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Moreno R, Yuste L, Morales G, Rojo F. Inactivation of Pseudomonas putida KT2440 pyruvate dehydrogenase relieves catabolite repression and improves the usefulness of this strain for degrading aromatic compounds. Microb Biotechnol 2024; 17:e14514. [PMID: 38923400 PMCID: PMC11196380 DOI: 10.1111/1751-7915.14514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
Pyruvate dehydrogenase (PDH) catalyses the irreversible decarboxylation of pyruvate to acetyl-CoA, which feeds the tricarboxylic acid cycle. We investigated how the loss of PDH affects metabolism in Pseudomonas putida. PDH inactivation resulted in a strain unable to utilize compounds whose assimilation converges at pyruvate, including sugars and several amino acids, whereas compounds that generate acetyl-CoA supported growth. PDH inactivation also resulted in the loss of carbon catabolite repression (CCR), which inhibits the assimilation of non-preferred compounds in the presence of other preferred compounds. Pseudomonas putida can degrade many aromatic compounds, most of which produce acetyl-CoA, making it useful for biotransformation and bioremediation. However, the genes involved in these metabolic pathways are often inhibited by CCR when glucose or amino acids are also present. Our results demonstrate that the PDH-null strain can efficiently degrade aromatic compounds even in the presence of other preferred substrates, which the wild-type strain does inefficiently, or not at all. As the loss of PDH limits the assimilation of many sugars and amino acids and relieves the CCR, the PDH-null strain could be useful in biotransformation or bioremediation processes that require growth with mixtures of preferred substrates and aromatic compounds.
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Affiliation(s)
- Renata Moreno
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
| | - Luis Yuste
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
| | - Gracia Morales
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
- Present address:
European UniversityMadridSpain
| | - Fernando Rojo
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
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2
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Dvořák P, Burýšková B, Popelářová B, Ebert BE, Botka T, Bujdoš D, Sánchez-Pascuala A, Schöttler H, Hayen H, de Lorenzo V, Blank LM, Benešík M. Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose. Nat Commun 2024; 15:2666. [PMID: 38531855 DOI: 10.1038/s41467-024-46812-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
To broaden the substrate scope of microbial cell factories towards renewable substrates, rational genetic interventions are often combined with adaptive laboratory evolution (ALE). However, comprehensive studies enabling a holistic understanding of adaptation processes primed by rational metabolic engineering remain scarce. The industrial workhorse Pseudomonas putida was engineered to utilize the non-native sugar D-xylose, but its assimilation into the bacterial biochemical network via the exogenous xylose isomerase pathway remained unresolved. Here, we elucidate the xylose metabolism and establish a foundation for further engineering followed by ALE. First, native glycolysis is derepressed by deleting the local transcriptional regulator gene hexR. We then enhance the pentose phosphate pathway by implanting exogenous transketolase and transaldolase into two lag-shortened strains and allow ALE to finetune the rewired metabolism. Subsequent multilevel analysis and reverse engineering provide detailed insights into the parallel paths of bacterial adaptation to the non-native carbon source, highlighting the enhanced expression of transaldolase and xylose isomerase along with derepressed glycolysis as key events during the process.
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Affiliation(s)
- Pavel Dvořák
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic.
| | - Barbora Burýšková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Barbora Popelářová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Birgitta E Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Cnr College Rd & Cooper Rd, St Lucia, QLD, QLD 4072, Australia
| | - Tibor Botka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Dalimil Bujdoš
- APC Microbiome Ireland, University College Cork, College Rd, Cork, T12 YT20, Ireland
- School of Microbiology, University College Cork, College Rd, Cork, T12 Y337, Ireland
| | - Alberto Sánchez-Pascuala
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Hannah Schöttler
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149, Münster, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149, Münster, Germany
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología CNB-CSIC, Cantoblanco, Darwin 3, 28049, Madrid, Spain
| | - Lars M Blank
- Institute of Applied Microbiology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
| | - Martin Benešík
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
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Molina-Henares MA, Ramos-González MI, Rinaldo S, Espinosa-Urgel M. Gene expression reprogramming of Pseudomonas alloputida in response to arginine through the transcriptional regulator ArgR. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001449. [PMID: 38511653 PMCID: PMC10963909 DOI: 10.1099/mic.0.001449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Different bacteria change their life styles in response to specific amino acids. In Pseudomonas putida (now alloputida) KT2440, arginine acts both as an environmental and a metabolic indicator that modulates the turnover of the intracellular second messenger c-di-GMP, and expression of biofilm-related genes. The transcriptional regulator ArgR, belonging to the AraC/XylS family, is key for the physiological reprogramming in response to arginine, as it controls transport and metabolism of the amino acid. To further expand our knowledge on the roles of ArgR, a global transcriptomic analysis of KT2440 and a null argR mutant growing in the presence of arginine was carried out. Results indicate that this transcriptional regulator influences a variety of cellular functions beyond arginine metabolism and transport, thus widening its regulatory role. ArgR acts as positive or negative modulator of the expression of several metabolic routes and transport systems, respiratory chain and stress response elements, as well as biofilm-related functions. The partial overlap between the ArgR regulon and those corresponding to the global regulators RoxR and ANR is also discussed.
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Affiliation(s)
- María Antonia Molina-Henares
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC. Profesor Albareda, 1. Granada 18008, Spain
| | - María Isabel Ramos-González
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC. Profesor Albareda, 1. Granada 18008, Spain
| | - Serena Rinaldo
- Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti - Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome, Italy
| | - Manuel Espinosa-Urgel
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC. Profesor Albareda, 1. Granada 18008, Spain
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4
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Tiwari R, Sathesh-Prabu C, Kim Y, Kuk Lee S. Simultaneous utilization of glucose and xylose by metabolically engineered Pseudomonas putida for the production of 3-hydroxypropionic acid. BIORESOURCE TECHNOLOGY 2024; 395:130389. [PMID: 38295962 DOI: 10.1016/j.biortech.2024.130389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/07/2024] [Accepted: 01/24/2024] [Indexed: 02/03/2024]
Abstract
Pseudomonas putida,a robust candidate for lignocellulosicbiomass-based biorefineries, encounters challenges in metabolizing xylose. In this study, Weimberg pathway was introduced intoP. putidaEM42 under a xylose-inducible promoter, resulting in slow cell growth (0.05 h-1) on xylose.Through adaptive laboratory evolution, an evolved strain exhibited highly enhanced growth on xylose (0.36 h-1), comparable to that on glucose (0.39 h-1). Whole genome sequencing identified four mutations, with two key mutations located inPP3380andPP2219. Reverse-engineered strain 8EM42_Xyl, harboring these two mutations, showed enhanced growth on xylose but co-utilizing glucose and xylose at a rate of 0.3 g/L/h. Furthermore, 8EM42_Xyl was employed for 3-hydroxypropionic acid (3HP) production from glucose and xylose by expressing malonyl-CoA reductase and acetyl-CoA carboxylase, yielding 29 g/L in fed-batch fermentation. Moreover, the engineered strain exhibited promising performance in 3HP production from empty palm fruit bunch hydrolysate, demonstrating its potential as a promising cell factory forbiorefineries.
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Affiliation(s)
- Rameshwar Tiwari
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Chandran Sathesh-Prabu
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Yuchan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Sung Kuk Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.
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5
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Moreno R, Rojo F. What are the signals that control catabolite repression in Pseudomonas? Microb Biotechnol 2024; 17:e14407. [PMID: 38227132 PMCID: PMC10832556 DOI: 10.1111/1751-7915.14407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Metabolically versatile bacteria exhibit a global regulatory response known as carbon catabolite repression (CCR), which prioritizes some carbon sources over others when all are present in sufficient amounts. This optimizes growth by distributing metabolite fluxes, but can restrict yields in biotechnological applications. The molecular mechanisms and preferred substrates for CCR vary between bacterial groups. Escherichia coli prioritizes glucose whereas Pseudomonas sp. prefer certain organic acids or amino acids. A significant issue in understanding (and potentially bypassing) CCR is the lack of information about the signals that trigger this regulatory response. In E. coli, several key compounds act as flux sensors, governing the flow of metabolites through catabolic pathways and preventing imbalances. These flux sensors can also modulate the CCR response. It has been suggested that the order of substrate preference is determined by carbon uptake flux rather than substrate identity. For Pseudomonas, much less information is available, as the signals that induce CCR are poorly understood. This article briefly discusses the available evidence on the signals that trigger CCR and the questions that remain to be answered in Pseudomonas.
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Affiliation(s)
- Renata Moreno
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
| | - Fernando Rojo
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
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Li J, Fu J, Yue C, Shang Y, Ye BC. Highly Efficient Biosynthesis of Protocatechuic Acid via Recombinant Pseudomonas putida KT2440. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37365996 DOI: 10.1021/acs.jafc.3c01511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Owing to their physiological activities, plant-derived phenolic acids, such as protocatechuic acid (PCA), have extensive applications and market prospects. However, traditional production processes present numerous challenges and cannot meet increasing market demands. Hence, we aimed to biosynthesize PCA by constructing an efficient microbial factory via metabolic engineering of Pseudomonas putida KT2440. Glucose metabolism was engineered by deleting the genes for gluconate 2-dehydrogenase to enhance PCA biosynthesis. To increase the biosynthetic metabolic flux, one extra copy of the genes aroGopt, aroQ, and aroB was inserted into the genome. The resultant strain, KGVA04, produced 7.2 g/L PCA. By inserting the degradation tags GSD and DAS to decrease the amount of shikimate dehydrogenase, PCA biosynthesis was increased to 13.2 g/L in shake-flask fermentation and 38.8 g/L in fed-batch fermentation. To the best of our knowledge, this was the first use of degradation tags to adjust the amount of a key enzyme at the protein level in P. putida KT2440, evidencing the remarkable potential of this method for naturally producing phenolic acids.
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Affiliation(s)
- Jin Li
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jianli Fu
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Cheng Yue
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yanzhe Shang
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
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7
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García-Franco A, Godoy P, Duque E, Ramos JL. Insights into the susceptibility of Pseudomonas putida to industrially relevant aromatic hydrocarbons that it can synthesize from sugars. Microb Cell Fact 2023; 22:22. [PMID: 36732770 PMCID: PMC9893694 DOI: 10.1186/s12934-023-02028-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/21/2023] [Indexed: 02/04/2023] Open
Abstract
Pseudomonas putida DOT-T1E is a highly solvent tolerant strain for which many genetic tools have been developed. The strain represents a promising candidate host for the synthesis of aromatic compounds-opening a path towards a green alternative to petrol-derived chemicals. We have engineered this strain to produce phenylalanine, which can then be used as a raw material for the synthesis of styrene via trans-cinnamic acid. To understand the response of this strain to the bioproducts of interest, we have analyzed the in-depth physiological and genetic response of the strain to these compounds. We found that in response to the exposure to the toxic compounds that the strain can produce, the cell launches a multifactorial response to enhance membrane impermeabilization. This process occurs via the activation of a cis to trans isomerase that converts cis unsaturated fatty acids to their corresponding trans isomers. In addition, the bacterial cells initiate a stress response program that involves the synthesis of a number of chaperones and ROS removing enzymes, such as peroxidases and superoxide dismutases. The strain also responds by enhancing the metabolism of glucose through the specific induction of the glucose phosphorylative pathway, Entner-Doudoroff enzymes, Krebs cycle enzymes and Nuo. In step with these changes, the cells induce two efflux pumps to extrude the toxic chemicals. Through analyzing a wide collection of efflux pump mutants, we found that the most relevant pump is TtgGHI, which is controlled by the TtgV regulator.
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Affiliation(s)
- Ana García-Franco
- Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas, c/Profesor Albareda nº 1, 18008, Granada, Spain
| | - Patricia Godoy
- Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas, c/Profesor Albareda nº 1, 18008, Granada, Spain
| | - Estrella Duque
- Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas, c/Profesor Albareda nº 1, 18008, Granada, Spain
| | - Juan Luis Ramos
- Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas, c/Profesor Albareda nº 1, 18008, Granada, Spain.
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8
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Bujdoš D, Popelářová B, Volke DC, Nikel PI, Sonnenschein N, Dvořák P. Engineering of Pseudomonas putida for accelerated co-utilization of glucose and cellobiose yields aerobic overproduction of pyruvate explained by an upgraded metabolic model. Metab Eng 2023; 75:29-46. [PMID: 36343876 DOI: 10.1016/j.ymben.2022.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/11/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
Pseudomonas putida KT2440 is an attractive bacterial host for biotechnological production of valuable chemicals from renewable lignocellulosic feedstocks as it can valorize lignin-derived aromatics or glucose obtainable from cellulose. P. putida EM42, a genome-reduced variant of strain KT2440 endowed with advantageous physiological properties, was recently engineered for growth on cellobiose, a major cellooligosaccharide product of enzymatic cellulose hydrolysis. Co-utilization of cellobiose and glucose was achieved in a mutant lacking periplasmic glucose dehydrogenase Gcd (PP_1444). However, the cause of the co-utilization phenotype remained to be understood and the Δgcd strain had a significant growth defect. In this study, we investigated the basis of the simultaneous uptake of the two sugars and accelerated the growth of P. putida EM42 Δgcd mutant for the bioproduction of valuable compounds from glucose and cellobiose. We show that the gcd deletion lifted the inhibition of the exogenous β-glucosidase BglC from Thermobifida fusca exerted by the intermediates of the periplasmic glucose oxidation pathway. The additional deletion of hexR gene, which encodes a repressor of the upper glycolysis genes, failed to restore rapid growth on glucose. The reduced growth rate of the Δgcd mutant was partially compensated by the implantation of heterologous glucose and cellobiose transporters (Glf from Zymomonas mobilis and LacY from Escherichia coli, respectively). Remarkably, this intervention resulted in the accumulation of pyruvate in aerobic P. putida cultures. We demonstrated that the excess of this key metabolic intermediate can be redirected to the enhanced biosynthesis of ethanol and lactate. The pyruvate overproduction phenotype was then unveiled by an upgraded genome-scale metabolic model constrained with proteomic and kinetic data. The model pointed to the saturation of glucose catabolism enzymes due to unregulated substrate uptake and it predicted improved bioproduction of pyruvate-derived chemicals by the engineered strain. This work sheds light on the co-metabolism of cellulosic sugars in an attractive biotechnological host and introduces a novel strategy for pyruvate overproduction in bacterial cultures under aerobic conditions.
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Affiliation(s)
- Dalimil Bujdoš
- Department of Experimental Biology (Section of Microbiology, Microbial Bioengineering Laboratory), Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Barbora Popelářová
- Department of Experimental Biology (Section of Microbiology, Microbial Bioengineering Laboratory), Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kgs, Lyngby, Denmark
| | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Pavel Dvořák
- Department of Experimental Biology (Section of Microbiology, Microbial Bioengineering Laboratory), Faculty of Science, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic.
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Collin B, Auffan M, Doelsch E, Proux O, Kieffer I, Ortet P, Santaella C. Bacterial Metabolites and Particle Size Determine Cerium Oxide Nanomaterial Biotransformation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16838-16847. [PMID: 36350260 DOI: 10.1021/acs.est.2c05280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Soil is a major receptor of manufactured nanomaterials (NMs) following unintentional releases or intentional uses. Ceria NMs have been shown to undergo biotransformation in plant and soil organisms with a partial Ce(IV) reduction into Ce(III), but the influence of environmentally widespread soil bacteria is poorly understood. We used high-energy resolution fluorescence-detected X-ray absorption spectroscopy (HERFD-XAS) with an unprecedented detection limit to assess Ce speciation in a model soil bacterium (Pseudomonas brassicacearum) exposed to CeO2 NMs of different sizes and shapes. The findings revealed that the CeO2 NM's size drives the biotransformation process. No biotransformation was observed for the 31 nm CeO2 NMs, contrary to 7 and 4 nm CeO2 NMs, with a Ce reduction of 64 ± 14% and 70 ± 15%, respectively. This major reduction appeared quickly, from the early exponential bacterial growth phase. Environmentally relevant organic acid metabolites secreted by Pseudomonas, especially in the rhizosphere, were investigated. The 2-keto-gluconic and citric acid metabolites alone were able to induce a significant reduction in 4 nm CeO2 NMs. The high biotransformation measured for <7 nm NMs would affect the fate of Ce in the soil and biota.
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Affiliation(s)
- Blanche Collin
- Aix Marseille Univ, CNRS, IRD, INRAE, Coll France, CEREGE, Aix-en-Provence, France
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 St-Paul-lez-Durance, France
| | - Mélanie Auffan
- Aix Marseille Univ, CNRS, IRD, INRAE, Coll France, CEREGE, Aix-en-Provence, France
| | - Emmanuel Doelsch
- CIRAD, UPR Recyclage et risque, F-34398 Montpellier, France
- Recyclage et risque, Univ Montpellier, CIRAD, Montpellier, France
| | - Olivier Proux
- BM30/CRG-FAME, ESRF, Université Grenoble Alpes, CNRS, IRSTEa, Météo France, IRD, OSUG, 38000 Grenoble, France
| | - Isabelle Kieffer
- BM30/CRG-FAME, ESRF, Université Grenoble Alpes, CNRS, IRSTEa, Météo France, IRD, OSUG, 38000 Grenoble, France
| | - Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 St-Paul-lez-Durance, France
| | - Catherine Santaella
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 St-Paul-lez-Durance, France
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10
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Kotecka K, Kawalek A, Modrzejewska-Balcerek M, Gawor J, Zuchniewicz K, Gromadka R, Bartosik AA. Functional Characterization of TetR-like Transcriptional Regulator PA3973 from Pseudomonas aeruginosa. Int J Mol Sci 2022; 23:ijms232314584. [PMID: 36498910 PMCID: PMC9736018 DOI: 10.3390/ijms232314584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
Pseudomonas aeruginosa, a human opportunistic pathogen, is a common cause of nosocomial infections. Its ability to survive under different conditions relies on a complex regulatory network engaging transcriptional regulators controlling metabolic pathways and capabilities to efficiently use the available resources. P. aeruginosa PA3973 encodes an uncharacterized TetR family transcriptional regulator. In this study, we applied a transcriptome profiling (RNA-seq), genome-wide identification of binding sites using ChIP-seq, as well as the phenotype analyses to unravel the biological role of PA3973. Transcriptional profiling of P. aeruginosa PAO1161 overexpressing PA3973 showed changes in the mRNA level of 648 genes. Concomitantly, ChIP-seq analysis identified more than 300 PA3973 binding sites in the P. aeruginosa genome. A 13 bp sequence motif was indicated as the binding site of PA3973. The PA3973 regulon encompasses the PA3972-PA3971 genes encoding a probable acyl-CoA dehydrogenase and a thioesterase. In vitro analysis showed PA3973 binding to PA3973p. Accordingly, the lack of PA3973 triggered increased expression of PA3972 and PA3971. The ∆PA3972-71 PAO1161 strain demonstrated impaired growth in the presence of stress-inducing agents hydroxylamine or hydroxyurea, thus suggesting the role of PA3972-71 in pathogen survival upon stress. Overall our results showed that TetR-type transcriptional regulator PA3973 has multiple binding sites in the P. aeruginosa genome and influences the expression of diverse genes, including PA3972-PA3971, encoding proteins with a proposed role in stress response.
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11
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Wirth NT, Gurdo N, Krink N, Vidal-Verdú À, Donati S, Férnandez-Cabezón L, Wulff T, Nikel PI. A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes. Metab Eng 2022; 74:83-97. [PMID: 36155822 DOI: 10.1016/j.ymben.2022.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/17/2022] [Accepted: 09/17/2022] [Indexed: 11/30/2022]
Abstract
Acetyl-coenzyme A (AcCoA) is a metabolic hub in virtually all living cells, serving as both a key precursor of essential biomass components and a metabolic sink for catabolic pathways for a large variety of substrates. Owing to this dual role, tight growth-production coupling schemes can be implemented around the AcCoA node. Building on this concept, a synthetic C2 auxotrophy was implemented in the platform bacterium Pseudomonas putida through an in silico-informed engineering approach. A growth-coupling strategy, driven by AcCoA demand, allowed for direct selection of an alternative sugar assimilation route-the phosphoketolase (PKT) shunt from bifidobacteria. Adaptive laboratory evolution forced the synthetic P. putida auxotroph to rewire its metabolic network to restore C2 prototrophy via the PKT shunt. Large-scale structural chromosome rearrangements were identified as possible mechanisms for adjusting the network-wide proteome profile, resulting in improved PKT-dependent growth phenotypes. 13C-based metabolic flux analysis revealed an even split between the native Entner-Doudoroff pathway and the synthetic PKT bypass for glucose processing, leading to enhanced carbon conservation. These results demonstrate that the P. putida metabolism can be radically rewired to incorporate a synthetic C2 metabolism, creating novel network connectivities and highlighting the importance of unconventional engineering strategies to support efficient microbial production.
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Affiliation(s)
- Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Nicolas Krink
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Àngela Vidal-Verdú
- Institute for Integrative Systems Biology I2SysBio (Universitat de València-CSIC), Calle del Catedràtic Agustin Escardino Benlloch 9, 46980, Paterna, Spain
| | - Stefano Donati
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Lorena Férnandez-Cabezón
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark.
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12
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Pseudomonas aeruginosa Pangenome: Core and Accessory Genes of a Highly Resourceful Opportunistic Pathogen. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:3-28. [DOI: 10.1007/978-3-031-08491-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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13
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Phale PS, Mohapatra B, Malhotra H, Shah BA. Eco-physiological portrait of a novel Pseudomonas sp. CSV86: an ideal host/candidate for metabolic engineering and bioremediation. Environ Microbiol 2021; 24:2797-2816. [PMID: 34347343 DOI: 10.1111/1462-2920.15694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/30/2022]
Abstract
Pseudomonas sp. CSV86, an Indian soil isolate, degrades wide range of aromatic compounds like naphthalene, benzoate and phenylpropanoids, amongst others. Isolate displays the unique and novel property of preferential utilization of aromatics over glucose and co-metabolizes them with organic acids. Interestingly, as compared to other Pseudomonads, strain CSV86 harbours only high-affinity glucokinase pathway (and absence of low-affinity oxidative route) for glucose metabolism. Such lack of gluconate loop might be responsible for the novel phenotype of preferential utilization of aromatics. The genome analysis and comparative functional mining indicated a large genome (6.79 Mb) with significant enrichment of regulators, transporters as well as presence of various secondary metabolite production clusters, suggesting its eco-physiological and metabolic versatility. Strain harbours various integrative conjugative elements (ICEs) and genomic islands, probably acquired through horizontal gene transfer events, leading to genome mosaicity and plasticity. Naphthalene degradation genes are arranged as regulonic clusters and found to be part of ICECSV86nah . Various eco-physiological properties and absence of major pathogenicity and virulence factors (risk group-1) in CSV86 suggest it to be an ideal candidate for bioremediation. Further, strain can serve as an ideal chassis for metabolic engineering to degrade various xenobiotics preferentially over simple carbon sources for efficient remediation.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
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14
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15
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Targeting Bacterial Gyrase with Cystobactamid, Fluoroquinolone, and Aminocoumarin Antibiotics Induces Distinct Molecular Signatures in Pseudomonas aeruginosa. mSystems 2021; 6:e0061021. [PMID: 34254824 PMCID: PMC8407119 DOI: 10.1128/msystems.00610-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The design of novel antibiotics relies on a profound understanding of their mechanism of action. While it has been shown that cellular effects of antibiotics cluster according to their molecular targets, we investigated whether compounds binding to different sites of the same target can be differentiated by their transcriptome or metabolome signatures. The effects of three fluoroquinolones, two aminocoumarins, and two cystobactamids, all inhibiting bacterial gyrase, on Pseudomonas aeruginosa at subinhibitory concentrations could be distinguished clearly by RNA sequencing as well as metabolomics. We observed a strong (2.8- to 212-fold) induction of autolysis-triggering pyocins in all gyrase inhibitors, which correlated with extracellular DNA (eDNA) release. Gyrase B-binding aminocoumarins induced the most pronounced changes, including a strong downregulation of phenazine and rhamnolipid virulence factors. Cystobactamids led to a downregulation of a glucose catabolism pathway. The study implies that clustering cellular mechanisms of action according to the primary target needs to take class-dependent variances into account. IMPORTANCE Novel antibiotics are urgently needed to tackle the growing worldwide problem of antimicrobial resistance. Bacterial pathogens possess few privileged targets for a successful therapy: the majority of existing antibiotics as well as current candidates in development target the complex bacterial machinery for cell wall synthesis, protein synthesis, or DNA replication. An important mechanistic question addressed by this study is whether inhibiting such a complex target at different sites with different compounds has similar or differentiated cellular consequences. Using transcriptomics and metabolomics, we demonstrate that three different classes of gyrase inhibitors can be distinguished by their molecular signatures in P. aeruginosa. We describe the cellular effects of a promising, recently identified gyrase inhibitor class, the cystobactamids, in comparison to those of the established gyrase A-binding fluoroquinolones and the gyrase B-binding aminocoumarins. The study results have implications for mode-of-action discovery approaches based on target-specific reference compounds, as they highlight the intraclass variability of cellular compound effects.
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16
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Nguyen AV, Lai B, Adrian L, Krömer JO. The anoxic electrode-driven fructose catabolism of Pseudomonas putida KT2440. Microb Biotechnol 2021; 14:1784-1796. [PMID: 34115443 PMCID: PMC8313287 DOI: 10.1111/1751-7915.13862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/20/2021] [Indexed: 11/29/2022] Open
Abstract
Pseudomonas putida (P. putida) is a microorganism of interest for various industrial processes, yet its strictly aerobic nature limits application. Despite previous attempts to adapt P. putida to anoxic conditions via genetic engineering or the use of a bioelectrochemical system (BES), the problem of energy shortage and internal redox imbalance persists. In this work, we aimed to provide the cytoplasmic metabolism with different monosaccharides, other than glucose, and explored the physiological response in P. putida KT2440 during bioelectrochemical cultivation. The periplasmic oxidation cascade was found to be able to oxidize a wide range of aldoses to their corresponding (keto-)aldonates. Unexpectedly, isomerization of the ketose fructose to mannose also enabled oxidation by glucose dehydrogenase, a new pathway uncovered for fructose metabolism in P. putida KT2440 in BES. Besides the isomerization, the remainder of fructose was imported into the cytoplasm and metabolized. This resulted in a higher NADPH/NADP+ ratio, compared to glucose. Comparative proteomics further revealed the upregulation of proteins in the lower central carbon metabolism during the experiment. These findings highlight that the choice of a substrate in BES can target cytosolic and periplasmic oxidation pathways, and that electrode-driven redox balancing can drive these pathways in P. putida under anaerobic conditions.
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Affiliation(s)
- Anh Vu Nguyen
- Department of Solar MaterialsHelmholtz Centre for Environmental Research ‐ UFZLeipzigGermany
| | - Bin Lai
- Department of Solar MaterialsHelmholtz Centre for Environmental Research ‐ UFZLeipzigGermany
| | - Lorenz Adrian
- Department of Environmental BiotechnologyHelmholtz Centre for Environmental Research ‐ UFZLeipzigGermany
- Chair of GeobiotechnologyTechnische Universität BerlinBerlinGermany
| | - Jens O. Krömer
- Department of Solar MaterialsHelmholtz Centre for Environmental Research ‐ UFZLeipzigGermany
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17
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Liang J, Gao S, Wu Z, Rijnaarts HHM, Grotenhuis T. DNA-SIP identification of phenanthrene-degrading bacteria undergoing bioaugmentation and natural attenuation in petroleum-contaminated soil. CHEMOSPHERE 2021; 266:128984. [PMID: 33234305 DOI: 10.1016/j.chemosphere.2020.128984] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/08/2020] [Accepted: 11/13/2020] [Indexed: 06/11/2023]
Abstract
DNA-stable isotope probing (SIP) with 13C labeled phenanthrene (PHE) as substrate was used to identify specific bacterial degraders during natural attenuation (NA) and bioaugmentation (BA) in petroleum contaminated soil. BA, with the addition of a bacterial suspension mixture named GZ, played a significant role in PHE degradation with a higher PHE removal rate (∼90%) than that of NA (∼80%) during the first 3 days, and remarkably altered microbial communities. Of the five strains introduced in BA, only two genera, particularly, Ochrobactrum, Rhodococcus were extensively responsible for PHE-degradation. Six (Bacillus sp., Acinetobacter sp., Xanthomonas sp., Conexibacter sp., Acinetobacter sp. and Staphylococcus sp.) and seven (Ochrobactrum sp., Rhodococcus sp., Alkanindiges sp., Williamsia sp., Sphingobium sp., Gillisia sp. and Massilia sp.) bacteria responsible for PHE degradation were identified in NA and BA treatments, respectively. This study reports for the first time the association of Xanthomonas sp., Williamsia sp., and Gillisia sp. to PHE degradation.
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Affiliation(s)
- Jidong Liang
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Sha Gao
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; Department of Environmental Technology, Wageningen University and Research, Wageningen, 6700AA, the Netherlands
| | - Zijun Wu
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Huub H M Rijnaarts
- Department of Environmental Technology, Wageningen University and Research, Wageningen, 6700AA, the Netherlands
| | - Tim Grotenhuis
- Department of Environmental Technology, Wageningen University and Research, Wageningen, 6700AA, the Netherlands
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18
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Xu C, Cao Q, Lan L. Glucose-Binding of Periplasmic Protein GltB Activates GtrS-GltR Two-Component System in Pseudomonas aeruginosa. Microorganisms 2021; 9:447. [PMID: 33670077 PMCID: PMC7927077 DOI: 10.3390/microorganisms9020447] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 12/14/2022] Open
Abstract
A two-component system GtrS-GltR is required for glucose transport activity in P. aeruginosa and plays a key role during P. aeruginosa-host interactions. However, the mechanism of action of GtrS-GltR has not been definitively established. Here, we show that gltB, which encodes a periplasmic glucose binding protein, is essential for the glucose-induced activation of GtrS-GltR in P. aeruginosa. We determined that GltB is capable of binding to membrane regulatory proteins including GtrS, the sensor kinase of the GtrS-GltR TCS. We observed that alanine substitution of glucose-binding residues abolishes the ability of GltB to promote the activation of GtrS-GltR. Importantly, like the gtrS deletion mutant, gltB deletion mutant showed attenuated virulence in both Drosophila melanogaster and mouse models of infection. In addition, using CHIP-seq experiments, we showed that the promoter of gltB is the major in vivo target of GltR. Collectively, these data suggest that periplasmic binding protein GltB and GtrS-GltR TCS form a complex regulatory circuit that regulates the virulence of P. aeruginosa in response to glucose.
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Affiliation(s)
- Chenchen Xu
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China;
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China;
| | - Qiao Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China;
| | - Lefu Lan
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China;
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China;
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai 201203, China
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19
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Li J, Ye BC. Metabolic engineering of Pseudomonas putida KT2440 for high-yield production of protocatechuic acid. BIORESOURCE TECHNOLOGY 2021; 319:124239. [PMID: 33254462 DOI: 10.1016/j.biortech.2020.124239] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 06/12/2023]
Abstract
Protocatechuic acid (PCA) has been widely utilized in conventional pharmaceutical, cosmetic and functional food industries. Currently, chemical synthesis and solvent extraction are the main methods for commercial production, indicating several disadvantages. In this study, we developed a method for the biosynthesis of PCA in Pseudomonas putida KT2440 in high yield. First, we developed constitutive promoters with different expression intensities for fine-tuned gene expression. Second, we improved the biosynthesis of "natural" PCA in P. putida KT2440 via multilevel metabolic engineering strategies: overexpression of rate-limiting enzymes, removal of negative regulators, attenuation of pathway competition, and enhancement of precursor supply. Finally, by further bioprocess engineering efforts, the best-producing strain reached a titer of 12.5 g/L PCA from glucose at 72 h in a shake flask and 21.7 g/L in fed-batch fermentation without antibiotic pressure. This was the highest PCA titer from glucose using metabolically engineered microbial cell factories reported to date.
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Affiliation(s)
- Jin Li
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
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20
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Song Y, Luo G, Zhu Y, Li T, Li C, He L, Zhao N, Zhao C, Yang J, Huang Q, Mu X, Tang X, Kang M, Wu S, He Y, Bao R. Pseudomonas aeruginosa antitoxin HigA functions as a diverse regulatory factor by recognizing specific pseudopalindromic DNA motifs. Environ Microbiol 2020; 23:1541-1558. [PMID: 33346387 DOI: 10.1111/1462-2920.15365] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 02/05/2023]
Abstract
Type II toxin-antitoxin (TA) systems modulate many essential cellular processes in prokaryotic organisms. Recent studies indicate certain type II antitoxins also transcriptionally regulate other genes, besides neutralizing toxin activity. Herein, we investigated the diverse transcriptional repression properties of type II TA antitoxin PaHigA from Pseudomonas aeruginosa. Biochemical and functional analyses showed that PaHigA recognized variable pseudopalindromic DNA sequences and repressed expression of multiple genes. Furthermore, we presented high resolution structures of apo-PaHigA, PaHigA-PhigBA and PaHigA-Ppa2440 complex, describing how the rearrangements of the HTH domain accounted for the different DNA-binding patterns among HigA homologues. Moreover, we demonstrated that the N-terminal loop motion of PaHigA was associated with its apo and DNA-bound states, reflecting a switch mechanism regulating HigA antitoxin function. Collectively, this work extends our understanding of how the PaHigB/HigA system regulates multiple metabolic pathways to balance the growth and stress response in P. aeruginosa and could guide further development of anti-TA oriented strategies for pathogen treatment.
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Affiliation(s)
- Yingjie Song
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Guihua Luo
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Yibo Zhu
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Tao Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Changcheng Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Lihui He
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ninglin Zhao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Chang Zhao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Jing Yang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Qin Huang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xingyu Mu
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xinyue Tang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Mei Kang
- Department of Laboratory medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Siying Wu
- Department of Laboratory medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yongxing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
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21
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Moxley-Paquette V, Lane D, Soong R, Ning P, Bastawrous M, Wu B, Pedram MZ, Haque Talukder MA, Ghafar-Zadeh E, Zverev D, Martin R, Macpherson B, Vargas M, Schmidig D, Graf S, Frei T, Al Adwan-Stojilkovic D, De Castro P, Busse F, Bermel W, Kuehn T, Kuemmerle R, Fey M, Decker F, Stronks H, Sullan RMA, Utz M, Simpson AJ. 5-Axis CNC Micromilling for Rapid, Cheap, and Background-Free NMR Microcoils. Anal Chem 2020; 92:15454-15462. [PMID: 33170641 DOI: 10.1021/acs.analchem.0c03126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The superior mass sensitivity of microcoil technology in nuclear magnetic resonance (NMR) spectroscopy provides potential for the analysis of extremely small-mass-limited samples such as eggs, cells, and tiny organisms. For optimal performance and efficiency, the size of the microcoil should be tailored to the size of the mass-limited sample of interest, which can be costly as mass-limited samples come in many shapes and sizes. Therefore, rapid and economic microcoil production methods are needed. One method with great potential is 5-axis computer numerical control (CNC) micromilling, commonly used in the jewelry industry. Most CNC milling machines are designed to process larger objects and commonly have a precision of >25 μm (making the machining of common spiral microcoils, for example, impossible). Here, a 5-axis MiRA6 CNC milling machine, specifically designed for the jewelry industry, with a 0.3 μm precision was used to produce working planar microcoils, microstrips, and novel microsensor designs, with some tested on the NMR in less than 24 h after the start of the design process. Sample wells could be built into the microsensor and could be machined at the same time as the sensors themselves, in some cases leaving a sheet of Teflon as thin as 10 μm between the sample and the sensor. This provides the freedom to produce a wide array of designs and demonstrates 5-axis CNC micromilling as a versatile tool for the rapid prototyping of NMR microsensors. This approach allowed the experimental optimization of a prototype microstrip for the analysis of two intact adult Daphnia magna organisms. In addition, a 3D volume slotted-tube resonator was produced that allowed for 2D 1H-13C NMR of D. magna neonates and exhibited 1H sensitivity (nLODω600 = 1.49 nmol s1/2) close to that of double strip lines, which themselves offer the best compromise between concentration and mass sensitivity published to date.
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Affiliation(s)
- Vincent Moxley-Paquette
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
| | - Daniel Lane
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
| | - Ronald Soong
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
| | - Paris Ning
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
| | - Monica Bastawrous
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
| | - Bing Wu
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
| | - Maysam Zamani Pedram
- Lassonde School of Engineering, York University, 4700 Keele Street, North York, Ontario, M3J 1P3, Canada.,Faculty of Medicine, Department of Radiology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Md Aminul Haque Talukder
- Lassonde School of Engineering, York University, 4700 Keele Street, North York, Ontario, M3J 1P3, Canada
| | - Ebrahim Ghafar-Zadeh
- Lassonde School of Engineering, York University, 4700 Keele Street, North York, Ontario, M3J 1P3, Canada
| | - Dimitri Zverev
- NSCNC Manufacturing Ltd., 1515 Broadway Street Unit 607, Port Coquitlam, British Columbia, V3C 6M2, Canada
| | - Richard Martin
- IMicrosolder, 57 Marshall Street West, Meaford, Ontario, N4L 1E4, Canada
| | - Bob Macpherson
- Apogee Steel Fabrication Inc., 3600 Erindale Station Road, Mississauga, Ontario, L5C 2T1, Canada
| | - Mike Vargas
- Apogee Steel Fabrication Inc., 3600 Erindale Station Road, Mississauga, Ontario, L5C 2T1, Canada
| | - Daniel Schmidig
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Stephan Graf
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Thomas Frei
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | | | - Peter De Castro
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Falko Busse
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Wolfgang Bermel
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Till Kuehn
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Rainer Kuemmerle
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Michael Fey
- Bruker Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821-3991, United States
| | - Frank Decker
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Henry Stronks
- Bruker Canada Ltd., 2800 High Point Drive, Milton, Ontario L9T 6P4, Canada
| | - Ruby May A Sullan
- Department of Physical and Environmental Science, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
| | - Marcel Utz
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - André J Simpson
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada.,Department of Physical and Environmental Science, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
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22
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Panayidou S, Georgiades K, Christofi T, Tamana S, Promponas VJ, Apidianakis Y. Pseudomonas aeruginosa core metabolism exerts a widespread growth-independent control on virulence. Sci Rep 2020; 10:9505. [PMID: 32528034 PMCID: PMC7289854 DOI: 10.1038/s41598-020-66194-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/13/2020] [Indexed: 02/04/2023] Open
Abstract
To assess the role of core metabolism genes in bacterial virulence - independently of their effect on growth - we correlated the genome, the transcriptome and the pathogenicity in flies and mice of 30 fully sequenced Pseudomonas strains. Gene presence correlates robustly with pathogenicity differences among all Pseudomonas species, but not among the P. aeruginosa strains. However, gene expression differences are evident between highly and lowly pathogenic P. aeruginosa strains in multiple virulence factors and a few metabolism genes. Moreover, 16.5%, a noticeable fraction of the core metabolism genes of P. aeruginosa strain PA14 (compared to 8.5% of the non-metabolic genes tested), appear necessary for full virulence when mutated. Most of these virulence-defective core metabolism mutants are compromised in at least one key virulence mechanism independently of auxotrophy. A pathway level analysis of PA14 core metabolism, uncovers beta-oxidation and the biosynthesis of amino-acids, succinate, citramalate, and chorismate to be important for full virulence. Strikingly, the relative expression among P. aeruginosa strains of genes belonging in these metabolic pathways is indicative of their pathogenicity. Thus, P. aeruginosa strain-to-strain virulence variation, remains largely obscure at the genome level, but can be dissected at the pathway level via functional transcriptomics of core metabolism.
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Affiliation(s)
- Stavria Panayidou
- Infection and Cancer Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Kaliopi Georgiades
- Infection and Cancer Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.,Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Theodoulakis Christofi
- Infection and Cancer Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Stella Tamana
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.
| | - Yiorgos Apidianakis
- Infection and Cancer Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.
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23
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Hua C, Wang T, Shao X, Xie Y, Huang H, Liu J, Zhang W, Zhang Y, Ding Y, Jiang L, Wang X, Deng X. Pseudomonas syringaedual‐function protein Lon switches between virulence and metabolism by acting as bothDNA‐binding transcriptional regulator and protease in different environments. Environ Microbiol 2020; 22:2968-2988. [DOI: 10.1111/1462-2920.15067] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Canfeng Hua
- Department of Biomedical SciencesCity University of Hong Kong, 83 Tat Chee Road, 16 Kowloon Tong, Hong Kong China
| | - Tingting Wang
- Department of Biomedical SciencesCity University of Hong Kong, 83 Tat Chee Road, 16 Kowloon Tong, Hong Kong China
| | - Xiaolong Shao
- Department of Biomedical SciencesCity University of Hong Kong, 83 Tat Chee Road, 16 Kowloon Tong, Hong Kong China
| | - Yingpeng Xie
- Department of Biomedical SciencesCity University of Hong Kong, 83 Tat Chee Road, 16 Kowloon Tong, Hong Kong China
| | - Hao Huang
- Department of Biomedical SciencesCity University of Hong Kong, 83 Tat Chee Road, 16 Kowloon Tong, Hong Kong China
| | - Jingui Liu
- Department of Biomedical SciencesCity University of Hong Kong, 83 Tat Chee Road, 16 Kowloon Tong, Hong Kong China
| | - Weitong Zhang
- Department of Biomedical SciencesCity University of Hong Kong, 83 Tat Chee Road, 16 Kowloon Tong, Hong Kong China
| | - Yingchao Zhang
- Department of Biomedical SciencesCity University of Hong Kong, 83 Tat Chee Road, 16 Kowloon Tong, Hong Kong China
| | - Yiqing Ding
- Department of Biomedical SciencesCity University of Hong Kong, 83 Tat Chee Road, 16 Kowloon Tong, Hong Kong China
| | - Lin Jiang
- Department of Biomedical SciencesCity University of Hong Kong, 83 Tat Chee Road, 16 Kowloon Tong, Hong Kong China
| | - Xin Wang
- Department of Biomedical SciencesCity University of Hong Kong, 83 Tat Chee Road, 16 Kowloon Tong, Hong Kong China
| | - Xin Deng
- Department of Biomedical SciencesCity University of Hong Kong, 83 Tat Chee Road, 16 Kowloon Tong, Hong Kong China
- Shenzhen Research InstituteCity University of Hong Kong Shenzhen Guangdong China
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24
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Nitschel R, Ankenbauer A, Welsch I, Wirth NT, Massner C, Ahmad N, McColm S, Borges F, Fotheringham I, Takors R, Blombach B. Engineering Pseudomonas putida KT2440 for the production of isobutanol. Eng Life Sci 2020; 20:148-159. [PMID: 32874178 PMCID: PMC7447888 DOI: 10.1002/elsc.201900151] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/08/2019] [Accepted: 12/10/2019] [Indexed: 11/06/2022] Open
Abstract
We engineered P. putida for the production of isobutanol from glucose by preventing product and precursor degradation, inactivation of the soluble transhydrogenase SthA, overexpression of the native ilvC and ilvD genes, and implementation of the feedback-resistant acetolactate synthase AlsS from Bacillus subtilis, ketoacid decarboxylase KivD from Lactococcus lactis, and aldehyde dehydrogenase YqhD from Escherichia coli. The resulting strain P. putida Iso2 produced isobutanol with a substrate specific product yield (Y Iso/S) of 22 ± 2 mg per gram of glucose under aerobic conditions. Furthermore, we identified the ketoacid decarboxylase from Carnobacterium maltaromaticum to be a suitable alternative for isobutanol production, since replacement of kivD from L. lactis in P. putida Iso2 by the variant from C. maltaromaticum yielded an identical YIso/S. Although P. putida is regarded as obligate aerobic, we show that under oxygen deprivation conditions this bacterium does not grow, remains metabolically active, and that engineered producer strains secreted isobutanol also under the non-growing conditions.
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Affiliation(s)
- Robert Nitschel
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Andreas Ankenbauer
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Ilona Welsch
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Nicolas T. Wirth
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Christoph Massner
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Naveed Ahmad
- Ingenza Ltd., Roslin Innovation CentreCharnock Bradley Building, Easter Bush CampusRoslinUK
| | - Stephen McColm
- Ingenza Ltd., Roslin Innovation CentreCharnock Bradley Building, Easter Bush CampusRoslinUK
| | - Frédéric Borges
- Laboratoire d'Ingénierie des Biomolécules (LIBio)Université de LorraineNancyFrance
| | - Ian Fotheringham
- Ingenza Ltd., Roslin Innovation CentreCharnock Bradley Building, Easter Bush CampusRoslinUK
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Bastian Blombach
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
- Microbial Biotechnology, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
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25
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Turner SE, Pang YY, O'Malley MR, Weisberg AJ, Fraser VN, Yan Q, Chang JH, Anderson JC. A DeoR-Type Transcription Regulator Is Required for Sugar-Induced Expression of Type III Secretion-Encoding Genes in Pseudomonas syringae pv. tomato DC3000. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:509-518. [PMID: 31829102 DOI: 10.1094/mpmi-10-19-0290-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The type III secretion system (T3SS) of plant-pathogenic Pseudomonas syringae is essential for virulence. Genes encoding the T3SS are not constitutively expressed and must be induced upon infection. Plant-derived metabolites, including sugars such as fructose and sucrose, are inducers of T3SS-encoding genes, yet the molecular mechanisms underlying perception of these host signals by P. syringae are unknown. Here, we report that sugar-induced expression of type III secretion A (setA), predicted to encode a DeoR-type transcription factor, is required for maximal sugar-induced expression of T3SS-associated genes in P. syringae DC3000. From a Tn5 transposon mutagenesis screen, we identified two independent mutants with insertions in setA. When both setA::Tn5 mutants were cultured in minimal medium containing fructose, genes encoding the T3SS master regulator HrpL and effector AvrRpm1 were expressed at lower levels relative to that of a wild-type strain. Decreased hrpL and avrRpm1 expression also occurred in a setA::Tn5 mutant in response to glucose, sucrose, galactose, and mannitol, demonstrating that setA is genetically required for T3SS induction by many different sugars. Expression of upstream regulators hrpR/S and rpoN was not altered in setA::Tn5, indicating that SetA positively regulates hrpL expression independently of increased transcription of these genes. In addition to decreased response to defined sugar signals, a setA::Tn5 mutant had decreased T3SS deployment during infection and was compromised in its ability to grow in planta and cause disease. These data suggest that SetA is necessary for P. syringae to effectively respond to T3SS-inducing sugar signals encountered during infection.
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Affiliation(s)
- Sydney E Turner
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
- Honors College, Oregon State University
| | - Yin-Yuin Pang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Megan R O'Malley
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Valerie N Fraser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
- Molecular and Cellular Biology Program, Oregon State University
| | - Qing Yan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
- Center for Genome Research and Biocomputing, Oregon State University
| | - Jeffrey C Anderson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
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26
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Rubio-Gómez JM, Santiago CM, Udaondo Z, Garitaonaindia MT, Krell T, Ramos JL, Daddaoua A. Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide. Front Microbiol 2020; 11:202. [PMID: 32153524 PMCID: PMC7044273 DOI: 10.3389/fmicb.2020.00202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/28/2020] [Indexed: 01/22/2023] Open
Abstract
Pseudomonas aeruginosa is an ubiquitous gram-negative opportunistic human pathogen which is not considered part of the human commensal gut microbiota. However, depletion of the intestinal microbiota (Dysbiosis) following antibiotic treatment facilitates the colonization of the intestinal tract by Multidrug-Resistant P. aeruginosa. One possible strategy is based on the use of functional foods with prebiotic activity. The bifidogenic effect of the prebiotic inulin and its hydrolyzed form (fructooligosaccharide: FOS) is well established since they promote the growth of specific beneficial (probiotic) gut bacteria such as bifidobacteria. Previous studies of the opportunistic nosocomial pathogen Pseudomonas aeruginosa PAO1 have shown that inulin and to a greater extent FOS reduce growth and biofilm formation, which was found to be due to a decrease in motility and exotoxin secretion. However, the transcriptional basis for these phenotypic alterations remains unclear. To address this question we conducted RNA-sequence analysis. Changes in the transcript level induced by inulin and FOS were similar, but a set of transcript levels were increased in response to inulin and reduced in the presence of FOS. In the presence of inulin or FOS, 260 and 217 transcript levels, respectively, were altered compared to the control to which no polysaccharide was added. Importantly, changes in transcript levels of 57 and 83 genes were found to be specific for either inulin or FOS, respectively, indicating that both compounds trigger different changes. Gene pathway analyses of differentially expressed genes (DEG) revealed a specific FOS-mediated reduction in transcript levels of genes that participate in several canonical pathways involved in metabolism and growth, motility, biofilm formation, β-lactamase resistance, and in the modulation of type III and VI secretion systems; results that have been partially verified by real time quantitative PCR measurements. Moreover, we have identified a genomic island formed by a cluster of 15 genes, encoding uncharacterized proteins, which were repressed in the presence of FOS. The analysis of isogenic mutants has shown that genes of this genomic island encode proteins involved in growth, biofilm formation and motility. These results indicate that FOS selectively modulates bacterial pathogenicity by interfering with different signaling pathways.
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Affiliation(s)
- José Manuel Rubio-Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Department of Pharmacology, School of Pharmacy, University of Granada, Granada, Spain
| | - Carlos Molina Santiago
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", University of Málaga, Málaga, Spain
| | - Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Mireia Tena Garitaonaindia
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan-Luis Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Abdelali Daddaoua
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
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27
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Molina L, Segura A, Duque E, Ramos JL. The versatility of Pseudomonas putida in the rhizosphere environment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 110:149-180. [PMID: 32386604 DOI: 10.1016/bs.aambs.2019.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This article addresses the lifestyle of Pseudomonas and focuses on how Pseudomonas putida can be used as a model system for biotechnological processes in agriculture, and in the removal of pollutants from soils. In this chapter we aim to show how a deep analysis using genetic information and experimental tests has helped to reveal insights into the lifestyle of Pseudomonads. Pseudomonas putida is a Plant Growth Promoting Rhizobacteria (PGPR) that establishes commensal relationships with plants. The interaction involves a series of functions encoded by core genes which favor nutrient mobilization, prevention of pathogen development and efficient niche colonization. Certain Pseudomonas putida strains harbor accessory genes that confer specific biodegradative properties and because these microorganisms can thrive on the roots of plants they can be exploited to remove pollutants via rhizoremediation, making the consortium plant/Pseudomonas a useful tool to combat pollution.
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Affiliation(s)
- Lázaro Molina
- CSIC- Estación Experimental del Zaidín, Granada, Spain
| | - Ana Segura
- CSIC- Estación Experimental del Zaidín, Granada, Spain
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28
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A multilocus sequence typing scheme of Pseudomonas putida for clinical and environmental isolates. Sci Rep 2019; 9:13980. [PMID: 31562354 PMCID: PMC6765009 DOI: 10.1038/s41598-019-50299-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 09/10/2019] [Indexed: 11/08/2022] Open
Abstract
Pseudomonas putida is a bacterium commonly found in soils, water and plants. Although P. putida group strains are considered to have low virulence, several nosocomial isolates with carbapenem- or multidrug-resistance have recently been reported. In the present study, we developed a multilocus sequence typing (MLST) scheme for P. putida. MLST loci and primers were selected and designed using the genomic information of 86 clinical isolates sequenced in this study as well as the sequences of 20 isolates previously reported. The genomes were categorised into 68 sequence types (STs). Significant linkage disequilibrium was detected for the 68 STs, indicating that the P. putida isolates are clonal. The MLST tree was similar to the haplotype network tree based on single nucleotide morphisms, demonstrating that our MLST scheme reflects the genetic diversity of P. putida group isolated from both clinical and environmental sites.
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29
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Potentiation of Aminoglycoside Lethality by C 4-Dicarboxylates Requires RpoN in Antibiotic-Tolerant Pseudomonas aeruginosa. Antimicrob Agents Chemother 2019; 63:AAC.01313-19. [PMID: 31383655 DOI: 10.1128/aac.01313-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/29/2019] [Indexed: 01/26/2023] Open
Abstract
Antibiotic tolerance contributes to the inability of standard antimicrobial therapies to clear the chronic Pseudomonas aeruginosa lung infections that often afflict patients with cystic fibrosis (CF). Metabolic potentiation of bactericidal antibiotics with carbon sources has emerged as a promising strategy to resensitize tolerant bacteria to antibiotic killing. Fumarate (FUM), a C4-dicarboxylate, has been recently shown to resensitize tolerant P. aeruginosa to killing by tobramycin (TOB), an aminoglycoside antibiotic, when used in combination (TOB+FUM). Fumarate and other C4-dicarboxylates are taken up intracellularly by transporters regulated by the alternative sigma factor RpoN. Once in the cell, FUM is metabolized, leading to enhanced electron transport chain activity, regeneration of the proton motive force, and increased TOB uptake. In this work, we demonstrate that a ΔrpoN mutant displays impaired FUM uptake and, consequently, nonsusceptibility to TOB+FUM treatment. RpoN was also found to be essential for susceptibility to other aminoglycoside and C4-dicarboxylate combinations. Importantly, RpoN loss-of-function mutations have been documented to evolve in the CF lung, and these loss-of-function alleles can also result in TOB+FUM nonsusceptibility. In a mixed-genotype population of wild-type and ΔrpoN cells, TOB+FUM specifically killed cells with RpoN function and spared the cells that lacked RpoN function. Unlike C4-dicarboylates, both d-glucose and l-arginine were able to potentiate TOB killing of ΔrpoN stationary-phase cells. Our findings raise the question of whether TOB+FUM will be a suitable treatment option in the future for CF patients infected with P. aeruginosa isolates that lack RpoN function.
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30
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Bharwad K, Rajkumar S. Rewiring the functional complexity between Crc, Hfq and sRNAs to regulate carbon catabolite repression in Pseudomonas. World J Microbiol Biotechnol 2019; 35:140. [DOI: 10.1007/s11274-019-2717-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/22/2019] [Indexed: 10/26/2022]
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31
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Poblete-Castro I, Wittmann C, Nikel PI. Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species. Microb Biotechnol 2019; 13:32-53. [PMID: 30883020 PMCID: PMC6922529 DOI: 10.1111/1751-7915.13400] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/17/2019] [Accepted: 02/23/2019] [Indexed: 11/30/2022] Open
Abstract
The use of renewable waste feedstocks is an environment‐friendly choice contributing to the reduction of waste treatment costs and increasing the economic value of industrial by‐products. Glycerol (1,2,3‐propanetriol), a simple polyol compound widely distributed in biological systems, constitutes a prime example of a relatively cheap and readily available substrate to be used in bioprocesses. Extensively exploited as an ingredient in the food and pharmaceutical industries, glycerol is also the main by‐product of biodiesel production, which has resulted in a progressive drop in substrate price over the years. Consequently, glycerol has become an attractive substrate in biotechnology, and several chemical commodities currently produced from petroleum have been shown to be obtained from this polyol using whole‐cell biocatalysts with both wild‐type and engineered bacterial strains. Pseudomonas species, endowed with a versatile and rich metabolism, have been adopted for the conversion of glycerol into value‐added products (ranging from simple molecules to structurally complex biopolymers, e.g. polyhydroxyalkanoates), and a number of metabolic engineering strategies have been deployed to increase the number of applications of glycerol as a cost‐effective substrate. The unique genetic and metabolic features of glycerol‐grown Pseudomonas are presented in this review, along with relevant examples of bioprocesses based on this substrate – and the synthetic biology and metabolic engineering strategies implemented in bacteria of this genus aimed at glycerol valorization.
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Affiliation(s)
- Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Natural Sciences, Universidad Andrés Bello, Santiago de Chile, Chile
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Universität des Saarlandes, Saarbrücken, Germany
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
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32
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Corona F, Martínez JL, Nikel PI. The global regulator Crc orchestrates the metabolic robustness underlying oxidative stress resistance in Pseudomonas aeruginosa. Environ Microbiol 2018; 21:898-912. [PMID: 30411469 DOI: 10.1111/1462-2920.14471] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 11/01/2018] [Accepted: 11/03/2018] [Indexed: 11/26/2022]
Abstract
The remarkable metabolic versatility of bacteria of the genus Pseudomonas enable their survival across very diverse environmental conditions. P. aeruginosa, one of the most relevant opportunistic pathogens, is a prime example of this adaptability. The interplay between regulatory networks that mediate these metabolic and physiological features is just starting to be explored in detail. Carbon catabolite repression, governed by the Crc protein, controls the availability of several enzymes and transporters involved in the assimilation of secondary carbon sources. Yet, the regulation exerted by Crc on redox metabolism of P. aeruginosa (hence, on the overall physiology) had hitherto been unexplored. In this study, we address the intimate connection between carbon catabolite repression and metabolic robustness of P. aeruginosa PAO1. In particular, we explored the interplay between oxidative stress, metabolic rearrangements in central carbon metabolism and the cellular redox state. By adopting a combination of quantitative physiology experiments, multiomic analyses, transcriptional patterns of key genes, measurement of metabolic activities in vitro and direct quantification of redox balances both in the wild-type strain and in an isogenic Δcrc derivative, we demonstrate that Crc orchestrates the overall response of P. aeruginosa to oxidative stress via reshaping of the core metabolic architecture in this bacterium.
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Affiliation(s)
- Fernando Corona
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - José Luis Martínez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Pablo I Nikel
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
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33
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Raneri M, Pinatel E, Peano C, Rampioni G, Leoni L, Bianconi I, Jousson O, Dalmasio C, Ferrante P, Briani F. Pseudomonas aeruginosa mutants defective in glucose uptake have pleiotropic phenotype and altered virulence in non-mammal infection models. Sci Rep 2018; 8:16912. [PMID: 30442901 PMCID: PMC6237876 DOI: 10.1038/s41598-018-35087-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/30/2018] [Indexed: 01/09/2023] Open
Abstract
Pseudomonas spp. are endowed with a complex pathway for glucose uptake that relies on multiple transporters. In this work we report the construction and characterization of Pseudomonas aeruginosa single and multiple mutants with unmarked deletions of genes encoding outer membrane (OM) and inner membrane (IM) proteins involved in glucose uptake. We found that a triple ΔgltKGF ΔgntP ΔkguT mutant lacking all known IM transporters (named GUN for Glucose Uptake Null) is unable to grow on glucose as unique carbon source. More than 500 genes controlling both metabolic functions and virulence traits show differential expression in GUN relative to the parental strain. Consistent with transcriptomic data, the GUN mutant displays a pleiotropic phenotype. Notably, the genome-wide transcriptional profile and most phenotypic traits differ between the GUN mutant and the wild type strain irrespective of the presence of glucose, suggesting that the investigated genes may have additional roles besides glucose transport. Finally, mutants carrying single or multiple deletions in the glucose uptake genes showed attenuated virulence relative to the wild type strain in Galleria mellonella, but not in Caenorhabditis elegans infection model, supporting the notion that metabolic functions may deeply impact P. aeruginosa adaptation to specific environments found inside the host.
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Affiliation(s)
- Matteo Raneri
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Eva Pinatel
- Istituto di Tecnologie Biomediche-CNR, Segrate, Italy
| | - Clelia Peano
- Istituto di Tecnologie Biomediche-CNR, Segrate, Italy
- Istituto Clinico Humanitas-CNR, Rozzano, Italy
| | - Giordano Rampioni
- Dipartimento di Scienze, Università degli Studi Roma Tre, Roma, Italy
| | - Livia Leoni
- Dipartimento di Scienze, Università degli Studi Roma Tre, Roma, Italy
| | - Irene Bianconi
- Centre for Integrative Biology, Università degli Studi di Trento, Trento, Italy
| | - Olivier Jousson
- Centre for Integrative Biology, Università degli Studi di Trento, Trento, Italy
| | - Chiara Dalmasio
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Palma Ferrante
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
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34
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Nikel PI, de Lorenzo V. Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism. Metab Eng 2018; 50:142-155. [DOI: 10.1016/j.ymben.2018.05.005] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 12/12/2022]
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35
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Udaondo Z, Ramos JL, Segura A, Krell T, Daddaoua A. Regulation of carbohydrate degradation pathways in Pseudomonas involves a versatile set of transcriptional regulators. Microb Biotechnol 2018; 11:442-454. [PMID: 29607620 PMCID: PMC5902321 DOI: 10.1111/1751-7915.13263] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/22/2018] [Accepted: 03/01/2018] [Indexed: 01/08/2023] Open
Abstract
Bacteria of the genus Pseudomonas are widespread in nature. In the last decades, members of this genus, especially Pseudomonas aeruginosa and Pseudomonas putida, have acquired great interest because of their interactions with higher organisms. Pseudomonas aeruginosa is an opportunistic pathogen that colonizes the lung of cystic fibrosis patients, while P. putida is a soil bacterium able to establish a positive interaction with the plant rhizosphere. Members of Pseudomonas genus have a robust metabolism for amino acids and organic acids as well as aromatic compounds; however, these microbes metabolize a very limited number of sugars. Interestingly, they have three-pronged metabolic system to generate 6-phosphogluconate from glucose suggesting an adaptation to efficiently consume this sugar. This review focuses on the description of the regulatory network of glucose utilization in Pseudomonas, highlighting the differences between P. putida and P. aeruginosa. Most interestingly, It is highlighted a functional link between glucose assimilation and exotoxin A production in P. aeruginosa. The physiological relevance of this connection remains unclear, and it needs to be established whether a similar relationship is also found in other bacteria.
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Affiliation(s)
- Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301W. Markham St., Slot 782, Little Rock, AR, 72205, USA
| | - Juan-Luis Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, C/ Profesor Albareda 1, E-18008, Granada, Spain
| | - Ana Segura
- Department of Environmental Protection, Estación Experimental del Zaidín, C/ Profesor Albareda 1, E-18008, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, C/ Profesor Albareda 1, E-18008, Granada, Spain
| | - Abdelali Daddaoua
- Department of Biochemistry and Molecular Biology II, Pharmacy School, Granada University, Granada, Spain
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