101
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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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102
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Batista MB, Teixeira CS, Sfeir MZT, Alves LPS, Valdameri G, Pedrosa FDO, Sassaki GL, Steffens MBR, de Souza EM, Dixon R, Müller-Santos M. PHB Biosynthesis Counteracts Redox Stress in Herbaspirillum seropedicae. Front Microbiol 2018; 9:472. [PMID: 29599762 PMCID: PMC5862806 DOI: 10.3389/fmicb.2018.00472] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 02/28/2018] [Indexed: 11/25/2022] Open
Abstract
The ability of bacteria to produce polyhydroxyalkanoates such as poly(3-hydroxybutyrate) (PHB) enables provision of a carbon storage molecule that can be mobilized under demanding physiological conditions. However, the precise function of PHB in cellular metabolism has not been clearly defined. In order to determine the impact of PHB production on global physiology, we have characterized the properties of a ΔphaC1 mutant strain of the diazotrophic bacterium Herbaspirillum seropedicae. The absence of PHB in the mutant strain not only perturbs redox balance and increases oxidative stress, but also influences the activity of the redox-sensing Fnr transcription regulators, resulting in significant changes in expression of the cytochrome c-branch of the electron transport chain. The synthesis of PHB is itself dependent on the Fnr1 and Fnr3 proteins resulting in a cyclic dependency that couples synthesis of PHB with redox regulation. Transcriptional profiling of the ΔphaC1 mutant reveals that the loss of PHB synthesis affects the expression of many genes, including approximately 30% of the Fnr regulon.
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Affiliation(s)
- Marcelo B Batista
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil.,Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Cícero S Teixeira
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Michelle Z T Sfeir
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Luis P S Alves
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Glaucio Valdameri
- Department of Clinical Analysis, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Guilherme L Sassaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria B R Steffens
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Emanuel M de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Marcelo Müller-Santos
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
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103
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Keohane CE, Steele AD, Fetzer C, Khowsathit J, Tyne DV, Moynié L, Gilmore MS, Karanicolas J, Sieber SA, Wuest WM. Promysalin Elicits Species-Selective Inhibition of Pseudomonas aeruginosa by Targeting Succinate Dehydrogenase. J Am Chem Soc 2018; 140:1774-1782. [PMID: 29300464 PMCID: PMC5869686 DOI: 10.1021/jacs.7b11212] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products have served as an inspiration to scientists both for their complex three-dimensional architecture and exquisite biological activity. Promysalin is one such Pseudomonad secondary metabolite that exhibits narrow-spectrum antibacterial activity, originally isolated from the rhizosphere. We herein utilize affinity-based protein profiling (AfBPP) to identify succinate dehydrogenase (Sdh) as the biological target of the natural product. The target was further validated in silico, in vitro, in vivo, and through the selection, and sequencing, of a resistant mutant. Succinate dehydrogenase plays an essential role in primary metabolism of Pseudomonas aeruginosa as the only enzyme that is involved both in the tricarboxylic acid cycle (TCA) and in respiration via the electron transport chain. These findings add credence to other studies that suggest that the TCA cycle is an understudied target in the development of novel therapeutics to combat P. aeruginosa, a significant pathogen in clinical settings.
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Affiliation(s)
- Colleen E. Keohane
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Andrew D. Steele
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Christian Fetzer
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Jittasak Khowsathit
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Daria Van Tyne
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02115, United States
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Lucile Moynié
- Division of Structural Biology, The University of Oxford, Headington Oxford, OX3 7BN, United Kingdom
- Biomedical Sciences Research Complex, University of St. Andrews, Fife Scotland, KY16 9ST, United Kingdom
| | - Michael S. Gilmore
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02115, United States
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - John Karanicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, United States
| | - Stephan A. Sieber
- Department of Chemistry, Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - William M. Wuest
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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104
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Nikel PI, de Lorenzo V. Assessing Carbon Source-Dependent Phenotypic Variability in Pseudomonas putida. Methods Mol Biol 2018; 1745:287-301. [PMID: 29476475 DOI: 10.1007/978-1-4939-7680-5_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The soil bacterium Pseudomonas putida is rapidly becoming a platform of choice for applications that require a microbial host highly resistant to different types of stresses and elevated rates of reducing power regeneration. P. putida is capable of growing in a wide variety of carbon sources that range from simple sugars to complex substrates such as aromatic compounds. Interestingly, the growth of the reference strain KT2440 on glycerol as the sole carbon source is characterized by a prolonged lag phase, not observed with other carbon substrates. This macroscopic phenomenon has been shown to be connected with the stochastic expression of the glp genes, which encode the enzymes needed for glycerol processing. In this protocol, we propose a general procedure to examine bacterial growth in small-scale cultures while monitoring the metabolic activity of individual cells. Assessing the metabolic capacity of single bacteria by means of fluorescence microscopy and flow cytometry, in combination with the analysis of the temporal takeoff of growth in single-cell cultures, is a simple and easy-to-implement approach. It can help to understand the link between macroscopic phenotypes (e.g., microbial growth in batch cultures) and stochastic phenomena at the genetic level. The implementation of these methodologies revealed that the adoption of a glycerol-metabolizing regime by P. putida KT2440 is not the result of a gradual change in the whole population, but it rather reflects a time-dependent bimodal switch between metabolically inactive (i.e., not growing) to fully active (i.e., growing) bacteria.
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Affiliation(s)
- Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
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105
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Dvořák P, Nikel PI, Damborský J, de Lorenzo V. Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol Adv 2017; 35:845-866. [DOI: 10.1016/j.biotechadv.2017.08.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 01/07/2023]
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106
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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] [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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107
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Yu S, Lai B, Plan MR, Hodson MP, Lestari EA, Song H, Krömer JO. Improved performance ofPseudomonas putidain a bioelectrochemical system through overexpression of periplasmic glucose dehydrogenase. Biotechnol Bioeng 2017; 115:145-155. [DOI: 10.1002/bit.26433] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/21/2017] [Accepted: 08/23/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Shiqin Yu
- Centre for Microbial Electrochemical Systems (CEMES); The University of Queensland; St Lucia Brisbane Australia
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane Australia
| | - Bin Lai
- Centre for Microbial Electrochemical Systems (CEMES); The University of Queensland; St Lucia Brisbane Australia
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane Australia
- Systems Biotechnology Group, Department for Solar Materials (SOMA); Helmholtz Centre for Environmental Research UFZ; Leipzig Germany
| | - Manuel R. Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN); The University of Queensland; St Lucia Brisbane Australia
- Metabolomics Australia (Queensland Node); The University of Queensland; St Lucia Brisbane Australia
| | - Mark P. Hodson
- Australian Institute for Bioengineering and Nanotechnology (AIBN); The University of Queensland; St Lucia Brisbane Australia
- Metabolomics Australia (Queensland Node); The University of Queensland; St Lucia Brisbane Australia
| | - Endah A. Lestari
- School of Chemical and Molecular Biosciences; The University of Queensland; St Lucia Brisbane Australia
| | - Hao Song
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering & Technology, and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin University; Tianjin China
| | - Jens O. Krömer
- Centre for Microbial Electrochemical Systems (CEMES); The University of Queensland; St Lucia Brisbane Australia
- Advanced Water Management Centre (AWMC); The University of Queensland; St Lucia Brisbane Australia
- Systems Biotechnology Group, Department for Solar Materials (SOMA); Helmholtz Centre for Environmental Research UFZ; Leipzig Germany
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108
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Martínez-García E, de Lorenzo V. Molecular tools and emerging strategies for deep genetic/genomic refactoring of Pseudomonas. Curr Opin Biotechnol 2017; 47:120-132. [DOI: 10.1016/j.copbio.2017.06.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/19/2017] [Indexed: 11/26/2022]
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109
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Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis. Essays Biochem 2017; 60:303-313. [PMID: 27903818 PMCID: PMC5264504 DOI: 10.1042/ebc20160015] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 07/24/2016] [Accepted: 08/05/2016] [Indexed: 12/14/2022]
Abstract
The chassis is the cellular host used as a recipient of engineered biological systems in synthetic biology. They are required to propagate the genetic information and to express the genes encoded in it. Despite being an essential element for the appropriate function of genetic circuits, the chassis is rarely considered in their design phase. Consequently, the circuits are transferred to model organisms commonly used in the laboratory, such as Escherichia coli, that may be suboptimal for a required function. In this review, we discuss some of the properties desirable in a versatile chassis and summarize some examples of alternative hosts for synthetic biology amenable for engineering. These properties include a suitable life style, a robust cell wall, good knowledge of its regulatory network as well as of the interplay of the host components with the exogenous circuits, and the possibility of developing whole-cell models and tuneable metabolic fluxes that could allow a better distribution of cellular resources (metabolites, ATP, nucleotides, amino acids, transcriptional and translational machinery). We highlight Pseudomonas putida, widely used in many different biotechnological applications as a prominent organism for synthetic biology due to its metabolic diversity, robustness and ease of manipulation.
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110
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Sánchez-Pascuala A, de Lorenzo V, Nikel PI. Refactoring the Embden-Meyerhof-Parnas Pathway as a Whole of Portable GlucoBricks for Implantation of Glycolytic Modules in Gram-Negative Bacteria. ACS Synth Biol 2017; 6:793-805. [PMID: 28121421 PMCID: PMC5440799 DOI: 10.1021/acssynbio.6b00230] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The
Embden–Meyerhof–Parnas (EMP) pathway is generally
considered to be the biochemical standard for glucose catabolism.
Alas, its native genomic organization and the control of gene expression
in Escherichia coli are both very intricate, which
limits the portability of the EMP pathway to other biotechnologically
important bacterial hosts that lack the route. In this work, the genes
encoding all the enzymes of the linear EMP route have been individually
recruited from the genome of E. coli K-12, edited in silico to remove their endogenous regulatory signals,
and synthesized de novo following a standard (GlucoBrick)
that enables their grouping in the form of functional modules at the
user’s will. After verifying their activity in several glycolytic
mutants of E. coli, the versatility of these
GlucoBricks was demonstrated in quantitative physiology tests and
biochemical assays carried out in Pseudomonas putida KT2440 and P. aeruginosa PAO1 as the heterologous
hosts. Specific configurations of GlucoBricks were also adopted to
streamline the downward circulation of carbon from hexoses to pyruvate
in E. coli recombinants, thereby resulting in
a 3-fold increase of poly(3-hydroxybutyrate) synthesis from glucose.
Refactoring whole metabolic blocks in the fashion described in this
work thus eases the engineering of biochemical processes where the
optimization of carbon traffic is facilitated by the operation of
the EMP pathway—which yields more ATP than other glycolytic
routes such as the Entner–Doudoroff pathway.
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Affiliation(s)
- Alberto Sánchez-Pascuala
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Pablo I. Nikel
- Systems and Synthetic Biology
Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
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111
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Isolation of Pseudomonas fluorescens species highly resistant to pentachlorobenzene. Folia Microbiol (Praha) 2017; 62:325-334. [PMID: 28188482 DOI: 10.1007/s12223-017-0501-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 01/26/2017] [Indexed: 10/20/2022]
Abstract
Polychlorinated aromatic compounds, including pentachlorobenzenes and hexachlorobenzenes, are recalcitrant industrial pollutants that cause adverse effects on living cells. In this paper, the isolation of Pseudomonas fluorescens species with high resistance to pentachlorobenzene (PeCB) is reported. It was found that, in contrast to its slightly negative effect on P. fluorescens growth, PeCB readily inhibited the cell growth of Serratia spp. and Escherichia coli strains, thus indicating that inhibition of bacterial growth by PeCB is species-dependent. Analysis of a P. fluorescens isolate revealed that the exposure to PeCB induced production of reactive oxygen species and led to an increase in the level of alkyl hydroperoxide reductase C (AhpC), an important enzyme enhancing the cell tolerance to organic hydroperoxides usually accumulated under oxidative stress. The putative mechanism conferring PeCB resistance to P. fluorescens and the potential use of P. fluorescens in bioremediation are discussed.
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112
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Abstract
Genomic studies focus on key metabolites and pathways that, despite their obvious anthropocentric design, keep being 'predicted', while this is only finding again what is already known. As increasingly more genomes are sequenced, this lightpost effect may account at least in part for our failure to understand the function of a continuously growing number of genes. Core metabolism often goes astray, accidentally producing a variety of unexpected compounds. Catabolism of these forgotten metabolites makes an essential part of the functions coded in metagenomes. Here, I explore the fate of a limited number of those: compounds resulting from radical reactions and molecules derived from some reactive intermediates produced during normal metabolism. I try both to update investigators with the most recent literature and to uncover old articles that may open up new research avenues in the genome exploration of metabolism. This should allow us to foresee further developments in experimental genomics and genome annotation.
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Affiliation(s)
- Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐Salpêtrière47 Boulevard de l'HôpitalParis75013France
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113
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Yu S, Plan MR, Winter G, Krömer JO. Metabolic Engineering of Pseudomonas putida KT2440 for the Production of para-Hydroxy Benzoic Acid. Front Bioeng Biotechnol 2016; 4:90. [PMID: 27965953 PMCID: PMC5124731 DOI: 10.3389/fbioe.2016.00090] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/10/2016] [Indexed: 11/13/2022] Open
Abstract
para-Hydroxy benzoic acid (PHBA) is the key component for preparing parabens, a common preservatives in food, drugs, and personal care products, as well as high-performance bioplastics such as liquid crystal polymers. Pseudomonas putida KT2440 was engineered to produce PHBA from glucose via the shikimate pathway intermediate chorismate. To obtain the PHBA production strain, chorismate lyase UbiC from Escherichia coli and a feedback resistant 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase encoded by gene aroGD146N were overexpressed individually and simultaneously. In addition, genes related to product degradation (pobA) or competing for the precursor chorismate (pheA and trpE) were deleted from the genome. To further improve PHBA production, the glucose metabolism repressor hexR was knocked out in order to increase erythrose 4-phosphate and NADPH supply. The best strain achieved a maximum titer of 1.73 g L−1 and a carbon yield of 18.1% (C-mol C-mol−1) in a non-optimized fed-batch fermentation. This is to date the highest PHBA concentration produced by P. putida using a chorismate lyase.
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Affiliation(s)
- Shiqin Yu
- Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Brisbane, QLD, Australia; Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, QLD, Australia
| | - Manuel R Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, Australia; Metabolomics Australia (Queensland Node), The University of Queensland, Brisbane, QLD, Australia
| | - Gal Winter
- Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Brisbane, QLD, Australia; Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, QLD, Australia; School of Science and Technology, The University of New England, Armidale, NSW, Australia
| | - Jens O Krömer
- Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Brisbane, QLD, Australia; Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, QLD, Australia
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114
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Poblete-Castro I, Borrero-de Acuña JM, Nikel PI, Kohlstedt M, Wittmann C. Host Organism: Pseudomonas putida. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ignacio Poblete-Castro
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - José M. Borrero-de Acuña
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program; National Spanish Center for Biotechnology (CNB-CSIC); Calle Darwin, 3 28049 Madrid, Spain
| | - Michael Kohlstedt
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
| | - Christoph Wittmann
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
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115
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Vegge CS, Jansen van Rensburg MJ, Rasmussen JJ, Maiden MCJ, Johnsen LG, Danielsen M, MacIntyre S, Ingmer H, Kelly DJ. Glucose Metabolism via the Entner-Doudoroff Pathway in Campylobacter: A Rare Trait that Enhances Survival and Promotes Biofilm Formation in Some Isolates. Front Microbiol 2016; 7:1877. [PMID: 27920773 PMCID: PMC5118423 DOI: 10.3389/fmicb.2016.01877] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/08/2016] [Indexed: 01/01/2023] Open
Abstract
Isolates of the zoonotic pathogen Campylobacter are generally considered to be unable to metabolize glucose due to lack of key glycolytic enzymes. However, the Entner-Doudoroff (ED) pathway has been identified in Campylobacter jejuni subsp. doylei and a few C. coli isolates. A systematic search for ED pathway genes in a wide range of Campylobacter isolates and in the C. jejuni/coli PubMLST database revealed that 1.7% of >6,000 genomes encoded a complete ED pathway, including both C. jejuni and C. coli from diverse clinical, environmental and animal sources. In rich media, glucose significantly enhanced stationary phase survival of a set of ED-positive C. coli isolates. Unexpectedly, glucose massively promoted floating biofilm formation in some of these ED-positive isolates. Metabolic profiling by gas chromatography–mass spectrometry revealed distinct responses to glucose in a low biofilm strain (CV1257) compared to a high biofilm strain (B13117), consistent with preferential diversion of hexose-6-phosphate to polysaccharide in B13117. We conclude that while the ED pathway is rare amongst Campylobacter isolates causing human disease (the majority of which would be of agricultural origin), some glucose-utilizing isolates exhibit specific fitness advantages, including stationary-phase survival and biofilm production, highlighting key physiological benefits of this pathway in addition to energy conservation.
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Affiliation(s)
- Christina S Vegge
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Copenhagen, Denmark
| | - Melissa J Jansen van Rensburg
- Department of Zoology, University of OxfordOxford, UK; NIHR Health Protection Research Unit in Gastrointestinal InfectionsOxford, UK
| | - Janus J Rasmussen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Copenhagen, Denmark
| | - Martin C J Maiden
- Department of Zoology, University of OxfordOxford, UK; NIHR Health Protection Research Unit in Gastrointestinal InfectionsOxford, UK
| | | | | | - Sheila MacIntyre
- School of Biological Sciences, University of Reading Reading, UK
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Copenhagen, Denmark
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield Sheffield, UK
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116
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Avendaño R, Chaves N, Fuentes P, Sánchez E, Jiménez JI, Chavarría M. Production of selenium nanoparticles in Pseudomonas putida KT2440. Sci Rep 2016; 6:37155. [PMID: 27845437 PMCID: PMC5109041 DOI: 10.1038/srep37155] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/25/2016] [Indexed: 11/09/2022] Open
Abstract
Selenium (Se) is an essential element for the cell that has multiple applications in medicine and technology; microorganisms play an important role in Se transformations in the environment. Here we report the previously unidentified ability of the soil bacterium Pseudomonas putida KT2440 to synthesize nanoparticles of elemental selenium (nano-Se) from selenite. Our results show that P. putida is able to reduce selenite aerobically, but not selenate, to nano-Se. Kinetic analysis indicates that, in LB medium supplemented with selenite (1 mM), reduction to nano-Se occurs at a rate of 0.444 mmol L−1 h−1 beginning in the middle-exponential phase and with a final conversion yield of 89%. Measurements with a transmission electron microscope (TEM) show that nano-Se particles synthesized by P. putida have a size range of 100 to 500 nm and that they are located in the surrounding medium or bound to the cell membrane. Experiments involving dynamic light scattering (DLS) show that, in aqueous solution, recovered nano-Se particles have a size range of 70 to 360 nm. The rapid kinetics of conversion, easy retrieval of nano-Se and the metabolic versatility of P. putida offer the opportunity to use this model organism as a microbial factory for production of selenium nanoparticles.
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Affiliation(s)
- Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200 San José, Costa Rica
| | - Nefertiti Chaves
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200 San José, Costa Rica
| | - Paola Fuentes
- Escuela de Química, Universidad de Costa Rica, 11501-2060 San José, Costa Rica.,Centro de Electroquímica y Energía Química (CELEQ), Universidad de Costa Rica, 11501-2060 San José, Costa Rica
| | - Ethel Sánchez
- Centro de Investigaciones en Estructuras Microscópicas (CIEMIC), Universidad de Costa Rica, 11501-2060 San José, Costa Rica
| | - Jose I Jiménez
- Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, UK
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200 San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060 San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060 San José, Costa Rica
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117
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Metabolic flux analyses of Pseudomonas aeruginosa cystic fibrosis isolates. Metab Eng 2016; 38:251-263. [PMID: 27637318 DOI: 10.1016/j.ymben.2016.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/07/2016] [Accepted: 09/11/2016] [Indexed: 01/22/2023]
Abstract
Pseudomonas aeruginosa is a metabolically versatile wide-ranging opportunistic pathogen. In humans P. aeruginosa causes infections of the skin, urinary tract, blood, and the lungs of Cystic Fibrosis patients. In addition, P. aeruginosa's broad environmental distribution, relatedness to biotechnologically useful species, and ability to form biofilms have made it the focus of considerable interest. We used 13C metabolic flux analysis (MFA) and flux balance analysis to understand energy and redox production and consumption and to explore the metabolic phenotypes of one reference strain and five strains isolated from the lungs of cystic fibrosis patients. Our results highlight the importance of the oxidative pentose phosphate and Entner-Doudoroff pathways in P. aeruginosa growth. Among clinical strains we report two divergent metabolic strategies and identify changes between genetically related strains that have emerged during a chronic infection of the same patient. MFA revealed that the magnitude of fluxes through the glyoxylate cycle correlates with growth rates.
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118
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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] [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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119
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Calero P, Jensen SI, Nielsen AT. Broad-Host-Range ProUSER Vectors Enable Fast Characterization of Inducible Promoters and Optimization of p-Coumaric Acid Production in Pseudomonas putida KT2440. ACS Synth Biol 2016; 5:741-53. [PMID: 27092814 DOI: 10.1021/acssynbio.6b00081] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Pseudomonas putida KT2440 has gained increasing interest as a host for the production of biochemicals. Because of the lack of a systematic characterization of inducible promoters in this strain, we generated ProUSER broad-host-expression plasmids that facilitate fast uracil-based cloning. A set of ProUSER-reporter vectors was further created to characterize different inducible promoters. The PrhaB and Pm promoters were orthogonal and showed titratable, high, and homogeneous expression. To optimize the production of p-coumaric acid, P. putida was engineered to prevent degradation of tyrosine and p-coumaric acid. Pm and PrhaB were used to control the expression of a tyrosine ammonia lyase or AroG* and TyrA* involved in tyrosine production, respectively. Pathway expression was optimized by modulating inductions, resulting in small-scale p-coumaric acid production of 1.2 mM, the highest achieved in Pseudomonads under comparable conditions. With broad-host-range compatibility, the ProUSER vectors will serve as useful tools for optimizing gene expression in a variety of bacteria.
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Affiliation(s)
- Patricia Calero
- Novo Nordisk Foundation Center
for Biosustainability, Technical University of Denmark, Kogle Allé
6, 2970 Hørsholm, Denmark
| | - Sheila I. Jensen
- Novo Nordisk Foundation Center
for Biosustainability, Technical University of Denmark, Kogle Allé
6, 2970 Hørsholm, Denmark
| | - Alex T. Nielsen
- Novo Nordisk Foundation Center
for Biosustainability, Technical University of Denmark, Kogle Allé
6, 2970 Hørsholm, Denmark
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120
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Aparicio T, Jensen SI, Nielsen AT, de Lorenzo V, Martínez-García E. The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42. Biotechnol J 2016; 11:1309-1319. [PMID: 27367544 DOI: 10.1002/biot.201600317] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 11/10/2022]
Abstract
Some strains of the soil bacterium Pseudomonas putida have become in recent years platforms of choice for hosting biotransformations of industrial interest. Despite availability of many genetic tools for this microorganism, genomic editing of the cell factory P. putida EM42 (a derivative of reference strain KT2440) is still a time-consuming endeavor. In this work we have investigated the in vivo activity of the Ssr protein encoded by the open reading frame T1E_1405 from Pseudomonas putida DOT-T1E, a plausible functional homologue of the β protein of the Red recombination system of λ phage of Escherichia coli. A test based on the phenotypes of pyrF mutants of P. putida (the yeast's URA3 ortholog) was developed for quantifying the ability of Ssr to promote invasion of the genomic DNA replication fork by synthetic oligonucleotides. The efficiency of the process was measured by monitoring the inheritance of the changes entered into pyrF by oligonucleotides bearing mutated sequences. Ssr fostered short and long genomic deletions/insertions at considerable frequencies as well as single-base swaps not affected by mismatch repair. These results not only demonstrate the feasibility of recombineering in P. putida, but they also enable a suite of multiplexed genomic manipulations in this biotechnologically important bacterium.
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Affiliation(s)
- Tomás Aparicio
- Systems Biology Program, National Center of Biotechnology CSIC, Madrid, Spain
| | - Sheila I Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Alex T Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Victor de Lorenzo
- Systems Biology Program, National Center of Biotechnology CSIC, Madrid, Spain.
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121
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Paralogous Regulators ArsR1 and ArsR2 of Pseudomonas putida KT2440 as a Basis for Arsenic Biosensor Development. Appl Environ Microbiol 2016; 82:4133-4144. [PMID: 27208139 DOI: 10.1128/aem.00606-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/25/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The remarkable metal resistance of many microorganisms is related to the presence of multiple metal resistance operons. Pseudomonas putida KT2440 can be considered a model for these microorganisms since its arsenic resistance is due to the action of proteins encoded by the two paralogous arsenic resistance operons ARS1 and ARS2. Both operons contain the genes encoding the transcriptional regulators ArsR1 and ArsR2 that control operon expression. We show here that purified ArsR1 and ArsR2 bind the trivalent salt of arsenic (arsenite) with similar affinities (~30 μM), whereas no binding is observed for the pentavalent salt (arsenate). Furthermore, trivalent salts of bismuth and antimony showed binding to both paralogues. The positions of cysteines, found to bind arsenic in other homologues, indicate that ArsR1 and ArsR2 employ different modes of arsenite recognition. Both paralogues are dimeric and possess significant thermal stability. Both proteins were used to construct whole-cell, lacZ-based biosensors. Whereas responses to bismuth were negligible, significant responses were observed for arsenite, arsenate, and antimony. Biosensors based on the P. putida arsB1 arsB2 arsenic efflux pump double mutant were significantly more sensitive than biosensors based on the wild-type strain. This sensitivity enhancement by pump mutation may be a convenient strategy for the construction of other biosensors. A frequent limitation found for other arsenic biosensors was their elevated background signal and interference by inorganic phosphate. The constructed biosensors show no interference by inorganic phosphate, are characterized by a very low background signal, and were found to be suitable to analyze environmental samples. IMPORTANCE Arsenic is at the top of the priority list of hazardous compounds issued by the U.S. Agency for Toxic Substances and Disease. The reason for the stunning arsenic resistance of many microorganisms is the existence of paralogous arsenic resistance operons. Pseudomonas putida KT2440 is a model organism for such bacteria, and their duplicated ars operons and in particular their ArsR transcription regulators have been studied in depth by in vivo approaches. Here we present an analysis of both purified ArsR paralogues by different biophysical techniques, and data obtained provide valuable insight into their structure and function. Particularly insightful was the comparison of ArsR effector profiles determined by in vitro and in vivo experimentation. We also report the use of both paralogues to construct robust and highly sensitive arsenic biosensors. Our finding that the deletion of both arsenic efflux pumps significantly increases biosensor sensitivity is of general relevance in the biosensor field.
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122
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D'Arrigo I, Bojanovič K, Yang X, Holm Rau M, Long KS. Genome-wide mapping of transcription start sites yields novel insights into the primary transcriptome ofPseudomonas putida. Environ Microbiol 2016; 18:3466-3481. [DOI: 10.1111/1462-2920.13326] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/01/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Isotta D'Arrigo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Klara Bojanovič
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Xiaochen Yang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Martin Holm Rau
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Katherine S. Long
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
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123
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Nikel PI, Chavarría M, Danchin A, de Lorenzo V. From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions. Curr Opin Chem Biol 2016; 34:20-29. [PMID: 27239751 DOI: 10.1016/j.cbpa.2016.05.011] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/04/2016] [Accepted: 05/10/2016] [Indexed: 01/14/2023]
Abstract
The soil bacterium Pseudomonas putida is endowed with a central carbon metabolic network capable of fulfilling high demands of reducing power. This situation arises from a unique metabolic architecture that encompasses the partial recycling of triose phosphates to hexose phosphates-the so-called EDEMP cycle. In this article, the value of P. putida as a bacterial chassis of choice for contemporary, industrially-oriented metabolic engineering is addressed. The biochemical properties that make this bacterium adequate for hosting biotransformations involving redox reactions as well as toxic compounds and intermediates are discussed. Finally, novel developments and open questions in the continuous quest for an optimal microbial cell factory are presented at the light of current and future needs in the area of biocatalysis.
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Affiliation(s)
- Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain.
| | - Max Chavarría
- Escuela de Química & CIPRONA, Universidad de Costa Rica, 11501-2060 San José, Costa Rica
| | - Antoine Danchin
- AMAbiotics SAS, Institut of Cardiometabolism and Nutrition (ICAN), Hôpital Universitaire de la Pitié-Salpêtrière, 75013 Paris, France
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain.
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124
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Gao SH, Fan L, Peng L, Guo J, Agulló-Barceló M, Yuan Z, Bond PL. Determining Multiple Responses of Pseudomonas aeruginosa PAO1 to an Antimicrobial Agent, Free Nitrous Acid. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:5305-5312. [PMID: 27116299 DOI: 10.1021/acs.est.6b00288] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Free nitrous acid (FNA) has recently been demonstrated as an antimicrobial agent on a range of micro-organisms, especially in wastewater-treatment systems. However, the antimicrobial mechanism of FNA is largely unknown. Here, we report that the antimicrobial effects of FNA are multitargeted. The response of a model denitrifier, Pseudomnas aeruginosa PAO1 (PAO1), common in wastewater treatment, was investigated in the absence and presence of inhibitory level of FNA (0.1 mg N/L) under anaerobic denitrifying conditions. This was achieved through coupling gene expression analysis, by RNA sequencing, and with a suite of physiological analyses. Various transcripts exhibited significant changes in abundance in the presence of FNA. Respiration was likely inhibited because denitrification activity was severely depleted, and decreased transcript levels of most denitrification genes occurred. As a consequence, the tricarboxylic acid (TCA) cycle was inhibited due to the lowered cellular redox state in the FNA-exposed cultures. Meanwhile, during FNA exposure, PAO1 rerouted its carbon metabolic pathway from the TCA cycle to pyruvate fermentation with acetate as the end product as a possible survival mechanism. Additionally, protein synthesis was significantly decreased, and ribosome preservation was evident. These findings improve our understanding of PAO1 in response to FNA and contribute toward the potential application for use of FNA as an antimicrobial agent.
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Affiliation(s)
- Shu-Hong Gao
- Advanced Water Management Centre, The University of Queensland , St. Lucia, Brisbane QLD 4072, Australia
| | - Lu Fan
- Advanced Water Management Centre, The University of Queensland , St. Lucia, Brisbane QLD 4072, Australia
- iCarbonX , Shenzhen 518053, China
| | - Lai Peng
- Advanced Water Management Centre, The University of Queensland , St. Lucia, Brisbane QLD 4072, Australia
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University , Coupure Links 653, Ghent 9000, Belgium
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland , St. Lucia, Brisbane QLD 4072, Australia
| | - Míriam Agulló-Barceló
- Advanced Water Management Centre, The University of Queensland , St. Lucia, Brisbane QLD 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland , St. Lucia, Brisbane QLD 4072, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland , St. Lucia, Brisbane QLD 4072, Australia
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125
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Johnson CW, Salvachúa D, Khanna P, Smith H, Peterson DJ, Beckham GT. Enhancing muconic acid production from glucose and lignin-derived aromatic compounds via increased protocatechuate decarboxylase activity. Metab Eng Commun 2016; 3:111-119. [PMID: 29468118 PMCID: PMC5779730 DOI: 10.1016/j.meteno.2016.04.002] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/01/2016] [Accepted: 04/21/2016] [Indexed: 11/28/2022] Open
Abstract
The conversion of biomass-derived sugars and aromatic molecules to cis,cis-muconic acid (referred to hereafter as muconic acid or muconate) has been of recent interest owing to its facile conversion to adipic acid, an important commodity chemical. Metabolic routes to produce muconate from both sugars and many lignin-derived aromatic compounds require the use of a decarboxylase to convert protocatechuate (PCA, 3,4-dihydroxybenzoate) to catechol (1,2-dihydroxybenzene), two central aromatic intermediates in this pathway. Several studies have identified the PCA decarboxylase as a metabolic bottleneck, causing an accumulation of PCA that subsequently reduces muconate production. A recent study showed that activity of the PCA decarboxylase is enhanced by co-expression of two genetically associated proteins, one of which likely produces a flavin-derived cofactor utilized by the decarboxylase. Using entirely genome-integrated gene expression, we have engineered Pseudomonas putida KT2440-derived strains to produce muconate from either aromatic molecules or sugars and demonstrate in both cases that co-expression of these decarboxylase associated proteins reduces PCA accumulation and enhances muconate production relative to strains expressing the PCA decarboxylase alone. In bioreactor experiments, co-expression increased the specific productivity (mg/g cells/h) of muconate from the aromatic lignin monomer p-coumarate by 50% and resulted in a titer of >15 g/L. In strains engineered to produce muconate from glucose, co-expression more than tripled the titer, yield, productivity, and specific productivity, with the best strain producing 4.92±0.48 g/L muconate. This study demonstrates that overcoming the PCA decarboxylase bottleneck can increase muconate yields from biomass-derived sugars and aromatic molecules in industrially relevant strains and cultivation conditions. We engineered Pseudomonas putida to produce muconate from p-coumarate and glucose. A protocatechuate decarboxylase was expressed with two associated proteins. Co-expression of these proteins reduced protocatechuate accumulation. Co-expression of these proteins reduced enhanced muconate production up to 3X. 15.6 g/L muconate was produced from p-coumarate and 4.92 g/L from glucose
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Affiliation(s)
- Christopher W Johnson
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
| | - Davinia Salvachúa
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
| | - Payal Khanna
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
| | - Holly Smith
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
| | - Darren J Peterson
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
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126
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Reduced expression of cytochrome oxidases largely explains cAMP inhibition of aerobic growth in Shewanella oneidensis. Sci Rep 2016; 6:24449. [PMID: 27076065 PMCID: PMC4830989 DOI: 10.1038/srep24449] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 03/29/2016] [Indexed: 12/20/2022] Open
Abstract
Inhibition of bacterial growth under aerobic conditions by elevated levels of cyclic adenosine 3′,5′-monophosphate (cAMP), first revealed more than 50 years ago, was attributed to accumulation of toxic methylglyoxal (MG). Here, we report a Crp-dependent mechanism rather than MG accumulation that accounts for the phenotype in Shewanella oneidensis, an emerging research model for the bacterial physiology. We show that a similar phenotype can be obtained by removing CpdA, a cAMP phosphodiesterase that appears more effective than its Escherichia coli counterpart. Although production of heme c and cytochromes c is correlated well with cAMP levels, neither is sufficient for the retarded growth. Quantities of overall cytochromes c increased substantially in the presence of elevated cAMP, a phenomenon resembling cells respiring on non-oxygen electron acceptors. In contrast, transcription of Crp-dependent genes encoding both cytochromes bd and cbb3 oxidases is substantially repressed under the same condition. Overall, our results suggest that cAMP of elevated levels drives cells into a low-energetic status, under which aerobic respiration is inhibited.
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127
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Beri D, Olson DG, Holwerda EK, Lynd LR. Nicotinamide cofactor ratios in engineered strains of Clostridium thermocellum and Thermoanaerobacterium saccharolyticum. FEMS Microbiol Lett 2016; 363:fnw091. [PMID: 27190292 DOI: 10.1093/femsle/fnw091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2016] [Indexed: 12/30/2022] Open
Abstract
Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are bacteria under investigation for production of biofuels from plant biomass. Thermoanaerobacterium saccharolyticum has been engineered to produce ethanol at high yield (>90% of theoretical) and titer (>70 g/l). Efforts to engineer C. thermocellum have not, to date, been as successful, and efforts are underway to transfer the ethanol production pathway from T. saccharolyticum to C. thermocellum One potential challenge in transferring metabolic pathways is the possibility of incompatible levels of nicotinamide cofactors. These cofactors (NAD(+), NADH, NADP(+) and NADPH) and their oxidation state are important in the context of microbial redox metabolism. In this study we directly measured the concentrations and reduced oxidized ratios of these cofactors in a number of strains of C. thermocellum and T. saccharolyticum by using acid/base extraction and enzymatic assays. We found that cofactor ratios are maintained in a fairly narrow range, regardless of the metabolic network modifications considered. We have found that the ratios are similar in both organisms, which is a relevant observation in the context of transferring the T. saccharolyticum ethanol production pathway to C. thermocellum.
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Affiliation(s)
- Dhananjay Beri
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Evert K Holwerda
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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128
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Lai B, Yu S, Bernhardt PV, Rabaey K, Virdis B, Krömer JO. Anoxic metabolism and biochemical production in Pseudomonas putida F1 driven by a bioelectrochemical system. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:39. [PMID: 26893611 PMCID: PMC4758010 DOI: 10.1186/s13068-016-0452-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/03/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Pseudomonas putida is a promising host for the bioproduction of chemicals, but its industrial applications are significantly limited by its obligate aerobic character. The aim of this paper is to empower the anoxic metabolism of wild-type Pseudomonas putida to enable bioproduction anaerobically, with the redox power from a bioelectrochemical system (BES). RESULTS The obligate aerobe Pseudomonas putida F1 was able to survive and produce almost exclusively 2-Keto-gluconate from glucose under anoxic conditions due to redox balancing with electron mediators in a BES. 2-Keto-gluconate, a precursor for industrial anti-oxidant production, was produced at an overall carbon yield of over 90 % based on glucose. Seven different mediator compounds were tested, and only those with redox potential above 0.207 V (vs standard hydrogen electrode) showed interaction with the cells. The productivity increased with the increasing redox potential of the mediator, indicating this was a key factor affecting the anoxic production process. P. putida cells survived under anaerobic conditions, and limited biofilm formation could be observed on the anode's surface. Analysis of the intracellular pools of ATP, ADP and AMP showed that cells had an increased adenylate energy charge suggesting that cells were able to generate energy using the anode as terminal electron acceptor. The analysis of NAD(H) and NADP(H) showed that in the presence of specific extracellular electron acceptors, the NADP(H) pool was more oxidised, while the NAD(H) pool was unchanged. This implies a growth limitation under anaerobic conditions due to a shortage of NADPH and provides a way to limit biomass formation, while allowing cell maintenance and catalysis at high purity and yield. CONCLUSIONS For the first time, this study proved the principle that a BES-driven bioconversion of glucose can be achieved for a wild-type obligate aerobe. This non-growth bioconversion was in high yields, high purity and also could deliver the necessary metabolic energy for cell maintenance. By combining this approach with metabolic engineering strategies, this could prove to be a powerful new way to produce bio-chemicals and fuels from renewables in both high yield and high purity.
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Affiliation(s)
- Bin Lai
- />Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Office 618, Gehrmann Building (60), St. Lucia, Brisbane, QLD 4072 Australia
- />Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Australia
| | - Shiqin Yu
- />Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Office 618, Gehrmann Building (60), St. Lucia, Brisbane, QLD 4072 Australia
- />Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Australia
| | - Paul V. Bernhardt
- />School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Korneel Rabaey
- />Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Ghent, Belgium
| | - Bernardino Virdis
- />Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Office 618, Gehrmann Building (60), St. Lucia, Brisbane, QLD 4072 Australia
- />Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Australia
| | - Jens O. Krömer
- />Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Office 618, Gehrmann Building (60), St. Lucia, Brisbane, QLD 4072 Australia
- />Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, Australia
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129
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Moreno-Forero SK, Rojas E, Beggah S, van der Meer JR. Comparison of differential gene expression to water stress among bacteria with relevant pollutant-degradation properties. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:91-102. [PMID: 26616826 DOI: 10.1111/1758-2229.12356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 11/15/2015] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
Abstract
Resistance to semi-dry environments has been considered a crucial trait for superior growth and survival of strains used for bioaugmentation in contaminated soils. In order to compare water stress programmes, we analyse differential gene expression among three phylogenetically different strains capable of aromatic compound degradation: Arthrobacter chlorophenolicus A6, Sphingomonas wittichii RW1 and Pseudomonas veronii 1YdBTEX2. Standardized laboratory-induced water stress was imposed by shock exposure of liquid cultures to water potential decrease, induced either by addition of solutes (NaCl, solute stress) or by addition of polyethylene glycol (matric stress), both at absolute similar stress magnitudes and at those causing approximately similar decrease of growth rates. Genome-wide differential gene expression was recorded by micro-array hybridizations. Growth of P. veronii 1YdBTEX2 was the most sensitive to water potential decrease, followed by S. wittichii RW1 and A. chlorophenolicus A6. The number of genes differentially expressed under decreasing water potential was lowest for A. chlorophenolicus A6, increasing with increasing magnitude of the stress, followed by S. wittichii RW1 and P. veronii 1YdBTEX2. Gene inspection and gene ontology analysis under stress conditions causing similar growth rate reduction indicated that common reactions among the three strains included diminished expression of flagellar motility and increased expression of compatible solutes (which were strain-specific). Furthermore, a set of common genes with ill-defined function was found between all strains, including ABC transporters and aldehyde dehydrogenases, which may constitute a core conserved response to water stress. The data further suggest that stronger reduction of growth rate of P. veronii 1YdBTEX2 under water stress may be an indirect result of the response demanding heavy NADPH investment, rather than the presence or absence of a suitable stress defence mechanism per se.
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Affiliation(s)
- Silvia K Moreno-Forero
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Edward Rojas
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Siham Beggah
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
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130
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Hollinshead WD, Rodriguez S, Martin HG, Wang G, Baidoo EEK, Sale KL, Keasling JD, Mukhopadhyay A, Tang YJ. Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δ pfk mutants. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:212. [PMID: 27766116 PMCID: PMC5057261 DOI: 10.1186/s13068-016-0630-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/28/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Glycolysis breakdowns glucose into essential building blocks and ATP/NAD(P)H for the cell, occupying a central role in its growth and bio-production. Among glycolytic pathways, the Entner Doudoroff pathway (EDP) is a more thermodynamically favorable pathway with fewer enzymatic steps than either the Embden-Meyerhof-Parnas pathway (EMPP) or the oxidative pentose phosphate pathway (OPPP). However, Escherichia coli do not use their native EDP for glucose metabolism. RESULTS Overexpression of edd and eda in E. coli to enhance EDP activity resulted in only a small shift in the flux directed through the EDP (~20 % of glycolysis flux). Disrupting the EMPP by phosphofructokinase I (pfkA) knockout increased flux through OPPP (~60 % of glycolysis flux) and the native EDP (~14 % of glycolysis flux), while overexpressing edd and eda in this ΔpfkA mutant directed ~70 % of glycolytic flux through the EDP. The downregulation of EMPP via the pfkA deletion significantly decreased the growth rate, while EDP overexpression in the ΔpfkA mutant failed to improve its growth rates due to metabolic burden. However, the reorganization of E. coli glycolytic strategies did reduce glucose catabolite repression. The ΔpfkA mutant in glucose medium was able to cometabolize acetate via the citric acid cycle and gluconeogenesis, while EDP overexpression in the ΔpfkA mutant repressed acetate flux toward gluconeogenesis. Moreover, 13C-pulse experiments in the ΔpfkA mutants showed unsequential labeling dynamics in glycolysis intermediates, possibly suggesting metabolite channeling (metabolites in glycolysis are pass from enzyme to enzyme without fully equilibrating within the cytosol medium). CONCLUSIONS We engineered E. coli to redistribute its native glycolytic flux. The replacement of EMPP by EDP did not improve E. coli glucose utilization or biomass growth, but alleviated catabolite repression. More importantly, our results supported the hypothesis of channeling in the glycolytic pathways, a potentially overlooked mechanism for regulating glucose catabolism and coutilization of other substrates. The presence of channeling in native pathways, if proven true, would affect synthetic biology applications and metabolic modeling.
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Affiliation(s)
- Whitney D. Hollinshead
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO USA
| | - Sarah Rodriguez
- Sandia National Laboratory, Livermore, CA USA
- Joint BioEnergy Institute, Emeryville, CA USA
| | - Hector Garcia Martin
- Joint BioEnergy Institute, Emeryville, CA USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA USA
| | - George Wang
- Joint BioEnergy Institute, Emeryville, CA USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA USA
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute, Emeryville, CA USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA USA
| | - Kenneth L. Sale
- Joint BioEnergy Institute, Emeryville, CA USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, CA USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA USA
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA USA
- Department of Bioengineering, University of California, Berkeley, CA USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé, DK2970 Hørsholm, Denmark
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA USA
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA USA
| | - Yinjie J. Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO USA
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131
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Zobel S, Benedetti I, Eisenbach L, de Lorenzo V, Wierckx N, Blank LM. Tn7-Based Device for Calibrated Heterologous Gene Expression in Pseudomonas putida. ACS Synth Biol 2015; 4:1341-51. [PMID: 26133359 DOI: 10.1021/acssynbio.5b00058] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The soil bacterium Pseudomonas putida is increasingly attracting considerable interest as a platform for advanced metabolic engineering through synthetic biology approaches. However, genomic context, gene copy number, and transcription/translation interplay often introduce considerable uncertainty to the design of reliable genetic constructs. In this work, we have established a standardized heterologous expression device in which the promoter strength is the only variable; the remaining parameters of the flow have stable default values. To this end, we tailored a mini-Tn7 delivery transposon vector that inserts the constructs in a single genomic locus of P. putida's chromosome. This was then merged with a promoter insertion site, an unvarying translational coupler, and a downstream location for placing the gene(s) of interest under fixed assembly rules. This arrangement was exploited to benchmark a collection of synthetic promoters with low transcriptional noise in this bacterial host. Growth experiments and flow cytometry with single-copy promoter-GFP constructs revealed a robust, constitutive behavior of these promoters, whose strengths and properties could be faithfully compared. This standardized expression device significantly extends the repertoire of tools available for reliable metabolic engineering and other genetic enhancements of P. putida.
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Affiliation(s)
- Sebastian Zobel
- Institute
of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Ilaria Benedetti
- Systems
Biology Program, Centro Nacional de Biotecnologia, CSIC, C/Darwin, 3 (Campus
de Cantoblanco), Madrid 28049, Spain
| | - Lara Eisenbach
- Institute
of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Victor de Lorenzo
- Systems
Biology Program, Centro Nacional de Biotecnologia, CSIC, C/Darwin, 3 (Campus
de Cantoblanco), Madrid 28049, Spain
| | - Nick Wierckx
- Institute
of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Lars M. Blank
- Institute
of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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132
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Arce-Rodríguez A, Calles B, Nikel PI, de Lorenzo V. The RNA chaperone Hfq enables the environmental stress tolerance super-phenotype ofPseudomonas putida. Environ Microbiol 2015; 18:3309-3326. [DOI: 10.1111/1462-2920.13052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/09/2015] [Accepted: 09/09/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Alejandro Arce-Rodríguez
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
| | - Belén Calles
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
| | - Pablo I. Nikel
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
| | - Víctor de Lorenzo
- Systems Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Campus de Cantoblanco Madrid 28049 Spain
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133
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Kuepper J, Dickler J, Biggel M, Behnken S, Jäger G, Wierckx N, Blank LM. Metabolic Engineering of Pseudomonas putida KT2440 to Produce Anthranilate from Glucose. Front Microbiol 2015; 6:1310. [PMID: 26635771 PMCID: PMC4656820 DOI: 10.3389/fmicb.2015.01310] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/09/2015] [Indexed: 11/29/2022] Open
Abstract
The Pseudomonas putida KT2440 strain was engineered in order to produce anthranilate (oAB, ortho-aminobenzoate), a precursor of the aromatic amino acid tryptophan, from glucose as sole carbon source. To enable the production of the metabolic intermediate oAB, the trpDC operon encoding an anthranilate phosphoribosyltransferase (TrpD) and an indole-3-glycerol phosphate synthase (TrpC), were deleted. In addition, the chorismate mutase (pheA) responsible for the conversion of chorismate over prephenate to phenylpyruvate was deleted in the background of the deletion of trpDC to circumvent a potential drain of precursor. To further increase the oAB production, a feedback insensitive version of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase encoded by the aroG (D146N) gene and an anthranilate synthase (trpE (S40F) G) were overexpressed separately and simultaneously in the deletion mutants. With optimized production conditions in a tryptophan-limited fed-batch process a maximum of 1.54 ± 0.3 g L(-1) (11.23 mM) oAB was obtained with the best performing engineered P. putida KT2440 strain (P. putida ΔtrpDC pSEVA234_aroG (D146N) _trpE (S40F) G).
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Affiliation(s)
- Jannis Kuepper
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), Rheinisch-Westfälische Technische Hochschule Aachen UniversityAachen, Germany
| | - Jasmin Dickler
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), Rheinisch-Westfälische Technische Hochschule Aachen UniversityAachen, Germany
| | - Michael Biggel
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), Rheinisch-Westfälische Technische Hochschule Aachen UniversityAachen, Germany
| | | | | | - Nick Wierckx
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), Rheinisch-Westfälische Technische Hochschule Aachen UniversityAachen, Germany
| | - Lars M. Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), Rheinisch-Westfälische Technische Hochschule Aachen UniversityAachen, Germany
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134
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Olavarria K, Marone MP, da Costa Oliveira H, Roncallo JC, da Costa Vasconcelos FN, da Silva LF, Gomez JGC. Quantifying NAD(P)H production in the upper Entner-Doudoroff pathway from Pseudomonas putida KT2440. FEBS Open Bio 2015; 5:908-15. [PMID: 26702395 PMCID: PMC4669411 DOI: 10.1016/j.fob.2015.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/29/2015] [Accepted: 11/03/2015] [Indexed: 11/04/2022] Open
Abstract
The first kinetic characterization of PputG6PDH-1 is presented. The relative production of NADH and NADPH by PputG6PDH-1 is quantified. The stoichiometric matrix of in silico metabolic models for Pseudomonas putida must be modified.
Despite the lack of biochemical information, all available in silico metabolic models of Pseudomonas putida KT2440 consider NADP as the only cofactor accepted by the glucose-6-phosphate dehydrogenases. Because the Entner–Doudoroff pathway is the main glycolytic route in this bacterium, determining how much NADH and NADPH are produced in the reaction catalyzed by these enzymes is very important for the correct interpretation of metabolic flux distributions. To determine the actual cofactor preference of the glucose-6-phosphate dehydrogenase encoded by the zwf-1 gene (PputG6PDH-1), the major isoform during growth on glucose, we purified this protein and studied its kinetic properties. Based on simple kinetic principles, we estimated the in vivo relative production of NADH and NADPH during the oxidation of glucose-6-phosphate (G6P). Contrary to the general assumption, our calculations showed that the reaction catalyzed by PputG6PDH-1 yields around 1/3 mol of NADPH and 2/3 mol of NADH per mol of oxidized G6P. Additionally, we obtained data suggesting that the reaction catalyzed by the 6-phosphogluconate dehydrogenase is active during growth on glucose, and it also produces NADH. These results indicate that the stoichiometric matrix of in silico models of P. putida KT2440 must be corrected and highlight the importance of considering the physiological concentrations of the involved metabolites to estimate the actual proportion of NADH and NADPH produced by a dehydrogenase.
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Affiliation(s)
- Karel Olavarria
- Departmento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
| | - Marina Pupke Marone
- Departmento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
| | | | - Juan Camilo Roncallo
- Departmento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
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135
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Udaondo Z, Molina L, Segura A, Duque E, Ramos JL. Analysis of the core genome and pangenome ofPseudomonas putida. Environ Microbiol 2015; 18:3268-3283. [DOI: 10.1111/1462-2920.13015] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/04/2015] [Accepted: 08/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Zulema Udaondo
- Biotechnology Technological Area; Abengoa Research; Calle Energía Solar 1, Building E, Campus Palmas Altas 41014 Sevilla Spain
| | - Lázaro Molina
- Department of Environmental Protection; Estación Experimental del Zaidín; Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1 18008 Granada Spain
| | - Ana Segura
- Biotechnology Technological Area; Abengoa Research; Calle Energía Solar 1, Building E, Campus Palmas Altas 41014 Sevilla Spain
| | - Estrella Duque
- Biotechnology Technological Area; Abengoa Research; Calle Energía Solar 1, Building E, Campus Palmas Altas 41014 Sevilla Spain
| | - Juan L. Ramos
- Biotechnology Technological Area; Abengoa Research; Calle Energía Solar 1, Building E, Campus Palmas Altas 41014 Sevilla Spain
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136
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Nikel PI, Chavarría M, Fuhrer T, Sauer U, de Lorenzo V. Pseudomonas putida KT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways. J Biol Chem 2015; 290:25920-32. [PMID: 26350459 DOI: 10.1074/jbc.m115.687749] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Indexed: 01/28/2023] Open
Abstract
The soil bacterium Pseudomonas putida KT2440 lacks a functional Embden-Meyerhof-Parnas (EMP) pathway, and glycolysis is known to proceed almost exclusively through the Entner-Doudoroff (ED) route. To investigate the raison d'être of this metabolic arrangement, the distribution of periplasmic and cytoplasmic carbon fluxes was studied in glucose cultures of this bacterium by using (13)C-labeled substrates, combined with quantitative physiology experiments, metabolite quantification, and in vitro enzymatic assays under both saturating and non-saturating, quasi in vivo conditions. Metabolic flux analysis demonstrated that 90% of the consumed sugar was converted into gluconate, entering central carbon metabolism as 6-phosphogluconate and further channeled into the ED pathway. Remarkably, about 10% of the triose phosphates were found to be recycled back to form hexose phosphates. This set of reactions merges activities belonging to the ED, the EMP (operating in a gluconeogenic fashion), and the pentose phosphate pathways to form an unforeseen metabolic architecture (EDEMP cycle). Determination of the NADPH balance revealed that the default metabolic state of P. putida KT2440 is characterized by a slight catabolic overproduction of reducing power. Cells growing on glucose thus run a biochemical cycle that favors NADPH formation. Because NADPH is required not only for anabolic functions but also for counteracting different types of environmental stress, such a cyclic operation may contribute to the physiological heftiness of this bacterium in its natural habitats.
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Affiliation(s)
- Pablo I Nikel
- From the Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Max Chavarría
- the Escuela de Química, Universidad de Costa Rica, 2060 San José, Costa Rica, and
| | - Tobias Fuhrer
- the Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Uwe Sauer
- the Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Víctor de Lorenzo
- From the Systems and Synthetic Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain,
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137
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Hollinshead WD, Henson WR, Abernathy M, Moon TS, Tang YJ. Rapid metabolic analysis of
Rhodococcus opacus
PD630 via parallel
13
C‐metabolite fingerprinting. Biotechnol Bioeng 2015; 113:91-100. [DOI: 10.1002/bit.25702] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 07/04/2015] [Accepted: 07/07/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Whitney D. Hollinshead
- Department of Energy, Environmental and Chemical EngineeringWashington University in St. LouisSt. LouisMissouri63130
| | - William R. Henson
- Department of Energy, Environmental and Chemical EngineeringWashington University in St. LouisSt. LouisMissouri63130
| | - Mary Abernathy
- Department of Energy, Environmental and Chemical EngineeringWashington University in St. LouisSt. LouisMissouri63130
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical EngineeringWashington University in St. LouisSt. LouisMissouri63130
| | - Yinjie J. Tang
- Department of Energy, Environmental and Chemical EngineeringWashington University in St. LouisSt. LouisMissouri63130
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138
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The glycerol-dependent metabolic persistence of Pseudomonas putida KT2440 reflects the regulatory logic of the GlpR repressor. mBio 2015; 6:mBio.00340-15. [PMID: 25827416 PMCID: PMC4453509 DOI: 10.1128/mbio.00340-15] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The growth of the soil bacterium Pseudomonas putida KT2440 on glycerol as the sole carbon source is characterized by a prolonged lag phase, not observed with other carbon substrates. We examined the bacterial growth in glycerol cultures while monitoring the metabolic activity of individual cells. Fluorescence microscopy and flow cytometry, as well as the analysis of the temporal start of growth in single-cell cultures, revealed that adoption of a glycerol-metabolizing regime was not the result of a gradual change in the whole population but rather reflected a time-dependent bimodal switch between metabolically inactive (i.e., nongrowing) and fully active (i.e., growing) bacteria. A transcriptional Φ(glpD-gfp) fusion (a proxy of the glycerol-3-phosphate [G3P] dehydrogenase activity) linked the macroscopic phenotype to the expression of the glp genes. Either deleting glpR (encoding the G3P-responsive transcriptional repressor that controls the expression of the glpFKRD gene cluster) or altering G3P formation (by overexpressing glpK, encoding glycerol kinase) abolished the bimodal glpD expression. These manipulations eliminated the stochastic growth start by shortening the otherwise long lag phase. Provision of glpR in trans restored the phenotypes lost in the ΔglpR mutant. The prolonged nongrowth regime of P. putida on glycerol could thus be traced to the regulatory device controlling the transcription of the glp genes. Since the physiological agonist of GlpR is G3P, the arrangement of metabolic and regulatory components at this checkpoint merges a positive feedback loop with a nonlinear transcriptional response, a layout fostering the observed time-dependent shift between two alternative physiological states. Phenotypic variation is a widespread attribute of prokaryotes that leads, inter alia, to the emergence of persistent bacteria, i.e., live but nongrowing members within a genetically clonal population. Persistence allows a fraction of cells to avoid the killing caused by conditions or agents that destroy most growing bacteria (e.g., some antibiotics). Known molecular mechanisms underlying the phenomenon include genetic changes, epigenetic variations, and feedback-based multistability. We show that a prolonged nongrowing state of the bacterial population can be brought about by a distinct regulatory architecture of metabolic genes when cells face specific nutrients (e.g., glycerol). Pseudomonas putida may have adopted the resulting carbon source-dependent metabolic bet hedging as an advantageous trait for exploring new chemical and nutritional landscapes. Defeating such naturally occurring adaptive features of environmental bacteria is instrumental in improving the performance of these microorganisms as whole-cell catalysts in a bioreactor setup.
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139
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Lieder S, Nikel PI, de Lorenzo V, Takors R. Genome reduction boosts heterologous gene expression in Pseudomonas putida. Microb Cell Fact 2015; 14:23. [PMID: 25890048 PMCID: PMC4352270 DOI: 10.1186/s12934-015-0207-7] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/11/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The implementation of novel platform organisms to be used as microbial cell factories in industrial applications is currently the subject of intense research. Ongoing efforts include the adoption of Pseudomonas putida KT2440 variants with a reduced genome as the functional chassis for biotechnological purposes. In these strains, dispensable functions removed include flagellar motility (1.1% of the genome) and a number of open reading frames expected to improve genotypic and phenotypic stability of the cells upon deletion (3.2% of the genome). RESULTS In this study, two previously constructed multiple-deletion P. putida strains were systematically evaluated as microbial cell factories for heterologous protein production and compared to the parental bacterium (strain KT2440) with regards to several industrially-relevant physiological traits. Energetic parameters were quantified at different controlled growth rates in continuous cultivations and both strains had a higher adenosine triphosphate content, increased adenylate energy charges, and diminished maintenance demands than the wild-type strain. Under all the conditions tested the mutants also grew faster, had enhanced biomass yields and showed higher viability, and displayed increased plasmid stability than the parental strain. In addition to small-scale shaken-flask cultivations, the performance of the genome-streamlined strains was evaluated in larger scale bioreactor batch cultivations taking a step towards industrial growth conditions. When the production of the green fluorescent protein (used as a model heterologous protein) was assessed in these cultures, the mutants reached a recombinant protein yield with respect to biomass up to 40% higher than that of P. putida KT2440. CONCLUSIONS The two streamlined-genome derivatives of P. putida KT2440 outcompeted the parental strain in every industrially-relevant trait assessed, particularly under the working conditions of a bioreactor. Our results demonstrate that these genome-streamlined bacteria are not only robust microbial cell factories on their own, but also a promising foundation for further biotechnological applications.
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Affiliation(s)
- Sarah Lieder
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
| | - Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain.
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain.
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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140
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Large-Scale 13C flux profiling reveals conservation of the Entner-Doudoroff pathway as a glycolytic strategy among marine bacteria that use glucose. Appl Environ Microbiol 2015; 81:2408-22. [PMID: 25616803 DOI: 10.1128/aem.03157-14] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine bacteria form one of the largest living surfaces on Earth, and their metabolic activity is of fundamental importance for global nutrient cycling. Here, we explored the largely unknown intracellular pathways in 25 microbes representing different classes of marine bacteria that use glucose: Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia of the Bacteriodetes phylum. We used (13)C isotope experiments to infer metabolic fluxes through their carbon core pathways. Notably, 90% of all strains studied use the Entner-Doudoroff (ED) pathway for glucose catabolism, whereas only 10% rely on the Embden-Meyerhof-Parnas (EMP) pathway. This result differed dramatically from the terrestrial model strains studied, which preferentially used the EMP pathway yielding high levels of ATP. Strains using the ED pathway exhibited a more robust resistance against the oxidative stress typically found in this environment. An important feature contributing to the preferential use of the ED pathway in the oceans could therefore be enhanced supply of NADPH through this pathway. The marine bacteria studied did not specifically rely on a distinct anaplerotic route, but the carboxylation of phosphoenolpyruvate (PEP) or pyruvate for fueling of the tricarboxylic acid (TCA) cycle was evenly distributed. The marine isolates studied belong to clades that dominate the uptake of glucose, a major carbon source for bacteria in seawater. Therefore, the ED pathway may play a significant role in the cycling of mono- and polysaccharides by bacterial communities in marine ecosystems.
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Nikel PI, Chavarría M. Quantitative Physiology Approaches to Understand and Optimize Reducing Power Availability in Environmental Bacteria. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_84] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Global genome comparative analysis reveals insights of resistome and life-style adaptation of Pseudomonas putida strain T2-2 in oral cavity. ScientificWorldJournal 2014; 2014:930727. [PMID: 25436236 PMCID: PMC4243125 DOI: 10.1155/2014/930727] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 09/08/2014] [Accepted: 09/14/2014] [Indexed: 11/25/2022] Open
Abstract
Most Pseudomonas putida strains are environmental microorganisms exhibiting a wide range of metabolic capability but certain strains have been reported as rare opportunistic pathogens and some emerged as multidrug resistant P. putida. This study aimed to assess the drug resistance profile of, via whole genome analysis, P. putida strain T2-2 isolated from oral cavity. At the same time, we also compared the nonenvironmental strain with environmentally isolated P. putida. In silico comparative genome analysis with available reference strains of P. putida shows that T2-2 has lesser gene counts on carbohydrate and aromatic compounds metabolisms, which suggested its little versatility. The detection of its edd gene also suggested T2-2's catabolism of glucose via ED pathway instead of EMP pathway. On the other hand, its drug resistance profile was observed via in silico gene prediction and most of the genes found were in agreement with drug-susceptibility testing in laboratory by automated VITEK 2. In addition, the finding of putative genes of multidrug resistance efflux pump and ATP-binding cassette transporters in this strain suggests a multidrug resistant phenotype. In summary, it is believed that multiple metabolic characteristics and drug resistance in P. putida strain T2-2 helped in its survival in human oral cavity.
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Martínez-García E, Nikel PI, Aparicio T, de Lorenzo V. Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression. Microb Cell Fact 2014; 13:159. [PMID: 25384394 PMCID: PMC4230525 DOI: 10.1186/s12934-014-0159-3] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 10/27/2014] [Indexed: 11/10/2022] Open
Abstract
Background Because of its adaptability to sites polluted with toxic chemicals, the model soil bacterium Pseudomonas putida is naturally endowed with a number of metabolic and stress-endurance qualities which have considerable value for hosting energy-demanding and redox reactions thereof. The growing body of knowledge on P. putida strain KT2440 has been exploited for the rational design of a derivative strain in which the genome has been heavily edited in order to construct a robust microbial cell factory. Results Eleven non-adjacent genomic deletions, which span 300 genes (i.e., 4.3% of the entire P. putida KT2440 genome), were eliminated; thereby enhancing desirable traits and eliminating attributes which are detrimental in an expression host. Since ATP and NAD(P)H availability – as well as genetic instability, are generally considered to be major bottlenecks for the performance of platform strains, a suite of functions that drain high-energy phosphate from the cells and/or consume NAD(P)H were targeted in particular, the whole flagellar machinery. Four prophages, two transposons, and three components of DNA restriction-modification systems were eliminated as well. The resulting strain (P. putida EM383) displayed growth properties (i.e., lag times, biomass yield, and specific growth rates) clearly superior to the precursor wild-type strain KT2440. Furthermore, it tolerated endogenous oxidative stress, acquired and replicated exogenous DNA, and survived better in stationary phase. The performance of a bi-cistronic GFP-LuxCDABE reporter system as a proxy of combined metabolic vitality, revealed that the deletions in P. putida strain EM383 brought about an increase of >50% in the overall physiological vigour. Conclusion The rationally modified P. putida strain allowed for the better functional expression of implanted genes by directly improving the metabolic currency that sustains the gene expression flow, instead of resorting to the classical genetic approaches (e.g., increasing the promoter strength in the DNA constructs of interest). Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0159-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Esteban Martínez-García
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Tomás Aparicio
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
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Martínez-García E, Nikel PI, Aparicio T, de Lorenzo V. Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression. Microb Cell Fact 2014. [PMID: 25384394 DOI: 10.1186/s12934-014-0159-3.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Because of its adaptability to sites polluted with toxic chemicals, the model soil bacterium Pseudomonas putida is naturally endowed with a number of metabolic and stress-endurance qualities which have considerable value for hosting energy-demanding and redox reactions thereof. The growing body of knowledge on P. putida strain KT2440 has been exploited for the rational design of a derivative strain in which the genome has been heavily edited in order to construct a robust microbial cell factory. RESULTS Eleven non-adjacent genomic deletions, which span 300 genes (i.e., 4.3% of the entire P. putida KT2440 genome), were eliminated; thereby enhancing desirable traits and eliminating attributes which are detrimental in an expression host. Since ATP and NAD(P)H availability - as well as genetic instability, are generally considered to be major bottlenecks for the performance of platform strains, a suite of functions that drain high-energy phosphate from the cells and/or consume NAD(P)H were targeted in particular, the whole flagellar machinery. Four prophages, two transposons, and three components of DNA restriction-modification systems were eliminated as well. The resulting strain (P. putida EM383) displayed growth properties (i.e., lag times, biomass yield, and specific growth rates) clearly superior to the precursor wild-type strain KT2440. Furthermore, it tolerated endogenous oxidative stress, acquired and replicated exogenous DNA, and survived better in stationary phase. The performance of a bi-cistronic GFP-LuxCDABE reporter system as a proxy of combined metabolic vitality, revealed that the deletions in P. putida strain EM383 brought about an increase of >50% in the overall physiological vigour. CONCLUSION The rationally modified P. putida strain allowed for the better functional expression of implanted genes by directly improving the metabolic currency that sustains the gene expression flow, instead of resorting to the classical genetic approaches (e.g., increasing the promoter strength in the DNA constructs of interest).
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Affiliation(s)
- Esteban Martínez-García
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Tomás Aparicio
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
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Moreno R, Rojo F. Features of pseudomonads growing at low temperatures: another facet of their versatility. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:417-426. [PMID: 25646532 DOI: 10.1111/1758-2229.12150] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pseudomonads are a diverse and ecologically successful group of γ-proteobacteria present in many environments (terrestrial, freshwater and marine), either free living or associated with plants or animals. Their success is at least partly based on their ability to grow over a wide range of temperatures, their capacity to withstand different kinds of stress and their great metabolic versatility. Although the optimal growth temperature of pseudomonads is usually close to 25–30°C, many strains can also grow between 5°C and 10°C, and some of them even close to 0°C. Such low temperatures strongly affect the physicochemical properties of macromolecules, forcing cells to evolve traits that optimize growth and help them withstand cold-induced stresses such as increased levels of reactive oxygen species, reduced membrane fluidity and enzyme activity, cold-induced protein denaturation and the greater stability of DNA and RNA secondary structures. This review gathers the information available on the strategies used by pseudomonads to adapt to low temperature growth, and briefly describes some of the biotechnological applications that might benefit from cold-adapted bacterial strains and enzymes, e.g., biotransformation or bioremediation processes to be performed at low temperatures.
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Kim J, Park W. Oxidative stress response in Pseudomonas putida. Appl Microbiol Biotechnol 2014; 98:6933-46. [PMID: 24957251 DOI: 10.1007/s00253-014-5883-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/04/2014] [Accepted: 06/05/2014] [Indexed: 11/30/2022]
Abstract
Pseudomonas putida is widely distributed in nature and is capable of degrading various organic compounds due to its high metabolic versatility. The survival capacity of P. putida stems from its frequent exposure to various endogenous and exogenous oxidative stresses. Oxidative stress is an unavoidable consequence of interactions with various reactive oxygen species (ROS)-inducing agents existing in various niches. ROS could facilitate the evolution of bacteria by mutating genomes. Aerobic bacteria maintain defense mechanisms against oxidative stress throughout their evolution. To overcome the detrimental effects of oxidative stress, P. putida has developed defensive cellular systems involving induction of stress-sensing proteins and detoxification enzymes as well as regulation of oxidative stress response networks. Genetic responses to oxidative stress in P. putida differ markedly from those observed in Escherichia coli and Salmonella spp. Two major redox-sensing transcriptional regulators, SoxR and OxyR, are present and functional in the genome of P. putida. However, the novel regulators FinR and HexR control many genes belonging to the E. coli SoxR regulon. Oxidative stress can be generated by exposure to antibiotics, and iron homeostasis in P. putida is crucial for bacterial cell survival during treatment with antibiotics. This review highlights and summarizes current knowledge of oxidative stress in P. putida, as a model soil bacterium, together with recent studies from molecular genetics perspectives.
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Affiliation(s)
- Jisun Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5Ga, Seungbuk-Ku, Seoul, 136-713, Republic of Korea
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The functional structure of central carbon metabolism in Pseudomonas putida KT2440. Appl Environ Microbiol 2014; 80:5292-303. [PMID: 24951791 DOI: 10.1128/aem.01643-14] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
What defines central carbon metabolism? The classic textbook scheme of central metabolism includes the Embden-Meyerhof-Parnas (EMP) pathway of glycolysis, the pentose phosphate pathway, and the citric acid cycle. The prevalence of this definition of central metabolism is, however, equivocal without experimental validation. We address this issue using a general experimental approach that combines the monitoring of transcriptional and metabolic flux changes between steady states on alternative carbon sources. This approach is investigated by using the model bacterium Pseudomonas putida with glucose, fructose, and benzoate as carbon sources. The catabolic reactions involved in the initial uptake and metabolism of these substrates are expected to show a correlated change in gene expressions and metabolic fluxes. However, there was no correlation for the reactions linking the 12 biomass precursor molecules, indicating a regulation mechanism other than mRNA synthesis for central metabolism. This result substantiates evidence for a (re)definition of central carbon metabolism including all reactions that are bound to tight regulation and transcriptional invariance. Contrary to expectations, the canonical Entner-Doudoroff and EMP pathways sensu stricto are not a part of central carbon metabolism in P. putida, as they are not regulated differently from the aromatic degradation pathway. The regulatory analyses presented here provide leads on a qualitative basis to address the use of alternative carbon sources by deregulation and overexpression at the transcriptional level, while rate improvements in central carbon metabolism require careful adjustment of metabolite concentrations, as regulation resides to a large extent in posttranslational and/or metabolic regulation.
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Berger A, Dohnt K, Tielen P, Jahn D, Becker J, Wittmann C. Robustness and plasticity of metabolic pathway flux among uropathogenic isolates of Pseudomonas aeruginosa. PLoS One 2014; 9:e88368. [PMID: 24709961 PMCID: PMC3977821 DOI: 10.1371/journal.pone.0088368] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/06/2014] [Indexed: 01/09/2023] Open
Abstract
Pseudomonas aeruginosa is a human pathogen that frequently causes urinary tract and catheter-associated urinary tract infections. Here, using 13C-metabolic flux analysis, we conducted quantitative analysis of metabolic fluxes in the model strain P. aeruginosa PAO1 and 17 clinical isolates. All P. aeruginosa strains catabolized glucose through the Entner-Doudoroff pathway with fully respiratory metabolism and no overflow. Together with other NADPH supplying reactions, this high-flux pathway provided by far more NADPH than needed for anabolism: a benefit for the pathogen to counteract oxidative stress imposed by the host. P. aeruginosa recruited the pentose phosphate pathway exclusively for biosynthesis. In contrast to glycolytic metabolism, which was conserved among all isolates, the flux through pyruvate metabolism, the tricarboxylic acid cycle, and the glyoxylate shunt was highly variable, likely caused by adaptive processes in individual strains during infection. This aspect of metabolism was niche-specific with respect to the corresponding flux because strains isolated from the urinary tract clustered separately from those originating from catheter-associated infections. Interestingly, most glucose-grown strains exhibited significant flux through the glyoxylate shunt. Projection into the theoretical flux space, which was computed using elementary flux-mode analysis, indicated that P. aeruginosa metabolism is optimized for efficient growth and exhibits significant potential for increasing NADPH supply to drive oxidative stress response.
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Affiliation(s)
- Antje Berger
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Katrin Dohnt
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Petra Tielen
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Judith Becker
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
- * E-mail:
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Nikel PI, de Lorenzo V. Robustness of Pseudomonas putida KT2440 as a host for ethanol biosynthesis. N Biotechnol 2014; 31:562-71. [PMID: 24572656 DOI: 10.1016/j.nbt.2014.02.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/10/2014] [Accepted: 02/15/2014] [Indexed: 12/01/2022]
Abstract
Expansion of the burgeoning biofuels agenda involves not only the design of suitable genetic and metabolic devices but also their deployment into suitable hosts that can endure the stress brought about by the products themselves. The microorganisms that are easiest to genetically manipulate for these endeavors (e.g. Escherichia coli) are often afflicted by an undesirable sensitivity to the very product that they are engineered to synthesize. In this context, we have examined the resistance to the stress arising from ethanol synthesis and/or its addition to cultures of recombinant Pseudomonas putida, using as a benchmark the same trait in an E. coli strain. To this end, ethanologenic strains of these two species were constructed by functionally expressing pdc (pyruvate decarboxylase) and adhB (alcohol dehydrogenase) from Zymomonas mobilis. Recombinants were compared under anoxic conditions as ethanol producers, and cell survival, stress resistance, and phenotypic stability were quantified in each case. P. putida consistently outperformed E. coli in every ethanol tolerance test conducted - whether the alcohol was produced endogenously or added exogenously. These results highlight the value of this bacterium as a microbial cell factory for the production of biofuels owing to its naturally pre-evolved ability to withstand different kinds of chemical stresses.
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Affiliation(s)
- Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid 28049, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid 28049, Spain.
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