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Weimer A, Pause L, Ries F, Kohlstedt M, Adrian L, Krömer J, Lai B, Wittmann C. Systems biology of electrogenic Pseudomonas putida - multi-omics insights and metabolic engineering for enhanced 2-ketogluconate production. Microb Cell Fact 2024; 23:246. [PMID: 39261865 PMCID: PMC11389600 DOI: 10.1186/s12934-024-02509-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/10/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND Pseudomonas putida KT2440 has emerged as a promising host for industrial bioproduction. However, its strictly aerobic nature limits the scope of applications. Remarkably, this microbe exhibits high bioconversion efficiency when cultured in an anoxic bio-electrochemical system (BES), where the anode serves as the terminal electron acceptor instead of oxygen. This environment facilitates the synthesis of commercially attractive chemicals, including 2-ketogluconate (2KG). To better understand this interesting electrogenic phenotype, we studied the BES-cultured strain on a systems level through multi-omics analysis. Inspired by our findings, we constructed novel mutants aimed at improving 2KG production. RESULTS When incubated on glucose, P. putida KT2440 did not grow but produced significant amounts of 2KG, along with minor amounts of gluconate, acetate, pyruvate, succinate, and lactate. 13C tracer studies demonstrated that these products are partially derived from biomass carbon, involving proteins and lipids. Over time, the cells exhibited global changes on both the transcriptomic and proteomic levels, including the shutdown of translation and cell motility, likely to conserve energy. These adaptations enabled the cells to maintain significant metabolic activity for several weeks. Acetate formation was shown to contribute to energy supply. Mutants deficient in acetate production demonstrated superior 2KG production in terms of titer, yield, and productivity. The ∆aldBI ∆aldBII double deletion mutant performed best, accumulating 2KG at twice the rate of the wild type and with an increased yield (0.96 mol/mol). CONCLUSIONS By integrating transcriptomic, proteomic, and metabolomic analyses, this work provides the first systems biology insight into the electrogenic phenotype of P. putida KT2440. Adaptation to anoxic-electrogenic conditions involved coordinated changes in energy metabolism, enabling cells to sustain metabolic activity for extended periods. The metabolically engineered mutants are promising for enhanced 2KG production under these conditions. The attenuation of acetate synthesis represents the first systems biology-informed metabolic engineering strategy for enhanced 2KG production in P. putida. This non-growth anoxic-electrogenic mode expands our understanding of the interplay between growth, glucose phosphorylation, and glucose oxidation into gluconate and 2KG in P. putida.
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Affiliation(s)
- Anna Weimer
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Laura Pause
- Systems Biotechnology Group, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Fabian Ries
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lorenz Adrian
- Department of Molecular Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jens Krömer
- Systems Biotechnology Group, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Bin Lai
- BMBF Junior Research Group Biophotovoltaics, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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Kulakowski S, Banerjee D, Scown CD, Mukhopadhyay A. Improving microbial bioproduction under low-oxygen conditions. Curr Opin Biotechnol 2023; 84:103016. [PMID: 37924688 DOI: 10.1016/j.copbio.2023.103016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/17/2023] [Accepted: 10/07/2023] [Indexed: 11/06/2023]
Abstract
Microbial bioconversion provides access to a wide range of sustainably produced chemicals and commodities. However, industrial-scale bioproduction process operations are preferred to be anaerobic due to the cost associated with oxygen transfer. Anaerobic bioconversion generally offers limited substrate utilization profiles, lower product yields, and reduced final product diversity compared with aerobic processes. Bioproduction under conditions of reduced oxygen can overcome the limitations of fully aerobic and anaerobic bioprocesses, but many microbial hosts are not developed for low-oxygen bioproduction. Here, we describe advances in microbial strain engineering involving the use of redox cofactor engineering, genome-scale metabolic modeling, and functional genomics to enable improved bioproduction processes under low oxygen and provide a viable path for scaling these bioproduction systems to industrial scales.
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Affiliation(s)
- Shawn Kulakowski
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Corinne D Scown
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Energy Analysis and Environmental Impacts Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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3
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McNaught KJ, Kuatsjah E, Zahn M, Prates ÉT, Shao H, Bentley GJ, Pickford AR, Gruber JN, Hestmark KV, Jacobson DA, Poirier BC, Ling C, San Marchi M, Michener WE, Nicora CD, Sanders JN, Szostkiewicz CJ, Veličković D, Zhou M, Munoz N, Kim YM, Magnuson JK, Burnum-Johnson KE, Houk KN, McGeehan JE, Johnson CW, Beckham GT. Initiation of fatty acid biosynthesis in Pseudomonas putida KT2440. Metab Eng 2023; 76:193-203. [PMID: 36796578 DOI: 10.1016/j.ymben.2023.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Deciphering the mechanisms of bacterial fatty acid biosynthesis is crucial for both the engineering of bacterial hosts to produce fatty acid-derived molecules and the development of new antibiotics. However, gaps in our understanding of the initiation of fatty acid biosynthesis remain. Here, we demonstrate that the industrially relevant microbe Pseudomonas putida KT2440 contains three distinct pathways to initiate fatty acid biosynthesis. The first two routes employ conventional β-ketoacyl-ACP synthase III enzymes, FabH1 and FabH2, that accept short- and medium-chain-length acyl-CoAs, respectively. The third route utilizes a malonyl-ACP decarboxylase enzyme, MadB. A combination of exhaustive in vivo alanine-scanning mutagenesis, in vitro biochemical characterization, X-ray crystallography, and computational modeling elucidate the presumptive mechanism of malonyl-ACP decarboxylation via MadB. Given that functional homologs of MadB are widespread throughout domain Bacteria, this ubiquitous alternative fatty acid initiation pathway provides new opportunities to target a range of biotechnology and biomedical applications.
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Affiliation(s)
- Kevin J McNaught
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Eugene Kuatsjah
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Michael Zahn
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Érica T Prates
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Huiling Shao
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA, 90095, USA
| | - Gayle J Bentley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Andrew R Pickford
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Josephine N Gruber
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Kelley V Hestmark
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Daniel A Jacobson
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Brenton C Poirier
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Chen Ling
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Myrsini San Marchi
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA, 90095, USA
| | - William E Michener
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA, 90095, USA
| | - Caralyn J Szostkiewicz
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Nathalie Munoz
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Young-Mo Kim
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jon K Magnuson
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kristin E Burnum-Johnson
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles, CA, 90095, USA
| | - John E McGeehan
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
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Scribani-Rossi C, Molina-Henares MA, Angeli S, Cutruzzolà F, Paiardini A, Espinosa-Urgel M, Rinaldo S. The phosphodiesterase RmcA contributes to the adaptation of Pseudomonas putida to l-arginine. FEMS Microbiol Lett 2023; 370:fnad077. [PMID: 37550221 PMCID: PMC10423028 DOI: 10.1093/femsle/fnad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/19/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023] Open
Abstract
Amino acids are crucial in nitrogen cycling and to shape the metabolism of microorganisms. Among them, arginine is a versatile molecule able to sustain nitrogen, carbon, and even ATP supply and to regulate multicellular behaviors such as biofilm formation. Arginine modulates the intracellular levels of 3'-5'cyclic diguanylic acid (c-di-GMP), a second messenger that controls biofilm formation, maintenance and dispersion. In Pseudomonas putida, KT2440, a versatile microorganism with wide biotechnological applications, modulation of c-di-GMP levels by arginine requires the transcriptional regulator ArgR, but the connections between arginine metabolism and c-di-GMP are not fully characterized. It has been recently demonstrated that arginine can be perceived by the opportunistic human pathogen Pseudomonas aeruginosa through the transducer RmcA protein (Redox regulator of c-di-GMP), which can directly decrease c-di-GMP levels and possibly affect biofilm architecture. A RmcA homolog is present in P. putida, but its function and involvement in arginine perceiving or biofilm life cycle had not been studied. Here, we present a preliminary characterization of the RmcA-dependent response to arginine in P. putida in modulating biofilm formation, c-di-GMP levels, and energy metabolism. This work contributes to further understanding the molecular mechanisms linking biofilm homeostasis and environmental adaptation.
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Affiliation(s)
- Chiara Scribani-Rossi
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - María Antonia Molina-Henares
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidin
, CSIC, Profesor Albareda, 1, Granada, 18008, Spain
| | - Simone Angeli
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Francesca Cutruzzolà
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Alessandro Paiardini
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Manuel Espinosa-Urgel
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidin
, 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, P.le Aldo Moro 5, 00185, Rome, Italy
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5
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Lu C, Akwafo EO, Wijffels RH, Martins Dos Santos VAP, Weusthuis RA. Metabolic engineering of Pseudomonas putida KT2440 for medium-chain-length fatty alcohol and ester production from fatty acids. Metab Eng 2023; 75:110-118. [PMID: 36494025 DOI: 10.1016/j.ymben.2022.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/03/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
Medium-chain-length fatty alcohols have broad applications in the surfactant, lubricant, and cosmetic industries. Their acetate esters are widely used as flavoring and fragrance substances. Pseudomonas putida KT2440 is a promising chassis for fatty alcohol and ester production at the industrial scale due to its robustness, versatility, and high oxidative capacity. However, P. putida has also numerous native alcohol dehydrogenases, which lead to the degradation of these alcohols and thereby hinder its use as an effective biocatalyst. Therefore, to harness its capacity as a producer, we constructed two engineered strains (WTΔpedFΔadhP, GN346ΔadhP) incapable of growing on mcl-fatty alcohols by deleting either a cytochrome c oxidase PedF and a short-chain alcohol dehydrogenase AdhP in P. putida or AdhP in P. putida GN346. Carboxylic acid reductase, phosphopantetheinyl transferase, and alcohol acetyltransferase were expressed in the engineered P. putida strains to produce hexyl acetate. Overexpression of transporters further increased 1-hexanol and hexyl acetate production. The optimal strain G23E-MPAscTP produced 93.8 mg/L 1-hexanol and 160.5 mg/L hexyl acetate, with a yield of 63.1%. The engineered strain is applicable for C6-C10 fatty alcohols and their acetate ester production. This study lays a foundation for P. putida being used as a microbial cell factory for sustainable synthesis of a broad range of products based on medium-chain-length fatty alcohols.
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Affiliation(s)
- Chunzhe Lu
- Bioprocess Engineering, Wageningen University and Research, Wageningen, the Netherlands
| | - Edward Ofori Akwafo
- Bioprocess Engineering, Wageningen University and Research, Wageningen, the Netherlands
| | - Rene H Wijffels
- Bioprocess Engineering, Wageningen University and Research, Wageningen, the Netherlands; Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Vitor A P Martins Dos Santos
- Bioprocess Engineering, Wageningen University and Research, Wageningen, the Netherlands; Lifeglimmer GmbH, Berlin, Germany
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Wageningen, the Netherlands.
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Solar Venero EC, Matera G, Vogel J, López NI, Tribelli PM. Small RNAs in the Antarctic bacterium Pseudomonas extremaustralis responsive to oxygen availability and oxidative stress. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:604-615. [PMID: 35689330 DOI: 10.1111/1758-2229.13084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Bacterial small non-coding RNAs (sRNAs) play key roles as genetic regulators, mediating in the adaptability to changing environmental conditions and stress responses. In this work, we analysed putative sRNAs identified by RNA-seq experiments in different aeration conditions in the extremophile bacterium P. extremaustralis. These analyses allowed the identification of 177 putative sRNAs under aerobiosis (A), microaerobiosis (M) and microaerobiosis after H2 O2 exposure (m-OS). The size and transcription profile of eight sRNAs with differential expression were verified by Northern blot. sRNA40, with unknown function but conserved in other Pseudomonas species, was selected to perform overexpression experiments followed by RNA-seq analysis. The overexpression of sRNA40 in P. extremaustralis resulted in significant expression changes of 19 genes with 14 differentially upregulated and five downregulated. Among the upregulated genes, eight transcripts corresponded to components of secretion systems, such as gspH, gspK, and gspM, belonging to the Type II secretion system, and rspO and rspP from Type III secretion system. Our results showed a novel sRNA which expression was triggered by low oxygen levels, and whose overexpression was associated with upregulation of selected components of protein secretion systems.
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Affiliation(s)
| | - Gianluca Matera
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Nancy I López
- IQUIBICEN-CONICET, Intendente Guiraldes 2160, 1428EGA, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428EGA, Buenos Aires, Argentina
| | - Paula M Tribelli
- IQUIBICEN-CONICET, Intendente Guiraldes 2160, 1428EGA, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428EGA, Buenos Aires, Argentina
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