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Ismail S, Giacinti G, Raynaud CD, Cameleyre X, Alfenore S, Guillouet S, Gorret N. Impact of the environmental parameters on single cell protein production and composition by Cupriavidus necator. J Biotechnol 2024; 388:83-95. [PMID: 38621427 DOI: 10.1016/j.jbiotec.2024.04.009] [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: 11/17/2023] [Revised: 01/26/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
Due to the rapid increase in the world's population, many developing countries are facing malnutrition problems, including famine and food insecurity. Particularly, the deficiency of protein sources becomes a serious problem for human and animal nutrition. In this context, Single Cell Proteins, could be exploited as an alternative source of unconventional proteins. The aim of the study was to investigate SCP production and composition by Cupriavidus necator under various environmental conditions, temperature and pH values. A mono-factorial approach was implemented using batch bioreactor cultures under well-controlled conditions. Results were compared in terms of bacterial growth and SCP composition (proteins, nucleic acids, amino acids and elemental formula). Complementary analyses were performed by flow cytometry to study cell morphology, membrane permeability and the presence of Poly(3-hydroxybutyrate) (PHB) production. Our data confirmed the ability of C. necator to produce high amount of proteins (69 %DW at 30 °C and pH7). The results showed that temperature and pH independently impact SCP production and composition. This impact was particularly observed at the highest temperature (40 °C) and also the lowest pH value (pH5) providing lower growth rates, cell elongation, changes in granularity and lower amounts of proteins (down to 44 %DW at pH5) and nucleic acids. These low percentages were related to the production of PHB production (up to 44 %DW at 40 °C) which is the first report of a PHB accumulation in C. necator under nutrient unlimited conditions.
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Affiliation(s)
- Siwar Ismail
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Géraldine Giacinti
- Laboratoire de Chimie Agro-Industrielle, LCA, Université de Toulouse, INRAe, Toulouse, France; Centre d'Application et de Traitement des Agro-Ressources (CATAR), Toulouse-INP, Toulouse, France
| | - Christine Delagado Raynaud
- Laboratoire de Chimie Agro-Industrielle, LCA, Université de Toulouse, INRAe, Toulouse, France; Centre d'Application et de Traitement des Agro-Ressources (CATAR), Toulouse-INP, Toulouse, France
| | - Xavier Cameleyre
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | | | - Nathalie Gorret
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
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Wang L, Yao J, Tu T, Yao B, Zhang J. Heterotrophic and autotrophic production of L-isoleucine and L-valine by engineered Cupriavidus necator H16. BIORESOURCE TECHNOLOGY 2024; 398:130538. [PMID: 38452952 DOI: 10.1016/j.biortech.2024.130538] [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: 12/23/2023] [Revised: 02/14/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Advancement in commodity chemical production from carbon dioxide (CO2) offers a promising path towards sustainable development goal. Cupriavidus necator is an ideal host to convert CO2 into high-value chemicals, thereby achieving this target. Here, C. necator was engineered for heterotrophic and autotrophic production of L-isoleucine and L-valine. Citramalate synthase was introduced to simplify isoleucine synthesis pathway. Blocking poly-hydroxybutyrate biosynthesis resulted in significant accumulation of isoleucine and valine. Besides, strategies like key enzymes screening and overexpressing, reducing power balancing and feedback inhibition removing were applied in strain modification. Finally, the maximum isoleucine and valine titers of the best isoleucine-producing and valine-producing strains reached 857 and 972 mg/L, respectively, in fed-batch fermentation using glucose as substrate, and 105 and 319 mg/L, respectively, in autotrophic fermentation using CO2 as substrate. This study provides a feasible solution for developing C. necator as a microbial factory to produce amino acids from CO2.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Diankristanti PA, Lin YC, Yi YC, Ng IS. Polyhydroxyalkanoates bioproduction from bench to industry: Thirty years of development towards sustainability. BIORESOURCE TECHNOLOGY 2024; 393:130149. [PMID: 38049017 DOI: 10.1016/j.biortech.2023.130149] [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: 11/09/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
The pursuit of carbon neutrality goals has sparked considerable interest in expanding bioplastics production from microbial cell factories. One prominent class of bioplastics, polyhydroxyalkanoates (PHA), is generated by specific microorganisms, serving as carbon and energy storage materials. To begin with, a native PHA producer, Cupriavidus necator (formerly Ralstonia eutropha) is extensively studied, covering essential topics such as carbon source selection, cultivation techniques, and accumulation enhancement strategies. Recently, various hosts including archaea, bacteria, cyanobacteria, yeast, and plants have been explored, stretching the limit of microbial PHA production. This review provides a comprehensive overview of current advancements in PHA bioproduction, spanning from the native to diversified cell factories. Recovery and purification techniques are discussed, and the current status of industrial applications is assessed as a critical milestone for startups. Ultimately, it concludes by addressing contemporary challenges and future prospects, offering insights into the path towards reduced carbon emissions and sustainable development goals.
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Affiliation(s)
| | - Yu-Chieh Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Ying-Chen Yi
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan; Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, USA
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan.
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Chacón M, Wongsirichot P, Winterburn J, Dixon N. Genetic and process engineering for polyhydroxyalkanoate production from pre- and post-consumer food waste. Curr Opin Biotechnol 2024; 85:103024. [PMID: 38056203 DOI: 10.1016/j.copbio.2023.103024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Biopolymers produced as microbial carbon storage systems, such as polyhydroxyalkanoates (PHAs), offer potential to be used in place of petrochemically derived plastics. Low-value organic feedstocks, such as food waste, have been explored as a potential substrate for the microbial production of PHAs. In this review, we discuss the biosynthesis, composition and producers of PHAs, with a particular focus on the genetic and process engineering efforts to utilise non-native substrates, derived from food waste from across the entire supply chain, for microbial growth and PHA production. We highlight a series of studies that have achieved impressive advances and discuss the challenges of producing PHAs with consistent composition and properties from mixed and variable food waste and by-products.
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Affiliation(s)
- Micaela Chacón
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester M1 7DN, UK
| | - Phavit Wongsirichot
- Department of Chemical Engineering, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - James Winterburn
- Department of Chemical Engineering, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Neil Dixon
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester M1 7DN, UK.
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Wang L, Luo H, Yao B, Yao J, Zhang J. Optimizing Hexose Utilization Pathways of Cupriavidus necator for Improving Growth and L-Alanine Production under Heterotrophic and Autotrophic Conditions. Int J Mol Sci 2023; 25:548. [PMID: 38203719 PMCID: PMC10778655 DOI: 10.3390/ijms25010548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Cupriavidus necator is a versatile microbial chassis to produce high-value products. Blocking the poly-β-hydroxybutyrate synthesis pathway (encoded by the phaC1AB1 operon) can effectively enhance the production of C. necator, but usually decreases cell density in the stationary phase. To address this problem, we modified the hexose utilization pathways of C. necator in this study by implementing strategies such as blocking the Entner-Doudoroff pathway, completing the phosphopentose pathway by expressing the gnd gene (encoding 6-phosphogluconate dehydrogenase), and completing the Embden-Meyerhof-Parnas pathway by expressing the pfkA gene (encoding 6-phosphofructokinase). During heterotrophic fermentation, the OD600 of the phaC1AB1-knockout strain increased by 44.8% with pfkA gene expression alone, and by 93.1% with gnd and pfkA genes expressing simultaneously. During autotrophic fermentation, gnd and pfkA genes raised the OD600 of phaC1AB1-knockout strains by 19.4% and 12.0%, respectively. To explore the effect of the pfkA gene on the production of C. necator, an alanine-producing C. necator was constructed by expressing the NADPH-dependent L-alanine dehydrogenase, alanine exporter, and knocking out the phaC1AB1 operon. The alanine-producing strain had maximum alanine titer and yield of 784 mg/L and 11.0%, respectively. And these values were significantly improved to 998 mg/L and 13.4% by expressing the pfkA gene. The results indicate that completing the Embden-Meyerhof-Parnas pathway by expressing the pfkA gene is an effective method to improve the growth and production of C. necator.
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Affiliation(s)
- Lei Wang
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (L.W.); (B.Y.)
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Bin Yao
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (L.W.); (B.Y.)
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (L.W.); (B.Y.)
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
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Ishihara S, Orita I, Matsumoto K, Fukui T. (R/S)-lactate/2-hydroxybutyrate dehydrogenases in and biosynthesis of block copolyesters by Ralstonia eutropha. Appl Microbiol Biotechnol 2023; 107:7557-7569. [PMID: 37773219 PMCID: PMC10656315 DOI: 10.1007/s00253-023-12797-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 10/01/2023]
Abstract
Bacterial polyhydroxyalkanoates (PHAs) are promising bio-based biodegradable polyesters. It was recently reported that novel PHA block copolymers composed of (R)-3-hydroxybutyrate (3HB) and (R)-2-hydroxybutyrate (2HB) were synthesized by Escherichia coli expressing PhaCAR, a chimeric enzyme of PHA synthases derived from Aeromonas caviae and Ralstonia eutropha. In this study, the sequence-regulating PhaCAR was applied in the natural PHA-producing bacterium, R. eutropha. During the investigation, (R/S)-2HB was found to exhibit strong growth inhibitory effects on the cells of R. eutropha. This was probably due to formation of excess 2-ketobutyrate (2KB) from (R/S)-2HB and the consequent L-valine depletion caused by dominant L-isoleucine synthesis attributed to the excess 2KB. Deletion analyses for genes of lactate dehydrogenase homologs identified cytochrome-dependent D-lactate dehydrogenase (Dld) and [Fe-S] protein-dependent L-lactate dehydrogenase as the enzymes responsible for sensitivity to (R)-2HB and (S)-2HB, respectively. The engineered R. eutropha strain (phaCAR+, ldhACd-hadACd+ encoding clostridial (R)-2-hydroxyisocaproate dehydrogenase and (R)-2-hydoroxyisocaproate CoA transferase, ∆dld) synthesized PHA containing 10 mol% of 2HB when cultivated on glucose with addition of sodium (RS)-2HB, and the 2HB composition in PHA increased up to 35 mol% by overexpression phaCAR. The solvent fractionation and NMR analyses showed that the resulting PHAs were most likely to be block polymers consisting of P(3HB-co-3HV) and P(2HB) segments, suggesting that PhaCAR functions as the sequence-regulating PHA synthase independently from genetic and metabolic backgrounds of the host cell. KEY POINTS: (R/S)-2-hydroxubutyrates (2HB) caused l-valine deletion in Ralstonia eutropha (R)- and (S)-lactate/2HB dehydrogenases functional in R. eutropha were identified The engineered R. eutropha synthesized block copolymers of 2HB-containing polyhydroxyalkanoates on glucose and 2HB.
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Affiliation(s)
- Shizuru Ishihara
- School of Life Science and Technology, Tokyo Institute of Technology, B-37 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
| | - Izumi Orita
- School of Life Science and Technology, Tokyo Institute of Technology, B-37 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
| | - Ken'ichiro Matsumoto
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, N13W8, Kita-ku, Sapporo, 060-8628, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, B-37 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
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González-Rojo S, Paniagua-García AI, Díez-Antolínez R. Biotransformation of starch-based wastewater into bioplastics: Optimization of poly(3-hydroxybutyrate) production by Cupriavidus necator DSM 545 using potato wastewater hydrolysate. WATER RESEARCH 2023; 247:120766. [PMID: 37897996 DOI: 10.1016/j.watres.2023.120766] [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: 07/27/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
Biodegradable biopolymers, such as polyhydroxyalkanoates (PHAs), have emerged as an alternative to petrochemical-based plastics. The present work explores the production of PHAs based on the biotransformation of potato processing wastewater and addresses two different strategies for PHA recovery. To this end, culture conditions for PHA synthesis by Cupriavidus necator DSM 545 were optimized on a laboratory scale using a response surface methodology-based experimental design. Optimal conditions rendered a PHB, poly(3-hydroxybutyrate), accumulation of 83.74 ± 2.37 % (5.1 ± 0.2 gL-1), a 1.4-fold increase compared to the initial conditions. Moreover, polymer extraction with non-halogenated agent improved PHB recovery compared to chloroform method (PHB yield up to 78.78 ± 0.57 %), while maintaining PHB purity. (99.83 ± 4.95 %). Overall, the present work demonstrated the potential valorization of starch-based wastewater by biotransformation into PHBs, a high value-added product, and showed that recovery approaches more eco-friendly than the traditional treatments could be applied to PHB recovery to some extent.
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Affiliation(s)
- S González-Rojo
- Centro de Biocombustibles y Bioproductos, Instituto Tecnológico Agrario de Castilla y León (ITACyL), Polígono Agroindustrial del Órbigo p. 2-6, Villarejo de Órbigo 24358, León, Spain.
| | - A I Paniagua-García
- Centro de Biocombustibles y Bioproductos, Instituto Tecnológico Agrario de Castilla y León (ITACyL), Polígono Agroindustrial del Órbigo p. 2-6, Villarejo de Órbigo 24358, León, Spain
| | - R Díez-Antolínez
- Centro de Biocombustibles y Bioproductos, Instituto Tecnológico Agrario de Castilla y León (ITACyL), Polígono Agroindustrial del Órbigo p. 2-6, Villarejo de Órbigo 24358, León, Spain
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An J, Ha B, Lee SK. Production of polyhydroxyalkanoates by the thermophile Cupriavidus cauae PHS1. BIORESOURCE TECHNOLOGY 2023; 371:128627. [PMID: 36646360 DOI: 10.1016/j.biortech.2023.128627] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
Thermophilic production of polyhydroxyalkanoate is considered a very promising way to overcome the problems that may arise when using mesophilic strains. This study reports the first thermophilic polyhydroxybutyrate-producing Cupriavidus species, which are known as the best polyhydroxybutyrate-producing microorganisms. Cupriavidus cauae PHS1 harbors a phbCABR cluster with high similarity to the corresponding proteins of C. necator H16 (80, 93, 96, and 97 %). This strain can produce polyhydroxybutyrate from a range of substrates, including acetate (5 g/L) and phenol (1 g/L), yielding 7.6 % and 18.9 % polyhydroxybutyrate, respectively. Moreover, the strain produced polyhydroxybutyrate at temperatures ranging from 25 to 50 °C, with the highest polyhydroxybutyrate content (47 °C) observed at 45 °C from gluconate. Additionally, the strain could incorporate 3-hydroxyvalerate (12.5 mol. %) into the polyhydroxybutyrate polymer using levulinic acid as a precursor. Thus, Cupriavidus cauae PHS1 may be a promising polyhydroxybutyrate producer as alternative for mesophilic polyhydroxybutyrate-producing Cupriavidus species.
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Affiliation(s)
- Jeongvin An
- School of Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Boram Ha
- School of Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sung Kuk Lee
- School of Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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Minimizing the Lag Phase of Cupriavidus necator Growth under Autotrophic, Heterotrophic, and Mixotrophic Conditions. Appl Environ Microbiol 2023; 89:e0200722. [PMID: 36719244 PMCID: PMC9972949 DOI: 10.1128/aem.02007-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Cupriavidus necator has the unique metabolic capability to grow under heterotrophic, autotrophic, and mixotrophic conditions. In the current work, we examined the effect of growth conditions on the metabolic responses of C. necator. In our lab-scale experiments, autotrophic growth was rapid, with a short lag phase as the exponential growth stage was initiated in 6 to 12 h. The lag phase extended significantly (>22 h) at elevated O2 and CO2 partial pressures, while the duration of the lag phase was independent of the H2 or N2 partial pressure. Under heterotrophic conditions with acetate as the organic substrate, the lag phase length was short (<12 h), but it increased with increasing acetate concentrations. When glucose and glycerol were provided as the organic substrate, the lag phase was consistently long (>12 h) regardless of the examined substrate concentrations (up to 10.0 g/L). In the transition experiments, C. necator cells showed rapid transitions from autotrophic to heterotrophic growth in less than 12 h and vice versa. Our experimental results indicate that C. necator can rapidly grow with both autotrophic and heterotrophic substrates, while the lag time substantially increases with nonacetate organic substrates (e.g., glucose or glycerol), high acetate concentrations, and high O2 and CO2 partial pressures. IMPORTANCE The current work investigated the inhibition of organic and gaseous substrates on the microbial adaption of Cupriavidus necator under several metabolic conditions commonly employed for commercial polyhydroxyalkanoate production. We also proposed a two-stage cultivation system to minimize the lag time required to change over between the heterotrophic, autotrophic, and mixotrophic pathways.
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Miyahara Y, Wang CT, Ishii-Hyakutake M, Tsuge T. Continuous Supply of Non-Combustible Gas Mixture for Safe Autotrophic Culture to Produce Polyhydroxyalkanoate by Hydrogen-Oxidizing Bacteria. Bioengineering (Basel) 2022; 9:bioengineering9100586. [PMID: 36290554 PMCID: PMC9598887 DOI: 10.3390/bioengineering9100586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 11/26/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are eco-friendly plastics that are thermoplastic and biodegradable in nature. The hydrogen-oxidizing bacterium Ralstonia eutropha can biosynthesize poly[(R)-3-hydroxybutyrate] [P(3HB)], the most common PHA, from carbon dioxide using hydrogen and oxygen as energy sources. In conventional autotrophic cultivation using R. eutropha, a gas mixture containing 75−80 vol% hydrogen is supplied; however, a gas mixture with such a high hydrogen content has a risk of explosion due to gas leakage. In this study, we aimed to develop an efficient cell culture system with a continuous supply of a non-combustible gas mixture (H2: O2: CO2: N2 = 3.8: 7.3: 13.0: 75.9) for safe autotrophic culture to produce P(3HB) by hydrogen-oxidizing bacteria, with a controlled hydrogen concentration under a lower explosive limit concentration. When the gas mixture was continuously supplied to the jar fermentor, the cell growth of R. eutropha H16 significantly improved compared to that in previous studies using flask cultures. Furthermore, an increased gas flow rate and agitation speed enhanced both cell growth and P(3HB) production. Nitrogen source deficiency promoted P(3HB) production, achieving up to 2.94 g/L P(3HB) and 89 wt% P(3HB) content in the cells after 144 h cultivation. R. eutropha NCIMB 11599, recombinant R. eutropha PHB-4, and Azohydromonas lata grew in a low-hydrogen-content gas mixture. R. eutropha H16 and recombinant R. eutropha PHB-4 expressing PHA synthase from Bacillus cereus YB-4 synthesized P(3HB) with a high weight-average molecular weight of 13.5−16.9 × 105. Thus, this autotrophic culture system is highly beneficial for PHA production from carbon dioxide using hydrogen-oxidizing bacteria as the risk of explosion is eliminated.
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Affiliation(s)
- Yuki Miyahara
- Correspondence: (Y.M.); (T.T.); Tel.: +81-45-924-5420 (T.T.)
| | | | | | - Takeharu Tsuge
- Correspondence: (Y.M.); (T.T.); Tel.: +81-45-924-5420 (T.T.)
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11
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Wang X, Luo H, Wang Y, Wang Y, Tu T, Qin X, Su X, Huang H, Bai Y, Yao B, Zhang J. Direct conversion of carbon dioxide to glucose using metabolically engineered Cupriavidus necator. BIORESOURCE TECHNOLOGY 2022; 362:127806. [PMID: 36031135 DOI: 10.1016/j.biortech.2022.127806] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Artificial synthesis of glucose, the monomer of starch, from renewable resources and CO2 is a promising method for addressing food crisis and alleviating climate change. Here, the construction of a microbial biocatalyst for glucose production from renewable resources and CO2 was reported. Initially, blocking the glucose catabolic pathway via deletion of glk gene generated a glucose-producing strain of Cupriavidus necator with titers of 24.7, 47.5 and 180.1 mg/L from fructose, glycerol and CO2, respectively. Subsequently, the Entner-Doudoroff pathway and polyhydroxybutyrate biosynthesis pathway were disrupted to further increase glucose accumulation. The maximum glucose titer and yield on biomass from CO2 reached 253.3 mg/L and 91.6 mg/L/OD600, respectively. Finally, the phosphatases that mediate the dephosphorylation of phosphorylated glucose were identified. Overexpression of HAD1 and cbbY2 could enhance glucose titer by 5.5-fold when fructose was used as sole carbon source. This study demonstrates a feasible route for microbial-based synthesis of glucose from CO2.
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Affiliation(s)
- Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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12
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Borrero‐de Acuña JM, Poblete‐Castro I. Rational engineering of natural polyhydroxyalkanoates producing microorganisms for improved synthesis and recovery. Microb Biotechnol 2022; 16:262-285. [PMID: 35792877 PMCID: PMC9871526 DOI: 10.1111/1751-7915.14109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
Microbial production of biopolymers derived from renewable substrates and waste streams reduces our heavy reliance on petrochemical plastics. One of the most important biodegradable polymers is the family of polyhydroxyalkanoates (PHAs), naturally occurring intracellular polyoxoesters produced for decades by bacterial fermentation of sugars and fatty acids at the industrial scale. Despite the advances, PHA production still suffers from heavy costs associated with carbon substrates and downstream processing to recover the intracellular product, thus restricting market positioning. In recent years, model-aided metabolic engineering and novel synthetic biology approaches have spurred our understanding of carbon flux partitioning through competing pathways and cellular resource allocation during PHA synthesis, enabling the rational design of superior biopolymer producers and programmable cellular lytic systems. This review describes these attempts to rationally engineering the cellular operation of several microbes to elevate PHA production on specific substrates and waste products. We also delve into genome reduction, morphology, and redox cofactor engineering to boost PHA biosynthesis. Besides, we critically evaluate engineered bacterial strains in various fermentation modes in terms of PHA productivity and the period required for product recovery.
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Affiliation(s)
| | - Ignacio Poblete‐Castro
- Biosystems Engineering LaboratoryDepartment of Chemical and Bioprocess EngineeringUniversidad de Santiago de Chile (USACH)SantiagoChile
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13
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Sohn YJ, Son J, Jo SY, Park SY, Yoo JI, Baritugo KA, Na JG, Choi JI, Kim HT, Joo JC, Park SJ. Chemoautotroph Cupriavidus necator as a potential game-changer for global warming and plastic waste problem: A review. BIORESOURCE TECHNOLOGY 2021; 340:125693. [PMID: 34365298 DOI: 10.1016/j.biortech.2021.125693] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Cupriavidus necator, a versatile microorganism found in both soil and water, can have both heterotrophic and lithoautotrophic metabolisms depending on environmental conditions. C. necator has been extensively examined for producing Polyhydroxyalkanoates (PHAs), the promising polyester alternatives to petroleum-based synthetic polymers because it has a superior ability for accumulating a considerable amount of PHAs from renewable resources. The development of metabolically engineered C. necator strains has led to their application for synthesizing biopolymers, biofuels and biochemicals such as ethanol, isobutanol and higher alcohols. Bio-based processes of recombinant C. necator have made much progress in production of these high-value products from biomass wastes, plastic wastes and even waste gases. In this review, we discuss the potential of C. necator as promising platform host strains that provide a great opportunity for developing a waste-based circular bioeconomy.
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Affiliation(s)
- Yu Jung Sohn
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seo Young Jo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Se Young Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jee In Yoo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Kei-Anne Baritugo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jeong Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea.
| | - Jong-Il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Korea.
| | - Hee Taek Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea.
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Gyeonggi-do, Republic of Korea.
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea.
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14
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Jahn M, Crang N, Janasch M, Hober A, Forsström B, Kimler K, Mattausch A, Chen Q, Asplund-Samuelsson J, Hudson EP. Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator. eLife 2021; 10:69019. [PMID: 34723797 PMCID: PMC8591527 DOI: 10.7554/elife.69019] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/30/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria must balance the different needs for substrate assimilation, growth
functions, and resilience in order to thrive in their environment. Of all
cellular macromolecules, the bacterial proteome is by far the most important
resource and its size is limited. Here, we investigated how the highly versatile
'knallgas' bacterium Cupriavidus necator reallocates protein
resources when grown on different limiting substrates and with different growth
rates. We determined protein quantity by mass spectrometry and estimated enzyme
utilization by resource balance analysis modeling. We found that C.
necator invests a large fraction of its proteome in functions that
are hardly utilized. Of the enzymes that are utilized, many are present in
excess abundance. One prominent example is the strong expression of CBB cycle
genes such as Rubisco during growth on fructose. Modeling and mutant competition
experiments suggest that CO2-reassimilation through Rubisco does not
provide a fitness benefit for heterotrophic growth, but is rather an investment
in readiness for autotrophy.
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Affiliation(s)
- Michael Jahn
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Nick Crang
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Markus Janasch
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Andreas Hober
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Björn Forsström
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Kyle Kimler
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Alexander Mattausch
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Qi Chen
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Asplund-Samuelsson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Elton Paul Hudson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
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15
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Subagyo DCH, Shimizu R, Orita I, Fukui T. Isopropanol production with reutilization of glucose-derived CO 2 by engineered Ralstonia eutropha. J Biosci Bioeng 2021; 132:479-486. [PMID: 34507913 DOI: 10.1016/j.jbiosc.2021.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 12/17/2022]
Abstract
Chemolithoautotrophic bacterium Ralstonia eutropha is a versatile host for production of various useful compounds including polyhydroxyalkanoates (PHAs) under both heterotrophic and autotrophic conditions. In this bacterium, Calvin-Benson-Bassham (CBB) cycle is functional even under heterotrophic conditions on sugars and reutilizes CO2 emitted through sugar metabolisms into PHA, leading to increase in yield of the storage polyester. This study focused on isopropanol production from glucose by engineered strains of R. eutropha. The isopropanol-producing strains were constructed by introduction of codon-optimized genes of acetoacetate decarboxylase (adc) and primary-secondary alcohol dehydrogenase (adh) from clostridia into glucose-utilizing and PHA-negative (ΔphaC1) strain of R. eutropha. Several genetic modifications showed that high expression of the isopropanol synthesis genes by using a strong synthetic promoter and deletion of NAD+-dependent (S)-3-hydroxybutyryl-CoA dehydrogenase genes (paaH1 and had) in addition to NADPH-dependent acetoacetyl-CoA reductase genes (phaB1 and phaB3) were effective for improving isopropanol production with low by-production of acetone. Isopropanol titer of 4.13 g/L was achieved by two-stage cultivation of the strain IP-007/pBj5c2-adh-adc, corresponding to overall yield of 0.6 mol mol-glucose-1. The fixation of sugar-derived CO2 during isopropanol synthesis was evaluated by 13C-labelling of the isopropanol produced from [1-13C]-glucose. The 13C-abundance in isopropanol synthesized by the engineered strain was significantly increased up to 4.8%, demonstrating actual reassimilation of CO2 emitted from glucose moiety by decarboxylation and potential contribution towards increase in the carbon yield of isopropanol on glucose.
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Affiliation(s)
- Dyah Candra Hapsari Subagyo
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Rie Shimizu
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Izumi Orita
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
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16
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Lee SM, Lee HJ, Kim SH, Suh MJ, Cho JY, Ham S, Jeon JM, Yoon JJ, Bhatia SK, Gurav R, Lee EY, Yang YH. Screening of the strictly xylose-utilizing Bacillus sp. SM01 for polyhydroxybutyrate and its co-culture with Cupriavidus necator NCIMB 11599 for enhanced production of PHB. Int J Biol Macromol 2021; 181:410-417. [PMID: 33775761 DOI: 10.1016/j.ijbiomac.2021.03.149] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 11/30/2022]
Abstract
Polyhydroxybutyrate (PHB) is a biodegradable plastic that can be used as an alternative to petrochemical-based plastics. PHB is produced by various microorganisms such as Ralstonia, Halomonas, and Bacillus species. However, there are very few strains that produce PHB using xylose, an abundant and inexpensive carbon source. In this study, ten xylose-utilizing PHB producers isolated from South Korean marine environments were screened and characterized. Among these isolates, Bacillus sp. SM01, a newly identified strain, produced the highest amount of PHB using xylose. Under optimal conditions, the maximum dry cell weight (DCW) was 3.41 ± 0.09 g/L, with 62% PHB content, and Bacillus sp. SM01 showed Poly (3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer production with propionate; however, the growth of Bacillus sp. SM01 was greatly inhibited by the presence of glucose. Co-culturing Bacillus sp. SM01 with Cupriavidus necator NCIMB 11599 resulted in increased DCW, PHB production, and utilization of glucose and xylose, the main sugar of lignocellulosic biomass, compared with the monoculture. Our results indicated that this co-culture system can be used to increase PHB production and overcome the limitation of sugar consumption associated with Bacillus sp. SM01 and C. necator.
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Affiliation(s)
- Sun Mi Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Hong-Ju Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sang Hyun Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Min Ju Suh
- Department of Biological Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jang Yeon Cho
- Department of Biological Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sion Ham
- Department of Biological Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jong-Min Jeon
- Green & Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Chungnam 331-825, Republic of Korea
| | - Jeong-Jun Yoon
- Green & Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Chungnam 331-825, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul 05029, Republic of Korea
| | - Ranjit Gurav
- Department of Biological Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul 05029, Republic of Korea.
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17
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Huong KH, Sevakumaran V, Amirul AA. P(3HB- co-4HB) as high value polyhydroxyalkanoate: its development over recent decades and current advances. Crit Rev Biotechnol 2021; 41:474-490. [PMID: 33726581 DOI: 10.1080/07388551.2020.1869685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Polyhydroxyalkanoate (PHA) is a biogenic polymer that has the potential to substitute synthetic plastic in numerous applications. This is due to its unique attribute of being a biodegradable and biocompatible thermoplastic, achievable through microbial fermentation from a broad utilizable range of renewable resources. Among all the PHAs discovered, poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] stands out as a next generation healthcare biomaterial for having high biopharmaceutical and medical value since it is highly compatible to mammalian tissue. This review provides a critical assessment and complete overview of the development and trend of P(3HB-co-4HB) research over the last few decades, highlighting aspects from the microbial strain discovery to metabolic engineering and bioprocess cultivation strategies. The article also outlines the relevance of P(3HB-co-4HB) as a material for high value-added products in numerous healthcare-related applications.
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Affiliation(s)
- Kai-Hee Huong
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Vigneswari Sevakumaran
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Kuala Terengganu, Terengganu, Malaysia
| | - A A Amirul
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia.,Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia.,Malaysian Institute of Pharmaceuticals and Nutraceuticals, NIBM, Gelugor, Penang, Malaysia
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18
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Biglari N, Orita I, Fukui T, Sudesh K. A study on the effects of increment and decrement repeated fed-batch feeding of glucose on the production of poly(3-hydroxybutyrate) [P(3HB)] by a newly engineered Cupriavidus necator NSDG-GG mutant in batch fill-and-draw fermentation. J Biotechnol 2020; 307:77-86. [DOI: 10.1016/j.jbiotec.2019.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/19/2019] [Accepted: 10/21/2019] [Indexed: 12/23/2022]
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19
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Modification of acetoacetyl-CoA reduction step in Ralstonia eutropha for biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from structurally unrelated compounds. Microb Cell Fact 2019; 18:147. [PMID: 31466527 PMCID: PMC6716841 DOI: 10.1186/s12934-019-1197-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/22/2019] [Indexed: 12/24/2022] Open
Abstract
Background Poly((R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate) [P(3HB-co-3HHx)] is a bacterial polyester with high biodegradability, even in marine environments. Ralstonia eutropha has been engineered for the biosynthesis of P(3HB-co-3HHx) from vegetable oils, but its production from structurally unrelated carbon sources remains unsatisfactory. Results Ralstonia eutropha strains capable of synthesizing P(3HB-co-3HHx) from not only fructose but also glucose and glycerol were constructed by integrating previously established engineering strategies. Further modifications were made at the acetoacetyl-CoA reduction step determining flux distribution responsible for the copolymer composition. When the major acetoacetyl-CoA reductase (PhaB1) was replaced by a low-activity paralog (PhaB2) or enzymes for reverse β-oxidation, copolyesters with high 3HHx composition were efficiently synthesized from glucose, possibly due to enhanced formation of butyryl-CoA from acetoacetyl-CoA via (S)-3HB-CoA. P(3HB-co-3HHx) composed of 7.0 mol% and 12.1 mol% 3HHx fractions, adequate for practical applications, were produced at cellular contents of 71.4 wt% and 75.3 wt%, respectively. The replacement by low-affinity mutants of PhaB1 had little impact on the PHA biosynthesis on glucose, but slightly affected those on fructose, suggesting altered metabolic regulation depending on the sugar-transport machinery. PhaB1 mostly acted in the conversion of acetoacetyl-CoA when the cells were grown on glycerol, as copolyester biosynthesis was severely impaired by the lack of phaB1. Conclusions The present results indicate the importance of flux distribution at the acetoacetyl-CoA node in R. eutropha for the biosynthesis of the PHA copolyesters with regulated composition from structurally unrelated compounds.
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20
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Van Houdt R, Provoost A, Van Assche A, Leys N, Lievens B, Mijnendonckx K, Monsieurs P. Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes. Genes (Basel) 2018; 9:genes9100507. [PMID: 30340417 PMCID: PMC6210171 DOI: 10.3390/genes9100507] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/11/2018] [Accepted: 10/15/2018] [Indexed: 12/16/2022] Open
Abstract
Cupriavidus metallidurans has been mostly studied because of its resistance to numerous heavy metals and is increasingly being recovered from other environments not typified by metal contamination. They host a large and diverse mobile gene pool, next to their native megaplasmids. Here, we used comparative genomics and global metabolic comparison to assess the impact of the mobilome on growth capabilities, nutrient utilization, and sensitivity to chemicals of type strain CH34 and three isolates (NA1, NA4 and H1130). The latter were isolated from water sources aboard the International Space Station (NA1 and NA4) and from an invasive human infection (H1130). The mobilome was expanded as prophages were predicted in NA4 and H1130, and a genomic island putatively involved in abietane diterpenoids metabolism was identified in H1130. An active CRISPR-Cas system was identified in strain NA4, providing immunity to a plasmid that integrated in CH34 and NA1. No correlation between the mobilome and isolation environment was found. In addition, our comparison indicated that the metal resistance determinants and properties are conserved among these strains and thus maintained in these environments. Furthermore, all strains were highly resistant to a wide variety of chemicals, much broader than metals. Only minor differences were observed in the phenomes (measured by phenotype microarrays), despite the large difference in mobilomes and the variable (shared by two or three strains) and strain-specific genomes.
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Affiliation(s)
- Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Ann Provoost
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Ado Van Assche
- Laboratory for Process Microbial Ecology and Bioinspirational Management, KU Leuven, B-2860 Sint-Katelijne-Waver, Belgium.
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management, KU Leuven, B-2860 Sint-Katelijne-Waver, Belgium.
| | - Kristel Mijnendonckx
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Pieter Monsieurs
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
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Biglari N, Ganjali Dashti M, Abdeshahian P, Orita I, Fukui T, Sudesh K. Enhancement of bioplastic polyhydroxybutyrate P(3HB) production from glucose by newly engineered strain Cupriavidus necator NSDG-GG using response surface methodology. 3 Biotech 2018; 8:330. [PMID: 30073115 DOI: 10.1007/s13205-018-1351-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/11/2018] [Indexed: 10/28/2022] Open
Abstract
This study aimed to enhance production of polyhydroxybutyrate P(3HB) by a newly engineered strain of Cupriavidus necator NSDG-GG by applying response surface methodology (RSM). From initial experiment of one-factor-at-a-time (OFAT), glucose and urea were found to be the most significant substrates as carbon and nitrogen sources, respectively, for the production of P(3HB). OFAT experiment results showed that the maximum biomass, P(3HB) content, and P(3HB) concentration of 8.95 g/L, 76 wt%, and 6.80 g/L were achieved at 25 g/L glucose and 0.54 g/L urea with an agitation rate of 200 rpm at 30 °C after 48 h. In this study, RSM was applied to optimize the three key variables (glucose concentration, urea concentration, and agitation speed) at a time to obtain optimal conditions in a multivariable system. Fermentation experiments were conducted in shaking flask by cultivation of C. necator NSDG-GG using various glucose concentrations (10-50 g/L), urea concentrations (0.27-0.73 g/L), and agitation speeds (150-250 rpm). The interaction between the variables studied was analyzed by ANOVA analysis. The RSM results indicated that the optimum cultivation conditions were 37.70 g/L glucose, 0.73 g/L urea, and 200 rpm agitation speed. The validation experiments under optimum conditions produced the highest biomass of 12.84 g/L, P(3HB) content of 92.16 wt%, and P(3HB) concentration of 11.83 g/L. RSM was found to be an efficient method in enhancing the production of biomass, P(3HB) content, and P(3HB) concentration by 43, 21, and 74%, respectively.
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22
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Crigler J, Bannerman-Akwei L, Cole AE, Eiteman MA, Altman E. Glucose can be transported and utilized in Escherichia coli by an altered or overproduced N-acetylglucosamine phosphotransferase system (PTS). Microbiology (Reading) 2018; 164:163-172. [DOI: 10.1099/mic.0.000596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jacob Crigler
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Laude Bannerman-Akwei
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
- Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Ashley E. Cole
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Mark A. Eiteman
- Biochemical Engineering, College of Engineering, University of Georgia, Athens, GA 30602, USA
| | - Elliot Altman
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
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Arikawa H, Matsumoto K, Fujiki T. Polyhydroxyalkanoate production from sucrose by Cupriavidus necator strains harboring csc genes from Escherichia coli W. Appl Microbiol Biotechnol 2017; 101:7497-7507. [PMID: 28889198 DOI: 10.1007/s00253-017-8470-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/26/2017] [Accepted: 07/30/2017] [Indexed: 01/05/2023]
Abstract
Cupriavidus necator H16 is the most promising bacterium for industrial production of polyhydroxyalkanoates (PHAs) because of their remarkable ability to accumulate them in the cells. With genetic modifications, this bacterium can produce poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx), which has better physical properties, as well as poly(3-hydroxybutyrate) (PHB) using plant oils and sugars as a carbon source. Considering production cost, sucrose is a very attractive raw material because it is inexpensive; however, this bacterium cannot assimilate sucrose. Here, we used the sucrose utilization (csc) genes of Escherichia coli W to generate C. necator strains that can assimilate sucrose. Especially, glucose-utilizing recombinant C. necator strains harboring the sucrose hydrolase gene (cscA) and sucrose permease gene (cscB) of E. coli W grew well on sucrose as a sole carbon source and accumulated PHB. In addition, strains introduced with a crotonyl-CoA reductase gene (ccr), ethylmalonyl-CoA decarboxylase gene (emd), and some other genetic modifications besides the csc genes and the glucose-utilizing mutations produced PHBHHx with a 3-hydroxyhexanoate (3HHx) content of maximum approximately 27 mol% from sucrose. Furthermore, when one of the PHBHHx-producing strains was cultured with sucrose solution in a fed-batch fermentation, PHBHHx with a 3HHx content of approximately 4 mol% was produced and reached 113 g/L for 65 h, which is approximately 1.5-fold higher than that produced using glucose solution.
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Affiliation(s)
- Hisashi Arikawa
- Bioproducts Research Group, Biotechnology Development Laboratories, KANEKA CORPORATION, 1-8 Miyamae-Cho, Takasago-Cho, Takasago, Hyogo, 676-8688, Japan.
| | - Keiji Matsumoto
- Bioproducts Research Group, Biotechnology Development Laboratories, KANEKA CORPORATION, 1-8 Miyamae-Cho, Takasago-Cho, Takasago, Hyogo, 676-8688, Japan
| | - Tetsuya Fujiki
- Bioproducts Research Group, Biotechnology Development Laboratories, KANEKA CORPORATION, 1-8 Miyamae-Cho, Takasago-Cho, Takasago, Hyogo, 676-8688, Japan
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Volodina E, Raberg M, Steinbüchel A. Engineering the heterotrophic carbon sources utilization range of Ralstonia eutropha H16 for applications in biotechnology. Crit Rev Biotechnol 2015; 36:978-991. [PMID: 26329669 DOI: 10.3109/07388551.2015.1079698] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Ralstonia eutropha H16 is an interesting candidate for the biotechnological production of polyesters consisting of hydroxy- and mercaptoalkanoates, and other compounds. It provides all the necessary characteristics, which are required for a biotechnological production strain. Due to its metabolic versatility, it can convert a broad range of renewable heterotrophic resources into diverse valuable compounds. High cell density fermentations of the non-pathogenic R. eutropha can be easily performed. Furthermore, this bacterium is accessible to engineering of its metabolism by genetic approaches having available a large repertoire of genetic tools. Since the complete genome sequence of R. eutropha H16 has become available, a variety of transcriptome, proteome and metabolome studies provided valuable data elucidating its complex metabolism and allowing a systematic biology approach. However, high production costs for bacterial large-scale production of biomass and biotechnologically valuable products are still an economic challenge. The application of inexpensive raw materials could significantly reduce the expenses. Therefore, the conversion of diverse substrates to polyhydroxyalkanoates by R. eutropha was steadily improved by optimization of cultivation conditions, mutagenesis and metabolic engineering. Industrial by-products and residual compounds like glycerol, and substrates containing high carbon content per weight like palm, soybean, corn oils as well as raw sugar-rich materials like molasses, starch and lignocellulose, are the most promising renewable substrates and were intensively studied.
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Affiliation(s)
- Elena Volodina
- a Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster , Münster , Germany and
| | - Matthias Raberg
- a Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster , Münster , Germany and
| | - Alexander Steinbüchel
- a Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster , Münster , Germany and.,b Environmental Science Department, King Abdulaziz University , Jeddah , Saudi Arabia
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New Insight into the Role of the Calvin Cycle: Reutilization of CO2 Emitted through Sugar Degradation. Sci Rep 2015; 5:11617. [PMID: 26130086 PMCID: PMC4486974 DOI: 10.1038/srep11617] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/01/2015] [Indexed: 01/25/2023] Open
Abstract
Ralstonia eutropha is a facultative chemolithoautotrophic bacterium that uses the Calvin–Benson–Bassham (CBB) cycle for CO2 fixation. This study showed that R. eutropha strain H16G incorporated 13CO2, emitted by the oxidative decarboxylation of [1-13C1]-glucose, into key metabolites of the CBB cycle and finally into poly(3-hydroxybutyrate) [P(3HB)] with up to 5.6% 13C abundance. The carbon yield of P(3HB) produced from glucose by the strain H16G was 1.2 times higher than that by the CBB cycle-inactivated mutants, in agreement with the possible fixation of CO2 estimated from the balance of energy and reducing equivalents through sugar degradation integrated with the CBB cycle. The results proved that the ‘gratuitously’ functional CBB cycle in R. eutropha under aerobic heterotrophic conditions participated in the reutilization of CO2 emitted during sugar degradation, leading to an advantage expressed as increased carbon yield of the storage compound. This is a new insight into the role of the CBB cycle, and may be applicable for more efficient utilization of biomass resources.
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Fukui T, Mukoyama M, Orita I, Nakamura S. Enhancement of glycerol utilization ability of Ralstonia eutropha H16 for production of polyhydroxyalkanoates. Appl Microbiol Biotechnol 2014; 98:7559-68. [PMID: 24878751 DOI: 10.1007/s00253-014-5831-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 05/13/2014] [Accepted: 05/13/2014] [Indexed: 11/25/2022]
Abstract
Ralstonia eutropha H16 is a well-studied bacterium with respect to biosynthesis of polyhydroxyalkanoates (PHAs), which has attracted attentions as biodegradable bio-based plastics. However, this strain shows quite poor growth on glycerol of which bulk supply has been increasing as a major by-product of biodiesel industries. This study examined enhancement of glycerol assimilation ability of R. eutropha H16 by introduction of the genes of aquaglyceroporin (glpF) and glycerol kinase (glpK) from Escherichia coli. Although introduction of glpFK Ec into the strain H16 using a multi-copy vector was not successful, a recombinant strain possessing glpFK Ec within the chromosome showed much faster growth on glycerol than H16. Further analyses clarified that weak expression of glpK Ec alone allowed to establish efficient glycerol assimilation pathway, indicating that the poor growth of H16 on glycerol was caused by insufficient kination activity to glycerol, as well as this strain had a potential ability for uptake of extracellular glycerol. The engineered strains expressing glpFK Ec or glpK Ec produced large amounts of poly[(R)-3-hydroxybutyrate] [P(3HB)] from glycerol with much higher productivity than H16. Unlike other glycerol-utilizable wild strains of R. eutropha, the H16-derived engineered strains accumulated P(3HB) with no significant decrease in molecular weights on glycerol, and the polydispersity index of the glycerol-based P(3HB) synthesized by the strains expressing glpFK Ec was lower than those by the parent strains. The present study demonstrated possibility of R. eutropha H16-based platform for production of useful compounds from inexpensive glycerol.
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Affiliation(s)
- Toshiaki Fukui
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan,
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Wang W, Yang S, Hunsinger GB, Pienkos PT, Johnson DK. Connecting lignin-degradation pathway with pre-treatment inhibitor sensitivity of Cupriavidus necator. Front Microbiol 2014; 5:247. [PMID: 24904560 PMCID: PMC4034039 DOI: 10.3389/fmicb.2014.00247] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 05/06/2014] [Indexed: 12/25/2022] Open
Abstract
To produce lignocellulosic biofuels economically, the complete release of monomers from the plant cell wall components, cellulose, hemicellulose, and lignin, through pre-treatment and hydrolysis (both enzymatic and chemical), and the efficient utilization of these monomers as carbon sources, is crucial. In addition, the identification and development of robust microbial biofuel production strains that can tolerate the toxic compounds generated during pre-treatment and hydrolysis is also essential. In this work, Cupriavidus necator was selected due to its capabilities for utilizing lignin monomers and producing polyhydroxylbutyrate (PHB), a bioplastic as well as an advanced biofuel intermediate. We characterized the growth kinetics of C. necator in pre-treated corn stover slurry as well as individually in the pre-sence of 11 potentially toxic compounds in the saccharified slurry. We found that C. necator was sensitive to the saccharified slurry produced from dilute acid pre-treated corn stover. Five out of 11 compounds within the slurry were characterized as toxic to C. necator, namely ammonium acetate, furfural, hydroxymethylfurfural (HMF), benzoic acid, and p-coumaric acid. Aldehydes (e.g., furfural and HMF) were more toxic than the acetate and the lignin degradation products benzoic acid and p-coumaric acid; furfural was identified as the most toxic compound. Although toxic to C. necator at high concentration, ammonium acetate, benzoic acid, and p-coumaric acid could be utilized by C. necator with a stimulating effect on C. necator growth. Consequently, the lignin degradation pathway of C. necator was reconstructed based on genomic information and literature. The efficient conversion of intermediate catechol to downstream products of cis,cis-muconate or 2-hydroxymuconate-6-semialdehyde may help improve the robustness of C. necator to benzoic acid and p-coumaric acid as well as improve PHB productivity.
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Affiliation(s)
- Wei Wang
- National Renewable Energy Laboratory, Biosciences CenterGolden, CO, USA
| | - Shihui Yang
- National Renewable Energy Laboratory, National Bioenergy CenterGolden, CO, USA
| | | | - Philip T. Pienkos
- National Renewable Energy Laboratory, National Bioenergy CenterGolden, CO, USA
| | - David K. Johnson
- National Renewable Energy Laboratory, Biosciences CenterGolden, CO, USA
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Biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) with co-expressed propionate permease (prpP), beta-ketothiolase B (bktB), and propionate-CoA synthase (prpE) in Escherichia coli. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2012.12.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Hawkins AS, McTernan PM, Lian H, Kelly RM, Adams MWW. Biological conversion of carbon dioxide and hydrogen into liquid fuels and industrial chemicals. Curr Opin Biotechnol 2013; 24:376-84. [PMID: 23510698 DOI: 10.1016/j.copbio.2013.02.017] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/18/2013] [Accepted: 02/19/2013] [Indexed: 12/12/2022]
Abstract
Non-photosynthetic routes for biological fixation of carbon dioxide into valuable industrial chemical precursors and fuels are moving from concept to reality. The development of 'electrofuel'-producing microorganisms leverages techniques in synthetic biology, genetic and metabolic engineering, as well as systems-level multi-omic analysis, directed evolution, and in silico modeling. Electrofuel processes are being developed for a range of microorganisms and energy sources (e.g. hydrogen, formate, electricity) to produce a variety of target molecules (e.g. alcohols, terpenes, alkenes). This review examines the current landscape of electrofuel projects with a focus on hydrogen-utilizing organisms covering the biochemistry of hydrogenases and carbonic anhydrases, kinetic and energetic analyses of the known carbon fixation pathways, and the state of genetic systems for current and prospective electrofuel-producing microorganisms.
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Affiliation(s)
- Aaron S Hawkins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, United States
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Impact of each individual component of the mutated PTS(Nag) on glucose uptake and phosphorylation in Ralstonia eutropha G⁺1. Appl Microbiol Biotechnol 2012; 95:735-44. [PMID: 22307500 DOI: 10.1007/s00253-012-3911-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/12/2012] [Accepted: 01/18/2012] [Indexed: 10/14/2022]
Abstract
A recent study of the UV-generated glucose-utilizing mutant Ralstonia eutropha G⁺1 comprising transcriptomic and proteomic analyses revealed clear evidence that glucose is transported by the N-acetylglucosamine-specific phosphotransferase system (PTS(Nag)), which is overexpressed in this mutant due to a derepression of the encoding nag operon by an identified insertion mutation in nagR (Raberg et al., Appl Environ Microbiol 77:2058-2070, 2011). The inability of the defined deletion mutant R. eutropha G⁺1∆nagFEC to utilize glucose confirms this finding. Furthermore, a missense mutation in nagE (membrane component comprising the cell membrane spanning EIIC(Nag) and the cytosolic domain EIIB(Nag)) was identified, which yields a substitution of an alanine by threonine at aa 153 of NagE and may affect glucose specificity of the mutated PTS(Nag) in R. eutropha G⁺1. The investigation of various generated deletion and substitution mutants of R. eutropha H16 and G⁺1 in this study was able to elucidate these phenomena. It could be shown that the porin NagC, encoded by nagC being part of the nag operon, is not necessary, while NagE is required and is probably responsible for glucose transport through the cell membrane. The intracellular phosphorylation of glucose is obviously mediated by the glucokinase GLK and not by NagF (cytosolic component comprising the three soluble domains EIIA(Nag), HPr(Nag), and EI(Nag)). Our data clearly indicate that the derepression of the nag operon is essential for glucose uptake. The point mutation in NagE is not an essential prerequisite for glucose transport although it increased glucose transport as observed in this study.
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