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Manoli MT, Gargantilla-Becerra Á, Del Cerro Sánchez C, Rivero-Buceta V, Prieto MA, Nogales J. A model-driven approach to upcycling recalcitrant feedstocks in Pseudomonas putida by decoupling PHA production from nutrient limitation. Cell Rep 2024; 43:113979. [PMID: 38517887 DOI: 10.1016/j.celrep.2024.113979] [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: 08/09/2023] [Revised: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 03/24/2024] Open
Abstract
Bacterial polyhydroxyalkanoates (PHAs) have emerged as promising eco-friendly alternatives to petroleum-based plastics since they are synthesized from renewable resources and offer exceptional properties. However, their production is limited to the stationary growth phase under nutrient-limited conditions, requiring customized strategies and costly two-phase bioprocesses. In this study, we tackle these challenges by employing a model-driven approach to reroute carbon flux and remove regulatory constraints using synthetic biology. We construct a collection of Pseudomonas putida-overproducing strains at the expense of plastics and lignin-related compounds using growth-coupling approaches. PHA production was successfully achieved during growth phase, resulting in the production of up to 46% PHA/cell dry weight while maintaining a balanced carbon-to-nitrogen ratio. Our strains are additionally validated under an upcycling scenario using enzymatically hydrolyzed polyethylene terephthalate as a feedstock. These findings have the potential to revolutionize PHA production and address the global plastic crisis by overcoming the complexities of traditional PHA production bioprocesses.
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Affiliation(s)
- Maria-Tsampika Manoli
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Álvaro Gargantilla-Becerra
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain; 3Systems Biotechnology Group, Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Carlos Del Cerro Sánchez
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Virginia Rivero-Buceta
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
| | - Juan Nogales
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain; 3Systems Biotechnology Group, Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain; CNB DNA Biofoundry (CNBio), CSIC, Madrid, Spain.
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2
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Chacón M, Wongsirichot P, Winterburn J, Dixon N. Genetic and process engineering for polyhydroxyalkanoate production from pre- and post-consumer food waste. Curr Opin Biotechnol 2024; 85:103024. [PMID: 38056203 DOI: 10.1016/j.copbio.2023.103024] [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: 08/29/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Biopolymers produced as microbial carbon storage systems, such as polyhydroxyalkanoates (PHAs), offer potential to be used in place of petrochemically derived plastics. Low-value organic feedstocks, such as food waste, have been explored as a potential substrate for the microbial production of PHAs. In this review, we discuss the biosynthesis, composition and producers of PHAs, with a particular focus on the genetic and process engineering efforts to utilise non-native substrates, derived from food waste from across the entire supply chain, for microbial growth and PHA production. We highlight a series of studies that have achieved impressive advances and discuss the challenges of producing PHAs with consistent composition and properties from mixed and variable food waste and by-products.
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Affiliation(s)
- Micaela Chacón
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester M1 7DN, UK
| | - Phavit Wongsirichot
- Department of Chemical Engineering, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - James Winterburn
- Department of Chemical Engineering, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Neil Dixon
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester M1 7DN, UK.
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3
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Benninghaus L, Zagami L, Tassini G, Meyer F, Wendisch VF. γ-Glutamylation of Isopropylamine by Fermentation. Chembiochem 2024; 25:e202300608. [PMID: 37987374 DOI: 10.1002/cbic.202300608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 11/22/2023]
Abstract
Glutamylation yields N-functionalized amino acids in several natural pathways. γ-Glutamylated amino acids may exhibit improved properties for their industrial application, e. g., as taste enhancers or in peptide drugs. γ-Glutamyl-isopropylamide (GIPA) can be synthesized from isopropylamine (IPA) and l-glutamate. In Pseudomonas sp. strain KIE171, GIPA is an intermediate in the biosynthesis of l-alaninol (2-amino-1-propanol), a precursor of the fluorochinolone antibiotic levofloxacin and of the chloroacetanilide herbicide metolachlor. In this study, fermentative production of GIPA with metabolically engineered Pseudomonas putida KT2440 using γ-glutamylmethylamide synthetase (GMAS) from Methylorubrum extorquens was established. Upon addition of IPA during growth with glycerol as carbon source in shake flasks, the recombinant strain produced up to 21.8 mM GIPA. In fed-batch bioreactor cultivations, GIPA accumulated to a titer of 11 g L-1 with a product yield of 0.11 g g-1 glycerol and a volumetric productivity of 0.24 g L-1 h-1 . To the best of our knowledge, this is the first fermentative production of GIPA.
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Affiliation(s)
- Leonie Benninghaus
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Laura Zagami
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Giulio Tassini
- School of Science Mathematics Physical and Natural Sciences, University of Florence, Piazza San Marco 4, 50121, Firenze, Italy
| | - Florian Meyer
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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4
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Aghaali Z, Naghavi MR. Biotechnological Approaches for Enhancing Polyhydroxyalkanoates (PHAs) Production: Current and Future Perspectives. Curr Microbiol 2023; 80:345. [PMID: 37731015 DOI: 10.1007/s00284-023-03452-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/19/2023] [Indexed: 09/22/2023]
Abstract
The benefits of biotechnology are not limited to genetic engineering, but it also displays its great impact on industrial uses of crops (e.g., biodegradable plastics). Polyhydroxyalkanoates (PHAs) make a diverse class of bio-based and biodegradable polymers naturally synthesized by numerous microorganisms. However, several C3 and C4 plants have also been genetically engineered to produce PHAs. The highest production yield of PHAs was obtained with a well-known C3 plant, Arabidopsis thaliana, upto 40% of the dry weight of the leaf. This review summarizes all biotechnological mechanisms that have been adopted with the goal of increasing PHAs production in bacteria and plant species alike. Moreover, the possibility of using some methods that have not been applied in bioplastic science are discussed with special attention to plants. These include producing PHAs in transgenic hairy roots and cell suspension cultures, making transformed bacteria and plants via transposons, constructing an engineered metabolon, and overexpressing of phaP and the ABC operon concurrently. Taken together, that biotechnology will be highly beneficial for reducing plastic pollution through the implementation of biotechnological strategies is taken for granted.
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Affiliation(s)
- Zahra Aghaali
- Department of Genetic and Plant Breeding, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Mohammad Reza Naghavi
- Division of Biotechnology, Department of Agronomy and Plant Breeding, College of Agricultural and Natural Resources, University of Tehran, Karaj, Iran.
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Alessio F, Lennert D, Sandra VD, Frederik W, Verhaeghe K, Koen VL, Joris R, Rosalia D. Glycerol used for denitrification in full-scale wastewater treatment plants: nitrous oxide emissions, sludge acclimatization, and other insights. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 88:645-657. [PMID: 37578880 PMCID: wst_2023_240 DOI: 10.2166/wst.2023.240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Glycerol is commonly employed for denitrification purposes in full-scale wastewater treatment. In non-acclimatized biomass, the glycerol is very inefficient resulting in a high C/N ratio and low-standard denitrification rates. The acclimatization is driven by the microbial enrichment of Saccharimonadales and Propionibacteriales as found in different sampled municipal sludges flanking the dominant presence of Burkholderiales. The selective strategy is based on a very efficient process in terms of C/N ratios and standard denitrification rates, but it leads to nitrite accumulation. As a result, severe and unexpected nitrous oxide emissions were found in full-scale with emission factors up to 2.5% kgN2O (kgKJNremoved)-1. Simultaneous dosage of isobutirate in a full-scale experiment could counter the nitrous oxide emissions. As nitrous oxide emissions were found proportional to the dosed glycerol-based COD, the authors suggest that, in case of acclimatization of biomass to glycerol, an emission factor based on the dosed COD should substitute the general nitrous oxide emission factors based on incoming or removed nitrogen to the plant.
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Affiliation(s)
- Fenu Alessio
- Aquafin NV, Dijkstraat 8, Aartselaar, Belgium E-mail:
| | | | | | | | | | | | - Roels Joris
- Aquafin NV, Dijkstraat 8, Aartselaar, Belgium
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6
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Mattioni Marchetti V, Hrabak J, Bitar I. Fosfomycin resistance mechanisms in Enterobacterales: an increasing threat. Front Cell Infect Microbiol 2023; 13:1178547. [PMID: 37469601 PMCID: PMC10352792 DOI: 10.3389/fcimb.2023.1178547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/31/2023] [Indexed: 07/21/2023] Open
Abstract
Antimicrobial resistance is well-known to be a global health and development threat. Due to the decrease of effective antimicrobials, re-evaluation in clinical practice of old antibiotics, as fosfomycin (FOS), have been necessary. FOS is a phosphonic acid derivate that regained interest in clinical practice for the treatment of complicated infection by multi-drug resistant (MDR) bacteria. Globally, FOS resistant Gram-negative pathogens are raising, affecting the public health, and compromising the use of the antibiotic. In particular, the increased prevalence of FOS resistance (FOSR) profiles among Enterobacterales family is concerning. Decrease in FOS effectiveness can be caused by i) alteration of FOS influx inside bacterial cell or ii) acquiring antimicrobial resistance genes. In this review, we investigate the main components implicated in FOS flow and report specific mutations that affect FOS influx inside bacterial cell and, thus, its effectiveness. FosA enzymes were identified in 1980 from Serratia marcescens but only in recent years the scientific community has started studying their spread. We summarize the global epidemiology of FosA/C2/L1-2 enzymes among Enterobacterales family. To date, 11 different variants of FosA have been reported globally. Among acquired mechanisms, FosA3 is the most spread variant in Enterobacterales, followed by FosA7 and FosA5. Based on recently published studies, we clarify and represent the molecular and genetic composition of fosA/C2 genes enviroment, analyzing the mechanisms by which such genes are slowly transmitting in emerging and high-risk clones, such as E. coli ST69 and ST131, and K. pneumoniae ST11. FOS is indicated as first line option against uncomplicated urinary tract infections and shows remarkable qualities in combination with other antibiotics. A rapid and accurate identification of FOSR type in Enterobacterales is difficult to achieve due to the lack of commercial phenotypic susceptibility tests and of rapid systems for MIC detection.
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Affiliation(s)
- Vittoria Mattioni Marchetti
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
- Unit of Microbiology and Clinical Microbiology, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
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7
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Eissenberger K, Ballesteros A, De Bisschop R, Bugnicourt E, Cinelli P, Defoin M, Demeyer E, Fürtauer S, Gioia C, Gómez L, Hornberger R, Ißbrücker C, Mennella M, von Pogrell H, Rodriguez-Turienzo L, Romano A, Rosato A, Saile N, Schulz C, Schwede K, Sisti L, Spinelli D, Sturm M, Uyttendaele W, Verstichel S, Schmid M. Approaches in Sustainable, Biobased Multilayer Packaging Solutions. Polymers (Basel) 2023; 15:polym15051184. [PMID: 36904425 PMCID: PMC10007551 DOI: 10.3390/polym15051184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 03/03/2023] Open
Abstract
The depletion of fossil resources and the growing demand for plastic waste reduction has put industries and academic researchers under pressure to develop increasingly sustainable packaging solutions that are both functional and circularly designed. In this review, we provide an overview of the fundamentals and recent advances in biobased packaging materials, including new materials and techniques for their modification as well as their end-of-life scenarios. We also discuss the composition and modification of biobased films and multilayer structures, with particular attention to readily available drop-in solutions, as well as coating techniques. Moreover, we discuss end-of-life factors, including sorting systems, detection methods, composting options, and recycling and upcycling possibilities. Finally, regulatory aspects are pointed out for each application scenario and end-of-life option. Moreover, we discuss the human factor in terms of consumer perception and acceptance of upcycling.
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Affiliation(s)
- Kristina Eissenberger
- Sustainable Packaging Institute SPI, Faculty of Life Sciences, Albstadt-Sigmaringen University, Anton-Günther-Str. 51, 72488 Sigmaringen, Germany
- Correspondence: (K.E.); (M.S.)
| | - Arantxa Ballesteros
- Centro Tecnológico ITENE, Parque Tecnológico, Carrer d’Albert Einstein 1, 46980 Paterna, Spain
| | - Robbe De Bisschop
- Centexbel, Textile Competence Centre, Etienne Sabbelaan 49, 8500 Kortrijk, Belgium
| | - Elodie Bugnicourt
- Graphic Packaging International, Fountain Plaza, Belgicastraat 7, 1930 Zaventem, Belgium
| | - Patrizia Cinelli
- Planet Bioplastics S.r.l., Via San Giovanni Bosco 23, 56127 Pisa, Italy
| | - Marc Defoin
- Bostik SA, 420 rue d’Estienne d’Orves, 92700 Colombes, France
| | - Elke Demeyer
- Centexbel, Textile Competence Centre, Etienne Sabbelaan 49, 8500 Kortrijk, Belgium
| | - Siegfried Fürtauer
- Fraunhofer Institute for Process Engineering and Packaging, Materials Development, Giggenhauser Str. 35, 85354 Freising, Germany
| | - Claudio Gioia
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Lola Gómez
- AIMPLAS, Plastics Technology Center, Valencia Parc Tecnologic, Carrer de Gustave Eiffel 4, 46980 Paterna, Spain
| | - Ramona Hornberger
- Fraunhofer Institute for Process Engineering and Packaging, Materials Development, Giggenhauser Str. 35, 85354 Freising, Germany
| | | | - Mara Mennella
- KNEIA S.L., Carrer d’Aribau 168-170, 08036 Barcelona, Spain
| | - Hasso von Pogrell
- AIMPLAS, Plastics Technology Center, Valencia Parc Tecnologic, Carrer de Gustave Eiffel 4, 46980 Paterna, Spain
| | | | - Angela Romano
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Antonella Rosato
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Nadja Saile
- Sustainable Packaging Institute SPI, Faculty of Life Sciences, Albstadt-Sigmaringen University, Anton-Günther-Str. 51, 72488 Sigmaringen, Germany
| | - Christian Schulz
- European Bioplastics e.V. (EUBP), Marienstr. 19/20, 10117 Berlin, Germany
| | - Katrin Schwede
- European Bioplastics e.V. (EUBP), Marienstr. 19/20, 10117 Berlin, Germany
| | - Laura Sisti
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Daniele Spinelli
- Next Technology Tecnotessile, Chemical Division, Via del Gelso 13, 59100 Prato, Italy
| | - Max Sturm
- Sustainable Packaging Institute SPI, Faculty of Life Sciences, Albstadt-Sigmaringen University, Anton-Günther-Str. 51, 72488 Sigmaringen, Germany
| | - Willem Uyttendaele
- Centexbel, Textile Competence Centre, Etienne Sabbelaan 49, 8500 Kortrijk, Belgium
| | | | - Markus Schmid
- Sustainable Packaging Institute SPI, Faculty of Life Sciences, Albstadt-Sigmaringen University, Anton-Günther-Str. 51, 72488 Sigmaringen, Germany
- Correspondence: (K.E.); (M.S.)
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8
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Microbially Synthesized Polymer-Metal Nanoparticles Composites as Promising Wound Dressings to Overcome Methicillin-Resistance Staphylococcus aureus Infections. Polymers (Basel) 2023; 15:polym15040920. [PMID: 36850204 PMCID: PMC9960834 DOI: 10.3390/polym15040920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/22/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
Antimicrobial resistance has been declared one of the top 10 global public health threats. Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of recurring skin and soft tissue infections in patients with chronic skin conditions such as diabetic foot infections, making the treatment of the ulcers challenging. Wound dressings combined with metal nanoparticles have been suggested to prevent and treat MRSA-infected wounds. However, these particles are commonly synthesized by chemical approaches. In this study, we developed bio-based silver (Bio-AgNPs) and copper oxide nanoparticles (CuONPs) polymer composites using a microbially produced polyester from the Polyhydroxyalkanoates (PHAs) family. Poly(3-hydroxyoctanoate)-co-(3-hydroxyhexanoate) (PHO) was synthesized by Pseudomonas putida and functionalized in-situ with Bio-AgNPs or ex-situ with CuONPs. PHO-CuONPs films did not inhibit MRSA growth, while a reduction of 6.0 log CFU/mL was achieved with PHO-Bio-AgNPs synthesized from silver nitrate (AgNO3) solution at 3.5 mM. Exposure of human fibroblast cells (HFF-1) to the bioactive films did not induce notable cytotoxicity and genotoxicity, as seen by a viability higher than 79% and no significant changes in basal DNA damage. However, exposure to PHO-Bio-AgNPs induced oxidative DNA damage in HFF-1 cells. No hemolytic potential was observed, while platelet aggregation was promoted and desired for wound healing. Here we demonstrate the biosynthesis of polymer-nanoparticle composites and their potential as bioactive films for MRSA treatment.
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9
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Park Y, Solhtalab M, Thongsomboon W, Aristilde L. Strategies of organic phosphorus recycling by soil bacteria: acquisition, metabolism, and regulation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:3-24. [PMID: 35001516 PMCID: PMC9306846 DOI: 10.1111/1758-2229.13040] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 05/12/2023]
Abstract
Critical to meeting cellular phosphorus (P) demand, soil bacteria deploy a number of strategies to overcome limitation in inorganic P (Pi ) in soils. As a significant contributor to P recycling, soil bacteria secrete extracellular enzymes to degrade organic P (Po ) in soils into the readily bioavailable Pi . In addition, several Po compounds can be transported directly via specific transporters and subsequently enter intracellular metabolic pathways. In this review, we highlight the strategies that soil bacteria employ to recycle Po from the soil environment. We discuss the diversity of extracellular phosphatases in soils, the selectivity of these enzymes towards various Po biomolecules and the influence of the soil environmental conditions on the enzyme's activities. Moreover, we outline the intracellular metabolic pathways for Po biosynthesis and transporter-assisted Po and Pi uptake at different Pi availabilities. We further highlight the regulatory mechanisms that govern the production of phosphatases, the expression of Po transporters and the key metabolic changes in P metabolism in response to environmental Pi availability. Due to the depletion of natural resources for Pi , we propose future studies needed to leverage bacteria-mediated P recycling from the large pools of Po in soils or organic wastes to benefit agricultural productivity.
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Affiliation(s)
- Yeonsoo Park
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
| | - Mina Solhtalab
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
| | - Wiriya Thongsomboon
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Chemistry, Faculty of ScienceMahasarakham UniversityMahasarakham44150Thailand
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
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10
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Benninghaus L, Walter T, Mindt M, Risse JM, Wendisch VF. Metabolic Engineering of Pseudomonas putida for Fermentative Production of l-Theanine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:9849-9858. [PMID: 34465093 DOI: 10.1021/acs.jafc.1c03240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
N-alkylated amino acids are intermediates of natural biological pathways and can be found incorporated in peptides or have physiological roles in their free form. The N-ethylated amino acid l-theanine shows taste-enhancing properties and health benefits. It naturally occurs in green tea as major free amino acid. Isolation of l-theanine from Camilla sinensis shows low efficiency, and chemical synthesis results in a racemic mixture. Therefore, biochemical approaches for the production of l-theanine gain increasing interest. Here, we describe metabolic engineering of Pseudomonas putida KT2440 for the fermentative production of l-theanine from monoethylamine and carbon sources glucose, glycerol, or xylose using heterologous enzymes from Methylorubrum extorquens for l-theanine production and heterologous enzymes from Caulobacter crescentus for growth with xylose. l-Theanine (15.4 mM) accumulated in shake flasks with minimal medium containing monoethylamine and glucose, 15.2 mM with glycerol and 7 mM with xylose. Fed-batch bioreactor cultures yielded l-theanine titers of 10 g L-1 with glucose plus xylose, 17.2 g L-1 with glycerol, 4 g L-1 with xylose, and 21 g L-1 with xylose plus glycerol, respectively. To the best of our knowledge, this is the first l-theanine process using P. putida and the first compatible with the use of various alternative carbon sources.
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Affiliation(s)
- Leonie Benninghaus
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld 33615, Germany
| | - Tatjana Walter
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld 33615, Germany
| | - Melanie Mindt
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld 33615, Germany
| | - Joe Max Risse
- Fermentation Technology, Technical Faculty and CeBiTec, Bielefeld University, Bielefeld 33615, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld 33615, Germany
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11
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Post-Transcriptional Control in the Regulation of Polyhydroxyalkanoates Synthesis. Life (Basel) 2021; 11:life11080853. [PMID: 34440597 PMCID: PMC8401924 DOI: 10.3390/life11080853] [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] [Received: 07/30/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 01/08/2023] Open
Abstract
The large production of non-degradable petrol-based plastics has become a major global issue due to its environmental pollution. Biopolymers produced by microorganisms such as polyhydroxyalkanoates (PHAs) are gaining potential as a sustainable alternative, but the high cost associated with their industrial production has been a limiting factor. Post-transcriptional regulation is a key step to control gene expression in changing environments and has been reported to play a major role in numerous cellular processes. However, limited reports are available concerning the regulation of PHA accumulation in bacteria, and many essential regulatory factors still need to be identified. Here, we review studies where the synthesis of PHA has been reported to be regulated at the post-transcriptional level, and we analyze the RNA-mediated networks involved. Finally, we discuss the forthcoming research on riboregulation, synthetic, and metabolic engineering which could lead to improved strategies for PHAs synthesis in industrial production, thereby reducing the costs currently associated with this procedure.
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12
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13
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Cook TB, Jacobson TB, Venkataraman MV, Hofstetter H, Amador-Noguez D, Thomas MG, Pfleger BF. Stepwise genetic engineering of Pseudomonas putida enables robust heterologous production of prodigiosin and glidobactin A. Metab Eng 2021; 67:112-124. [PMID: 34175462 DOI: 10.1016/j.ymben.2021.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/14/2021] [Accepted: 06/19/2021] [Indexed: 12/21/2022]
Abstract
Polyketide synthases (PKS) and nonribosomal peptide synthetases (NRPS) comprise biosynthetic pathways that provide access to diverse, often bioactive natural products. Metabolic engineering can improve production metrics to support characterization and drug-development studies, but often native hosts are difficult to genetically manipulate and/or culture. For this reason, heterologous expression is a common strategy for natural product discovery and characterization. Many bacteria have been developed to express heterologous biosynthetic gene clusters (BGCs) for producing polyketides and nonribosomal peptides. In this article, we describe tools for using Pseudomonas putida, a Gram-negative soil bacterium, as a heterologous host for producing natural products. Pseudomonads are known to produce many natural products, but P. putida production titers have been inconsistent in the literature and often low compared to other hosts. In recent years, synthetic biology tools for engineering P. putida have greatly improved, but their application towards production of natural products is limited. To demonstrate the potential of P. putida as a heterologous host, we introduced BGCs encoding the synthesis of prodigiosin and glidobactin A, two bioactive natural products synthesized from a combination of PKS and NRPS enzymology. Engineered strains exhibited robust production of both compounds after a single chromosomal integration of the corresponding BGC. Next, we took advantage of a set of genome-editing tools to increase titers by modifying transcription and translation of the BGCs and increasing the availability of auxiliary proteins required for PKS and NRPS activity. Lastly, we discovered genetic modifications to P. putida that affect natural product synthesis, including a strategy for removing a carbon sink that improves product titers. These efforts resulted in production strains capable of producing 1.1 g/L prodigiosin and 470 mg/L glidobactin A.
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Affiliation(s)
- Taylor B Cook
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Tyler B Jacobson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Maya V Venkataraman
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Heike Hofstetter
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael G Thomas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
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14
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Lhamo P, Behera SK, Mahanty B. Process optimization, metabolic engineering interventions and commercialization of microbial polyhydroxyalkanoates production - A state-of-the art review. Biotechnol J 2021; 16:e2100136. [PMID: 34132046 DOI: 10.1002/biot.202100136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/29/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022]
Abstract
Microbial polyhydroxyalkanoates (PHAs) produced using renewable resources could be the best alternative for conventional plastics. Despite their incredible potential, commercial production of PHAs remains very low. Nevertheless, sincere attempts have been made by researchers to improve the yield and economic viability of PHA production by utilizing low-cost agricultural or industrial wastes. In this context, the use of efficient microbial culture or consortia, adoption of experimental design to trace ideal growth conditions, nutritional requirements, and intervention of metabolic engineering tools have gained significant attention. This review has been structured to highlight the important microbial sources for PHA production, use of conventional and non-conventional substrates, product optimization using experimental design, metabolic engineering strategies, and global players in the commercialization of PHA in the past two decades. The challenges about PHA recovery and analysis have also been discussed which possess indirect hurdle while expanding the horizon of PHA-based bioplastics. Selection of appropriate microorganism and substrate plays a vital role in improving the productivity and characteristics of PHAs. Experimental design-based bioprocess, use of metabolic engineering tools, and optimal product recovery techniques are invaluable in this dimension. Optimization strategies, which are being explored in isolation, need to be logically integrated for the successful commercialization of microbial PHAs.
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Affiliation(s)
- Pema Lhamo
- Department of Biotechnology, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Shishir Kumar Behera
- Industrial Ecology Research Group, School of Chemical Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Biswanath Mahanty
- Department of Biotechnology, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
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15
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Matuszewska M, Maciąg T, Rajewska M, Wierzbicka A, Jafra S. The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482. Sci Rep 2021; 11:10994. [PMID: 34040089 PMCID: PMC8154892 DOI: 10.1038/s41598-021-90488-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/12/2021] [Indexed: 02/04/2023] Open
Abstract
Pseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound ("cluster 17") and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.
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Affiliation(s)
- Marta Matuszewska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Tomasz Maciąg
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Magdalena Rajewska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Aldona Wierzbicka
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland.
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16
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Borrero-de Acuña JM, Rohde M, Saldias C, Poblete-Castro I. Fed-Batch mcl- Polyhydroxyalkanoates Production in Pseudomonas putida KT2440 and Δ phaZ Mutant on Biodiesel-Derived Crude Glycerol. Front Bioeng Biotechnol 2021; 9:642023. [PMID: 33796510 PMCID: PMC8007980 DOI: 10.3389/fbioe.2021.642023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/18/2021] [Indexed: 11/13/2022] Open
Abstract
Crude glycerol has emerged as a suitable feedstock for the biotechnological production of various industrial chemicals given its high surplus catalyzed by the biodiesel industry. Pseudomonas bacteria metabolize the polyol into several biopolymers, including alginate and medium-chain-length poly(3-hydroxyalkanoates) (mcl-PHAs). Although P. putida is a suited platform to derive these polyoxoesters from crude glycerol, the attained concentrations in batch and fed-batch cultures are still low. In this study, we employed P. putida KT2440 and the hyper-PHA producer ΔphaZ mutant in two different fed-batch modes to synthesize mcl-PHAs from raw glycerol. Initially, the cells grew in a batch phase (μmax 0.21 h–1) for 22 h followed by a carbon-limiting exponential feeding, where the specific growth rate was set at 0.1 (h–1), resulting in a cell dry weight (CDW) of nearly 50 (g L–1) at 40 h cultivation. During the PHA production stage, we supplied the substrate at a constant rate of 50 (g h–1), where the KT2440 and the ΔphaZ produced 9.7 and 12.7 gPHA L–1, respectively, after 60 h cultivation. We next evaluated the PHA production ability of the P. putida strains using a DO-stat approach under nitrogen depletion. Citric acid was the main by-product secreted by the cells, accumulating in the culture broth up to 48 (g L–1) under nitrogen limitation. The mutant ΔphaZ amassed 38.9% of the CDW as mcl-PHA and exhibited a specific PHA volumetric productivity of 0.34 (g L–1 h–1), 48% higher than the parental KT2440 under the same growth conditions. The biosynthesized mcl-PHAs had average molecular weights ranging from 460 to 505 KDa and a polydispersity index (PDI) of 2.4–2.6. Here, we demonstrated that the DO-stat feeding approach in high cell density cultures enables the high yield production of mcl-PHA in P. putida strains using the industrial crude glycerol, where the fed-batch process selection is essential to exploit the superior biopolymer production hallmarks of engineered bacterial strains.
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Affiliation(s)
- José Manuel Borrero-de Acuña
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility of Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Cesar Saldias
- Departamento de Química Física, Facultad de Química y Farmacia, Pontificia Universidad Católica de Chile, Macul, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Faculty of Life Sciences, Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
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17
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Zhang Y, Li Z, Liu Y, Cen X, Liu D, Chen Z. Systems metabolic engineering of Vibrio natriegens for the production of 1,3-propanediol. Metab Eng 2021; 65:52-65. [PMID: 33722653 DOI: 10.1016/j.ymben.2021.03.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/28/2021] [Accepted: 03/06/2021] [Indexed: 11/18/2022]
Abstract
The economic viability of current bio-production systems is often limited by its low productivity due to slow cell growth and low substrate uptake rate. The fastest-growing bacterium Vibrio natriegens is a highly promising next-generation workhorse of the biotechnology industry which can utilize various industrially relevant carbon sources with high substrate uptake rates. Here, we demonstrate the first systematic engineering example of V. natriegens for the heterologous production of 1,3-propanediol (1,3-PDO) from glycerol. Systems metabolic engineering strategies have been applied in this study to develop a superior 1,3-PDO producer, including: (1) heterologous pathway construction and optimization; (2) engineering cellular transcriptional regulators and global transcriptomic analysis; (3) enhancing intracellular reducing power by cofactor engineering; (4) reducing the accumulation of toxic intermediate by pathway engineering; (5) systematic engineering of glycerol oxidation pathway to eliminate byproduct formation. A final engineered strain can efficiently produce 1,3-PDO with a titer of 56.2 g/L, a yield of 0.61 mol/mol, and an average productivity of 2.36 g/L/h. The strategies described in this study would be useful for engineering V. natriegens as a potential chassis for the production of other useful chemicals and biofuels.
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Affiliation(s)
- Ye Zhang
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Zihua Li
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yu Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xuecong Cen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Dehua Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan, 523808, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Zhen Chen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan, 523808, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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18
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Wang S, Fu C, Liu K, Cui J, Hu H, Wang W, Zhang X. Engineering a Synthetic Pathway for Gentisate in Pseudomonas Chlororaphis P3. Front Bioeng Biotechnol 2021; 8:622226. [PMID: 33553126 PMCID: PMC7862547 DOI: 10.3389/fbioe.2020.622226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/30/2020] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas chlororaphis P3 has been well-engineered as a platform organism for biologicals production due to enhanced shikimate pathway and excellent physiological and genetic characteristics. Gentisate displays high antiradical and antioxidant activities and is an important intermediate that can be used as a precursor for drugs. Herein, a plasmid-free biosynthetic pathway of gentisate was constructed by connecting the endogenous degradation pathway from 3-hydroxybenzoate in Pseudomonas for the first time. As a result, the production of gentisate reached 365 mg/L from 3-HBA via blocking gentisate conversion and enhancing the gentisate precursors supply through the overexpression of the rate-limiting step. With a close-up at the future perspectives, a series of bioactive compounds could be achieved by constructing synthetic pathways in conventional Pseudomonas to establish a cell factory.
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Affiliation(s)
- Songwei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Cong Fu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Kaiquan Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Department of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Jiajia Cui
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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19
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Wang Q, Yu D, Wang X, Chu G, He T, Zhao J. Development of novel denitrifying nitrite accumulation and phosphorus removal (DNAPR) process for offering an alternative pretreatment to achieve mainstream Anammox. BIORESOURCE TECHNOLOGY 2021; 319:124164. [PMID: 33002785 DOI: 10.1016/j.biortech.2020.124164] [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: 08/17/2020] [Revised: 09/17/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
For achieving mainstream anaerobic ammonium oxidation (Anammox), there is a need to achieve organic carbon and phosphorus removal meanwhile supplying nitrite (NO2--N). Based on this demand, a novel anaerobic/anoxic/aerobic operated denitrifying nitrite accumulation and phosphorus removal (DNAPR) process was proposed for treating synthetic municipal and nitrate (NO3--N) wastewaters simultaneously (volume ratio of 5:1). By adjusting influent composition, discharging anaerobic-end supernatant, shortening anoxic duration, and adding a short aerobic stage, DNAPR process achieved promising and stable nitrate-to-nitrite transformation (78.35%) and phosphorus removal (98.34%) performance. Moreover, effluent with chemical oxygen demand of 16.63 mg/L, nitrite of 54.16 mg/L, orthophosphate of 0.37 mg/L, and nitrite to ammonia ratio of 1.3 were finally obtained after 141-day operation. Microbiological analysis showed that Thauera (34.9%) and unclassified_f_Rhodobacteraceae (6.79%) were both responsible for DNAPR. Therefore, DNAPR, serving as promising alternative pretreatment, might possess significance for achieving mainstream Anammox.
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Affiliation(s)
- Qiuying Wang
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, PR China
| | - Deshuang Yu
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, PR China
| | - Xiaoxia Wang
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, PR China
| | - Guangyu Chu
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, PR China
| | - Tonghui He
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, PR China
| | - Ji Zhao
- School of Environmental Science and Engineering, Qingdao University, Qingdao 266071, PR China.
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20
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Mezzina MP, Manoli MT, Prieto MA, Nikel PI. Engineering Native and Synthetic Pathways in Pseudomonas putida for the Production of Tailored Polyhydroxyalkanoates. Biotechnol J 2020; 16:e2000165. [PMID: 33085217 DOI: 10.1002/biot.202000165] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/16/2020] [Indexed: 12/16/2022]
Abstract
Growing environmental concern sparks renewed interest in the sustainable production of (bio)materials that can replace oil-derived goods. Polyhydroxyalkanoates (PHAs) are isotactic polymers that play a critical role in the central metabolism of producer bacteria, as they act as dynamic reservoirs of carbon and reducing equivalents. PHAs continue to attract industrial attention as a starting point toward renewable, biodegradable, biocompatible, and versatile thermoplastic and elastomeric materials. Pseudomonas species have been known for long as efficient biopolymer producers, especially for medium-chain-length PHAs. The surge of synthetic biology and metabolic engineering approaches in recent years offers the possibility of exploiting the untapped potential of Pseudomonas cell factories for the production of tailored PHAs. In this article, an overview of the metabolic and regulatory circuits that rule PHA accumulation in Pseudomonas putida is provided, and approaches leading to the biosynthesis of novel polymers (e.g., PHAs including nonbiological chemical elements in their structures) are discussed. The potential of novel PHAs to disrupt existing and future market segments is closer to realization than ever before. The review is concluded by pinpointing challenges that currently hinder the wide adoption of bio-based PHAs, and strategies toward programmable polymer biosynthesis from alternative substrates in engineered P. putida strains are proposed.
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Affiliation(s)
- Mariela P Mezzina
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, 2800, Denmark
| | - María Tsampika Manoli
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas «Margarita Salas» (CIB-CSIC), Polymer Biotechnology Group, Madrid, 28040, Spain.,Spanish National Research Council (SusPlast-CSIC), Interdisciplinary Platform for Sustainable Plastics Toward a Circular Economy, Madrid, 28040, Spain
| | - M Auxiliadora Prieto
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas «Margarita Salas» (CIB-CSIC), Polymer Biotechnology Group, Madrid, 28040, Spain.,Spanish National Research Council (SusPlast-CSIC), Interdisciplinary Platform for Sustainable Plastics Toward a Circular Economy, Madrid, 28040, Spain
| | - Pablo I Nikel
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, 2800, Denmark
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21
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Zhang T, Cao J, Zhang Y, Fang F, Feng Q, Luo J. Achieving efficient nitrite accumulation in glycerol-driven partial denitrification system: Insights of influencing factors, shift of microbial community and metabolic function. BIORESOURCE TECHNOLOGY 2020; 315:123844. [PMID: 32688259 DOI: 10.1016/j.biortech.2020.123844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
Partial denitrification (PD), which could provide sufficient nitrite for subsequent anaerobic ammonium oxidation, is a novel strategy for mainstream nitrogen removal. In this study, the performance of using glycerol as electron donor for nitrite accumulation in PD process was evaluated. Results showed that a C/N of 4.5 was effective for nitrite production (average nitrite accumulation rate: 34.32 mg N h-1 gMLVSS-1; average nitrate-to-nitrite transformation ratio (NTR): 91.1%) with pH ranging from 6.0 to 9.0. Also, a stable nitrite accumulation was achieved in long-term operation with the average NTR of 80.1%. Mechanism investigation found that the denitrifying bacteria Saccharibacteria (77.9%) was enriched in glycerol-driven reactors. Moreover, the enzymatic activity as well as the encoding genes (i.e. narG, narH and napA) involved in nitrate reduction were much higher than that for nitrite reduction (i.e. nirK), and this disparity was responsible for the efficient nitrite accumulation in glycerol-driven PD system.
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Affiliation(s)
- Teng Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Jiashun Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China; Guohe Environmental Research Institute (Nanjing) Co, Ltd, Nanjing 211599, China
| | - Yilei Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Fang Fang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China; Guohe Environmental Research Institute (Nanjing) Co, Ltd, Nanjing 211599, China
| | - Qian Feng
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China; Guohe Environmental Research Institute (Nanjing) Co, Ltd, Nanjing 211599, China
| | - Jingyang Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China; Guohe Environmental Research Institute (Nanjing) Co, Ltd, Nanjing 211599, China.
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22
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Carbon Source Influence on Extracellular pH Changes along Bacterial Cell-Growth. Genes (Basel) 2020; 11:genes11111292. [PMID: 33142974 PMCID: PMC7693008 DOI: 10.3390/genes11111292] [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: 09/28/2020] [Revised: 10/24/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023] Open
Abstract
The effect of initial pH on bacterial cell-growth and its change over time was studied under aerobic heterotrophic conditions by using three bacterial strains: Escherichia coli ATCC 25922, Pseudomonas putida KT2440, and Pseudomonas pseudoalcaligenes CECT 5344. In Luria-Bertani (LB) media, pH evolved by converging to a certain value that is specific for each bacterium. By contrast, in the buffered Minimal Medium (MM), pH was generally more stable along the growth curve. In MM with glucose as carbon source, a slight acidification of the medium was observed for all strains. In the case of E. coli, a sudden drop in pH was observed during exponential cell growth that was later recovered at initial pH 7 or 8, but was irreversible below pH 6, thus arresting further cell-growth. When using other carbon sources in MM at a fixed initial pH, pH changes depended mainly on the carbon source itself. While glucose, glycerol, or octanoate slightly decreased extracellular pH, more oxidized carbon sources, such as citrate, 2-furoate, 2-oxoglutarate, and fumarate, ended up with the alkalinization of the medium. These observations are in accordance with pH change predictions using genome-scale metabolic models for the three strains, thus revealing the metabolic reasons behind pH change. Therefore, we conclude that the composition of the medium, specifically the carbon source, determines pH change during bacterial growth to a great extent and unravel the main molecular mechanism behind this phenotype. These findings pave the way for predicting pH changes in a given bacterial culture and may anticipate the interspecies interactions and fitness of bacteria in their environment.
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23
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Li Y, Yang S, Jin D, Jia X. Optimization of medium‐chain‐length polyhydroxyalkanoate production by
Pseudomonas putida
KT2440 from co‐metabolism of glycerol and octanoate. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ying Li
- Department of Biochemical Engineering School of Chemical Engineering and Technology, Tianjin University Tianjin China
- Frontier Science Centre for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology, Tianjin University Tianjin China
| | - Songyuan Yang
- Department of Biochemical Engineering School of Chemical Engineering and Technology, Tianjin University Tianjin China
- Frontier Science Centre for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology, Tianjin University Tianjin China
| | - Dayao Jin
- Department of Biochemical Engineering School of Chemical Engineering and Technology, Tianjin University Tianjin China
- Frontier Science Centre for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology, Tianjin University Tianjin China
| | - Xiaoqiang Jia
- Department of Biochemical Engineering School of Chemical Engineering and Technology, Tianjin University Tianjin China
- Frontier Science Centre for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE) School of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin) Tianjin China
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24
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A four-microorganism three-step fermentation process for producing medium-chain-length polyhydroxyalkanoate from starch. 3 Biotech 2020; 10:352. [PMID: 32766094 DOI: 10.1007/s13205-020-02347-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/18/2020] [Indexed: 12/11/2022] Open
Abstract
In this study, a four-microorganism three-step fermentation process was established for producing medium-chain-length polyhydroxyalkanoate (mcl-PHA) from starch, which was used as the sole carbon source. The four microorganisms used for this process were Aspergillus niger, Saccharomyces cerevisiae L2612, Acetobacter orientalis, and Pseudomonas putida KT2440-acs. The initial carbon source starch concentration was set to 30 g/L, the maximum glucose concentration reached 17.66 g/L at 48 h after starch hydrolysis, and then, 2.36 g/L of acetic acid was obtained at 96 h. The final output of mcl-PHA was 0.5 g/L at 144 h, overall productivity for mcl-PHA was 3.47 mg/(L·h) and the total starch to mcl-PHA yield for the process was 16.67 mg/g. Although the overall yield and conversion rate of this process were not high, this is the first attempt to produce mcl-PHA using starch as a substrate, and it provides a feasible strategy for producing PHA from kitchen waste. The production process of mcl-PHA with a clear flora structure and short fermentation cycle was realized.
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Zhang X, Lin Y, Wu Q, Wang Y, Chen GQ. Synthetic Biology and Genome-Editing Tools for Improving PHA Metabolic Engineering. Trends Biotechnol 2020; 38:689-700. [DOI: 10.1016/j.tibtech.2019.10.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 12/17/2022]
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26
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Regulation of filamentation by bacteria and its impact on the productivity of compounds in biotechnological processes. Appl Microbiol Biotechnol 2020; 104:4631-4642. [DOI: 10.1007/s00253-020-10590-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 12/29/2022]
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27
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Biosynthesis of polyhydroxyalkanoates from sucrose by metabolically engineered Escherichia coli strains. Int J Biol Macromol 2020; 149:593-599. [DOI: 10.1016/j.ijbiomac.2020.01.254] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/23/2020] [Accepted: 01/25/2020] [Indexed: 02/07/2023]
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Engineering of glycerol utilization in Pseudomonas chlororaphis GP72 for enhancing phenazine-1-carboxylic acid production. World J Microbiol Biotechnol 2020; 36:49. [PMID: 32157439 DOI: 10.1007/s11274-020-02824-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 02/29/2020] [Indexed: 12/25/2022]
Abstract
Glycerol is a by-product of biodiesel, and it has a great application prospect to be transformed to synthesize high value-added compounds. Pseudomonas chlororaphis GP72 isolated from the green pepper rhizosphere is a plant growth promoting rhizobacteria that can utilize amount of glycerol to synthesize phenazine-1-carboxylic acid (PCA). PCA has been commercially registered as "Shenqinmycin" in China due to its characteristics of preventing pepper blight and rice sheath blight. The aim of this study was to engineer glycerol utilization pathway in P. chlororaphis GP72. First, the two genes glpF and glpK from the glycerol metabolism pathway were overexpressed in GP72ANO separately. Then, the two genes were co-expressed in GP72ANO, improving PCA production from 729.4 mg/L to 993.4 mg/L at 36 h. Moreover, the shunt pathway was blocked to enhance glycerol utilization, resulting in 1493.3 mg/L PCA production. Additionally, we confirmed the inhibition of glpR on glycerol metabolism pathway in P. chlororaphis GP72. This study provides a good example for improving the utilization of glycerol to synthesize high value-added compounds in Pseudomonas.
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Construction of a "nutrition supply-detoxification" coculture consortium for medium-chain-length polyhydroxyalkanoate production with a glucose-xylose mixture. J Ind Microbiol Biotechnol 2020; 47:343-354. [PMID: 32140930 DOI: 10.1007/s10295-020-02267-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/23/2020] [Indexed: 10/24/2022]
Abstract
In this study, we constructed a coculture consortium comprising engineered Pseudomonas putida KT2440 and Escherichia coli MG1655. Provision of "related" carbon sources and synthesis of medium-chain-length polyhydroxyalkanoates (mcl-PHAs) were separately assigned to these strains via a modular construction strategy. To avoid growth competition, a preference for the use of a carbon source was constructed. Further, the main intermediate metabolite acetate played an important role in constructing the expected "nutrition supply-detoxification" relationship between these strains. The coculture consortium showed a remarkable increase in the mcl-PHA titer (0.541 g/L) with a glucose-xylose mixture (1:1). Subsequently, the titer of mcl-PHA produced by the coculture consortium when tested with actual lignocellulosic hydrolysate (0.434 g/L) was similar to that achieved with laboratory sugars' mixture (0.469 g/L). These results indicate a competitive potential of the engineered E. coli-P. putida coculture consortium for mcl-PHA production with lignocellulosic hydrolysate.
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30
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Martinez S, Déziel E. Changes in polyhydroxyalkanoate granule accumulation make optical density measurement an unreliable method for estimating bacterial growth in Burkholderia thailandensis. Can J Microbiol 2020; 66:256-262. [PMID: 31917612 DOI: 10.1139/cjm-2019-0342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optical density (OD) measurement is the standard method used in microbiology for estimating bacterial concentrations in cultures. However, most studies do not compare these measurements with viable cell counts and assume that they reflect the real cell concentration. Burkholderia thailandensis was recently identified as a polyhydroxyalkanoate (PHA) producer. PHA biosynthesis seems to be coded by an orthologue of the Cupriavidus necator phaC gene. When growing cultures of wild-type strain E264 and an isogenic phaC mutant, we noted a difference in their OD600 values, although viable cell counts indicated similar growth. Investigating the cellular morphologies of both strains, we found that under our conditions the wild-type strain was full of PHA granules, deforming the cells, while the mutant contained no granules. These factors apparently affected the light scattering, making the OD600 values no longer representative of cell density. We show a direct correlation between OD600 values and the accumulation of PHA. We conclude that OD measurement is unreliable for growth evaluation of B. thailandensis because of PHA production. This study also suggests that B. thailandensis could represent an excellent candidate for PHA bioproduction. Correlation between OD measurements and viable cell counts should be verified in any study performed with B. thailandensis.
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Affiliation(s)
- Sarah Martinez
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, Quebec, Canada.,Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, Quebec, Canada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, Quebec, Canada.,Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, Quebec, Canada
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31
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Wroe JA, Johnson CT, García AJ. Bacteriophage delivering hydrogels reduce biofilm formation in vitro and infection in vivo. J Biomed Mater Res A 2019; 108:39-49. [PMID: 31443115 DOI: 10.1002/jbm.a.36790] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022]
Abstract
Implanted orthopedic devices become infected more frequently than any other implanted surgical device. These infections can be extremely costly and result in significant patient morbidity. Current treatment options typically involve the long term, systemic administration of a combination of antibiotics, often followed by implant removal. Here we engineered an injectable hydrogel capable of encapsulating Pseudomonas aeruginosa bacteriophage and delivering active phage to the site of bone infections. Bacteriophage retain their bacteriolytic activity after encapsulation and release from the hydrogel, and their rate of release from the hydrogel can be controlled by gel formulation. Bacteriophage-encapsulating hydrogels effectively kill their host bacteria in both planktonic and biofilm phenotypes in vitro without influencing the metabolic activity of human mesenchymal stromal cells. Bacteriophage-encapsulating hydrogels were used to treat murine radial segmental defects infected with P. aeruginosa. The hydrogels achieved a 4.7-fold reduction in live P. aeruginosa counts at the infection site compared to bacteriophage-free hydrogels at 7 days postimplantation. These results support the development of bacteriophage-delivering hydrogels to treat local bone infections.
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Affiliation(s)
- James A Wroe
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia.,Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| | - Christopher T Johnson
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia.,Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| | - Andrés J García
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia.,Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia
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Hassan EA, Abd‐Alla MH, Zohri AA, Ragaey MM, Ali SM. Production of butanol and polyhydroxyalkanoate from industrial waste by Clostridium beijerinckiiASU10. INTERNATIONAL JOURNAL OF ENERGY RESEARCH 2019; 43:3640-3652. [DOI: 10.1002/er.4514] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 02/26/2019] [Indexed: 09/02/2023]
Affiliation(s)
- Elhagag Ahmed Hassan
- Botany and Microbiology Department, Faculty of ScienceAssiut University Assiut Egypt
| | | | | | - Marwa M. Ragaey
- Botany Department, Faculty of ScienceNew Valley University El‐Kharja Egypt
| | - Shimaa Mohamed Ali
- Botany Department, Faculty of ScienceNew Valley University El‐Kharja Egypt
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Yang S, Li S, Jia X. Production of medium chain length polyhydroxyalkanoate from acetate by engineered Pseudomonas putida KT2440. ACTA ACUST UNITED AC 2019; 46:793-800. [DOI: 10.1007/s10295-019-02159-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 03/05/2019] [Indexed: 11/27/2022]
Abstract
Abstract
Pseudomonas putida was metabolically engineered to produce medium chain length polyhydroxyalkanoate (mcl-PHA) from acetate, a promising carbon source to achieve cost-effective microbial processes. As acetate is known to be harmful to cell growth, P. putida KT2440 was screened from three Pseudomonas strains (P. putida KT2440, P. putida NBRC14164, and P. aeruginosa PH1) as the host with the highest tolerance to 10 g/L of acetate in the medium. Subsequently, P. putida KT2440 was engineered by amplifying the acetate assimilation pathway, including overexpression of the acs (encoding acetyl-CoA synthetase) route and construction of the ackA-pta (encoding acetate kinase-phosphotransacetylase) pathway. The acs overexpressing P. putida KT2440 showed a remarkable increase of mcl-PHA titer (+ 92%), mcl-PHA yield (+ 50%), and cellular mcl-PHA content (+ 43%) compared with the wild-type P. putida KT2440, which indicated that acetate could be a potential substrate for biochemical production of mcl-PHA by engineered P. putida.
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Affiliation(s)
- Songyuan Yang
- 0000 0004 1761 2484 grid.33763.32 Department of Biological Engineering, School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology Tianjin University 300350 Tianjin People’s Republic of China
| | - Suhang Li
- 0000 0004 1761 2484 grid.33763.32 Department of Biological Engineering, School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology Tianjin University 300350 Tianjin People’s Republic of China
| | - Xiaoqiang Jia
- 0000 0004 1761 2484 grid.33763.32 Department of Biological Engineering, School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology Tianjin University 300350 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
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Glycerol metabolism and its regulation in lactic acid bacteria. Appl Microbiol Biotechnol 2019; 103:5079-5093. [DOI: 10.1007/s00253-019-09830-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 01/09/2023]
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35
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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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36
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Kim SK, Yoon PK, Kim SJ, Woo SG, Rha E, Lee H, Yeom SJ, Kim H, Lee DH, Lee SG. CRISPR interference-mediated gene regulation in Pseudomonas putida KT2440. Microb Biotechnol 2019; 13:210-221. [PMID: 30793496 PMCID: PMC6922533 DOI: 10.1111/1751-7915.13382] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 01/08/2023] Open
Abstract
Targeted gene regulation is indispensable for reprogramming a cellular network to modulate a microbial phenotype. Here, we adopted the type II CRISPR interference (CRISPRi) system for simple and efficient regulation of target genes in Pseudomonas putida KT2440. A single CRISPRi plasmid was generated to express a nuclease-deficient Cas9 gene and a designed single guide RNA, under control of l-rhamnose-inducible Prha BAD and the constitutive Biobrick J23119 promoter respectively. Two target genes were selected to probe the CRISPRi-mediated gene regulation: exogenous green fluorescent protein on the multicopy plasmid and endogenous glpR on the P. putida KT2440 chromosome, encoding GlpR, a transcriptional regulator that represses expression of the glpFKRD gene cluster for glycerol utilization. The CRISPRi system successfully repressed the two target genes, as evidenced by a reduction in the fluorescence intensity and the lag phase of P. putida KT2440 cell growth on glycerol. Furthermore, CRISPRi-mediated repression of glpR improved both the cell growth and glycerol utilization, resulting in the enhanced production of mevalonate in an engineered P. putida KT2440 harbouring heterologous genes for the mevalonate pathway. CRISPRi is expected to become a robust tool to reprogram P. putida KT2440 for the development of microbial cell factories producing industrially valuable products.
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Affiliation(s)
- Seong Keun Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Paul K Yoon
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Soo-Jung Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Seung-Gyun Woo
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Eugene Rha
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Hyewon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Soo-Jin Yeom
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Korea
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37
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Pavan ME, Venero ES, Egoburo DE, Pavan EE, López NI, Julia Pettinari M. Glycerol inhibition of melanin biosynthesis in the environmental Aeromonas salmonicida 34mel T. Appl Microbiol Biotechnol 2018; 103:1865-1876. [PMID: 30539256 DOI: 10.1007/s00253-018-9545-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 02/06/2023]
Abstract
The environmental strain Aeromonas salmonicida subsp. pectinolytica 34melT produces abundant melanin through the homogentisate pathway in several culture media, but unexpectedly not when grown in a medium containing glycerol. Using this observation as a starting point, this study investigated the underlying causes of the inhibition of melanin synthesis by glycerol, to shed light on factors that affect melanin production in this microorganism. The effect of different carbon sources on melanin formation was related to the degree of oxidation of their C atoms, as the more reduced substrates delayed melanization more than the more oxidized ones, although only glycerol completely abolished melanin production. Glyphosate, an inhibitor of aromatic amino acid synthesis, did not affect melanization, while bicyclopyrone, an inhibitor of 4-hydroxyphenylpyruvate dioxygenase (Hpd), the enzyme responsible for the synthesis of homogentisate, prevented melanin synthesis. These results showed that melanin production in 34melT depends on the degradation of aromatic amino acids from the growth medium and not on de novo aromatic amino acid synthesis. The presence of glycerol changed the secreted protein profile, but none of the proteins affected could be directly connected with melanin synthesis or transport. Transcription analysis of hpd, encoding the key enzyme for melanin synthesis, showed a clear inhibition caused by glycerol. The results obtained in this work indicate that a significant decrease in the transcription of hpd, together with a more reduced intracellular state, would lead to the abolishment of melanin synthesis observed. The effect of glycerol on melanization can thus be attributed to a combination of metabolic and regulatory effects.
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Affiliation(s)
- María Elisa Pavan
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Esmeralda Solar Venero
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Diego E Egoburo
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Esteban E Pavan
- Biomedical Technologies Laboratory, Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy
| | - Nancy I López
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina. .,IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - M Julia Pettinari
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina. .,IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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38
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Mindt M, Walter T, Risse JM, Wendisch VF. Fermentative Production of N-Methylglutamate From Glycerol by Recombinant Pseudomonas putida. Front Bioeng Biotechnol 2018; 6:159. [PMID: 30474025 PMCID: PMC6237917 DOI: 10.3389/fbioe.2018.00159] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/16/2018] [Indexed: 12/02/2022] Open
Abstract
N-methylated amino acids are present in diverse biological molecules in bacteria, archaea and eukaryotes. There is an increasing interest in this molecular class of alkylated amino acids by the pharmaceutical and chemical industries. N-alkylated amino acids have desired functions such as higher proteolytic stability, enhanced membrane permeability and longer peptide half-lives, which are important for the peptide-based drugs, the so-called peptidomimetics. Chemical synthesis of N-methylated amino acids often is limited by incomplete stereoselectivity, over-alkylation or the use of hazardous chemicals. Here, we describe metabolic engineering of Pseudomonas putida KT2440 for the fermentative production of N-methylglutamate from simple carbon sources and monomethylamine. P. putida KT2440, which is generally recognized as safe and grows with glucose and the alternative feedstock glycerol as sole carbon and energy source, was engineered for the production of N-methylglutamate using heterologous enzymes from Methylobacterium extorquens. About 3.9 g L−1N-methylglutamate accumulated within 48 h in shake flask cultures with minimal medium containing monomethylamine and glycerol. A fed-batch cultivation process yielded a N-methylglutamate titer of 17.9 g L−1.
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Affiliation(s)
- Melanie Mindt
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Tatjana Walter
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Joe Max Risse
- Fermentation Technology, Technical Faculty and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
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39
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Urbina L, Wongsirichot P, Corcuera MÁ, Gabilondo N, Eceiza A, Winterburn J, Retegi A. Application of cider by-products for medium chain length polyhydroxyalkanoate production by Pseudomonas putida KT2440. Eur Polym J 2018. [DOI: 10.1016/j.eurpolymj.2018.08.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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40
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Nielsen C, Rahman A, Rehman AU, Walsh MK, Miller CD. Food waste conversion to microbial polyhydroxyalkanoates. Microb Biotechnol 2017; 10:1338-1352. [PMID: 28736901 PMCID: PMC5658610 DOI: 10.1111/1751-7915.12776] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 06/17/2017] [Indexed: 12/16/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are biopolymers with desirable material properties similar to petrochemically derived plastics. PHAs are naturally produced by a wide range of microorganisms as a carbon storage mechanism and can accumulate to significantly high levels. PHAs are an environmentally friendly alternative to their petroleum counterparts because they can be easily degraded, potentially reducing the burden on municipal waste systems. Nevertheless, widespread use of PHAs is not currently realistic due to a variety of factors. One of the major constraints of large-scale PHA production is the cost of carbon substrate for PHA-producing microbes. The cost of production could potentially be reduced with the use of waste carbon from food-related processes. Food wastage is a global issue and therefore harbours immense potential to create valuable bioproducts. This article's main focus is to examine the state of the art of converting food-derived waste into carbon substrates for microbial metabolism and subsequent conversion into PHAs.
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Affiliation(s)
- Chad Nielsen
- Department of Biological EngineeringUtah State University4105 Old Main HillLoganUT84322‐4105USA
| | - Asif Rahman
- Bioengineering BranchSpace BioSciences DivisionNASA Ames Research CenterMoffett FieldCA94035‐1000USA
- COSMIAC Research CenterUniversity of New MexicoAlbuquerqueNM87106USA
| | - Asad Ur Rehman
- Department of Biological EngineeringUtah State University4105 Old Main HillLoganUT84322‐4105USA
- Institute of Industrial BiotechnologyGovernment College UniversityKatchery RoadLahorePakistan
| | - Marie K. Walsh
- Department of Nutrition, Dietetics, and Food SciencesUtah State University8700 Old Main HillLoganUT84322‐8700USA
| | - Charles D. Miller
- Department of Biological EngineeringUtah State University4105 Old Main HillLoganUT84322‐4105USA
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Combinatorial metabolic engineering of Pseudomonas putida KT2440 for efficient mineralization of 1,2,3-trichloropropane. Sci Rep 2017; 7:7064. [PMID: 28765600 PMCID: PMC5539299 DOI: 10.1038/s41598-017-07435-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/23/2017] [Indexed: 01/03/2023] Open
Abstract
An industrial waste, 1,2,3-trichloropropane (TCP), is toxic and extremely recalcitrant to biodegradation. To date, no natural TCP degraders able to mineralize TCP aerobically have been isolated. In this work, we engineered a biosafety Pseudomonas putida strain KT2440 for aerobic mineralization of TCP by implantation of a synthetic biodegradation pathway into the chromosome and further improved TCP mineralization using combinatorial engineering strategies. Initially, a synthetic pathway composed of haloalkane dehalogenase, haloalcohol dehalogenase and epoxide hydrolase was functionally assembled for the conversion of TCP into glycerol in P. putida KT2440. Then, the growth lag-phase of using glycerol as a growth precursor was eliminated by deleting the glpR gene, significantly enhancing the flux of carbon through the pathway. Subsequently, we improved the oxygen sequestering capacity of this strain through the heterologous expression of Vitreoscilla hemoglobin, which makes this strain able to mineralize TCP under oxygen-limited conditions. Lastly, we further improved intracellular energy charge (ATP/ADP ratio) and reducing power (NADPH/NADP+ ratio) by deleting flagella-related genes in the genome of P. putida KT2440. The resulting strain (named KTU-TGVF) could efficiently utilize TCP as the sole source of carbon for growth. Degradation studies in a bioreactor highlight the value of this engineered strain for TCP bioremediation.
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Rizzo MG, Chines V, Franco D, Nicolò MS, Guglielmino SP. The role of glutamine in Pseudomonas mediterranea in biotechnological processes. N Biotechnol 2017; 37:144-151. [DOI: 10.1016/j.nbt.2016.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/24/2016] [Accepted: 04/21/2016] [Indexed: 11/29/2022]
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Fontaine P, Mosrati R, Corroler D. Medium chain length polyhydroxyalkanoates biosynthesis in Pseudomonas putida mt-2 is enhanced by co-metabolism of glycerol/octanoate or fatty acids mixtures. Int J Biol Macromol 2017; 98:430-435. [PMID: 28174083 DOI: 10.1016/j.ijbiomac.2017.01.115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 01/16/2017] [Accepted: 01/25/2017] [Indexed: 10/20/2022]
Abstract
The synthesis of medium chain length polyhydroxyalkanoates (mcl-PHAs) by Pseudomonas putida mt-2 was investigated under nitrogen-rich then deficient conditions with glycerol/octanoate or long-chain fatty acids (LCFAs) as carbon sources. When mixed, glycerol and octanoate were co-assimilated regardless of nitrogen availability but provided that glycerol uptake has been already triggered under non-limiting nutrient conditions. This concomitant consumption allowed to enhance mcl-PHAs accumulation (up to 57% of cell dry weight (CDW)) under both non-limiting and nitrogen deficient conditions. Octanoate then mostly drove anabolism of the polyester with 3-hydroxyoctanoate (3HO) synthesized as the main monomer (83%). If the preferred PHA precursor octanoate was supplied, glycerol was mainly involved in cell growth and/or maintenance but very little in PHA production even under nitrogen starvation. P. putida cells accumulated higher amounts of mcl-PHAs when grown on mixtures of LCFAs compared to LCFAs supplied as single substrate (25% and 9% of CDW, respectively). However, only a weak enrichment of the polyester was observed after transfer of cells in a fresh nitrogen-free medium containing the same combination of LCFAs. Some typical units within the polyester were related to the LCFAs ratio supplied in the medium indicating that tailor-made monomers could be synthesized.
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Affiliation(s)
- Paul Fontaine
- Normandie Univ., UNICAEN, UR ABTE, 14000 Caen, France
| | - Ridha Mosrati
- Normandie Univ., UNICAEN, UR ABTE, 14000 Caen, France
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Sharma PK, Fu J, Spicer V, Krokhin OV, Cicek N, Sparling R, Levin DB. Global changes in the proteome of Cupriavidus necator H16 during poly-(3-hydroxybutyrate) synthesis from various biodiesel by-product substrates. AMB Express 2016; 6:36. [PMID: 27184362 PMCID: PMC4870535 DOI: 10.1186/s13568-016-0206-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/07/2016] [Indexed: 01/13/2023] Open
Abstract
Synthesis of poly-[3-hydroxybutyrate] (PHB) by Cupriavidus necator H16 in batch cultures was evaluated using three biodiesel-derived by-products as the sole carbon sources: waste glycerol (REG-80, refined to 80 % purity with negligible free fatty acids); glycerol bottom (REG-GB, with up to 65 % glycerol and 35 % free fatty acids), and free fatty acids (REG-FFA, with up to 75 % FFA and no glycerol). All the three substrates supported growth and PHB production by C. necator, with polymer accumulation ranging from 9 to 84 % cell dry weight (cdw), depending on the carbon source. To help understand these differences, proteomic analysis indicated that although C. necator H16 was able to accumulate PHB during growth on all three biodiesel by-products, no changes in the levels of PHB synthesis enzymes were observed. However, significant changes in the levels of expression were observed for two Phasin proteins involved with PHB accumulation, and for a number of gene products in the fatty acid β-oxidation pathway, the Glyoxylate Shunt, and the hydrogen (H2) synthesis pathways in C. necator cells cultured with different substrates. The glycerol transport protein (GlpF) was induced in REG-GB and REG-80 glycerol cultures only. Cupriavidus necator cells cultured with REG-GB and REG-FFA showed up-regulation of β-oxidation and Glyoxylate Shunt pathways proteins at 24 h pi, but H2 synthesis pathways enzymes were significantly down-regulated, compared with cells cultured with waste glycerol. Our data confirmed earlier observations of constitutive expression of PHB synthesis proteins, but further suggested that C. necator H16 cells growing on biodiesel-derived glycerol were under oxidative stress.
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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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Integrated transcriptomic and proteomic analysis of the bile stress response in probiotic Lactobacillus salivarius LI01. J Proteomics 2016; 150:216-229. [PMID: 27585996 DOI: 10.1016/j.jprot.2016.08.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/24/2016] [Accepted: 08/25/2016] [Indexed: 12/11/2022]
Abstract
Lactobacillus salivarius LI01, isolated from healthy humans, has demonstrated probiotic properties in the prevention and treatment of liver failure. Tolerance to bile stress is crucial to allow lactobacilli to survive in the gastrointestinal tract and exert their benefits. In this work, we used a Digital Gene Expression transcriptomic and iTRAQ LC-MS/MS proteomic approach to examine the characteristics of LI01 in response to bile stress. Using culture medium with or without 0.15% ox bile, 591 differentially transcribed genes and 347 differentially expressed proteins were detected in LI01. Overall, we found the bile resistance of LI01 to be based on a highly remodeled cell envelope and a reinforced bile efflux system rather than on the activity of bile salt hydrolases. Additionally, some differentially expressed genes related to regulatory systems, the general stress response and central metabolism processes, also play roles in stress sensing, bile-induced damage prevention and energy efficiency. Moreover, bile salts appear to enhance proteolysis and amino acid uptake (especially aromatic amino acids) by LI01, which may support the liver protection properties of this strain. Altogether, this study establishes a model of global response mechanism to bile stress in L. salivarius LI01. BIOLOGICAL SIGNIFICANCE L. salivarius strain LI01 exhibits not only antibacterial and antifungal properties but also exerts a good health-promoting effect in acute liver failure. As a potential probiotic strain, the bile-tolerance trait of strain LI01 is important, though this has not yet been explored. In this study, an analysis based on DGE and iTRAQ was performed to investigate the gene expression in strain LI01 under bile stress at the mRNA and protein levels, respectively. To our knowledge, this work also represents the first combined transcriptomic and proteomic analysis of the bile stress response mechanism in L. salivarius.
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Tiso T, Sabelhaus P, Behrens B, Wittgens A, Rosenau F, Hayen H, Blank LM. Creating metabolic demand as an engineering strategy in Pseudomonas putida - Rhamnolipid synthesis as an example. Metab Eng Commun 2016; 3:234-244. [PMID: 29142825 PMCID: PMC5678820 DOI: 10.1016/j.meteno.2016.08.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 07/19/2016] [Accepted: 08/06/2016] [Indexed: 12/12/2022] Open
Abstract
Metabolic engineering of microbial cell factories for the production of heterologous secondary metabolites implicitly relies on the intensification of intracellular flux directed toward the product of choice. Apart from reactions following peripheral pathways, enzymes of the central carbon metabolism are usually targeted for the enhancement of precursor supply. In Pseudomonas putida, a Gram-negative soil bacterium, central carbon metabolism, i.e., the reactions required for the synthesis of all 12 biomass precursors, was shown to be regulated at the metabolic level and not at the transcriptional level. The bacterium's central carbon metabolism appears to be driven by demand to react rapidly to ever-changing environmental conditions. In contrast, peripheral pathways that are only required for growth under certain conditions are regulated transcriptionally. In this work, we show that this regulation regime can be exploited for metabolic engineering. We tested this driven-by-demand metabolic engineering strategy using rhamnolipid production as an example. Rhamnolipid synthesis relies on two pathways, i.e., fatty acid de novo synthesis and the rhamnose pathway, providing the required precursors hydroxyalkanoyloxy-alkanoic acid (HAA) and activated (dTDP-)rhamnose, respectively. In contrast to single-pathway molecules, rhamnolipid synthesis causes demand for two central carbon metabolism intermediates, i.e., acetyl-CoA for HAA and glucose-6-phosphate for rhamnose synthesis. Following the above-outlined strategy of driven by demand, a synthetic promoter library was developed to identify the optimal expression of the two essential genes (rhlAB) for rhamnolipid synthesis. The best rhamnolipid-synthesizing strain had a yield of 40% rhamnolipids on sugar [CmolRL/CmolGlc], which is approximately 55% of the theoretical yield. The rate of rhamnolipid synthesis of this strain was also high. Compared to an exponentially growing wild type, the rhamnose pathway increased its flux by 300%, whereas the flux through de novo fatty acid synthesis increased by 50%. We show that the central carbon metabolism of P. putida is capable of meeting the metabolic demand generated by engineering transcription in peripheral pathways, thereby enabling a significant rerouting of carbon flux toward the product of interest, in this case, rhamnolipids of industrial interest. Synthetic demand was created by the introduction of the rhamnolipid synthesis genes. A high demand was achieved using a strong synthetic promoter. Pseudomonas putida responded to demand by increasing flux towards required central carbon metabolites. High rhamnolipid carbon yield of 40% was achieved.
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Key Words
- Biosurfactant
- CCM, central carbon metabolism
- CDW, cell dry weight
- Driven by demand
- ED pathway, Entner-Doudoroff pathway
- FBA, flux balance analysis
- HAA, hydroxyalkanoyloxy-alkanoic acid
- LPS, lipopolysaccharide
- Metabolic control
- Non-pathogenic Pseudomonas
- PHA, polyhydroxyalkanoate
- PP pathway, pentose phosphate pathway
- RL, rhamnolipid
- Rhamnolipid
- Synthetic promoter
- TCA, tricarboxylic acid
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Affiliation(s)
- Till Tiso
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074 Aachen, Germany
| | - Petra Sabelhaus
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074 Aachen, Germany
| | - Beate Behrens
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, D-48149 Münster, Germany
| | - Andreas Wittgens
- Ulm Center for Peptide Pharmaceuticals, Ulm University, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Frank Rosenau
- Ulm Center for Peptide Pharmaceuticals, Ulm University, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, D-48149 Münster, Germany
| | - Lars Mathias Blank
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074 Aachen, Germany
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Mi J, Sydow A, Schempp F, Becher D, Schewe H, Schrader J, Buchhaupt M. Investigation of plasmid-induced growth defect in Pseudomonas putida. J Biotechnol 2016; 231:167-173. [DOI: 10.1016/j.jbiotec.2016.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 02/03/2016] [Accepted: 06/06/2016] [Indexed: 02/07/2023]
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Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol. Microb Cell Fact 2016; 15:73. [PMID: 27142075 PMCID: PMC4855977 DOI: 10.1186/s12934-016-0470-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/24/2016] [Indexed: 02/02/2023] Open
Abstract
Background Given its high surplus and low cost, glycerol has emerged as interesting carbon substrate for the synthesis of value-added chemicals. The soil bacterium Pseudomonas putida KT2440 can use glycerol to synthesize medium-chain-length poly(3-hydroxyalkanoates) (mcl-PHA), a class of biopolymers of industrial interest. Here, glycerol metabolism in P. putida KT2440 was studied on the level of gene expression (transcriptome) and metabolic fluxes (fluxome), using precisely adjusted chemostat cultures, growth kinetics and stoichiometry, to gain a systematic understanding of the underlying metabolic and regulatory network. Results Glycerol-grown P. putida KT2440 has a maintenance energy requirement [0.039 (mmolglycerol (gCDW h)−1)] that is about sixteen times lower than that of other bacteria, such as Escherichia coli, which provides a great advantage to use this substrate commercially. The shift from carbon (glycerol) to nitrogen (ammonium) limitation drives the modulation of specific genes involved in glycerol metabolism, transport electron chain, sensors to assess the energy level of the cell, and PHA synthesis, as well as changes in flux distribution to increase the precursor availability for PHA synthesis (Entner–Doudoroff pathway and pyruvate metabolism) and to reduce respiration (glyoxylate shunt). Under PHA-producing conditions (N-limitation), a higher PHA yield was achieved at low dilution rate (29.7 wt% of CDW) as compared to a high rate (12.8 wt% of CDW). By-product formation (succinate, malate) was specifically modulated under these regimes. On top of experimental data, elementary flux mode analysis revealed the metabolic potential of P. putida KT2440 to synthesize PHA and identified metabolic engineering targets towards improved production performance on glycerol. Conclusion This study revealed the complex interplay of gene expression levels and metabolic fluxes under PHA- and non-PHA producing conditions using the attractive raw material glycerol as carbon substrate. This knowledge will form the basis for the development of future metabolically engineered hyper-PHA-producing strains derived from the versatile bacterium P. putida KT2440.
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