1
|
Wang Z, Hou X, Shang G, Deng G, Luo K, Peng M. Exploring Fatty Acid β-Oxidation Pathways in Bacteria: From General Mechanisms to DSF Signaling and Pathogenicity in Xanthomonas. Curr Microbiol 2024; 81:336. [PMID: 39223428 DOI: 10.1007/s00284-024-03866-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Fatty acids (FAs) participate in extensive physiological activities such as energy metabolism, transcriptional control, and cell signaling. In bacteria, FAs are degraded and utilized through various metabolic pathways, including β-oxidation. Over the past ten years, significant progress has been made in studying FA oxidation in bacteria, particularly in E. coli, where the processes and roles of FA β-oxidation have been comprehensively elucidated. Here, we provide an update on the new research achievements in FAs β-oxidation in bacteria. Using Xanthomonas as an example, we introduce the oxidation process and regulation mechanism of the DSF-family quorum sensing signal. Based on current findings, we propose the specific enzymes required for β-oxidation of several specific FAs. Finally, we discuss the future outlook on scientific issues that remain to be addressed. This paper supplies theoretical guidance for further study of the FA β-oxidation pathway with particular emphasis on its connection to the pathogenicity mechanisms of bacteria.
Collapse
Affiliation(s)
- Zhiyong Wang
- Hubei Engineering Research Center of Selenium Food Nutrition and Health Intelligent Technology College of Biological and Food Engineering, Hubei Minzu University, Enshi, 445000, China
| | - Xue Hou
- Hubei Engineering Research Center of Selenium Food Nutrition and Health Intelligent Technology College of Biological and Food Engineering, Hubei Minzu University, Enshi, 445000, China
| | - Guohui Shang
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Guangai Deng
- Hubei Engineering Research Center of Selenium Food Nutrition and Health Intelligent Technology College of Biological and Food Engineering, Hubei Minzu University, Enshi, 445000, China
| | - Kai Luo
- Hubei Engineering Research Center of Selenium Food Nutrition and Health Intelligent Technology College of Biological and Food Engineering, Hubei Minzu University, Enshi, 445000, China
| | - Mu Peng
- Hubei Engineering Research Center of Selenium Food Nutrition and Health Intelligent Technology College of Biological and Food Engineering, Hubei Minzu University, Enshi, 445000, China.
| |
Collapse
|
2
|
Santolin L, Riedel SL, Brigham CJ. Synthetic biology toolkit of Ralstonia eutropha (Cupriavidus necator). Appl Microbiol Biotechnol 2024; 108:450. [PMID: 39207499 PMCID: PMC11362209 DOI: 10.1007/s00253-024-13284-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024]
Abstract
Synthetic biology encompasses many kinds of ideas and techniques with the common theme of creating something novel. The industrially relevant microorganism, Ralstonia eutropha (also known as Cupriavidus necator), has long been a subject of metabolic engineering efforts to either enhance a product it naturally makes (polyhydroxyalkanoate) or produce novel bioproducts (e.g., biofuels and other small molecule compounds). Given the metabolic versatility of R. eutropha and the existence of multiple molecular genetic tools and techniques for the organism, development of a synthetic biology toolkit is underway. This toolkit will allow for novel, user-friendly design that can impart new capabilities to R. eutropha strains to be used for novel application. This article reviews the different synthetic biology techniques currently available for modifying and enhancing bioproduction in R. eutropha. KEY POINTS: • R. eutropha (C. necator) is a versatile organism that has been examined for many applications. • Synthetic biology is being used to design more powerful strains for bioproduction. • A diverse synthetic biology toolkit is being developed to enhance R. eutropha's capabilities.
Collapse
Affiliation(s)
- Lara Santolin
- Technische Universität Berlin, Institute of Biotechnology, Chair of Bioprocess Engineering, Berlin, Germany
| | - Sebastian L Riedel
- Berliner Hochschule Für Technik, Department VIII - Mechanical Engineering, Event Technology and Process Engineering, Environmental and Bioprocess Engineering Laboratory, Berlin, Germany.
| | - Christopher J Brigham
- Department of Bioengineering, University of Massachusetts Dartmouth, North Dartmouth, MA, USA.
| |
Collapse
|
3
|
Zhila NO, Sapozhnikova KY, Kiselev EG, Shishatskaya EI, Volova TG. Biosynthesis of Polyhydroxyalkanoates in Cupriavidus necator B-10646 on Saturated Fatty Acids. Polymers (Basel) 2024; 16:1294. [PMID: 38732762 PMCID: PMC11085183 DOI: 10.3390/polym16091294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/20/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024] Open
Abstract
It has been established that the wild-type Cupriavidus necator B-10646 strain uses saturated fatty acids (SFAs) for growth and polyhydroxyalkanoate (PHA) synthesis. It uses lauric (12:0), myristic (14:0), palmitic (16:0) and stearic (18:0) acids as carbon sources; moreover, the elongation of the C-chain negatively affects the biomass and PHA yields. When bacteria grow on C12 and C14 fatty acids, the total biomass and PHA yields are comparable up to 7.5 g/L and 75%, respectively, which twice exceed the values that occur on longer C16 and C18 acids. Regardless of the type of SFAs, bacteria synthesize poly(3-hydroxybutyrate), which have a reduced crystallinity (Cx from 40 to 57%) and a molecular weight typical for poly(3-hydroxybutyrate) (P(3HB)) (Mw from 289 to 465 kDa), and obtained polymer samples demonstrate melting and degradation temperatures with a gap of about 100 °C. The ability of bacteria to assimilate SFAs opens up the possibility of attracting the synthesis of PHAs on complex fat-containing substrates, including waste.
Collapse
Affiliation(s)
- Natalia O. Zhila
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (K.Y.S.); (E.G.K.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
| | - Kristina Yu. Sapozhnikova
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (K.Y.S.); (E.G.K.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
| | - Evgeniy G. Kiselev
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (K.Y.S.); (E.G.K.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
| | - Ekaterina I. Shishatskaya
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (K.Y.S.); (E.G.K.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
| | - Tatiana G. Volova
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (K.Y.S.); (E.G.K.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
| |
Collapse
|
4
|
Hernández-Herreros N, Rivero-Buceta V, Pardo I, Prieto MA. Production of poly(3-hydroxybutyrate)/poly(lactic acid) from industrial wastewater by wild-type Cupriavidus necator H16. WATER RESEARCH 2024; 249:120892. [PMID: 38007895 DOI: 10.1016/j.watres.2023.120892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/28/2023]
Abstract
The massive production of urban and industrial wastes has created a clear need for alternative waste management processes. One of the more promising strategies is to use waste as raw material for the production of biopolymers such as polyhydroxyalkanoates (PHAs). In this work, a lactate-enriched stream obtained by anaerobic digestion (AD) of wastewater (WW) from a candy production plant was used as a feedstock for PHA production in wild-type Cupriavidus necator H16. Unexpectedly, we observed the accumulation of poly(3-hydroxybutyrate)/poly(lactic acid) (P(3HB)/PLA), suggesting that the non-engineered strain already possesses the metabolic potential to produce these polymers of interest. The systematic study of factors, such as incubation time, nitrogen and lactate concentration, influencing the synthesis of P(3HB)/PLA allowed the production of a panel of polymers in a resting cell system with tailored lactic acid (LA) content according to the GC-MS of the biomass. Further biomass extraction suggested the presence of methanol soluble low molecular weight molecules containing LA, while 1 % LA could be detected in the purified polymer fraction. These results suggested that the cells are producing a blend of polymers. A proteomic analysis of C. necator resting cells under P(3HB)/PLA production conditions provides new insights into the latent pathways involved in this process. This study is a proof of concept demonstrating that LA can polymerize in a non-modified organism and paves the way for new metabolic engineering approaches for lactic acid polymer production in the model bacterium C. necator H16.
Collapse
Affiliation(s)
- Natalia Hernández-Herreros
- Microbial & Plant Biotechnology Department. Polymer Biotechnology Group. Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Virginia Rivero-Buceta
- Microbial & Plant Biotechnology Department. Polymer Biotechnology Group. Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Isabel Pardo
- Microbial & Plant Biotechnology Department. Polymer Biotechnology Group. Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Microbial & Plant Biotechnology Department. Polymer Biotechnology Group. Biological Research Centre Margarita Salas, Spanish National Research Council (CIB-CSIC), Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
| |
Collapse
|
5
|
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
|
6
|
Medium-Chain-Length Fatty Acid Catabolism in Cupriavidus necator H16: Transcriptome Sequencing Reveals Differences from Long-Chain-Length Fatty Acid β-Oxidation and Involvement of Several Homologous Genes. Appl Environ Microbiol 2023; 89:e0142822. [PMID: 36541797 PMCID: PMC9888253 DOI: 10.1128/aem.01428-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The number of genes encoding β-oxidation enzymes in Cupriavidus necator H16 (synonym, Ralstonia eutropha H16) is high, but only the operons A0459-A0464 and A1526-A1531, each encoding four genes for β-oxidation enzymes, were expressed during growth with long-chain-length fatty acids (LCFAs). However, we observed that C. necator ΔA0459-A0464 ΔA1526-A1531 and C. necator H16 showed the same growth behavior during growth with decanoic acid and shorter FAs. The negative effect of the deletion of these two operons increased with an increasing chain length of the utilized FAs. Transcriptome sequencing (RNA-Seq) revealed the expression profiles of genes involved in the catabolism of medium-chain-length fatty acids (MCFAs) in C. necator H16. Operon A0459-A0464 was expressed only during growth with nonanoic acid, whereas operon A1526-A1531 was highly expressed during growth with octanoic and nonanoic acid. The gene clusters B1187-B1192 and B0751-B0759 showed a log2 fold change in expression of up to 4.29 and 4.02, respectively, during growth with octanoic acid and up to 8.82 and 5.50, respectively, with nonanoic acid compared to sodium gluconate-grown cells. Several acyl-CoA ligases catalyze the activation of MCFAs with coenzyme A (CoA), but fadD3 (A3288), involved in activation of LCFAs, was not detected. The expression profiles of C. necator strain ΔA0459-A0464 ΔA1526-A1531 showed that the growth with nonanoic acid resulted in the expression of further β-oxidation enzyme-encoding genes. Additional insights into the transport of FAs in C. necator H16 revealed the complexity and putative involvement of the DegV-like protein encoded by A0463 in the transport of odd-chain-length FAs and of siderophore biosynthesis in the transport mechanism. IMPORTANCE Although Cupriavidus necator H16 has been used in several studies to produce polyhydroxyalkanoates from various lipids, the fatty acid metabolism is poorly understood. The β-oxidation of long-chain-length FAs has been investigated, but the tremendous number of homologous genes encoding β-oxidation enzymes hides the potential for variances in the expressed genes for catabolism of shorter FAs. The catabolism of medium-chain-length FAs and connected pathways has not been investigated yet. As more sustainable substrates such as lipids and the production of fatty acids and fatty acid derivates become more critical with the dependency on fossil-based substances, understanding the complex metabolism in this highly diverse workhorse for biotechnology, C. necator, is inevitable. For further metabolic engineering and construction of production strains, we investigated the metabolism during growth on medium-chain-length FAs by RNA-Seq.
Collapse
|
7
|
Piecha CR, Alves TC, Zanini MLDO, Corrêa CDPL, Leite FPL, Galli V, Diaz PS. Application of the solid-state fermentation process and its variations in PHA production: a review. Arch Microbiol 2022; 205:11. [PMID: 36460824 DOI: 10.1007/s00203-022-03336-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/25/2022] [Accepted: 11/14/2022] [Indexed: 12/04/2022]
Abstract
Solid-state fermentation (SSF) is a type of fermentation process with potential to use agro-industrial by-products as a carbon source. Nonetheless, there are few studies evaluating SSF compared to submerged fermentation (SmF) to produce polyhydroxyalkanoates (PHAs). Different methodologies are available associating the two processes. In general, the studies employ a 1st step by SSF to hydrolyze the agro-industrial by-products used as a carbon source, and a 2nd step to produce PHA that can be carried out by SmF or SSF. This paper reviewed and compared the different methodologies described in the literature to assess their potential for use in PHA production. The studies evaluated showed that highest PHA yields (86.2% and 82.3%) were achieved by associating SSF and SmF by Cupriavidus necator. Meanwhile, in methodologies using only SSF, Bacillus produced the highest yields (62% and 56.8%). Since PHA (%) does not necessarily represent a higher production by biomass, the productivity parameter was also compared between studies. We observed that the highest productivity results did not necessarily represent the highest PHA (%). C. necator presented the highest PHA yields associating SSF and SmF, however, is not the most suitable microorganism for PHA production by SSF. Concomitant use of C. necator and Bacillus is suggested for future studies in SSF. Also, it discusses the lack of studies on the association of the two fermentation methodologies, and on the scaling of SSF process for PHA production. In addition to demonstrating the need for standardization of results, for comparison between different methodologies.
Collapse
Affiliation(s)
- Camila Rios Piecha
- Bioprocess Technology Laboratory, Biotechnology, Technological Development Center, Federal University of Pelotas, RS, Zip Code 96010-90, Pelotas, Brazil.
| | - Taisha Carvalho Alves
- Center for Chemical, Pharmaceutical and Food Science, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Maria Luiza de Oliveira Zanini
- Bioprocess Technology Laboratory, Biotechnology, Technological Development Center, Federal University of Pelotas, RS, Zip Code 96010-90, Pelotas, Brazil
| | - Caroline de Paula Lopes Corrêa
- Bioprocess Technology Laboratory, Biotechnology, Technological Development Center, Federal University of Pelotas, RS, Zip Code 96010-90, Pelotas, Brazil
| | - Fábio Pereira Leivas Leite
- Bioprocess Technology Laboratory, Biotechnology, Technological Development Center, Federal University of Pelotas, RS, Zip Code 96010-90, Pelotas, Brazil
| | - Vanessa Galli
- Bioprocess Technology Laboratory, Biotechnology, Technological Development Center, Federal University of Pelotas, RS, Zip Code 96010-90, Pelotas, Brazil
| | - Patrícia Silva Diaz
- Bioprocess Technology Laboratory, Biotechnology, Technological Development Center, Federal University of Pelotas, RS, Zip Code 96010-90, Pelotas, Brazil
| |
Collapse
|
8
|
Son HF, Ahn JW, Hong J, Seok J, Jin KS, Kim KJ. Crystal structure of multi-functional enzyme FadB from Cupriavidus necator: Non-formation of FadAB complex. Arch Biochem Biophys 2022; 730:109391. [PMID: 36087768 DOI: 10.1016/j.abb.2022.109391] [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: 05/19/2022] [Revised: 08/14/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022]
Abstract
Cupriavidus necator H16 is a gram-negative chemolithoautotrophic bacterium that has been extensively studied for biosynthesis and biodegradation of polyhydroxyalkanoate (PHA) plastics. To improve our understanding of fatty acid metabolism for PHA production, we determined the crystal structure of multi-functional enoyl-CoA hydratase from Cupriavidus necator H16 (CnFadB). The predicted model of CnFadB created by AlphaFold was used to solve the phase problem during determination of the crystal structure of the protein. The CnFadB structure consists of two distinctive domains, an N-terminal enol-CoA hydratase (ECH) domain and a C-terminal 3-hydroxyacyl-CoA dehydrogenase (HAD) domain, and the substrate- and cofactor-binding modes of these two functional domains were identified. Unlike other known FadB enzymes that exist as dimers complexed with FadA, CnFadB functions as a monomer without forming a complex with CnFadA. Small angle X-ray scattering (SAXS) measurement further proved that CnFadB exists as a monomer in solution. The non-sequential action of FadA and FadB in C. necator appears to affect β-oxidation and PHA synthesis/degradation.
Collapse
Affiliation(s)
- Hyeoncheol Francis Son
- Clean Energy Research Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Jae-Woo Ahn
- Postech Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea; Center for Biomolecular Capture Technology, Bio Open Innovation Center, Pohang University of Science and Technology, 47 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jiyeon Hong
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea
| | - Jihye Seok
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, 80 Jigokro-127-beongil, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 Four KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566, Republic of Korea.
| |
Collapse
|
9
|
A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications. PLoS Comput Biol 2022; 18:e1010106. [PMID: 35604933 PMCID: PMC9166356 DOI: 10.1371/journal.pcbi.1010106] [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: 11/06/2021] [Revised: 06/03/2022] [Accepted: 04/14/2022] [Indexed: 11/29/2022] Open
Abstract
Exploiting biological processes to recycle renewable carbon into high value platform chemicals provides a sustainable and greener alternative to current reliance on petrochemicals. In this regard Cupriavidus necator H16 represents a particularly promising microbial chassis due to its ability to grow on a wide range of low-cost feedstocks, including the waste gas carbon dioxide, whilst also naturally producing large quantities of polyhydroxybutyrate (PHB) during nutrient-limited conditions. Understanding the complex metabolic behaviour of this bacterium is a prerequisite for the design of successful engineering strategies for optimising product yields. We present a genome-scale metabolic model (GSM) of C. necator H16 (denoted iCN1361), which is directly constructed from the BioCyc database to improve the readability and reusability of the model. After the initial automated construction, we have performed extensive curation and both theoretical and experimental validation. By carrying out a genome-wide essentiality screening using a Transposon-directed Insertion site Sequencing (TraDIS) approach, we showed that the model could predict gene knockout phenotypes with a high level of accuracy. Importantly, we indicate how experimental and computational predictions can be used to improve model structure and, thus, model accuracy as well as to evaluate potential false positives identified in the experiments. Finally, by integrating transcriptomics data with iCN1361 we create a condition-specific model, which, importantly, better reflects PHB production in C. necator H16. Observed changes in the omics data and in-silico-estimated alterations in fluxes were then used to predict the regulatory control of key cellular processes. The results presented demonstrate that iCN1361 is a valuable tool for unravelling the system-level metabolic behaviour of C. necator H16 and can provide useful insights for designing metabolic engineering strategies. Genome-scale metabolic models (GSMs) provide a tool for unravelling the complex metabolic behaviour of bacteria and how they adapt to changing environments and genetic perturbations, and thus offer invaluable insights for biotechnology applications. For a GSM to be used efficiently for strain development purposes, however, the model must be easily readable and reusable by other researchers, whilst being able to predict metabolic behaviour with a high level of accuracy. In this work, we developed a GSM for Cupriavidus necator H16 that is linked to the BioCyc database, which provides an efficient way of application, model update, integration of experimental data and network visualisation for other researchers. Using our model, we demonstrate how integrating experimental observations, including Transposon-directed Insertion site Sequencing (TraDIS) and omics data, can be used to compensate for the lack of regulatory, kinetic and thermodynamic information in GSMs, and thus improve model accuracy. Importantly, we found that TraDIS in vivo screening and GSM analysis are complementary approaches, which can be used in combination to provide reliable gene essentiality predictions. Overall, our results offer an informed strategy for the deliberate manipulation of C. necator H16 metabolic capabilities, towards its industrial application to convert greenhouse gases into biochemicals and biofuels.
Collapse
|
10
|
Arikawa H, Sato S. Impact of various β-ketothiolase genes on PHBHHx production in Cupriavidus necator H16 derivatives. Appl Microbiol Biotechnol 2022; 106:3021-3032. [PMID: 35451630 DOI: 10.1007/s00253-022-11928-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 11/02/2022]
Abstract
Poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] (PHBHHx) is a type of biopolyester of the polyhydroxyalkanoate group (PHA). Due to a wide range of properties resulting from the alteration of the (R)-3-hydroxyhexanoate (3HHx) composition, PHBHHx is getting a lot of attention as a substitute to conventional plastic materials for various applications. Cupriavidus necator H16 is the most promising PHA producer and has been genetically engineered to produce PHBHHx efficiently for many years. Nevertheless, the role of individual genes involved in PHBHHx biosynthesis is not well elaborated. C. necator H16 possesses six potential physiologically active β-ketothiolase genes identified by transcriptome analysis, i.e., phaA, bktB, bktC (h16_A0170), h16_A0462, h16_A1528, and h16_B0759. In this study, we focused on the functionality of these genes in vivo in relation to 3HHx monomer supply. Gene deletion experiments identified BktB and H16_A1528 as important β-ketothiolases for C6 metabolism in β-oxidation. Furthermore, in the bktB/h16_A1528 double-deletion strain, the proportion of 3HHx composition of PHBHHx produced from sugar was very low, whereas that from plant oil was significantly higher. In fact, the proportion reached 36.2 mol% with overexpression of (R)-specifc enoyl-CoA hydratase (PhaJ) and PHA synthase. Furthermore, we demonstrated high-density production (196 g/L) of PHBHHx with high 3HHx (32.5 mol%) by fed-batch fermentation with palm kernel oil. The PHBHHx was amorphous according to the differential scanning calorimetry analysis. KEY POINTS: • Role of six β-ketothiolases in PHBHHx biosynthesis was investigated in vivo. • Double-deletion of bktB/h16_A1528 results in high 3HHx composition with plant oil. • Amorphous PHBHHx with 32.5 mol% 3HHx was produced in high density by jar fermenter.
Collapse
Affiliation(s)
- Hisashi Arikawa
- Green Planet Research Group, Agri-Bio & Supplement Research Laboratories, KANEKA CORPORATION, 1-8 Miyamae-Cho, Takasago-Cho, Takasago, Hyogo, 676-8688, Japan.
| | - Shunsuke Sato
- Green Planet Research Group, Agri-Bio & Supplement Research Laboratories, KANEKA CORPORATION, 1-8 Miyamae-Cho, Takasago-Cho, Takasago, Hyogo, 676-8688, Japan
| |
Collapse
|
11
|
Influence of emulsified plant oil composition on growth and biopolymer production of Cupriavidus necator DSM 545. FOOD AND BIOPRODUCTS PROCESSING 2022. [DOI: 10.1016/j.fbp.2021.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
12
|
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
|
13
|
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
|
14
|
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
|
15
|
Insights in the Degradation of Medium-Chain Length Dicarboxylic Acids in Cupriavidus necator H16 reveal Differences in β-Oxidation between Dicarboxylic Acids and Fatty Acids. Appl Environ Microbiol 2021; 88:e0187321. [PMID: 34731045 DOI: 10.1128/aem.01873-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many homologous genes encoding β-oxidation enzymes were found in the genome of Cupriavidus necator H16 (synonym: Ralstonia eutropha H16). By proteome analysis, the degradation of adipic acid was investigated and showed differences to the degradation of hexanoic acid. During β-oxidation of adipic acid, activation with coenzyme A (CoA) is catalyzed by the two-subunit acyl-CoA ligase encoded by B0198 and B0199. The operon is completed by B0200 encoding a thiolase catalyzing the cleavage of acetyl-CoA at the end of the β-oxidation cycle. Strain C. necator ΔB0198-B0200 showed improved growth on adipic acid. Potential substitutes are B1239 for B0198-B0199 and A0170 as well as A1445 for B0200. A deletion mutant without all three thiolases showed diminished growth. The deletion of detected acyl-CoA dehydrogenase encoded by B2555 has an altered phenotype grown with sebacic acid but not adipic acid. With hexanoic acid, acyl-CoA dehydrogenase encoded by B0087 was detected on 2D gels. Both enzymes are active with adipoyl-CoA and hexanoyl-CoA as substrates, but specific activity indicates a higher activity of B2555 with adipoyl-CoA. 2D gels, growth experiments and enzyme assays suggest the specific expression of B2555 for the degradation of dicarboxylic acids. In C. necator H16 the degradation of carboxylic acids potentially changes with an increasing chain length. Two operons involved in growth with long-chain fatty acids seem to be replaced during growth on medium-chain carboxylic acids. Only two deletion mutants showed diminished growth. Replacement of deleted genes with one of the numerous homologous is likely. Importance The biotechnologically interesting bacterium Cupriavidus necator H16 was thoroughly investigated. Fifteen years ago, it was sequenced entirely and annotated (Pohlmann et al., 2006). Nevertheless, the degradation of monocarboxylic fatty acids and dicarboxylic acids has not been elucidated completely. C. necator is used to produce value-added products from affordable substrates. One of our investigations ' primary targets is the biotechnological production of organic acids with different and specific chain lengths. The versatile metabolism of carboxylic acids recommends C. necator H16 as a candidate for producing value-added organic products. Therefore, the metabolism of these compounds is of interest, and for different applications in industry, understanding such central metabolic pathways is crucial.
Collapse
|
16
|
Azubuike CC, Gatehouse AMR, Howard TP. pCAT vectors overcome inefficient electroporation of Cupriavidus necator H16. N Biotechnol 2021; 65:20-30. [PMID: 34333160 DOI: 10.1016/j.nbt.2021.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/06/2021] [Accepted: 07/24/2021] [Indexed: 10/20/2022]
Abstract
Cupriavidus necator H16 is a chemolithoautotroph with a range of industrial biotechnological applications. Advanced metabolic engineering in the bacterium, however, is impeded by low transformation efficiency, making it difficult to introduce and screen new genetic functions rapidly. This study systematically characterized the broad host range plasmids pBHR1, pBBR1MCS-2 and pKT230 used frequently for C. necator engineering. Kanamycin resistance cassette (KanR) and a truncated sequence of the replication origin (Rep) are contributing factors to C. necator low electroporation transformation efficiency. Consequently, a series of modular minimal plasmids, named pCAT, were constructed. pCAT vectors transform C. necator H16 with a > 3000-fold higher efficiency (up to 107 CFU/μg DNA) compared to control plasmids. Further, pCAT vectors are highly stable, expressing reporter proteins over several days of serial cultivation in the absence of selection pressure. Finally, they can be assembled rapidly from PCR or synthesized DNA fragments, and restriction-ligation reactions can be efficiently electroporated directly into C. necator, circumventing the requirement to use Escherichia coli for plasmid maintenance or propagation. This study demonstrates that an understanding of the behaviour of the constituent parts of plasmids in a host is key to efficient propagation of genetic information, while offering new methods for engineering a bacterium with desirable industrial biotechnological features.
Collapse
Affiliation(s)
- Christopher C Azubuike
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RX, United Kingdom; Department of Microbiology, Faculty of Science, University of Port Harcourt, East-West Road, P.M.B. 5323, Choba, Port Harcourt, Rivers State, Nigeria
| | - Angharad M R Gatehouse
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RX, United Kingdom
| | - Thomas P Howard
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RX, United Kingdom.
| |
Collapse
|
17
|
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
|
18
|
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
|
19
|
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
|
20
|
Ding R, Hu S, Xu M, Hu Q, Jiang S, Xu K, Tremblay PL, Zhang T. The facile and controllable synthesis of a bacterial cellulose/polyhydroxybutyrate composite by co-culturing Gluconacetobacter xylinus and Ralstonia eutropha. Carbohydr Polym 2021; 252:117137. [DOI: 10.1016/j.carbpol.2020.117137] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/24/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
|
21
|
Volova T, Sapozhnikova K, Zhila N. Cupriavidus necator B-10646 growth and polyhydroxyalkanoates production on different plant oils. Int J Biol Macromol 2020; 164:121-130. [DOI: 10.1016/j.ijbiomac.2020.07.095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/26/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
|
22
|
Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle. Proc Natl Acad Sci U S A 2020; 117:22452-22461. [PMID: 32820073 PMCID: PMC7486775 DOI: 10.1073/pnas.2012288117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Calvin cycle is the most important carbon fixation pathway in the biosphere. However, its carboxylating enzyme Rubisco also accepts oxygen, thus producing 2-phosphoglycolate. Phosphoglycolate salvage pathways were extensively studied in photoautotrophs but remain uncharacterized in chemolithoautotrophs using the Calvin cycle. Here, we study phosphoglycolate salvage in the chemolithoautotrophic model bacterium Cupriavidus necator H16. We demonstrate that this bacterium mainly reassimilates 2-phosphoglycolate via the glycerate pathway. Upon disruption of this pathway, a secondary route, which we term the malate cycle, supports photorespiration by completely oxidizing 2-phosphoglycolate to CO2. While the malate cycle was not previously known to metabolize 2-phosphoglycolate in nature, a bioinformatic analysis suggests that it may support phosphoglycolate salvage in diverse chemoautotrophic bacteria. Carbon fixation via the Calvin cycle is constrained by the side activity of Rubisco with dioxygen, generating 2-phosphoglycolate. The metabolic recycling of phosphoglycolate was extensively studied in photoautotrophic organisms, including plants, algae, and cyanobacteria, where it is referred to as photorespiration. While receiving little attention so far, aerobic chemolithoautotrophic bacteria that operate the Calvin cycle independent of light must also recycle phosphoglycolate. As the term photorespiration is inappropriate for describing phosphoglycolate recycling in these nonphotosynthetic autotrophs, we suggest the more general term “phosphoglycolate salvage.” Here, we study phosphoglycolate salvage in the model chemolithoautotroph Cupriavidus necator H16 (Ralstonia eutropha H16) by characterizing the proxy process of glycolate metabolism, performing comparative transcriptomics of autotrophic growth under low and high CO2 concentrations, and testing autotrophic growth phenotypes of gene deletion strains at ambient CO2. We find that the canonical plant-like C2 cycle does not operate in this bacterium, and instead, the bacterial-like glycerate pathway is the main route for phosphoglycolate salvage. Upon disruption of the glycerate pathway, we find that an oxidative pathway, which we term the malate cycle, supports phosphoglycolate salvage. In this cycle, glyoxylate is condensed with acetyl coenzyme A (acetyl-CoA) to give malate, which undergoes two oxidative decarboxylation steps to regenerate acetyl-CoA. When both pathways are disrupted, autotrophic growth is abolished at ambient CO2. We present bioinformatic data suggesting that the malate cycle may support phosphoglycolate salvage in diverse chemolithoautotrophic bacteria. This study thus demonstrates a so far unknown phosphoglycolate salvage pathway, highlighting important diversity in microbial carbon fixation metabolism.
Collapse
|
23
|
Applying Statistical Design of Experiments To Understanding the Effect of Growth Medium Components on Cupriavidus necator H16 Growth. Appl Environ Microbiol 2020; 86:AEM.00705-20. [PMID: 32561588 PMCID: PMC7440812 DOI: 10.1128/aem.00705-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/31/2020] [Indexed: 01/06/2023] Open
Abstract
Chemically defined media (CDM) for cultivation of C. necator vary in components and compositions. This lack of consensus makes it difficult to optimize new processes for the bacterium. This study employed statistical design of experiments (DOE) to understand how basic components of defined media affect C. necator growth. Our growth model predicts that C. necator can be cultivated to high cell density with components held at low concentrations, arguing that CDM for large-scale cultivation of the bacterium for industrial purposes will be economically competitive. Although existing CDM for the bacterium are without amino acids, addition of a few amino acids to growth medium shortened lag phase of growth. The interactions highlighted by our growth model show how factors can interact with each other during a process to positively or negatively affect process output. This approach is efficient, relying on few well-structured experimental runs to gain maximum information on a biological process, growth. Cupriavidus necator H16 is gaining significant attention as a microbial chassis for range of biotechnological applications. While the bacterium is a major producer of bioplastics, its lithoautotrophic and versatile metabolic capabilities make the bacterium a promising microbial chassis for biofuels and chemicals using renewable resources. It remains necessary to develop appropriate experimental resources to permit controlled bioengineering and system optimization of this microbe. In this study, we employed statistical design of experiments to gain understanding of the impact of components of defined media on C. necator growth and built a model that can predict the bacterium’s cell density based on medium components. This highlighted medium components, and interaction between components, having the most effect on growth: fructose, amino acids, trace elements, CaCl2, and Na2HPO4 contributed significantly to growth (t values of <−1.65 or >1.65); copper and histidine were found to interact and must be balanced for robust growth. Our model was experimentally validated and found to correlate well (r2 = 0.85). Model validation at large culture scales showed correlations between our model-predicted growth ranks and experimentally determined ranks at 100 ml in shake flasks (ρ = 0.87) and 1 liter in a bioreactor (ρ = 0.90). Our approach provides valuable and quantifiable insights on the impact of medium components on cell growth and can be applied to model other C. necator responses that are crucial for its deployment as a microbial chassis. This approach can be extended to other nonmodel microbes of medical and industrial biotechnological importance. IMPORTANCE Chemically defined media (CDM) for cultivation of C. necator vary in components and compositions. This lack of consensus makes it difficult to optimize new processes for the bacterium. This study employed statistical design of experiments (DOE) to understand how basic components of defined media affect C. necator growth. Our growth model predicts that C. necator can be cultivated to high cell density with components held at low concentrations, arguing that CDM for large-scale cultivation of the bacterium for industrial purposes will be economically competitive. Although existing CDM for the bacterium are without amino acids, addition of a few amino acids to growth medium shortened lag phase of growth. The interactions highlighted by our growth model show how factors can interact with each other during a process to positively or negatively affect process output. This approach is efficient, relying on few well-structured experimental runs to gain maximum information on a biological process, growth.
Collapse
|
24
|
Enhanced Triacylglycerol Metabolism Contributes to Efficient Oil Utilization and High-Level Production of Salinomycin in Streptomyces albus ZD11. Appl Environ Microbiol 2020; 86:AEM.00763-20. [PMID: 32532869 DOI: 10.1128/aem.00763-20] [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: 04/13/2020] [Accepted: 05/31/2020] [Indexed: 11/20/2022] Open
Abstract
Streptomyces is well known for biosynthesis of secondary metabolites with diverse bioactivities. Although oils have been employed as carbon sources to produce polyketide antibiotics for several industrial Streptomyces strains, the intrinsic correlation between oil utilization and high production of antibiotics still remains unclear. In this study, we investigated the correlation between oil metabolism and salinomycin biosynthesis in Streptomyces albus ZD11, which employs soybean oil as the main carbon source. Comparative genomic analysis revealed the enrichment of genes related to triacylglycerol (TAG) metabolism in S. albus ZD11. Transcriptomic profiling further confirmed the enhancement of TAG metabolism and acyl coenzyme A biosynthesis in S. albus ZD11. Multiple secreted lipases, which catalyze TAG hydrolysis, were seen to be working in a synergistic and complementary manner in aiding the efficient and stable hydrolyzation of TAGs. Together, our results suggest that enhanced TAG hydrolysis and fatty acid degradation contribute to the high efficiency of oil utilization in S. albus ZD11 in order to provide abundant carbon precursors for cell growth and salinomycin biosynthesis.IMPORTANCE In order to obtain high-level production of antibiotics, oils have been used as the main carbon source for some Streptomyces strains. Based on multiomics analysis, this study provides insight into the relationship between triacylglycerol (TAG) metabolism and antibiotic biosynthesis in S. albus ZD11, an oil-preferring industrial Streptomyces strain. Our investigation into TAG hydrolysis yielded further evidence that this strain utilizes complicated strategies enabling an efficient TAG metabolism. In addition, a novel secreted lipase was identified that exhibited highly hydrolytic activity for medium- and long-chain TAGs. Our findings represent a good start toward clarifying the complicated relationship between TAG catabolism and high-level antibiotic production in the industrial strains.
Collapse
|
25
|
Yaashikaa P, Senthil Kumar P, Varjani SJ, Saravanan A. A review on photochemical, biochemical and electrochemical transformation of CO2 into value-added products. J CO2 UTIL 2019. [DOI: 10.1016/j.jcou.2019.05.017] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
26
|
In-Line Monitoring of Polyhydroxyalkanoate (PHA) Production during High-Cell-Density Plant Oil Cultivations Using Photon Density Wave Spectroscopy. Bioengineering (Basel) 2019; 6:bioengineering6030085. [PMID: 31546779 PMCID: PMC6783927 DOI: 10.3390/bioengineering6030085] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 12/25/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are biodegradable plastic-like materials with versatile properties. Plant oils are excellent carbon sources for a cost-effective PHA production, due to their high carbon content, large availability, and comparatively low prices. Additionally, efficient process development and control is required for competitive PHA production, which can be facilitated by on-line or in-line monitoring devices. To this end, we have evaluated photon density wave (PDW) spectroscopy as a new process analytical technology for Ralstonia eutropha (Cupriavidus necator) H16 plant oil cultivations producing polyhydroxybutyrate (PHB) as an intracellular polymer. PDW spectroscopy was used for in-line recording of the reduced scattering coefficient µs’ and the absorption coefficient µa at 638 nm. A correlation of µs’ with the cell dry weight (CDW) and µa with the residual cell dry weight (RCDW) was observed during growth, PHB accumulation, and PHB degradation phases in batch and pulse feed cultivations. The correlation was used to predict CDW, RCDW, and PHB formation in a high-cell-density fed-batch cultivation with a productivity of 1.65 gPHB·L−1·h−1 and a final biomass of 106 g·L−1 containing 73 wt% PHB. The new method applied in this study allows in-line monitoring of CDW, RCDW, and PHA formation.
Collapse
|
27
|
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: 20] [Impact Index Per Article: 4.0] [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
|
28
|
Arenas-López C, Locker J, Orol D, Walter F, Busche T, Kalinowski J, Minton NP, Kovács K, Winzer K. The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:150. [PMID: 31236137 PMCID: PMC6572756 DOI: 10.1186/s13068-019-1489-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/07/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND 3-Hydroxypropionic acid (3-HP) is a promising platform chemical with various industrial applications. Several metabolic routes to produce 3-HP from organic substrates such as sugars or glycerol have been implemented in yeast, enterobacterial species and other microorganisms. In this study, the native 3-HP metabolism of Cupriavidus necator was investigated and manipulated as it represents a promising chassis for the production of 3-HP and other fatty acid derivatives from CO2 and H2. RESULTS When testing C. necator for its tolerance towards 3-HP, it was noted that it could utilise the compound as the sole source of carbon and energy, a highly undesirable trait in the context of biological 3-HP production which required elimination. Inactivation of the methylcitrate pathway needed for propionate utilisation did not affect the organism's ability to grow on 3-HP. Putative genes involved in 3-HP degradation were identified by bioinformatics means and confirmed by transcriptomic analyses, the latter revealing considerably increased expression in the presence of 3-HP. Genes identified in this manner encoded three putative (methyl)malonate semialdehyde dehydrogenases (mmsA1, mmsA2 and mmsA3) and two putative dehydrogenases (hpdH and hbdH). These genes, which are part of three separate mmsA operons, were inactivated through deletion of the entire coding region, either singly or in various combinations, to engineer strains unable to grow on 3-HP. Whilst inactivation of single genes or double deletions could only delay but not abolish growth, a triple ∆mmsA1∆mmsA2∆mmsA3 knock-out strain was unable utilise 3-HP as the sole source of carbon and energy. Under the used conditions this strain was also unable to co-metabolise 3-HP alongside other carbon and energy sources such as fructose and CO2/H2. Further analysis suggested primary roles for the different mmsA operons in the utilisation of β-alanine generating substrates (mmsA1), degradation of 3-HP (mmsA2), and breakdown of valine (mmsA3). CONCLUSIONS Three different (methyl)malonate semialdehyde dehydrogenases contribute to 3-HP breakdown in C. necator H16. The created triple ∆mmsA1∆mmsA2∆mmsA3 knock-out strain represents an ideal chassis for autotrophic 3-HP production.
Collapse
Affiliation(s)
- Christian Arenas-López
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Jessica Locker
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Diego Orol
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Frederik Walter
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Nigel P. Minton
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Katalin Kovács
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Klaus Winzer
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| |
Collapse
|
29
|
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
|
30
|
Yu J. Fixation of carbon dioxide by a hydrogen-oxidizing bacterium for value-added products. World J Microbiol Biotechnol 2018; 34:89. [PMID: 29886519 DOI: 10.1007/s11274-018-2473-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/04/2018] [Indexed: 01/03/2023]
Abstract
With rapid technology progress and cost reduction, clean hydrogen from water electrolysis driven by renewable powers becomes a potential feedstock for CO2 fixation by hydrogen-oxidizing bacteria. Cupriavidus necator (formally Ralstonia eutropha), a representative member of the lithoautotrophic prokaryotes, is a promising producer of polyhydroxyalkanoates and single cell proteins. This paper reviews the fundamental properties of the hydrogen-oxidizing bacterium, the metabolic activities under limitation of individual gases and nutrients, and the value-added products from CO2, including the products with large potential markets. Gas fermentation and bioreactor safety are discussed for achieving high cell density and high productivity of desired products under chemolithotrophic conditions. The review also updates the recent research activities in metabolic engineering of C. necator to produce novel metabolites from CO2.
Collapse
Affiliation(s)
- Jian Yu
- Hawaii Natural Energy Institute, University of Hawaii at Manoa, Honolulu, USA.
| |
Collapse
|
31
|
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]
|
32
|
Thakur IS, Kumar M, Varjani SJ, Wu Y, Gnansounou E, Ravindran S. Sequestration and utilization of carbon dioxide by chemical and biological methods for biofuels and biomaterials by chemoautotrophs: Opportunities and challenges. BIORESOURCE TECHNOLOGY 2018; 256:478-490. [PMID: 29459105 DOI: 10.1016/j.biortech.2018.02.039] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
To meet the CO2 emission reduction targets, carbon dioxide capture and utilization (CCU) comes as an evolve technology. CCU concept is turning into a feedstock and technologies have been developed for transformation of CO2 into useful organic products. At industrial scale, utilization of CO2 as raw material is not much significant as compare to its abundance. Mechanisms in nature have evolved for carbon concentration, fixation and utilization. Assimilation and subsequent conversion of CO2 into complex molecules are performed by the photosynthetic and chemolithotrophic organisms. In the last three decades, substantial research is carry out to discover chemical and biological conversion of CO2 in various synthetic and biological materials, such as carboxylic acids, esters, lactones, polymer biodiesel, bio-plastics, bio-alcohols, exopolysaccharides. This review presents an over view of catalytic transformation of CO2 into biofuels and biomaterials by chemical and biological methods.
Collapse
Affiliation(s)
- Indu Shekhar Thakur
- School of Environmental Sciences, JawaharNehru University, New Delhi 110067, India; Bioenergy and Energy Planning Research Group (BPE), IIC, ENAC, Station 18, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - Manish Kumar
- School of Environmental Sciences, JawaharNehru University, New Delhi 110067, India
| | - Sunita J Varjani
- Gujarat Pollution Control Board, Sector-10A, Gandhinagar 382010, Gujarat, India; Bioenergy and Energy Planning Research Group (BPE), IIC, ENAC, Station 18, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China.
| | - Edgard Gnansounou
- Bioenergy and Energy Planning Research Group (BPE), IIC, ENAC, Station 18, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - Sindhu Ravindran
- Microbial Processes and Technology Division, CSIR-NIIST, Trivandrum, India
| |
Collapse
|
33
|
Heterologous expression of phaC2 gene and poly-3-hydroxyalkanoate production by recombinant Cupriavidus necator strains using canola oil as carbon source. N Biotechnol 2018; 40:200-206. [DOI: 10.1016/j.nbt.2017.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 06/06/2017] [Accepted: 08/10/2017] [Indexed: 11/18/2022]
|
34
|
Raberg M, Volodina E, Lin K, Steinbüchel A. Ralstonia eutrophaH16 in progress: Applications beside PHAs and establishment as production platform by advanced genetic tools. Crit Rev Biotechnol 2017; 38:494-510. [DOI: 10.1080/07388551.2017.1369933] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Matthias Raberg
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Elena Volodina
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Kaichien Lin
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
35
|
Alagesan S, Minton NP, Malys N. 13C-assisted metabolic flux analysis to investigate heterotrophic and mixotrophic metabolism in Cupriavidus necator H16. Metabolomics 2017; 14:9. [PMID: 29238275 PMCID: PMC5715045 DOI: 10.1007/s11306-017-1302-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/22/2017] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Cupriavidus necator H16 is a gram-negative bacterium, capable of lithoautotrophic growth by utilizing hydrogen as an energy source and fixing carbon dioxide (CO2) through Calvin-Benson-Bassham (CBB) cycle. The potential to utilize synthesis gas (Syngas) and the prospects of rerouting carbon from polyhydroxybutyrate synthesis to value-added compounds makes C. necator an excellent chassis for industrial application. OBJECTIVES In the context of lack of sufficient quantitative information of the metabolic pathways and to advance in rational metabolic engineering for optimized product synthesis in C. necator H16, we carried out a metabolic flux analysis based on steady-state 13C-labelling. METHODS In this study, steady-state carbon labelling experiments, using either d-[1-13C]fructose or [1,2-13C]glycerol, were undertaken to investigate the carbon flux through the central carbon metabolism in C. necator H16 under heterotrophic and mixotrophic growth conditions, respectively. RESULTS We found that the CBB cycle is active even under heterotrophic condition, and growth is indeed mixotrophic. While Entner-Doudoroff (ED) pathway is shown to be the major route for sugar degradation, tricarboxylic acid (TCA) cycle is highly active in mixotrophic condition. Enhanced flux is observed in reductive pentose phosphate pathway (redPPP) under the mixotrophic condition to supplement the precursor requirement for CBB cycle. The flux distribution was compared to the mRNA abundance of genes encoding enzymes involved in key enzymatic reactions of the central carbon metabolism. CONCLUSION This study leads the way to establishing 13C-based quantitative fluxomics for rational pathway engineering in C. necator H16.
Collapse
Affiliation(s)
- Swathi Alagesan
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University Park, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University Park, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Naglis Malys
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University Park, The University of Nottingham, Nottingham, NG7 2RD, UK.
| |
Collapse
|
36
|
Waste date seed oil extract as an alternative feedstock for Poly(3-hydroxybutyrate) synthesis. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
37
|
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]
|
38
|
Byloos B, Coninx I, Van Hoey O, Cockell C, Nicholson N, Ilyin V, Van Houdt R, Boon N, Leys N. The Impact of Space Flight on Survival and Interaction of Cupriavidus metallidurans CH34 with Basalt, a Volcanic Moon Analog Rock. Front Microbiol 2017; 8:671. [PMID: 28503167 PMCID: PMC5408026 DOI: 10.3389/fmicb.2017.00671] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/31/2017] [Indexed: 11/13/2022] Open
Abstract
Microbe-mineral interactions have become of interest for space exploration as microorganisms could be used to biomine from extra-terrestrial material and extract elements useful as micronutrients in life support systems. This research aimed to identify the impact of space flight on the long-term survival of Cupriavidus metallidurans CH34 in mineral water and the interaction with basalt, a lunar-type rock in preparation for the ESA spaceflight experiment, BIOROCK. Therefore, C. metallidurans CH34 cells were suspended in mineral water supplemented with or without crushed basalt and send for 3 months on board the Russian FOTON-M4 capsule. Long-term storage had a significant impact on cell physiology and energy status (by flow cytometry analysis, plate count and intracellular ATP measurements) as 60% of cells stored on ground lost their cell membrane potential, only 17% were still active, average ATP levels per cell were significantly lower and cultivability dropped to 1%. The cells stored in the presence of basalt and exposed to space flight conditions during storage however showed less dramatic changes in physiology, with only 16% of the cells lost their cell membrane potential and 24% were still active, leading to a higher cultivability (50%) and indicating a general positive effect of basalt and space flight on survival. Microbe-mineral interactions and biofilm formation was altered by spaceflight as less biofilm was formed on the basalt during flight conditions. Leaching from basalt also changed (measured with ICP-OES), showing that cells release more copper from basalt and the presence of cells also impacted iron and magnesium concentration irrespective of the presence of basalt. The flight conditions thus could counteract some of the detrimental effects observed after the 3 month storage conditions.
Collapse
Affiliation(s)
- Bo Byloos
- Microbiology Unit, Belgian Nuclear Research Centre, SCK•CENMol, Belgium.,Center for Microbial Ecology and Technology, Ghent UniversityGhent, Belgium
| | - Ilse Coninx
- Microbiology Unit, Belgian Nuclear Research Centre, SCK•CENMol, Belgium
| | - Olivier Van Hoey
- Research in Dosimetric Applications, Belgian Nuclear Research Centre, SCK•CENMol, Belgium
| | - Charles Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of EdinburghEdinburgh, UK
| | - Natasha Nicholson
- UK Centre for Astrobiology, School of Physics and Astronomy, University of EdinburghEdinburgh, UK
| | - Vyacheslav Ilyin
- Institute of Medical and Biological Problems of Russian Academy of SciencesMoscow, Russia
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre, SCK•CENMol, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Ghent UniversityGhent, Belgium
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre, SCK•CENMol, Belgium
| |
Collapse
|
39
|
Sharma PK, Fu J, Spicer V, Krokhin OV, Cicek N, Sparling R, Levin DB. Global changes in the proteome of Cupriavidus necator H16 during poly-(3-hydroxybutyrate) synthesis from various biodiesel by-product substrates. AMB Express 2016; 6:36. [PMID: 27184362 PMCID: PMC4870535 DOI: 10.1186/s13568-016-0206-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/07/2016] [Indexed: 01/13/2023] Open
Abstract
Synthesis of poly-[3-hydroxybutyrate] (PHB) by Cupriavidus necator H16 in batch cultures was evaluated using three biodiesel-derived by-products as the sole carbon sources: waste glycerol (REG-80, refined to 80 % purity with negligible free fatty acids); glycerol bottom (REG-GB, with up to 65 % glycerol and 35 % free fatty acids), and free fatty acids (REG-FFA, with up to 75 % FFA and no glycerol). All the three substrates supported growth and PHB production by C. necator, with polymer accumulation ranging from 9 to 84 % cell dry weight (cdw), depending on the carbon source. To help understand these differences, proteomic analysis indicated that although C. necator H16 was able to accumulate PHB during growth on all three biodiesel by-products, no changes in the levels of PHB synthesis enzymes were observed. However, significant changes in the levels of expression were observed for two Phasin proteins involved with PHB accumulation, and for a number of gene products in the fatty acid β-oxidation pathway, the Glyoxylate Shunt, and the hydrogen (H2) synthesis pathways in C. necator cells cultured with different substrates. The glycerol transport protein (GlpF) was induced in REG-GB and REG-80 glycerol cultures only. Cupriavidus necator cells cultured with REG-GB and REG-FFA showed up-regulation of β-oxidation and Glyoxylate Shunt pathways proteins at 24 h pi, but H2 synthesis pathways enzymes were significantly down-regulated, compared with cells cultured with waste glycerol. Our data confirmed earlier observations of constitutive expression of PHB synthesis proteins, but further suggested that C. necator H16 cells growing on biodiesel-derived glycerol were under oxidative stress.
Collapse
|
40
|
Parlane NA, Gupta SK, Rubio-Reyes P, Chen S, Gonzalez-Miro M, Wedlock DN, Rehm BHA. Self-Assembled Protein-Coated Polyhydroxyalkanoate Beads: Properties and Biomedical Applications. ACS Biomater Sci Eng 2016; 3:3043-3057. [PMID: 33445349 DOI: 10.1021/acsbiomaterials.6b00355] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are biological polyesters that can be naturally produced by a range of bacteria as water-insoluble inclusions composed of a PHA core coated with PHA synthesis, structural, and regulatory proteins. These naturally self-assembling shell-core particles have been recently conceived as biomaterials that can be bioengineered as biologically active beads for medical applications. Protein engineering of PHA-associated proteins enabled the production of PHA-protein assemblies exhibiting biologically active protein-based functions relevant for applications as vaccines or diagnostics. Here we provide an overview of the recent advances in bioengineering of PHA particles toward the display of biomedically relevant protein functions such as selected disease-specific antigens as diagnostic tools or for the design of particulate subunit vaccines against infectious diseases such as tuberculosis, meningitis, pneumonia, and hepatitis C.
Collapse
Affiliation(s)
- Natalie A Parlane
- AgResearch, Hopkirk Research Institute, Palmerston North 4442, New Zealand
| | - Sandeep K Gupta
- AgResearch, Hopkirk Research Institute, Palmerston North 4442, New Zealand
| | - Patricia Rubio-Reyes
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Shuxiong Chen
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Majela Gonzalez-Miro
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - D Neil Wedlock
- AgResearch, Hopkirk Research Institute, Palmerston North 4442, New Zealand
| | - Bernd H A Rehm
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.,MacDiarmid Institute for Advanced Materials and Nanotechnology, Kelburn Parade, Wellington 6140, New Zealand
| |
Collapse
|
41
|
A study on the relation between poly(3-hydroxybutyrate) depolymerases or oligomer hydrolases and molecular weight of polyhydroxyalkanoates accumulating in Cupriavidus necator H16. J Biotechnol 2016; 227:94-102. [DOI: 10.1016/j.jbiotec.2016.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/25/2016] [Accepted: 04/04/2016] [Indexed: 01/23/2023]
|
42
|
Schmidt M, Ienczak JL, Quines LK, Zanfonato K, Schmidell W, Aragão GMF. POLY(3-HYDROXYBUTYRATE) PRODUCTION BY Cupriavidus necator SUPPLEMENTED WITH MINIEMULSIFIED SOYBEAN OIL. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2016. [DOI: 10.1590/0104-6632.20160331s00003394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- M. Schmidt
- Federal University of Santa Catarina, Brazil
| | | | | | | | | | | |
Collapse
|
43
|
Chen JS, Colón B, Dusel B, Ziesack M, Way JC, Torella JP. Production of fatty acids in Ralstonia eutropha H16 by engineering β-oxidation and carbon storage. PeerJ 2015; 3:e1468. [PMID: 26664804 PMCID: PMC4675107 DOI: 10.7717/peerj.1468] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/12/2015] [Indexed: 12/23/2022] Open
Abstract
Ralstonia eutropha H16 is a facultatively autotrophic hydrogen-oxidizing bacterium capable of producing polyhydroxybutyrate (PHB)-based bioplastics. As PHB's physical properties may be improved by incorporation of medium-chain-length fatty acids (MCFAs), and MCFAs are valuable on their own as fuel and chemical intermediates, we engineered R. eutropha for MCFA production. Expression of UcFatB2, a medium-chain-length-specific acyl-ACP thioesterase, resulted in production of 14 mg/L laurate in wild-type R. eutropha. Total fatty acid production (22 mg/L) could be increased up to 2.5-fold by knocking out PHB synthesis, a major sink for acetyl-CoA, or by knocking out the acyl-CoA ligase fadD3, an entry point for fatty acids into β-oxidation. As ΔfadD3 mutants still consumed laurate, and because the R. eutropha genome is predicted to encode over 50 acyl-CoA ligases, we employed RNA-Seq to identify acyl-CoA ligases upregulated during growth on laurate. Knockouts of the three most highly upregulated acyl-CoA ligases increased fatty acid yield significantly, with one strain (ΔA2794) producing up to 62 mg/L free fatty acid. This study demonstrates that homologous β-oxidation systems can be rationally engineered to enhance fatty acid production, a strategy that may be employed to increase yield for a range of fuels, chemicals, and PHB derivatives in R. eutropha.
Collapse
Affiliation(s)
- Janice S. Chen
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, United States
- Current affiliation: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Brendan Colón
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States
| | - Brendon Dusel
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, United States
| | - Marika Ziesack
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States
| | - Jeffrey C. Way
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, United States
| | - Joseph P. Torella
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States
| |
Collapse
|
44
|
Kawashima Y, Orita I, Nakamura S, Fukui T. Compositional regulation of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) by replacement of granule-associated protein in Ralstonia eutropha. Microb Cell Fact 2015; 14:187. [PMID: 26597300 PMCID: PMC4657207 DOI: 10.1186/s12934-015-0380-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/04/2015] [Indexed: 11/10/2022] Open
Abstract
Background Phasin (PhaP), a kind of polyhydroxyalkanoate (PHA) granule-associated proteins, has a role in controlling the properties of PHA granules surface, and is thought to have influence on PHA biosynthesis in PHA-producing bacteria. This study focused on the phaP1Re locus in Ralstonia eutropha as a site of chromosomal modification for production of flexible poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) [P(3HB-co-3HHx)] from soybean oil. Results Considering the high expression level of phaP1Re, phaJAc [encoding (R)-specific enoyl-CoA hydratase from Aeromonas caviae] was inserted into the downstream of phaP1Re on chromosome 1 of R. eutropha strain NSDG harboring phaCNSDG (encoding PHA synthase with broad substrate specificity). The constructed strain efficiently accumulated P(3HB-co-3HHx) on soybean oil with higher 3HHx composition when compared to the previous strain having phaJAc within pha operon. Insertion of the second phaCNSDG along with phaJAc at the phaP1Re locus led to incorporation of much larger 3HHx fraction into PHA chains, although the molecular weight was markedly reduced. The R. eutropha strains were further engineered by replacing phaP1Re with phaPAc (encoding phasin from A. caviae) on the chromosome. Interestingly, the phasin replacement increased 3HHx composition in the soybean oil-based PHA with keeping high cellular contents, nevertheless no modification was conducted in the metabolic pathways. Kinetic and Western blot analyses of PHA synthase using cellular insoluble fractions strongly suggested that the phasin replacement not only enhanced activity of PHA synthase from A. caviae but also increased affinity especially to longer (R)-3HHx-CoA. It was supposed that the increased affinity of PHA synthase to (R)-3HHx-CoA was responsible for the higher 3HHx composition in the copolyester. Conclusions The downstream of phaP1Re was a useful site for integration of genes to be overexpressed during PHA accumulation in R. eutropha. The results also clarified that polymerization properties of PHA synthase was affected by the kind of phasin co-existed on the surface of PHA granules, leading to altered composition of the resulting P(3HB-co-3HHx). The phasin replacement is a novel engineering strategy for regulation of composition of PHA copolyesters. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0380-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yui Kawashima
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
| | - Izumi Orita
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
| | - Satoshi Nakamura
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
| | - Toshiaki Fukui
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
| |
Collapse
|
45
|
Volodina E, Raberg M, Steinbüchel A. Engineering the heterotrophic carbon sources utilization range of Ralstonia eutropha H16 for applications in biotechnology. Crit Rev Biotechnol 2015; 36:978-991. [PMID: 26329669 DOI: 10.3109/07388551.2015.1079698] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Ralstonia eutropha H16 is an interesting candidate for the biotechnological production of polyesters consisting of hydroxy- and mercaptoalkanoates, and other compounds. It provides all the necessary characteristics, which are required for a biotechnological production strain. Due to its metabolic versatility, it can convert a broad range of renewable heterotrophic resources into diverse valuable compounds. High cell density fermentations of the non-pathogenic R. eutropha can be easily performed. Furthermore, this bacterium is accessible to engineering of its metabolism by genetic approaches having available a large repertoire of genetic tools. Since the complete genome sequence of R. eutropha H16 has become available, a variety of transcriptome, proteome and metabolome studies provided valuable data elucidating its complex metabolism and allowing a systematic biology approach. However, high production costs for bacterial large-scale production of biomass and biotechnologically valuable products are still an economic challenge. The application of inexpensive raw materials could significantly reduce the expenses. Therefore, the conversion of diverse substrates to polyhydroxyalkanoates by R. eutropha was steadily improved by optimization of cultivation conditions, mutagenesis and metabolic engineering. Industrial by-products and residual compounds like glycerol, and substrates containing high carbon content per weight like palm, soybean, corn oils as well as raw sugar-rich materials like molasses, starch and lignocellulose, are the most promising renewable substrates and were intensively studied.
Collapse
Affiliation(s)
- Elena Volodina
- a Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster , Münster , Germany and
| | - Matthias Raberg
- a Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster , Münster , Germany and
| | - Alexander Steinbüchel
- a Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster , Münster , Germany and.,b Environmental Science Department, King Abdulaziz University , Jeddah , Saudi Arabia
| |
Collapse
|
46
|
Prieto A, Escapa IF, Martínez V, Dinjaski N, Herencias C, de la Peña F, Tarazona N, Revelles O. A holistic view of polyhydroxyalkanoate metabolism inPseudomonas putida. Environ Microbiol 2015; 18:341-57. [DOI: 10.1111/1462-2920.12760] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 12/12/2014] [Accepted: 12/20/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Auxiliadora Prieto
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Isabel F. Escapa
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Virginia Martínez
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Nina Dinjaski
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Cristina Herencias
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Fernando de la Peña
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Natalia Tarazona
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| | - Olga Revelles
- Department of Environmental Biology; Centro de Investigaciones Biológicas; CSIC; Madrid 28040 Spain
| |
Collapse
|
47
|
Huschner F, Grousseau E, Brigham CJ, Plassmeier J, Popovic M, Rha C, Sinskey AJ. Development of a feeding strategy for high cell and PHA density fed-batch fermentation of Ralstonia eutropha H16 from organic acids and their salts. Process Biochem 2015. [DOI: 10.1016/j.procbio.2014.12.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
48
|
Zhila N, Kalacheva G, Volova T. Fatty acid composition and polyhydroxyalkanoates production by Cupriavidus eutrophus B-10646 cells grown on different carbon sources. Process Biochem 2015. [DOI: 10.1016/j.procbio.2014.10.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
49
|
Gruber S, Hagen J, Schwab H, Koefinger P. Reprint of “Versatile and stable vectors for efficient gene expression in Ralstonia eutropha H16”. J Biotechnol 2014; 192 Pt B:410-8. [DOI: 10.1016/j.jbiotec.2014.09.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
50
|
Gruber S, Hagen J, Schwab H, Koefinger P. Versatile and stable vectors for efficient gene expression in Ralstonia eutropha H16. J Biotechnol 2014; 186:74-82. [DOI: 10.1016/j.jbiotec.2014.06.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/11/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
|