30344889 PMCID: PMC6186047 DOI: 10.1186/s40793-018-0323-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 09/24/2018] [Indexed: 12/28/2022] Open
Abstract
Members of the genus Cylindrospermopsis represent an important environmental and health concern. Strains CS-508 and MVCC14 of C. raciborskii were isolated from freshwater reservoirs located in Australia and Uruguay, respectively. While CS-508 has been reported as non-toxic, MVCC14 is a saxitoxin (STX) producer. We annotated the draft genomes of these C. raciborskii strains using the assembly of reads obtained from Illumina MiSeq sequencing. The final assemblies resulted in genome sizes close to 3.6 Mbp for both strains and included 3202 ORFs for CS-508 (in 163 contigs) and 3560 ORFs for MVCC14 (in 99 contigs). Finally, both the average nucleotide identity (ANI) and the similarity of gene content indicate that these two genomes should be considered as strains of the C. raciborskii species.
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Affiliation(s)
- Juan J Fuentes-Valdés
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile
- Department of Chemical and Bioprocess Engineering, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
| | - Katia Soto-Liebe
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, 8940577 Santiago, Chile
| | - Javier Tamames
- Systems Biology Program, CNB, CSIC, Calle Darwin 3, 28049 Madrid, Spain
| | - Lucy Belmar
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile
| | | | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
| | - Mónica Vásquez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile
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11
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Alcamán-Arias ME, Pedrós-Alió C, Tamames J, Fernández C, Pérez-Pantoja D, Vásquez M, Díez B. Diurnal Changes in Active Carbon and Nitrogen Pathways Along the Temperature Gradient in Porcelana Hot Spring Microbial Mat. Front Microbiol 2018; 9:2353. [PMID: 30333812 PMCID: PMC6176055 DOI: 10.3389/fmicb.2018.02353] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 09/13/2018] [Indexed: 01/14/2023] Open
Abstract
Composition, carbon and nitrogen uptake, and gene transcription of microbial mat communities in Porcelana neutral hot spring (Northern Chilean Patagonia) were analyzed using metagenomics, metatranscriptomics and isotopically labeled carbon (H13CO3) and nitrogen (15NH4Cl and K15NO3) assimilation rates. The microbial mat community included 31 phyla, of which only Cyanobacteria and Chloroflexi were dominant. At 58°C both phyla co-occurred, with similar contributions in relative abundances in metagenomes and total transcriptional activity. At 66°C, filamentous anoxygenic phototrophic Chloroflexi were >90% responsible for the total transcriptional activity recovered, while Cyanobacteria contributed most metagenomics and metatranscriptomics reads at 48°C. According to such reads, phototrophy was carried out both through oxygenic photosynthesis by Cyanobacteria (mostly Mastigocladus) and anoxygenic phototrophy due mainly to Chloroflexi. Inorganic carbon assimilation through the Calvin-Benson cycle was almost exclusively due to Mastigocladus, which was the main primary producer at lower temperatures. Two other CO2 fixation pathways were active at certain times and temperatures as indicated by transcripts: 3-hydroxypropionate (3-HP) bi-cycle due to Chloroflexi and 3-hydroxypropionate-4-hydroxybutyrate (HH) cycle carried out by Thaumarchaeota. The active transcription of the genes involved in these C-fixation pathways correlated with high in situ determined carbon fixation rates. In situ measurements of ammonia assimilation and nitrogen fixation (exclusively attributed to Cyanobacteria and mostly to Mastigocladus sp.) showed these were the most important nitrogen acquisition pathways at 58 and 48°C. At 66°C ammonia oxidation genes were actively transcribed (mostly due to Thaumarchaeota). Reads indicated that denitrification was present as a nitrogen sink at all temperatures and that dissimilatory nitrate reduction to ammonia (DNRA) contributed very little. The combination of metagenomic and metatranscriptomic analysis with in situ assimilation rates, allowed the reconstruction of day and night carbon and nitrogen assimilation pathways together with the contribution of keystone microorganisms in this natural hot spring microbial mat.
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Affiliation(s)
- María E. Alcamán-Arias
- Department of Oceanography, Universidad de Concepción, Concepción, Chile
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Climate and Resilience Research, Universidad de Chile, Santiago, Chile
| | - Carlos Pedrós-Alió
- Programa de Biología de Sistemas, Centro Nacional de Biotecnología – Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Javier Tamames
- Programa de Biología de Sistemas, Centro Nacional de Biotecnología – Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Camila Fernández
- Department of Oceanography, Universidad de Concepción, Concepción, Chile
- Laboratoire d’Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre-et-Marie-Curie, Centre National de la Recherche Scientifique, Banyuls-sur-Mer, France
- Fondap IDEAL, Universidad Austral de Chile, Valdivia, Chile
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Mónica Vásquez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Climate and Resilience Research, Universidad de Chile, Santiago, Chile
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Fonseca A, Ishoey T, Espinoza C, Pérez-Pantoja D, Manghisi A, Morabito M, Salas-Burgos A, Gallardo VA. Genomic features of "Candidatus Venteria ishoeyi", a new sulfur-oxidizing macrobacterium from the Humboldt Sulfuretum off Chile. PLoS One 2017; 12:e0188371. [PMID: 29236755 PMCID: PMC5728499 DOI: 10.1371/journal.pone.0188371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 11/06/2017] [Indexed: 12/13/2022] Open
Abstract
The Humboldt Sulfuretum (HS), in the productive Humboldt Eastern Boundary Current Upwelling Ecosystem, extends under the hypoxic waters of the Peru-Chile Undercurrent (ca. 6°S and ca. 36°S). Studies show that primeval sulfuretums held diverse prokaryotic life, and, while rare today, still sustain species-rich giant sulfur-oxidizing bacterial communities. We here present the genomic features of a new bacteria of the HS, "Candidatus Venteria ishoeyi" ("Ca. V. ishoeyi") in the family Thiotrichaceae.Three identical filaments were micro-manipulated from reduced sediments collected off central Chile; their DNA was extracted, amplified, and sequenced by a Roche 454 GS FLX platform. Using three sequenced libraries and through de novo genome assembly, a draft genome of 5.7 Mbp, 495 scaffolds, and a N50 of 70 kbp, was obtained. The 16S rRNA gene phylogenetic analysis showed that "Ca. V. ishoeyi" is related to non-vacuolate forms presently known as Beggiatoa or Beggiatoa-like forms. The complete set of genes involved in respiratory nitrate-reduction to dinitrogen was identified in "Ca. V. ishoeyi"; including genes likely leading to ammonification. As expected, the sulfur-oxidation pathway reported for other sulfur-oxidizing bacteria were deduced and also, key inorganic and organic carbon acquisition related genes were identified. Unexpectedly, the genome of "Ca. V. ishoeyi" contained numerous CRISPR repeats and an I-F CRISPR-Cas type system gene coding array. Findings further show that, as a member of an eons-old marine ecosystem, "Ca. V. ishoeyi" contains the needed metabolic plasticity for life in an increasingly oxygenated and variable ocean.
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Affiliation(s)
- Alexis Fonseca
- Department of Pharmacology, University of Concepcion, Concepcion, Chile
- Department of Oceanography, University of Concepcion, Concepcion, Chile
| | - Thomas Ishoey
- Independent consultant, Encinitas, California, United States of America
| | - Carola Espinoza
- Department of Oceanography, University of Concepcion, Concepcion, Chile
- College of Ocean Science and Resources, Institute Marine Affairs and Resource Management, National Taiwan Ocean University, Keelung, Taiwan
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, San Joaquin, Santiago, Chile
| | - Antonio Manghisi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Marina Morabito
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | | | - Víctor A. Gallardo
- Department of Oceanography, University of Concepcion, Concepcion, Chile
- College of Ocean Science and Resources, Institute Marine Affairs and Resource Management, National Taiwan Ocean University, Keelung, Taiwan
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Svenningsen NB, Damgaard M, Rasmussen M, Pérez-Pantoja D, Nybroe O, Nicolaisen MH. Cupriavidus pinatubonensis AEO106 deals with copper-induced oxidative stress before engaging in biodegradation of the herbicide 4-chloro-2-methylphenoxyacetic acid. BMC Microbiol 2017; 17:211. [PMID: 29084513 PMCID: PMC5663122 DOI: 10.1186/s12866-017-1119-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/19/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Microbial degradation of phenoxy acid (PA) herbicides in agricultural soils is important to minimize herbicide leaching to groundwater reservoirs. Degradation may, however, be hampered by exposure of the degrader bacteria to toxic metals as copper (Cu) in the soil environment. Exposure to Cu leads to accumulation of intracellular reactive oxygen species (ROS) in some bacteria, but it is not known how Cu-derived ROS and an ensuing oxidative stress affect the degradation of PA herbicides. Based on the previously proposed paradigm that bacteria deal with environmental stress before they engage in biodegradation, we studied how the degradation of the PA herbicide 2-methyl-4-chlorophenoxyacetic acid (MCPA) by the model PA degrader Cupriavidus pinatubonensis AEO106 was affected by Cu exposure. RESULTS Exposure of C. pinatubonensis in batch culture to sublethal concentrations of Cu increased accumulation of ROS measured by the oxidant sensing probe 2,7-dichlorodihydrofluorescein diacetate and flow cytometry, and resulted in upregulation of a gene encoding a protein belong to the Ohr/OsmC protein family. The ohr/osmC gene was also highly induced by H2O2 exposure suggesting that it is involved in the oxidative stress response in C. pinatubonensis. The increased ROS accumulation and increased expression of the oxidative stress defense coincided with a delay in the catabolic performance, since both expression of the catabolic tfdA gene and MCPA mineralization were delayed compared to unexposed control cells. CONCLUSIONS The current study suggests that Cu-induced ROS accumulation in C. pinatubonensis activates a stress response involving the product of the ohr/osmC gene. Further, the stress response is launched before induction of the catabolic tfdA gene and mineralization occurs.
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Affiliation(s)
- Nanna Bygvraa Svenningsen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Mette Damgaard
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Maria Rasmussen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, San Joaquín, Santiago, Chile
| | - Ole Nybroe
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Mette Haubjerg Nicolaisen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark.
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Nikel PI, Pérez-Pantoja D, de Lorenzo V. Pyridine nucleotide transhydrogenases enable redox balance of Pseudomonas putida during biodegradation of aromatic compounds. Environ Microbiol 2016; 18:3565-3582. [PMID: 27348295 DOI: 10.1111/1462-2920.13434] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/23/2016] [Indexed: 11/26/2022]
Abstract
The metabolic versatility of the soil bacterium Pseudomonas putida is reflected by its ability to execute strong redox reactions (e.g., mono- and di-oxygenations) on aromatic substrates. Biodegradation of aromatics occurs via the pathway encoded in the archetypal TOL plasmid pWW0, yet the effect of running such oxidative route on redox balance against the background metabolism of P. putida remains unexplored. To answer this question, the activity of pyridine nucleotide transhydrogenases (that catalyze the reversible interconversion of NADH and NADPH) was inspected under various physiological and oxidative stress regimes. The genome of P. putida KT2440 encodes a soluble transhydrogenase (SthA) and a membrane-bound, proton-pumping counterpart (PntAB). Mutant strains, lacking sthA and/or pntAB, were subjected to a panoply of genetic, biochemical, phenomic and functional assays in cells grown on customary carbon sources (e.g., citrate) versus difficult-to-degrade aromatic substrates. The results consistently indicated that redox homeostasis is compromised in the transhydrogenases-defective variant, rendering the mutant sensitive to oxidants. This metabolic deficiency was, however, counteracted by an increase in the activity of NADP+ -dependent dehydrogenases in central carbon metabolism. Taken together, these observations demonstrate that transhydrogenases enable a redox-adjusting mechanism that comes into play when biodegradation reactions are executed to metabolize unusual carbon compounds.
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Affiliation(s)
- Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Danilo Pérez-Pantoja
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Concepción, 4030000 Concepción, Chile
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain.
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Akkaya Ö, Nikel PI, Pérez-Pantoja D, de Lorenzo V. DNA damage elicits a different SOS response in Pseudomonas putida and Escherichia coli. N Biotechnol 2016. [DOI: 10.1016/j.nbt.2016.06.1401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Kim J, Pérez-Pantoja D, Silva-Rocha R, Oliveros JC, de Lorenzo V. High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2. Environ Microbiol 2015; 18:3327-3341. [PMID: 26373670 DOI: 10.1111/1462-2920.13054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/30/2015] [Accepted: 09/12/2015] [Indexed: 11/28/2022]
Abstract
Pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the TOL plasmid pWW0 along with other chromosomally encoded activities. Tiling arrays of densely overlapping oligonucleotides were designed to cover every gene involved in this process, allowing dissection of operon structures and exposing the interplay of plasmid and chromosomal functions. All xyl sequences were transcribed in response to aromatic substrates and the 3'-termini of both upper and lower mRNA operons extended beyond their coding regions, i.e. the 3'-end of the lower operon mRNA penetrated into the convergent xylS regulatory gene. Furthermore, xylR mRNA for the master m-xylene responsive regulator of the system was decreased by aromatic substrates, while the cognate upper operon mRNA was evenly stable throughout its full length. RNA sequencing confirmed these data at a single nucleotide level and refined the formerly misannotated xylL sequence. The chromosomal ortho route for degradation of benzoate (the ben, cat clusters and some pca genes) was activated by this aromatic, but not by the TOL substrates, toluene or m-xylene. We advocate this scenario as a testbed of natural retroactivity between a pre-existing metabolic network and a new biochemical pathway implanted through gene transfer.
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Affiliation(s)
- Juhyun Kim
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Danilo Pérez-Pantoja
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Rafael Silva-Rocha
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Juan Carlos Oliveros
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain.
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Svenningsen NB, Pérez-Pantoja D, Nikel PI, Nicolaisen MH, de Lorenzo V, Nybroe O. Pseudomonas putida mt-2 tolerates reactive oxygen species generated during matric stress by inducing a major oxidative defense response. BMC Microbiol 2015; 15:202. [PMID: 26445482 PMCID: PMC4595014 DOI: 10.1186/s12866-015-0542-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 10/02/2015] [Indexed: 01/09/2023] Open
Abstract
Background Soil bacteria typically thrive in water-limited habitats that cause an inherent matric stress to the cognate cells. Matric stress gives rise to accumulation of intracellular reactive oxygen species (ROS), which in turn may induce oxidative stress, and even promote mutagenesis. However, little is known about the impact of ROS induced by water limitation on bacteria performing important processes as pollutant biodegradation in the environment. We have rigorously examined the physiological consequences of the rise of intracellular ROS caused by matric stress for the toluene- and xylene-degrading soil bacterium Pseudomonas putida mt-2. Methods For the current experiments, controlled matric potential stress was delivered to P. putida cells by addition of polyethylene glycol to liquid cultures, and ROS formation in individual cells monitored by a specific dye. The physiological response to ROS was then quantified by both RT-qPCR of RNA transcripts from genes accredited as proxies of oxidative stress and the SOS response along with cognate transcriptional GFP fusions to the promoters of the same genes. Results Extensive matric stress at −1.5 MPa clearly increased intracellular accumulation of ROS. The expression of the two major oxidative defense genes katA and ahpC, as well as the hydroperoxide resistance gene osmC, was induced under matric stress. Different induction profiles of the reporters were related to the severity of the stress. To determine if matric stress lead to induction of the SOS-response, we constructed a DNA damage-inducible bioreporter based on the LexA-controlled phage promoter PPP3901. According to bioreporter analysis, this gene was expressed during extensive matric stress. Despite this DNA-damage mediated gene induction, we observed no increase in the mutation frequency as monitored by emergence of rifampicin-resistant colonies. Conclusions Under conditions of extensive matric stress, we observed a direct link between matric stress, ROS formation, induction of ROS-detoxifying functions and (partial) activation of the SOS system. However, such a stress-response regime did not translate into a general DNA mutagenesis status. Taken together, the data suggest that P. putida mt-2 can cope with this archetypal environmental stress while preserving genome stability, a quality that strengthens the status of this bacterium for biotechnological purposes.
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Affiliation(s)
- Nanna B Svenningsen
- Department of Plant and Environmental Sciences, Section of Genetics and Microbiology, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
| | - Danilo Pérez-Pantoja
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/ Darwin 3, 28049, Madrid, Spain.
| | - Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/ Darwin 3, 28049, Madrid, Spain.
| | - Mette H Nicolaisen
- Department of Plant and Environmental Sciences, Section of Genetics and Microbiology, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/ Darwin 3, 28049, Madrid, Spain.
| | - Ole Nybroe
- Department of Plant and Environmental Sciences, Section of Genetics and Microbiology, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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Pérez-Pantoja D, Kim J, Silva-Rocha R, de Lorenzo V. The differential response of thePbenpromoter ofPseudomonas putida mt-2 to BenR and XylS prevents metabolic conflicts inm-xylene biodegradation. Environ Microbiol 2014; 17:64-75. [DOI: 10.1111/1462-2920.12443] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 02/13/2014] [Accepted: 02/21/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Danilo Pérez-Pantoja
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnologia; Madrid Spain
| | - Juhyun Kim
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnologia; Madrid Spain
| | - Rafael Silva-Rocha
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnologia; Madrid Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnologia; Madrid Spain
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Jiménez JI, Pérez-Pantoja D, Chavarría M, Díaz E, de Lorenzo V. A second chromosomal copy of thecatAgene endowsPseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environ Microbiol 2014; 16:1767-78. [DOI: 10.1111/1462-2920.12361] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 12/10/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Jose I. Jiménez
- Centro de Investigaciones Biológicas; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
- Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| | - Danilo Pérez-Pantoja
- Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| | - Max Chavarría
- Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| | - Eduardo Díaz
- Centro de Investigaciones Biológicas; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| | - Víctor de Lorenzo
- Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Nikel PI, Pérez-Pantoja D, de Lorenzo V. Why are chlorinated pollutants so difficult to degrade aerobically? Redox stress limits 1,3-dichloroprop-1-ene metabolism by Pseudomonas pavonaceae. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120377. [PMID: 23479756 DOI: 10.1098/rstb.2012.0377] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chlorinated pollutants are hardly biodegradable under oxic conditions, but they can often be metabolized by anaerobic bacteria through organohalide respiration reactions. In an attempt to identify bottlenecks limiting aerobic catabolism of 1,3-dichloroprop-1-ene (1,3-DCP; a widely used organohalide) in Pseudomonas pavonaceae, the possible physiological restrictions for this process were surveyed. Flow cytometry and a bioluminescence reporter of metabolic state revealed that cells treated with 1,3-DCP experienced an intense stress that could be traced to the endogenous production of reactive oxygen species (ROS) during the metabolism of the compound. Cells exposed to 1,3-DCP also manifested increased levels of D-glucose-6-P 1-dehydrogenase activity (G6PDH, an enzyme key to the synthesis of reduced NADPH), observed under both glycolytic and gluconeogenic growth regimes. The increase in G6PDH activity, as well as cellular hydroperoxide levels, correlated with the generation of ROS. Additionally, the high G6PDH activity was paralleled by the accumulation of D-glucose-6-P, suggesting a metabolic flux shift that favours the production of NADPH. Thus, G6PDH and its cognate substrate seem to play an important role in P. pavonaceae under redox stress caused by 1,3-DCP, probably by increasing the rate of NADPH turnover. The data suggest that oxidative stress associated with the biodegradation of 1,3-DCP reflects a significant barrier for the evolution of aerobic pathways for chlorinated compounds, thereby allowing for the emergence of anaerobic counterparts.
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Affiliation(s)
- Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid 28049, Spain
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Chavarría M, Nikel PI, Pérez-Pantoja D, de Lorenzo V. The Entner-Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress. Environ Microbiol 2013; 15:1772-85. [PMID: 23301697 DOI: 10.1111/1462-2920.12069] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 12/03/2012] [Accepted: 12/03/2012] [Indexed: 11/27/2022]
Abstract
Glucose catabolism of Pseudomonas putida is carried out exclusively through the Entner-Doudoroff (ED) pathway due to the absence of 6-phosphofructokinase. In order to activate the Embden-Meyerhof-Parnas (EMP) route we transferred the pfkA gene from Escherichia coli to a P. putida wild-type strain as well as to an eda mutant, i.e. lacking 2-keto-3-deoxy-6-phosphogluconate aldolase. PfkA(E. coli) failed to redirect the carbon flow from the ED route towards the EMP pathway, suggesting that ED was essential for sugar catabolism. The presence of PfkA(E. coli) was detrimental for growth, which could be traced to the reduction of ATP and NAD(P)H pools along with alteration of the NAD(P)H/NADP(+) ratio. Pseudomonas putida cells carrying PfkA(E. coli) became highly sensitive to diamide and hydrogen peroxide, the response to which is very demanding of NADPH. The inhibitory effect of PfkA(E. coli) could in part be relieved by methionine, the synthesis of which relies much on NADPH. These results expose the role of the ED pathway for generating the redox currency (NADPH) that is required for counteracting oxidative stress. It is thus likely that environmental bacteria that favour the ED pathway over the EMP pathway do so in order to gear their aerobic metabolism to endure oxidative-related insults.
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Affiliation(s)
- Max Chavarría
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología CNB-CSIC, 28049 Madrid, Spain
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Silva-Rocha R, Pérez-Pantoja D, de Lorenzo V. Decoding the genetic networks of environmental bacteria: regulatory moonlighting of the TOL system of Pseudomonas putida mt-2. ISME J 2012; 7:229-32. [PMID: 22895160 DOI: 10.1038/ismej.2012.98] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rafael Silva-Rocha
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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Pérez-Pantoja D, Donoso R, Agulló L, Córdova M, Seeger M, Pieper DH, González B. Genomic analysis of the potential for aromatic compounds biodegradation in Burkholderiales. Environ Microbiol 2011; 14:1091-117. [PMID: 22026719 DOI: 10.1111/j.1462-2920.2011.02613.x] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The relevance of the β-proteobacterial Burkholderiales order in the degradation of a vast array of aromatic compounds, including several priority pollutants, has been largely assumed. In this review, the presence and organization of genes encoding oxygenases involved in aromatics biodegradation in 80 Burkholderiales genomes is analysed. This genomic analysis underscores the impressive catabolic potential of this bacterial lineage, comprising nearly all of the central ring-cleavage pathways reported so far in bacteria and most of the peripheral pathways involved in channelling of a broad diversity of aromatic compounds. The more widespread pathways in Burkholderiales include protocatechuate ortho ring-cleavage, catechol ortho ring-cleavage, homogentisate ring-cleavage and phenylacetyl-CoA ring-cleavage pathways found in at least 60% of genomes analysed. In general, a genus-specific pattern of positional ordering of biodegradative genes is observed in the catabolic clusters of these pathways indicating recent events in its evolutionary history. In addition, a significant bias towards secondary chromosomes, now termed chromids, is observed in the distribution of catabolic genes across multipartite genomes, which is consistent with a genus-specific character. Strains isolated from environmental sources such as soil, rhizosphere, sediment or sludge show a higher content of catabolic genes in their genomes compared with strains isolated from human, animal or plant hosts, but no significant difference is found among Alcaligenaceae, Burkholderiaceae and Comamonadaceae families, indicating that habitat is more of a determinant than phylogenetic origin in shaping aromatic catabolic versatility.
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Affiliation(s)
- Danilo Pérez-Pantoja
- Center for Advanced Studies in Ecology and Biodiversity, Millennium Nucleus in Plant Functional Genomics, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Santiago, Chile
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Donoso RA, Pérez-Pantoja D, González B. Strict and direct transcriptional repression of thepobAgene by benzoate avoids 4-hydroxybenzoate degradation in the pollutant degrader bacteriumCupriavidus necatorJMP134. Environ Microbiol 2011; 13:1590-600. [DOI: 10.1111/j.1462-2920.2011.02470.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Lykidis A, Pérez-Pantoja D, Ledger T, Mavromatis K, Anderson IJ, Ivanova NN, Hooper SD, Lapidus A, Lucas S, González B, Kyrpides NC. The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader. PLoS One 2010; 5:e9729. [PMID: 20339589 PMCID: PMC2842291 DOI: 10.1371/journal.pone.0009729] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 02/17/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Cupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source. METHODOLOGY/PRINCIPAL FINDINGS Its genome consists of four replicons (two chromosomes and two plasmids) containing a total of 6631 protein coding genes. Comparative analysis identified 1910 core genes common to the four genomes compared (C. necator JMP134, C. necator H16, C. metallidurans CH34, R. solanacearum GMI1000). Although secondary chromosomes found in the Cupriavidus, Ralstonia, and Burkholderia lineages are all derived from plasmids, analyses of the plasmid partition proteins located on those chromosomes indicate that different plasmids gave rise to the secondary chromosomes in each lineage. The C. necator JMP134 genome contains 300 genes putatively involved in the catabolism of aromatic compounds and encodes most of the central ring-cleavage pathways. This strain also shows additional metabolic capabilities towards alicyclic compounds and the potential for catabolism of almost all proteinogenic amino acids. This remarkable catabolic potential seems to be sustained by a high degree of genetic redundancy, most probably enabling this catabolically versatile bacterium with different levels of metabolic responses and alternative regulation necessary to cope with a challenging environment. From the comparison of Cupriavidus genomes, it is possible to state that a broad metabolic capability is a general trait for Cupriavidus genus, however certain specialization towards a nutritional niche (xenobiotics degradation, chemolithoautotrophy or symbiotic nitrogen fixation) seems to be shaped mostly by the acquisition of "specialized" plasmids. CONCLUSIONS/SIGNIFICANCE The availability of the complete genome sequence for C. necator JMP134 provides the groundwork for further elucidation of the mechanisms and regulation of chloroaromatic compound biodegradation.
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Affiliation(s)
- Athanasios Lykidis
- Department of Energy (DOE)-Joint Genome Institute, Walnut Creek, California, United States of America.
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Pérez-Pantoja D, Donoso RA, Sánchez MA, González B. Genuine genetic redundancy in maleylacetate-reductase-encoding genes involved in degradation of haloaromatic compounds by Cupriavidus necator JMP134. Microbiology (Reading) 2009; 155:3641-3651. [DOI: 10.1099/mic.0.032086-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Maleylacetate reductases (MAR) are required for biodegradation of several substituted aromatic compounds. To date, the functionality of two MAR-encoding genes (tfdF
I and tfdF
II) has been reported in Cupriavidus necator JMP134(pJP4), a known degrader of aromatic compounds. These two genes are located in tfd gene clusters involved in the turnover of 2,4-dichlorophenoxyacetate (2,4-D) and 3-chlorobenzoate (3-CB). The C. necator JMP134 genome comprises at least three other genes that putatively encode MAR (tcpD, hqoD and hxqD), but confirmation of their functionality and their role in the catabolism of haloaromatic compounds has not been assessed. RT-PCR expression analyses of C. necator JMP134 cells exposed to 2,4-D, 3-CB, 2,4,6-trichlorophenol (2,4,6-TCP) or 4-fluorobenzoate (4-FB) showed that tfdF
I and tfdF
II are induced by haloaromatics channelled to halocatechols as intermediates. In contrast, 2,4,6-TCP only induces tcpD, and any haloaromatic compounds tested did not induce hxqD and hqoD. However, the tcpD, hxqD and hqoD gene products showed MAR activity in cell extracts and provided the MAR function for 2,4-D catabolism when heterologously expressed in MAR-lacking strains. Growth tests for mutants of the five MAR-encoding genes in strain JMP134 showed that none of these genes is essential for degradation of the tested compounds. However, the role of tfdF
I/tfdF
II and tcpD genes in the expression of MAR activity during catabolism of 2,4-D and 2,4,6-TCP, respectively, was confirmed by enzyme activity tests in mutants. These results reveal a striking example of genetic redundancy in the degradation of aromatic compounds.
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Affiliation(s)
- Danilo Pérez-Pantoja
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Millennium Nucleus on Microbial Ecology and Environmental Microbiology and Biotechnology, NM-EMBA, Center for Advanced Studies in Ecology and Biodiversity, CASEB, Santiago, Chile
| | - Raúl A. Donoso
- Facultad de Ingeniería y Ciencia, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Miguel A. Sánchez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Millennium Nucleus on Microbial Ecology and Environmental Microbiology and Biotechnology, NM-EMBA, Center for Advanced Studies in Ecology and Biodiversity, CASEB, Santiago, Chile
| | - Bernardo González
- Facultad de Ingeniería y Ciencia, Universidad Adolfo Ibáñez, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, P. Universidad Católica de Chile, Millennium Nucleus on Microbial Ecology and Environmental Microbiology and Biotechnology, NM-EMBA, Center for Advanced Studies in Ecology and Biodiversity, CASEB, Santiago, Chile
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Pérez-Pantoja D, De la Iglesia R, Pieper DH, González B. Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacteriumCupriavidus necatorJMP134. FEMS Microbiol Rev 2008; 32:736-94. [DOI: 10.1111/j.1574-6976.2008.00122.x] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Trefault N, De la Iglesia R, Molina AM, Manzano M, Ledger T, Pérez-Pantoja D, Sánchez MA, Stuardo M, González B. Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways. Environ Microbiol 2004; 6:655-68. [PMID: 15186344 DOI: 10.1111/j.1462-2920.2004.00596.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ralstonia eutropha JMP134 (pJP4) is a useful model for the study of bacterial degradation of substituted aromatic pollutants. Several key degrading capabilities, encoded by tfd genes, are located in the 88 kb, self-transmissible, IncP-1 beta plasmid pJP4. The complete sequence of the 87,688 nucleotides of pJP4, encoding 83 open reading frames (ORFs), is reported. Most of the coding sequence corresponds to a well-conserved IncP-1 beta backbone and the previously reported tfd genes. In addition, we found hypothetical proteins putatively involved in the transport of aromatic compounds and short-chain fatty acid oxidation. ORFs related to mobile elements, including the Tn501-encoded mercury resistance determinants, an IS1071-based composite transposon and a cryptic class II transposon, are also present in pJP4. These mobile elements are inefficient in transposition and are located in two regions of pJP4 that are rich in remnants of lateral gene transfer events. pJP4 plasmid was able to capture chromosomal genes and form hybrid plasmids with the IncP-1 alpha plasmid RP4. These observations are integrated into a model for the evolution of pJP4, which reveals mechanisms of bacterial adaptation to degrade pollutants.
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MESH Headings
- Adaptation, Physiological
- Base Composition
- Biodegradation, Environmental
- Cupriavidus necator/genetics
- Cupriavidus necator/metabolism
- DNA Transposable Elements
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- Drug Resistance, Bacterial/genetics
- Environmental Pollutants/metabolism
- Gene Order
- Gene Transfer, Horizontal
- Genes, Bacterial
- Hydrocarbons, Aromatic/metabolism
- Mercury Compounds/toxicity
- Molecular Sequence Data
- Open Reading Frames
- Operon
- Plasmids/genetics
- Recombination, Genetic
- Sequence Analysis, DNA
- Transcription, Genetic
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Affiliation(s)
- N Trefault
- Laboratorio de Microbiología, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, and Millennium Institute for Fundamental and Applied Biology, Santiago, Chile
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Pérez-Pantoja D, Ledger T, Pieper DH, González B. Efficient turnover of chlorocatechols is essential for growth of Ralstonia eutropha JMP134(pJP4) in 3-chlorobenzoic acid. J Bacteriol 2003; 185:1534-42. [PMID: 12591870 PMCID: PMC148064 DOI: 10.1128/jb.185.5.1534-1542.2003] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ralstonia eutropha JMP134(pJP4) degrades 3-chlorobenzoate (3-CB) by using two not completely isofunctional, pJP4-encoded chlorocatechol degradation gene clusters, tfdC(I)D(I)E(I)F(I) and tfdD(II)C(II)E(II)F(II). Introduction of several copies of each gene cluster into R. eutropha JMP222, which lacks pJP4 and thus accumulates chlorocatechols from 3-CB, allows the derivatives to grow in this substrate. However, JMP222 derivatives containing one chromosomal copy of each cluster did not grow in 3-CB. The failure to grow in 3-CB was the result of accumulation of chlorocatechols due to the limiting activity of chlorocatechol 1,2-dioxygenase (TfdC), the first enzyme in the chlorocatechol degradation pathway. Micromolar concentrations of 3- and 4-chlorocatechol inhibited the growth of strains JMP134 and JMP222 in benzoate, and cells of strain JMP222 exposed to 3 mM 3-CB exhibited a 2-order-of-magnitude decrease in viability. This toxicity effect was not observed with strain JMP222 harboring multiple copies of the tfdC(I) gene, and the derivative of strain JMP222 containing tfdC(I)D(I)E(I)F(I) plus multiple copies of the tfdC(I) gene could efficiently grow in 3-CB. In addition, tfdC(I) and tfdC(II) gene mutants of strain JMP134 exhibited no growth and impaired growth in 3-CB, respectively. The introduction into strain JMP134 of the xylS-xylXYZL genes, encoding a broad-substrate-range benzoate 1,2-dioxygenase system and thus increasing the transformation of 3-CB into chlorocatechols, resulted in derivatives that exhibited a sharp decrease in the ability to grow in 3-CB. These observations indicate that the dosage of chlorocatechol-transforming genes is critical for growth in 3-CB. This effect depends on a delicate balance between chlorocatechol-producing and chlorocatechol-consuming reactions.
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Affiliation(s)
- D Pérez-Pantoja
- Laboratorio de Microbiología, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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Ledger T, Pieper DH, Pérez-Pantoja D, González B. Novel insights into the interplay between peripheral reactions encoded by xyl genes and the chlorocatechol pathway encoded by tfd genes for the degradation of chlorobenzoates by Ralstonia eutropha JMP134. Microbiology (Reading) 2002; 148:3431-3440. [PMID: 12427935 DOI: 10.1099/00221287-148-11-3431] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Many bacteria can grow on chloroaromatic pollutants because they can transform them into chlorocatechols, which are further degraded by enzymes of a specialized ortho-cleavage pathway. Ralstonia eutropha JMP134 is able to grow on 3-chlorobenzoate by using two pJP4-encoded, ortho-cleavage chlorocatechol degradation gene clusters (tfdC(I)D(I)E(I)F(I) and tfdD(II)C(II)E(II)F(II)). Very little is known about the acquisition of new catabolic genes encoding enzymes that lead to the formation of chlorocatechols in R. eutropha JMP134. The effect on the catabolic properties of an R. eutropha JMP134 derivative that received the xylS-xylXYZL gene module, encoding the xylS-regulated expression of the broad-substrate-range toluate 1,2-dioxygenase (xylXYZ) and the 1,2-dihydro-1,2-dihydroxytoluate dehydrogenase (xylL) from pWW0, which allows the transformation of 4-chlorobenzoate into 4-chlorocatechol, was studied. Such a derivative could efficiently grow on 4-chlorobenzoate. Unexpectedly, this derivative also grew on 3,5-dichlorobenzoate, a substrate for XylXYZL but not an inducer of the XylS regulatory protein. The ability to grow on 4-chlorobenzoate or 3,5-dichlorobenzoate was also observed in derivatives of strain JMP134 containing the xyl gene module but lacking xylS, indicating the presence of an xylS-like element in R. eutropha with an inducer profile different from that of the pWW0-encoded regulator. Growth on 4-chlorobenzoate was also observed after introduction of the xyl gene module into strain JMP222, a JMP134 derivative lacking pJP4, but only if multiple copies of tfdC(I)D(I)E(I)F(I) or tfdD(II)C(II)E(II)F(II) were present. However, only the derivative containing multiple copies of tfdD(II)C(II)E(II)F(II) was able to grow on 3,5-dichlorobenzoate. These observations indicate that although the acquisition of new catabolic genes actually enhances the catabolic abilities of R. eutropha JMP134, these new properties are strongly influenced by the dosage of the tfd genes, the presence of a chromosomal xylS-like regulatory element and the different contributions of the tfd gene clusters.
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Affiliation(s)
- Thomas Ledger
- Laboratorio de Microbiologı́a, Departamento de Genética Molecular y Microbiologı́a, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D Santiago, Chile1
| | - Dietmar H Pieper
- Division of Microbiology, National Research Centre for Biotechnology - GBF, Braunschweig, Germany2
| | - Danilo Pérez-Pantoja
- Laboratorio de Microbiologı́a, Departamento de Genética Molecular y Microbiologı́a, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D Santiago, Chile1
| | - Bernardo González
- Laboratorio de Microbiologı́a, Departamento de Genética Molecular y Microbiologı́a, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D Santiago, Chile1
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Plumeier I, Pérez-Pantoja D, Heim S, González B, Pieper DH. Importance of different tfd genes for degradation of chloroaromatics by Ralstonia eutropha JMP134. J Bacteriol 2002; 184:4054-64. [PMID: 12107121 PMCID: PMC135226 DOI: 10.1128/jb.184.15.4054-4064.2002] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The tfdC(I)D(I)E(I)F(I,) and tfdD(II)C(II)E(II)F(II) gene modules of plasmid pJP4 of Ralstonia eutropha JMP134 encode complete sets of functional enzymes for the transformation of chlorocatechols into 3-oxoadipate, which are all expressed during growth on 2,4-dichlorophenoxyacetate (2,4-D). However, activity of tfd(I)-encoded enzymes was usually higher than that of tfd(II)-encoded enzymes, both in the wild-type strain grown on 2,4-D and in 3-chlorobenzoate-grown derivatives harboring only one tfd gene module. The tfdD(II)-encoded chloromuconate cycloisomerase exhibited special kinetic properties, with high activity against 3-chloromuconate and poor activity against 2-chloromuconate and unsubstituted muconate, thus explaining the different phenotypic behaviors of R. eutropha strains containing different tfd gene modules. The enzyme catalyzes the formation of an equilibrium between 2-chloromuconate and 5-chloro- and 2-chloromuconolactone and very inefficiently catalyzes dehalogenation to form trans-dienelactone as the major product, thus differing from all (chloro)muconate cycloisomerases described thus far.
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Affiliation(s)
- Iris Plumeier
- Department of Environmental Biotechnology, GBF-German Research Center for Biotechnology, D-38124 Braunschweig, Germany
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Pérez-Pantoja D, Guzmán L, Manzano M, Pieper DH, González B. Role of tfdC(I)D(I)E(I)F(I) and tfdD(II)C(II)E(II)F(II) gene modules in catabolism of 3-chlorobenzoate by Ralstonia eutropha JMP134(pJP4). Appl Environ Microbiol 2000; 66:1602-8. [PMID: 10742248 PMCID: PMC92029 DOI: 10.1128/aem.66.4.1602-1608.2000] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The enzymes chlorocatechol-1,2-dioxygenase, chloromuconate cycloisomerase, dienelactone hydrolase, and maleylacetate reductase allow Ralstonia eutropha JMP134(pJP4) to degrade chlorocatechols formed during growth in 2,4-dichlorophenoxyacetate or 3-chlorobenzoate (3-CB). There are two gene modules located in plasmid pJP4, tfdC(I)D(I)E(I)F(I) (module I) and tfdD(II)C(II)E(II)F(II) (module II), putatively encoding these enzymes. To assess the role of both tfd modules in the degradation of chloroaromatics, each module was cloned into the medium-copy-number plasmid vector pBBR1MCS-2 under the control of the tfdR regulatory gene. These constructs were introduced into R. eutropha JMP222 (a JMP134 derivative lacking pJP4) and Pseudomonas putida KT2442, two strains able to transform 3-CB into chlorocatechols. Specific activities in cell extracts of chlorocatechol-1,2-dioxygenase (tfdC), chloromuconate cycloisomerase (tfdD), and dienelactone hydrolase (tfdE) were 2 to 50 times higher for microorganisms containing module I compared to those containing module II. In contrast, a significantly (50-fold) higher activity of maleylacetate reductase (tfdF) was observed in cell extracts of microorganisms containing module II compared to module I. The R. eutropha JMP222 derivative containing tfdR-tfdC(I)D(I)E(I)F(I) grew four times faster in liquid cultures with 3-CB as a sole carbon and energy source than in cultures containing tfdR-tfdD(II)C(II)E(II)F(II). In the case of P. putida KT2442, only the derivative containing module I was able to grow in liquid cultures of 3-CB. These results indicate that efficient degradation of 3-CB by R. eutropha JMP134(pJP4) requires the two tfd modules such that TfdCDE is likely supplied primarily by module I, while TfdF is likely supplied by module II.
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Affiliation(s)
- D Pérez-Pantoja
- Laboratorio de Microbiología, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
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