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Zhao L, Cai Z, Li Y, Zhang Y. Engineering Rubisco to enhance CO 2 utilization. Synth Syst Biotechnol 2024; 9:55-68. [PMID: 38273863 PMCID: PMC10809010 DOI: 10.1016/j.synbio.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/15/2023] [Accepted: 12/25/2023] [Indexed: 01/27/2024] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a pivotal enzyme that mediates the fixation of CO2. As the most abundant protein on earth, Rubisco has a significant impact on global carbon, water, and nitrogen cycles. However, the significantly low carboxylation activity and competing oxygenase activity of Rubisco greatly impede high carbon fixation efficiency. This review first summarizes the current efforts in directly or indirectly modifying plant Rubisco, which has been challenging due to its high conservation and limitations in chloroplast transformation techniques. However, recent advancements in understanding Rubisco biogenesis with the assistance of chaperones have enabled successful heterologous expression of all Rubisco forms, including plant Rubisco, in microorganisms. This breakthrough facilitates the acquisition and evaluation of modified proteins, streamlining the measurement of their activity. Moreover, the establishment of a screening system in E. coli opens up possibilities for obtaining high-performance mutant enzymes through directed evolution. Finally, this review emphasizes the utilization of Rubisco in microorganisms, not only expanding their carbon-fixing capabilities but also holding significant potential for enhancing biotransformation processes.
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Affiliation(s)
- Lei Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Cai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanping Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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Baumschabl M, Mitic BM, Troyer C, Hann S, Ata Ö, Mattanovich D. A native phosphoglycolate salvage pathway of the synthetic autotrophic yeast Komagataella phaffii. MICROLIFE 2023; 5:uqad046. [PMID: 38234447 PMCID: PMC10791038 DOI: 10.1093/femsml/uqad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/10/2023] [Accepted: 12/09/2023] [Indexed: 01/19/2024]
Abstract
Synthetic autotrophs can serve as chassis strains for bioproduction from CO2 as a feedstock to take measures against the climate crisis. Integration of the Calvin-Benson-Bassham (CBB) cycle into the methylotrophic yeast Komagataella phaffii (Pichia pastoris) enabled it to use CO2 as the sole carbon source. The key enzyme in this cycle is ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzing the carboxylation step. However, this enzyme is error prone to perform an oxygenation reaction leading to the production of toxic 2-phosphoglycolate. Native autotrophs have evolved different recycling pathways for 2-phosphoglycolate. However, for synthetic autotrophs, no information is available for the existence of such pathways. Deletion of CYB2 in the autotrophic K. phaffii strain led to the accumulation of glycolate, an intermediate in phosphoglycolate salvage pathways, suggesting that such a pathway is enabled by native K. phaffii enzymes. 13C tracer analysis with labeled glycolate indicated that the yeast pathway recycling phosphoglycolate is similar to the plant salvage pathway. This orthogonal yeast pathway may serve as a sensor for RuBisCO oxygenation, and as an engineering target to boost autotrophic growth rates in K. phaffii.
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Affiliation(s)
- Michael Baumschabl
- Austrian Centre of Industrial Biotechnology, Vienna 1190, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Bernd M Mitic
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna 1190, Austria
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Analytical Chemistry, Vienna 1190, Austria
| | - Christina Troyer
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Analytical Chemistry, Vienna 1190, Austria
| | - Stephan Hann
- Austrian Centre of Industrial Biotechnology, Vienna 1190, Austria
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Analytical Chemistry, Vienna 1190, Austria
| | - Özge Ata
- Austrian Centre of Industrial Biotechnology, Vienna 1190, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology, Vienna 1190, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna 1190, Austria
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Tang R, Yuan X, Yang J. Problems and corresponding strategies for converting CO 2 into value-added products in Cupriavidus necator H16 cell factories. Biotechnol Adv 2023; 67:108183. [PMID: 37286176 DOI: 10.1016/j.biotechadv.2023.108183] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/17/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
Elevated CO2 emissions have substantially altered the worldwide climate, while the excessive reliance on fossil fuels has exacerbated the energy crisis. Therefore, the conversion of CO2 into fuel, petroleum-based derivatives, drug precursors, and other value-added products is expected. Cupriavidus necator H16 is the model organism of the "Knallgas" bacterium and is considered to be a microbial cell factory as it can convert CO2 into various value-added products. However, the development and application of C. necator H16 cell factories has several limitations, including low efficiency, high cost, and safety concerns arising from the autotrophic metabolic characteristics of the strains. In this review, we first considered the autotrophic metabolic characteristics of C. necator H16, and then categorized and summarized the resulting problems. We also provided a detailed discussion of some corresponding strategies concerning metabolic engineering, trophic models, and cultivation mode. Finally, we provided several suggestions for improving and combining them. This review might help in the research and application of the conversion of CO2 into value-added products in C. necator H16 cell factories.
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Affiliation(s)
- Ruohao Tang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China; Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong Province, People's Republic of China
| | - Xianzheng Yuan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, Shandong Province, People's Republic of China
| | - Jianming Yang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, People's Republic of China.
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4
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Yu X, Catanescu CO, Bird RE, Satagopan S, Baum ZJ, Lotti Diaz LM, Zhou QA. Trends in Research and Development for CO 2 Capture and Sequestration. ACS OMEGA 2023; 8:11643-11664. [PMID: 37033841 PMCID: PMC10077574 DOI: 10.1021/acsomega.2c05070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
Technological and medical advances over the past few decades epitomize human capabilities. However, the increased life expectancies and concomitant land-use changes have significantly contributed to the release of ∼830 gigatons of CO2 into the atmosphere over the last three decades, an amount comparable to the prior two and a half centuries of CO2 emissions. The United Nations has adopted a pledge to achieve "net zero", i.e., yearly removing as much CO2 from the atmosphere as the amount emitted due to human activities, by the year 2050. Attaining this goal will require a concerted effort by scientists, policy makers, and industries all around the globe. The development of novel materials on industrial scales to selectively remove CO2 from mixtures of gases makes it possible to mitigate CO2 emissions using a multipronged approach. Broadly, the CO2 present in the atmosphere can be captured using materials and processes for biological, chemical, and geological technologies that can sequester CO2 while also reducing our dependence on fossil-fuel reserves. In this review, we used the curated literature available in the CAS Content Collection to present a systematic analysis of the various approaches taken by scientists and industrialists to restore carbon balance in the environment. Our analysis highlights the latest trends alongside the associated challenges.
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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.
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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
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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.
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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.
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Srisawat P, Higuchi-Takeuchi M, Numata K. Microbial autotrophic biorefineries: Perspectives for biopolymer production. Polym J 2022. [DOI: 10.1038/s41428-022-00675-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
AbstractThe use of autotrophic microorganisms to fabricate biochemical products has attracted much attention in both academia and industry. Unlike heterotrophic microorganisms that require carbohydrates and amino acids for growth, autotrophic microorganisms have evolved to utilize either light (photoautotrophs) or chemical compounds (chemolithotrophs) to fix carbon dioxide (CO2) and drive metabolic processes. Several biotechnological approaches, including synthetic biology and metabolic engineering, have been proposed to harness autotrophic microorganisms as a sustainable/green production platform for commercially essential products such as biofuels, commodity chemicals, and biopolymers. Here, we review the recent advances in natural autotrophic microorganisms (photoautotrophic and chemoautotrophic), focusing on the biopolymer production. We present current state-of-the-art technologies to engineer autotrophic microbial cell factories for efficient biopolymer production.
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Strittmatter CS, Eggers J, Biesgen V, Pauels I, Becker F, Steinbüchel A. The reliance of glycerol utilization by Cupriavidus necator on CO 2 fixation and improved glycerol catabolism. Appl Microbiol Biotechnol 2022; 106:2541-2555. [PMID: 35325274 DOI: 10.1007/s00253-022-11842-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 11/29/2022]
Abstract
While crude glycerol is a cheap carbon source for industrial-scale cultivation of microorganisms, its application relies on fast growth and conversion. The biopolymer producing Cupriavidus necator H16 (synonym: Ralstonia eutropha H16) grows poorly on glycerol. The heterologous expression of glycerol facilitator glpF, glycerol kinase glpK, and glycerol dehydrogenase glpD from E. coli accelerated the growth considerably. The naturally occurring glycerol utilization is inhibited by low glycerol kinase activity. A limited heterotrophic growth promotes the dependency on autotrophic growth by carbon dioxide (CO2) fixation and refixation. As mixotrophic growth occurs in the wildtype due to low consumption rates of glycerol, CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle is essential. The deletion of both cbbX copies encoding putative RuBisCO-activases (AAA + ATPase) resulted in a sharp slowdown of growth and glycerol consumption. Activase activity is necessary for functioning carboxylation by RuBisCO. Each of the two copies compensates for the loss of the other, as suggested by observed expression levels. The strong tendency towards autotrophy supports previous investigations of glycerol growth and emphasizes the versatility of the metabolism of C. necator H16. Mixotrophy with glycerol-utilization and CO2 fixation with a high dependence on the CBB is automatically occurring unless transportation and degradation of glycerol are optimized. Parallel engineering of CO2 fixation and glycerol degradation is suggested towards application for value-added production from crude glycerol. KEY POINTS: • Growth on glycerol is highly dependent on efficient carbon fixation via CBB cycle. • CbbX is essential for the efficiency of RuBisCO in C. necator H16. • Expression of glycerol degradation pathway enzymes accelerates glycerol utilization.
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Affiliation(s)
- Carl Simon Strittmatter
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Jessica Eggers
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Vanessa Biesgen
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Inga Pauels
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Florian Becker
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany
| | - Alexander Steinbüchel
- Insitut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universtität Münster, Münster, Germany. .,Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia.
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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]
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Manikandan NA, Pakshirajan K, Pugazhenthi G. A novel rotating wide gap annular bioreactor (Taylor-Couette type flow) for polyhydroxybutyrate production by Ralstonia eutropha using carob pod extract. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 299:113591. [PMID: 34455350 DOI: 10.1016/j.jenvman.2021.113591] [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: 01/31/2021] [Revised: 08/09/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
An annular bioreactor (ABR) with wide gap was used for PHB production from Ralstonia eutropha. Hydrodynamic studies demonstrated the uniform distribution of fluid in the ABR due to the Taylor-Couette flow. Thereafter, the ABR was operated at different agitation and sparging rates to study its effect on R. eutropha growth and PHB production. The ABR operated at 500 rpm with air sparge rate of 0.8 vvm yielded a maximum PHB concentration of 14.89 g/L, which was nearly 1.4 times that obtained using a conventional stirred-tank bioreactor (STBR). Furthermore, performances of the bioreactors were compared by operating the reactors under fed-batch mode. At the end of 90 h of operation, the ABR resulted in a very high PHB production of 70.8 g/L. But STBR resulted in a low PHB concentration of 44.2 g/L. The superior performance was due to enhanced oxygen and nutrient mass transfer in the ABR.
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Affiliation(s)
- N Arul Manikandan
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Kannan Pakshirajan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
| | - G Pugazhenthi
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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Pan H, Wang J, Wu H, Li Z, Lian J. Synthetic biology toolkit for engineering Cupriviadus necator H16 as a platform for CO 2 valorization. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:212. [PMID: 34736496 PMCID: PMC8570001 DOI: 10.1186/s13068-021-02063-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 10/25/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND CO2 valorization is one of the effective methods to solve current environmental and energy problems, in which microbial electrosynthesis (MES) system has proved feasible and efficient. Cupriviadus necator (Ralstonia eutropha) H16, a model chemolithoautotroph, is a microbe of choice for CO2 conversion, especially with the ability to be employed in MES due to the presence of genes encoding [NiFe]-hydrogenases and all the Calvin-Benson-Basham cycle enzymes. The CO2 valorization strategy will make sense because the required hydrogen can be produced from renewable electricity independently of fossil fuels. MAIN BODY In this review, synthetic biology toolkit for C. necator H16, including genetic engineering vectors, heterologous gene expression elements, platform strain and genome engineering, and transformation strategies, is firstly summarized. Then, the review discusses how to apply these tools to make C. necator H16 an efficient cell factory for converting CO2 to value-added products, with the examples of alcohols, fatty acids, and terpenoids. The review is concluded with the limitation of current genetic tools and perspectives on the development of more efficient and convenient methods as well as the extensive applications of C. necator H16. CONCLUSIONS Great progress has been made on genetic engineering toolkit and synthetic biology applications of C. necator H16. Nevertheless, more efforts are expected in the near future to engineer C. necator H16 as efficient cell factories for the conversion of CO2 to value-added products.
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Affiliation(s)
- Haojie Pan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jia Wang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Haoliang Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhongjian Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China.
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Sohn YJ, Son J, Jo SY, Park SY, Yoo JI, Baritugo KA, Na JG, Choi JI, Kim HT, Joo JC, Park SJ. Chemoautotroph Cupriavidus necator as a potential game-changer for global warming and plastic waste problem: A review. BIORESOURCE TECHNOLOGY 2021; 340:125693. [PMID: 34365298 DOI: 10.1016/j.biortech.2021.125693] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Cupriavidus necator, a versatile microorganism found in both soil and water, can have both heterotrophic and lithoautotrophic metabolisms depending on environmental conditions. C. necator has been extensively examined for producing Polyhydroxyalkanoates (PHAs), the promising polyester alternatives to petroleum-based synthetic polymers because it has a superior ability for accumulating a considerable amount of PHAs from renewable resources. The development of metabolically engineered C. necator strains has led to their application for synthesizing biopolymers, biofuels and biochemicals such as ethanol, isobutanol and higher alcohols. Bio-based processes of recombinant C. necator have made much progress in production of these high-value products from biomass wastes, plastic wastes and even waste gases. In this review, we discuss the potential of C. necator as promising platform host strains that provide a great opportunity for developing a waste-based circular bioeconomy.
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Affiliation(s)
- Yu Jung Sohn
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seo Young Jo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Se Young Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jee In Yoo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Kei-Anne Baritugo
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jeong Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea.
| | - Jong-Il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Korea.
| | - Hee Taek Kim
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea.
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Gyeonggi-do, Republic of Korea.
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea.
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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]
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Synthetic Biology Approaches To Enhance Microalgal Productivity. Trends Biotechnol 2021; 39:1019-1036. [PMID: 33541719 DOI: 10.1016/j.tibtech.2020.12.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022]
Abstract
The major bottleneck in commercializing biofuels and other commodities produced by microalgae is the high cost associated with phototrophic cultivation. Improving microalgal productivities could be a solution to this problem. Synthetic biology methods have recently been used to engineer the downstream production pathways in several microalgal strains. However, engineering upstream photosynthetic and carbon fixation metabolism to enhance growth, productivity, and yield has barely been explored in microalgae. We describe strategies to improve the generation of reducing power from light, as well as to improve the assimilation of CO2 by either the native Calvin cycle or synthetic alternatives. Overall, we are optimistic that recent technological advances will prompt long-awaited breakthroughs in microalgal research.
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15
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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.
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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.
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16
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Bernhardsgrütter I, Stoffel GM, Miller TE, Erb TJ. CO 2-converting enzymes for sustainable biotechnology: from mechanisms to application. Curr Opin Biotechnol 2021; 67:80-87. [PMID: 33508634 DOI: 10.1016/j.copbio.2021.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/20/2020] [Accepted: 01/05/2021] [Indexed: 01/28/2023]
Abstract
To realize a circular, carbon-neutral economy, it will become important to utilize the greenhouse gas CO2 as a sustainable carbon source. Carboxylases, the enzymes that capture and convert gaseous CO2 are the prime candidates to pave the way towards realizing this vision of a CO2-based bio-economy. In the last couple of years, the interest in using and engineering carboxylases has been steadily growing. Here, we discuss how basic research on the mechanism of CO2 binding and activation by carboxylases opened the way to develop new-to-nature CO2-fixing enzymes that found application in the development of synthetic CO2-fixation pathways and their further realization in vitro and in vivo. These pioneering efforts in the field pave the way to realize a diverse CO2-fixation biochemistry that can find application in biocatalysis, biotechnology, and artificial photosynthesis.
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Affiliation(s)
- Iria Bernhardsgrütter
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Gabriele Mm Stoffel
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Tarryn E Miller
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany; Center for Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany.
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17
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Flamholz AI, Dugan E, Blikstad C, Gleizer S, Ben-Nissan R, Amram S, Antonovsky N, Ravishankar S, Noor E, Bar-Even A, Milo R, Savage DF. Functional reconstitution of a bacterial CO 2 concentrating mechanism in Escherichia coli. eLife 2020; 9:59882. [PMID: 33084575 PMCID: PMC7714395 DOI: 10.7554/elife.59882] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
Many photosynthetic organisms employ a CO2 concentrating mechanism (CCM) to increase the rate of CO2 fixation via the Calvin cycle. CCMs catalyze ≈50% of global photosynthesis, yet it remains unclear which genes and proteins are required to produce this complex adaptation. We describe the construction of a functional CCM in a non-native host, achieved by expressing genes from an autotrophic bacterium in an Escherichia coli strain engineered to depend on rubisco carboxylation for growth. Expression of 20 CCM genes enabled E. coli to grow by fixing CO2 from ambient air into biomass, with growth in ambient air depending on the components of the CCM. Bacterial CCMs are therefore genetically compact and readily transplanted, rationalizing their presence in diverse bacteria. Reconstitution enabled genetic experiments refining our understanding of the CCM, thereby laying the groundwork for deeper study and engineering of the cell biology supporting CO2 assimilation in diverse organisms.
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Affiliation(s)
- Avi I Flamholz
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Eli Dugan
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Roee Ben-Nissan
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Shira Amram
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Sumedha Ravishankar
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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18
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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: 23] [Impact Index Per Article: 5.8] [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.
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19
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Zhou Y, Whitney S. Directed Evolution of an Improved Rubisco; In Vitro Analyses to Decipher Fact from Fiction. Int J Mol Sci 2019; 20:ijms20205019. [PMID: 31658746 PMCID: PMC6834295 DOI: 10.3390/ijms20205019] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 01/01/2023] Open
Abstract
Inaccuracies in biochemically characterizing the amount and CO2-fixing properties of the photosynthetic enzyme Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase continue to hamper an accurate evaluation of Rubisco mutants selected by directed evolution. Here, we outline an analytical pipeline for accurately quantifying Rubisco content and kinetics that averts the misinterpretation of directed evolution outcomes. Our study utilizes a new T7-promoter regulated Rubisco Dependent Escherichia coli (RDE3) screen to successfully select for the first Rhodobacter sphaeroides Rubisco (RsRubisco) mutant with improved CO2-fixing properties. The RsRubisco contains four amino acid substitutions in the large subunit (RbcL) and an improved carboxylation rate (kcatC, up 27%), carboxylation efficiency (kcatC/Km for CO2, increased 17%), unchanged CO2/O2 specificity and a 40% lower holoenzyme biogenesis capacity. Biochemical analysis of RsRubisco chimers coding one to three of the altered amino acids showed Lys-83-Gln and Arg-252-Leu substitutions (plant RbcL numbering) together, but not independently, impaired holoenzyme (L8S8) assembly. An N-terminal Val-11-Ile substitution did not affect RsRubisco catalysis or assembly, while a Tyr-345-Phe mutation alone conferred the improved kinetics without an effect on RsRubisco production. This study confirms the feasibility of improving Rubisco by directed evolution using an analytical pipeline that can identify false positives and reliably discriminate carboxylation enhancing amino acids changes from those influencing Rubisco biogenesis (solubility).
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Affiliation(s)
- Yu Zhou
- Australian Research Council Center of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 0200, Australia.
| | - Spencer Whitney
- Australian Research Council Center of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 0200, Australia.
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20
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Satagopan S, North JA, Arbing MA, Varaljay VA, Haines SN, Wildenthal JA, Byerly KM, Shin A, Tabita FR. Structural Perturbations of Rhodopseudomonas palustris Form II RuBisCO Mutant Enzymes That Affect CO2 Fixation. Biochemistry 2019; 58:3880-3892. [DOI: 10.1021/acs.biochem.9b00617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sriram Satagopan
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Justin A. North
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark A. Arbing
- UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Vanessa A. Varaljay
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sidney N. Haines
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - John A. Wildenthal
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kathryn M. Byerly
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Annie Shin
- UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - F. Robert Tabita
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
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21
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Selection of Cyanobacterial ( Synechococcus sp. Strain PCC 6301) RubisCO Variants with Improved Functional Properties That Confer Enhanced CO 2-Dependent Growth of Rhodobacter capsulatus, a Photosynthetic Bacterium. mBio 2019; 10:mBio.01537-19. [PMID: 31337726 PMCID: PMC6650557 DOI: 10.1128/mbio.01537-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RubisCO catalysis has a significant impact on mitigating greenhouse gas accumulation and CO2 conversion to food, fuel, and other organic compounds required to sustain life. Because RubisCO-dependent CO2 fixation is severely compromised by oxygen inhibition and other physiological constraints, improving RubisCO’s kinetic properties to enhance growth in the presence of atmospheric O2 levels has been a longstanding goal. In this study, RubisCO variants with superior structure-functional properties were selected which resulted in enhanced growth of an autotrophic host organism (R. capsulatus), indicating that RubisCO function was indeed growth limiting. It is evident from these results that genetically engineered RubisCO with kinetically enhanced properties can positively impact growth rates in primary producers. Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a ubiquitous enzyme that catalyzes the conversion of atmospheric CO2 into organic carbon in primary producers. All naturally occurring RubisCOs have low catalytic turnover rates and are inhibited by oxygen. Evolutionary adaptations of the enzyme and its host organisms to changing atmospheric oxygen concentrations provide an impetus to artificially evolve RubisCO variants under unnatural selective conditions. A RubisCO deletion strain of the nonsulfur purple photosynthetic bacterium Rhodobacter capsulatus was previously used as a heterologous host for directed evolution and suppressor selection studies that led to the identification of a conserved hydrophobic region near the active site where amino acid substitutions selectively impacted the enzyme’s sensitivity to O2. In this study, structural alignments, mutagenesis, suppressor selection, and growth complementation with R. capsulatus under anoxic or oxygenic conditions were used to analyze the importance of semiconserved residues in this region of Synechococcus RubisCO. RubisCO mutant substitutions were identified that provided superior CO2-dependent growth capabilities relative to the wild-type enzyme. Kinetic analyses of the mutant enzymes indicated that enhanced growth performance was traceable to differential interactions of the enzymes with CO2 and O2. Effective residue substitutions also appeared to be localized to two other conserved hydrophobic regions of the holoenzyme. Structural comparisons and similarities indicated that regions identified in this study may be targeted for improvement in RubisCOs from other sources, including crop plants.
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22
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Engqvist MKM, Rabe KS. Applications of Protein Engineering and Directed Evolution in Plant Research. PLANT PHYSIOLOGY 2019; 179:907-917. [PMID: 30626612 PMCID: PMC6393796 DOI: 10.1104/pp.18.01534] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/25/2018] [Indexed: 05/06/2023]
Abstract
Engineered proteins can be used to optimize desired traits in plants; even though recent advances have resulted in new application areas, certain methodological challenges remain.
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Affiliation(s)
- Martin K M Engqvist
- Department of Biology and Biological Engineering, Chalmers University of Technology, Division of Systems and Synthetic Biology, Gothenburg, Sweden
| | - Kersten S Rabe
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Group for Molecular Evolution, Karlsruhe, Germany
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23
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Liu D, Ramya RCS, Mueller-Cajar O. Surveying the expanding prokaryotic Rubisco multiverse. FEMS Microbiol Lett 2018; 364:3983162. [PMID: 28854711 DOI: 10.1093/femsle/fnx156] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/19/2017] [Indexed: 11/12/2022] Open
Abstract
The universal, but catalytically modest, CO2-fixing enzyme Rubisco is currently experiencing intense interest by researchers aiming to enhance crop photosynthesis. These efforts are mostly focused on the highly conserved hexadecameric enzyme found in land plants. In comparison, prokaryotic organisms harbor a far greater diversity in Rubisco forms. Recent work towards improving our appreciation of microbial Rubisco properties and harnessing their potential is surveyed. New structural models are providing informative glimpses into catalytic subtleties and diverse oligomeric states. Ongoing characterization is informing us about the conservation of constraints, such as sugar phosphate inhibition and the associated dependence on Rubisco activase helper proteins. Prokaryotic Rubiscos operate under a far wider range of metabolic contexts than the photosynthetic function of higher plant enzymes. Relaxed selection pressures may have resulted in the exploration of a larger volume of sequence space than permitted in organisms performing oxygenic photosynthesis. To tap into the potential of microbial Rubiscos, in vivo selection systems are being used to discover functional metagenomic Rubiscos. Various directed evolution systems to optimize their function have been developed. It is anticipated that this approach will provide access to biotechnologically valuable enzymes that cannot be encountered in the higher plant Rubisco space.
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Affiliation(s)
- Di Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | | | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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24
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Antonovsky N, Gleizer S, Milo R. Engineering carbon fixation in E. coli : from heterologous RuBisCO expression to the Calvin–Benson–Bassham cycle. Curr Opin Biotechnol 2017; 47:83-91. [DOI: 10.1016/j.copbio.2017.06.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/13/2017] [Indexed: 11/26/2022]
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