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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Blanco FG, Machatschek R, Keller M, Hernández-Arriaga AM, Godoy MS, Tarazona NA, Prieto MA. Nature-inspired material binding peptides with versatile polyester affinities and binding strengths. Int J Biol Macromol 2023; 253:126760. [PMID: 37683751 DOI: 10.1016/j.ijbiomac.2023.126760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
Biodegradable polyesters, such as polyhydroxyalkanoates (PHAs), are having a tremendous impact on biomedicine. However, these polymers lack functional moieties to impart functions like targeted delivery of molecules. Inspired by native GAPs, such as phasins and their polymer-binding and surfactant properties, we generated small material binding peptides (MBPs) for polyester surface functionalization using a rational approach based on amphiphilicity. Here, two peptides of 48 amino acids derived from phasins PhaF and PhaI from Pseudomonas putida, MinP and the novel-designed MinI, were assessed for their binding towards two types of PHAs, PHB and PHOH. In vivo, fluorescence studies revealed selective binding towards PHOH, whilst in vitro binding experiments using the Langmuir-Blodgett technique coupled to ellipsometry showed KD in the range of nM for all polymers and MBPs. Marked morphological changes of the polymer surface upon peptide adsorption were shown by BAM and AFM for PHOH. Moreover, both MBPs were successfully used to immobilize cargo proteins on the polymer surfaces. Altogether, this work shows that by redesigning the amphiphilicity of phasins, a high affinity but lower specificity to polyesters can be achieved in vitro. Furthermore, the MBPs demonstrated binding to PET, showing potential to bind cargo molecules also to synthetic polyesters.
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Affiliation(s)
- Francisco G Blanco
- Polymer Biotechnology Group, Plant and Microbial Biotechnology Department, Margarita Salas Centre for Biological Research (CIB - CSIC), Madrid, Spain; Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Rainhard Machatschek
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, Kantstraße 55, 14513 Teltow, Germany
| | - Manuela Keller
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, Kantstraße 55, 14513 Teltow, Germany
| | - Ana M Hernández-Arriaga
- Polymer Biotechnology Group, Plant and Microbial Biotechnology Department, Margarita Salas Centre for Biological Research (CIB - CSIC), Madrid, Spain; Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Manuel S Godoy
- Polymer Biotechnology Group, Plant and Microbial Biotechnology Department, Margarita Salas Centre for Biological Research (CIB - CSIC), Madrid, Spain; Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Natalia A Tarazona
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, Kantstraße 55, 14513 Teltow, Germany.
| | - M Auxiliadora Prieto
- Polymer Biotechnology Group, Plant and Microbial Biotechnology Department, Margarita Salas Centre for Biological Research (CIB - CSIC), Madrid, Spain; Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Blanco FG, Vázquez R, Hernández-Arriaga AM, García P, Prieto MA. Enzybiotic-mediated antimicrobial functionalization of polyhydroxyalkanoates. Front Bioeng Biotechnol 2023; 11:1220336. [PMID: 37449090 PMCID: PMC10336440 DOI: 10.3389/fbioe.2023.1220336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Polymeric nanoparticles (NPs) present some ideal properties as biomedical nanocarriers for targeted drug delivery such as enhanced translocation through body barriers. Biopolymers, such as polyhydroxyalkanoates (PHAs) are gaining attention as nanocarrier biomaterials due to their inherent biocompatibility, biodegradability, and ability to be vehiculized through hydrophobic media, such as the lung surfactant (LS). Upon colonization of the lung alveoli, below the LS layer, Streptococcus pneumoniae, causes community-acquired pneumonia, a severe respiratory condition. In this work, we convert PHA NPs into an antimicrobial material by the immobilization of an enzybiotic, an antimicrobial enzyme, via a minimal PHA affinity tag. We first produced the fusion protein M711, comprising the minimized PHA affinity tag, MinP, and the enzybiotic Cpl-711, which specifically targets S. pneumoniae. Then, a PHA nanoparticulate suspension with adequate physicochemical properties for pulmonary delivery was formulated, and NPs were decorated with M711. Finally, we assessed the antipneumococcal activity of the nanosystem against planktonic and biofilm forms of S. pneumoniae. The resulting system displayed sustained antimicrobial activity against both, free and sessile cells, confirming that tag-mediated immobilization of enzybiotics on PHAs is a promising platform for bioactive antimicrobial functionalization.
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Affiliation(s)
- Francisco G. Blanco
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Margarita Salas Center for Biological Research (CIB–CSIC), Madrid, Spain
- Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Roberto Vázquez
- Protein Engineering Against Antibiotic Resistance Group, Microbial and Plant Biotechnology Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Ana M. Hernández-Arriaga
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Margarita Salas Center for Biological Research (CIB–CSIC), Madrid, Spain
- Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Pedro García
- Protein Engineering Against Antibiotic Resistance Group, Microbial and Plant Biotechnology Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - M. Auxiliadora Prieto
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Margarita Salas Center for Biological Research (CIB–CSIC), Madrid, Spain
- Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
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Goswami M, Rekhi P, Debnath M, Ramakrishna S. Microbial Polyhydroxyalkanoates Granules: An Approach Targeting Biopolymer for Medical Applications and Developing Bone Scaffolds. Molecules 2021; 26:860. [PMID: 33562111 PMCID: PMC7915662 DOI: 10.3390/molecules26040860] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
Microbial polyhydroxyalkanoates (PHA) are proteinaceous storage granules ranging from 100 nm to 500 nm. Bacillus sp. serve as unique bioplastic sources of short-chain length and medium-chain length PHA showcasing properties such as biodegradability, thermostability, and appreciable mechanical strength. The PHA can be enhanced by adding functional groups to make it a more industrially useful biomaterial. PHA blends with hydroxyapatite to form nanocomposites with desirable features of compressibility. The reinforced matrices result in nanocomposites that possess significantly improved mechanical and thermal properties both in solid and melt states along with enhanced gas barrier properties compared to conventional filler composites. These superior qualities extend the polymeric composites' applications to aggressive environments where the neat polymers are likely to fail. This nanocomposite can be used in different industries as nanofillers, drug carriers for packaging essential hormones and microcapsules, etc. For fabricating a bone scaffold, electrospun nanofibrils made from biocomposite of hydroxyapatite and polyhydroxy butyrate, a form of PHA, can be incorporated with the targeted tissue. The other methods for making a polymer scaffold, includes gas foaming, lyophilization, sol-gel, and solvent casting method. In this review, PHA as a sustainable eco-friendly NextGen biomaterial from bacterial sources especially Bacillus cereus, and its application for fabricating bone scaffold using different strategies for bone regeneration have been discussed.
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Affiliation(s)
- Moushmi Goswami
- Department of Biosciences, Manipal University Jaipur, Rajasthan 303007, India; (M.G.); (P.R.)
| | - Pavni Rekhi
- Department of Biosciences, Manipal University Jaipur, Rajasthan 303007, India; (M.G.); (P.R.)
| | - Mousumi Debnath
- Department of Biosciences, Manipal University Jaipur, Rajasthan 303007, India; (M.G.); (P.R.)
| | - Seeram Ramakrishna
- Department of Mechanical Engineering, National University of Singapore, Singapore 119260, Singapore;
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