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Yang J, Son JH, Kim H, Cho S, Na JG, Yeon YJ, Lee J. Mevalonate production from ethanol by direct conversion through acetyl-CoA using recombinant Pseudomonas putida, a novel biocatalyst for terpenoid production. Microb Cell Fact 2019; 18:168. [PMID: 31601210 PMCID: PMC6786281 DOI: 10.1186/s12934-019-1213-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 09/17/2019] [Indexed: 01/13/2023] Open
Abstract
Background Bioethanol is one of the most representative eco-friendly fuels developed to replace the non-renewable fossil fuels and is the most successful commercially available bio-conversion technology till date. With the availability of inexpensive carbon sources, such as cellulosic biomass, bioethanol production has become cheaper and easier to perform, which can facilitate the development of methods for converting ethanol into higher value-added biochemicals. In this study, a bioconversion process using Pseudomonas putida as a biocatalyst was established, wherein ethanol was converted to mevalonate. Since ethanol can be converted directly to acetyl-CoA, bypassing its conversion to pyruvate, there is a possibility that ethanol can be converted to mevalonate without producing pyruvate-derived by-products. Furthermore, P. putida seems to be highly resistant to the toxicity caused by terpenoids, and thus can be useful in conducting terpenoid production research. Results In this study, we first expressed the core genes responsible for mevalonate production (atoB, mvaS, and mvaE) in P. putida and mevalonate production was confirmed. Thereafter, through an improvement in genetic stability and ethanol metabolism manipulation, mevalonate production was enhanced up to 2.39-fold (1.70 g/L vs. 4.07 g/L) from 200 mM ethanol with an enhancement in reproducibility of mevalonate production. Following this, the metabolic characteristics related to ethanol catabolism and mevalonate production were revealed by manipulations to reduce fatty acid biosynthesis and optimize pH by batch fermentation. Finally, we reached a product yield of 0.41 g mevalonate/g ethanol in flask scale culture and 0.32 g mevalonate/g ethanol in batch fermentation. This is the highest experimental yield obtained from using carbon sources other than carbohydrates till date and it is expected that further improvements will be made through the development of fermentation methods. Conclusion Pseudomonas putida was investigated as a biocatalyst that can efficiently convert ethanol to mevalonate, the major precursor for terpenoid production, and this research is expected to open new avenues for the production of terpenoids using microorganisms that have not yet reached the stage of mass production.
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Affiliation(s)
- Jeongmo Yang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Ji Hee Son
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Hyeonsoo Kim
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Sukhyeong Cho
- C1 Gas Refinery R&D Center, Sogang University, Seoul, 04107, Republic of Korea
| | - Jeong-Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Young Joo Yeon
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, 25457, Republic of Korea
| | - Jinwon Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea.
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Li W, Jayakody LN, Franden MA, Wehrmann M, Daun T, Hauer B, Blank LM, Beckham GT, Klebensberger J, Wierckx N. Laboratory evolution reveals the metabolic and regulatory basis of ethylene glycol metabolism by
Pseudomonas putida
KT2440. Environ Microbiol 2019; 21:3669-3682. [DOI: 10.1111/1462-2920.14703] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Wing‐Jin Li
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBt RWTH Aachen University Worringerweg 1, 52074 Aachen Germany
| | - Lahiru N. Jayakody
- National Bioenergy Center National Renewable Energy Laboratory Golden CO 80401 USA
| | - Mary Ann Franden
- National Bioenergy Center National Renewable Energy Laboratory Golden CO 80401 USA
| | - Matthias Wehrmann
- University of Stuttgart Institute of Biochemistry and Technical Biochemistry Allmandring 31, 70569 Stuttgart Germany
| | - Tristan Daun
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBt RWTH Aachen University Worringerweg 1, 52074 Aachen Germany
| | - Bernhard Hauer
- University of Stuttgart Institute of Biochemistry and Technical Biochemistry Allmandring 31, 70569 Stuttgart Germany
| | - Lars M. Blank
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBt RWTH Aachen University Worringerweg 1, 52074 Aachen Germany
| | - Gregg T. Beckham
- National Bioenergy Center National Renewable Energy Laboratory Golden CO 80401 USA
| | - Janosch Klebensberger
- University of Stuttgart Institute of Biochemistry and Technical Biochemistry Allmandring 31, 70569 Stuttgart Germany
| | - Nick Wierckx
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBt RWTH Aachen University Worringerweg 1, 52074 Aachen Germany
- Institute of Bio‐ and Geosciences IBG‐1: Biotechnology Forschungszentrum Jülich, 52425 Jülich Germany
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53
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Veselova MA, Plyuta VA, Khmel IA. Volatile Compounds of Bacterial Origin: Structure, Biosynthesis, and Biological Activity. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719030160] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Orellana-Saez M, Pacheco N, Costa JI, Mendez KN, Miossec MJ, Meneses C, Castro-Nallar E, Marcoleta AE, Poblete-Castro I. In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential. Front Microbiol 2019; 10:1154. [PMID: 31178851 PMCID: PMC6543543 DOI: 10.3389/fmicb.2019.01154] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
We obtained the complete genome sequence of the psychrotolerant extremophile Pseudomonas sp. MPC6, a natural Polyhydroxyalkanoates (PHAs) producing bacterium able to rapidly grow at low temperatures. Genomic and phenotypic analyses allowed us to situate this isolate inside the Pseudomonas fluorescens phylogroup of pseudomonads as well as to reveal its metabolic versatility and plasticity. The isolate possesses the gene machinery for metabolizing a variety of toxic aromatic compounds such as toluene, phenol, chloroaromatics, and TNT. In addition, it can use both C6- and C5-carbon sugars like xylose and arabinose as carbon substrates, an uncommon feature for bacteria of this genus. Furthermore, Pseudomonas sp. MPC6 exhibits a high-copy number of genes encoding for enzymes involved in oxidative and cold-stress response that allows it to cope with high concentrations of heavy metals (As, Cd, Cu) and low temperatures, a finding that was further validated experimentally. We then assessed the growth performance of MPC6 on glycerol using a temperature range from 0 to 45°C, the latter temperature corresponding to the limit at which this Antarctic isolate was no longer able to propagate. On the other hand, the MPC6 genome comprised considerably less virulence and drug resistance factors as compared to pathogenic Pseudomonas strains, thus supporting its safety. Unexpectedly, we found five PHA synthases within the genome of MPC6, one of which clustered separately from the other four. This PHA synthase shared only 40% sequence identity at the amino acid level against the only PHA polymerase described for Pseudomonas (63-1 strain) able to produce copolymers of short- and medium-chain length PHAs. Batch cultures for PHA synthesis in Pseudomonas sp. MPC6 using sugars, decanoate, ethylene glycol, and organic acids as carbon substrates result in biopolymers with different monomer compositions. This indicates that the PHA synthases play a critical role in defining not only the final chemical structure of the biosynthesized PHA, but also the employed biosynthetic pathways. Based on the results obtained, we conclude that Pseudomonas sp. MPC6 can be exploited as a bioremediator and biopolymer factory, as well as a model strain to unveil molecular mechanisms behind adaptation to cold and extreme environments.
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Affiliation(s)
- Matias Orellana-Saez
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Nicolas Pacheco
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - José I Costa
- Integrative Microbiology Group, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Katterinne N Mendez
- Center for Bioinformatics and Integrative Biology, Faculty of Life Science, Universidad Andres Bello, Santiago, Chile
| | - Matthieu J Miossec
- Computational Genomics Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Science, Universidad Andres Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Faculty of Life Science, Universidad Andres Bello, Santiago, Chile
| | - Andrés E Marcoleta
- Integrative Microbiology Group, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
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Salvador M, Abdulmutalib U, Gonzalez J, Kim J, Smith AA, Faulon JL, Wei R, Zimmermann W, Jimenez JI. Microbial Genes for a Circular and Sustainable Bio-PET Economy. Genes (Basel) 2019; 10:E373. [PMID: 31100963 PMCID: PMC6562992 DOI: 10.3390/genes10050373] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 02/03/2023] Open
Abstract
Plastics have become an important environmental concern due to their durability and resistance to degradation. Out of all plastic materials, polyesters such as polyethylene terephthalate (PET) are amenable to biological degradation due to the action of microbial polyester hydrolases. The hydrolysis products obtained from PET can thereby be used for the synthesis of novel PET as well as become a potential carbon source for microorganisms. In addition, microorganisms and biomass can be used for the synthesis of the constituent monomers of PET from renewable sources. The combination of both biodegradation and biosynthesis would enable a completely circular bio-PET economy beyond the conventional recycling processes. Circular strategies like this could contribute to significantly decreasing the environmental impact of our dependence on this polymer. Here we review the efforts made towards turning PET into a viable feedstock for microbial transformations. We highlight current bottlenecks in degradation of the polymer and metabolism of the monomers, and we showcase fully biological or semisynthetic processes leading to the synthesis of PET from sustainable substrates.
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Affiliation(s)
- Manuel Salvador
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Umar Abdulmutalib
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Jaime Gonzalez
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Juhyun Kim
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Alex A Smith
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
- SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
- CNRS-UMR8030/Laboratoire iSSB, Université Paris-Saclay, 91000 Évry, France.
| | - Ren Wei
- Department of Microbiology and Bioprocess Technology, Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany.
| | - Wolfgang Zimmermann
- Department of Microbiology and Bioprocess Technology, Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany.
| | - Jose I Jimenez
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
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56
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Taniguchi I, Yoshida S, Hiraga K, Miyamoto K, Kimura Y, Oda K. Biodegradation of PET: Current Status and Application Aspects. ACS Catal 2019. [DOI: 10.1021/acscatal.8b05171] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ikuo Taniguchi
- Department of Polymer Science, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Shosuke Yoshida
- Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Kazumi Hiraga
- Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kenji Miyamoto
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yoshiharu Kimura
- Department of Polymer Science, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kohei Oda
- Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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57
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The PedS2/PedR2 Two-Component System Is Crucial for the Rare Earth Element Switch in Pseudomonas putida KT2440. mSphere 2018; 3:3/4/e00376-18. [PMID: 30158283 PMCID: PMC6115532 DOI: 10.1128/msphere.00376-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The function of lanthanides for methanotrophic and methylotrophic bacteria is gaining increasing attention, while knowledge about the role of rare earth elements (REEs) in nonmethylotrophic bacteria is still limited. The present study investigates the recently described differential expression of the two PQQ-EDHs of P. putida in response to lanthanides. We demonstrate that a specific TCS is crucial for their inverse regulation and provide evidence for a dual regulatory function of the LuxR-type response regulator involved. Thus, our study represents the first detailed characterization of the molecular mechanism underlying the REE switch of PQQ-EDHs in a nonmethylotrophic bacterium and stimulates subsequent investigations for the identification of additional genes or phenotypic traits that might be coregulated during REE-dependent niche adaptation. In Pseudomonas putida KT2440, two pyrroloquinoline quinone-dependent ethanol dehydrogenases (PQQ-EDHs) are responsible for the periplasmic oxidation of a broad variety of volatile organic compounds (VOCs). Depending on the availability of rare earth elements (REEs) of the lanthanide series (Ln3+), we have recently reported that the transcription of the genes encoding the Ca2+-utilizing enzyme PedE and the Ln3+-utilizing enzyme PedH are inversely regulated. With adaptive evolution experiments, site-specific mutations, transcriptional reporter fusions, and complementation approaches, we now demonstrate that the PedS2/PedR2 (PP_2671/PP_2672) two-component system (TCS) plays a central role in the observed REE-mediated switch of PQQ-EDHs in P. putida. We provide evidence that in the absence of lanthanum (La3+), the sensor histidine kinase PedS2 phosphorylates its cognate LuxR-type response regulator PedR2, which in turn not only activates pedE gene transcription but is also involved in repression of pedH. Our data further suggest that the presence of La3+ lowers kinase activity of PedS2, either by the direct binding of the metal ions to the periplasmic region of PedS2 or by an uncharacterized indirect interaction, leading to reduced levels of phosphorylated PedR2. Consequently, the decreasing pedE expression and concomitant alleviation of pedH repression causes—in conjunction with the transcriptional activation of the pedH gene by a yet unknown regulatory module—the Ln3+-dependent transition from PedE- to PedH-catalyzed oxidation of alcoholic VOCs. IMPORTANCE The function of lanthanides for methanotrophic and methylotrophic bacteria is gaining increasing attention, while knowledge about the role of rare earth elements (REEs) in nonmethylotrophic bacteria is still limited. The present study investigates the recently described differential expression of the two PQQ-EDHs of P. putida in response to lanthanides. We demonstrate that a specific TCS is crucial for their inverse regulation and provide evidence for a dual regulatory function of the LuxR-type response regulator involved. Thus, our study represents the first detailed characterization of the molecular mechanism underlying the REE switch of PQQ-EDHs in a nonmethylotrophic bacterium and stimulates subsequent investigations for the identification of additional genes or phenotypic traits that might be coregulated during REE-dependent niche adaptation.
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58
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Franden MA, Jayakody LN, Li WJ, Wagner NJ, Cleveland NS, Michener WE, Hauer B, Blank LM, Wierckx N, Klebensberger J, Beckham GT. Engineering Pseudomonas putida KT2440 for efficient ethylene glycol utilization. Metab Eng 2018; 48:197-207. [DOI: 10.1016/j.ymben.2018.06.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/02/2018] [Accepted: 06/05/2018] [Indexed: 10/14/2022]
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59
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Functional Role of Lanthanides in Enzymatic Activity and Transcriptional Regulation of Pyrroloquinoline Quinone-Dependent Alcohol Dehydrogenases in Pseudomonas putida KT2440. mBio 2017; 8:mBio.00570-17. [PMID: 28655819 PMCID: PMC5487730 DOI: 10.1128/mbio.00570-17] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The oxidation of alcohols and aldehydes is crucial for detoxification and efficient catabolism of various volatile organic compounds (VOCs). Thus, many Gram-negative bacteria have evolved periplasmic oxidation systems based on pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ-ADHs) that are often functionally redundant. Here we report the first description and characterization of a lanthanide-dependent PQQ-ADH (PedH) in a nonmethylotrophic bacterium based on the use of purified enzymes from the soil-dwelling model organism Pseudomonas putida KT2440. PedH (PP_2679) exhibits enzyme activity on a range of substrates similar to that of its Ca2+-dependent counterpart PedE (PP_2674), including linear and aromatic primary and secondary alcohols, as well as aldehydes, but only in the presence of lanthanide ions, including La3+, Ce3+, Pr3+, Sm3+, or Nd3+ Reporter assays revealed that PedH not only has a catalytic function but is also involved in the transcriptional regulation of pedE and pedH, most likely acting as a sensory module. Notably, the underlying regulatory network is responsive to as little as 1 to 10 nM lanthanum, a concentration assumed to be of ecological relevance. The present study further demonstrates that the PQQ-dependent oxidation system is crucial for efficient growth with a variety of volatile alcohols. From these results, we conclude that functional redundancy and inverse regulation of PedE and PedH represent an adaptive strategy of P. putida KT2440 to optimize growth with volatile alcohols in response to the availability of different lanthanides.IMPORTANCE Because of their low bioavailability, lanthanides have long been considered biologically inert. In recent years, however, the identification of lanthanides as a cofactor in methylotrophic bacteria has attracted tremendous interest among various biological fields. The present study reveals that one of the two PQQ-ADHs produced by the model organism P. putida KT2440 also utilizes lanthanides as a cofactor, thus expanding the scope of lanthanide-employing bacteria beyond the methylotrophs. Similar to the system described in methylotrophic bacteria, a complex regulatory network is involved in lanthanide-responsive switching between the two PQQ-ADHs encoded by P. putida KT2440. We further show that the functional production of at least one of the enzymes is crucial for efficient growth with several volatile alcohols. Overall, our study provides a novel understanding of the redundancy of PQQ-ADHs observed in many organisms and further highlights the importance of lanthanides for bacterial metabolism, particularly in soil environments.
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60
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Park SJ, Kwak MK, Kang SO. Schiff bases of putrescine with methylglyoxal protect from cellular damage caused by accumulation of methylglyoxal and reactive oxygen species in Dictyostelium discoideum. Int J Biochem Cell Biol 2017; 86:54-66. [PMID: 28330789 DOI: 10.1016/j.biocel.2017.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 02/08/2023]
Abstract
Polyamines protect protein glycation in cells against the advanced glycation end product precursor methylglyoxal, which is inevitably produced during glycolysis, and the enzymes that detoxify this α-ketoaldehyde have been widely studied. Nonetheless, nonenzymatic methylglyoxal-scavenging molecules have not been sufficiently studied either in vitro or in vivo. Here, we hypothesized reciprocal regulation between polyamines and methylglyoxal modeled in Dictyostelium grown in a high-glucose medium. We based our hypothesis on the reaction between putrescine and methylglyoxal in putrescine-deficient (odc-) or putrescine-overexpressing (odcoe) cells. In these strains, growth and cell cycle were found to be dependent on cellular methylglyoxal and putrescine contents. The odc- cells showed growth defects and underwent G1 phase cell cycle arrest, which was efficiently reversed by exogenous putrescine. Cellular methylglyoxal, reactive oxygen species (ROS), and glutathione levels were remarkably changed in odcoe cells and odc̄ cells. These results revealed that putrescine may act as an intracellular scavenger of methylglyoxal and ROS. Herein, we observed interactions of putrescine and methylglyoxal via formation of a Schiff base complex, by UV-vis spectroscopy, and confirmed this adduct by liquid chromatography with mass spectrometry via electrospray ionization. Schiff bases were isolated, analyzed, and predicted to have molecular masses ranging from 124 to 130. We showed that cellular putrescine-methylglyoxal Schiff bases were downregulated in proportion to the levels of endogenous or exogenous putrescine and glutathione in the odc mutants. The putrescine-methylglyoxal Schiff base affected endogenous metabolite levels. This is the first report showing that cellular methylglyoxal functions as a signaling molecule through reciprocal interactions with polyamines by forming Schiff bases.
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Affiliation(s)
- Seong-Jun Park
- Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Min-Kyu Kwak
- Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea.
| | - Sa-Ouk Kang
- Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea.
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Poblete-Castro I, Borrero-de Acuña JM, Nikel PI, Kohlstedt M, Wittmann C. Host Organism: Pseudomonas putida. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ignacio Poblete-Castro
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - José M. Borrero-de Acuña
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program; National Spanish Center for Biotechnology (CNB-CSIC); Calle Darwin, 3 28049 Madrid, Spain
| | - Michael Kohlstedt
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
| | - Christoph Wittmann
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
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Zhang Y, Jiang T, Sheng B, Long Y, Gao C, Ma C, Xu P. Coexistence of two d-lactate-utilizing systems in Pseudomonas putida KT2440. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:699-707. [PMID: 27264531 DOI: 10.1111/1758-2229.12429] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/13/2016] [Accepted: 05/24/2016] [Indexed: 06/05/2023]
Abstract
It is advantageous for rhizosphere-dwelling microorganisms to utilize organic acids such as lactate. Pseudomonas putida KT2440 is one of the most widely studied rhizosphere-dwelling model organisms. The P. putida KT2440 genome contains an NAD-dependent d-lactate dehydrogenase encoding gene, but mutation of this gene does not play a role in d-lactate utilization. Instead, it was found that d-lactate utilization in P. putida KT2440 proceeds via a multidomain NAD-independent d-lactate dehydrogenase with a C-terminal domain containing several Fe-S cluster-binding motifs (Fe-S d-iLDH) and glycolate oxidase, which is widely distributed in various microorganisms. Both Fe-S d-iLDH and glycolate oxidase were identified to be membrane-bound proteins. Neither Fe-S d-iLDH nor glycolate oxidase is constitutively expressed but both of them can be induced by either enantiomer of lactate in P. putida KT2440. This study shows a case in which an environmental microbe contains two types of enzymes specific for d-lactate utilization.
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Affiliation(s)
- Yingxin Zhang
- State Key Laboratory of Microbial Technology and School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Tianyi Jiang
- State Key Laboratory of Microbial Technology and School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, People's Republic of China
| | - Binbin Sheng
- State Key Laboratory of Microbial Technology and School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Yangdanyu Long
- State Key Laboratory of Microbial Technology and School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Chao Gao
- State Key Laboratory of Microbial Technology and School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology and School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
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63
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Ethylene Glycol Metabolism in the Acetogen Acetobacterium woodii. J Bacteriol 2016; 198:1058-65. [PMID: 26787767 DOI: 10.1128/jb.00942-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/12/2016] [Indexed: 01/11/2023] Open
Abstract
UNLABELLED The acetogenic bacterium Acetobacterium woodii is able to grow by the oxidation of diols, such as 1,2-propanediol, 2,3-butanediol, or ethylene glycol. Recent analyses demonstrated fundamentally different ways for oxidation of 1,2-propanediol and 2,3-butanediol. Here, we analyzed the metabolism of ethylene glycol. Our data demonstrate that ethylene glycol is dehydrated to acetaldehyde, which is then disproportionated to ethanol and acetyl coenzyme A (acetyl-CoA). The latter is further converted to acetate, and this pathway is coupled to ATP formation by substrate-level phosphorylation. Apparently, the product ethanol is in part further oxidized and the reducing equivalents are recycled by reduction of CO2 to acetate in the Wood-Ljungdahl pathway. Biochemical data as well as the results of protein synthesis analysis are consistent with the hypothesis that the propane diol dehydratase (PduCDE) and CoA-dependent propionaldehyde dehydrogenase (PduP) proteins, encoded by the pdu gene cluster, also catalyze ethylene glycol dehydration to acetaldehyde and its CoA-dependent oxidation to acetyl-CoA. Moreover, genes encoding bacterial microcompartments as part of the pdu gene cluster are also expressed during growth on ethylene glycol, arguing for a dual function of the Pdu microcompartment system. IMPORTANCE Acetogenic bacteria are characterized by their ability to use CO2 as a terminal electron acceptor by a specific pathway, the Wood-Ljungdahl pathway, enabling in most acetogens chemolithoautotrophic growth with H2 and CO2. However, acetogens are very versatile and can use a wide variety of different substrates for growth. Here we report on the elucidation of the pathway for utilization of ethylene glycol by the model acetogen Acetobacterium woodii. This diol is degraded by dehydration to acetaldehyde followed by a disproportionation to acetate and ethanol. We present evidence that this pathway is catalyzed by the same enzyme system recently described for the utilization of 1,2-propanediol. The enzymes for ethylene glycol utilization seem to be encapsulated in protein compartments, known as bacterial microcompartments.
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Kishi M, Kawai M, Toda T. Heterotrophic utilization of ethylene glycol and propylene glycol by Chlorella protothecoides. ALGAL RES 2015. [DOI: 10.1016/j.algal.2015.04.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Wierckx N, Prieto MA, Pomposiello P, de Lorenzo V, O'Connor K, Blank LM. Plastic waste as a novel substrate for industrial biotechnology. Microb Biotechnol 2015; 8:900-3. [PMID: 26482561 PMCID: PMC4621443 DOI: 10.1111/1751-7915.12312] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 07/07/2015] [Accepted: 07/14/2015] [Indexed: 01/26/2023] Open
Affiliation(s)
- Nick Wierckx
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany
| | - M Auxiliadora Prieto
- Biological Research Center, The Spanish National Research Council (CIB-CSIC), C/ Ramiro de Maeztu, 9, Madrid, 28040, Spain
| | | | - Victor de Lorenzo
- National Center of Biotechnology, The Spanish National Research Council (CNB-CSIC), C/Darwin, 3, Campus of Cantoblanco, Madrid, 28049, Spain
| | - Kevin O'Connor
- School of Biomolecular and Biomedical Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.,Bioplastech, NovaUCD, University College Dublin, Belfield Innovation Park, Belfield, Dublin 4, Ireland
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany
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Vallon T, Simon O, Rendgen-Heugle B, Frana S, Mückschel B, Broicher A, Siemann-Herzberg M, Pfannenstiel J, Hauer B, Huber A, Breuer M, Takors R. Applying systems biology tools to studyn-butanol degradation inPseudomonas putidaKT2440. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400051] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Tobias Vallon
- Institute of Biochemical Engineering; University of Stuttgart; Stuttgart Germany
| | - Oliver Simon
- Proteomics Core Facility of the Life Science Center; University of Hohenheim; Stuttgart Germany
| | - Beate Rendgen-Heugle
- Institute of Biochemical Engineering; University of Stuttgart; Stuttgart Germany
| | - Sabine Frana
- Institute of Biochemical Engineering; University of Stuttgart; Stuttgart Germany
| | - Björn Mückschel
- Institute of Technical Biochemistry; University of Stuttgart; Stuttgart Germany
| | - Alexander Broicher
- Institute of Biochemical Engineering; University of Stuttgart; Stuttgart Germany
| | | | - Jens Pfannenstiel
- Proteomics Core Facility of the Life Science Center; University of Hohenheim; Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; University of Stuttgart; Stuttgart Germany
| | - Achim Huber
- Proteomics Core Facility of the Life Science Center; University of Hohenheim; Stuttgart Germany
| | - Michael Breuer
- BASF SE; Fine Chemicals and Biocatalysis Research; Ludwigshafen Germany
| | - Ralf Takors
- Institute of Biochemical Engineering; University of Stuttgart; Stuttgart Germany
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Analysis of the molecular response of Pseudomonas putida KT2440 to the next-generation biofuel n-butanol. J Proteomics 2015; 122:11-25. [PMID: 25829261 DOI: 10.1016/j.jprot.2015.03.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 02/25/2015] [Accepted: 03/10/2015] [Indexed: 11/24/2022]
Abstract
UNLABELLED To increase the efficiency of biocatalysts a thorough understanding of the molecular response of the biocatalyst to precursors, products and environmental conditions applied in bioconversions is essential. Here we performed a comprehensive proteome and phospholipid analysis to characterize the molecular response of the potential biocatalyst Pseudomonas putida KT2440 to the next-generation biofuel n-butanol. Using complementary quantitative proteomics approaches we were able to identify and quantify 1467 proteins, corresponding to 28% of the total KT2440 proteome. 256 proteins were altered in abundance in response to n-butanol. The proteome response entailed an increased abundance of enzymes involved in n-butanol degradation including quinoprotein alcohol dehydrogenases, aldehyde dehydrogenases and enzymes of fatty acid beta oxidation. From these results we were able to construct a pathway for the metabolism of n-butanol in P. putida. The initial oxidation of n-butanol is catalyzed by at least two quinoprotein ethanol dehydrogenases (PedE and PedH). Growth of mutants lacking PedE and PedH on n-butanol was significantly impaired, but not completely inhibited, suggesting that additional alcohol dehydrogenases can at least partially complement their function in KT2440. Furthermore, phospholipid profiling revealed a significantly increased abundance of lyso-phospholipids in response to n-butanol, indicating a rearrangement of the lipid bilayer. BIOLOGICAL SIGNIFICANCE n-butanol is an important bulk chemical and a promising alternative to gasoline as a transportation fuel. Due to environmental concerns as well as increasing energy prices there is a growing interest in sustainable and cost-effective biotechnological production processes for the production of bulk chemicals and transportation fuels from renewable resources. n-butanol fermentation is well established in Clostridiae, but the efficiency of n-butanol production is mainly limited by its toxicity. Therefore bacterial strains with higher intrinsic tolerance to n-butanol have to be selected as hosts for n-butanol production. Pseudomonas bacteria are metabolically very versatile and exhibit a high intrinsic tolerance to organic solvents making them suitable candidates for bioconversion processes. A prerequisite for a potential production of n-butanol in Pseudomonas bacteria is a thorough understanding of the molecular adaption processes caused by n-butanol and the identification of enzymes involved in n-butanol metabolization. This work describes the impact of n-butanol on the proteome and the phospholipid composition of the reference strain P. putida KT2440. The high proteome coverage of our proteomics survey allowed us to reconstruct the degradation pathway of n-butanol and to monitor the changes in the energy metabolism of KT2440 induced by n-butanol. Key enzymes involved in n-butanol degradation identified in study will be interesting targets for optimization of n-butanol production in Pseudomonads. The present work and the identification of key enzymes involved in butanol metabolism may serve as a fundament to develop new or improve existing strategies for the biotechnological production of the next-generation biofuel n-butanol in Pseudomonads.
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Audrain B, Farag MA, Ryu CM, Ghigo JM. Role of bacterial volatile compounds in bacterial biology. FEMS Microbiol Rev 2015; 39:222-33. [PMID: 25725014 DOI: 10.1093/femsre/fuu013] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Bacterial interactions with neighboring microorganisms via production of small metabolites enable bacteria to respond and adapt to environmental changes. The study of intercellular interactions primarily focused on soluble metabolites, but bacteria also produce and release into their headspace a wide variety of volatile secondary metabolites, the ecological roles of which have generally been overlooked. However, bacterial volatile compounds are known to contribute to interkingdom interactions (plant, fungi and nematodes), and recent studies also identified their at-a-distance influence on bacterial behavior. The present review describes the biological roles of bacterial volatile compounds in inter- and intraspecies bacterial interactions, a new and yet unexplored research area, with potential clinical and industrial applications.
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Affiliation(s)
- Bianca Audrain
- Institut Pasteur, Genetics of Biofilms Unit, Department of Microbiology, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Mohamed A Farag
- Cairo University, Faculty of Pharmacy, Pharmacognosy Department, Kasr El Aini Street, P.B. 11562, Cairo, Egypt
| | - Choong-Min Ryu
- KRIBB, Molecular Phytobacteriology Laboratory, Daejeon 305-806, South Korea
| | - Jean-Marc Ghigo
- Institut Pasteur, Genetics of Biofilms Unit, Department of Microbiology, 28 rue du Dr Roux, 75724 Paris cedex 15, France
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Simon O, Klaiber I, Huber A, Pfannstiel J. Comprehensive proteome analysis of the response of Pseudomonas putida KT2440 to the flavor compound vanillin. J Proteomics 2014; 109:212-27. [PMID: 25026441 DOI: 10.1016/j.jprot.2014.07.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/25/2014] [Accepted: 07/06/2014] [Indexed: 12/15/2022]
Abstract
UNLABELLED Understanding of the molecular response of bacteria to precursors, products and environmental conditions applied in bioconversions is essential for optimizing whole-cell biocatalysis. To investigate the molecular response of the potential biocatalyst Pseudomonas putida KT2440 to the flavor compound vanillin we applied complementary gel- and LC-MS-based quantitative proteomics approaches. Our comprehensive proteomics survey included cytoplasmic and membrane proteins and led to the identification and quantification of 1614 proteins, corresponding to 30% of the total KT2440 proteome. 662 proteins were altered in abundance during growth on vanillin as sole carbon source as compared to growth on glucose. The proteome response entailed an increased abundance of enzymes involved in vanillin degradation, significant changes in central energy metabolism and an activation of solvent tolerance mechanisms. With respect to vanillin metabolism, particularly enzymes belonging to the β-ketoadipate pathway including a transcriptional regulator and porins specific for vanillin uptake increased in abundance. However, catabolism of vanillin was not dependent on vanillin dehydrogenase (Vdh), as shown by quantitative proteome analysis of a Vdh-deficient KT2440 mutant (GN235). Other aldehyde dehydrogenases that were significantly increased in abundance in response to vanillin may replace Vdh and thus may represent interesting targets for improving vanillin production in P. putida KT2440. BIOLOGICAL SIGNIFICANCE The high demand for the flavor compound vanillin by the food and fragrance industry makes natural vanillin from vanilla pods a scarce and expensive resource rendering its biotechnological production economically attractive. Pseudomonas bacteria are metabolically very versatile and accept a broad range of hydrocarbons as carbon source making them suitable candidates for bioconversion processes. This work describes the impact of vanillin on the metabolism of the reference strain P. putida KT2440 on a proteome wide scale. The high proteome coverage of our proteomics survey allowed us to analyze the regulation of whole protein networks instead of single proteins. We were able to reconstruct the complete degradation pathway of vanillin and to monitor the changes in the energy metabolism of KT2440 induced by vanillin as sole carbon source. Vanillin dehydrogenase (Vdh) was not mandatory for vanillin degradation in KT2440 and may be substituted by other aldehyde dehydrogenases that were up-regulated in a wild-type as well as in a Vdh-deficient strain in the presence of vanillin. Aldehyde dehydrogenases, vanillin specific porins and efflux pump systems identified in study will be interesting targets for optimization of vanillin production in Pseudomonas bacteria. Furthermore, several mechanisms of solvent tolerance were induced by vanillin in KT2440. These include increased abundance of several efflux pump systems, chaperones as well as enzymes involved in cyclopropane fatty acid synthesis and trehalose formation. The present work will deepen the understanding of metabolism of aromatic compounds in P. putida and may lead to a more comprehensive understanding of solvent tolerance mechanisms in Gram-negative bacteria in general. Moreover, it will serve as a basis for further strain developments for a biotechnological production of vanillin in P. putida KT2440 or other Pseudomonas strains, highlighting the role of proteomics surveys as a powerful screening technology.
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Affiliation(s)
- Oliver Simon
- Department of Biosensorics, Institute of Physiology, University of Hohenheim, August von Hartmann-Str. 3, 70599 Stuttgart, Germany
| | - Iris Klaiber
- Proteomics Core Facility of the Life Science Center, University of Hohenheim, August von Hartmann-Str. 3, 70599 Stuttgart, Germany
| | - Armin Huber
- Department of Biosensorics, Institute of Physiology, University of Hohenheim, August von Hartmann-Str. 3, 70599 Stuttgart, Germany; Proteomics Core Facility of the Life Science Center, University of Hohenheim, August von Hartmann-Str. 3, 70599 Stuttgart, Germany
| | - Jens Pfannstiel
- Proteomics Core Facility of the Life Science Center, University of Hohenheim, August von Hartmann-Str. 3, 70599 Stuttgart, Germany.
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