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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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Morlino MS, Serna García R, Savio F, Zampieri G, Morosinotto T, Treu L, Campanaro S. Cupriavidus necator as a platform for polyhydroxyalkanoate production: An overview of strains, metabolism, and modeling approaches. Biotechnol Adv 2023; 69:108264. [PMID: 37775073 DOI: 10.1016/j.biotechadv.2023.108264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Cupriavidus necator is a bacterium with a high phenotypic diversity and versatile metabolic capabilities. It has been extensively studied as a model hydrogen oxidizer, as well as a producer of polyhydroxyalkanoates (PHA), plastic-like biopolymers with a high potential to substitute petroleum-based materials. Thanks to its adaptability to diverse metabolic lifestyles and to the ability to accumulate large amounts of PHA, C. necator is employed in many biotechnological processes, with particular focus on PHA production from waste carbon sources. The large availability of genomic information has enabled a characterization of C. necator's metabolism, leading to the establishment of metabolic models which are used to devise and optimize culture conditions and genetic engineering approaches. In this work, the characteristics of available C. necator strains and genomes are reviewed, underlining how a thorough comprehension of the genetic variability of C. necator is lacking and it could be instrumental for wider application of this microorganism. The metabolic paradigms of C. necator and how they are connected to PHA production and accumulation are described, also recapitulating the variety of carbon substrates used for PHA accumulation, highlighting the most promising strategies to increase the yield. Finally, the review describes and critically analyzes currently available genome-scale metabolic models and reduced metabolic network applications commonly employed in the optimization of PHA production. Overall, it appears that the capacity of C. necator of performing CO2 bioconversion to PHA is still underexplored, both in biotechnological applications and in metabolic modeling. However, the accurate characterization of this organism and the efforts in using it for gas fermentation can help tackle this challenging perspective in the future.
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Affiliation(s)
- Maria Silvia Morlino
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Rebecca Serna García
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain
| | - Filippo Savio
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Guido Zampieri
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Tomas Morosinotto
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Laura Treu
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
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Hathi ZJ, Haque MA, Priya A, Qin ZH, Huang S, Lam CH, Ladakis D, Pateraki C, Mettu S, Koutinas A, Du C, Lin CSK. Fermentative bioconversion of food waste into biopolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) using Cupriavidus necator. ENVIRONMENTAL RESEARCH 2022; 215:114323. [PMID: 36115419 DOI: 10.1016/j.envres.2022.114323] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/20/2022] [Accepted: 09/07/2022] [Indexed: 05/27/2023]
Abstract
Dependency on plastic commodities has led to a recurrent increase in their global production every year. Conventionally, plastic products are derived from fossil fuels, leading to severe environmental concerns. The recent coronavirus disease 2019 pandemic has triggered an increase in medical waste. Conversely, it has disrupted the supply chain of personal protective equipment (PPE). Valorisation of food waste was performed to cultivate C. necator for fermentative production of biopolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). The increase in biomass, PHBV yield and molar 3-hydroxy valerate (3HV) content was estimated after feeding volatile fatty acids. The fed-batch fermentation strategy reported in this study produced 15.65 ± 0.14 g/L of biomass with 5.32 g/L of PHBV with 50% molar 3HV content. This is a crucial finding, as molar concentration of 3HV can be modulated to suit the specification of biopolymer (film or fabric). The strategy applied in this study addresses the issue of global food waste burden and subsequently generates biopolymer PHBV, turning waste to wealth.
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Affiliation(s)
- Zubeen J Hathi
- School of Energy and Environment, City University of Hong Kong, Tat Chee Ave, Kowloon, Hong Kong
| | - Md Ariful Haque
- School of Energy and Environment, City University of Hong Kong, Tat Chee Ave, Kowloon, Hong Kong
| | - Anshu Priya
- School of Energy and Environment, City University of Hong Kong, Tat Chee Ave, Kowloon, Hong Kong
| | - Zi-Hao Qin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Ave, Kowloon, Hong Kong
| | - Shuquan Huang
- School of Energy and Environment, City University of Hong Kong, Tat Chee Ave, Kowloon, Hong Kong
| | - Chun Ho Lam
- School of Energy and Environment, City University of Hong Kong, Tat Chee Ave, Kowloon, Hong Kong
| | - Dimitris Ladakis
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Chrysanthi Pateraki
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Srinivas Mettu
- Chemical and Environmental Engineering, School of Engineering, RMIT University, Melbourne, Victoria, 3000, Australia
| | - Apostolis Koutinas
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Chenyu Du
- School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, United Kingdom
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Ave, Kowloon, Hong Kong.
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Davison PA, Tu W, Xu J, Della Valle S, Thompson IP, Hunter CN, Huang WE. Engineering a Rhodopsin-Based Photo-Electrosynthetic System in Bacteria for CO 2 Fixation. ACS Synth Biol 2022; 11:3805-3816. [PMID: 36264158 PMCID: PMC9680020 DOI: 10.1021/acssynbio.2c00397] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A key goal of synthetic biology is to engineer organisms that can use solar energy to convert CO2 to biomass, chemicals, and fuels. We engineered a light-dependent electron transfer chain by integrating rhodopsin and an electron donor to form a closed redox loop, which drives rhodopsin-dependent CO2 fixation. A light-driven proton pump comprising Gloeobacter rhodopsin (GR) and its cofactor retinal have been assembled in Ralstonia eutropha (Cupriavidus necator) H16. In the presence of light, this strain fixed inorganic carbon (or bicarbonate) leading to 20% growth enhancement, when formate was used as an electron donor. We found that an electrode from a solar panel can replace organic compounds to serve as the electron donor, mediated by the electron shuttle molecule riboflavin. In this new autotrophic and photo-electrosynthetic system, GR is augmented by an external photocell for reductive CO2 fixation. We demonstrated that this hybrid photo-electrosynthetic pathway can drive the engineered R. eutropha strain to grow using CO2 as the sole carbon source. In this system, a bioreactor with only two inputs, light and CO2, enables the R. eutropha strain to perform a rhodopsin-dependent autotrophic growth. Light energy alone, supplied by a solar panel, can drive the conversion of CO2 into biomass with a maximum electron transfer efficiency of 20%.
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Affiliation(s)
- Paul A. Davison
- Plants,
Photosynthesis and Soil, School of Biosciences, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Weiming Tu
- Department
of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom
| | - Jiabao Xu
- Department
of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom
| | - Simona Della Valle
- Department
of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom
| | - Ian P. Thompson
- Department
of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom
| | - C. Neil Hunter
- Plants,
Photosynthesis and Soil, School of Biosciences, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Wei E. Huang
- Department
of Engineering Science, University of Oxford, OxfordOX1 3PJ, United Kingdom,. Tel: +44 1865 283786
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The Carbon Source Effect on the Production of Ralstonia eutropha H16 and Proteomic Response Underlying Targeting the Bioconversion with Solar Fuels. Appl Biochem Biotechnol 2022; 194:3212-3227. [PMID: 35349090 DOI: 10.1007/s12010-022-03887-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 03/14/2022] [Indexed: 12/21/2022]
Abstract
Chemoautotrophic bacterium Ralstonia eutropha H16 can fix CO2 to bioplastic and is potentially useful for CO2 neutralization. Targeting the solar fuel-based plastic biomanufactory, the polyhydroxybutyrate (PHB) production between heterotrophy and chemoautotrophy conditions was evaluated and the proteomic responses of the R. eutropha H16 cells to different carbon and energy sources were investigated. The results show that the chemoautotrophic mode hardly affected the cellular PHB accumulation capacity. Benefited from the high coverage proteome data, the global response of R. eutropha H16 to different carbon and energy sources was presented with a 95% KEGG pathway annotation, and the genome-wide location-related protein expression pattern was also identified. PHB depolymerase Q0K9H3 was found as a key protein responding to the low carbon input while CO2 and H2 were used, and will be a new regulation target for further high PHB production based on solar fuels.
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Pan H, Wang J, Wu H, Li Z, Lian J. Synthetic biology toolkit for engineering Cupriviadus necator H16 as a platform for CO 2 valorization. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:212. [PMID: 34736496 PMCID: PMC8570001 DOI: 10.1186/s13068-021-02063-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 10/25/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND CO2 valorization is one of the effective methods to solve current environmental and energy problems, in which microbial electrosynthesis (MES) system has proved feasible and efficient. Cupriviadus necator (Ralstonia eutropha) H16, a model chemolithoautotroph, is a microbe of choice for CO2 conversion, especially with the ability to be employed in MES due to the presence of genes encoding [NiFe]-hydrogenases and all the Calvin-Benson-Basham cycle enzymes. The CO2 valorization strategy will make sense because the required hydrogen can be produced from renewable electricity independently of fossil fuels. MAIN BODY In this review, synthetic biology toolkit for C. necator H16, including genetic engineering vectors, heterologous gene expression elements, platform strain and genome engineering, and transformation strategies, is firstly summarized. Then, the review discusses how to apply these tools to make C. necator H16 an efficient cell factory for converting CO2 to value-added products, with the examples of alcohols, fatty acids, and terpenoids. The review is concluded with the limitation of current genetic tools and perspectives on the development of more efficient and convenient methods as well as the extensive applications of C. necator H16. CONCLUSIONS Great progress has been made on genetic engineering toolkit and synthetic biology applications of C. necator H16. Nevertheless, more efforts are expected in the near future to engineer C. necator H16 as efficient cell factories for the conversion of CO2 to value-added products.
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Affiliation(s)
- Haojie Pan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jia Wang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Haoliang Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhongjian Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China.
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Intasian P, Prakinee K, Phintha A, Trisrivirat D, Weeranoppanant N, Wongnate T, Chaiyen P. Enzymes, In Vivo Biocatalysis, and Metabolic Engineering for Enabling a Circular Economy and Sustainability. Chem Rev 2021; 121:10367-10451. [PMID: 34228428 DOI: 10.1021/acs.chemrev.1c00121] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the industrial revolution, the rapid growth and development of global industries have depended largely upon the utilization of coal-derived chemicals, and more recently, the utilization of petroleum-based chemicals. These developments have followed a linear economy model (produce, consume, and dispose). As the world is facing a serious threat from the climate change crisis, a more sustainable solution for manufacturing, i.e., circular economy in which waste from the same or different industries can be used as feedstocks or resources for production offers an attractive industrial/business model. In nature, biological systems, i.e., microorganisms routinely use their enzymes and metabolic pathways to convert organic and inorganic wastes to synthesize biochemicals and energy required for their growth. Therefore, an understanding of how selected enzymes convert biobased feedstocks into special (bio)chemicals serves as an important basis from which to build on for applications in biocatalysis, metabolic engineering, and synthetic biology to enable biobased processes that are greener and cleaner for the environment. This review article highlights the current state of knowledge regarding the enzymatic reactions used in converting biobased wastes (lignocellulosic biomass, sugar, phenolic acid, triglyceride, fatty acid, and glycerol) and greenhouse gases (CO2 and CH4) into value-added products and discusses the current progress made in their metabolic engineering. The commercial aspects and life cycle assessment of products from enzymatic and metabolic engineering are also discussed. Continued development in the field of metabolic engineering would offer diversified solutions which are sustainable and renewable for manufacturing valuable chemicals.
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Affiliation(s)
- Pattarawan Intasian
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Nopphon Weeranoppanant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Chemical Engineering, Faculty of Engineering, Burapha University, 169, Long-hard Bangsaen, Saensook, Muang, Chonburi 20131, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
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Gutschmann B, Bock MCE, Jahns S, Neubauer P, Brigham CJ, Riedel SL. Untargeted metabolomics analysis of Ralstonia eutropha during plant oil cultivations reveals the presence of a fucose salvage pathway. Sci Rep 2021; 11:14267. [PMID: 34253787 PMCID: PMC8275744 DOI: 10.1038/s41598-021-93720-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Process engineering of biotechnological productions can benefit greatly from comprehensive analysis of microbial physiology and metabolism. Ralstonia eutropha (syn. Cupriavidus necator) is one of the best studied organisms for the synthesis of biodegradable polyhydroxyalkanoate (PHA). A comprehensive metabolomic study during bioreactor cultivations with the wild-type (H16) and an engineered (Re2058/pCB113) R. eutropha strain for short- and or medium-chain-length PHA synthesis has been carried out. PHA production from plant oil was triggered through nitrogen limitation. Sample quenching allowed to conserve the metabolic states of the cells for subsequent untargeted metabolomic analysis, which consisted of GC-MS and LC-MS analysis. Multivariate data analysis resulted in identification of significant changes in concentrations of oxidative stress-related metabolites and a subsequent accumulation of antioxidative compounds. Moreover, metabolites involved in the de novo synthesis of GDP-L-fucose as well as the fucose salvage pathway were identified. The related formation of fucose-containing exopolysaccharides potentially supports the emulsion-based growth of R. eutropha on plant oils.
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Affiliation(s)
- Björn Gutschmann
- grid.6734.60000 0001 2292 8254Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Martina C. E. Bock
- grid.6734.60000 0001 2292 8254Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Stefan Jahns
- grid.6734.60000 0001 2292 8254Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Peter Neubauer
- grid.6734.60000 0001 2292 8254Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Christopher J. Brigham
- grid.422596.e0000 0001 0639 028XSchool of Engineering, Wentworth Institute of Technology, Boston, MA USA
| | - Sebastian L. Riedel
- grid.6734.60000 0001 2292 8254Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
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9
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Chen W, Wang Z, Xu W, Tian R, Zeng J. Dibutyl phthalate contamination accelerates the uptake and metabolism of sugars by microbes in black soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:114332. [PMID: 32182534 DOI: 10.1016/j.envpol.2020.114332] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/21/2020] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
Dibutyl phthalate (DBP) is widely used as plasticizer and has been detected in the environment, posing a threat to animal health. However, the effects of DBP on agricultural microbiomes are not known. In this study, DBP levels in black soil were evaluated, and the impact of DBP contamination on the uptake and metabolism of sugars in microbes was assessed by glucose absorption tests, metaproteomics, metabolomics, enzyme activity assays and computational simulation analysis. The results indicated that DBP contamination accelerated glucose consumption and upregulated the expression of porins and periplasmic monosaccharide ATP-binding cassette (ABC) transporter solute-binding proteins (SBPs). DBP and its metabolic intermediates (carboxymuconate and butanol) may form a stable complex with sugar transporters and enhance the rigidity and stability of these proteins. Sugar metabolism resulting in the generation of ATP and reducing agent (NADPH), as well as the expression of some key enzymes (dehydrogenases) were also upregulated by DBP treatment. Moreover, a diverse bacterial community appears to utilize sugar, suggesting that there are widespread effects of DBP contamination on soil microbial ecosystems. The results of this study provide a theoretical basis for investigating the toxicological effects of DBP on microbes in black soil.
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Affiliation(s)
- Wenjing Chen
- Center for Ecological Research, Northeast Forestry University, Heilongjiang Province, Harbin, 150040, China; Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, 161006, China; College of Life Sciences, Agriculture and Forestry, Qiqihar University, Heilongjiang Province, Qiqihar, 161006, China.
| | - Zhigang Wang
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, 161006, China; College of Life Sciences, Agriculture and Forestry, Qiqihar University, Heilongjiang Province, Qiqihar, 161006, China.
| | - Weihui Xu
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, 161006, China; College of Life Sciences, Agriculture and Forestry, Qiqihar University, Heilongjiang Province, Qiqihar, 161006, China.
| | - Renmao Tian
- Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL, 60501, USA.
| | - Jin Zeng
- Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
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10
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Dalsasso RR, Pavan FA, Bordignon SE, Aragão GMFD, Poletto P. Polyhydroxybutyrate (PHB) production by Cupriavidus necator from sugarcane vinasse and molasses as mixed substrate. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.07.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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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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12
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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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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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Xiong B, Li Z, Liu L, Zhao D, Zhang X, Bi C. Genome editing of Ralstonia eutropha using an electroporation-based CRISPR-Cas9 technique. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:172. [PMID: 29951116 PMCID: PMC6011247 DOI: 10.1186/s13068-018-1170-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 06/12/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Ralstonia eutropha is an important bacterium for the study of polyhydroxyalkanoates (PHAs) synthesis and CO2 fixation, which makes it a potential strain for industrial PHA production and attractive host for CO2 conversion. Although the bacterium is not recalcitrant to genetic manipulation, current methods for genome editing based on group II introns or single crossover integration of a suicide plasmid are inefficient and time-consuming, which limits the genetic engineering of this organism. Thus, developing an efficient and convenient method for R. eutropha genome editing is imperative. RESULTS An efficient genome editing method for R. eutropha was developed using an electroporation-based CRISPR-Cas9 technique. In our study, the electroporation efficiency of R. eutropha was found to be limited by its restriction-modification (RM) systems. By searching the putative RM systems in R. eutropha H16 using REBASE database and comparing with that in E. coli MG1655, five putative restriction endonuclease genes which are related to the RM systems in R. eutropha were predicated and disrupted. It was found that deletion of H16_A0006 and H16_A0008-9 increased the electroporation efficiency 1658 and 4 times, respectively. Fructose was found to reduce the leaky expression of the arabinose-inducible pBAD promoter, which was used to optimize the expression of cas9, enabling genome editing via homologous recombination based on CRISPR-Cas9 in R. eutropha. A total of five genes were edited with efficiencies ranging from 78.3 to 100%. The CRISPR-Cpf1 system and the non-homologous end joining mechanism were also investigated, but failed to yield edited strains. CONCLUSIONS We present the first genome editing method for R. eutropha using an electroporation-based CRISPR-Cas9 approach, which significantly increased the efficiency and decreased time to manipulate this facultative chemolithoautotrophic microbe. The novel technique will facilitate more advanced researches and applications of R. eutropha for PHA production and CO2 conversion.
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Affiliation(s)
- Bin Xiong
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Zhongkang Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- University of Sciences and Technology of China, Hefei, 230026 People’s Republic of China
| | - Li Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- University of Sciences and Technology of China, Hefei, 230026 People’s Republic of China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
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Raberg M, Volodina E, Lin K, Steinbüchel A. Ralstonia eutrophaH16 in progress: Applications beside PHAs and establishment as production platform by advanced genetic tools. Crit Rev Biotechnol 2017; 38:494-510. [DOI: 10.1080/07388551.2017.1369933] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Matthias Raberg
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Elena Volodina
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Kaichien Lin
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
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16
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Sharma PK, Fu J, Spicer V, Krokhin OV, Cicek N, Sparling R, Levin DB. Global changes in the proteome of Cupriavidus necator H16 during poly-(3-hydroxybutyrate) synthesis from various biodiesel by-product substrates. AMB Express 2016; 6:36. [PMID: 27184362 PMCID: PMC4870535 DOI: 10.1186/s13568-016-0206-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/07/2016] [Indexed: 01/13/2023] Open
Abstract
Synthesis of poly-[3-hydroxybutyrate] (PHB) by Cupriavidus necator H16 in batch cultures was evaluated using three biodiesel-derived by-products as the sole carbon sources: waste glycerol (REG-80, refined to 80 % purity with negligible free fatty acids); glycerol bottom (REG-GB, with up to 65 % glycerol and 35 % free fatty acids), and free fatty acids (REG-FFA, with up to 75 % FFA and no glycerol). All the three substrates supported growth and PHB production by C. necator, with polymer accumulation ranging from 9 to 84 % cell dry weight (cdw), depending on the carbon source. To help understand these differences, proteomic analysis indicated that although C. necator H16 was able to accumulate PHB during growth on all three biodiesel by-products, no changes in the levels of PHB synthesis enzymes were observed. However, significant changes in the levels of expression were observed for two Phasin proteins involved with PHB accumulation, and for a number of gene products in the fatty acid β-oxidation pathway, the Glyoxylate Shunt, and the hydrogen (H2) synthesis pathways in C. necator cells cultured with different substrates. The glycerol transport protein (GlpF) was induced in REG-GB and REG-80 glycerol cultures only. Cupriavidus necator cells cultured with REG-GB and REG-FFA showed up-regulation of β-oxidation and Glyoxylate Shunt pathways proteins at 24 h pi, but H2 synthesis pathways enzymes were significantly down-regulated, compared with cells cultured with waste glycerol. Our data confirmed earlier observations of constitutive expression of PHB synthesis proteins, but further suggested that C. necator H16 cells growing on biodiesel-derived glycerol were under oxidative stress.
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17
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Ribeiro PLL, de Souza Silva G, Druzian JI. Evaluation of the effects of crude glycerol on the production and properties of novel polyhydroxyalkanoate copolymers containing high 11-hydroxyoctadecanoate byCupriavidus necatorIPT 029 andBacillus megateriumIPT 429. POLYM ADVAN TECHNOL 2015. [DOI: 10.1002/pat.3725] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Paulo Leonardo Lima Ribeiro
- Department of Chemical Engineering, Polytechnic School; Federal University of Bahia; 210-630 Salvador City BA Brazil
| | - Graciete de Souza Silva
- Department of Bromatological Analysis, College of Pharmacy; Federal University of Bahia; 171-970 Salvador City BA Brazil
| | - Janice Izabel Druzian
- Department of Bromatological Analysis, College of Pharmacy; Federal University of Bahia; 171-970 Salvador City BA Brazil
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18
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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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19
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Prieto A, Escapa IF, Martínez V, Dinjaski N, Herencias C, de la Peña F, Tarazona N, Revelles O. A holistic view of polyhydroxyalkanoate metabolism inPseudomonas putida. Environ Microbiol 2015; 18:341-57. [DOI: 10.1111/1462-2920.12760] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 12/12/2014] [Accepted: 12/20/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Auxiliadora Prieto
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Isabel F. Escapa
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Virginia Martínez
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Nina Dinjaski
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Cristina Herencias
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Fernando de la Peña
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Natalia Tarazona
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Olga Revelles
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
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20
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Chien CC, Wang LJ, Lin WR. Polyhydroxybutyrate accumulation by a cadmium-resistant strain of Cupriavidus taiwanensis. J Taiwan Inst Chem Eng 2014. [DOI: 10.1016/j.jtice.2014.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Profile of secreted hydrolases, associated proteins, and SlpA in Thermoanaerobacterium saccharolyticum during the degradation of hemicellulose. Appl Environ Microbiol 2014; 80:5001-11. [PMID: 24907337 DOI: 10.1128/aem.00998-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thermoanaerobacterium saccharolyticum, a Gram-positive thermophilic anaerobic bacterium, grows robustly on insoluble hemicellulose, which requires a specialized suite of secreted and transmembrane proteins. We report here the characterization of proteins secreted by this organism. Cultures were grown on hemicellulose, glucose, xylose, starch, and xylan in pH-controlled bioreactors, and samples were analyzed via spotted microarrays and liquid chromatography-mass spectrometry. Key hydrolases and transporters employed by T. saccharolyticum for growth on hemicellulose were, for the most part, hitherto uncharacterized and existed in two clusters (Tsac_1445 through Tsac_1464 for xylan/xylose and Tsac_1344 through Tsac_1349 for starch). A phosphotransferase system subunit, Tsac_0032, also appeared to be exclusive to growth on glucose. Previously identified hydrolases that showed strong conditional expression changes included XynA (Tsac_1459), XynC (Tsac_0897), and a pullulanase, Apu (Tsac_1342). An omnipresent transcript and protein making up a large percentage of the overall secretome, Tsac_0361, was tentatively identified as the primary S-layer component in T. saccharolyticum, and deletion of the Tsac_0361 gene resulted in gross morphological changes to the cells. The view of hemicellulose degradation revealed here will be enabling for metabolic engineering efforts in biofuel-producing organisms that degrade cellulose well but lack the ability to catabolize C5 sugars.
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22
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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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23
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Study of metabolic network of Cupriavidus necator DSM 545 growing on glycerol by applying elementary flux modes and yield space analysis. J Ind Microbiol Biotechnol 2014; 41:913-30. [PMID: 24715530 DOI: 10.1007/s10295-014-1439-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/13/2014] [Indexed: 10/25/2022]
Abstract
A metabolic network consisting of 48 reactions was established to describe intracellular processes during growth and poly-3-hydroxybutyrate (PHB) production for Cupriavidus necator DSM 545. Glycerol acted as the sole carbon source during exponential, steady-state cultivation conditions. Elementary flux modes were obtained by the program Metatool and analyzed by using yield space analysis. Four sets of elementary modes were obtained, depending on whether the pair NAD/NADH or FAD/FADH2 contributes to the reaction of glycerol-3-phosphate dehydrogenase (GLY-3-P DH), and whether 6-phosphogluconate dehydrogenase (6-PG DH) is present or not. Established metabolic network and the related system of equations provide multiple solutions for the simultaneous synthesis of PHB and biomass; this number of solutions can be further increased if NAD/NADH or FAD/FADH2 were assumed to contribute in the reaction of GLY-3-P DH. As a major outcome, it was demonstrated that experimentally determined yields for biomass and PHB with respect to glycerol fit well to the values obtained in silico when the Entner-Doudoroff pathway (ED) dominates over the glycolytic pathway; this is also the case if the Embden-Meyerhof-Parnas pathway dominates over the ED.
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24
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Grousseau E, Blanchet E, Déléris S, Albuquerque MGE, Paul E, Uribelarrea JL. Impact of sustaining a controlled residual growth on polyhydroxybutyrate yield and production kinetics in Cupriavidus necator. BIORESOURCE TECHNOLOGY 2013; 148:30-38. [PMID: 24035890 DOI: 10.1016/j.biortech.2013.08.120] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 07/31/2013] [Accepted: 08/02/2013] [Indexed: 06/02/2023]
Abstract
In this study a complementary modeling and experimental approach was used to explore how growth controls the NADPH generation and availability, and the resulting impact on PHB (polyhydroxybutyrate) yields and kinetics. The results show that the anabolic demand allowed the NADPH production through the Entner-Doudoroff (ED) pathway, leading to a high maximal theoretical PHB production yield of 0.89 C mole C mole(-1); whereas without biomass production, NADPH regeneration is only possible via the isocitrate dehydrogenase leading to a theoretical yield of 0.67 C mole C mole(-1). Furthermore, the maximum specific rate of NADPH produced at maximal growth rate (to fulfil biomass requirement) was found to be the maximum set in every conditions, which by consequence determines the maximal PHB production rate. These results imply that sustaining a controlled residual growth improves the PHB specific production rate without altering production yield.
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Affiliation(s)
- Estelle Grousseau
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France; INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France; VEOLIA Environnement, Centre de Recherche sur l'Eau, Chemin de la Digue, BP 76, F-78603 Maisons-Laffitte Cedex, France.
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25
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Five-step continuous production of PHB analyzed by elementary flux, modes, yield space analysis and high structured metabolic model. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Špoljarić IV, Lopar M, Koller M, Muhr A, Salerno A, Reiterer A, Malli K, Angerer H, Strohmeier K, Schober S, Mittelbach M, Horvat P. Mathematical modeling of poly[(R)-3-hydroxyalkanoate] synthesis by Cupriavidus necator DSM 545 on substrates stemming from biodiesel production. BIORESOURCE TECHNOLOGY 2013; 133:482-494. [PMID: 23454805 DOI: 10.1016/j.biortech.2013.01.126] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/21/2013] [Accepted: 01/22/2013] [Indexed: 06/01/2023]
Abstract
Two low structured mathematical models for fed-batch production of polyhydroxybutyrate and poly[hydroxybutyrate-co-hydroxyvalerate] by Cupriavidus necator DSM 545 on renewable substrates (glycerol and fatty acid methyl esters-FAME) combined with glucose and valeric acid, were established. The models were used for development/optimization of feeding strategies of carbon and nitrogen sources concerning PHA content and polymer/copolymer composition. Glycerol/glucose fermentation featured a max. specific growth rate of 0.171 h(-1), a max. specific production rate of 0.038 h(-1) and a PHB content of 64.5%, whereas the FAME/valeric acid fermentation resulted in a max. specific growth rate of 0.046 h(-1), a max. specific production rate of 0.07 h(-1) and 63.6% PHBV content with 4.3% of 3-hydroxyvalerate (3HV) in PHBV. A strong inhibition of glycerol consumption by glucose was confirmed (inhibition constant ki,G=4.28×10(-4) g L(-1)). Applied concentration of FAME (10-12 g L(-1)) positively influenced on PHBV synthesis. HV/PHBV ratio depends on applied VA concentration.
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Affiliation(s)
- Ivna Vrana Špoljarić
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
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27
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Multiple propionyl coenzyme A-supplying pathways for production of the bioplastic poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in Haloferax mediterranei. Appl Environ Microbiol 2013; 79:2922-31. [PMID: 23435886 DOI: 10.1128/aem.03915-12] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Haloferax mediterranei is able to accumulate the bioplastic poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) with more than 10 mol% 3-hydroxyvalerate (3HV) from unrelated carbon sources. However, the pathways that produce propionyl coenzyme A (propionyl-CoA), an important precursor of 3HV monomer, have not yet been determined. Bioinformatic analysis of H. mediterranei genome indicated that this strain uses multiple pathways for propionyl-CoA biosynthesis, including the citramalate/2-oxobutyrate pathway, the aspartate/2-oxobutyrate pathway, the methylmalonyl-CoA pathway, and a novel 3-hydroxypropionate pathway. Cofeeding of pathway intermediates and inactivating pathway-specific genes supported that these four pathways were indeed involved in the biosynthesis of 3HV monomer. The novel 3-hydroxypropionate pathway that couples CO2 assimilation with PHBV biosynthesis was further confirmed by analysis of (13)C positional enrichment in 3HV. Notably, (13)C metabolic flux analysis showed that the citramalate/2-oxobutyrate pathway (53.0% flux) and the 3-hydroxypropionate pathway (30.6% flux) were the two main generators of propionyl-CoA from glucose. In addition, genetic perturbation on the transcriptome of the ΔphaEC mutant (deficient in PHBV accumulation) revealed that a considerable number of genes in the four propionyl-CoA synthetic pathways were significantly downregulated. We determined for the first time four propionyl-CoA-supplying pathways for PHBV production in haloarchaea, particularly including a new 3-hydroxypropionate pathway. These results would provide novel strategies for the production of PHBV with controllable 3HV molar fraction.
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28
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Liu H, Luo Y, Han J, Wu J, Wu Z, Feng D, Cai S, Li M, Liu J, Zhou J, Xiang H. Proteome Reference Map of Haloarcula hispanica and Comparative Proteomic and Transcriptomic Analysis of Polyhydroxyalkanoate Biosynthesis under Genetic and Environmental Perturbations. J Proteome Res 2013; 12:1300-15. [PMID: 23301558 DOI: 10.1021/pr300969m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hailong Liu
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Yuanming Luo
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Jing Han
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Jinhua Wu
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Zhenfang Wu
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Deqin Feng
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Shuangfeng Cai
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Ming Li
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Jingfang Liu
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Jian Zhou
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Hua Xiang
- State Key
Laboratory of Microbial Resources, Institute
of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
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Autotrophic production of stable-isotope-labeled arginine in Ralstonia eutropha strain H16. Appl Environ Microbiol 2012; 78:7884-90. [PMID: 22941075 DOI: 10.1128/aem.01972-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
With the aim of improving industrial-scale production of stable-isotope (SI)-labeled arginine, we have developed a system for the heterologous production of the arginine-containing polymer cyanophycin in recombinant strains of Ralstonia eutropha under lithoautotrophic growth conditions. We constructed an expression plasmid based on the cyanophycin synthetase gene (cphA) of Synechocystis sp. strain PCC6308 under the control of the strong P(cbbL) promoter of the R. eutropha H16 cbb(c) operon (coding for autotrophic CO(2) fixation). In batch cultures growing on H(2) and CO(2) as sole sources of energy and carbon, respectively, the cyanophycin content of cells reached 5.5% of cell dry weight (CDW). However, in the absence of selection (i.e., in antibiotic-free medium), plasmid loss led to a substantial reduction in yield. We therefore designed a novel addiction system suitable for use under lithoautotrophic conditions. Based on the hydrogenase transcription factor HoxA, this system mediated stabilized expression of cphA during lithoautotrophic cultivation without the need for antibiotics. The maximum yield of cyanophycin was 7.1% of CDW. To test the labeling efficiency of our expression system under actual production conditions, cells were grown in 10-liter-scale fermentations fed with (13)CO(2) and (15)NH(4)Cl, and the (13)C/(15)N-labeled cyanophycin was subsequently extracted by treatment with 0.1 M HCl; 2.5 to 5 g of [(13)C/(15)N]arginine was obtained per fed-batch fermentation, corresponding to isotope enrichments of 98.8% to 99.4%.
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Kaddor C, Voigt B, Hecker M, Steinbüchel A. Impact of the Core Components of the Phosphoenolpyruvate-Carbohydrate Phosphotransferase System, HPr and EI, on Differential Protein Expression in Ralstonia eutropha H16. J Proteome Res 2012; 11:3624-36. [DOI: 10.1021/pr300042f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Chlud Kaddor
- Institut für
Molekulare
Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse
3, D-48149 Münster, Germany
| | - Birgit Voigt
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität, Friedrich-Ludwig-Jahn-Straße
15, D-17489 Greifswald, Germany
| | - Michael Hecker
- Institut für Mikrobiologie, Ernst-Moritz-Arndt Universität, Friedrich-Ludwig-Jahn-Straße
15, D-17489 Greifswald, Germany
| | - Alexander Steinbüchel
- Institut für
Molekulare
Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse
3, D-48149 Münster, Germany
- King Abdul Aziz University, Jeddah 22254,
Saudi Arabia
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31
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Proteomic phenotyping of Novosphingobium nitrogenifigens reveals a robust capacity for simultaneous nitrogen fixation, polyhydroxyalkanoate production, and resistance to reactive oxygen species. Appl Environ Microbiol 2012; 78:4802-15. [PMID: 22582058 DOI: 10.1128/aem.00274-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Novosphingobium nitrogenifigens Y88(T) (Y88) is a free-living, diazotrophic Alphaproteobacterium, capable of producing 80% of its biomass as the biopolymer polyhydroxybutyrate (PHB). We explored the potential utility of this species as a polyhydroxybutyrate production strain, correlating the effects of glucose, nitrogen availability, dissolved oxygen concentration, and extracellular pH with polyhydroxybutyrate production and changes in the Y88 proteomic profile. Using two-dimensional differential in-gel electrophoresis and tandem mass spectrometry, we identified 217 unique proteins from six growth conditions. We observed reproducible, characteristic proteomic signatures for each of the physiological states we examined. We identified proteins that changed in abundance in correlation with either nitrogen fixation, dissolved oxygen concentration, or acidification of the growth medium. The proteins that correlated with nitrogen fixation were identified either as known nitrogen fixation proteins or as novel proteins that we predict play roles in aspects of nitrogen fixation based on their proteomic profiles. In contrast, the proteins involved in central carbon and polyhydroxybutyrate metabolism were constitutively abundant, consistent with the constitutive polyhydroxybutyrate production that we observed in this species. Three proteins with roles in detoxification of reactive oxygen species were identified in this obligate aerobe. The most abundant protein in all experiments was a polyhydroxyalkanoate granule-associated protein, phasin. The full-length isoform of this protein has a long, intrinsically disordered Ala/Pro/Lys-rich N-terminal segment, a feature that appears to be unique to sphingomonad phasins. The data suggest that Y88 has potential as a PHB production strain due to its aerobic tolerance and metabolic orientation toward polyhydroxybutyrate accumulation, even in low-nitrogen growth medium.
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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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Escapa IF, García JL, Bühler B, Blank LM, Prieto MA. The polyhydroxyalkanoate metabolism controls carbon and energy spillage in Pseudomonas putida. Environ Microbiol 2012; 14:1049-63. [PMID: 22225632 DOI: 10.1111/j.1462-2920.2011.02684.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The synthesis and degradation of polyhydroxyalkanoates (PHAs), the storage polymer of many bacteria, is linked to the operation of central carbon metabolism. To rationalize the impact of PHA accumulation on central carbon metabolism of the prototype bacterium Pseudomonas putida, we have revisited PHA production in quantitative physiology experiments in the wild-type strain vs. a PHA negative mutant growing under low nitrogen conditions. When octanoic acid was used as PHA precursor and as carbon and energy source, we have detected higher intracellular flux via acetyl-CoA in the mutant strain than in the wild type, which correlates with the stimulation of the TCA cycle and glyoxylate shunt observed on the transcriptional level. The mutant defective in carbon and energy storage spills the additional resources, releasing CO(2) instead of generating biomass. Hence, P. putida operates the metabolic network to optimally exploit available resources and channels excess carbon and energy to storage via PHA, without compromising growth. These findings demonstrate that the PHA metabolism plays a critical role in synchronizing global metabolism to availability of resources in PHA-producing microorganisms.
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Affiliation(s)
- I F Escapa
- Environmental Biology Department, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
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34
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Identification of mutation points in Cupriavidus necator NCIMB 11599 and genetic reconstitution of glucose-utilization ability in wild strain H16 for polyhydroxyalkanoate production. J Biosci Bioeng 2012; 113:63-9. [DOI: 10.1016/j.jbiosc.2011.09.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/21/2011] [Accepted: 09/21/2011] [Indexed: 11/19/2022]
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35
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Franz A, Rehner R, Kienle A, Grammel H. Rapid selection of glucose-utilizing variants of the polyhydroxyalkanoate producer Ralstonia eutropha H16 by incubation with high substrate levels. Lett Appl Microbiol 2011; 54:45-51. [DOI: 10.1111/j.1472-765x.2011.03171.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Jaremko M, Yu J. The initial metabolic conversion of levulinic acid in Cupriavidus necator. J Biotechnol 2011; 155:293-8. [PMID: 21821073 DOI: 10.1016/j.jbiotec.2011.07.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 07/16/2011] [Accepted: 07/22/2011] [Indexed: 11/18/2022]
Abstract
Levulinic acid or 4-ketovaleric acid is a potential renewable substrate for production of polyhydroxyalkanoates. In this work, the initial reactions of LA metabolism by Cupriavidus necator were examined in vitro. The organic acid was converted by membrane-bound crude enzymes obtained from the cells pre-grown on LA, while no LA activity was detected from cells pre-grown on acetic acid. Acetyl-CoA and propionyl-CoA were two major intermediates in the initial reactions of LA conversion. A mass balance on propionyl-CoA accounts for 84 mol% of LA added in vitro. It explains an interesting phenomenon that 3-hydroxbutyrate and 3-hydroxyvalerate are two major monomers of the biopolyester formed from LA, instead of 4-hydroxvalerate that has the similar chemical structure of LA as the precursor. A Monod model was used to describe the kinetics of LA utilization as a sole carbon source or a co-substrate of glucose and fructose. The μ(max) and K(m) of LA alone were 0.26 h⁻¹ and 0.01 g/L, respectively. The content and composition of PHA are also dependent on the culture conditions such as carbon to nitrogen ratio. The in vitro observation is supported by the high utilization rate of LA and the high molar percentage of 3HB and 3HV in the PHA derived from LA.
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Affiliation(s)
- Matt Jaremko
- Hawai'i Natural Energy Institute, University of Hawai'i at Mānoa, 1680 East West Road, POST 109, Honolulu, HI 96822, USA.
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Park JM, Kim TY, Lee SY. Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production. BMC SYSTEMS BIOLOGY 2011; 5:101. [PMID: 21711532 PMCID: PMC3154180 DOI: 10.1186/1752-0509-5-101] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 06/28/2011] [Indexed: 11/28/2022]
Abstract
Background Ralstonia eutropha H16, found in both soil and water, is a Gram-negative lithoautotrophic bacterium that can utillize CO2 and H2 as its sources of carbon and energy in the absence of organic substrates. R. eutropha H16 can reach high cell densities either under lithoautotrophic or heterotrophic conditions, which makes it suitable for a number of biotechnological applications. It is the best known and most promising producer of polyhydroxyalkanoates (PHAs) from various carbon substrates and is an environmentally important bacterium that can degrade aromatic compounds. In order to make R. eutropha H16 a more efficient and robust biofactory, system-wide metabolic engineering to improve its metabolic performance is essential. Thus, it is necessary to analyze its metabolic characteristics systematically and optimize the entire metabolic network at systems level. Results We present the lithoautotrophic genome-scale metabolic model of R. eutropha H16 based on the annotated genome with biochemical and physiological information. The stoichiometic model, RehMBEL1391, is composed of 1391 reactions including 229 transport reactions and 1171 metabolites. Constraints-based flux analyses were performed to refine and validate the genome-scale metabolic model under environmental and genetic perturbations. First, the lithoautotrophic growth characteristics of R. eutropha H16 were investigated under varying feeding ratios of gas mixture. Second, the genome-scale metabolic model was used to design the strategies for the production of poly[R-(-)-3hydroxybutyrate] (PHB) under different pH values and carbon/nitrogen source uptake ratios. It was also used to analyze the metabolic characteristics of R. eutropha when the phosphofructokinase gene was expressed. Finally, in silico gene knockout simulations were performed to identify targets for metabolic engineering essential for the production of 2-methylcitric acid in R. eutropha H16. Conclusion The genome-scale metabolic model, RehMBEL1391, successfully represented metabolic characteristics of R. eutropha H16 at systems level. The reconstructed genome-scale metabolic model can be employed as an useful tool for understanding its metabolic capabilities, predicting its physiological consequences in response to various environmental and genetic changes, and developing strategies for systems metabolic engineering to improve its metabolic performance.
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Affiliation(s)
- Jong Myoung Park
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
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Kaddor C, Steinbüchel A. Effects of homologous phosphoenolpyruvate-carbohydrate phosphotransferase system proteins on carbohydrate uptake and poly(3-Hydroxybutyrate) accumulation in Ralstonia eutropha H16. Appl Environ Microbiol 2011; 77:3582-90. [PMID: 21478317 PMCID: PMC3127587 DOI: 10.1128/aem.00218-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 03/29/2011] [Indexed: 11/20/2022] Open
Abstract
Seven gene loci encoding putative proteins of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PEP-PTS) were identified in the genome of Ralstonia eutropha H16 by in silico analysis. Except the N-acetylglucosamine-specific PEP-PTS, an additional complete PEP-PTS is lacking in strain H16. Based on these findings, we generated single and multiple deletion mutants defective mainly in the PEP-PTS genes to investigate their influence on carbon source utilization, growth behavior, and poly(3-hydroxybutyrate) (PHB) accumulation. As supposed, the H16 ΔfrcACB and H16 ΔnagFEC mutants exhibited no growth when cultivated on fructose and N-acetylglucosamine, respectively. Furthermore, a transposon mutant with a ptsM-ptsH insertion site did not grow on both carbon sources. The observed phenotype was not complemented, suggesting that it results from an interaction of genes or a polar effect caused by the Tn5::mob insertion. ptsM, ptsH, and ptsI single, double, and triple mutants stored much less PHB than the wild type (about 10 to 39% [wt/wt] of cell dry weight) and caused reduced PHB production in mutants lacking the H16_A2203, H16_A0384, frcACB, or nagFEC genes. In contrast, mutant H16 ΔH16_A0384 accumulated 11.5% (wt/wt) more PHB than the wild type when grown on gluconate and suppressed partially the negative effect of the ptsMHI deletion on PHB synthesis. Based on our experimental data, we discussed whether the PEP-PTS homologous proteins in R. eutropha H16 are exclusively involved in the complex sugar transport system or whether they are also involved in cellular regulatory functions of carbon and PHB metabolism.
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Affiliation(s)
- Chlud Kaddor
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149 Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149 Münster, Germany
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