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Ortega Ramírez CA, Ching T, Yoza B, Li QX. Glycerol-assisted degradation of dibenzothiophene by Paraburkholderia sp. C3 is associated with polyhydroxyalkanoate granulation. CHEMOSPHERE 2022; 291:133054. [PMID: 34838841 DOI: 10.1016/j.chemosphere.2021.133054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/06/2021] [Accepted: 11/22/2021] [Indexed: 05/28/2023]
Abstract
Glycerol is a biodiesel byproduct. In the present study, glycerol was used as a co-substrate during biodegradation of dibenzothiophene (DBT) by Paraburkholderia sp. C3. Polycyclic aromatic hydrocarbons (PAHs) are a group of persistent, ubiquitous and carcinogenic chemicals found in the environment. DBT is a major sulfur-containing PAH. The chemical properties of DBT make it an ideal model pollutant for examining the bioremediation of higher molecular weight PAHs. Bioremediation uses microbial catalysis for removal of environmental pollutants. Environmental microorganisms that encounter aromatic substrates such as heterocyclic PAHs develop unique characteristics that allow the uptake and assimilation of these cytotoxic substrates. Microbial adaptations include changes in membrane lipid composition, secretion of surface-active compounds and accumulation of lipid granules to withstand chemical toxicity. Biostimulation using more readily metabolized substrates can increase the biodegradation rate of PAHs, but the molecular mechanisms are not well understood. We analyzed the DBT biodegradation kinetics in C3, proteome changes and TEM micrographs in different culturing conditions. We utilized 2-bromoalkanoic lipid metabolic inhibitors to establish a correlation between polyhydroxyalkanoate (PHA) granule formation and the enhancement of DBT biodegradation induced by glycerol. This is the first description linking PHA biosynthesis, DBT biodegradation and 2-bromoalkanoic acids in a Paraburkholderia species.
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Affiliation(s)
- Camila A Ortega Ramírez
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Travers Ching
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Brandon Yoza
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA.
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Kukurugya MA, Mendonca CM, Solhtalab M, Wilkes RA, Thannhauser TW, Aristilde L. Multi-omics analysis unravels a segregated metabolic flux network that tunes co-utilization of sugar and aromatic carbons in Pseudomonas putida. J Biol Chem 2019; 294:8464-8479. [PMID: 30936206 DOI: 10.1074/jbc.ra119.007885] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/26/2019] [Indexed: 11/06/2022] Open
Abstract
Pseudomonas species thrive in different nutritional environments and can catabolize divergent carbon substrates. These capabilities have important implications for the role of these species in natural and engineered carbon processing. However, the metabolic phenotypes enabling Pseudomonas to utilize mixed substrates remain poorly understood. Here, we employed a multi-omics approach involving stable isotope tracers, metabolomics, fluxomics, and proteomics in Pseudomonas putida KT2440 to investigate the constitutive metabolic network that achieves co-utilization of glucose and benzoate, respectively a monomer of carbohydrate polymers and a derivative of lignin monomers. Despite nearly equal consumption of both substrates, metabolite isotopologues revealed nonuniform assimilation throughout the metabolic network. Gluconeogenic flux of benzoate-derived carbons from the tricarboxylic acid cycle did not reach the upper Embden-Meyerhof-Parnas pathway nor the pentose-phosphate pathway. These latter two pathways were populated exclusively by glucose-derived carbons through a cyclic connection with the Entner-Doudoroff pathway. We integrated the 13C-metabolomics data with physiological parameters for quantitative flux analysis, demonstrating that the metabolic segregation of the substrate carbons optimally sustained biosynthetic flux demands and redox balance. Changes in protein abundance partially predicted the metabolic flux changes in cells grown on the glucose:benzoate mixture versus on glucose alone. Notably, flux magnitude and directionality were also maintained by metabolite levels and regulation of phosphorylation of key metabolic enzymes. These findings provide new insights into the metabolic architecture that affords adaptability of P. putida to divergent carbon substrates and highlight regulatory points at different metabolic nodes that may underlie the high nutritional flexibility of Pseudomonas species.
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Affiliation(s)
- Matthew A Kukurugya
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Caroll M Mendonca
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Mina Solhtalab
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Rebecca A Wilkes
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
| | | | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States.
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Cloning and characterisation of four catA genes located on the chromosome and large plasmid of Pseudomonas putida ND6. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Kohlstedt M, Starck S, Barton N, Stolzenberger J, Selzer M, Mehlmann K, Schneider R, Pleissner D, Rinkel J, Dickschat JS, Venus J, B.J.H. van Duuren J, Wittmann C. From lignin to nylon: Cascaded chemical and biochemical conversion using metabolically engineered Pseudomonas putida. Metab Eng 2018; 47:279-293. [DOI: 10.1016/j.ymben.2018.03.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/02/2018] [Accepted: 03/04/2018] [Indexed: 12/31/2022]
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Jõesaar M, Viggor S, Heinaru E, Naanuri E, Mehike M, Leito I, Heinaru A. Strategy of Pseudomonas pseudoalcaligenes C70 for effective degradation of phenol and salicylate. PLoS One 2017; 12:e0173180. [PMID: 28257519 PMCID: PMC5336314 DOI: 10.1371/journal.pone.0173180] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/16/2017] [Indexed: 01/08/2023] Open
Abstract
Phenol- and naphthalene-degrading indigenous Pseudomonas pseudoalcaligenes strain C70 has great potential for the bioremediation of polluted areas. It harbours two chromosomally located catechol meta pathways, one of which is structurally and phylogenetically very similar to the Pseudomonas sp. CF600 dmp operon and the other to the P. stutzeri AN10 nah lower operon. The key enzymes of the catechol meta pathway, catechol 2,3-dioxygenase (C23O) from strain C70, PheB and NahH, have an amino acid identity of 85%. The metabolic and regulatory phenotypes of the wild-type and the mutant strain C70ΔpheB lacking pheB were evaluated. qRT-PCR data showed that in C70, the expression of pheB- and nahH-encoded C23O was induced by phenol and salicylate, respectively. We demonstrate that strain C70 is more effective in the degradation of phenol and salicylate, especially at higher substrate concentrations, when these compounds are present as a mixture; i.e., when both pathways are expressed. Moreover, NahH is able to substitute for the deleted PheB in phenol degradation when salicylate is also present in the growth medium. The appearance of a yellow intermediate 2-hydroxymuconic semialdehyde was followed by the accumulation of catechol in salicylate-containing growth medium, and lower expression levels and specific activities of the C23O of the sal operon were detected. However, the excretion of the toxic intermediate catechol to the growth medium was avoided when the growth medium was supplemented with phenol, seemingly due to the contribution of the second meta pathway encoded by the phe genes.
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Affiliation(s)
- Merike Jõesaar
- Institute of Molecular and Cell Biology, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Signe Viggor
- Institute of Molecular and Cell Biology, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Eeva Heinaru
- Institute of Molecular and Cell Biology, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Eve Naanuri
- Institute of Molecular and Cell Biology, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Maris Mehike
- Institute of Molecular and Cell Biology, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Ivo Leito
- Institute of Chemistry, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Ain Heinaru
- Institute of Molecular and Cell Biology, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
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Dueholm MS, Marques IG, Karst SM, D'Imperio S, Tale VP, Lewis D, Nielsen PH, Nielsen JL. Survival and activity of individual bioaugmentation strains. BIORESOURCE TECHNOLOGY 2015; 186:192-199. [PMID: 25817029 DOI: 10.1016/j.biortech.2015.02.111] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/25/2015] [Accepted: 02/27/2015] [Indexed: 06/04/2023]
Abstract
Successful application of bioaugmentation for enhanced degradation of environmental pollutants is often limited by the lack of methods to monitor the survival and activity of individual bioaugmentation strains. However, recent advancements in sequencing technologies and molecular techniques now allow us to address these limitations. Here a complementing set of general applicable molecular methods are presented that provides detailed information on the performance of individual bioaugmentation strains under in situ conditions. The approach involves genome sequencing to establish highly specific qPCR and RT-qPCR tools for cell enumerations and expression of involved genes, stable isotope probing to follow growth on the target compounds and GFP-tagging to visualize the bioaugmentation strains directly in samples, all in combination with removal studies of the target compounds. The concept of the approach is demonstrated through a case study involving degradation of aromatic hydrocarbons in activated sludge augmented with the bioaugmentation strain Pseudomonas monteilii SB3078.
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Affiliation(s)
- Morten S Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Irina G Marques
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Søren M Karst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Seth D'Imperio
- Novozymes Biologicals, Inc., 5400 Corporate Circle, Salem, VA 24153, United States
| | - Vaibhav P Tale
- Novozymes Biologicals, Inc., 5400 Corporate Circle, Salem, VA 24153, United States
| | - Derrick Lewis
- Novozymes Biologicals, Inc., 5400 Corporate Circle, Salem, VA 24153, United States
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark
| | - Jeppe Lund Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark.
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Boyd DR, Sharma ND, Berberian MV, Cleij M, Hardacre C, Ljubez V, McConville G, Stevenson PJ, Kulakov LA, Allen CCR. Arenecis-Diol Dehydrogenase-Catalysed Regio- and Stereoselective Oxidation of Arene-, Cycloalkane- and Cycloalkene-cis-diols to Yield Catechols and Chiral α-Ketols. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500189] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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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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