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Hernández-Herreros N, Rodríguez A, Galán B, Auxiliadora Prieto M. Boosting hydrogen production in Rhodospirillum rubrum by syngas-driven photoheterotrophic adaptive evolution. BIORESOURCE TECHNOLOGY 2024; 406:130972. [PMID: 38876276 DOI: 10.1016/j.biortech.2024.130972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024]
Abstract
Rhodospirillum rubrum is a photosynthetic purple non-sulphur bacterium with great potential to be used for complex waste valorisation in biotechnological applications due to its metabolic versatility. This study investigates the production of hydrogen (H2) and polyhydroxyalkanoates (PHA) by R. rubrum from syngas under photoheterotrophic conditions. An adaptive laboratory evolution strategy (ALE) has been carried out to improve the yield of the process. After 200 generations, two evolved strains were selected that showed reduced lag phase and enhanced poly-3-hydroxybutyrate (PHB) and H2 synthesis compared to the parental strain. Genomic analysis of the photo-adapted (PA) variants showed four genes with single point mutations, including the photosynthesis gene expression regulator PpsR. The proteome of the variants suggested that the adapted variants overproduced H2 due to a more efficient CO oxidation through the CO-dehydrogenase enzyme complex and confirmed that energy acquisition was enhanced through overexpression of the photosynthetic system and metal cofactors essential for pigment biosynthesis.
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Affiliation(s)
- Natalia Hernández-Herreros
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Alberto Rodríguez
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Beatriz Galán
- Microbial & Plant Biotechnology Department, Environmental Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Microbial & Plant Biotechnology Department, Polymer Biotechnology Group, Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
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2
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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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3
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Hernández-Herreros N, Rivero-Buceta V, Pardo I, Prieto MA. Production of poly(3-hydroxybutyrate)/poly(lactic acid) from industrial wastewater by wild-type Cupriavidus necator H16. WATER RESEARCH 2024; 249:120892. [PMID: 38007895 DOI: 10.1016/j.watres.2023.120892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/28/2023]
Abstract
The massive production of urban and industrial wastes has created a clear need for alternative waste management processes. One of the more promising strategies is to use waste as raw material for the production of biopolymers such as polyhydroxyalkanoates (PHAs). In this work, a lactate-enriched stream obtained by anaerobic digestion (AD) of wastewater (WW) from a candy production plant was used as a feedstock for PHA production in wild-type Cupriavidus necator H16. Unexpectedly, we observed the accumulation of poly(3-hydroxybutyrate)/poly(lactic acid) (P(3HB)/PLA), suggesting that the non-engineered strain already possesses the metabolic potential to produce these polymers of interest. The systematic study of factors, such as incubation time, nitrogen and lactate concentration, influencing the synthesis of P(3HB)/PLA allowed the production of a panel of polymers in a resting cell system with tailored lactic acid (LA) content according to the GC-MS of the biomass. Further biomass extraction suggested the presence of methanol soluble low molecular weight molecules containing LA, while 1 % LA could be detected in the purified polymer fraction. These results suggested that the cells are producing a blend of polymers. A proteomic analysis of C. necator resting cells under P(3HB)/PLA production conditions provides new insights into the latent pathways involved in this process. This study is a proof of concept demonstrating that LA can polymerize in a non-modified organism and paves the way for new metabolic engineering approaches for lactic acid polymer production in the model bacterium C. necator H16.
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Affiliation(s)
- Natalia Hernández-Herreros
- Microbial & Plant Biotechnology Department. Polymer Biotechnology Group. Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Virginia Rivero-Buceta
- Microbial & Plant Biotechnology Department. Polymer Biotechnology Group. Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Isabel Pardo
- Microbial & Plant Biotechnology Department. Polymer Biotechnology Group. Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Microbial & Plant Biotechnology Department. Polymer Biotechnology Group. Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
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4
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Manoli MT, Blanco FG, Rivero-Buceta V, Kniewel R, Alarcon SH, Salgado S, Prieto MA. Heterologous constitutive production of short-chain-length polyhydroxyalkanoates in Pseudomonas putida KT2440: the involvement of IbpA inclusion body protein. Front Bioeng Biotechnol 2023; 11:1275036. [PMID: 38026847 PMCID: PMC10646324 DOI: 10.3389/fbioe.2023.1275036] [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: 08/09/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Designing cell factories for the production of novel polyhydroxyalkanoates (PHAs) via smart metabolic engineering is key to obtain à la carte materials with tailored physicochemical properties. To this end, we used the model medium-chain-length-PHA producing bacterium, P. putida KT2440 as a chassis, which is characterized by its metabolic versatility and stress tolerance. Different PHA biosynthetic modules were assembled in expression plasmids using the Golden gate/MoClo modular assembly technique to implement an orthogonal short-chain-lengh-PHA (scl-PHA) switch in a "deaf" PHA mutant. This was specifically constructed to override endogenous multilevel regulation of PHA synthesis in the native strain. We generated a panel of engineered approaches carrying the genes from Rhodospirillum rubrum, Cupriavidus necator and Pseudomonas pseudoalcaligenes, demonstrating that diverse scl-PHAs can be constitutively produced in the chassis strain to varying yields from 23% to 84% PHA/CDW. Co-feeding assays of the most promising engineered strain harboring the PHA machinery from C. necator resulted to a panel of PHBV from 0.6% to 19% C5 monomeric incorporation. Chromosomally integrated PHA machineries with high PhaCCn synthase dosage successfully resulted in 68% PHA/CDW production. Interestingly, an inverse relationship between PhaC synthase dosage and granule size distribution was demonstrated in the heterologous host. In this vein, it is proposed the key involvement of inclusion body protein IbpA to the heterologous production of tailored PHA in P. putida KT2440.
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Affiliation(s)
- Maria-Tsampika Manoli
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Francisco G. Blanco
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Virginia Rivero-Buceta
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Ryan Kniewel
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Sandra Herrera Alarcon
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Sergio Salgado
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - M. Auxiliadora Prieto
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
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5
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Martínez MDLÁM, Urzúa LS, Carrillo YA, Ramírez MB, Morales LJM. Polyhydroxybutyrate Metabolism in Azospirillum brasilense and Its Applications, a Review. Polymers (Basel) 2023; 15:3027. [PMID: 37514417 PMCID: PMC10383645 DOI: 10.3390/polym15143027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Gram-negative Azospirillum brasilense accumulates approximately 80% of polyhydroxybutyrate (PHB) as dry cell weight. For this reason, this bacterium has been characterized as one of the main microorganisms that produce PHB. PHB is synthesized inside bacteria by the polymerization of 3-hydroxybutyrate monomers. In this review, we are focusing on the analysis of the PHB production by A. brasilense in order to understand the metabolism during PHB accumulation. First, the carbon and nitrogen sources used to improve PHB accumulation are discussed. A. brasilense accumulates more PHB when it is grown on a minimal medium containing a high C/N ratio, mainly from malate and ammonia chloride, respectively. The metabolic pathways to accumulate and mobilize PHB in A. brasilense are mentioned and compared with those of other microorganisms. Next, we summarize the available information to understand the role of the genes involved in the regulation of PHB metabolism as well as the role of PHB in the physiology of Azospirillum. Finally, we made a comparison between the properties of PHB and polypropylene, and we discussed some applications of PHB in biomedical and commercial areas.
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Affiliation(s)
- María de Los Ángeles Martínez Martínez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Lucía Soto Urzúa
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Yovani Aguilar Carrillo
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Mirian Becerril Ramírez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Luis Javier Martínez Morales
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
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6
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Dong H, Yang X, Shi J, Xiao C, Zhang Y. Exploring the Feasibility of Cell-Free Synthesis as a Platform for Polyhydroxyalkanoate (PHA) Production: Opportunities and Challenges. Polymers (Basel) 2023; 15:polym15102333. [PMID: 37242908 DOI: 10.3390/polym15102333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
The extensive utilization of traditional petroleum-based plastics has resulted in significant damage to the natural environment and ecological systems, highlighting the urgent need for sustainable alternatives. Polyhydroxyalkanoates (PHAs) have emerged as promising bioplastics that can compete with petroleum-based plastics. However, their production technology currently faces several challenges, primarily focused on high costs. Cell-free biotechnologies have shown significant potential for PHA production; however, despite recent progress, several challenges still need to be overcome. In this review, we focus on the status of cell-free PHA synthesis and compare it with microbial cell-based PHA synthesis in terms of advantages and drawbacks. Finally, we present prospects for the development of cell-free PHA synthesis.
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Affiliation(s)
- Huaming Dong
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xue Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Jingjing Shi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Chunqiao Xiao
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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7
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Kalia VC, Patel SKS, Lee JK. Exploiting Polyhydroxyalkanoates for Biomedical Applications. Polymers (Basel) 2023; 15:polym15081937. [PMID: 37112084 PMCID: PMC10144186 DOI: 10.3390/polym15081937] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Polyhydroxyalkanoates (PHA) are biodegradable plastic. Numerous bacteria produce PHAs under environmental stress conditions, such as excess carbon-rich organic matter and limitations of other nutritional elements such as potassium, magnesium, oxygen, phosphorus, and nitrogen. In addition to having physicochemical properties similar to fossil-fuel-based plastics, PHAs have unique features that make them ideal for medical devices, such as easy sterilization without damaging the material itself and easy dissolution following use. PHAs can replace traditional plastic materials used in the biomedical sector. PHAs can be used in a variety of biomedical applications, including medical devices, implants, drug delivery devices, wound dressings, artificial ligaments and tendons, and bone grafts. Unlike plastics, PHAs are not manufactured from petroleum products or fossil fuels and are, therefore, environment-friendly. In this review, a recent overview of applications of PHAs with special emphasis on biomedical sectors, including drug delivery, wound healing, tissue engineering, and biocontrols, are discussed.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
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Liang B, Zhang X, Wang F, Miao C, Ji Y, Huang Z, Gu P, Liu X, Fan X, Li Q. Production of polyhydroxyalkanoate by mixed cultivation of Brevundimonas diminuta R79 and Pseudomonas balearica R90. Int J Biol Macromol 2023; 234:123667. [PMID: 36796552 DOI: 10.1016/j.ijbiomac.2023.123667] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
The microflora in the activated sludge of propylene oxide saponification wastewater is characterized by a clear succession after enrichment and domestication, and the specifically enriched strains can significantly increase the yield of polyhydroxyalkanoate. In this study, Pseudomonas balearica R90 and Brevundimonas diminuta R79, which are dominant strain after domestication, were selected as models to examine the interactive mechanisms associated with the synthesis of polyhydroxyalkanoate by co-cultured strains. RNA-Seq analysis revealed the up-regulated expression of the acs and phaA genes of strains R79 and R90 in the co-culture group, which enhanced their utilization of acetic acid and synthesis of poly-β-hydroxybutyrate. Cell dry weight and the yield of poly-β-hydroxybutyrate in the co-culture group were accordingly considerably higher than those in the respective pure culture groups. In addition, two-component system, quorum-sensing, flagellar synthesis-related, and chemotaxis-related genes were enriched in strain R90, thereby indicating that compared with the R79 strain, R90 can adapt more rapidly to a domesticated environment. Expression of the acs gene was higher in R79 than in R90, and consequently, strain R79 could more efficiently assimilate acetate in the domesticated environment, and thus predominated in the culture population at the end of the fermentation period.
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Affiliation(s)
- Boya Liang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Xiujun Zhang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Fang Wang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Changfeng Miao
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Yan Ji
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Zhaosong Huang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Xiaoli Liu
- Key Laboratory of Marine Biotechnology in Universities of Shandong, School of Life Sciences, Ludong University, Yantai, China
| | - Xiangyu Fan
- School of Biological Science and Technology, University of Jinan, Jinan, China.
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, China.
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9
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β-oxidation-polyhydroxyalkanoates synthesis relationship in Pseudomonas putida KT2440 revisited. Appl Microbiol Biotechnol 2023; 107:1863-1874. [PMID: 36763117 PMCID: PMC10006253 DOI: 10.1007/s00253-023-12413-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/11/2023]
Abstract
Pseudomonas putida KT2440 is a well-known model organism for the medium-chain-length (mcl) polyhydroxyalkanoate (PHA) accumulation. (R)-Specific enoyl-coenzyme A hydratase (PhaJ) was considered to be the main supplier of monomers for PHA synthesis by converting the β-oxidation intermediate, trans-2-enoyl-CoA to (R)-3-hydroxyacyl-CoA when fatty acids (FA) are used. Three PhaJ homologues, PhaJ1, PhaJ4 and MaoC, are annotated in P. putida KT2440. To investigate the relationship of fatty acids-PHA metabolism and the role of each PhaJ in PHA biosynthesis in P. putida KT2440, a series of P. putida KT2440 knockouts was obtained. PHA content and monomer composition in wild type (WT) and mutants under different growth conditions were analysed. PhaJ4 was the main monomer supplier for PHA synthesis with FA as sole carbon and energy source, with preference towards C8 and C10 substrate, whereas PhaJ1 showed preference for the C6 substrate. However, when all three PhaJ homologues were deleted, the mutant still accumulated PHA up to 10.7% of the cell dry weight (CDW). The deletion of (R)-3-hydroxydecanoyl-ACP:CoA transacylase (PhaG), which connects de novo FA and PHA synthesis pathways, while causing a further 1.8-fold decrease in PHA content, did not abolish PHA accumulation. Further proteome analysis revealed quinoprotein alcohol dehydrogenases PedE and PedH as potential monomer suppliers, but when these were deleted, the PHA level remained at 2.2-14.8% CDW depending on the fatty acid used and whether nitrogen limitation was applied. Therefore, it is likely that some other non-specific dehydrogenases supply monomers for PHA synthesis, demonstrating the redundancy of PHA metabolism. KEY POINTS: • β-oxidation intermediates are converted to PHA monomers by hydratases PhaJ1, PhaJ4 and MaoC in Pseudomonas putida KT2440. • When these are deleted, the PHA level decreases, but it is not abolished. • PHA non-specific enzyme(s) also contributes to PHA metabolism in KT2440.
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10
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Mohanan N, Wong MCH, Budisa N, Levin DB. Polymer-Degrading Enzymes of Pseudomonas chloroaphis PA23 Display Broad Substrate Preferences. Int J Mol Sci 2023; 24:ijms24054501. [PMID: 36901931 PMCID: PMC10003648 DOI: 10.3390/ijms24054501] [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: 01/02/2023] [Revised: 01/27/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023] Open
Abstract
Although many bacterial lipases and PHA depolymerases have been identified, cloned, and characterized, there is very little information on the potential application of lipases and PHA depolymerases, especially intracellular enzymes, for the degradation of polyester polymers/plastics. We identified genes encoding an intracellular lipase (LIP3), an extracellular lipase (LIP4), and an intracellular PHA depolymerase (PhaZ) in the genome of the bacterium Pseudomonas chlororaphis PA23. We cloned these genes into Escherichia coli and then expressed, purified, and characterized the biochemistry and substrate preferences of the enzymes they encode. Our data suggest that the LIP3, LIP4, and PhaZ enzymes differ significantly in their biochemical and biophysical properties, structural-folding characteristics, and the absence or presence of a lid domain. Despite their different properties, the enzymes exhibited broad substrate specificity and were able to hydrolyze both short- and medium-chain length polyhydroxyalkanoates (PHAs), para-nitrophenyl (pNP) alkanoates, and polylactic acid (PLA). Gel Permeation Chromatography (GPC) analyses of the polymers treated with LIP3, LIP4, and PhaZ revealed significant degradation of both the biodegradable as well as the synthetic polymers poly(ε-caprolactone) (PCL) and polyethylene succinate (PES).
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Affiliation(s)
- Nisha Mohanan
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Michael C.-H. Wong
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, MB R3T 2N2, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, MB R3T 2N2, Canada
- Biocatalysis Group, Technical University of Berlin, Müller-Breslau-Str. 10, D-10623 Berlin, Germany
- Correspondence: or (N.B.); (D.B.L.); Tel.: +1-204-474-7429
| | - David B. Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
- Correspondence: or (N.B.); (D.B.L.); Tel.: +1-204-474-7429
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11
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Grey A, Costeira R, Lorenzo E, O’Kane S, McCaul MV, McCarthy T, Jordan SF, Allen CCR, Kelleher BP. Biogeochemical properties of blue carbon sediments influence the distribution and monomer composition of bacterial polyhydroxyalkanoates (PHA). BIOGEOCHEMISTRY 2023; 162:359-380. [PMID: 36873379 PMCID: PMC9971093 DOI: 10.1007/s10533-022-01008-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/25/2022] [Indexed: 06/18/2023]
Abstract
UNLABELLED Coastal wetlands are highly efficient 'blue carbon' sinks which contribute to mitigating climate change through the long-term removal of atmospheric CO2 and capture of carbon (C). Microorganisms are integral to C sequestration in blue carbon sediments and face a myriad of natural and anthropogenic pressures yet their adaptive responses are poorly understood. One such response in bacteria is the alteration of biomass lipids, specifically through the accumulation of polyhydroxyalkanoates (PHAs) and alteration of membrane phospholipid fatty acids (PLFA). PHAs are highly reduced bacterial storage polymers that increase bacterial fitness in changing environments. In this study, we investigated the distribution of microbial PHA, PLFA profiles, community structure and response to changes in sediment geochemistry along an elevation gradient from intertidal to vegetated supratidal sediments. We found highest PHA accumulation, monomer diversity and expression of lipid stress indices in elevated and vegetated sediments where C, nitrogen (N), PAH and heavy metals increased, and pH was significantly lower. This was accompanied by a reduction in bacterial diversity and a shift to higher abundances of microbial community members favouring complex C degradation. Results presented here describe a connection between bacterial PHA accumulation, membrane lipid adaptation, microbial community composition and polluted C rich sediments. GRAPHICAL ABSTRACT Geochemical, microbiological and polyhydroxyalkanoate (PHA) gradient in a blue carbon zone. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10533-022-01008-5.
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Affiliation(s)
- Anthony Grey
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Ricardo Costeira
- The School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland
| | - Emmaline Lorenzo
- Department of Chemistry, University of Kansas, Lawrence, 66045 USA
| | - Sean O’Kane
- National Centre for Geocomputation, Maynooth University, Maynooth, Ireland
| | - Margaret V. McCaul
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin 4, Ireland
| | - Tim McCarthy
- National Centre for Geocomputation, Maynooth University, Maynooth, Ireland
| | - Sean F. Jordan
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin 4, Ireland
| | | | - Brian P. Kelleher
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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12
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Bioconversion of Used Transformer Oil into Polyhydroxyalkanoates by Acinetobacter sp. Strain AAAID-1.5. Polymers (Basel) 2022; 15:polym15010097. [PMID: 36616449 PMCID: PMC9824233 DOI: 10.3390/polym15010097] [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: 11/23/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
In this research, the utilisation of used transformer oil (UTO) as carbon feedstock for the production of polyhydroxyalkanoate (PHA) was targeted; with a view to reducing the environmental challenges associated with the disposal of the used oil and provision of an alternative to non-biodegradable synthetic plastic. Acinetobacter sp. strain AAAID-1.5 is a PHA-producing bacterium recently isolated from a soil sample collected in Penang, Malaysia. The PHA-producing capability of this bacterium was assessed through laboratory experiments in a shake flask biosynthesis under controlled culture conditions. The effect of some biosynthesis factors on growth and polyhydroxyalkanoate (PHA) accumulation was also investigated, the structural composition of the PHA produced by the organism was established, and the characteristics of the polymer were determined using standard analytical methods. The results indicated that the bacteria could effectively utilise UTO and produce PHA up to 34% of its cell dry weight. Analysis of the effect of some biosynthesis factors revealed that the concentration of carbon substrate, incubation time, the concentration of yeast extract and utilisation of additional carbon substrates could influence the growth and polymer accumulation in the test organism. Manipulation of culture conditions resulted in an enhanced accumulation of the PHA. The data obtained from GC-MS and NMR analyses indicated that the PHA produced might have been composed of 3-hydroxyoctadecanoate and 3-hydroxyhexadecanoate as the major monomers. The physicochemical analysis of a sample of the polymer revealed an amorphous elastomer with average molecular weight and polydispersity index (PDI) of 110 kDa and 2.01, respectively. The melting and thermal degradation temperatures were 88 °C and 268 °C, respectively. The findings of this work indicated that used transformer oil could be used as an alternative carbon substrate for PHA biosynthesis. Also, Acinetobacter sp. strain AAAID-1.5 could serve as an effective agent in the bioconversion of waste oils, especially UTO, to produce biodegradable plastics. These may undoubtedly provide a foundation for further exploration of UTO as an alternative carbon substrate in the biosynthesis of specific polyhydroxyalkanoates.
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13
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Czajka JJ, Banerjee D, Eng T, Menasalvas J, Yan C, Munoz NM, Poirier BC, Kim YM, Baker SE, Tang YJ, Mukhopadhyay A. Tuning a high performing multiplexed-CRISPRi Pseudomonas putida strain to further enhance indigoidine production. Metab Eng Commun 2022; 15:e00206. [PMID: 36158112 PMCID: PMC9494242 DOI: 10.1016/j.mec.2022.e00206] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022] Open
Abstract
In this study, a 14-gene edited Pseudomonas putida KT2440 strain for heterologous indigoidine production was examined using three distinct omic datasets. Transcriptomic data indicated that CRISPR/dCpf1-interference (CRISPRi) mediated multiplex repression caused global gene expression changes, implying potential undesirable changes in metabolic flux. 13C-metabolic flux analysis (13C-MFA) revealed that the core P. putida flux network after CRISPRi repression was conserved, with moderate reduction of TCA cycle and pyruvate shunt activity along with glyoxylate shunt activation during glucose catabolism. Metabolomic results identified a change in intracellular TCA metabolites and extracellular metabolite secretion profiles (sugars and succinate overflow) in the engineered strains. These omic analyses guided further strain engineering, with a random mutagenesis screen first identifying an optimal ribosome binding site (RBS) for Cpf1 that enabled stronger product-substrate pairing (1.6-fold increase). Then, deletion strains were constructed with excision of the PHA operon (ΔphaAZC-IID) resulting in a 2.2-fold increase in indigoidine titer over the optimized Cpf1-RBS construct at the end of the growth phase (∼6 h). The maximum indigoidine titer (at 72 h) in the ΔphaAZC-IID strain had a 1.5-fold and 1.8-fold increase compared to the optimized Cpf1-RBS construct and the original strain, respectively. Overall, this study demonstrated that integration of omic data types is essential for understanding responses to complex metabolic engineering designs and directly quantified the effect of such modifications on central metabolism.
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Affiliation(s)
- Jeffrey J Czajka
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Thomas Eng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Javier Menasalvas
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chunsheng Yan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nathalie Munoz Munoz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Brenton C Poirier
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Scott E Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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14
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LeBlanc N, Charles TC. Bacterial genome reductions: Tools, applications, and challenges. Front Genome Ed 2022; 4:957289. [PMID: 36120530 PMCID: PMC9473318 DOI: 10.3389/fgeed.2022.957289] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial cells are widely used to produce value-added products due to their versatility, ease of manipulation, and the abundance of genome engineering tools. However, the efficiency of producing these desired biomolecules is often hindered by the cells’ own metabolism, genetic instability, and the toxicity of the product. To overcome these challenges, genome reductions have been performed, making strains with the potential of serving as chassis for downstream applications. Here we review the current technologies that enable the design and construction of such reduced-genome bacteria as well as the challenges that limit their assembly and applicability. While genomic reductions have shown improvement of many cellular characteristics, a major challenge still exists in constructing these cells efficiently and rapidly. Computational tools have been created in attempts at minimizing the time needed to design these organisms, but gaps still exist in modelling these reductions in silico. Genomic reductions are a promising avenue for improving the production of value-added products, constructing chassis cells, and for uncovering cellular function but are currently limited by their time-consuming construction methods. With improvements to and the creation of novel genome editing tools and in silico models, these approaches could be combined to expedite this process and create more streamlined and efficient cell factories.
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Affiliation(s)
- Nicole LeBlanc
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- *Correspondence: Nicole LeBlanc,
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- Metagenom Bio Life Science Inc., Waterloo, ON, Canada
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15
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Polyhydroxyalkanoate Production by Caenibius tardaugens from Steroidal Endocrine Disruptors. Microorganisms 2022; 10:microorganisms10040706. [PMID: 35456754 PMCID: PMC9027588 DOI: 10.3390/microorganisms10040706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 12/10/2022] Open
Abstract
The α-proteobacterium Caenibius tardaugens can use estrogens and androgens as the sole carbon source. These compounds are steroidal endocrine disruptors that are found contaminating soil and aquatic ecosystems. Here, we show that C. tardaugens, which has been considered as a valuable biocatalyst for aerobic steroidal hormone decontamination, is also able to produce polyhydroxyalkanoates (PHA), biodegradable and biocompatible polyesters of increasing biotechnological interest as a sustainable alternative to classical oil-derived polymers. Steroid catabolism yields a significant amount of propionyl-CoA that is metabolically directed towards PHA production through condensation into 3-ketovaleryl-CoA, rendering a PHA rich in 3-hydroxyvalerate. To the best of our knowledge, this is the first report where PHAs are produced from steroids as carbon sources.
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16
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Abstract
Polyhydroxyalkanoates (PHAs) are polyesters produced by numerous microorganisms for energy and carbon storage. Simultaneous synthesis and degradation of PHA drives a dynamic cycle linked to the central carbon metabolism, which modulates numerous and diverse bacterial processes, such as stress endurance, pathogenesis, and persistence. Here, we analyze the role of the PHA cycle in conferring robustness to the model bacterium P. putida KT2440. To assess the effect of this cycle in the cell, we began by constructing a PHA depolymerase (PhaZ) mutant strain that had its PHA cycle blocked. We then restored the flux through the cycle in the context of an engineered library of P. putida strains harboring differential levels of PhaZ. High-throughput phenotyping analyses of this collection of strains revealed significant changes in response to PHA cycle performance impacting cell number and size, PHA accumulation, and production of extracellular (R)-hydroxyalkanoic acids. To understand the metabolic changes at the system level due to PHA turnover, we contextualized these physiological data using the genome-scale metabolic model iJN1411. Model-based predictions suggest successive metabolic steady states during the growth curve and an important carbon flux rerouting driven by the activity of the PHA cycle. Overall, we demonstrate that modulating the activity of the PHA cycle gives us control over the carbon metabolism of P. putida, which in turn will give us the ability to tailor cellular mechanisms driving stress tolerance, e.g., defenses against oxidative stress, and any potential biotechnological applications. IMPORTANCE Despite large research efforts devoted to understanding the flexible metabolism of Pseudomonas beyond the role of key regulatory players, the metabolic basis powering the dynamic control of its biological fitness under disturbance conditions remains largely unknown. Among other metabolic hubs, the so-called PHA cycle, involving simultaneous synthesis and degradation of PHAs, is emerging as a pivotal metabolic trait powering metabolic robustness and resilience in this bacterial group. Here, we provide evidence suggesting that metabolic states in Pseudomonas can be anticipated, controlled, and engineered by tailoring the flux through the PHA cycle. Overall, our study suggests that the PHA cycle is a promising metabolic target toward achieving control over bacterial metabolic robustness. This is likely to open up a broad range of applications in areas as diverse as pathogenesis and biotechnology.
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17
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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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18
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Li D, Ma X, Yin F, Qiu Y, Yan X. Creating biotransformation of volatile fatty acids and octanoate as co-substrate to high yield medium-chain-length polyhydroxyalkanoate. BIORESOURCE TECHNOLOGY 2021; 331:125031. [PMID: 33798859 DOI: 10.1016/j.biortech.2021.125031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Using mixed microbial consortium (MMC) to accumulate polyhydroxyalkanoate (PHA) is an effective strategy to solve high production cost and reduce the amount of excess sludge. In this study, a process for the production of short-chain-length and medium-chain-length PHA using volatile fatty acids (VFAs) from pretreated wood hydrolysate synergistic with octanoate as co-substrate was proposed. The effects of co-substrate ratios on PHA accumulation ability and physical properties were investigated. The incorporation of co-substrate accelerated the time of PHA and 3-hydroxyoctanoate reaching the maximum production (1834 and 280 mg COD/L). The highest PHA content was 53.0% (w/w), which was equivalent to that reported previously. The biopolymer films possessed high tensile strength, Young's modulus, and could be used in the field of water vapor barrier requirements. The accumulation strategy applied for converting fermentation products VFAs and octanoate co-substrate into high value and yield PHA could potentially demonstrate the valuable for low-cost large-scale production.
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Affiliation(s)
- Dongna Li
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300222, PR China
| | - Xiaojun Ma
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300222, PR China.
| | - Fen Yin
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300222, PR China
| | - Yujuan Qiu
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300222, PR China
| | - Xu Yan
- College of Light Industry Science and Engineering, Tianjin University of Science & Technology, Tianjin 300222, PR China
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19
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Blanco FG, Hernández N, Rivero-Buceta V, Maestro B, Sanz JM, Mato A, Hernández-Arriaga AM, Prieto MA. From Residues to Added-Value Bacterial Biopolymers as Nanomaterials for Biomedical Applications. NANOMATERIALS 2021; 11:nano11061492. [PMID: 34200068 PMCID: PMC8228158 DOI: 10.3390/nano11061492] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 12/16/2022]
Abstract
Bacterial biopolymers are naturally occurring materials comprising a wide range of molecules with diverse chemical structures that can be produced from renewable sources following the principles of the circular economy. Over the last decades, they have gained substantial interest in the biomedical field as drug nanocarriers, implantable material coatings, and tissue-regeneration scaffolds or membranes due to their inherent biocompatibility, biodegradability into nonhazardous disintegration products, and their mechanical properties, which are similar to those of human tissues. The present review focuses upon three technologically advanced bacterial biopolymers, namely, bacterial cellulose (BC), polyhydroxyalkanoates (PHA), and γ-polyglutamic acid (PGA), as models of different carbon-backbone structures (polysaccharides, polyesters, and polyamides) produced by bacteria that are suitable for biomedical applications in nanoscale systems. This selection models evidence of the wide versatility of microorganisms to generate biopolymers by diverse metabolic strategies. We highlight the suitability for applied sustainable bioprocesses for the production of BC, PHA, and PGA based on renewable carbon sources and the singularity of each process driven by bacterial machinery. The inherent properties of each polymer can be fine-tuned by means of chemical and biotechnological approaches, such as metabolic engineering and peptide functionalization, to further expand their structural diversity and their applicability as nanomaterials in biomedicine.
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Affiliation(s)
- Francisco G. Blanco
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), 28040 Madrid, Spain; (F.G.B.); (N.H.); (V.R.-B.); (A.M.); (A.M.H.-A.)
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Biological Research Centre Margarita Salas, CIB-CSIC, 28040 Madrid, Spain
| | - Natalia Hernández
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), 28040 Madrid, Spain; (F.G.B.); (N.H.); (V.R.-B.); (A.M.); (A.M.H.-A.)
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Biological Research Centre Margarita Salas, CIB-CSIC, 28040 Madrid, Spain
| | - Virginia Rivero-Buceta
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), 28040 Madrid, Spain; (F.G.B.); (N.H.); (V.R.-B.); (A.M.); (A.M.H.-A.)
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Biological Research Centre Margarita Salas, CIB-CSIC, 28040 Madrid, Spain
| | - Beatriz Maestro
- Host-Parasite Interplay in Pneumococcal Infection Group, Microbial and Plant Biotechnology Department, Biological Research Centre Margarita Salas, CIB-CSIC, 28040 Madrid, Spain; (B.M.); (J.M.S.)
| | - Jesús M. Sanz
- Host-Parasite Interplay in Pneumococcal Infection Group, Microbial and Plant Biotechnology Department, Biological Research Centre Margarita Salas, CIB-CSIC, 28040 Madrid, Spain; (B.M.); (J.M.S.)
| | - Aránzazu Mato
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), 28040 Madrid, Spain; (F.G.B.); (N.H.); (V.R.-B.); (A.M.); (A.M.H.-A.)
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Biological Research Centre Margarita Salas, CIB-CSIC, 28040 Madrid, Spain
| | - Ana M. Hernández-Arriaga
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), 28040 Madrid, Spain; (F.G.B.); (N.H.); (V.R.-B.); (A.M.); (A.M.H.-A.)
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Biological Research Centre Margarita Salas, CIB-CSIC, 28040 Madrid, Spain
| | - M. Auxiliadora Prieto
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), 28040 Madrid, Spain; (F.G.B.); (N.H.); (V.R.-B.); (A.M.); (A.M.H.-A.)
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Biological Research Centre Margarita Salas, CIB-CSIC, 28040 Madrid, Spain
- Correspondence:
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20
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Koch M, Forchhammer K. Polyhydroxybutyrate: A Useful Product of Chlorotic Cyanobacteria. Microb Physiol 2021; 31:67-77. [PMID: 33979794 DOI: 10.1159/000515617] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/02/2021] [Indexed: 11/19/2022]
Abstract
Polyhydroxybutyrate (PHB) is a carbon polymer with diverse functions, varying greatly on the organism producing it. This microreview describes the current knowledge about PHB metabolism, structure, and different physiological roles with a special focus on cyanobacteria. Despite the physiological function of PHB in the cyanobacterial phylum still being unknown, these organisms provide the unique opportunity to directly convert atmospheric CO2 into bioplastic using a solar-based process. Recent research on PHB metabolism in the cyanobacterial model organism Synechocystis revealed a sophisticated control of PHB granule formation. Novel insights about the metabolic background of PHB synthesis resulted in the engineering of the first cyanobacterial superproducer strain.
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Affiliation(s)
- Moritz Koch
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Eberhard Karls University Tübingen, Tübingen, Germany
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21
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Li HL, Deng RX, Wang W, Liu KQ, Hu HB, Huang XQ, Zhang XH. Biosynthesis and Characterization of Medium-Chain-Length Polyhydroxyalkanoate with an Enriched 3-Hydroxydodecanoate Monomer from a Pseudomonas chlororaphis Cell Factory. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3895-3903. [PMID: 33759523 DOI: 10.1021/acs.jafc.1c00500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Polyhydroxyalkanoates (PHAs) have been reported with agricultural and medical applications in virtue of their biodegradable and biocompatible properties. Here, we systematically engineered three modules for the enhanced biosynthesis of medium-chain-length polyhydroxyalkanoate (mcl-PHA) in Pseudomonas chlororaphis HT66. The phzE, fadA, and fadB genes were deleted to block the native phenazine pathway and weaken the fatty acid β-oxidation pathway. Additionally, a PHA depolymerase gene phaZ was knocked out to prevent the degradation of mcl-PHA. Three genes involved in the mcl-PHA biosynthesis pathway were co-overexpressed to increase carbon flux. The engineered strain HT4Δ::C1C2J exhibited an 18.2 g/L cell dry weight with 84.9 wt % of mcl-PHA in a shake-flask culture, and the 3-hydroxydodecanoate (3HDD) monomer was increased to 71.6 mol %. Thermophysical and mechanical properties of mcl-PHA were improved with an enriched ratio of 3HDD. This study demonstrated a rational metabolic engineering approach to enhance the production of mcl-PHA with the enriched dominant monomer and improved material properties.
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Affiliation(s)
- Hui-Ling Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ru-Xiang Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kai-Quan Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, China
| | - Hong-Bo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xian-Qing Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Hong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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22
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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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Dabrowska D, Mozejko-Ciesielska J, Pokój T, Ciesielski S. Transcriptome Changes in Pseudomonas putida KT2440 during Medium-Chain-Length Polyhydroxyalkanoate Synthesis Induced by Nitrogen Limitation. Int J Mol Sci 2020; 22:ijms22010152. [PMID: 33375721 PMCID: PMC7801951 DOI: 10.3390/ijms22010152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas putida’s versatility and metabolic flexibility make it an ideal biotechnological platform for producing valuable chemicals, such as medium-chain-length polyhydroxyalkanoates (mcl-PHAs), which are considered the next generation bioplastics. This bacterium responds to environmental stimuli by rearranging its metabolism to improve its fitness and increase its chances of survival in harsh environments. Mcl-PHAs play an important role in central metabolism, serving as a reservoir of carbon and energy. Due to the complexity of mcl-PHAs’ metabolism, the manner in which P. putida changes its transcriptome to favor mcl-PHA synthesis in response to environmental stimuli remains unclear. Therefore, our objective was to investigate how the P. putida KT2440 wild type and mutants adjust their transcriptomes to synthesize mcl-PHAs in response to nitrogen limitation when supplied with sodium gluconate as an external carbon source. We found that, under nitrogen limitation, mcl-PHA accumulation is significantly lower in the mutant deficient in the stringent response than in the wild type or the rpoN mutant. Transcriptome analysis revealed that, under N-limiting conditions, 24 genes were downregulated and 21 were upregulated that were common to all three strains. Additionally, potential regulators of these genes were identified: the global anaerobic regulator (Anr, consisting of FnrA, Fnrb, and FnrC), NorR, NasT, the sigma54-dependent transcriptional regulator, and the dual component NtrB/NtrC regulator all appear to play important roles in transcriptome rearrangement under N-limiting conditions. The role of these regulators in mcl-PHA synthesis is discussed.
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Affiliation(s)
- Dorota Dabrowska
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (D.D.); (T.P.)
| | - Justyna Mozejko-Ciesielska
- Department of Microbiology and Mycology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
| | - Tomasz Pokój
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (D.D.); (T.P.)
| | - Slawomir Ciesielski
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (D.D.); (T.P.)
- Correspondence: ; Tel.: +48-89-5234162
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24
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Bandopadhyay S, Liquet Y González JE, Henderson KB, Anunciado MB, Hayes DG, DeBruyn JM. Soil Microbial Communities Associated With Biodegradable Plastic Mulch Films. Front Microbiol 2020; 11:587074. [PMID: 33281783 PMCID: PMC7691482 DOI: 10.3389/fmicb.2020.587074] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/20/2020] [Indexed: 11/13/2022] Open
Abstract
Agricultural plastic mulch films provide a favorable soil microclimate for plant growth, improving crop yields. Biodegradable plastic mulch films (BDMs) have emerged as a sustainable alternative to widely used non-biodegradable polyethylene (PE) films. BDMs are tilled into the soil after use and are expected to biodegrade under field conditions. However, little is known about the microbes involved in biodegradation and the relationships between microbes and plastics in soils. In order to capture the consortium of soil microbes associated with (and thus likely degrading) BDMs, agriculturally-weathered plastics from two locations were studied alongside laboratory enrichment experiments to assess differences in the microbial communities associated with BDMs and PE films. Using a combination of amplicon sequencing and quantitative PCR (qPCR), we observed that agriculturally-weathered plastics hosted an enrichment of fungi and an altered bacterial community composition compared to the surrounding soil. Notably, Methylobacterium, Arthrobacter, and Sphingomonas were enriched on BDMs compared to non-biodegradable PE. In laboratory enrichment cultures, microbial consortia were able to degrade the plastics, and the composition of the microbial communities was influenced by the composition of the BDMs. Our initial characterization of the microbial communities associated with biodegradable plastic mulch films, or the biodegradable "plastisphere," lays the groundwork for understanding biodegradation dynamics of biodegradable plastics in the environment.
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Affiliation(s)
- Sreejata Bandopadhyay
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States
| | - José E Liquet Y González
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States
| | - Kelsey B Henderson
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States
| | - Marife B Anunciado
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States
| | - Douglas G Hayes
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States
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25
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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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Ankenbauer A, Schäfer RA, Viegas SC, Pobre V, Voß B, Arraiano CM, Takors R. Pseudomonas putida KT2440 is naturally endowed to withstand industrial-scale stress conditions. Microb Biotechnol 2020; 13:1145-1161. [PMID: 32267616 PMCID: PMC7264900 DOI: 10.1111/1751-7915.13571] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 03/11/2020] [Accepted: 03/15/2020] [Indexed: 12/17/2022] Open
Abstract
Pseudomonas putida is recognized as a very promising strain for industrial application due to its high redox capacity and frequently observed tolerance towards organic solvents. In this research, we studied the metabolic and transcriptional response of P. putida KT2440 exposed to large-scale heterogeneous mixing conditions in the form of repeated glucose shortage. Cellular responses were mimicked in an experimental setup comprising a stirred tank reactor and a connected plug flow reactor. We deciphered that a stringent response-like transcriptional regulation programme is frequently induced, which seems to be linked to the intracellular pool of 3-hydroxyalkanoates (3-HA) that are known to serve as precursors for polyhydroxyalkanoates (PHA). To be precise, P. putida is endowed with a survival strategy likely to access cellular PHA, amino acids and glycogen in few seconds under glucose starvation to obtain ATP from respiration, thereby replenishing the reduced ATP levels and the adenylate energy charge. Notably, cells only need 0.4% of glucose uptake to build those 3-HA-based energy buffers. Concomitantly, genes that are related to amino acid catabolism and β-oxidation are upregulated during the transient absence of glucose. Furthermore, we provide a detailed list of transcriptional short- and long-term responses that increase the cellular maintenance by about 17% under the industrial-like conditions tested.
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Affiliation(s)
- Andreas Ankenbauer
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Richard A. Schäfer
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Sandra C. Viegas
- ITQBInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República2780‐157OeirasPortugal
| | - Vânia Pobre
- ITQBInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República2780‐157OeirasPortugal
| | - Björn Voß
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Cecília M. Arraiano
- ITQBInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República2780‐157OeirasPortugal
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartAllmandring 3170569StuttgartGermany
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Sanz D, García JL, Díaz E. Expanding the current knowledge and biotechnological applications of the oxygen-independent ortho-phthalate degradation pathway. Environ Microbiol 2020; 22:3478-3493. [PMID: 32510798 DOI: 10.1111/1462-2920.15119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/31/2020] [Accepted: 06/03/2020] [Indexed: 11/29/2022]
Abstract
ortho-Phthalate derives from industrially produced phthalate esters, which are massively used as plasticizers and constitute major emerging environmental pollutants. The pht pathway for the anaerobic bacterial biodegradation of o-phthalate involves its activation to phthaloyl-CoA followed by decarboxylation to benzoyl-CoA. Here, we have explored further the pht peripheral pathway in denitrifying bacteria and shown that it requires also an active transport system for o-phthalate uptake that belongs to the poorly characterized class of TAXI-TRAP transporters. The construction of a fully functional pht cassette combining both catabolic and transport genes allowed to expand the o-phthalate degradation ecological trait to heterologous hosts. Unexpectedly, the pht cassette also allowed the aerobic conversion of o-phthalate to benzoyl-CoA when coupled to a functional box central pathway. Hence, the pht pathway may constitute an evolutionary acquisition for o-phthalate degradation by bacteria that thrive either in anoxic environments or in environments that face oxygen limitations and that rely on benzoyl-CoA, rather than on catecholic central intermediates, for the aerobic catabolism of aromatic compounds. Finally, the recombinant pht cassette was used both to screen for functional aerobic box pathways in bacteria and to engineer recombinant biocatalysts for o-phthalate bioconversion into sustainable bioplastics, e.g., polyhydroxybutyrate, in plastic recycling industrial processes.
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Affiliation(s)
- David Sanz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
| | - José L García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
| | - Eduardo Díaz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
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28
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Mato A, Blanco FG, Maestro B, Sanz JM, Pérez-Gil J, Prieto MA. Dissecting the Polyhydroxyalkanoate-Binding Domain of the PhaF Phasin: Rational Design of a Minimized Affinity Tag. Appl Environ Microbiol 2020; 86:e00570-20. [PMID: 32303541 PMCID: PMC7267194 DOI: 10.1128/aem.00570-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/10/2020] [Indexed: 12/13/2022] Open
Abstract
Phasin PhaF from Pseudomonas putida consists of a modular protein whose N-terminal domain (BioF) has been demonstrated to be responsible for binding to the polyhydroxyalkanoate (PHA) granule. BioF has been exploited for biotechnological purposes as an affinity tag in the functionalization of PHA beads with fusion proteins both in vivo and in vitro The structural model of this domain suggests an amphipathic α-helical conformation with the hydrophobic residues facing the PHA granule. In this work, we analyzed the mean hydrophobicity and the hydrophobic moment of the native BioF tag to rationally design shorter versions that maintain affinity for the granule. Hybrid proteins containing the green fluorescent protein (GFP) fused to the BioF derivatives were studied for in vivo localization on PHA, stability on the surface of the PHA granule against pH, temperature, and ionic strength, and their possible influence on PHA synthesis. Based on the results obtained, a minimized BioF tag for PHA functionalization has been proposed (MinP) that retains similar binding properties but possesses an attractive biotechnological potential derived from its reduced size. The MinP tag was further validated by analyzing the functionality and stability of the fusion proteins MinP-β-galactosidase and MinP-CueO from Escherichia coliIMPORTANCE Polyhydroxyalkanoates (PHAs) are biocompatible, nontoxic, and biodegradable biopolymers with exceptional applications in the industrial and medical fields. The complex structure of the PHA granule can be exploited as a toolbox to display molecules of interest on their surface. Phasins, the most abundant group of proteins on the granule, have been employed as anchoring tags to obtain functionalized PHA beads for high-affinity bioseparation, enzyme immobilization, diagnostics, or cell targeting. Here, a shorter module based on the previously designed BioF tag has been demonstrated to maintain the affinity for the PHA granule, with higher stability and similar functionalization efficiency. The use of a 67% shorter peptide, which maintains the binding properties of the entire protein, constitutes an advantage for the immobilization of recombinant proteins on the PHA surface both in vitro and in vivo.
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Affiliation(s)
- Aranzazu Mato
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Francisco G Blanco
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Beatriz Maestro
- Host-Parasite Interplay in Pneumococcal Infection Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
| | - Jesús M Sanz
- Host-Parasite Interplay in Pneumococcal Infection Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Jesús Pérez-Gil
- Biochemical and Molecular Biology Department, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - M Auxiliadora Prieto
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
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29
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Characterization of an intracellular poly(3-hydroxyalkanoate) depolymerase from the soil bacterium, Pseudomonas putida LS46. Polym Degrad Stab 2020. [DOI: 10.1016/j.polymdegradstab.2020.109127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Velázquez-Sánchez C, Espín G, Peña C, Segura D. The Modification of Regulatory Circuits Involved in the Control of Polyhydroxyalkanoates Metabolism to Improve Their Production. Front Bioeng Biotechnol 2020; 8:386. [PMID: 32426348 PMCID: PMC7204398 DOI: 10.3389/fbioe.2020.00386] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/07/2020] [Indexed: 11/13/2022] Open
Abstract
Poly-(3-hydroxyalkanoates) (PHAs) are bacterial carbon and energy storage compounds. These polymers are synthesized under conditions of nutritional imbalance, where a nutrient is growth-limiting while there is still enough carbon source in the medium. On the other side, the accumulated polymer is mobilized under conditions of nutrient accessibility or by limitation of the carbon source. Thus, it is well known that the accumulation of PHAs is affected by the availability of nutritional resources and this knowledge has been used to establish culture conditions favoring high productivities. In addition to this effect of the metabolic status on PHAs accumulation, several genetic regulatory networks have been shown to drive PHAs metabolism, so the expression of the PHAs genes is under the influence of global or specific regulators. These regulators are thought to coordinate PHAs synthesis and mobilization with the rest of bacterial physiology. While the metabolic and biochemical knowledge related to the biosynthesis of these polymers has led to the development of processes in bioreactors for high-level production and also to the establishment of strategies for metabolic engineering for the synthesis of modified biopolymers, the use of knowledge related to the regulatory circuits controlling PHAs metabolism for strain improvement is scarce. A better understanding of the genetic control systems involved could serve as the foundation for new strategies for strain modification in order to increase PHAs production or to adjust the chemical structure of these biopolymers. In this review, the regulatory systems involved in the control of PHAs metabolism are examined, with emphasis on those acting at the level of expression of the enzymes involved and their potential modification for strain improvement, both for higher titers, or manipulation of polymer properties. The case of the PHAs producer Azotobacter vinelandii is taken as an example of the complexity and variety of systems controlling the accumulation of these interesting polymers in response to diverse situations, many of which could be engineered to improve PHAs production.
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Affiliation(s)
- Claudia Velázquez-Sánchez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Carlos Peña
- Departamento Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Daniel Segura
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Development of a CRISPR/Cas9n-based tool for metabolic engineering of Pseudomonas putida for ferulic acid-to-polyhydroxyalkanoate bioconversion. Commun Biol 2020; 3:98. [PMID: 32139868 PMCID: PMC7058019 DOI: 10.1038/s42003-020-0824-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/12/2020] [Indexed: 12/18/2022] Open
Abstract
Ferulic acid is a ubiquitous phenolic compound in lignocellulose, which is recognized for its role in the microbial carbon catabolism and industrial value. However, its recalcitrance and toxicity poses a challenge for ferulic acid-to-bioproducts bioconversion. Here, we develop a genome editing strategy for Pseudomonas putida KT2440 using an integrated CRISPR/Cas9n-λ-Red system with pyrF as a selection marker, which maintains cell viability and genetic stability, increases mutation efficiency, and simplifies genetic manipulation. Via this method, four functional modules, comprised of nine genes involved in ferulic acid catabolism and polyhydroxyalkanoate biosynthesis, were integrated into the genome, generating the KTc9n20 strain. After metabolic engineering and optimization of C/N ratio, polyhydroxyalkanoate production was increased to ~270 mg/L, coupled with ~20 mM ferulic acid consumption. This study not only establishes a simple and efficient genome editing strategy, but also offers an encouraging example of how to apply this method to improve microbial aromatic compound bioconversion. Yueyue Zhou et al. develop a genetic engineering method that increases the production of polyhydroxyalkanoate from ferulic acid, which is toxic at high concentrations. This study provides insight into the bioconversion of the aromatic compound in Pseudomonas.
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33
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Production of Polyhydroxyalkanoates and Extracellular Products Using Pseudomonas Corrugata and P. Mediterranea: A Review. Bioengineering (Basel) 2019; 6:bioengineering6040105. [PMID: 31739507 PMCID: PMC6955742 DOI: 10.3390/bioengineering6040105] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/10/2019] [Accepted: 11/12/2019] [Indexed: 11/16/2022] Open
Abstract
Some strains of Pseudomonas corrugata (Pco) and P. mediterranea (Pme) efficiently synthesize medium-chain-length polyhydroxyalkanoates elastomers (mcl-PHA) and extracellular products on related and unrelated carbon sources. Yield and composition are dependent on the strain, carbon source, fermentation process, and any additives. Selected Pco strains produce amorphous and sticky mcl-PHA, whereas strains of Pme produce, on high grade and partially refined biodiesel glycerol, a distinctive filmable PHA, very different from the conventional microbial mcl-PHA, suitable for making blends with polylactide acid. However, the yields still need to be improved and production costs lowered. An integrated process has been developed to recover intracellular mcl-PHA and extracellular bioactive molecules. Transcriptional regulation studies during PHA production contribute to understanding the metabolic potential of Pco and Pme strains. Data available suggest that pha biosynthesis genes and their regulations will be helpful to develop new, integrated strategies for cost-effective production.
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34
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Salvachúa D, Rydzak T, Auwae R, De Capite A, Black BA, Bouvier JT, Cleveland NS, Elmore JR, Huenemann JD, Katahira R, Michener WE, Peterson DJ, Rohrer H, Vardon DR, Beckham GT, Guss AM. Metabolic engineering of Pseudomonas putida for increased polyhydroxyalkanoate production from lignin. Microb Biotechnol 2019; 13:290-298. [PMID: 31468725 PMCID: PMC6922519 DOI: 10.1111/1751-7915.13481] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/10/2019] [Indexed: 12/01/2022] Open
Abstract
Microbial conversion offers a promising strategy for overcoming the intrinsic heterogeneity of the plant biopolymer, lignin. Soil microbes that natively harbour aromatic‐catabolic pathways are natural choices for chassis strains, and Pseudomonas putida KT2440 has emerged as a viable whole‐cell biocatalyst for funnelling lignin‐derived compounds to value‐added products, including its native carbon storage product, medium‐chain‐length polyhydroxyalkanoates (mcl‐PHA). In this work, a series of metabolic engineering targets to improve mcl‐PHA production are combined in the P. putida chromosome and evaluated in strains growing in a model aromatic compound, p‐coumaric acid, and in lignin streams. Specifically, the PHA depolymerase gene phaZ was knocked out, and the genes involved in β‐oxidation (fadBA1 and fadBA2) were deleted. Additionally, to increase carbon flux into mcl‐PHA biosynthesis, phaG, alkK, phaC1 and phaC2 were overexpressed. The best performing strain – which contains all the genetic modifications detailed above – demonstrated a 53% and 200% increase in mcl‐PHA titre (g l−1) and a 20% and 100% increase in yield (g mcl‐PHA per g cell dry weight) from p‐coumaric acid and lignin, respectively, compared with the wild type strain. Overall, these results present a promising strain to be employed in further process development for enhancing mcl‐PHA production from aromatic compounds and lignin.
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Affiliation(s)
- Davinia Salvachúa
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Thomas Rydzak
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Raquel Auwae
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Annette De Capite
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Brenna A Black
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Jason T Bouvier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nicholas S Cleveland
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Joshua R Elmore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jay D Huenemann
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Rui Katahira
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - William E Michener
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Darren J Peterson
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Holly Rohrer
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Derek R Vardon
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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Bustamante D, Segarra S, Tortajada M, Ramón D, del Cerro C, Auxiliadora Prieto M, Iglesias JR, Rojas A. In silico prospection of microorganisms to produce polyhydroxyalkanoate from whey: Caulobacter segnis DSM 29236 as a suitable industrial strain. Microb Biotechnol 2019; 12:487-501. [PMID: 30702206 PMCID: PMC6465232 DOI: 10.1111/1751-7915.13371] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 12/20/2018] [Accepted: 12/26/2018] [Indexed: 11/29/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are polyesters of microbial origin that can be synthesized by prokaryotes from noble sugars or lipids and from complex renewable substrates. They are an attractive alternative to conventional plastics because they are biodegradable and can be produced from renewable resources, such as the surplus of whey from dairy companies. After an in silico screening to search for ß-galactosidase and PHA polymerase genes, several bacteria were identified as potential PHA producers from whey based on their ability to hydrolyse lactose. Among them, Caulobacter segnis DSM 29236 was selected as a suitable strain to develop a process for whey surplus valorization. This microorganism accumulated 31.5% of cell dry weight (CDW) of poly(3-hydroxybutyrate) (PHB) with a titre of 1.5 g l-1 in batch assays. Moreover, the strain accumulated 37% of CDW of PHB and 9.3 g l-1 in fed-batch mode of operation. This study reveals this species as a PHA producer and experimentally validates the in silico bioprospecting strategy for selecting microorganisms for waste re-valorization.
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Affiliation(s)
- Daniel Bustamante
- Biopolis, S.L. Parque Científico Universidad de Valenciaedf. 2 C/Catedrático Agustín Escardino, 946980PaternaValenciaSpain
| | - Silvia Segarra
- Biopolis, S.L. Parque Científico Universidad de Valenciaedf. 2 C/Catedrático Agustín Escardino, 946980PaternaValenciaSpain
| | - Marta Tortajada
- Biopolis, S.L. Parque Científico Universidad de Valenciaedf. 2 C/Catedrático Agustín Escardino, 946980PaternaValenciaSpain
| | - Daniel Ramón
- Biopolis, S.L. Parque Científico Universidad de Valenciaedf. 2 C/Catedrático Agustín Escardino, 946980PaternaValenciaSpain
| | - Carlos del Cerro
- Microbial and Plant Biotechnology DepartmentCentro de Investigaciones BiológicasMadridSpain
- Present address:
National Renewable Energy Laboratory (NREL)15013 Denver West ParkwayGoldenCO80401USA
| | | | - José Ramón Iglesias
- Corporación Alimentaria Peñasanta (CAPSA) Polígono Industrial0, 33199Granda, AsturiasSpain
| | - Antonia Rojas
- Biopolis, S.L. Parque Científico Universidad de Valenciaedf. 2 C/Catedrático Agustín Escardino, 946980PaternaValenciaSpain
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Zhao F, Liu X, Kong A, Zhao Y, Fan X, Ma T, Gao W, Wang S, Yang C. Screening of endogenous strong promoters for enhanced production of medium-chain-length polyhydroxyalkanoates in Pseudomonas mendocina NK-01. Sci Rep 2019; 9:1798. [PMID: 30755729 PMCID: PMC6372614 DOI: 10.1038/s41598-019-39321-z] [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: 09/05/2018] [Accepted: 01/21/2019] [Indexed: 01/02/2023] Open
Abstract
Polyhydroxyalkanoate (PHA) can be produced by microorganisms from renewable resources and is regarded as a promising bioplastic to replace petroleum-based plastics. Pseudomonas mendocina NK-01 is a medium-chain-length PHA (mcl-PHA)-producing strain and its whole-genome sequence is currently available. The yield of mcl-PHA in P. mendocina NK-01 is expected to be improved by applying a promoter engineering strategy. However, a limited number of well-characterized promoters has greatly restricted the application of promoter engineering for increasing the yield of mcl-PHA in P. mendocina NK-01. In this work, 10 endogenous promoters from P. mendocina NK-01 were identified based on RNA-seq and promoter prediction results. Subsequently, 10 putative promoters were characterized for their strength through the expression of a reporter gene gfp. As a result, five strong promoters designated as P4, P6, P9, P16 and P25 were identified based on transcriptional level and GFP fluorescence intensity measurements. To evaluate whether the screened promoters can be used to enhance transcription of PHA synthase gene (phaC), the three promoters P4, P6 and P16 were separately integrated into upstream of the phaC operon in the genome of P. mendocina NK-01, resulting in the recombinant strains NKU-4C1, NKU-6C1 and NKU-16C1. As expected, the transcriptional levels of phaC1 and phaC2 in the recombinant strains were increased as shown by real-time quantitative RT-PCR. The phaZ gene encoding PHA depolymerase was further deleted to construct the recombinant strains NKU-∆phaZ-4C1, NKU-∆phaZ-6C1 and NKU-∆phaZ-16C1. The results from shake-flask fermentation indicated that the mcl-PHA titer of recombinant strain NKU-∆phaZ-16C1 was increased from 17 to 23 wt% compared with strain NKU-∆phaZ. This work provides a feasible method to discover strong promoters in P. mendocina NK-01 and highlights the potential of the screened endogenous strong promoters for metabolic engineering of P. mendocina NK-01 to increase the yield of mcl-PHA.
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Affiliation(s)
- Fengjie Zhao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Xiangsheng Liu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Annie Kong
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Yuxin Zhao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Xu Fan
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China
| | - Weixia Gao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
| | - Shufang Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin, 300071, China.
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Chen Z, Zhang C, Shen L, Li H, Peng Y, Wang H, He N, Li Q, Wang Y. Synthesis of Short-Chain-Length and Medium-Chain-Length Polyhydroxyalkanoate Blends from Activated Sludge by Manipulating Octanoic Acid and Nonanoic Acid as Carbon Sources. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:11043-11054. [PMID: 30265532 DOI: 10.1021/acs.jafc.8b04001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The effects of octanoic acid/nonanoic acid and acclimation time on the synthesis of short-chain-length and medium-chain-length PHA blends from activated sludge were investigated. An increased concentration (847-1366 mg/L) of PHAs resulted from 4-month acclimation compared with the concentration derived from 2-month acclimation (450-1126 mg/L). The content of octanoic acid had a positive linear relationship with the content of even-numbered carbon monomers among the PHAs. The blending products were identified mainly with scl-PHAs during the 2-month acclimation period and were thereafter dominated by mcl-PHAs until 4 months of acclimation. Thermal properties analysis demonstrated that the products derived from 4-month acclimation were a mixture of scl-PHAs and mcl-PHAs rather than a copolymer of scl-PHAs and mcl-PHAs. High-throughput sequencing results indicated that Pseudofulvimonas, Paracoccus, and Blastocatella were the dominant genera that might be responsible for scl-PHAs production during the 2-month acclimation period, whereas Comamonas and Pseudomonas that were responsible for mcl-PHAs production then became the dominant genera after 4-months acclimation.
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Affiliation(s)
- Zheng Chen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361001 , People's Republic of China
- Department of Environmental Science, School of Environmental Science and Engineering, Tan Kah Kee College , Xiamen University , Zhangzhou 363105 , People's Republic of China
- Zhejiang Provincial Key Laboratory of Watershed Science and Health , Wenzhou Medical University , Wenzhou 325035 , People's Republic of China
- Key Laboratory of Measurement and Control System for Coastal Environment , Fuqing Branch of Fujian Normal University , Fuqing 350300 , People's Republic of China
| | - Chuanpan Zhang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361001 , People's Republic of China
| | - Liang Shen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361001 , People's Republic of China
| | - Heng Li
- Department of Environmental Science, School of Environmental Science and Engineering, Tan Kah Kee College , Xiamen University , Zhangzhou 363105 , People's Republic of China
| | - Yajuan Peng
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361001 , People's Republic of China
| | - Haitao Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361001 , People's Republic of China
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361001 , People's Republic of China
| | - Qingbiao Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361001 , People's Republic of China
- College of Food and Biological Engineering , Jimei University , Xiamen 361021 , People's Republic of China
| | - Yuanpeng Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361001 , People's Republic of China
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Burkholderia xenovorans LB400 possesses a functional polyhydroxyalkanoate anabolic pathway encoded by the pha genes and synthesizes poly(3-hydroxybutyrate) under nitrogen-limiting conditions. Int Microbiol 2018; 21:47-57. [DOI: 10.1007/s10123-018-0004-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/27/2018] [Accepted: 03/27/2018] [Indexed: 10/16/2022]
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Kutralam-Muniasamy G, Corona-Hernandez J, Narayanasamy RK, Marsch R, Pérez-Guevara F. Phylogenetic diversification and developmental implications of poly-(R)-3-hydroxyalkanoate gene cluster assembly in prokaryotes. FEMS Microbiol Lett 2018; 364:3888817. [PMID: 28655209 DOI: 10.1093/femsle/fnx135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/23/2017] [Indexed: 11/13/2022] Open
Abstract
Many polyhydroxyalkanoates (PHAs) system genes, such as phaC, phaA, phaB, phaR, phaP and phaZ, are often found to be organised in the form of operon-like clusters. In this study, a genome survey was performed to identify such clustered PHA systems among 256 prokaryotic organisms. These data were then used to generate a comprehensive 16S rRNA species tree depicting the phylogenetic distribution of the observed clusters with diverse gene arrangements. In addition, the gene occurrences and physical linkages between PHA system genes were quantitatively estimated. From this, we identified a centrally connected hub gene, i.e. the phaC gene of PHA. Furthermore, a comparative investigation was performed between the clusters of PHA and glycogen, which decoded the role of the hub gene in the cluster organisation of both systems. Together, these findings suggest that the highly connected hub gene might contribute substantively towards the organisation and maintenance of the gene network connectivity in the clusters, particularly in the storage reserve systems.
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Affiliation(s)
- Gurusamy Kutralam-Muniasamy
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
| | - Juan Corona-Hernandez
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
| | - Ravi-Kumar Narayanasamy
- Department of Infectomics y Molecular Pathogenesis, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
| | - Rodolfo Marsch
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
| | - Fermín Pérez-Guevara
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México.,Nanoscience and Nanotechnology Program, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, México D.F. 07360, México
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Tiso T, Zauter R, Tulke H, Leuchtle B, Li WJ, Behrens B, Wittgens A, Rosenau F, Hayen H, Blank LM. Designer rhamnolipids by reduction of congener diversity: production and characterization. Microb Cell Fact 2017; 16:225. [PMID: 29241456 PMCID: PMC5729600 DOI: 10.1186/s12934-017-0838-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 12/05/2017] [Indexed: 01/19/2023] Open
Abstract
Background Rhamnolipids are biosurfactants featuring surface-active properties that render them suitable for a broad range of industrial applications. These properties include their emulsification and foaming capacity, critical micelle concentration, and ability to lower surface tension. Further, aspects like biocompatibility and environmental friendliness are becoming increasingly important. Rhamnolipids are mainly produced by pathogenic bacteria like Pseudomonas aeruginosa. We previously designed and constructed a recombinant Pseudomonas putida KT2440, which synthesizes rhamnolipids by decoupling production from host-intrinsic regulations and cell growth. Results Here, the molecular structure of the rhamnolipids, i.e., different congeners produced by engineered P. putida are reported. Natural rhamnolipid producers can synthesize mono- and di-rhamnolipids, containing one or two rhamnose molecules, respectively. Of each type of rhamnolipid four main congeners are produced, deviating in the chain lengths of the β-hydroxy-fatty acids. The resulting eight main rhamnolipid congeners with variable numbers of hydrophobic/hydrophilic residues and their mixtures feature different physico-chemical properties that might lead to diverse applications. We engineered a microbial cell factory to specifically produce three different biosurfactant mixtures: a mixture of di- and mono-rhamnolipids, mono-rhamnolipids only, and hydroxyalkanoyloxy alkanoates, the precursors of rhamnolipid synthesis, consisting only of β-hydroxy-fatty acids. To support the possibility of second generation biosurfactant production with our engineered microbial cell factory, we demonstrate rhamnolipid production from sustainable carbon sources, including glycerol and xylose. A simple purification procedure resulted in biosurfactants with purities of up to 90%. Finally, through determination of properties specific for surface active compounds, we were able to show that the different mixtures indeed feature different physico-chemical characteristics. Conclusions The approach demonstrated here is a first step towards the production of designer biosurfactants, tailor-made for specific applications by purposely adjusting the congener composition of the mixtures. Not only were we able to genetically engineer our cell factory to produce specific biosurfactant mixtures, but we also showed that the products are suited for different applications. These designer biosurfactants can be produced as part of a biorefinery from second generation carbon sources such as xylose. Electronic supplementary material The online version of this article (10.1186/s12934-017-0838-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Till Tiso
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Rabea Zauter
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Hannah Tulke
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Bernd Leuchtle
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Wing-Jin Li
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Beate Behrens
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, 48149, Münster, Germany.,Doehler GmbH, Riedstraße 7-9, 64295, Darmstadt, Germany
| | - Andreas Wittgens
- Ulm Center for Peptide Pharmaceuticals (U-PEP), Ulm-University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Frank Rosenau
- Ulm Center for Peptide Pharmaceuticals (U-PEP), Ulm-University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Lars Mathias Blank
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
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Ray S, Kalia VC. Biomedical Applications of Polyhydroxyalkanoates. Indian J Microbiol 2017; 57:261-269. [PMID: 28904409 PMCID: PMC5574769 DOI: 10.1007/s12088-017-0651-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/20/2017] [Indexed: 12/24/2022] Open
Abstract
Polyhydroxyalkanoates (PHA) are produced by a large number of microbes under stress conditions such as high carbon (C) availability and limitations of nutrients such as nitrogen, potassium, phosphorus, magnesium, and oxygen. Here, microbes store C as granules of PHAs-energy reservoir. PHAs have properties, which are quite similar to those of synthetic plastics. The unique properties, which make them desirable materials for biomedical applications is their biodegradability, biocompatibility, and non-toxicity. PHAs have been found suitable for various medical applications: biocontrol agents, drug carriers, biodegradable implants, tissue engineering, memory enhancers, and anticancer agents.
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Affiliation(s)
- Subhasree Ray
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
- Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
- Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
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Zamarro MT, Barragán MJL, Carmona M, García JL, Díaz E. Engineering a bzd cassette for the anaerobic bioconversion of aromatic compounds. Microb Biotechnol 2017; 10:1418-1425. [PMID: 28736925 PMCID: PMC5658619 DOI: 10.1111/1751-7915.12746] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 05/11/2017] [Accepted: 05/11/2017] [Indexed: 01/26/2023] Open
Abstract
Microorganisms able to degrade aromatic contaminants constitute potential valuable biocatalysts to deal with a significant reusable carbon fraction suitable for eco‐efficient valorization processes. Metabolic engineering of anaerobic pathways for degradation and recycling of aromatic compounds is an almost unexplored field. In this work, we present the construction of a functional bzd cassette encoding the benzoyl‐CoA central pathway for the anaerobic degradation of benzoate. The bzd cassette has been used to expand the ability of some denitrifying bacteria to use benzoate as sole carbon source under anaerobic conditions, and it paves the way for future pathway engineering of efficient anaerobic biodegraders of aromatic compounds whose degradation generates benzoyl‐CoA as central intermediate. Moreover, a recombinant Azoarcus sp. CIB strain harbouring the bzd cassette was shown to behave as a valuable biocatalyst for anaerobic toluene valorization towards the synthesis of poly‐3‐hydroxybutyrate (PHB), a biodegradable and biocompatible polyester of increasing biotechnological interest as a sustainable alternative to classical oil‐derived polymers.
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Affiliation(s)
- María Teresa Zamarro
- Centro de Investigaciones Biológicas, CSIC, C/Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - María J L Barragán
- Centro de Investigaciones Biológicas, CSIC, C/Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Manuel Carmona
- Centro de Investigaciones Biológicas, CSIC, C/Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - José Luis García
- Centro de Investigaciones Biológicas, CSIC, C/Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Eduardo Díaz
- Centro de Investigaciones Biológicas, CSIC, C/Ramiro de Maeztu, 9, 28040, Madrid, Spain
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Andin N, Longieras A, Veronese T, Marcato F, Molina-Jouve C, Uribelarrea JL. Improving carbon and energy distribution by coupling growth and medium chain length polyhydroxyalkanoate production from fatty acids by Pseudomonas putida KT2440. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-016-0449-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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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45
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García-Hidalgo J, Acebal C, de la Mata I, Arroyo M. Developing an efficient strategy for immobilization of PHB depolymerase on magnetite-based nanoparticles for degrading polyhydroxybutyrate in acidic conditions. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1315942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Javier García-Hidalgo
- Departamento de Bioquímica y Biología Molecular I, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Carmen Acebal
- Departamento de Bioquímica y Biología Molecular I, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Isabel de la Mata
- Departamento de Bioquímica y Biología Molecular I, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Miguel Arroyo
- Departamento de Bioquímica y Biología Molecular I, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
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Licciardello G, Ferraro R, Russo M, Strozzi F, Catara AF, Bella P, Catara V. Transcriptome analysis of Pseudomonas mediterranea and P. corrugata plant pathogens during accumulation of medium-chain-length PHAs by glycerol bioconversion. N Biotechnol 2016; 37:39-47. [PMID: 27445200 DOI: 10.1016/j.nbt.2016.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 06/11/2016] [Accepted: 07/16/2016] [Indexed: 11/30/2022]
Abstract
Pseudomonas corrugata and P. mediterranea are soil inhabitant bacteria, generally living as endophytes on symptomless plants and bare soil, but also capable of causing plant diseases. They share a similar genome size and a high proteome similarity. P. corrugata produces many biomolecules which play an important role in bacterial cell survival and fitness. Both species produce different medium-chain-length PHAs (mcl-PHAs) from the bioconversion of glycerol to a transparent film in P. mediterranea and a sticky elastomer in P. corrugata. In this work, using RNA-seq we investigated the transcriptional profiles of both bacteria at the early stationary growth phase with glycerol as the carbon source. Quantitative analysis of P. mediterranea transcripts versus P. corrugata revealed that 1756 genes were differentially expressed. A total of 175 genes were significantly upregulated in P. mediterranea, while 217 were downregulated. The largest group of upregulated genes was related to transport systems and stress response, energy and central metabolism, and carbon metabolism. Expression levels of most genes coding for enzymes related to PHA biosynthesis and central metabolic pathways showed no differences or only slight variations in pyruvate metabolism. The most relevant result was the significantly increased expression in P. mediterranea of genes involved in alginate production, an important exopolysaccharide, which in other Pseudomonas spp. plays a key role as a virulence factor or in stress tolerance and shows many industrial applications. In conclusion, the results provide useful information on the co-production of mcl-PHAs and alginate from glycerol as carbon source by P. mediterranea in the design of new strategies of genetic regulation to improve the yield of bioproducts or bacterial fitness.
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Affiliation(s)
- Grazia Licciardello
- Parco Scientifico e Tecnologico della Sicilia s.c.p.a. Via V. Lancia 57, 95121 Catania, Italy.
| | - Rosario Ferraro
- Parco Scientifico e Tecnologico della Sicilia s.c.p.a. Via V. Lancia 57, 95121 Catania, Italy
| | - Marcella Russo
- Parco Scientifico e Tecnologico della Sicilia s.c.p.a. Via V. Lancia 57, 95121 Catania, Italy
| | - Francesco Strozzi
- Parco Tecnologico Padano, via Einstein - Loc. Cascina Codazza 26900, Lodi, Italy
| | - Antonino F Catara
- Parco Scientifico e Tecnologico della Sicilia s.c.p.a. Via V. Lancia 57, 95121 Catania, Italy
| | - Patrizia Bella
- Dipartimento di Scienze Agrarie e Forestali Università degli Studi di Palermo, Viale delle Scienze, 13, 90128, Palermo, Italy
| | - Vittoria Catara
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Via S. Sofia 100, 95123 Catania Italy
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47
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Cheng J, Charles TC. Novel polyhydroxyalkanoate copolymers produced in Pseudomonas putida by metagenomic polyhydroxyalkanoate synthases. Appl Microbiol Biotechnol 2016; 100:7611-27. [PMID: 27333909 DOI: 10.1007/s00253-016-7666-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/01/2016] [Accepted: 06/04/2016] [Indexed: 10/21/2022]
Abstract
Bacterially produced biodegradable polyhydroxyalkanoates (PHAs) with versatile properties can be achieved using different PHA synthases (PhaCs). This work aims to expand the diversity of known PhaCs via functional metagenomics and demonstrates the use of these novel enzymes in PHA production. Complementation of a PHA synthesis-deficient Pseudomonas putida strain with a soil metagenomic cosmid library retrieved 27 clones expressing either class I, class II, or unclassified PHA synthases, and many did not have close sequence matches to known PhaCs. The composition of PHA produced by these clones was dependent on both the supplied growth substrates and the nature of the PHA synthase, with various combinations of short-chain-length (SCL) and medium-chain-length (MCL) PHA. These data demonstrate the ability to isolate diverse genes for PHA synthesis by functional metagenomics and their use for the production of a variety of PHA polymer and copolymer mixtures.
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Affiliation(s)
- Jiujun Cheng
- Department of Biology and Centre for Bioengineering and Biotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Trevor C Charles
- Department of Biology and Centre for Bioengineering and Biotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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48
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Bresan S, Sznajder A, Hauf W, Forchhammer K, Pfeiffer D, Jendrossek D. Polyhydroxyalkanoate (PHA) Granules Have no Phospholipids. Sci Rep 2016; 6:26612. [PMID: 27222167 PMCID: PMC4879537 DOI: 10.1038/srep26612] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/05/2016] [Indexed: 12/11/2022] Open
Abstract
Polyhydroxybutyrate (PHB) granules, also designated as carbonosomes, are supra-molecular complexes in prokaryotes consisting of a PHB polymer core and a surface layer of structural and functional proteins. The presence of suspected phospholipids in the surface layer is based on in vitro data of isolated PHB granules and is often shown in cartoons of the PHB granule structure in reviews on PHB metabolism. However, the in vivo presence of a phospholipid layer has never been demonstrated. We addressed this topic by the expression of fusion proteins of DsRed2EC and other fluorescent proteins with the phospholipid-binding domain (LactC2) of lactadherin in three model organisms. The fusion proteins specifically localized at the cell membrane of Ralstonia eutropha but did not co-localize with PHB granules. The same result was obtained for Pseudomonas putida, a species that accumulates another type of polyhydroxyalkanoate (PHA) granules related to PHB. Notably, DsRed2EC-LactC2 expressed in Magnetospirillum gryphiswaldense was detected at the position of membrane-enclosed magnetosome chains and at the cytoplasmic membrane but not at PHB granules. In conclusion, the carbonosomes of representatives of α-proteobacteria, β-proteobacteria and γ-proteobacteria have no phospholipids in vivo and we postulate that the PHB/PHA granule surface layers in natural producers generally are free of phospholipids and consist of proteins only.
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Affiliation(s)
| | - Anna Sznajder
- Institute of Microbiology, University Stuttgart, Germany
| | - Waldemar Hauf
- Department of Organismic Interactions, Eberhard Karls Universität Tübingen, Germany
| | - Karl Forchhammer
- Department of Organismic Interactions, Eberhard Karls Universität Tübingen, Germany
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49
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Engineering a predatory bacterium as a proficient killer agent for intracellular bio-products recovery: The case of the polyhydroxyalkanoates. Sci Rep 2016; 6:24381. [PMID: 27087466 PMCID: PMC4834554 DOI: 10.1038/srep24381] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/22/2016] [Indexed: 02/04/2023] Open
Abstract
This work examines the potential of the predatory bacterium Bdellovibrio bacteriovorus HD100, an obligate predator of other Gram-negative bacteria, as an external cell-lytic agent for recovering valuable intracellular bio-products produced by prey cultures. The bio-product targets to be recovered were polyhydroxyalkanoates (PHAs) produced naturally by Pseudomonas putida and Cupriavidus necator, or by recombinant Escherichia coli strains. B. bacteriovorus with a mutated PHA depolymerase gene to prevent the unwanted breakdown of the bio-product allowed the recovery of up to 80% of that accumulated by the prey bacteria, even at high biomass concentrations. This innovative downstream process highlights how B. bacteriovorus can be used as a novel, biological lytic agent for the inexpensive, industrial scale recovery of intracellular products from different Gram-negative prey cultures.
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50
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Beuker J, Steier A, Wittgens A, Rosenau F, Henkel M, Hausmann R. Integrated foam fractionation for heterologous rhamnolipid production with recombinant Pseudomonas putida in a bioreactor. AMB Express 2016; 6:11. [PMID: 26860613 PMCID: PMC4747948 DOI: 10.1186/s13568-016-0183-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 01/29/2016] [Indexed: 11/10/2022] Open
Abstract
Heterologeous production of rhamnolipids in Pseudomonas putida is characterized by advantages of a non-pathogenic host and avoidance of the native quorum sensing regulation in Pseudomonas aeruginosa. Yet, downstream processing is a major problem in rhamnolipid production and increases in complexity at low rhamnolipid titers and when using chemical foam control. This leaves the necessity of a simple concentrating and purification method. Foam fractionation is an elegant method for in situ product removal when producing microbial surfactants. However, up to now in situ foam fractionation is nearly exclusively reported for the production of surfactin with Bacillus subtilis. So far no cultivation integrated foam fractionation process for rhamnolipid production has been reported. This is probably due to excessive bacterial foam enrichment in that system. In this article a simple integrated foam fractionation process is reported for heterologous rhamnolipid production in a bioreactor with easily manageable bacterial foam enrichments. Rhamnolipids were highly concentrated in the foam during the cultivation process with enrichment factors up to 200. The described process was evaluated at different pH, media compositions and temperatures. Foam fractionation processes were characterized by calculating procedural parameter including rhamnolipid and bacterial enrichment, rhamnolipid recovery, YX/S, YP/X, and specific as well as volumetric productivities. Comparing foam fractionation parameters of the rhamnolipid process with the surfactin process a high effectiveness of the integrated foam fractionation for rhamnolipid production was demonstrated.
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