1
|
Huong KH, Orita I, Fukui T. Microaerobic insights into production of polyhydroxyalkanoates containing 3-hydroxyhexanoate via native reverse β-oxidation from glucose in Ralstonia eutropha H16. Microb Cell Fact 2024; 23:21. [PMID: 38221622 PMCID: PMC10788006 DOI: 10.1186/s12934-024-02294-4] [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: 10/17/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024] Open
Abstract
BACKGROUND Ralstonia eutropha H16, a facultative chemolitoautotroph, is an important workhorse for bioindustrial production of useful compounds such as polyhydroxyalkanoates (PHAs). Despite the extensive studies to date, some of its physiological properties remain not fully understood. RESULTS This study demonstrated that the knallgas bacterium exhibited altered PHA production behaviors under slow-shaking condition, as compared to its usual aerobic condition. One of them was a notable increase in PHA accumulation, ranging from 3.0 to 4.5-fold in the mutants lacking of at least two NADPH-acetoacetyl-CoA reductases (PhaB1, PhaB3 and/or phaB2) when compared to their respective aerobic counterpart, suggesting the probable existence of (R)-3HB-CoA-providing route(s) independent on PhaBs. Interestingly, PHA production was still considerably high even with an excess nitrogen source under this regime. The present study further uncovered the conditional activation of native reverse β-oxidation (rBOX) allowing formation of (R)-3HHx-CoA, a crucial precursor for poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) [P(3HB-co-3HHx)], solely from glucose. This native rBOX led to the natural incorporation of 3.9 mol% 3HHx in a triple phaB-deleted mutant (∆phaB1∆phaB1∆phaB2-C2). Gene deletion experiments elucidated that the native rBOX was mediated by previously characterized (S)-3HB-CoA dehydrogenases (PaaH1/Had), β-ketothiolase (BktB), (R)-2-enoyl-CoA hydratase (PhaJ4a), and unknown crotonase(s) and reductase(s) for crotonyl-CoA to butyryl-CoA conversion prior to elongation. The introduction of heterologous enzymes, crotonyl-CoA carboxylase/reductase (Ccr) and ethylmalonyl-CoA decarboxylase (Emd) along with (R)-2-enoyl-CoA hydratase (PhaJ) aided the native rBOX, resulting in remarkably high 3HHx composition (up to 37.9 mol%) in the polyester chains under the low-aerated condition. CONCLUSION These findings shed new light on the robust characteristics of Ralstonia eutropha H16 and have the potential for the development of new strategies for practical P(3HB-co-3HHx) copolyesters production from sugars under low-aerated conditions.
Collapse
Affiliation(s)
- Kai-Hee Huong
- 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.
| |
Collapse
|
2
|
Oh SJ, Choi TR, Kim HJ, Shin N, Hwang JH, Kim HJ, Bhatia SK, Kim W, Yeon YJ, Yang YH. Maximization of 3-hydroxyhexanoate fraction in poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) using lauric acid with engineered Cupriavidus necator H16. Int J Biol Macromol 2024; 256:128376. [PMID: 38007029 DOI: 10.1016/j.ijbiomac.2023.128376] [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: 07/05/2023] [Revised: 10/16/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023]
Abstract
As polyhydroxybutyrate (P(3HB)) was struggling with mechanical properties, efforts have been directed towards increasing mole fraction of 3-hydroxyhexanoate (3HHx) in P(3HB-co-3HHx) to improve the properties of polyhydroxyalkanoates (PHAs). Although genetic modification had significant results, there were several issues related to cell growth and PHA production by deletion of PHA synthetic genes. To find out easier strategy for high 3HHx mole fraction without gene deletion, Cupriavidus necator H16 containing phaC2Ra-phaACn-phaJ1Pa was examined with various oils resulting that coconut oil gave the highest 3HHx mole fraction. When fatty acid composition analysis with GC-MS was applied, coconut oil was found to have very different composition from other vegetable oil containing very high lauric acid (C12) content. To find out specific fatty acid affecting 3HHx fraction, different fatty acids from caproic acid (C6) to stearic acid (C18) was evaluated and the 3HHx mole fraction was increased to 26.5 ± 1.6 % using lauric acid. Moreover, the 3HHx mole fraction could be controlled from 9 % to 31.1 % by mixing bean oil and lauric acid with different ratios. Produced P(3HB-co-3HHx) exhibited higher molecular than P(3HB-co-3HHx) from phaB-deletion mutant. This study proposes another strategy to increase 3HHx mole fraction with easier way by modifying substrate composition without applying deletion tools.
Collapse
Affiliation(s)
- Suk Jin Oh
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Tae-Rim Choi
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Hyun Joong Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Nara Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jeong Hyeon Hwang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Hyun Jin Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul, Republic of Korea
| | - Wooseong Kim
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Young Joo Yeon
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea.
| |
Collapse
|
3
|
Gerlach MS, Neubauer P, Gimpel M. Improved preculture management for Cupriavidus necator cultivations. Biotechnol Lett 2023; 45:1487-1493. [PMID: 37828291 PMCID: PMC10635987 DOI: 10.1007/s10529-023-03436-1] [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: 07/11/2023] [Revised: 08/30/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023]
Abstract
OBJECTIVES Research on hydrogenases from Cupriavidus necator has been ongoing for more than two decades and still today the common methods for culture inoculation are used. These methods were never adapted to the requirements of modified bacterial strains, resulting in different physiological states of the bacteria in the precultures, which in turn lead prolonged and different lag-phases. RESULTS In order to obtain uniform and always equally fit precultures for inoculation, we have established in this study an optimized protocol for precultures of the derivative of C. necator HF210 (C. necator HP80) which is used for homologous overexpression of the genes for the NAD+-reducing soluble hydrogenase (SH). We compared different media for preculture growth and determined the optimal time point for harvest. The protocol obtained in this study is based on two subsequent precultures, the first one in complex nutrient broth medium (NB) and a second one in fructose -nitrogen mineral salt medium (FN). CONCLUSION Despite having two subsequent precultures our protocol reduces the preculture time to less than 30 h and provides reproducible precultures for cultivation of C. necator HP80.
Collapse
Affiliation(s)
- Michelle-Sophie Gerlach
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstr. 76, ACK24, 13355, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstr. 76, ACK24, 13355, Berlin, Germany
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstr. 76, ACK24, 13355, Berlin, Germany.
| |
Collapse
|
4
|
Ebu SM, Ray L, Panda AN, Gouda SK. De novo assembly and comparative genome analysis for polyhydroxyalkanoates-producing Bacillus sp. BNPI-92 strain. J Genet Eng Biotechnol 2023; 21:132. [PMID: 37991636 PMCID: PMC10665291 DOI: 10.1186/s43141-023-00578-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/26/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Certain Bacillus species play a vital role in polyhydroxyalkanoate (PHA) production. However, most of these isolates did not properly identify to species level when scientifically had been reported. RESULTS From NGS analysis, 5719 genes were predicted in the de novo genome assembly. Based on genome annotation using RAST server, 5,527,513 bp sequences were predicted with 5679 bp number of protein-coding sequence. Its genome sequence contains 35.1% and 156 GC content and contigs, respectively. In RAST server analysis, subsystem (43%) and non-subsystem coverage (57%) were generated. Ortho Venn comparative genome analysis indicated that Bacillus sp. BNPI-92 shared 2930 gene cluster (core gene) with B. cereus ATCC 14579 T (AE016877), B. paranthracis Mn5T (MACE01000012), B. thuringiensis ATCC 10792 T (ACNF01000156), and B. antrics Amen T (AE016879) strains. For our strain, the maximum gene cluster (190) was shared with B. cereus ATCC 14579 T (AE016877). For Ortho Venn pair wise analysis, the maximum overlapping gene clusters thresholds have been detected between Bacillus s p.BNPI-92 and Ba. cereus ATCC 14579 T (5414). Average nucleotide identity (ANI) such as OriginalANI and OrthoANI, in silicon digital DND-DNA hybridization (isDDH), Type (Strain) Genome Server (TYGS), and Genome-Genome Distance Calculator (GGDC) were more essentially related Bacillus sp. BNPI-92 with B. cereus ATCC 14579 T strain. Therefore, based on the combination of RAST annotation, OrthoVenn server, ANI and isDDH result Bacillus sp.BNPI-92 strain was strongly confirmed to be a B. cereus type strain. It was designated as B. cereus BNPI-92 strain. In B. cereus BNPI-92 strain whole genome sequence, PHA biosynthesis encoding genes such as phaP, phaQ, phaR (PHA synthesis repressor phaR gene sequence), phaB/phbB, and phaC were predicted on the same operon. These gene clusters were designated as phaPQRBC. However, phaA was located on other operons. CONCLUSIONS This newly obtained isolate was found to be new a strain based on comparative genomic analysis and it was also observed as a potential candidate for PHA biosynthesis.
Collapse
Affiliation(s)
- Seid Mohammed Ebu
- Department of Applied Biology, SoANS, Adama Science and Technology University, Oromia, Ethiopia.
| | - Lopamudra Ray
- School of Law, Campus -16 Adjunct Faculty, School of Biotech, Campus-11 KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Ananta N Panda
- School of Biotechnology, Campus-11 KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Sudhansu K Gouda
- School of Biotechnology, Campus-11 KIIT University, Bhubaneswar, Odisha, 751024, India
| |
Collapse
|
5
|
Manoli MT, Blanco FG, Rivero-Buceta V, Kniewel R, Alarcon SH, Salgado S, Prieto MA. Heterologous constitutive production of short-chain-length polyhydroxyalkanoates in Pseudomonas putida KT2440: the involvement of IbpA inclusion body protein. Front Bioeng Biotechnol 2023; 11:1275036. [PMID: 38026847 PMCID: PMC10646324 DOI: 10.3389/fbioe.2023.1275036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Designing cell factories for the production of novel polyhydroxyalkanoates (PHAs) via smart metabolic engineering is key to obtain à la carte materials with tailored physicochemical properties. To this end, we used the model medium-chain-length-PHA producing bacterium, P. putida KT2440 as a chassis, which is characterized by its metabolic versatility and stress tolerance. Different PHA biosynthetic modules were assembled in expression plasmids using the Golden gate/MoClo modular assembly technique to implement an orthogonal short-chain-lengh-PHA (scl-PHA) switch in a "deaf" PHA mutant. This was specifically constructed to override endogenous multilevel regulation of PHA synthesis in the native strain. We generated a panel of engineered approaches carrying the genes from Rhodospirillum rubrum, Cupriavidus necator and Pseudomonas pseudoalcaligenes, demonstrating that diverse scl-PHAs can be constitutively produced in the chassis strain to varying yields from 23% to 84% PHA/CDW. Co-feeding assays of the most promising engineered strain harboring the PHA machinery from C. necator resulted to a panel of PHBV from 0.6% to 19% C5 monomeric incorporation. Chromosomally integrated PHA machineries with high PhaCCn synthase dosage successfully resulted in 68% PHA/CDW production. Interestingly, an inverse relationship between PhaC synthase dosage and granule size distribution was demonstrated in the heterologous host. In this vein, it is proposed the key involvement of inclusion body protein IbpA to the heterologous production of tailored PHA in P. putida KT2440.
Collapse
Affiliation(s)
- Maria-Tsampika Manoli
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Francisco G. Blanco
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Virginia Rivero-Buceta
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Ryan Kniewel
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Sandra Herrera Alarcon
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Sergio Salgado
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - M. Auxiliadora Prieto
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| |
Collapse
|
6
|
Aghaali Z, Naghavi MR. Biotechnological Approaches for Enhancing Polyhydroxyalkanoates (PHAs) Production: Current and Future Perspectives. Curr Microbiol 2023; 80:345. [PMID: 37731015 DOI: 10.1007/s00284-023-03452-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/19/2023] [Indexed: 09/22/2023]
Abstract
The benefits of biotechnology are not limited to genetic engineering, but it also displays its great impact on industrial uses of crops (e.g., biodegradable plastics). Polyhydroxyalkanoates (PHAs) make a diverse class of bio-based and biodegradable polymers naturally synthesized by numerous microorganisms. However, several C3 and C4 plants have also been genetically engineered to produce PHAs. The highest production yield of PHAs was obtained with a well-known C3 plant, Arabidopsis thaliana, upto 40% of the dry weight of the leaf. This review summarizes all biotechnological mechanisms that have been adopted with the goal of increasing PHAs production in bacteria and plant species alike. Moreover, the possibility of using some methods that have not been applied in bioplastic science are discussed with special attention to plants. These include producing PHAs in transgenic hairy roots and cell suspension cultures, making transformed bacteria and plants via transposons, constructing an engineered metabolon, and overexpressing of phaP and the ABC operon concurrently. Taken together, that biotechnology will be highly beneficial for reducing plastic pollution through the implementation of biotechnological strategies is taken for granted.
Collapse
Affiliation(s)
- Zahra Aghaali
- Department of Genetic and Plant Breeding, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Mohammad Reza Naghavi
- Division of Biotechnology, Department of Agronomy and Plant Breeding, College of Agricultural and Natural Resources, University of Tehran, Karaj, Iran.
| |
Collapse
|
7
|
Collas F, Dronsella BB, Kubis A, Schann K, Binder S, Arto N, Claassens NJ, Kensy F, Orsi E. Engineering the biological conversion of formate into crotonate in Cupriavidus necator. Metab Eng 2023; 79:49-65. [PMID: 37414134 DOI: 10.1016/j.ymben.2023.06.015] [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: 03/14/2023] [Revised: 06/08/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
To advance the sustainability of the biobased economy, our society needs to develop novel bioprocesses based on truly renewable resources. The C1-molecule formate is increasingly proposed as carbon and energy source for microbial fermentations, as it can be efficiently generated electrochemically from CO2 and renewable energy. Yet, its biotechnological conversion into value-added compounds has been limited to a handful of examples. In this work, we engineered the natural formatotrophic bacterium C. necator as cell factory to enable biological conversion of formate into crotonate, a platform short-chain unsaturated carboxylic acid of biotechnological relevance. First, we developed a small-scale (150-mL working volume) cultivation setup for growing C. necator in minimal medium using formate as only carbon and energy source. By using a fed-batch strategy with automatic feeding of formic acid, we could increase final biomass concentrations 15-fold compared to batch cultivations in flasks. Then, we engineered a heterologous crotonate pathway in the bacterium via a modular approach, where each pathway section was assessed using multiple candidates. The best performing modules included a malonyl-CoA bypass for increasing the thermodynamic drive towards the intermediate acetoacetyl-CoA and subsequent conversion to crotonyl-CoA through partial reverse β-oxidation. This pathway architecture was then tested for formate-based biosynthesis in our fed-batch setup, resulting in a two-fold higher titer, three-fold higher productivity, and five-fold higher yield compared to the strain not harboring the bypass. Eventually, we reached a maximum product titer of 148.0 ± 6.8 mg/L. Altogether, this work consists in a proof-of-principle integrating bioprocess and metabolic engineering approaches for the biological upgrading of formate into a value-added platform chemical.
Collapse
Affiliation(s)
| | - Beau B Dronsella
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Karin Schann
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
| | | | - Enrico Orsi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
| |
Collapse
|
8
|
Jämsä T, Tervasmäki P, Pitkänen JP, Salusjärvi L. Inactivation of poly(3-hydroxybutyrate) (PHB) biosynthesis in 'Knallgas' bacterium Xanthobacter sp. SoF1. AMB Express 2023; 13:75. [PMID: 37452197 PMCID: PMC10349022 DOI: 10.1186/s13568-023-01577-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
Aerobic hydrogen-oxidizing 'Knallgas' bacteria are promising candidates for microbial cell factories due to their ability to use hydrogen and carbon dioxide as the sole energy and carbon sources, respectively. These bacteria can convert atmospheric CO2 to chemicals which could help to mitigate climate change by replacing fossil fuel-based chemicals. A known method to enhance the product yield is to disrupt competing metabolic pathways in the host organism. One such pathway in many 'Knallgas' bacteria is polyhydroxybutyrate (PHB) biosynthesis. In this study, the PHB biosynthesis genes of a non-model 'Knallgas' bacterium Xanthobacter sp. SoF1 were identified. Consequently, the phaA, phaB and phaC genes were individually deleted and the resulting knockouts were evaluated for their ability to produce PHB in autotrophic shake flask and small-scale bioreactor cultivations. The results demonstrate that PHB production was inactivated in the phaC1 knockout strain, which advances the development of Xanthobacter sp. SoF1 as a production host.
Collapse
Affiliation(s)
- Tytti Jämsä
- VTT Technical Research Centre of Finland Ltd., 02150, Espoo, Finland.
| | | | | | - Laura Salusjärvi
- VTT Technical Research Centre of Finland Ltd., 02150, Espoo, Finland
| |
Collapse
|
9
|
Xie Z, Wang D, Ben Fekih I, Yu Y, Li Y, Alwathnani H, Herzberg M, Rensing C. Whole Genome Sequence Analysis of Cupriavidus necator C39, a Multiple Heavy Metal(loid) and Antibiotic Resistant Bacterium Isolated from a Gold/Copper Mine. Microorganisms 2023; 11:1518. [PMID: 37375020 DOI: 10.3390/microorganisms11061518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Here a multiple heavy metal and antibiotic resistant bacterium Cupriavidus necator C39 (C. necator C39) was isolated from a Gold-Copper mine in Zijin, Fujian, China. C. necator C39 was able to tolerate intermediate concentrations of heavy metal(loid)s in Tris Minimal (TMM) Medium (Cu(II) 2 mM, Zn(II) 2 mM, Ni(II) 0.2 mM, Au(III) 70 μM and As(III) 2.5 mM). In addition, high resistance to multiple antibiotics was experimentally observed. Moreover, strain C39 was able to grow on TMM medium containing aromatic compounds such as benzoate, phenol, indole, p-hydroxybenzoic acid or phloroglucinol anhydrous as the sole carbon sources. The complete genome of this strain revealed 2 circular chromosomes and 1 plasmid, and showed the closest type strain is C. necator N-1T based on Genome BLAST Distance Phylogeny. The arsenic-resistance (ars) cluster GST-arsR-arsICBR-yciI and a scattered gene encoding the putative arsenite efflux pump ArsB were identified on the genome of strain C39, which thereby may provide the bacterium a robust capability for arsenic resistance. Genes encoding multidrug resistance efflux pump may confer high antibiotic resistance to strain C39. Key genes encoding functions in degradation pathways of benzene compounds, including benzoate, phenol, benzamide, catechol, 3- or 4-fluorobenzoate, 3- or 4-hydroxybenzoate and 3,4-dihydroxybenzoate, indicated its potential for degrading those benzene compounds.
Collapse
Affiliation(s)
- Zhenchen Xie
- Institute of Environmental Microbiology, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dan Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ibtissem Ben Fekih
- Institute of Environmental Microbiology, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Functional and Evolutionary Entomology, Terra, Gembloux Agro-Bio Tech, University of Liege, Passage des Deportes-2, B-5030 Gembloux, Belgium
| | - Yanshuang Yu
- Institute of Environmental Microbiology, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanping Li
- Institute of Environmental Microbiology, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hend Alwathnani
- Department of Botany and Microbiology, King Saud University, Riyadh 11495, Saudi Arabia
| | - Martin Herzberg
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle, Germany
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Complete genome sequence of Aquitalea pelogenes USM4 (JCM19919), a polyhydroxyalkanoate producer. Arch Microbiol 2023; 205:66. [PMID: 36645481 DOI: 10.1007/s00203-023-03406-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
Polyhydroxyalkanoate (PHA) is a type of biopolymer produced by most bacteria and archaea, resembling thermoplastic with biodegradability and biocompatibility features. Here, we report the complete genome of a PHA producer, Aquitalea sp. USM4, isolated from Perak, Malaysia. This bacterium possessed a 4.2 Mb circular chromosome and a 54,370 bp plasmid. A total of 4067 predicted protein-coding sequences, 87 tRNA genes, and 25 rRNA operons were identified using PGAP. Based on ANI and dDDH analysis, the Aquitalea sp. USM4 is highly similar to Aquitalea pelogenes. We also identified genes, including acetyl-CoA (phaA), acetoacetyl-CoA (phaB), PHA synthase (phaC), enoyl-CoA hydratase (phaJ), and phasin (phaP), which play an important role in PHA production in Aquitalea sp. USM4. The heterologous expression of phaC1 from Aquitalea sp. USM4 in Cupriavidus necator PHB-4 was able to incorporate six different types of PHA monomers, which are 3-hydroxybutyrate (3HB), 3-hydroxyvalerate (3HV), 4-hydroxybutyrate (4HB), 5-hydroxyvalerate (5HV), 3-hydroxyhexanoate (3HHx) and isocaproic acid (3H4MV) with suitable precursor substrates. This is the first complete genome sequence of the genus Aquitalea among the 22 genome sequences from 4 Aquitalea species listed in the GOLD database, which provides an insight into its genome evolution and molecular machinery responsible for PHA biosynthesis.
Collapse
|
12
|
An efficient and reusable N,N-dimethylacetamide/LiCl solvent system for the extraction of high-purity polyhydroxybutyrate from bacterial biomass. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
13
|
Tan HT, Chek MF, Neoh SZ, Ang SL, Yoshida S, Hakoshima T, Sudesh K. Characterization of the polyhydroxyalkanoate (PHA) synthase from Ideonella sakaiensis, a bacterium that is capable of degrading and assimilating poly(ethylene terephthalate). Polym Degrad Stab 2022. [DOI: 10.1016/j.polymdegradstab.2022.110160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
14
|
Yoon J, Bae J, Kang S, Cho BK, Oh MK. Poly-3-hydroxybutyrate production in acetate minimal medium using engineered Methylorubrum extorquens AM1. BIORESOURCE TECHNOLOGY 2022; 353:127127. [PMID: 35398538 DOI: 10.1016/j.biortech.2022.127127] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Acetate is regarded as a sustainable microbial feedstock that is synthesized from biowastes such as synthesis gas (syngas), carbon dioxide, lignocellulose, or organic waste. In this study, Methylorubrum extorquens AM1 was engineered to improve the production of bioplastic poly-3-hydroxybutyrate (PHB) using acetate as the sole carbon source. To utilize acetate as a carbon source and methanol as an energy source, acs encoding acetyl-CoA synthetase and fdh from Burkholderia stabilis were overexpressed, while ftfL involved in the assimilation of methanol into formyl-tetrahydrofolate was deleted. The yields of biomass and PHB from acetate significantly improved, and the growth rate and PHB content of the bacteria increased. In addition, sustainability of the PHB production was demonstrated using acetate derived from carbon dioxide and syngas. This study shows that biopolymers could be synthesized efficiently using acetate as the sole carbon source through metabolic engineering and the supply of energy cofactors.
Collapse
Affiliation(s)
- Jihee Yoon
- Department of Chemical and Biological Engineering, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jiyun Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Seulgi Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea.
| |
Collapse
|
15
|
Saito S, Imai R, Miyahara Y, Nakagawa M, Orita I, Tsuge T, Fukui T. Biosynthesis of Poly(3-hydroxybutyrate- co-3-hydroxyhexanoate) From Glucose by Escherichia coli Through Butyryl-CoA Formation Driven by Ccr-Emd Combination. Front Bioeng Biotechnol 2022; 10:888973. [PMID: 35646875 PMCID: PMC9134075 DOI: 10.3389/fbioe.2022.888973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/11/2022] [Indexed: 11/29/2022] Open
Abstract
Poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)] is a practical kind of bacterial polyhydroxyalkanoates (PHAs). A previous study has established an artificial pathway for the biosynthesis of P(3HB-co-3HHx) from structurally unrelated sugars in Ralstonia eutropha, in which crotonyl-CoA carboxylase/reductase (Ccr) and ethylmalonyl-CoA decarboxylase (Emd) are a key combination for generation of butyryl-CoA and the following chain elongation. This study focused on the installation of the artificial pathway into Escherichia coli. The recombinant strain of E. coli JM109 harboring 11 heterologous genes including Ccr and Emd produced P(3HB-co-3HHx) composed of 14 mol% 3HHx with 41 wt% of dry cellular weight from glucose. Further investigations revealed that the C6 monomer (R)-3HHx-CoA was not supplied by (R)-specific reduction of 3-oxohexanoyl-CoA but by (R)-specific hydration of 2-hexenoyl-CoA formed through reverse β-oxidation after the elongation from C4 to C6. While contribution of the reverse β-oxidation to the conversion of the C4 intermediates was very limited, crotonyl-CoA, a precursor of butyryl-CoA, was generated by dehydration of (R)-3HB-CoA. Several modifications previously reported for enhancement of bioproduction in E. coli were examined for the copolyester synthesis. Elimination of the global regulator Cra or PdhR as well as the block of acetate formation resulted in poor PHA synthesis. The strain lacking RNase G accumulated more PHA but with almost no 3HHx unit. Introduction of the phosphite oxidation system for regeneration of NADPH led to copolyester synthesis with the higher cellular content and higher 3HHx composition by two-stage cultivation with phosphite than those in the absence of phosphite.
Collapse
Affiliation(s)
- Shu Saito
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ryu Imai
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuki Miyahara
- School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Mari Nakagawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Izumi Orita
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Takeharu Tsuge
- School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| |
Collapse
|
16
|
Olavarria K, Pijman YO, Cabrera R, van Loosdrecht MCM, Wahl SA. Engineering an acetoacetyl-CoA reductase from Cupriavidus necator toward NADH preference under physiological conditions. Sci Rep 2022; 12:3757. [PMID: 35260659 PMCID: PMC8904767 DOI: 10.1038/s41598-022-07663-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/21/2022] [Indexed: 11/09/2022] Open
Abstract
The coupling of PHB generation with NADH reoxidation is required to generate PHB as a fermentation product. A fundamental trait to accomplish this feature is to express a functional NADH-preferring acetoacetyl-CoA reductase, engaged in PHB accumulation. One way to obtain such a reductase is by engineering the cofactor preference of the acetoacetyl-CoA reductase encoded by the phaB1 gene from Cupriavidus necator (AARCn1). Aiming to have a deeper understanding of the structural determinants of the cofactor preference in AARCn1, and to obtain an NADH-preferring acetoacetyl-CoA reductase derived from this protein, some engineered enzymes were expressed, purified and kinetically characterized, together with the parental AARCn1. One of these engineered enzymes, Chimera 5, experimentally showed a selectivity ratio ((kcat/KM)NADH/(kcat/KM)NADPH) ≈ 18, which is 160 times higher than the selectivity ratio experimentally observed in the parental AARCn1. A thermodynamic-kinetic approach was employed to estimate the cofactor preference and flux capacity of Chimera 5 under physiological conditions. According to this approach, Chimera 5 could prefer NADH over NADPH between 25 and 150 times. Being a derivative of AARCn1, Chimera 5 should be readily functional in Escherichia coli and C. necator. Moreover, with the expected expression level, its activity should be enough to sustain PHB accumulation fluxes similar to the fluxes previously observed in these biotechnologically relevant cell factories.
Collapse
Affiliation(s)
- Karel Olavarria
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands. .,Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6700 EH, Wageningen, The Netherlands.
| | - Yared O Pijman
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Ricardo Cabrera
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Región Metropolitana, Chile
| | - Mark C M van Loosdrecht
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - S Aljoscha Wahl
- Departement Biotechnologie, Faculteit Technische Natuurwetenschappen, Technische Universiteit Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| |
Collapse
|
17
|
Chin JHC, Samian MR, Normi YM. Characterization of polyhydroxyalkanoate production capacity, composition and weight synthesized by Burkholderia cepacia JC-1 from various carbon sources. Heliyon 2022; 8:e09174. [PMID: 35368536 PMCID: PMC8971576 DOI: 10.1016/j.heliyon.2022.e09174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/27/2021] [Accepted: 03/17/2022] [Indexed: 12/17/2022] Open
Abstract
Polyhydroxyalkanoates (PHA) are microbial polymers that have received widespread attention in recent decades as potential alternatives to some petrochemical-based plastics. However, widespread use of PHA is often impeded by its cost of production. Therefore, the search for and systematic investigation of versatile microbial PHA producers capable of using various carbon sources, even in the form of animal fats, for PHA biosynthesis is desirable. This study highlights the PHA production capacity, monomer composition and molecular weight synthesized by Burkholderia cepacia JC-1, a locally isolated strain from soil, from various carbon sources. In the category of simple sugars and plant oils, the use of glucose and palm oil at C:N ratio of 40 resulted in the highest accumulation of 52 wt% and 36 wt% poly(3-hydroxybutyrate) [P(3HB)] homopolymer and dry cell weight of 2.56 g/L and 3.17 g/L, respectively. Interestingly, B. cepacia JC-1 was able to directly utilize animal-derived lipid in the form of crude and extracted chicken fat, resulting in appreciable dry cell weight and PHA contents of up to 3.19 g/L and 47 wt% respectively, surpassing even that of palm oil in the group of triglycerides as substrates. The presence of antibiotics (streptomycin) in cultivation medium did not significantly affect cell growth and polymer production. The supply of sodium pentanoate as a co-substrate resulted in the incorporation of 3-hydroxyvalerate (3HV) monomer at fractions up to 37 mol%. The molecular weight of polymers produced from glucose, palm oil and chicken fat were in the range of 991–2118 kDa, higher than some reported studies involving native strains. The results from this study form an important basis for possible improvements in using B. cepacia JC-1 and crude chicken fats in solid form for PHA production in the future.
Collapse
Affiliation(s)
- Julian Hock-Chye Chin
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Mohd Razip Samian
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Bimolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| |
Collapse
|
18
|
Improved polyhydroxybutyrate production by Cupriavidus necator and the photocatalyst graphitic carbon nitride from fructose under low light intensity. Int J Biol Macromol 2022; 203:526-534. [PMID: 35120931 DOI: 10.1016/j.ijbiomac.2022.01.179] [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: 11/13/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/21/2022]
Abstract
The photocatalyst graphitic carbon nitride (g-C3N4) is known to photostimulate the production of the bioplastic polyhydroxybutyrate (PHB) by Cupriavidus necator. In previous studies, the combination of C. necator and g-C3N4 increased PHB yield from either an organic or inorganic carbon substrate under a light intensity of 4200 lx. Here, different parameters including light intensity, pH, temperature, nitrogen and carbon concentrations, aeration, and inoculum size were explored to maximize PHB production by hybrid photosynthesis from fructose and visible light. A g-C3N4/C. necator culture grown with a lower light intensity of 2100 lx, an inoculum size of 128.30 × 106 CFU ml-1, and constant aeration produced 7.16 g l-1 d-1 PHB with a product yield from fructose of 60.94%. Furthermore, the ratio of incident photons harvested by g-C3N4 converted into NADPH+H+ by C. necator for PHB production was improved to 19.74% after the process optimization. In comparison, the PHB production rate of a non-optimized g-C3N4/C. necator system exposed to 4200 lx was only 2.94 g l-1 d-1 with a product yield from fructose of 33.29%. These results demonstrate that hybrid photosynthesis productivity can be significantly augmented by decreasing light intensity and adjusting other parameters, which is promising for future bioproduction applications.
Collapse
|
19
|
McGregor C, Minton NP, Kovács K. Biosynthesis of Poly(3HB- co-3HP) with Variable Monomer Composition in Recombinant Cupriavidus necator H16. ACS Synth Biol 2021; 10:3343-3352. [PMID: 34762808 DOI: 10.1021/acssynbio.1c00283] [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: 11/29/2022]
Abstract
Polyhydroxyalkanoates are attractive alternatives to traditional plastics. However, although polyhydroxybutyrate (PHB) is produced in large quantities by Cupriavidus necator H16, its properties are far from ideal for the manufacture of plastic products. These properties may be improved through its coproduction with 3-hydroxypropionate (3HP), which leads to the formation of the copolymer poly(3-hydroxybutyrate-co-3-hydroxypropionate) (poly(3HB-co-3HP). To achieve this, a pathway was designed to enable C. necator H16 to convert β-alanine to 3HP. The initial low levels of incorporation of 3HP into the copolymer were overcome by the overproduction of the native propionyl-CoA transferase together with PHA synthase from Chromobacterium sp. USM2. Following optimization of 3HP incorporation into the copolymer, the molar fraction of 3HP could be controlled by cultivation in medium containing different concentrations of β-alanine. Between 0 and 80 mol % 3HP could be achieved. Further supplementation with 2 mM cysteine increased the maximum 3HP molar fraction to 89%. Additionally, the effect of deletions of the phaA and phaB1 genes of the phaCAB operon on 3HP molar fraction were investigated. A phaAB1 double knockout resulted in a copolymer containing 91 mol % 3HP without the need for cysteine supplementation.
Collapse
Affiliation(s)
- Callum McGregor
- BBSRC/EPSRC Synthetic Biology Research Centre, The University of Nottingham, Nottingham NG7 2RD, U.K
| | - Nigel P. Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, The University of Nottingham, Nottingham NG7 2RD, U.K
| | - Katalin Kovács
- BBSRC/EPSRC Synthetic Biology Research Centre, The University of Nottingham, Nottingham NG7 2RD, U.K
- School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, U.K
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
The over-expression of phasin and regulator genes promoting the synthesis of polyhydroxybutyrate in Cupriavidus necator H16 under non-stress conditions. Appl Environ Microbiol 2021; 88:e0145821. [PMID: 34731058 DOI: 10.1128/aem.01458-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cupriavidus necator H16 is an ideal strain for polyhydroxybutyrate (PHB) production from CO2. Low-oxygen-stress can induce PHB synthesis in C. necator H16 while reducing bacterial growth under chemoautotrophic culture. The optimum growth and PHB synthesis of C. necator H16 cannot be achieved simultaneously, which restricts PHB production. The present study was initiated to address the issue through comparative transcriptome and gene function analysis. Firstly, the comparative transcriptome of C. necator H16 chemoautotrophically cultured under low-oxygen-stress and non-stress conditions was studied. Three types of transcription different genes were discovered: PHB enzymatic synthesis, PHB granulation, and regulators. Under low-oxygen-stress condition, acetoacetyl-CoA reductase gene phaB2, PHB synthase gene phaC2, phasins genes phaP1 and phaP2, regulators genes uspA and rpoN were up-regulated 3.0, 2.5, 1.8, 2.7, 3.5, 1.6 folds, respectively. Secondly, the functions of up-regulated genes and their applications in PHB synthesis were further studied. It was found that the over-expression of phaP1, phaP2, uspA, and rpoN can induce PHB synthesis under non-stress condition, while phaB2 and phaC2 have no significant effect. Under the optimum condition, PHB percentage content in C. necator H16 was respectively increased by 37.2%, 28.4%, 15.8%, and 41.0% with the over-expression of phaP1, phaP2, uspA, and rpoN, and the corresponding PHB production increased by 49.8%, 42.9%, 47.0%, and 77.5% under non-stress chemoautotrophic conditions. Similar promotion by phaP1, phaP2, uspA, and rpoN was observed in heterotrophically cultured C. necator H16. The PHB percentage content and PHB production were respectively increased by 54.4% and 103.1% with the over-expression of rpoN under non-stress heterotrophic conditions. Importance Microbial fixation of CO2 is an effective way to reduce greenhouse gases. Some microbes such as C. necator H16 usually accumulate PHB when they grow under stress. Low-oxygen-stress can induce PHB synthesis when C. necator H16 is autotrophically cultured with CO2, H2, and O2, while under stress, growth is restricted and total PHB yield is reduced. Achieving the optimal bacterial growth and PHB synthesis at the same time is an ideal condition for transforming CO2 into PHB by C. necator H16. The present study was initiated to clarify the molecular basis of low-oxygen-stress promoting PHB accumulation and to realize the optimal PHB production by C. necator H16. Genes up-regulated under non-stress conditions were identified through comparative transcriptome analysis and over-expression of phasin and regulator genes were demonstrated to promote PHB synthesis in C. necator H16.
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
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.
Collapse
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.
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Lim H, Chuah JA, Chek MF, Tan HT, Hakoshima T, Sudesh K. Identification of regions affecting enzyme activity, substrate binding, dimer stabilization and polyhydroxyalkanoate (PHA) granule morphology in the PHA synthase of Aquitalea sp. USM4. Int J Biol Macromol 2021; 186:414-423. [PMID: 34246679 DOI: 10.1016/j.ijbiomac.2021.07.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/23/2021] [Accepted: 07/05/2021] [Indexed: 11/28/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are biopolyesters synthesized by microorganisms as intracellular energy reservoirs under stressful environmental conditions. PHA synthase (PhaC) is the key enzyme responsible for PHA biosynthesis, but the importance of its N- and C-terminal ends still remains elusive. Six plasmid constructs expressing truncation variants of Aquitalea sp. USM4 PhaC (PhaC1As) were generated and heterologously expressed in Cupriavidus necator PHB-4. Removal of the first six residues at the N-terminus enabled the modulation of PHA composition without altering the PHA content in cells. Meanwhile, deletion of 13 amino acids from the C-terminus greatly affected the catalytic activity of PhaC1As, retaining only 1.1-7.4% of the total activity. Truncation(s) at the N- and/or C-terminus of PhaC1As gradually diminished the incorporation of comonomer units, and revealed that the N-terminal region is essential for PhaC1As dimerization whereas the C-terminal region is required for stabilization. Notably, transmission electron microscopy analysis showed that PhaC modification affected the morphology of intracellular PHA granules, which until now is only known to be regulated by phasins. This study provided substantial evidence and highlighted the significance of both the N- and C-termini of PhaC1As in regulating intracellular granule morphology, activity, substrate specificity, dimerization and stability of the synthase.
Collapse
Affiliation(s)
- Hui Lim
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Jo-Ann Chuah
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Min Fey Chek
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hua Tiang Tan
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia.
| |
Collapse
|
26
|
Jeremy Wong HS, Huong KH, Shafie NAH, Amirul AAA. Genetic incorporation of oil-utilizing ability in Cupriavidus malaysiensis USMAA2-4 for sustainable polyhydroxyalkanoates production from palm olein and 1-pentanol. J Biotechnol 2021; 337:71-79. [PMID: 34233208 DOI: 10.1016/j.jbiotec.2021.07.001] [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] [Received: 01/06/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 11/25/2022]
Abstract
The sustainability in polyhydroxyalkanoates (PHA) production is drawing increasing attention as the effort to increase the economic feasibility for commercialization pursues. Oleic acid is widely preferred by bacteria but its employment for PHA production makes sustainability rather dubious. This study showed promising poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] content of 68 wt % by lipase genes-harbouring Cupriavidus malaysiensis USMAA2-4 transformant from palm olein and 1-pentanol. High oleic acid content and low oil saturation caused palm olein to outperform crude palm oil, crude palm kernel oil and soybean oil due to its preference for oleic acid shown by previous screening. The transformant showed 8-fold and 40-fold higher lipase activity compared to C. necator H16 and its wild-type respectively. The transformant was unaffected by Co2+ but the growth of C. necator H16 was inversely proportional to Co2+ concentration and the employment of 1-pentanol also ceased its growth and PHA accumulation. Although the inhibitory effect of Fe2+, Cu2+ and Zn2+ at high molarity on LipA decreased PHA content of C. malaysiensis USMAA2-4 transformant by 23-24 wt %, the lipase activity was restorable with high molarity of Ca2+, thus resulted in higher PHA content. The transformant enabled the employment of low-cost 1-pentanol as the precursor for cost-effective PHA production and its preference for palm olein contributed to higher sustainability.
Collapse
Affiliation(s)
- Hau Seung Jeremy Wong
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, 11800, Malaysia; Centre for Chemical Biology, Sains@USM, Bayan Lepas, Penang, 11900, Malaysia.
| | - Kai Hee Huong
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, 11800, Malaysia; Centre for Chemical Biology, Sains@USM, Bayan Lepas, Penang, 11900, Malaysia.
| | | | - Al-Ashraf Abdullah Amirul
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, 11800, Malaysia; Centre for Chemical Biology, Sains@USM, Bayan Lepas, Penang, 11900, Malaysia.
| |
Collapse
|
27
|
Gascoyne JL, Bommareddy RR, Heeb S, Malys N. Engineering Cupriavidus necator H16 for the autotrophic production of (R)-1,3-butanediol. Metab Eng 2021; 67:262-276. [PMID: 34224897 PMCID: PMC8449065 DOI: 10.1016/j.ymben.2021.06.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/08/2021] [Accepted: 06/30/2021] [Indexed: 11/20/2022]
Abstract
Butanediols are widely used in the synthesis of polymers, specialty chemicals and important chemical intermediates. Optically pure R-form of 1,3-butanediol (1,3-BDO) is required for the synthesis of several industrial compounds and as a key intermediate of β-lactam antibiotic production. The (R)-1,3-BDO can only be produced by application of a biocatalytic process. Cupriavidus necator H16 is an established production host for biosynthesis of biodegradable polymer poly-3-hydroxybutryate (PHB) via acetyl-CoA intermediate. Therefore, the utilisation of acetyl-CoA or its upstream precursors offers a promising strategy for engineering biosynthesis of value-added products such as (R)-1,3-BDO in this bacterium. Notably, C. necator H16 is known for its natural capacity to fix carbon dioxide (CO2) using hydrogen as an electron donor. Here, we report engineering of this facultative lithoautotrophic bacterium for heterotrophic and autotrophic production of (R)-1,3-BDO. Implementation of (R)-3-hydroxybutyraldehyde-CoA- and pyruvate-dependent biosynthetic pathways in combination with abolishing PHB biosynthesis and reducing flux through the tricarboxylic acid cycle enabled to engineer strain, which produced 2.97 g/L of (R)-1,3-BDO and achieved production rate of nearly 0.4 Cmol Cmol−1 h−1 autotrophically. This is first report of (R)-1,3-BDO production from CO2. Engineering of chemolithoautotroph C. necator H16 for (R)-1,3-butanediol production. Implementation of (R)-3-hydroxybutyraldehyde-CoA- and pyruvate-dependent pathways for (R)-1,3-butanediol biosynthesis. Redirecting carbon flux for (R)-1,3-butanediol biosynthesis. Achieved 2.97 g/L of (R)-1,3-butanediol with production rate of nearly 0.4 Cmol/(Cmol h) autotrophically. First report of (R)-1,3-butanediol production from carbon dioxide.
Collapse
Affiliation(s)
- Joshua Luke Gascoyne
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Rajesh Reddy Bommareddy
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Stephan Heeb
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Naglis Malys
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Biodiscovery Institute, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom.
| |
Collapse
|
28
|
In Vivo Characterization and Application of the PHA Synthase from Azotobacter vinelandii for the Biosynthesis of Polyhydroxyalkanoate Containing 4-Hydroxybutyrate. Polymers (Basel) 2021; 13:polym13101576. [PMID: 34069008 PMCID: PMC8156725 DOI: 10.3390/polym13101576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 11/26/2022] Open
Abstract
Polyhydroxyalkanoate (PHA) is a biodegradable thermoplastic naturally synthesized by many microorganisms, and the PHA synthase (PhaC) is known to be the key enzyme involved in determining the material properties and monomer composition of the produced PHA. The ability to exploit widely distributed, commonly found soil microorganisms such as Azotobacter vinelandii to synthesize PHA containing the lipase-degradable 4-hydroxybutyrate (4HB) monomer will allow for convenient production of biocompatible and flexible PHA. Comparisons between the A. vinelandii wild type and mutant strains, with and without a surface layer (S-layer), respectively, in terms of gene or amino acid sequences, synthase activity, granule morphology, and PHA productivity, revealed that the S-layer is the sole factor affecting PHA biosynthesis by A. vinelandii. Based on PHA biosynthesis using different carbon sources, the PhaC of A. vinelandii showed specificity for short-chain-length PHA monomers, making it a member of the Class I PHA synthases. In addition, it was proven that the PhaC of A. vinelandii has the inherent ability to polymerize 4-hydroxybutyrate (4HB) and the mediated accumulation of PHA with 4HB fractions ranging from 10 mol% to as high as 22 mol%. The synthesis of biocompatible PHA containing tailorable amounts of 4HB with an expanded range of elasticity and lipase-degradability will enable a wider range of applications in the biomedical field.
Collapse
|
29
|
Revalorization of adsorbed residual oil in spent bleaching clay as a sole carbon source for polyhydroxyalkanoate (PHA) accumulation in Cupriavidus necator Re2058/pCB113. Polym J 2020. [DOI: 10.1038/s41428-020-00418-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
30
|
Park YL, Choi TR, Han YH, Song HS, Park JY, Bhatia SK, Gurav R, Choi KY, Kim YG, Yang YH. Effects of osmolytes on salt resistance of Halomonas socia CKY01 and identification of osmolytes-related genes by genome sequencing. J Biotechnol 2020; 322:21-28. [DOI: 10.1016/j.jbiotec.2020.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/09/2020] [Accepted: 07/09/2020] [Indexed: 10/23/2022]
|
31
|
Stöckl M, Harms S, Dinges I, Dimitrova S, Holtmann D. From CO 2 to Bioplastic - Coupling the Electrochemical CO 2 Reduction with a Microbial Product Generation by Drop-in Electrolysis. CHEMSUSCHEM 2020; 13:4086-4093. [PMID: 32677318 PMCID: PMC7496250 DOI: 10.1002/cssc.202001235] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/01/2020] [Indexed: 05/19/2023]
Abstract
CO2 has been electrochemically reduced to the intermediate formate, which was subsequently used as sole substrate for the production of the polymer polyhydroxybutyrate (PHB) by the microorganism Cupriavidus necator. Faradaic efficiencies (FE) up to 54 % have been reached with Sn-based gas-diffusion electrodes in physiological electrolyte. The formate containing electrolyte can be used directly as drop-in solution in the following biological polymer production by resting cells. 56 mg PHB L-1 and a ratio of 34 % PHB per cell dry weight were achieved. The calculated overall FE for the process was as high as 4 %. The direct use of the electrolyte as drop-in media in the bioconversion enables simplified processes with a minimum of intermediate purification effort. Thus, an optimal coupling between electrochemical and biotechnological processes can be realized.
Collapse
Affiliation(s)
- Markus Stöckl
- Electrochemistry, Industrial BiotechnologyDECHEMA Research InstituteTheodor-Heuss-Allee 2560486Frankfurt am MainGermany
| | - Svenja Harms
- Electrochemistry, Industrial BiotechnologyDECHEMA Research InstituteTheodor-Heuss-Allee 2560486Frankfurt am MainGermany
| | - Ida Dinges
- Electrochemistry, Industrial BiotechnologyDECHEMA Research InstituteTheodor-Heuss-Allee 2560486Frankfurt am MainGermany
- Institute for Anorganic and Analytic ChemistryGoethe-Universität Frankfurt am MainMax-von-Laue-Straße 760438Frankfurt am MainGermany
| | - Steliyana Dimitrova
- Electrochemistry, Industrial BiotechnologyDECHEMA Research InstituteTheodor-Heuss-Allee 2560486Frankfurt am MainGermany
| | - Dirk Holtmann
- Electrochemistry, Industrial BiotechnologyDECHEMA Research InstituteTheodor-Heuss-Allee 2560486Frankfurt am MainGermany
- Institute of Bioprocess Engineering and Pharmaceutical TechnologyUniversity of Applied Sciences MittelhessenWiesenstrasse 1435390GiessenGermany
| |
Collapse
|
32
|
Pander B, Mortimer Z, Woods C, McGregor C, Dempster A, Thomas L, Maliepaard J, Mansfield R, Rowe P, Krabben P. Hydrogen oxidising bacteria for production of single‐cell protein and other food and feed ingredients. ENGINEERING BIOLOGY 2020; 4:21-24. [PMID: 36970394 PMCID: PMC9996702 DOI: 10.1049/enb.2020.0005] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/04/2020] [Indexed: 11/19/2022] Open
Abstract
Using hydrogen oxidising bacteria to produce protein and other food and feed ingredients is a form of industrial biotechnology that is gaining traction. The technology fixes carbon dioxide into products without the light requirements of agriculture and biotech that rely on primary producers such as plants and algae while promising higher growth rates, drastically less land, fresh water, and mineral requirements. The significant body of scientific knowledge on hydrogen oxidising bacteria continues to grow and genetic engineering tools are well developed for specific species. The scale-up success of other types of gas- fermentation using carbon monoxide or methane has paved the way for scale-up of a process that uses a mix of hydrogen, oxygen, and carbon dioxide to produce bacteria as a food and feed ingredients in a highly sustainable fashion.
Collapse
Affiliation(s)
| | - Zahara Mortimer
- School of Lifesciences University of Nottingham Nottingham UK
| | - Craig Woods
- Deep Branch Biotechnology Ltd Nottingham UK
- School of Lifesciences University of Nottingham Nottingham UK
| | - Callum McGregor
- Deep Branch Biotechnology Ltd Nottingham UK
- School of Lifesciences University of Nottingham Nottingham UK
| | - Andrew Dempster
- School of Lifesciences University of Nottingham Nottingham UK
| | | | - Joshua Maliepaard
- Deep Branch Biotechnology Ltd Nottingham UK
- Leiden Academic Centre for Drug Research University of Leiden Leiden The Netherlands
| | - Robert Mansfield
- Deep Branch Biotechnology Ltd Nottingham UK
- School of Lifesciences University of Nottingham Nottingham UK
| | - Peter Rowe
- Deep Branch Biotechnology Ltd Nottingham UK
| | | |
Collapse
|
33
|
Tan HT, Chek MF, Lakshmanan M, Foong CP, Hakoshima T, Sudesh K. Evaluation of BP-M-CPF4 polyhydroxyalkanoate (PHA) synthase on the production of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from plant oil using Cupriavidus necator transformants. Int J Biol Macromol 2020; 159:250-257. [PMID: 32417540 DOI: 10.1016/j.ijbiomac.2020.05.064] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 04/25/2020] [Accepted: 05/10/2020] [Indexed: 01/24/2023]
Abstract
Among the various types of polyhydroxyalkanoate (PHA), poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)] has a high potential to serve as commercial bioplastic due to its striking resemblance to petroleum-based plastics. In this study, five different genotypes of Cupriavidusnecator transformants harbouring the phaCBP-M-CPF4 gene (including PHB¯4/pBBR1-CBP-M-CPF4) were developed to evaluate the efficiency of 3HHx monomer incorporation. The fraction of 3-hydroxyhexanoate (3HHx) monomer that was incorporated into the PHA synthesized by these C. necator transformants using palm oil as the sole carbon source, was examined. Overall, co-expression of enoyl-CoA hydratase gene (phaJ1) from Pseudomonas aeruginosa, along with PHA synthase (PhaC), increased the 3HHx composition in the PHA copolymer. The differences in the enzyme activities of β-ketothiolase (PhaACn) and NADPH-dependent acetoacetyl-CoA reductase (PhaBCn) of the C. necator mutant hosts used in this study, were observed to alter the 3HHx composition and molecular weight of the PHA copolymer produced. The 3HHx fractions in the P(3HB-co-3HHx) produced by these C. necator transformants ranged between 1 and 18 mol%, while the weight-average molecular weight ranged from 0.7 × 106 to 1.8 × 106 Da. PhaCBP-M-CPF4 displayed a typical initial lag-phase and a relatively low synthase activity in the in vitro enzyme assay, which is thought to be the reason for the higher molecular weights of PHA obtained in this study.
Collapse
Affiliation(s)
- Hua Tiang Tan
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia USM, 11800, Pulau Pinang, Malaysia
| | - Min Fey Chek
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Manoj Lakshmanan
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia USM, 11800, Pulau Pinang, Malaysia; USM-RIKEN International Center for Aging Science (URICAS), School of Biological Sciences, Universiti Sains Malaysia USM, 11800, Pulau Pinang, Malaysia
| | - Choon Pin Foong
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia USM, 11800, Pulau Pinang, Malaysia; USM-RIKEN International Center for Aging Science (URICAS), School of Biological Sciences, Universiti Sains Malaysia USM, 11800, Pulau Pinang, Malaysia.
| |
Collapse
|
34
|
Choi TR, Jeon JM, Bhatia SK, Gurav R, Han YH, Park YL, Park JY, Song HS, Park HY, Yoon JJ, Seo SO, Yang YH. Production of Low Molecular Weight P(3HB-co-3HV) by Butyrateacetoacetate CoA-transferase (cftAB) in Escherichia coli. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0366-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
35
|
Sangkharak K, Paichid N, Yunu T, Prasertsan P. Enhancing the degradation of mixed polycyclic aromatic hydrocarbon and medium-chain-length polyhydroxyalkanoate production by mixed bacterial cultures using modified repeated batch fermentation. J Appl Microbiol 2020; 129:554-564. [PMID: 32162457 DOI: 10.1111/jam.14638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/04/2020] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
AIMS To increase the biodegradation of phenanthrene (PHE), pyrene (PYR) and fluoranthene (FLU) through mixed cultures of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria, using modified repeated batch fermentation. METHODS AND RESULTS Novel bacterial strains of Pseudomonas putida, Pseudomonas sp. and Ralstonia eutropha were cultivated and the biodegradation and conversion of mixed PAH to medium-chain-length polyhydroxyalkanoates (MCL-PHA) was determined. The highest degradation of PAH (100%) and PHA production (50·0%) was obtained in medium containing 30 mmol l-1 of mixed PAH after three cycles of repeated batch fermentation. The concentration of PAH in the reactor was increased from 30 to 90 mmol l-1 with repeated additions of PAH, and bacteria were able to produce PHA at 40% of cell dry mass. The MCL-PHA were identified by gas chromatography/mass spectroscopy, with the 3-hydroxydecanoate (3-HD) monomer higher than 75 mol.%. CONCLUSIONS This study demonstrated that the biodegradation of PHE, PYR and FLU was enhanced by modified repeated batch fermentation using a mixed culture of bacteria. In addition, this fermentation strategy also increased the production of PHA, with an increase in monomer composition. SIGNIFICANCE AND IMPACT OF THE STUDY This was the first study to describe the enhancement of the degradation of mixed solutions of PHE, PYR and FLU, and PHA production, using novel mixed bacterial cultures and modified repeated batch fermentation. The MCL-PHA formed had uniquely high 3-HD content.
Collapse
Affiliation(s)
- K Sangkharak
- Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung, Thailand
| | - N Paichid
- Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung, Thailand
| | - T Yunu
- Department of Chemistry, Faculty of Science, Thaksin University, Phatthalung, Thailand
| | - P Prasertsan
- Research and Development Office, Prince of Songkla University, Songkhla, Thailand
| |
Collapse
|
36
|
Tan IKP, Foong CP, Tan HT, Lim H, Zain NAA, Tan YC, Hoh CC, Sudesh K. Polyhydroxyalkanoate (PHA) synthase genes and PHA-associated gene clusters in Pseudomonas spp. and Janthinobacterium spp. isolated from Antarctica. J Biotechnol 2020; 313:18-28. [PMID: 32171790 DOI: 10.1016/j.jbiotec.2020.03.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/31/2022]
Abstract
The polyhydroxyalkanoate (PHA) producing capability of four bacterial strains isolated from Antarctica was reported in a previous study. This study analyzed the PHA synthase genes and the PHA-associated gene clusters from the two antarctic Pseudomonas isolates (UMAB-08 and UMAB-40) and the two antarctic Janthinobacterium isolates (UMAB-56 and UMAB-60) through whole-genome sequence analysis. The Pseudomonas isolates were found to carry PHA synthase genes which fall into two different PHA gene clusters, namely Class I and Class II, which are involved in the biosynthesis of short-chain-length-PHA (SCL-PHA) and medium-chain-length-PHA (MCL-PHA), respectively. On the other hand, the Janthinobacterium isolates carry a Class I and an uncharacterized putative PHA synthase genes. No other gene involved in PHA synthesis was detected in close proximity to the uncharacterized putative PHA synthase gene in the Janthinobacterium isolates, therefore it falls into a separate clade from the ordinary Class I, II, III and IV clades of PHA synthase (PhaC) phylogenetic tree. Multiple sequence alignment showed that the uncharacterized putative PHA synthase gene contains all the highly conserved amino acid residues and the proposed catalytic triad of PHA synthase. PHA biosynthesis and in vitro PhaC enzymatic assay results showed that this uncharacterized putative PHA synthase from Janthinobacterium sp. UMAB-60 is funtional. This report adds new knowledge to the PHA synthase database as we describe scarce information of PHA synthase genes and PHA-associated gene clusters from the antarctic bacterial isolates (extreme and geographically isolated environment) and comparing with those from non-antarctic PHA-producing bacteria.
Collapse
Affiliation(s)
- Irene Kit Ping Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Choon Pin Foong
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
| | - Hua Tiang Tan
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
| | - Hui Lim
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
| | - Noor-Afiqah Ahmad Zain
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
| | - Yung Chie Tan
- Department of Science and Technology, Codon Genomics S/B, Taman Dutamas, Balakong, 43200 Seri Kembangan, Malaysia
| | - Chee Choong Hoh
- Department of Science and Technology, Codon Genomics S/B, Taman Dutamas, Balakong, 43200 Seri Kembangan, Malaysia
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia.
| |
Collapse
|
37
|
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]
|
38
|
Zainab-L I, Sudesh K. High cell density culture of Cupriavidus necator H16 and improved biological recovery of polyhydroxyalkanoates using mealworms. J Biotechnol 2019; 305:35-42. [DOI: 10.1016/j.jbiotec.2019.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 11/26/2022]
|
39
|
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.
Collapse
|
40
|
Skoog E, Shin JH, Saez-Jimenez V, Mapelli V, Olsson L. Biobased adipic acid – The challenge of developing the production host. Biotechnol Adv 2018; 36:2248-2263. [DOI: 10.1016/j.biotechadv.2018.10.012] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/18/2018] [Accepted: 10/27/2018] [Indexed: 11/28/2022]
|
41
|
Segawa M, Wen C, Orita I, Nakamura S, Fukui T. Two NADH-dependent (S)-3-hydroxyacyl-CoA dehydrogenases from polyhydroxyalkanoate-producing Ralstonia eutropha. J Biosci Bioeng 2018; 127:294-300. [PMID: 30243533 DOI: 10.1016/j.jbiosc.2018.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/20/2018] [Accepted: 08/22/2018] [Indexed: 12/28/2022]
Abstract
Ralstonia eutropha H16 contains both NADH- and NADPH-dependent reduction activities to acetoacetyl-CoA, and the NADPH-dependent activity is mediated by PhaB paralogs with (R)-stereospecificity providing (R)-3-hydroxybutyryl (3HB)-CoA monomer for poly((R)-3-hydroxybutyrate) synthesis. In contrast, the gene encoding the NADH-dependent enzyme has not been identified to date. This study focused on the NADH-dependent dehydrogenase with (S)-stereospecificity in R. eutropha, as the (S)-specific reduction of acetoacetyl-CoA potentially competed with the polyester biosynthesis via (R)-3HB-CoA. The NADH-dependent reduction activity decreased to one-half when the gene for H16_A0282 (PaaH1), one of two homologs of clostridial NADH-3HB-CoA dehydrogenase, was deleted. The enzyme responsible for the remaining activity was partially purified and identified as H16_A0602 (Had) belonging to a different family from PaaH1. Gene disruption analysis elucidated that most of the NADH-dependent activity was mediated by PaaH1 and Had. The kinetic analysis using the recombinant enzymes indicated that PaaH1 and Had were both NADH-dependent 3-hydroxyacyl-CoA dehydrogenases with rather broad substrate specificity to 3-oxoacyl-CoAs of C4 to C8. The deletion of had in the R. eutropha strain previously engineered for biosynthesis of poly((R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate) led to decrease in the C6 composition of the copolyester synthesized from soybean oil, suggesting the role of Had in (S)-specific reduction of 3-oxohexanoyl-CoA with reverse β-oxidation direction. Crotonase ((S)-specific enoyl-CoA hydratase) in R. eutropha H16 was also partially purified and identified as H16_A3307.
Collapse
Affiliation(s)
- Mutsumi Segawa
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Cheng Wen
- 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
| | - Satoshi Nakamura
- 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.
| |
Collapse
|
42
|
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.
Collapse
|
43
|
Li Z, Li G, Chen X, Xia Z, Yao J, Yang B, Lei L, Hou Y. Water Splitting-Biosynthetic Hybrid System for CO 2 Conversion using Nickel Nanoparticles Embedded in N-Doped Carbon Nanotubes. CHEMSUSCHEM 2018; 11:2382-2387. [PMID: 29809320 DOI: 10.1002/cssc.201800878] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/27/2018] [Indexed: 06/08/2023]
Abstract
CO2 reduction has drawn increasing attention owing to the concern of global warming. Water splitting-biosynthetic hybrid systems are novel and efficient approaches for CO2 conversion. Intimate coupling of electrocatalysts and biosynthesis requires the catalysts possess both high catalytic performance and excellent biocompatibility, which is a bottleneck of developing such catalysts. Here, a complex of Ni nanoparticles embedded in N-doped carbon nanotubes (Ni@N-C) is synthesized as a hydrogen evolution reaction electrocatalyst and is coupled with a hydrogen oxidizing autotroph, Cupriavidus necator H16, to convert CO2 to poly-β-hydroxybutyrate. In Ni@N-C, the Ni nanoparticles are encapsulated in N-C nanotubes, which prevents bacteria from direct contact with Ni and inhibits Ni2+ leaching. As a result, Ni@N-C exhibits excellent biocompatibility and stability. This work demonstrates that electrocatalysts and biosynthesis can be intimately coupled through rational catalyst design.
Collapse
Affiliation(s)
- Zhongjian Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hanzghou, 310027, China
- College of Chemical and Biological Engineering, Zhejiang University, Hanzghou, 310027, China
| | - Gang Li
- College of Chemical and Biological Engineering, Zhejiang University, Hanzghou, 310027, China
| | - Xinlu Chen
- College of Chemical and Biological Engineering, Zhejiang University, Hanzghou, 310027, China
| | - Zheng Xia
- College of Chemical and Biological Engineering, Zhejiang University, Hanzghou, 310027, China
| | - Jiani Yao
- College of Chemical and Biological Engineering, Zhejiang University, Hanzghou, 310027, China
| | - Bin Yang
- College of Chemical and Biological Engineering, Zhejiang University, Hanzghou, 310027, China
| | - Lecheng Lei
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hanzghou, 310027, China
- College of Chemical and Biological Engineering, Zhejiang University, Hanzghou, 310027, China
| | - Yang Hou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hanzghou, 310027, China
- College of Chemical and Biological Engineering, Zhejiang University, Hanzghou, 310027, China
| |
Collapse
|
44
|
Kutralam-Muniasamy G, Peréz-Guevara F. Genome characteristics dictate poly-R-(3)-hydroxyalkanoate production in Cupriavidus necator H16. World J Microbiol Biotechnol 2018; 34:79. [DOI: 10.1007/s11274-018-2460-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/19/2018] [Indexed: 11/28/2022]
|
45
|
Biosynthesis of polyhydroxyalkanoates using Cupriavidus necator H16 and its application for particleboard production. JOURNAL OF POLYMER RESEARCH 2018. [DOI: 10.1007/s10965-018-1521-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
46
|
Black WB, Zhang L, Kamoku C, Liao JC, Li H. Rearrangement of Coenzyme A-Acylated Carbon Chain Enables Synthesis of Isobutanol via a Novel Pathway in Ralstonia eutropha. ACS Synth Biol 2018; 7:794-800. [PMID: 29429336 DOI: 10.1021/acssynbio.7b00409] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Coenzyme A (CoA)-dependent pathways have been explored extensively for the biosynthesis of fuels and chemicals. While CoA-dependent mechanisms are widely used to elongate carbon chains in a linear fashion, branch-making chemistry has not been incorporated. In this study, we demonstrated the production of isobutanol, a branched-chain alcohol that can be used as a gasoline substitute, using a novel CoA-dependent pathway in recombinant Ralstonia eutropha H16. The designed pathway is constituted of three modules: chain elongation, rearrangement, and modification. We first integrated and optimized the chain elongation and modification modules, and we achieved the production of ∼200 mg/L n-butanol from fructose or ∼30 mg/L from formate by engineered R. eutropha. Subsequently, we incorporated the rearrangement module, which features a previously uncharacterized, native isobutyryl-CoA mutase in R. eutropha. The engineered strain produced ∼30 mg/L isobutanol from fructose. The carbon skeleton rearrangement chemistry demonstrated here may be used to expand the range of the chemicals accessible with CoA-dependent pathways.
Collapse
Affiliation(s)
- William B. Black
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, California 90697, United States
| | - Linyue Zhang
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, California 90697, United States
| | - Cody Kamoku
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, California 90697, United States
| | - James C. Liao
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Han Li
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, California 90697, United States
| |
Collapse
|
47
|
Production of (3-hydroxybutyrate-co-3-hydroxyhexanoate) copolymer from coffee waste oil using engineered Ralstonia eutropha. Bioprocess Biosyst Eng 2017; 41:229-235. [DOI: 10.1007/s00449-017-1861-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/25/2017] [Indexed: 10/18/2022]
|
48
|
Murugan P, Gan CY, Sudesh K. Biosynthesis of P(3HB- co -3HHx) with improved molecular weights from a mixture of palm olein and fructose by Cupriavidus necator Re2058/pCB113. Int J Biol Macromol 2017; 102:1112-1119. [DOI: 10.1016/j.ijbiomac.2017.05.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/18/2017] [Accepted: 05/01/2017] [Indexed: 10/19/2022]
|
49
|
Over expression of GroESL in Cupriavidus necator for heterotrophic and autotrophic isopropanol production. Metab Eng 2017; 42:74-84. [DOI: 10.1016/j.ymben.2017.05.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/30/2017] [Accepted: 05/31/2017] [Indexed: 01/09/2023]
|
50
|
Reversal of β-oxidative pathways for the microbial production of chemicals and polymer building blocks. Metab Eng 2017; 42:33-42. [PMID: 28550000 DOI: 10.1016/j.ymben.2017.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/28/2017] [Accepted: 05/22/2017] [Indexed: 12/30/2022]
Abstract
β-Oxidation is the ubiquitous metabolic strategy to break down fatty acids. In the course of this four-step process, two carbon atoms are liberated per cycle from the fatty acid chain in the form of acetyl-CoA. However, typical β-oxidative strategies are not restricted to monocarboxylic (fatty) acid degradation only, but can also be involved in the utilization of aromatic compounds, amino acids and dicarboxylic acids. Each enzymatic step of a typical β-oxidation cycle is reversible, offering the possibility to also take advantage of reversed metabolic pathways for applied purposes. In such cases, 3-oxoacyl-CoA thiolases, which catalyze the final chain-shortening step in the catabolic direction, mediate the condensation of an acyl-CoA starter molecule with acetyl-CoA in the anabolic direction. Subsequently, the carbonyl-group at C3 is stepwise reduced and dehydrated yielding a chain-elongated product. In the last years, several β-oxidation pathways have been studied in detail and reversal of these pathways already proved to be a promising strategy for the production of chemicals and polymer building blocks in several industrially relevant microorganisms. This review covers recent advancements in this field and discusses constraints and bottlenecks of this metabolic strategy in comparison to alternative production pathways.
Collapse
|