1
|
Santolin L, Eichenroth RSJ, Cornehl P, Wortmann H, Forbrig C, Schulze A, Haq IU, Brantl S, Rappsilber J, Riedel SL, Neubauer P, Gimpel M. Elucidating regulation of polyhydroxyalkanoate metabolism in Ralstonia eutropha: Identification of transcriptional regulators from phasin and depolymerase genes. J Biol Chem 2024; 300:107523. [PMID: 38969063 DOI: 10.1016/j.jbc.2024.107523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/24/2024] [Accepted: 06/20/2024] [Indexed: 07/07/2024] Open
Abstract
Despite the ever-growing research interest in polyhydroxyalkanoates (PHAs) as green plastic alternatives, our understanding of the regulatory mechanisms governing PHA synthesis, storage, and degradation in the model organism Ralstonia eutropha remains limited. Given its importance for central carbon metabolism, PHA homeostasis is probably controlled by a complex network of transcriptional regulators. Understanding this fine-tuning is the key for developing improved PHA production strains thereby boosting the application of PHAs. We conducted promoter pull-down assays with crude protein extracts from R. eutropha Re2058/pCB113, followed by liquid chromatography with tandem mass spectrometry, to identify putative transcriptional regulators involved in the expression control of PHA metabolism, specifically targeting phasin phaP1 and depolymerase phaZ3 and phaZ5 genes. The impact on promoter activity was studied in vivo using β-galactosidase assays and the most promising candidates were heterologously produced in Escherichia coli, and their interaction with the promoters investigated in vitro by electrophoretic mobility shift assays. We could show that R. eutropha DNA-binding xenobiotic response element-family-like protein H16_B1672, specifically binds the phaP1 promoter in vitro with a KD of 175 nM and represses gene expression from this promoter in vivo. Protein H16_B1672 also showed interaction with both depolymerase promoters in vivo and in vitro suggesting a broader role in the regulation of PHA metabolism. Furthermore, in vivo assays revealed that the H-NS-like DNA-binding protein H16_B0227 and the peptidyl-prolyl cis-trans isomerase PpiB, strongly repress gene expression from PphaP1 and PphaZ3, respectively. In summary, this study provides new insights into the regulation of PHA metabolism in R. eutropha, uncovering specific interactions of novel transcriptional regulators.
Collapse
Affiliation(s)
- Lara Santolin
- Technische Universität Berlin, Chair of Bioprocess Engineering, Berlin, Germany
| | | | - Paul Cornehl
- Technische Universität Berlin, Chair of Bioprocess Engineering, Berlin, Germany
| | - Henrike Wortmann
- Technische Universität Berlin, Chair of Bioprocess Engineering, Berlin, Germany
| | - Christian Forbrig
- Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Anne Schulze
- Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Inam Ul Haq
- Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Sabine Brantl
- Matthias-Schleiden-Institut für Genetik, Bioinformatik und Molekulare Botanik, AG Bakteriengenetik, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Juri Rappsilber
- Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Sebastian Lothar Riedel
- Technische Universität Berlin, Chair of Bioprocess Engineering, Berlin, Germany; Berliner Hochschule für Technik, Environmental and Bioprocess Engineering Laboratory, Berlin, Germany
| | - Peter Neubauer
- Technische Universität Berlin, Chair of Bioprocess Engineering, Berlin, Germany
| | - Matthias Gimpel
- Technische Universität Berlin, Chair of Bioprocess Engineering, Berlin, Germany.
| |
Collapse
|
2
|
Hudson EP. The Calvin Benson cycle in bacteria: New insights from systems biology. Semin Cell Dev Biol 2024; 155:71-83. [PMID: 37002131 DOI: 10.1016/j.semcdb.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
The Calvin Benson cycle in phototrophic and chemolithoautotrophic bacteria has ecological and biotechnological importance, which has motivated study of its regulation. I review recent advances in our understanding of how the Calvin Benson cycle is regulated in bacteria and the technologies used to elucidate regulation and modify it, and highlight differences between and photoautotrophic and chemolithoautotrophic models. Systems biology studies have shown that in oxygenic phototrophic bacteria, Calvin Benson cycle enzymes are extensively regulated at post-transcriptional and post-translational levels, with multiple enzyme activities connected to cellular redox status through thioredoxin. In chemolithoautotrophic bacteria, regulation is primarily at the transcriptional level, with effector metabolites transducing cell status, though new methods should now allow facile, proteome-wide exploration of biochemical regulation in these models. A biotechnological objective is to enhance CO2 fixation in the cycle and partition that carbon to a product of interest. Flux control of CO2 fixation is distributed over multiple enzymes, and attempts to modulate gene Calvin cycle gene expression show a robust homeostatic regulation of growth rate, though the synthesis rates of products can be significantly increased. Therefore, de-regulation of cycle enzymes through protein engineering may be necessary to increase fluxes. Non-canonical Calvin Benson cycles, if implemented with synthetic biology, could have reduced energy demand and enzyme loading, thus increasing the attractiveness of these bacteria for industrial applications.
Collapse
Affiliation(s)
- Elton P Hudson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
| |
Collapse
|
3
|
Arhar S, Rauter T, Stolterfoht-Stock H, Lambauer V, Kratzer R, Winkler M, Karava M, Kourist R, Emmerstorfer-Augustin A. CO 2-based production of phytase from highly stable expression plasmids in Cupriavidus necator H16. Microb Cell Fact 2024; 23:9. [PMID: 38172920 PMCID: PMC10763379 DOI: 10.1186/s12934-023-02280-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Existing plasmid systems offer a fundamental foundation for gene expression in Cupriavidus necator; however, their applicability is constrained by the limitations of conjugation. Low segregational stabilities and plasmid copy numbers, particularly in the absence of selection pressure, pose challenges. Phytases, recognized for their widespread application as supplements in animal feed to enhance phosphate availability, present an intriguing prospect for heterologous production in C. necator. The establishment of stable, high-copy number plasmid that can be electroporated would support the utilization of C. necator for the production of single-cell protein from CO2. RESULTS In this study, we introduce a novel class of expression plasmids specifically designed for electroporation. These plasmids contain partitioning systems to boost segregation stability, eliminating the need for selection pressure. As a proof of concept, we successfully produced Escherichia coli derived AppA phytase in C. necator H16 PHB- 4 using these improved plasmids. Expression was directed by seven distinct promoters, encompassing the constitutive j5 promoter, hydrogenase promoters, and those governing the Calvin-Benson-Bassham cycle. The phytase activities observed in recombinant C. necator H16 strains ranged from 2 to 50 U/mg of total protein, contingent upon the choice of promoter and the mode of cell cultivation - heterotrophic or autotrophic. Further, an upscaling experiment conducted in a 1 l fed-batch gas fermentation system resulted in the attainment of the theoretical biomass. Phytase activity reached levels of up to 22 U/ml. CONCLUSION The new expression system presented in this study offers a highly efficient platform for protein production and a wide array of synthetic biology applications. It incorporates robust promoters that exhibit either constitutive activity or can be selectively activated when cells transition from heterotrophic to autotrophic growth. This versatility makes it a powerful tool for tailored gene expression. Moreover, the potential to generate active phytases within C. necator H16 holds promising implications for the valorization of CO2 in the feed industry.
Collapse
Affiliation(s)
- Simon Arhar
- Austrian Centre of Industrial Biotechnology, acib GmbH, Krenngasse 37, Graz, 8010, Austria
| | - Thomas Rauter
- Austrian Centre of Industrial Biotechnology, acib GmbH, Krenngasse 37, Graz, 8010, Austria
| | | | - Vera Lambauer
- Austrian Centre of Industrial Biotechnology, acib GmbH, Krenngasse 37, Graz, 8010, Austria
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, Graz, 8010, Austria
| | - Regina Kratzer
- Austrian Centre of Industrial Biotechnology, acib GmbH, Krenngasse 37, Graz, 8010, Austria
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, Graz, 8010, Austria
| | - Margit Winkler
- Austrian Centre of Industrial Biotechnology, acib GmbH, Krenngasse 37, Graz, 8010, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, Graz, 8010, Austria
| | - Marianna Karava
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, Graz, 8010, Austria
| | - Robert Kourist
- Austrian Centre of Industrial Biotechnology, acib GmbH, Krenngasse 37, Graz, 8010, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, Graz, 8010, Austria
| | - Anita Emmerstorfer-Augustin
- Austrian Centre of Industrial Biotechnology, acib GmbH, Krenngasse 37, Graz, 8010, Austria.
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, Graz, 8010, Austria.
- BioTechMed-Graz, Graz, Austria.
| |
Collapse
|
4
|
Continuous-flow membrane bioreactor enhances enrichment and culture of autotrophic nitrifying bacteria by removing extracellular free organic carbon. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:42378-42389. [PMID: 36648712 DOI: 10.1007/s11356-023-25253-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 01/07/2023] [Indexed: 01/18/2023]
Abstract
An activated sludge system can be inoculated with enriched nitrifying bacteria to enhance NH4+-N removal, or enriched nitrifying bacteria can be added directly to a river to remove NH4+-N. However, the enrichment culture is still generally inefficient and the technical bottleneck has not been clarified. Previous studies have shown that extracellular free organic carbon (EFOC) inhibits the growth of some autotrophic bacteria, and separating EFOC during culture with a membrane bioreactor (MBR) promotes the continuous growth of autotrophic bacteria and CO2 fixation. However, whether a membrane bioreactor can also be used to enrich and culture autotrophic nitrifying bacteria by separating EFOC has not been verified. In this study, an MBR was constructed to separate EFOC during the culture of nitrifying bacteria in activated sludge to confirm that the MBR better enriches and cultures nitrifying bacteria than a sequencing batch reactor (SBR). Our results showed that after culture for 34 days, the rate of NH4+-N removal and the nitrification rate by nitrifying bacteria in the MBR were 2.20-fold and 1.42-fold higher than in the SBR, respectively. The abundance of Nitrospira in the MBR was also 7.23-fold greater than in the SBR at the end of the experimental period. After 34 days, the average concentration of EFOC and the average EFOC/bacterial organic carbon ratio in the MBR were only 53% and 37% of those in the SBR, respectively. A correlation analysis suggested that the timely removal by the MBR of the EFOC generated during the culture process may be an important factor in promoting the growth of autotrophic nitrifying bacteria. The possible mechanism by which the MBR separates EFOC to the growth of promote autotrophic nitrifying bacteria is discussed from the perspective of the inhibitory effect of EFOC on cbb gene transcription. Our experimental results suggest a new approach to enhancing the enrichment of autotrophic nitrifying bacteria and extending the application of MBRs.
Collapse
|
5
|
Calvey CH, Sànchez I Nogué V, White AM, Kneucker CM, Woodworth SP, Alt HM, Eckert CA, Johnson CW. Improving growth of Cupriavidus necator H16 on formate using adaptive laboratory evolution-informed engineering. Metab Eng 2023; 75:78-90. [PMID: 36368470 DOI: 10.1016/j.ymben.2022.10.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022]
Abstract
Conversion of CO2 to value-added products presents an opportunity to reduce GHG emissions while generating revenue. Formate, which can be generated by the electrochemical reduction of CO2, has been proposed as a promising intermediate compound for microbial upgrading. Here we present progress towards improving the soil bacterium Cupriavidus necator H16, which is capable of growing on formate as its sole source of carbon and energy using the Calvin-Benson-Bassham (CBB) cycle, as a host for formate utilization. Using adaptive laboratory evolution, we generated several isolates that exhibited faster growth rates on formate. The genomes of these isolates were sequenced, and resulting mutations were systematically reintroduced by metabolic engineering, to identify those that improved growth. The metabolic impact of several mutations was investigated further using RNA-seq transcriptomics. We found that deletion of a transcriptional regulator implicated in quorum sensing, PhcA, reduced expression of several operons and led to improved growth on formate. Growth was also improved by deleting large genomic regions present on the extrachromosomal megaplasmid pHG1, particularly two hydrogenase operons and the megaplasmid CBB operon, one of two copies present in the genome. Based on these findings, we generated a rationally engineered ΔphcA and megaplasmid-deficient strain that exhibited a 24% faster maximum growth rate on formate. Moreover, this strain achieved a 7% growth rate improvement on succinate and a 19% increase on fructose, demonstrating the broad utility of microbial genome reduction. This strain has the potential to serve as an improved microbial chassis for biological conversion of formate to value-added products.
Collapse
Affiliation(s)
- Christopher H Calvey
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Violeta Sànchez I Nogué
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Aleena M White
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Colin M Kneucker
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Sean P Woodworth
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Hannah M Alt
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Carrie A Eckert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| |
Collapse
|
6
|
Kim S, Jang YJ, Gong G, Lee SM, Um Y, Kim KH, Ko JK. Engineering Cupriavidus necator H16 for enhanced lithoautotrophic poly(3-hydroxybutyrate) production from CO 2. Microb Cell Fact 2022; 21:231. [PMCID: PMC9636797 DOI: 10.1186/s12934-022-01962-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Background A representative hydrogen-oxidizing bacterium Cupriavidus necator H16 has attracted much attention as hosts to recycle carbon dioxide (CO2) into a biodegradable polymer, poly(R)-3-hydroxybutyrate (PHB). Although C. necator H16 has been used as a model PHB producer, the PHB production rate from CO2 is still too low for commercialization. Results Here, we engineer the carbon fixation metabolism to improve CO2 utilization and increase PHB production. We explore the possibilities to enhance the lithoautotrophic cell growth and PHB production by introducing additional copies of transcriptional regulators involved in Calvin Benson Bassham (CBB) cycle. Both cbbR and regA-overexpressing strains showed the positive phenotypes for 11% increased biomass accumulation and 28% increased PHB production. The transcriptional changes of key genes involved in CO2—fixing metabolism and PHB production were investigated. Conclusions The global transcriptional regulator RegA plays an important role in the regulation of carbon fixation and shows the possibility to improve autotrophic cell growth and PHB accumulation by increasing its expression level. This work represents another step forward in better understanding and improving the lithoautotrophic PHB production by C. necator H16. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01962-7.
Collapse
Affiliation(s)
- Soyoung Kim
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Yong Jae Jang
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Gyeongtaek Gong
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
| | - Sun-Mi Lee
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
| | - Youngsoon Um
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
| | - Kyoung Heon Kim
- grid.222754.40000 0001 0840 2678Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 Republic of Korea
| | - Ja Kyong Ko
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
| |
Collapse
|
7
|
Lin L, Huang H, Zhang X, Dong L, Chen Y. Hydrogen-oxidizing bacteria and their applications in resource recovery and pollutant removal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155559. [PMID: 35483467 DOI: 10.1016/j.scitotenv.2022.155559] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/16/2022] [Accepted: 04/23/2022] [Indexed: 06/14/2023]
Abstract
Hydrogen oxidizing bacteria (HOB), a type of chemoautotroph, are a group of bacteria from different genera that share the ability to oxidize H2 and fix CO2 to provide energy and synthesize cellular material. Recently, HOB have received growing attention due to their potential for CO2 capture and waste recovery. This review provides a comprehensive overview of the biological characteristics of HOB and their application in resource recovery and pollutant removal. Firstly, the enzymes, genes and corresponding regulation systems responsible for the key metabolic processes of HOB are discussed in detail. Then, the enrichment and cultivation methods including the coupled water splitting-biosynthetic system cultivation, mixed cultivation and two-stage cultivation strategies for HOB are summarized, which is the critical prerequisite for their application. On the basis, recent advances of HOB application in the recovery of high-value products and the removal of pollutants are presented. Finally, the key points for future investigation are proposed that more attention should be paid to the main limitations in the large-scale industrial application of HOB, including the mass transfer rate of the gases, the safety of the production processes and products, and the commercial value of the products.
Collapse
Affiliation(s)
- Lin Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xin Zhang
- Shanghai Municipal Engineering Design Institute (Group) Co. LTD, 901 Zhongshan North Second Rd, Shanghai 200092, China
| | - Lei Dong
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Municipal Engineering Design Institute (Group) Co. LTD, 901 Zhongshan North Second Rd, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| |
Collapse
|
8
|
Bolay P, Schlüter S, Grimm S, Riediger M, Hess WR, Klähn S. The transcriptional regulator RbcR controls ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes in the cyanobacterium Synechocystis sp. PCC 6803. THE NEW PHYTOLOGIST 2022; 235:432-445. [PMID: 35377491 DOI: 10.1111/nph.18139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Oxygenic photosynthesis evolved in cyanobacteria, primary producers of striking ecological importance. Like plants, cyanobacteria use the Calvin-Benson-Bassham cycle for CO2 fixation, fuelled by ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). In a competitive reaction this enzyme also fixes O2 which makes it rather ineffective. To mitigate this problem, cyanobacteria evolved a CO2 concentrating mechanism (CCM) to pool CO2 in the vicinity of RuBisCO. However, the regulation of these carbon (C) assimilatory systems is understood only partially. Using the model Synechocystis sp. PCC 6803 we characterized an essential LysR-type transcriptional regulator encoded by gene sll0998. Transcript profiling of a knockdown mutant revealed diminished expression of several genes involved in C acquisition, including rbcLXS, sbtA and ccmKL encoding RuBisCO and parts of the CCM, respectively. We demonstrate that the Sll0998 protein binds the rbcL promoter and acts as a RuBisCO regulator (RbcR). We propose ATTA(G/A)-N5 -(C/T)TAAT as the binding motif consensus. Our data validate RbcR as a regulator of inorganic C assimilation and define the regulon controlled by it. Biological CO2 fixation can sustain efforts to reduce its atmospheric concentrations and is fundamental for the light-driven production of chemicals directly from CO2 . Information about the involved regulatory and physiological processes is crucial to engineer cyanobacterial cell factories.
Collapse
Affiliation(s)
- Paul Bolay
- Department of Solar Materials, Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Susan Schlüter
- Department of Solar Materials, Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Samuel Grimm
- Department of Solar Materials, Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Matthias Riediger
- Genetics & Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Stephan Klähn
- Department of Solar Materials, Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| |
Collapse
|
9
|
Pavan M, Reinmets K, Garg S, Mueller AP, Marcellin E, Köpke M, Valgepea K. Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy. Metab Eng 2022; 71:117-141. [DOI: 10.1016/j.ymben.2022.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
|
10
|
Ma Z, Liu D, Liu M, Cao Y, Song H. From CO<sub>2</sub> to high value-added products: Advances on carbon sequestration by <italic>Ralstonia eutropha</italic> H16. CHINESE SCIENCE BULLETIN-CHINESE 2021. [DOI: 10.1360/tb-2021-0584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
11
|
Jahn M, Crang N, Janasch M, Hober A, Forsström B, Kimler K, Mattausch A, Chen Q, Asplund-Samuelsson J, Hudson EP. Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator. eLife 2021; 10:69019. [PMID: 34723797 PMCID: PMC8591527 DOI: 10.7554/elife.69019] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/30/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria must balance the different needs for substrate assimilation, growth
functions, and resilience in order to thrive in their environment. Of all
cellular macromolecules, the bacterial proteome is by far the most important
resource and its size is limited. Here, we investigated how the highly versatile
'knallgas' bacterium Cupriavidus necator reallocates protein
resources when grown on different limiting substrates and with different growth
rates. We determined protein quantity by mass spectrometry and estimated enzyme
utilization by resource balance analysis modeling. We found that C.
necator invests a large fraction of its proteome in functions that
are hardly utilized. Of the enzymes that are utilized, many are present in
excess abundance. One prominent example is the strong expression of CBB cycle
genes such as Rubisco during growth on fructose. Modeling and mutant competition
experiments suggest that CO2-reassimilation through Rubisco does not
provide a fitness benefit for heterotrophic growth, but is rather an investment
in readiness for autotrophy.
Collapse
Affiliation(s)
- Michael Jahn
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Nick Crang
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Markus Janasch
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Andreas Hober
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Björn Forsström
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Kyle Kimler
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Alexander Mattausch
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Qi Chen
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Asplund-Samuelsson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Elton Paul Hudson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| |
Collapse
|
12
|
Subagyo DCH, Shimizu R, Orita I, Fukui T. Isopropanol production with reutilization of glucose-derived CO 2 by engineered Ralstonia eutropha. J Biosci Bioeng 2021; 132:479-486. [PMID: 34507913 DOI: 10.1016/j.jbiosc.2021.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 12/17/2022]
Abstract
Chemolithoautotrophic bacterium Ralstonia eutropha is a versatile host for production of various useful compounds including polyhydroxyalkanoates (PHAs) under both heterotrophic and autotrophic conditions. In this bacterium, Calvin-Benson-Bassham (CBB) cycle is functional even under heterotrophic conditions on sugars and reutilizes CO2 emitted through sugar metabolisms into PHA, leading to increase in yield of the storage polyester. This study focused on isopropanol production from glucose by engineered strains of R. eutropha. The isopropanol-producing strains were constructed by introduction of codon-optimized genes of acetoacetate decarboxylase (adc) and primary-secondary alcohol dehydrogenase (adh) from clostridia into glucose-utilizing and PHA-negative (ΔphaC1) strain of R. eutropha. Several genetic modifications showed that high expression of the isopropanol synthesis genes by using a strong synthetic promoter and deletion of NAD+-dependent (S)-3-hydroxybutyryl-CoA dehydrogenase genes (paaH1 and had) in addition to NADPH-dependent acetoacetyl-CoA reductase genes (phaB1 and phaB3) were effective for improving isopropanol production with low by-production of acetone. Isopropanol titer of 4.13 g/L was achieved by two-stage cultivation of the strain IP-007/pBj5c2-adh-adc, corresponding to overall yield of 0.6 mol mol-glucose-1. The fixation of sugar-derived CO2 during isopropanol synthesis was evaluated by 13C-labelling of the isopropanol produced from [1-13C]-glucose. The 13C-abundance in isopropanol synthesized by the engineered strain was significantly increased up to 4.8%, demonstrating actual reassimilation of CO2 emitted from glucose moiety by decarboxylation and potential contribution towards increase in the carbon yield of isopropanol on glucose.
Collapse
Affiliation(s)
- Dyah Candra Hapsari Subagyo
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Rie Shimizu
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Izumi Orita
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
| |
Collapse
|
13
|
Phenn J, Pané-Farré J, Meukow N, Klein A, Troitzsch A, Tan P, Fuchs S, Wagner GE, Lichtenegger S, Steinmetz I, Kohler C. RegAB Homolog of Burkholderia pseudomallei is the Master Regulator of Redox Control and involved in Virulence. PLoS Pathog 2021; 17:e1009604. [PMID: 34048488 PMCID: PMC8191878 DOI: 10.1371/journal.ppat.1009604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/10/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022] Open
Abstract
Burkholderia pseudomallei, the etiological agent of melioidosis in humans and animals, often occupies environmental niches and infection sites characterized by limited concentrations of oxygen. Versatile genomic features enable this pathogen to maintain its physiology and virulence under hypoxia, but the crucial regulatory networks employed to switch from oxygen dependent respiration to alternative terminal electron acceptors (TEA) like nitrate, remains poorly understood. Here, we combined a Tn5 transposon mutagenesis screen and an anaerobic growth screen to identify a two-component signal transduction system with homology to RegAB. We show that RegAB is not only essential for anaerobic growth, but also for full virulence in cell lines and a mouse infection model. Further investigations of the RegAB regulon, using a global transcriptomic approach, identified 20 additional regulators under transcriptional control of RegAB, indicating a superordinate role of RegAB in the B. pseudomallei anaerobiosis regulatory network. Of the 20 identified regulators, NarX/L and a FNR homolog were selected for further analyses and a role in adaptation to anaerobic conditions was demonstrated. Growth experiments identified nitrate and intermediates of the denitrification process as the likely signal activateing RegAB, NarX/L, and probably of the downstream regulators Dnr or NsrR homologs. While deletions of individual genes involved in the denitrification process demonstrated their important role in anaerobic fitness, they showed no effect on virulence. This further highlights the central role of RegAB as the master regulator of anaerobic metabolism in B. pseudomallei and that the complete RegAB-mediated response is required to achieve full virulence. In summary, our analysis of the RegAB-dependent modulon and its interconnected regulons revealed a key role for RegAB of B. pseudomallei in the coordination of the response to hypoxic conditions and virulence, in the environment and the host.
Collapse
Affiliation(s)
- Julia Phenn
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Nikolai Meukow
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Annelie Klein
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Anne Troitzsch
- Department for Microbial Physiology and Molecular Biology, University Greifswald, Greifswald, Germany
| | - Patrick Tan
- Genome Institute of Singapore, Singapore, Republic of Singapore
- Duke-NUS Medical School Singapore, Singapore, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Republic of Singapore
| | - Stephan Fuchs
- FG13 Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode, Germany
| | - Gabriel E Wagner
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Sabine Lichtenegger
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Ivo Steinmetz
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Christian Kohler
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
14
|
Zhang S, Wang L, Fu X, Tsang YF, Maiti K. A continuous flow membrane bio-reactor releases the feedback inhibition of self-generated free organic carbon on cbb gene transcription of a typical chemoautotrophic bacterium to improve its CO 2 fixation efficiency. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:143186. [PMID: 33131832 DOI: 10.1016/j.scitotenv.2020.143186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/25/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Since the free organic carbon (FOC) generated by chemoautotrophic bacterium self has a feedback inhibition effect on its growth and carbon fixation, a continuous flow membrane bio-reactor was designed to remove extracellular FOC (EFOC) and release its inhibition effect. The promotion effect of membrane reactor on growth and carbon fixation of typical chemoautotrophic bacterium and its mechanism were studied. The accumulated apparent carbon fixation yield in membrane reactor was 3.24 times that in the control reactor. The EFOC per unit bacteria and cbb gene transcription level in membrane reactor were about 0.41 times and 11.18 times that in control reactor in late stage, respectively. Membrane reactor separated out EFOC, especially the small molecules, which facilitated the release of intracellular FOC, thereby releasing the inhibition of FOC on cbb gene transcription, thus promoting growth and carbon fixation of the typical chemoautotrophic bacterium. This study lays a foundation for enhancing carbon fixation by chemoautotrophic bacteria and expands the application field of membrane reactor.
Collapse
Affiliation(s)
- Saiwei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, China; Department of Oceanography and Coastal Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA, USA
| | - Lei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, China.
| | - Xiaohua Fu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, China
| | - Yiu Fai Tsang
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, New Territories, Hong Kong SAR, China
| | - Kanchan Maiti
- Department of Oceanography and Coastal Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA, USA
| |
Collapse
|
15
|
Panich J, Fong B, Singer SW. Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO 2. Trends Biotechnol 2021; 39:412-424. [PMID: 33518389 DOI: 10.1016/j.tibtech.2021.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 02/08/2023]
Abstract
Decelerating global warming is one of the predominant challenges of our time and will require conversion of CO2 to usable products and commodity chemicals. Of particular interest is the production of fuels, because the transportation sector is a major source of CO2 emissions. Here, we review recent technological advances in metabolic engineering of the hydrogen-oxidizing bacterium Cupriavidus necator H16, a chemolithotroph that naturally consumes CO2 to generate biomass. We discuss recent successes in biofuel production using this organism, and the implementation of electrolysis/artificial photosynthesis approaches that enable growth of C. necator using renewable electricity and CO2. Last, we discuss prospects of improving the nonoptimal growth of C. necator in ambient concentrations of CO2.
Collapse
Affiliation(s)
- Justin Panich
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Bonnie Fong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Steven W Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| |
Collapse
|
16
|
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: 22] [Impact Index Per Article: 3.7] [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
|