1
|
Höper R, Komkova D, Zavřel T, Steuer R. A quantitative description of light-limited cyanobacterial growth using flux balance analysis. PLoS Comput Biol 2024; 20:e1012280. [PMID: 39102434 DOI: 10.1371/journal.pcbi.1012280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 06/26/2024] [Indexed: 08/07/2024] Open
Abstract
The metabolism of phototrophic cyanobacteria is an integral part of global biogeochemical cycles, and the capability of cyanobacteria to assimilate atmospheric CO2 into organic carbon has manifold potential applications for a sustainable biotechnology. To elucidate the properties of cyanobacterial metabolism and growth, computational reconstructions of genome-scale metabolic networks play an increasingly important role. Here, we present an updated reconstruction of the metabolic network of the cyanobacterium Synechocystis sp. PCC 6803 and its quantitative evaluation using flux balance analysis (FBA). To overcome limitations of conventional FBA, and to allow for the integration of experimental analyses, we develop a novel approach to describe light absorption and light utilization within the framework of FBA. Our approach incorporates photoinhibition and a variable quantum yield into the constraint-based description of light-limited phototrophic growth. We show that the resulting model is capable of predicting quantitative properties of cyanobacterial growth, including photosynthetic oxygen evolution and the ATP/NADPH ratio required for growth and cellular maintenance. Our approach retains the computational and conceptual simplicity of FBA and is readily applicable to other phototrophic microorganisms.
Collapse
Affiliation(s)
- Rune Höper
- Institute for Biology, Theoretical Biology (ITB), Humboldt-University of Berlin, Berlin, Germany
| | - Daria Komkova
- Institute for Biology, Theoretical Biology (ITB), Humboldt-University of Berlin, Berlin, Germany
| | - Tomáš Zavřel
- Department of Adaptive Biotechnologies, Global Change Research Institute of the Czech Academy of Sciences, Brno, Czechia
| | - Ralf Steuer
- Institute for Biology, Theoretical Biology (ITB), Humboldt-University of Berlin, Berlin, Germany
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| |
Collapse
|
2
|
Victoria AJ, Astbury MJ, McCormick AJ. Engineering highly productive cyanobacteria towards carbon negative emissions technologies. Curr Opin Biotechnol 2024; 87:103141. [PMID: 38735193 DOI: 10.1016/j.copbio.2024.103141] [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: 02/28/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/14/2024]
Abstract
Cyanobacteria are a diverse and ecologically important group of photosynthetic prokaryotes that contribute significantly to the global carbon cycle through the capture of CO2 as biomass. Cyanobacterial biotechnology could play a key role in a sustainable bioeconomy through negative emissions technologies (NETs), such as carbon sequestration or bioproduction. However, the primary issues of low productivities and high infrastructure costs currently limit the commercialisation of such applications. The isolation of several fast-growing strains and recent advancements in molecular biology tools now offer promising new avenues for improving yields, including metabolic engineering approaches guided by high-throughput screening and metabolic models. Furthermore, emerging research on engineering coculture communities could help to develop more robust culturing systems to support broader NET applications.
Collapse
Affiliation(s)
- Angelo J Victoria
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EH9 3BF UK; Centre for Engineering Biology, School of Biological Sciences, University of Edinburgh, EH9 3BF UK
| | - Michael J Astbury
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EH9 3BF UK; Centre for Engineering Biology, School of Biological Sciences, University of Edinburgh, EH9 3BF UK
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EH9 3BF UK; Centre for Engineering Biology, School of Biological Sciences, University of Edinburgh, EH9 3BF UK.
| |
Collapse
|
3
|
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
|
4
|
Tüllinghoff A, Djaya‐Mbissam H, Toepel J, Bühler B. Light-driven redox biocatalysis on gram-scale in Synechocystis sp. PCC 6803 via an in vivo cascade. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2074-2083. [PMID: 37439151 PMCID: PMC10502755 DOI: 10.1111/pbi.14113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/08/2023] [Accepted: 06/18/2023] [Indexed: 07/14/2023]
Abstract
The photosynthetic light reaction in cyanobacteria constitutes a highly attractive tool for productive biocatalysis, as it can provide redox reactions with high-energy reduction equivalents using sunlight and water as sources of energy and electrons, respectively. Here, we describe the first artificial light-driven redox cascade in Synechocystis sp. PCC 6803 to convert cyclohexanone to the polymer building block 6-hydroxyhexanoic acid (6-HA). Co-expression of a Baeyer-Villiger monooxygenase (BVMO) and a lactonase, both from Acidovorax sp. CHX100, enabled this two-step conversion with an activity of up to 63.1 ± 1.0 U/gCDW without accumulating inhibitory ε-caprolactone. Thereby, one of the key limitations of biocatalytic reactions, that is, reactant inhibition or toxicity, was overcome. In 2 L stirred-tank-photobioreactors, the process could be stabilized for 48 h, forming 23.50 ± 0.84 mm (3.11 ± 0.12 g/L) 6-HA. The high specificity enabling a product yield (YP/S ) of 0.96 ± 0.01 mol/mol and the remarkable biocatalyst-related yield of 3.71 ± 0.21 g6-HA /gCDW illustrate the potential of producing this non-toxic product in a synthetic cascade. The fine-tuning of the energy burden on the catalyst was found to be crucial, which indicates a limitation by the metabolic capacity of the cells possibly being compromised by biocatalysis-related reductant withdrawal. Intriguingly, energy balancing revealed that the biotransformation could tap surplus electrons derived from the photosynthetic light reaction and thereby relieve photosynthetic sink limitation. This study shows the feasibility of light-driven biocatalytic cascade operation in cyanobacteria and highlights respective metabolic limitations and engineering targets to unleash the full potential of photosynthesis.
Collapse
Affiliation(s)
- Adrian Tüllinghoff
- Helmholtz‐Centre for Environmental Research – UFZ, PermoserstrLeipzigGermany
| | | | - Jörg Toepel
- Helmholtz‐Centre for Environmental Research – UFZ, PermoserstrLeipzigGermany
| | - Bruno Bühler
- Helmholtz‐Centre for Environmental Research – UFZ, PermoserstrLeipzigGermany
| |
Collapse
|
5
|
Kugler A, Stensjö K. Optimal energy and redox metabolism in the cyanobacterium Synechocystis sp. PCC 6803. NPJ Syst Biol Appl 2023; 9:47. [PMID: 37739963 PMCID: PMC10516873 DOI: 10.1038/s41540-023-00307-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 09/01/2023] [Indexed: 09/24/2023] Open
Abstract
Understanding energy and redox homeostasis and carbon partitioning is crucial for systems metabolic engineering of cell factories. Carbon metabolism alone cannot achieve maximal accumulation of metabolites in production hosts, since an efficient production of target molecules requires energy and redox balance, in addition to carbon flow. The interplay between cofactor regeneration and heterologous production in photosynthetic microorganisms is not fully explored. To investigate the optimality of energy and redox metabolism, while overproducing alkenes-isobutene, isoprene, ethylene and 1-undecene, in the cyanobacterium Synechocystis sp. PCC 6803, we applied stoichiometric metabolic modelling. Our network-wide analysis indicates that the rate of NAD(P)H regeneration, rather than of ATP, controls ATP/NADPH ratio, and thereby bioproduction. The simulation also implies that energy and redox balance is interconnected with carbon and nitrogen metabolism. Furthermore, we show that an auxiliary pathway, composed of serine, one-carbon and glycine metabolism, supports cellular redox homeostasis and ATP cycling. The study revealed non-intuitive metabolic pathways required to enhance alkene production, which are mainly driven by a few key reactions carrying a high flux. We envision that the presented comparative in-silico metabolic analysis will guide the rational design of Synechocystis as a photobiological production platform of target chemicals.
Collapse
Affiliation(s)
- Amit Kugler
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE-751 20, Uppsala, Sweden
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE-751 20, Uppsala, Sweden.
| |
Collapse
|
6
|
Germann AT, Nakielski A, Dietsch M, Petzel T, Moser D, Triesch S, Westhoff P, Axmann IM. A systematic overexpression approach reveals native targets to increase squalene production in Synechocystis sp. PCC 6803. FRONTIERS IN PLANT SCIENCE 2023; 14:1024981. [PMID: 37324717 PMCID: PMC10266222 DOI: 10.3389/fpls.2023.1024981] [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: 08/22/2022] [Accepted: 04/28/2023] [Indexed: 06/17/2023]
Abstract
Cyanobacteria are a promising platform for the production of the triterpene squalene (C30), a precursor for all plant and animal sterols, and a highly attractive intermediate towards triterpenoids, a large group of secondary plant metabolites. Synechocystis sp. PCC 6803 natively produces squalene from CO2 through the MEP pathway. Based on the predictions of a constraint-based metabolic model, we took a systematic overexpression approach to quantify native Synechocystis gene's impact on squalene production in a squalene-hopene cyclase gene knock-out strain (Δshc). Our in silico analysis revealed an increased flux through the Calvin-Benson-Bassham cycle in the Δshc mutant compared to the wildtype, including the pentose phosphate pathway, as well as lower glycolysis, while the tricarboxylic acid cycle predicted to be downregulated. Further, all enzymes of the MEP pathway and terpenoid synthesis, as well as enzymes from the central carbon metabolism, Gap2, Tpi and PyrK, were predicted to positively contribute to squalene production upon their overexpression. Each identified target gene was integrated into the genome of Synechocystis Δshc under the control of the rhamnose-inducible promoter Prha. Squalene production was increased in an inducer concentration dependent manner through the overexpression of most predicted genes, which are genes of the MEP pathway, ispH, ispE, and idi, leading to the greatest improvements. Moreover, we were able to overexpress the native squalene synthase gene (sqs) in Synechocystis Δshc, which reached the highest production titer of 13.72 mg l-1 reported for squalene in Synechocystis sp. PCC 6803 so far, thereby providing a promising and sustainable platform for triterpene production.
Collapse
Affiliation(s)
- Anna T. Germann
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andreas Nakielski
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Maximilian Dietsch
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tim Petzel
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Daniel Moser
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Sebastian Triesch
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
| | - Philipp Westhoff
- Plant Metabolism and Metabolomics Laboratory, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ilka M. Axmann
- Institute for Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
7
|
Yu J, Zhu H, Wang H, Shutes B, Niu T. Effect of butachlor on Microcystis aeruginosa: Cellular and molecular mechanisms of toxicity. JOURNAL OF HAZARDOUS MATERIALS 2023; 449:131042. [PMID: 36827725 DOI: 10.1016/j.jhazmat.2023.131042] [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: 10/17/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
The rapid development of agriculture increases the release of butachlor into aquatic environments. As a dominant species causing cyanobacterial blooms, Microcystis aeruginosa (M. aeruginosa) can produce microcystin and poses threats to aquatic ecosystems and human health. However, the impact of butachlor on M. aeruginosa remains unclarified. Therefore, the physiochemical responses of M. aeruginosa to butachlor were investigated, and the relevant underlying molecular mechanism was highlighted. There were no significant changes (P > 0.05) in the growth and physiology of M. aeruginosa at the low concentrations of butachlor (0-0.1 mg/L), which evidenced a high level of butachlor tolerance in Microcystis aeruginosa. For the high concentrations of butachlor (4-30 mg/L), the inhibition of photosynthetic activity, disruption of cell ultrastructure, and oxidative stress were dominant toxic effects on M. aeruginosa. Additionally, the impaired cellular integrity and lipid peroxidation may be attributed to the substantial elevations of extracellular microcystin-LR concentration. Downregulation of genes associated with photosynthesis, energy metabolism, and oxidative stress was inferred to be responsible for the growth suppression of M. aeruginosa in 30 mg/L butachlor treatment. The upregulation of gene sets involved in nitrogen metabolism may illustrate the specific effort to sustain the steady concentration of intracellular microcystin-LR. These findings dissect the response mechanism of M. aeruginosa to butachlor toxicity and provide valuable reference for the evaluation of potential risk caused by butachlor in aquatic environments.
Collapse
Affiliation(s)
- Jing Yu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Hui Zhu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Heli Wang
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China
| | - Brian Shutes
- Department of Natural Sciences, Middlesex University, Hendon, London NW4 4BT, UK
| | - Tingting Niu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| |
Collapse
|
8
|
Assessing and reducing phenotypic instability in cyanobacteria. Curr Opin Biotechnol 2023; 80:102899. [PMID: 36724584 DOI: 10.1016/j.copbio.2023.102899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/23/2022] [Accepted: 01/06/2023] [Indexed: 01/31/2023]
Abstract
Cyanobacteria have promising potential as sustainable cell factories. However, one challenge that is still largely unreported in scaling-up cyanobacteria bioproduction is phenotypic instability, where the emergence and selection of nonproducing cells leading to loss in production has longer evolutionary timescales to take place in industrial-scale bioreactors. Quantifying phenotypic instability early on in strain development allows researchers to make informed decisions on whether to proceed with scalable designs, or if present, devise countermeasures to reduce instability. One particularly effective strategy to mitigate instability is the use of genome-scale metabolic models to design growth-coupled production strains. In silico studies have predicted that creating certain cofactor imbalances or removing recycling reactions in cyanobacteria can be exploited to stably produce a wide variety of metabolites.
Collapse
|
9
|
Barone GD, Hubáček M, Malihan-Yap L, Grimm HC, Nikkanen L, Pacheco CC, Tamagnini P, Allahverdiyeva Y, Kourist R. Towards the rate limit of heterologous biotechnological reactions in recombinant cyanobacteria. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:4. [PMID: 36609316 PMCID: PMC9825001 DOI: 10.1186/s13068-022-02237-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/04/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Cyanobacteria have emerged as highly efficient organisms for the production of chemicals and biofuels. Yet, the productivity of the cell has been low for commercial application. Cyanobacterial photobiotransformations utilize photosynthetic electrons to form reducing equivalents, such as NADPH-to-fuel biocatalytic reactions. These photobiotransformations are a measure to which extent photosynthetic electrons can be deviated toward heterologous biotechnological processes, such as the production of biofuels. By expressing oxidoreductases, such as YqjM from Bacillus subtilis in Synechocystis sp. PCC 6803, a high specific activity was obtained in the reduction of maleimides. Here, we investigated the possibility to accelerate the NAD(P)H-consuming redox reactions by addition of carbohydrates as exogenous carbon sources such as D-Glucose under light and darkness. RESULTS A 1.7-fold increase of activity (150 µmol min-1 gDCW-1) was observed upon addition of D-Glucose at an OD750 = 2.5 (DCW = 0.6 g L-1) in the biotransformation of 2-methylmaleimide. The stimulating effect of D-Glucose was also observed at higher cell densities in light and dark conditions as well as in the reduction of other substrates. No increase in both effective photosynthetic yields of Photosystem II and Photosystem I was found upon D-Glucose addition. However, we observed higher NAD(P)H fluorescence when D-Glucose was supplemented, suggesting increased glycolytic activity. Moreover, the system was scaled-up (working volume of 200 mL) in an internally illuminated Bubble Column Reactor exhibiting a 2.4-fold increase of specific activity under light-limited conditions. CONCLUSIONS Results show that under photoautotrophic conditions at a specific activity of 90 µmol min-1 gDCW-1, the ene-reductase YqjM in Synechocystis sp. PCC 6803 is not NAD(P)H saturated, which is an indicator that an increase of the rates of heterologous electron consuming processes for catalysis and biofuel production will require funnelling further reducing power from the photosynthetic chain toward heterologous processes.
Collapse
Affiliation(s)
- Giovanni Davide Barone
- grid.410413.30000 0001 2294 748XBiocatalysis and Protein Engineering, Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria ,grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Michal Hubáček
- grid.1374.10000 0001 2097 1371Laboratory of Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Lenny Malihan-Yap
- grid.410413.30000 0001 2294 748XBiocatalysis and Protein Engineering, Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Hanna C. Grimm
- grid.410413.30000 0001 2294 748XBiocatalysis and Protein Engineering, Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Lauri Nikkanen
- grid.1374.10000 0001 2097 1371Laboratory of Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Catarina C. Pacheco
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Paula Tamagnini
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal ,grid.5808.50000 0001 1503 7226Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Yagut Allahverdiyeva
- grid.1374.10000 0001 2097 1371Laboratory of Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
| | - Robert Kourist
- grid.410413.30000 0001 2294 748XBiocatalysis and Protein Engineering, Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria
| |
Collapse
|
10
|
Systems biology's role in leveraging microalgal biomass potential: Current status and future perspectives. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
11
|
Shlosberg Y, Spungin D, Schuster G, Berman-Frank I, Adir N. Trichodesmium erythraeum produces a higher photocurrent than other cyanobacterial species in bio-photo electrochemical cells. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148910. [PMID: 35944660 DOI: 10.1016/j.bbabio.2022.148910] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
The increase in world energy consumption, and the worries from potential future disasters that may derive from climate change have stimulated the development of renewable energy technologies. One promising method is the utilization of whole photosynthetic cyanobacterial cells to produce photocurrent in a bio-photo electrochemical cell (BPEC). The photocurrent can be derived from either the respiratory or photosynthetic pathways, via the redox couple NADP+/NADPH mediating cyclic electron transport between photosystem I inside the cells, and the anode. In the past, most studies have utilized the fresh-water cyanobacterium Synechocystis sp. PCC 6803 (Syn). Here, we show that the globally important marine cyanobacterium Trichodesmium erythraeum flourishing in the subtropical oceans can provide improved currents as compared to Syn. We applied 2D-fluorescence measurements to detect the secretion of NADPH and show that the resulting photocurrent production is enhanced by increasing the electrolyte salinity, Further enhancement of the photocurrent can be obtained by the addition of electron mediators such as NAD+, NADP+, cytochrome C, vitamin B1, or potassium ferricyanide. Finally, we produce photocurrent from additional cyanobacterial species: Synechocystis sp. PCC6803, Synechococcus elongatus PCC7942, Acaryochloris marina MBIC 11017, and Spirulina, using their cultivation media as electrolytes for the BPEC.
Collapse
Affiliation(s)
- Yaniv Shlosberg
- Grand Technion Energy Program, Technion, Haifa 32000, Israel; Schulich Faculty of Chemistry, Technion, Haifa 320000, Israel
| | - Dina Spungin
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Gadi Schuster
- Grand Technion Energy Program, Technion, Haifa 32000, Israel; Faculty of Biology, Technion, Haifa 32000, Israel
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Noam Adir
- Grand Technion Energy Program, Technion, Haifa 32000, Israel; Schulich Faculty of Chemistry, Technion, Haifa 320000, Israel.
| |
Collapse
|
12
|
Agarwal P, Soni R, Kaur P, Madan A, Mishra R, Pandey J, Singh S, Singh G. Cyanobacteria as a Promising Alternative for Sustainable Environment: Synthesis of Biofuel and Biodegradable Plastics. Front Microbiol 2022; 13:939347. [PMID: 35903468 PMCID: PMC9325326 DOI: 10.3389/fmicb.2022.939347] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
With the aim to alleviate the increasing plastic burden and carbon footprint on Earth, the role of certain microbes that are capable of capturing and sequestering excess carbon dioxide (CO2) generated by various anthropogenic means was studied. Cyanobacteria, which are photosynthetic prokaryotes, are promising alternative for carbon sequestration as well as biofuel and bioplastic production because of their minimal growth requirements, higher efficiency of photosynthesis and growth rates, presence of considerable amounts of lipids in thylakoid membranes, and cosmopolitan nature. These microbes could prove beneficial to future generations in achieving sustainable environmental goals. Their role in the production of polyhydroxyalkanoates (PHAs) as a source of intracellular energy and carbon sink is being utilized for bioplastic production. PHAs have emerged as well-suited alternatives for conventional plastics and are a parallel competitor to petrochemical-based plastics. Although a lot of studies have been conducted where plants and crops are used as sources of energy and bioplastics, cyanobacteria have been reported to have a more efficient photosynthetic process strongly responsible for increased production with limited land input along with an acceptable cost. The biodiesel production from cyanobacteria is an unconventional choice for a sustainable future as it curtails toxic sulfur release and checks the addition of aromatic hydrocarbons having efficient oxygen content, with promising combustion potential, thus making them a better choice. Here, we aim at reporting the application of cyanobacteria for biofuel production and their competent biotechnological potential, along with achievements and constraints in its pathway toward commercial benefits. This review article also highlights the role of various cyanobacterial species that are a source of green and clean energy along with their high potential in the production of biodegradable plastics.
Collapse
|
13
|
Introduction of NADH-dependent nitrate assimilation in Synechococcus sp. PCC 7002 improves photosynthetic production of 2-methyl-1-butanol and isobutanol. Metab Eng 2022; 69:87-97. [PMID: 34774761 PMCID: PMC9026717 DOI: 10.1016/j.ymben.2021.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/09/2021] [Accepted: 11/05/2021] [Indexed: 02/06/2023]
Abstract
Cyanobacteria hold promise for renewable chemical production due to their photosynthetic nature, but engineered strains frequently display poor production characteristics. These difficulties likely arise in part due to the distinctive photoautotrophic metabolism of cyanobacteria. In this work, we apply a genome-scale metabolic model of the cyanobacteria Synechococus sp. PCC 7002 to identify strain designs accounting for this unique metabolism that are predicted to improve the production of various biofuel alcohols (e.g. 2-methyl-1-butanol, isobutanol, and 1-butanol) synthesized via an engineered biosynthesis pathway. Using the model, we identify that the introduction of a large, non-native NADH-demand into PCC 7002's metabolic network is predicted to enhance production of these alcohols by promoting NADH-generating reactions upstream of the production pathways. To test this, we construct strains of PCC 7002 that utilize a heterologous, NADH-dependent nitrite reductase in place of the native, ferredoxin-dependent enzyme to create an NADH-demand in the cells when grown on nitrate-containing media. We find that photosynthetic production of both isobutanol and 2-methyl-1-butanol is significantly improved in the engineered strain background relative to that in a wild-type background. We additionally identify that the use of high-nutrient media leads to a substantial prolongment of the production curve in our alcohol production strains. The metabolic engineering strategy identified and tested in this work presents a novel approach to engineer cyanobacterial production strains that takes advantage of a unique aspect of their metabolism and serves as a basis on which to further develop strains with improved production of these alcohols and related products.
Collapse
|
14
|
Tong T, Chen X, Hu G, Wang XL, Liu GQ, Liu L. Engineering microbial metabolic energy homeostasis for improved bioproduction. Biotechnol Adv 2021; 53:107841. [PMID: 34610353 DOI: 10.1016/j.biotechadv.2021.107841] [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: 06/16/2021] [Revised: 08/25/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
Metabolic energy (ME) homeostasis is essential for the survival and proper functioning of microbial cell factories. However, it is often disrupted during bioproduction because of inefficient ME supply and excessive ME consumption. In this review, we propose strategies, including reinforcement of the capacity of ME-harvesting systems in autotrophic microorganisms; enhancement of the efficiency of ME-supplying pathways in heterotrophic microorganisms; and reduction of unessential ME consumption by microbial cells, to address these issues. This review highlights the potential of biotechnology in the engineering of microbial ME homeostasis and provides guidance for the higher efficient bioproduction of microbial cell factories.
Collapse
Affiliation(s)
- Tian Tong
- Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha 410004, China; International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Xiao-Ling Wang
- Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha 410004, China; International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China
| | - Gao-Qiang Liu
- Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha 410004, China; International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology of Hunan Province, Central South University of Forestry and Technology, Changsha 410004, China.
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
| |
Collapse
|
15
|
Shabestary K, Hernández HP, Miao R, Ljungqvist E, Hallman O, Sporre E, Branco Dos Santos F, Hudson EP. Cycling between growth and production phases increases cyanobacteria bioproduction of lactate. Metab Eng 2021; 68:131-141. [PMID: 34601120 DOI: 10.1016/j.ymben.2021.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/03/2021] [Accepted: 09/25/2021] [Indexed: 01/23/2023]
Abstract
Decoupling growth from product synthesis is a promising strategy to increase carbon partitioning and maximize productivity in cell factories. However, reduction in both substrate uptake rate and metabolic activity in the production phase are an underlying problem for upscaling. Here, we used CRISPR interference to repress growth in lactate-producing Synechocystis sp. PCC 6803. Carbon partitioning to lactate in the production phase exceeded 90%, but CO2 uptake was severely reduced compared to uptake during the growth phase. We characterized strains during the onset of growth arrest using transcriptomics and proteomics. Multiple genes involved in ATP homeostasis were regulated once growth was inhibited, which suggests an alteration of energy charge that may lead to reduced substrate uptake. In order to overcome the reduced metabolic activity and take advantage of increased carbon partitioning, we tested a novel production strategy that involved alternating growth arrest and recovery by periodic addition of an inducer molecule to activate CRISPRi. Using this strategy, we maintained lactate biosynthesis in Synechocystis for 30 days in a constant light turbidostat cultivation. Cumulative lactate titers were also increased by 100% compared to a constant growth-arrest regime, and reached 1 g/L. Further, the cultivation produced lactate for 30 days, compared to 20 days for the non-growth arrest cultivation. Periodic growth arrest could be applicable for other products, and in cyanobacteria, could be linked to internal circadian rhythms that persist in constant light.
Collapse
Affiliation(s)
- Kiyan Shabestary
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Hugo Pineda Hernández
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, the Netherlands
| | - Rui Miao
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Emil Ljungqvist
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Olivia Hallman
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Emil Sporre
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Filipe Branco Dos Santos
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, the Netherlands
| | - Elton P Hudson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
| |
Collapse
|
16
|
Hobisch M, Spasic J, Malihan‐Yap L, Barone GD, Castiglione K, Tamagnini P, Kara S, Kourist R. Internal Illumination to Overcome the Cell Density Limitation in the Scale-up of Whole-Cell Photobiocatalysis. CHEMSUSCHEM 2021; 14:3219-3225. [PMID: 34138524 PMCID: PMC8456840 DOI: 10.1002/cssc.202100832] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/11/2021] [Indexed: 05/28/2023]
Abstract
Cyanobacteria have the capacity to use photosynthesis to fuel their metabolism, which makes them highly promising production systems for the sustainable production of chemicals. Yet, their dependency on visible light limits the cell-density, which is a challenge for the scale-up. Here, it was shown with the example of a light-dependent biotransformation that internal illumination in a bubble column reactor equipped with wireless light emitters (WLEs) could overcome this limitation. Cells of the cyanobacterium Synechocystis sp. PCC 6803 expressing the gene of the ene-reductase YqjM were used for the reduction of 2-methylmaleimide to (R)-2-methylsuccinimide with high optical purity (>99 % ee). Compared to external source of light, illumination by floating wireless light emitters allowed a more than two-fold rate increase. Under optimized conditions, product formation rates up to 3.7 mm h-1 and specific activities of up to 65.5 U gDCW -1 were obtained, allowing the reduction of 40 mm 2-methylmaleimide with 650 mg isolated enantiopure product (73 % yield). The results demonstrate the principle of internal illumination as a means to overcome the intrinsic cell density limitation of cyanobacterial biotransformations, obtaining high reaction rates in a scalable photobioreactor.
Collapse
Affiliation(s)
- Markus Hobisch
- Department of Biological and Chemical EngineeringBiocatalysis and Bioprocessing GroupAarhus UniversityGustav Wieds Vej 108000AarhusDenmark
- Institute of Molecular BiotechnologyGraz University of TechnologyNAWI GrazBioTechMedPetersgasse 148010GrazAustria
| | - Jelena Spasic
- Institute of Molecular BiotechnologyGraz University of TechnologyNAWI GrazBioTechMedPetersgasse 148010GrazAustria
- i3S – Instituto de Investigação e Inovação em Saúde Universidade do Porto & IBMC – Instituto de Biologia Molecular e CelularR. Alfredo Allen 2084200-135PortoPortugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do PortoRua do Campo Alegre, Edifício FC44169-007PortoPortugal
| | - Lenny Malihan‐Yap
- Institute of Molecular BiotechnologyGraz University of TechnologyNAWI GrazBioTechMedPetersgasse 148010GrazAustria
| | - Giovanni Davide Barone
- Institute of Molecular BiotechnologyGraz University of TechnologyNAWI GrazBioTechMedPetersgasse 148010GrazAustria
- i3S – Instituto de Investigação e Inovação em Saúde Universidade do Porto & IBMC – Instituto de Biologia Molecular e CelularR. Alfredo Allen 2084200-135PortoPortugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do PortoRua do Campo Alegre, Edifício FC44169-007PortoPortugal
| | - Kathrin Castiglione
- Institute of Bioprocess EngineeringDepartment of Chemical and BioengineeringFriedrich-Alexander-Universität Erlangen-NürnbergPaul-Gordan-Straße 391052ErlangenGermany
| | - Paula Tamagnini
- i3S – Instituto de Investigação e Inovação em Saúde Universidade do Porto & IBMC – Instituto de Biologia Molecular e CelularR. Alfredo Allen 2084200-135PortoPortugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do PortoRua do Campo Alegre, Edifício FC44169-007PortoPortugal
| | - Selin Kara
- Department of Biological and Chemical EngineeringBiocatalysis and Bioprocessing GroupAarhus UniversityGustav Wieds Vej 108000AarhusDenmark
| | - Robert Kourist
- Institute of Molecular BiotechnologyGraz University of TechnologyNAWI GrazBioTechMedPetersgasse 148010GrazAustria
| |
Collapse
|
17
|
Liu Y, Benitez MG, Chen J, Harrison E, Khusnutdinova AN, Mahadevan R. Opportunities and Challenges for Microbial Synthesis of Fatty Acid-Derived Chemicals (FACs). Front Bioeng Biotechnol 2021; 9:613322. [PMID: 33575251 PMCID: PMC7870715 DOI: 10.3389/fbioe.2021.613322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
Global warming and uneven distribution of fossil fuels worldwide concerns have spurred the development of alternative, renewable, sustainable, and environmentally friendly resources. From an engineering perspective, biosynthesis of fatty acid-derived chemicals (FACs) is an attractive and promising solution to produce chemicals from abundant renewable feedstocks and carbon dioxide in microbial chassis. However, several factors limit the viability of this process. This review first summarizes the types of FACs and their widely applications. Next, we take a deep look into the microbial platform to produce FACs, give an outlook for the platform development. Then we discuss the bottlenecks in metabolic pathways and supply possible solutions correspondingly. Finally, we highlight the most recent advances in the fast-growing model-based strain design for FACs biosynthesis.
Collapse
Affiliation(s)
- Yilan Liu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Mauricio Garcia Benitez
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Jinjin Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Emma Harrison
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Anna N. Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
18
|
Yao L, Shabestary K, Björk SM, Asplund-Samuelsson J, Joensson HN, Jahn M, Hudson EP. Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes. Nat Commun 2020; 11:1666. [PMID: 32245970 PMCID: PMC7125299 DOI: 10.1038/s41467-020-15491-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/13/2020] [Indexed: 11/09/2022] Open
Abstract
Cyanobacteria are model organisms for photosynthesis and are attractive for biotechnology applications. To aid investigation of genotype-phenotype relationships in cyanobacteria, we develop an inducible CRISPRi gene repression library in Synechocystis sp. PCC 6803, where we aim to target all genes for repression. We track the growth of all library members in multiple conditions and estimate gene fitness. The library reveals several clones with increased growth rates, and these have a common upregulation of genes related to cyclic electron flow. We challenge the library with 0.1 M L-lactate and find that repression of peroxiredoxin bcp2 increases growth rate by 49%. Transforming the library into an L-lactate-secreting Synechocystis strain and sorting top lactate producers enriches clones with sgRNAs targeting nutrient assimilation, central carbon metabolism, and cyclic electron flow. In many examples, productivity can be enhanced by repression of essential genes, which are difficult to access by transposon insertion.
Collapse
Affiliation(s)
- Lun Yao
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Kiyan Shabestary
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Sara M Björk
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Johannes Asplund-Samuelsson
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Haakan N Joensson
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Michael Jahn
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Elton P Hudson
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden. .,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
| |
Collapse
|
19
|
Malek Shahkouhi A, Motamedian E. Reconstruction of a regulated two-cell metabolic model to study biohydrogen production in a diazotrophic cyanobacterium Anabaena variabilis ATCC 29413. PLoS One 2020; 15:e0227977. [PMID: 31978122 PMCID: PMC6980584 DOI: 10.1371/journal.pone.0227977] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/03/2020] [Indexed: 12/21/2022] Open
Abstract
Anabaena variabilis is a diazotrophic filamentous cyanobacterium that differentiates to heterocysts and produces hydrogen as a byproduct. Study on metabolic interactions of the two differentiated cells provides a better understanding of its metabolism especially for improving hydrogen production. To this end, a genome-scale metabolic model for Anabaena variabilis ATCC 29413, iAM957, was reconstructed and evaluated in this research. Then, the model and transcriptomic data of the vegetative and heterocyst cells were applied to construct a regulated two-cell metabolic model. The regulated model improved prediction for biomass in high radiation levels. The regulated model predicts that heterocysts provide an oxygen-free environment and then, this model was used to find strategies for improving hydrogen production in heterocysts. The predictions indicate that the removal of uptake hydrogenase improves hydrogen production which is consistent with previous empirical research. Furthermore, the regulated model proposed activation of some reactions to provide redox cofactors which are required for improving hydrogen production up to 60% by bidirectional hydrogenase.
Collapse
Affiliation(s)
- Ali Malek Shahkouhi
- Department of Biotechnology, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Motamedian
- Department of Biotechnology, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
20
|
Thiel K, Patrikainen P, Nagy C, Fitzpatrick D, Pope N, Aro EM, Kallio P. Redirecting photosynthetic electron flux in the cyanobacterium Synechocystis sp. PCC 6803 by the deletion of flavodiiron protein Flv3. Microb Cell Fact 2019; 18:189. [PMID: 31690310 PMCID: PMC6833302 DOI: 10.1186/s12934-019-1238-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/23/2019] [Indexed: 01/20/2023] Open
Abstract
Background Oxygen-evolving photoautotrophic organisms, like cyanobacteria, protect their photosynthetic machinery by a number of regulatory mechanisms, including alternative electron transfer pathways. Despite the importance in modulating the electron flux distribution between the photosystems, alternative electron transfer routes may compete with the solar-driven production of CO2-derived target chemicals in biotechnological systems under development. This work focused on engineered cyanobacterial Synechocystis sp. PCC 6803 strains, to explore possibilities to rescue excited electrons that would normally be lost to molecular oxygen by an alternative acceptor flavodiiron protein Flv1/3—an enzyme that is natively associated with transfer of electrons from PSI to O2, as part of an acclimation strategy towards varying environmental conditions. Results The effects of Flv1/3 inactivation by flv3 deletion were studied in respect to three alternative end-products, sucrose, polyhydroxybutyrate and glycogen, while the photosynthetic gas fluxes were monitored by Membrane Inlet Mass Spectrometry (MIMS) to acquire information on cellular carbon uptake, and the production and consumption of O2. The results demonstrated that a significant proportion of the excited electrons derived from photosynthetic water cleavage was lost to molecular oxygen via Flv1/3 in cells grown under high CO2, especially under high light intensities. In flv3 deletion strains these electrons could be re-routed to increase the relative metabolic flux towards the monitored target products, but the carbon distribution and the overall efficiency were determined by the light conditions and the genetic composition of the respective pathways. At the same time, the total photosynthetic capacity of the Δflv3 strains was systematically reduced, and accompanied by upregulation of oxidative glycolytic metabolism in respect to controls with the native Flv1/3 background. Conclusions The observed metabolic changes and respective production profiles were proposedly linked with the lack of Flv1/3-mediated electron transfer, and the associated decrease in the intracellular ATP/NADPH ratio, which is bound to affect the metabolic carbon partitioning in the flv3-deficient cells. While the deletion of flv3 could offer a strategy for enhancing the photosynthetic production of desired chemicals in cyanobacteria under specified conditions, the engineered target pathways have to be carefully selected to align with the intracellular redox balance of the cells.
Collapse
Affiliation(s)
- Kati Thiel
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turun Yliopisto, Finland
| | - Pekka Patrikainen
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turun Yliopisto, Finland
| | - Csaba Nagy
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turun Yliopisto, Finland
| | - Duncan Fitzpatrick
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turun Yliopisto, Finland
| | - Nicolas Pope
- Department of Future Technologies, University of Turku, 20014, Turun Yliopisto, Finland
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turun Yliopisto, Finland
| | - Pauli Kallio
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turun Yliopisto, Finland. .,, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland.
| |
Collapse
|
21
|
Du W, Jongbloets JA, Guillaume M, van de Putte B, Battaglino B, Hellingwerf KJ, Branco dos Santos F. Exploiting Day- and Night-Time Metabolism of Synechocystis sp. PCC 6803 for Fitness-Coupled Fumarate Production around the Clock. ACS Synth Biol 2019; 8:2263-2269. [PMID: 31553573 PMCID: PMC6804261 DOI: 10.1021/acssynbio.9b00289] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Indexed: 01/18/2023]
Abstract
Cyanobacterial cell factories are widely researched for the sustainable production of compounds directly from CO2. Their application, however, has been limited for two reasons. First, traditional approaches have been shown to lead to unstable cell factories that lose their production capability when scaled to industrial levels. Second, the alternative approaches developed so far are mostly limited to growing conditions, which are not always the case in industry, where nongrowth periods tend to occur (e.g., darkness). We tackled both by generalizing the concept of growth-coupled production to fitness coupling. The feasibility of this new approach is demonstrated for the production of fumarate by constructing the first stable dual-strategy cell factory. We exploited circadian metabolism using both systems and synthetic biology tools, resulting in the obligatorily coupling of fumarate to either biomass or energy production. Resorting to laboratory evolution experiments, we show that this engineering approach is more stable than conventional methods.
Collapse
Affiliation(s)
- Wei Du
- Molecular
Microbial Physiology Group, Faculty of Life Sciences, Swammerdam Institute
of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Joeri A. Jongbloets
- Molecular
Microbial Physiology Group, Faculty of Life Sciences, Swammerdam Institute
of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Max Guillaume
- Molecular
Microbial Physiology Group, Faculty of Life Sciences, Swammerdam Institute
of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Bram van de Putte
- Molecular
Microbial Physiology Group, Faculty of Life Sciences, Swammerdam Institute
of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Beatrice Battaglino
- Applied
Science and Technology Department, Politecnico
di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Centre
for Sustainable Future Technologies, Istituto
Italiano di Tecnologia, Environment Park, Via Livorno 60, 10144 Torino, Italy
| | - Klaas J. Hellingwerf
- Molecular
Microbial Physiology Group, Faculty of Life Sciences, Swammerdam Institute
of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Filipe Branco dos Santos
- Molecular
Microbial Physiology Group, Faculty of Life Sciences, Swammerdam Institute
of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| |
Collapse
|
22
|
Alter TB, Ebert BE. Determination of growth-coupling strategies and their underlying principles. BMC Bioinformatics 2019; 20:447. [PMID: 31462231 PMCID: PMC6714386 DOI: 10.1186/s12859-019-2946-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 06/12/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Metabolic coupling of product synthesis and microbial growth is a prominent approach for maximizing production performance. Growth-coupling (GC) also helps stabilizing target production and allows the selection of superior production strains by adaptive laboratory evolution. To support the implementation of growth-coupling strain designs, we seek to identify biologically relevant, metabolic principles that enforce strong growth-coupling on the basis of reaction knockouts. RESULTS We adapted an established bilevel programming framework to maximize the minimally guaranteed production rate at a fixed, medium growth rate. Using this revised formulation, we identified various GC intervention strategies for metabolites of the central carbon metabolism, which were examined for GC generating principles under diverse conditions. Curtailing the metabolism to render product formation an essential carbon drain was identified as one major strategy generating strong coupling of metabolic activity and target synthesis. Impeding the balancing of cofactors and protons in the absence of target production was the underlying principle of all other strategies and further increased the GC strength of the aforementioned strategies. CONCLUSION Maximizing the minimally guaranteed production rate at a medium growth rate is an attractive principle for the identification of strain designs that couple growth to target metabolite production. Moreover, it allows for controlling the inevitable compromise between growth coupling strength and the retaining of microbial viability. With regard to the corresponding metabolic principles, generating a dependency between the supply of global metabolic cofactors and product synthesis appears to be advantageous in enforcing strong GC for any metabolite. Deriving such strategies manually, is a hard task, due to which we suggest incorporating computational metabolic network analyses in metabolic engineering projects seeking to determine GC strain designs.
Collapse
Affiliation(s)
- Tobias B Alter
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
| | - Birgitta E Ebert
- Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany. .,Present Address: Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.
| |
Collapse
|
23
|
iMet: A graphical user interface software tool to merge metabolic networks. Heliyon 2019; 5:e01766. [PMID: 31286073 PMCID: PMC6587100 DOI: 10.1016/j.heliyon.2019.e01766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 04/10/2019] [Accepted: 05/15/2019] [Indexed: 11/23/2022] Open
Abstract
Nowadays, studying microorganisms has become faster and deeper than the last decades, thanks to the modeling of genome-scale metabolic networks. Completed genome sequencing projects of microorganisms and annotating these sequences have provided a worthwhile platform for reconstructing and modeling genome-scale metabolic networks. The genome-scale metabolic network reconstruction is a laborious and time-consuming task which needs an extensive study and search in different types of databases. Furthermore, it also requires an iterative process of creating and curating the obtained network, particularly with experimental methods. Hence, different types of reconstructions and models of a targeted microorganism can be found with different qualities, as the goal and need of researchers differ. Due to these circumstances, scientists have to continue with only one of the reconstructed metabolic networks of each microorganism and ignore the rest in their in silico works. It is clear that having a tool which merges different metabolic networks of a single organism can be a useful and effective way to study them with minimal cost and time. To meet this need, we have developed iMet, the standalone graphical user interface (GUI) software tool to merge multiple reconstructed metabolic networks of microorganisms. As a case study, we merged three reconstructed metabolic networks of a cyanobacterium using iMet, and then all of them (including the new merged one) became modeled. The results of our evaluations including Flux Balance Analysis (FBA), revealed enhancing metabolic network coverage as well as increasing yield of desired products in the new obtained model.
Collapse
|
24
|
Vieira V, Maia P, Rocha M, Rocha I. Comparison of pathway analysis and constraint-based methods for cell factory design. BMC Bioinformatics 2019; 20:350. [PMID: 31221092 PMCID: PMC6585037 DOI: 10.1186/s12859-019-2934-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Computational strain optimisation methods (CSOMs) have been successfully used to exploit genome-scale metabolic models, yielding strategies useful for allowing compound overproduction in metabolic cell factories. Minimal cut sets are particularly interesting since their definition allows searching for intervention strategies that impose strong growth-coupling phenotypes, and are not subject to optimality bias when compared with simulation-based CSOMs. However, since both types of methods have different underlying principles, they also imply different ways to formulate metabolic engineering problems, posing an obstacle when comparing their outputs. RESULTS In this work, we perform an in-depth analysis of potential strategies that can be obtained with both methods, providing a critical comparison of performance, robustness, predicted phenotypes as well as strategy structure and size. To this end, we devised a pipeline including enumeration of strategies from evolutionary algorithms (EA) and minimal cut sets (MCS), filtering and flux analysis of predicted mutants to optimize the production of succinic acid in Saccharomyces cerevisiae. We additionally attempt to generalize problem formulations for MCS enumeration within the context of growth-coupled product synthesis. Strategies from evolutionary algorithms show the best compromise between acceptable growth rates and compound overproduction. However, constrained MCSs lead to a larger variety of phenotypes with several degrees of growth-coupling with production flux. The latter have proven useful in revealing the importance, in silico, of the gamma-aminobutyric acid shunt and manipulation of cofactor pools in growth-coupled designs for succinate production, mechanisms which have also been touted as potentially useful for metabolic engineering. CONCLUSIONS The two main groups of CSOMs are valuable for finding growth-coupled mutants. Despite the limitations in maximum growth rates and large strategy sizes, MCSs help uncover novel mechanisms for compound overproduction and thus, analyzing outputs from both methods provides a richer overview on strategies that can be potentially carried over in vivo.
Collapse
Affiliation(s)
- Vítor Vieira
- Centro de Engenharia Biológica, Universidade do Minho, Braga, Portugal
| | | | - Miguel Rocha
- Centro de Engenharia Biológica, Universidade do Minho, Braga, Portugal
| | - Isabel Rocha
- Centro de Engenharia Biológica, Universidade do Minho, Braga, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| |
Collapse
|
25
|
Farrokh P, Sheikhpour M, Kasaeian A, Asadi H, Bavandi R. Cyanobacteria as an eco-friendly resource for biofuel production: A critical review. Biotechnol Prog 2019; 35:e2835. [PMID: 31063628 DOI: 10.1002/btpr.2835] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/07/2019] [Accepted: 04/24/2019] [Indexed: 12/26/2022]
Abstract
Cyanobacteria are photosynthetic microorganisms which can be found in various environmental habitats. These photosynthetic bacteria are considered as promising feedstock for the production of the third- and the fourth-generation biofuels. The main subject of this review is highlighting the significant aspects of the biofuel production from cyanobacteria. The most recent investigations about the extraction or separation of the bio-oil from cyanobacteria are also adduced in the present review. Moreover, the genetic engineering of cyanobacteria for improving biofuel production and the impact of bioinformatics studies on the designing better-engineered strains are mentioned. The large-scale biofuel production is challenging, so the economic considerations to provide inexpensive biofuels are also cited. It seems that the future of biofuels is strongly dependent to the following items; understanding the metabolic pathways of the cyanobacterial species, progression in the construction of the engineered cyanobacteria, and inexpensive large-scale cultivation of them.
Collapse
Affiliation(s)
- Parisa Farrokh
- Department of cell and molecular biology, School of Biology, Damghan University, Damghan, Iran.,Institute of Biological Sciences, Damghan University, Damghan, Iran
| | - Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Alibakhsh Kasaeian
- Faculty of New Science and Technologies, University of Tehran, Tehran, Iran
| | - Hassan Asadi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Roya Bavandi
- Branch-Marine Science and Technology Faculty, Islamic Azad University North Tehran, Tehran, Iran
| |
Collapse
|
26
|
Lasry Testa R, Delpino C, Estrada V, Diaz SM. In silico strategies to couple production of bioethanol with growth in cyanobacteria. Biotechnol Bioeng 2019; 116:2061-2073. [DOI: 10.1002/bit.26998] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 04/11/2019] [Accepted: 04/25/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Romina Lasry Testa
- Planta Piloto de Ingeniería Química (PLAPIQUI)Universidad Nacional del Sur (UNS)‐CONICETBahía Blanca Argentina
| | - Claudio Delpino
- Planta Piloto de Ingeniería Química (PLAPIQUI)Universidad Nacional del Sur (UNS)‐CONICETBahía Blanca Argentina
| | - Vanina Estrada
- Planta Piloto de Ingeniería Química (PLAPIQUI)Universidad Nacional del Sur (UNS)‐CONICETBahía Blanca Argentina
| | - Soledad M. Diaz
- Planta Piloto de Ingeniería Química (PLAPIQUI)Universidad Nacional del Sur (UNS)‐CONICETBahía Blanca Argentina
| |
Collapse
|
27
|
Pérez AA, Chen Q, Hernández HP, Branco dos Santos F, Hellingwerf KJ. On the use of oxygenic photosynthesis for the sustainable production of commodity chemicals. PHYSIOLOGIA PLANTARUM 2019; 166:413-427. [PMID: 30829400 PMCID: PMC6850307 DOI: 10.1111/ppl.12946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 05/13/2023]
Abstract
A sustainable society will have to largely refrain from the use of fossil carbon deposits. In such a regime, renewable electricity can be harvested as a primary source of energy. However, as for the synthesis of carbon-based materials from bulk chemicals, an alternative is required. A sustainable approach towards this is the synthesis of commodity chemicals from CO2 , water and sunlight. Multiple paths to achieve this have been designed and tested in the domains of chemistry and biology. In the latter, the use of both chemotrophic and phototrophic organisms has been advocated. 'Direct conversion' of CO2 and H2 O, catalyzed by an oxyphototroph, has excellent prospects to become the most economically competitive of these transformations, because of the relative ease of scale-up of this process. Significantly, for a wide range of energy and commodity products, a proof of principle via engineering of the corresponding production organism has been provided. In the optimization of a cyanobacterial production organism, a wide range of aspects has to be addressed. Of these, here we will put our focus on: (1) optimizing the (carbon) flux to the desired product; (2) increasing the genetic stability of the producing organism and (3) maximizing its energy conversion efficiency. Significant advances have been made on all these three aspects during the past 2 years and these will be discussed: (1) increasing the carbon partitioning to >50%; (2) aligning product formation with the growth of the cells and (3) expanding the photosynthetically active radiation region for oxygenic photosynthesis.
Collapse
Affiliation(s)
- Adam A. Pérez
- Molecular Microbial Physiology GroupSwammerdam Institute for Life Sciences, University of Amsterdam1098 XH AmsterdamThe Netherlands
- Photanol BVMatrix VAmsterdam, 1098 XHThe Netherlands
| | - Que Chen
- Molecular Microbial Physiology GroupSwammerdam Institute for Life Sciences, University of Amsterdam1098 XH AmsterdamThe Netherlands
| | - Hugo Pineda Hernández
- Molecular Microbial Physiology GroupSwammerdam Institute for Life Sciences, University of Amsterdam1098 XH AmsterdamThe Netherlands
| | - Filipe Branco dos Santos
- Molecular Microbial Physiology GroupSwammerdam Institute for Life Sciences, University of Amsterdam1098 XH AmsterdamThe Netherlands
| | - Klaas J. Hellingwerf
- Molecular Microbial Physiology GroupSwammerdam Institute for Life Sciences, University of Amsterdam1098 XH AmsterdamThe Netherlands
- Photanol BVMatrix VAmsterdam, 1098 XHThe Netherlands
| |
Collapse
|
28
|
Garlapati D, Chandrasekaran M, Devanesan A, Mathimani T, Pugazhendhi A. Role of cyanobacteria in agricultural and industrial sectors: an outlook on economically important byproducts. Appl Microbiol Biotechnol 2019; 103:4709-4721. [PMID: 31030286 DOI: 10.1007/s00253-019-09811-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/29/2019] [Accepted: 03/31/2019] [Indexed: 01/22/2023]
Abstract
Cyanobacteria are potential organisms, which are used as food, feed and fuel. The unique characters of cyanobacteria include short generation times, their ubiquitous presence and efficient nitrogen fixing potential. Cyanobacteria are unique organisms performing photosynthesis, bioremediation of wastewater, high biomass and biofuel productions etc. They are also used in the treatment of industrial and domestic wastewaters for the utilization or removal of ammonia, phosphates and other heavy metals (Cr, Pb, Co, Cu, Zn). Biomasses of cyanobacteria are used as biofertilizers for the improvement of nutrient or mineral status and water-holding capacity of the soil. The secondary metabolites of cyanobacteria are used in pharmaceuticals, nutraceutical and chemical industries. In the industrial sector, value-added products from cyanobacteria such as pigments, enzymes and exopolysaccharides are being produced in large scales for biomedical and health applications. Age-old applications of cyanobacteria in agroecosystems as biofertilizers (Anabaena sp; Nostoc sp.) and in industrial sectors as food products (Spirulina) have motivated the researchers to come up with much more specific applications of cyanobacteria both in agricultural and in industrial sectors. Therefore, considering the effectiveness and efficiency of cyanobacteria, the present review has enlisted the standout qualities of cyanobacteria and their potential applications in agricultural and industrial sectors for the benefit of human beings and environment.
Collapse
Affiliation(s)
- Deviram Garlapati
- National Centre for Coastal Research (NCCR), Ministry of Earth Sciences (MoES), Chennai, Tamil Nadu, 600 100, India
| | - Muthukumar Chandrasekaran
- National Centre for Coastal Research (NCCR), Ministry of Earth Sciences (MoES), Chennai, Tamil Nadu, 600 100, India
| | - ArulAnanth Devanesan
- Department of Food Quality and Safety, Gilat Research Center, Agricultural Research Organization, 85280, Negev, MP, Israel
| | - Thangavel Mathimani
- Department of Energy and Environment, National Institute of Technology, Tiruchirappalli, Tamil Nadu, 620015, India
| | - Arivalagan Pugazhendhi
- Innovative Green Product Synthesis and Renewable Environment Development Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
| |
Collapse
|
29
|
Selão TT, Jebarani J, Ismail NA, Norling B, Nixon PJ. Enhanced Production of D-Lactate in Cyanobacteria by Re-Routing Photosynthetic Cyclic and Pseudo-Cyclic Electron Flow. FRONTIERS IN PLANT SCIENCE 2019; 10:1700. [PMID: 32117327 PMCID: PMC7025493 DOI: 10.3389/fpls.2019.01700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/03/2019] [Indexed: 05/22/2023]
Abstract
Cyanobacteria are promising chassis strains for the photosynthetic production of platform and specialty chemicals from carbon dioxide. Their efficient light harvesting and metabolic flexibility abilities have allowed a wide range of biomolecules, such as the bioplastic polylactate precursor D-lactate, to be produced, though usually at relatively low yields. In order to increase photosynthetic electron flow towards the production of D-lactate, we have generated several strains of the marine cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) with deletions in genes involved in cyclic or pseudo-cyclic electron flow around photosystem I. Using a variant of the Chlamydomonas reinhardtii D-lactate dehydrogenase (LDHSRT, engineered to efficiently utilize NADPH in vivo), we have shown that deletion of either of the two flavodiiron flv homologs (involved in pseudo-cyclic electron transport) or the Syn7002 pgr5 homolog (proposed to be a vital part of the cyclic electron transport pathway) is able to increase D-lactate production in Syn7002 strains expressing LDHSRT and the Escherichia coli LldP (lactate permease), especially at low temperature (25°C) and 0.04% (v/v) CO2, though at elevated temperatures (38°C) and/or high (1%) CO2 concentrations, the effect was less obvious. The Δpgr5 background seemed to be particularly beneficial at 25°C and 0.04% (v/v) CO2, with a nearly 7-fold increase in D-lactate accumulation in comparison to the wild-type background (≈1000 vs ≈150 mg/L) and decreased side effects in comparison to the flv deletion strains. Overall, our results show that manipulation of photosynthetic electron flow is a viable strategy to increase production of platform chemicals in cyanobacteria under ambient conditions.
Collapse
Affiliation(s)
- Tiago Toscano Selão
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jasmin Jebarani
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nurul Aina Ismail
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Birgitta Norling
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Peter Julian Nixon
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Life Sciences, Imperial College London, London, United Kingdom
- *Correspondence: Peter Julian Nixon,
| |
Collapse
|
30
|
Shabestary K, Anfelt J, Ljungqvist E, Jahn M, Yao L, Hudson EP. Targeted Repression of Essential Genes To Arrest Growth and Increase Carbon Partitioning and Biofuel Titers in Cyanobacteria. ACS Synth Biol 2018; 7:1669-1675. [PMID: 29874914 DOI: 10.1021/acssynbio.8b00056] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Photoautotrophic production of fuels and chemicals by cyanobacteria typically gives lower volumetric productivities and titers than heterotrophic production. Cyanobacteria cultures become light limited above an optimal cell density, so that this substrate is not supplied to all cells sufficiently. Here, we investigate genetic strategies for a two-phase cultivation, where biofuel-producing Synechocystis cultures are limited to an optimal cell density through inducible CRISPR interference (CRISPRi) repression of cell growth. Fixed CO2 is diverted to ethanol or n-butanol. Among the most successful strategies was partial repression of citrate synthase gltA. Strong repression (>90%) of gltA at low culture densities increased carbon partitioning to n-butanol 5-fold relative to a nonrepression strain, but sacrificed volumetric productivity due to severe growth restriction. CO2 fixation continued for at least 3 days after growth was arrested. By targeting sgRNAs to different regions of the gltA gene, we could modulate GltA expression and carbon partitioning between growth and product to increase both specific and volumetric productivity. These growth arrest strategies can be useful for improving performance of other photoautotrophic processes.
Collapse
Affiliation(s)
- Kiyan Shabestary
- KTH—Royal Institute of Technology. School of Engineering Sciences in Chemistry, Biotechnology, and Health, Science for Life Laboratory, Stockholm, SE-171 21 Sweden
| | - Josefine Anfelt
- KTH—Royal Institute of Technology. School of Engineering Sciences in Chemistry, Biotechnology, and Health, Science for Life Laboratory, Stockholm, SE-171 21 Sweden
| | - Emil Ljungqvist
- KTH—Royal Institute of Technology. School of Engineering Sciences in Chemistry, Biotechnology, and Health, Science for Life Laboratory, Stockholm, SE-171 21 Sweden
| | - Michael Jahn
- KTH—Royal Institute of Technology. School of Engineering Sciences in Chemistry, Biotechnology, and Health, Science for Life Laboratory, Stockholm, SE-171 21 Sweden
| | - Lun Yao
- KTH—Royal Institute of Technology. School of Engineering Sciences in Chemistry, Biotechnology, and Health, Science for Life Laboratory, Stockholm, SE-171 21 Sweden
| | - Elton P. Hudson
- KTH—Royal Institute of Technology. School of Engineering Sciences in Chemistry, Biotechnology, and Health, Science for Life Laboratory, Stockholm, SE-171 21 Sweden
| |
Collapse
|
31
|
Du W, Jongbloets JA, van Boxtel C, Pineda Hernández H, Lips D, Oliver BG, Hellingwerf KJ, Branco dos Santos F. Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and photoautotrophic growth. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:38. [PMID: 29456625 PMCID: PMC5809919 DOI: 10.1186/s13068-018-1037-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/31/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microbial bioengineering has the potential to become a key contributor to the future development of human society by providing sustainable, novel, and cost-effective production pipelines. However, the sustained productivity of genetically engineered strains is often a challenge, as spontaneous non-producing mutants tend to grow faster and take over the population. Novel strategies to prevent this issue of strain instability are urgently needed. RESULTS In this study, we propose a novel strategy applicable to all microbial production systems for which a genome-scale metabolic model is available that aligns the production of native metabolites to the formation of biomass. Based on well-established constraint-based analysis techniques such as OptKnock and FVA, we developed an in silico pipeline-FRUITS-that specifically 'Finds Reactions Usable in Tapping Side-products'. It analyses a metabolic network to identify compounds produced in anabolism that are suitable to be coupled to growth by deletion of their re-utilization pathway(s), and computes their respective biomass and product formation rates. When applied to Synechocystis sp. PCC6803, a model cyanobacterium explored for sustainable bioproduction, a total of nine target metabolites were identified. We tested our approach for one of these compounds, acetate, which is used in a wide range of industrial applications. The model-guided engineered strain shows an obligatory coupling between acetate production and photoautotrophic growth as predicted. Furthermore, the stability of acetate productivity in this strain was confirmed by performing prolonged turbidostat cultivations. CONCLUSIONS This work demonstrates a novel approach to stabilize the production of target compounds in cyanobacteria that culminated in the first report of a photoautotrophic growth-coupled cell factory. The method developed is generic and can easily be extended to any other modeled microbial production system.
Collapse
Affiliation(s)
- Wei Du
- Molecular Microbial Physiology Group, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Joeri A. Jongbloets
- Molecular Microbial Physiology Group, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Coco van Boxtel
- Systems Bioinformatics/Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)/Netherlands Institute for Systems Biology, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Hugo Pineda Hernández
- Molecular Microbial Physiology Group, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - David Lips
- Molecular Microbial Physiology Group, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Brett G. Oliver
- Systems Bioinformatics/Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)/Netherlands Institute for Systems Biology, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Modelling of Biological Process, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Klaas J. Hellingwerf
- Molecular Microbial Physiology Group, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Filipe Branco dos Santos
- Molecular Microbial Physiology Group, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| |
Collapse
|
32
|
Zhou J, Meng H, Zhang W, Li Y. Production of Industrial Chemicals from CO 2 by Engineering Cyanobacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:97-116. [PMID: 30091093 DOI: 10.1007/978-981-13-0854-3_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
As photosynthetic prokaryotes, cyanobacteria can directly convert CO2 to organic compounds and grow rapidly using sunlight as the sole source of energy. The direct biosynthesis of chemicals from CO2 and sunlight in cyanobacteria is therefore theoretically more attractive than using glucose as carbon source in heterotrophic bacteria. To date, more than 20 different target chemicals have been synthesized from CO2 in cyanobacteria. However, the yield and productivity of the constructed strains is about 100-fold lower than what can be obtained using heterotrophic bacteria, and only a few products reached the gram level. The main bottleneck in optimizing cyanobacterial cell factories is the relative complexity of the metabolism of photoautotrophic bacteria. In heterotrophic bacteria, energy metabolism is integrated with the carbon metabolism, so that glucose can provide both energy and carbon for the synthesis of target chemicals. By contrast, the energy and carbon metabolism of cyanobacteria are separated. First, solar energy is converted into chemical energy and reducing power via the light reactions of photosynthesis. Subsequently, CO2 is reduced to organic compounds using this chemical energy and reducing power. Finally, the reduced CO2 provides the carbon source and chemical energy for the synthesis of target chemicals and cell growth. Consequently, the unique nature of the cyanobacterial energy and carbon metabolism determines the specific metabolic engineering strategies required for these organisms. In this chapter, we will describe the specific characteristics of cyanobacteria regarding their metabolism of carbon and energy, summarize and analyze the specific strategies for the production of chemicals in cyanobacteria, and propose metabolic engineering strategies which may be most suitable for cyanobacteria.
Collapse
Affiliation(s)
- Jie Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hengkai Meng
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wei Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, 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, China.
| |
Collapse
|
33
|
6S RNA plays a role in recovery from nitrogen depletion in Synechocystis sp. PCC 6803. BMC Microbiol 2017; 17:229. [PMID: 29216826 PMCID: PMC5721685 DOI: 10.1186/s12866-017-1137-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/27/2017] [Indexed: 12/30/2022] Open
Abstract
Background The 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. While its role is well-characterized in some heterotrophic bacteria, we subjected a cyanobacterial homolog to functional analysis, thereby extending the scope of 6S RNA action to the special challenges of photoautotrophic lifestyles. Results Physiological characterization of a 6S RNA deletion strain (ΔssaA) demonstrates a delay in the recovery from nitrogen starvation. Significantly decelerated phycobilisome reassembly and glycogen degradation are accompanied with reduced photosynthetic activity compared to the wild type. Transcriptome profiling further revealed that predominantly genes encoding photosystem components, ATP synthase, phycobilisomes and ribosomal proteins were negatively affected in ΔssaA. In vivo pull-down studies of the RNA polymerase complex indicated that the presence of 6S RNA promotes the recruitment of the cyanobacterial housekeeping σ factor SigA, concurrently supporting dissociation of group 2 σ factors during recovery from nitrogen starvation. Conclusions The combination of genetic, physiological and biochemical studies reveals the homologue of 6S RNA as an integral part of the cellular response of Synechocystis sp. PCC 6803 to changing nitrogen availability. According to these results, 6S RNA supports a rapid acclimation to changing nitrogen supply by accelerating the switch from group 2 σ factors SigB, SigC and SigE to SigA-dependent transcription. We therefore introduce the cyanobacterial 6S RNA as a novel candidate regulator of RNA polymerase sigma factor recruitment in Synechocystis sp. PCC 6803. Further studies on mechanistic features of the postulated interaction should shed additional light on the complexity of transcriptional regulation in cyanobacteria. Electronic supplementary material The online version of this article (10.1186/s12866-017-1137-9) contains supplementary material, which is available to authorized users.
Collapse
|
34
|
Mellor SB, Vavitsas K, Nielsen AZ, Jensen PE. Photosynthetic fuel for heterologous enzymes: the role of electron carrier proteins. PHOTOSYNTHESIS RESEARCH 2017; 134:329-342. [PMID: 28285375 DOI: 10.1007/s11120-017-0364-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/27/2017] [Indexed: 05/21/2023]
Abstract
Plants, cyanobacteria, and algae generate a surplus of redox power through photosynthesis, which makes them attractive for biotechnological exploitations. While central metabolism consumes most of the energy, pathways introduced through metabolic engineering can also tap into this source of reducing power. Recent work on the metabolic engineering of photosynthetic organisms has shown that the electron carriers such as ferredoxin and flavodoxin can be used to couple heterologous enzymes to photosynthetic reducing power. Because these proteins have a plethora of interaction partners and rely on electrostatically steered complex formation, they form productive electron transfer complexes with non-native enzymes. A handful of examples demonstrate channeling of photosynthetic electrons to drive the activity of heterologous enzymes, and these focus mainly on hydrogenases and cytochrome P450s. However, competition from native pathways and inefficient electron transfer rates present major obstacles, which limit the productivity of heterologous reactions coupled to photosynthesis. We discuss specific approaches to address these bottlenecks and ensure high productivity of such enzymes in a photosynthetic context.
Collapse
Affiliation(s)
- Silas Busck Mellor
- Copenhagen Plant Science Center, Center for Synthetic Biology 'bioSYNergy', Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Konstantinos Vavitsas
- Copenhagen Plant Science Center, Center for Synthetic Biology 'bioSYNergy', Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Agnieszka Zygadlo Nielsen
- Copenhagen Plant Science Center, Center for Synthetic Biology 'bioSYNergy', Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Poul Erik Jensen
- Copenhagen Plant Science Center, Center for Synthetic Biology 'bioSYNergy', Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
| |
Collapse
|
35
|
Use of CellNetAnalyzer in biotechnology and metabolic engineering. J Biotechnol 2017; 261:221-228. [DOI: 10.1016/j.jbiotec.2017.05.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 01/28/2023]
|
36
|
Hagemann M, Hess WR. Systems and synthetic biology for the biotechnological application of cyanobacteria. Curr Opin Biotechnol 2017; 49:94-99. [PMID: 28843192 DOI: 10.1016/j.copbio.2017.07.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis. Their evolutionary relation to plastids in eukaryotic phototrophs and their increasing utilization as green cell factories initiated the use of systems biology approaches early on. For select model strains, extensive 'omics' data sets have been generated, and genome-wide models have been elucidated. Moreover, the results obtained may be used for the optimization of cyanobacterial metabolism, which can direct the biotechnological production of biofuels or chemical feedstock. Synthetic biology approaches permit the rational construction of novel metabolic pathways that are based on the combination of multiple enzymatic activities of different origins. In addition, the manipulation of whole metabolic networks by CRISPR-based and sRNA-based technologies with multiple parallel targets will further stimulate the use of cyanobacteria for diverse applications in basic research and biotechnology.
Collapse
Affiliation(s)
- Martin Hagemann
- University of Rostock, Institute of Biological Sciences, Plant Physiology, A.-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Schänzlestr. 1, D-79104 Freiburg, Germany
| |
Collapse
|
37
|
Purdy HM, Reed JL. Evaluating the capabilities of microbial chemical production using genome-scale metabolic models. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
38
|
Motwalli O, Essack M, Jankovic BR, Ji B, Liu X, Ansari HR, Hoehndorf R, Gao X, Arold ST, Mineta K, Archer JAC, Gojobori T, Mijakovic I, Bajic VB. In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria. BMC Genomics 2017; 18:33. [PMID: 28056772 PMCID: PMC5217662 DOI: 10.1186/s12864-016-3389-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/07/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Finding a source from which high-energy-density biofuels can be derived at an industrial scale has become an urgent challenge for renewable energy production. Some microorganisms can produce free fatty acids (FFA) as precursors towards such high-energy-density biofuels. In particular, photosynthetic cyanobacteria are capable of directly converting carbon dioxide into FFA. However, current engineered strains need several rounds of engineering to reach the level of production of FFA to be commercially viable; thus new chassis strains that require less engineering are needed. Although more than 120 cyanobacterial genomes are sequenced, the natural potential of these strains for FFA production and excretion has not been systematically estimated. RESULTS Here we present the FFA SC (FFASC), an in silico screening method that evaluates the potential for FFA production and excretion of cyanobacterial strains based on their proteomes. A literature search allowed for the compilation of 64 proteins, most of which influence FFA production and a few of which affect FFA excretion. The proteins are classified into 49 orthologous groups (OGs) that helped create rules used in the scoring/ranking of algorithms developed to estimate the potential for FFA production and excretion of an organism. Among 125 cyanobacterial strains, FFASC identified 20 candidate chassis strains that rank in their FFA producing and excreting potential above the specifically engineered reference strain, Synechococcus sp. PCC 7002. We further show that the top ranked cyanobacterial strains are unicellular and primarily include Prochlorococcus (order Prochlorales) and marine Synechococcus (order Chroococcales) that cluster phylogenetically. Moreover, two principal categories of enzymes were shown to influence FFA production the most: those ensuring precursor availability for the biosynthesis of lipids, and those involved in handling the oxidative stress associated to FFA synthesis. CONCLUSION To our knowledge FFASC is the first in silico method to screen cyanobacteria proteomes for their potential to produce and excrete FFA, as well as the first attempt to parameterize the criteria derived from genetic characteristics that are favorable/non-favorable for this purpose. Thus, FFASC helps focus experimental evaluation only on the most promising cyanobacteria.
Collapse
Affiliation(s)
- Olaa Motwalli
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Magbubah Essack
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Boris R. Jankovic
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Boyang Ji
- Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Xinyao Liu
- SABIC Corporate Research and Development (CRD), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Hifzur Rahman Ansari
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Robert Hoehndorf
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Katsuhiko Mineta
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - John A. C. Archer
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Ivan Mijakovic
- Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Vladimir B. Bajic
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| |
Collapse
|
39
|
Kopka J, Schmidt S, Dethloff F, Pade N, Berendt S, Schottkowski M, Martin N, Dühring U, Kuchmina E, Enke H, Kramer D, Wilde A, Hagemann M, Friedrich A. Systems analysis of ethanol production in the genetically engineered cyanobacterium Synechococcus sp. PCC 7002. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:56. [PMID: 28286551 PMCID: PMC5340023 DOI: 10.1186/s13068-017-0741-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/23/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Future sustainable energy production can be achieved using mass cultures of photoautotrophic microorganisms, which are engineered to synthesize valuable products directly from CO2 and sunlight. As cyanobacteria can be cultivated in large scale on non-arable land, these phototrophic bacteria have become attractive organisms for production of biofuels. Synechococcus sp. PCC 7002, one of the cyanobacterial model organisms, provides many attractive properties for biofuel production such as tolerance of seawater and high light intensities. RESULTS Here, we performed a systems analysis of an engineered ethanol-producing strain of the cyanobacterium Synechococcus sp. PCC 7002, which was grown in artificial seawater medium over 30 days applying a 12:12 h day-night cycle. Biosynthesis of ethanol resulted in a final accumulation of 0.25% (v/v) ethanol, including ethanol lost due to evaporation. The cultivation experiment revealed three production phases. The highest production rate was observed in the initial phase when cells were actively growing. In phase II growth of the producer strain stopped, but ethanol production rate was still high. Phase III was characterized by a decrease of both ethanol production and optical density of the culture. Metabolomics revealed that the carbon drain due to ethanol diffusion from the cell resulted in the expected reduction of pyruvate-based intermediates. Carbon-saving strategies successfully compensated the decrease of central intermediates of carbon metabolism during the first phase of fermentation. However, during long-term ethanol production the producer strain showed clear indications of intracellular carbon limitation. Despite the decreased levels of glycolytic and tricarboxylic acid cycle intermediates, soluble sugars and even glycogen accumulated in the producer strain. The changes in carbon assimilation patterns are partly supported by proteome analysis, which detected decreased levels of many enzymes and also revealed the stress phenotype of ethanol-producing cells. Strategies towards improved ethanol production are discussed. CONCLUSIONS Systems analysis of ethanol production in Synechococcus sp. PCC 7002 revealed initial compensation followed by increasing metabolic limitation due to excessive carbon drain from primary metabolism.
Collapse
Affiliation(s)
- Joachim Kopka
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Stefanie Schmidt
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Frederik Dethloff
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Max-Planck-Institute of Psychiatry, Kraepelinstraße 2-10, 80804 Munich, Germany
| | - Nadin Pade
- Institute of Biological Sciences, Plant Physiology, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Susanne Berendt
- Algenol Biofuels Germany GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | | | - Nico Martin
- Algenol Biofuels Germany GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Ulf Dühring
- Algenol Biofuels Germany GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Ekaterina Kuchmina
- Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Heike Enke
- Algenol Biofuels Germany GmbH, Magnusstraße 11, 12489 Berlin, Germany
- Cyano Biotech GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Dan Kramer
- Algenol Biofuels Germany GmbH, Magnusstraße 11, 12489 Berlin, Germany
- Cyano Biotech GmbH, Magnusstraße 11, 12489 Berlin, Germany
| | - Annegret Wilde
- Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Martin Hagemann
- Institute of Biological Sciences, Plant Physiology, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | | |
Collapse
|
40
|
Shabestary K, Hudson EP. Computational metabolic engineering strategies for growth-coupled biofuel production by Synechocystis. Metab Eng Commun 2016; 3:216-226. [PMID: 29468126 PMCID: PMC5779732 DOI: 10.1016/j.meteno.2016.07.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/31/2016] [Accepted: 07/19/2016] [Indexed: 11/28/2022] Open
Abstract
Chemical and fuel production by photosynthetic cyanobacteria is a promising technology but to date has not reached competitive rates and titers. Genome-scale metabolic modeling can reveal limitations in cyanobacteria metabolism and guide genetic engineering strategies to increase chemical production. Here, we used constraint-based modeling and optimization algorithms on a genome-scale model of Synechocystis PCC6803 to find ways to improve productivity of fermentative, fatty-acid, and terpene-derived fuels. OptGene and MOMA were used to find heuristics for knockout strategies that could increase biofuel productivity. OptKnock was used to find a set of knockouts that led to coupling between biofuel and growth. Our results show that high productivity of fermentation or reversed beta-oxidation derived alcohols such as 1-butanol requires elimination of NADH sinks, while terpenes and fatty-acid based fuels require creating imbalances in intracellular ATP and NADPH production and consumption. The FBA-predicted productivities of these fuels are at least 10-fold higher than those reported so far in the literature. We also discuss the physiological and practical feasibility of implementing these knockouts. This work gives insight into how cyanobacteria could be engineered to reach competitive biofuel productivities.
Collapse
Affiliation(s)
| | - Elton P. Hudson
- School of Biotechnology, KTH - Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| |
Collapse
|
41
|
Enhanced limonene production in cyanobacteria reveals photosynthesis limitations. Proc Natl Acad Sci U S A 2016; 113:14225-14230. [PMID: 27911807 DOI: 10.1073/pnas.1613340113] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Terpenes are the major secondary metabolites produced by plants, and have diverse industrial applications as pharmaceuticals, fragrance, solvents, and biofuels. Cyanobacteria are equipped with efficient carbon fixation mechanism, and are ideal cell factories to produce various fuel and chemical products. Past efforts to produce terpenes in photosynthetic organisms have gained only limited success. Here we engineered the cyanobacterium Synechococcus elongatus PCC 7942 to efficiently produce limonene through modeling guided study. Computational modeling of limonene flux in response to photosynthetic output has revealed the downstream terpene synthase as a key metabolic flux-controlling node in the MEP (2-C-methyl-d-erythritol 4-phosphate) pathway-derived terpene biosynthesis. By enhancing the downstream limonene carbon sink, we achieved over 100-fold increase in limonene productivity, in contrast to the marginal increase achieved through stepwise metabolic engineering. The establishment of a strong limonene flux revealed potential synergy between photosynthate output and terpene biosynthesis, leading to enhanced carbon flux into the MEP pathway. Moreover, we show that enhanced limonene flux would lead to NADPH accumulation, and slow down photosynthesis electron flow. Fine-tuning ATP/NADPH toward terpene biosynthesis could be a key parameter to adapt photosynthesis to support biofuel/bioproduct production in cyanobacteria.
Collapse
|
42
|
Hendry JI, Prasannan CB, Joshi A, Dasgupta S, Wangikar PP. Metabolic model of Synechococcus sp. PCC 7002: Prediction of flux distribution and network modification for enhanced biofuel production. BIORESOURCE TECHNOLOGY 2016; 213:190-197. [PMID: 27036328 DOI: 10.1016/j.biortech.2016.02.128] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 05/18/2023]
Abstract
Flux Balance Analysis was performed with the Genome Scale Metabolic Model of a fast growing cyanobacterium Synechococcus sp. PCC 7002 to gain insights that would help in engineering the organism as a production host. Gene essentiality and synthetic lethality analysis revealed a reduced metabolic robustness under genetic perturbation compared to the heterotrophic bacteria Escherichia coli. Under glycerol heterotrophy the reducing equivalents were generated from tricarboxylic acid cycle rather than the oxidative pentose phosphate pathway. During mixotrophic growth in glycerol the photosynthetic electron transport chain was predominantly used for ATP synthesis with a photosystem I/photosystem II flux ratio higher than that observed under autotrophy. An exhaustive analysis of all possible double reaction knock outs was performed to reroute fixed carbon towards ethanol and butanol production. It was predicted that only ∼10% of fixed carbon could be diverted for ethanol and butanol production.
Collapse
Affiliation(s)
- John I Hendry
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Charulata B Prasannan
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Aditi Joshi
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Santanu Dasgupta
- Reliance Technology Group, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai 400701, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India; DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Mumbai 400076, India; Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India.
| |
Collapse
|
43
|
Zavřel T, Červený J, Knoop H, Steuer R. Optimizing cyanobacterial product synthesis: Meeting the challenges. Bioengineered 2016; 7:490-496. [PMID: 27420605 PMCID: PMC5241762 DOI: 10.1080/21655979.2016.1207017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The synthesis of renewable bioproducts using photosynthetic microorganisms holds great promise. Sustainable industrial applications, however, are still scarce and the true limits of phototrophic production remain unknown. One of the limitations of further progress is our insufficient understanding of the quantitative changes in photoautotrophic metabolism that occur during growth in dynamic environments. We argue that a proper evaluation of the intra- and extracellular factors that limit phototrophic production requires the use of highly-controlled cultivation in photobioreactors, coupled to real-time analysis of production parameters and their evaluation by predictive computational models. In this addendum, we discuss the importance and challenges of systems biology approaches for the optimization of renewable biofuels production. As a case study, we present the utilization of a state-of-the-art experimental setup together with a stoichiometric computational model of cyanobacterial metabolism for quantitative evaluation of ethylene production by a recombinant cyanobacterium Synechocystis sp. PCC 6803.
Collapse
Affiliation(s)
- Tomáš Zavřel
- a Department of Adaptive Biotechnologies , Global Change Research Institute, Academy of Science of the Czech Republic , Drásov , Czech Republic
| | - Jan Červený
- a Department of Adaptive Biotechnologies , Global Change Research Institute, Academy of Science of the Czech Republic , Drásov , Czech Republic
| | - Henning Knoop
- b Institut für Theoretische Biologie, Humboldt-Universität zu Berlin , Berlin , Germany
| | - Ralf Steuer
- b Institut für Theoretische Biologie, Humboldt-Universität zu Berlin , Berlin , Germany
| |
Collapse
|
44
|
Tobalina L, Pey J, Planes FJ. Direct calculation of minimal cut sets involving a specific reaction knock-out. Bioinformatics 2016; 32:2001-7. [PMID: 27153694 DOI: 10.1093/bioinformatics/btw072] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 02/02/2016] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION The concept of Minimal Cut Sets (MCSs) is used in metabolic network modeling to describe minimal groups of reactions or genes whose simultaneous deletion eliminates the capability of the network to perform a specific task. Previous work showed that MCSs where closely related to Elementary Flux Modes (EFMs) in a particular dual problem, opening up the possibility to use the tools developed for computing EFMs to compute MCSs. Until recently, however, there existed no method to compute an EFM with some specific characteristic, meaning that, in the case of MCSs, the only strategy to obtain them was to enumerate them using, for example, the standard K-shortest EFMs algorithm. RESULTS In this work, we adapt the recently developed theory to compute EFMs satisfying several constraints to the calculation of MCSs involving a specific reaction knock-out. Importantly, we emphasize that not all the EFMs in the dual problem correspond to real MCSs, and propose a new formulation capable of correctly identifying the MCS wanted. Furthermore, this formulation brings interesting insights about the relationship between the primal and the dual problem of the MCS computation. AVAILABILITY AND IMPLEMENTATION A Matlab-Cplex implementation of the proposed algorithm is available as a supplementary material CONTACT fplanes@ceit.es SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Luis Tobalina
- CEIT and Tecnun, University of Navarra, San Sebastián 20018, Spain
| | - Jon Pey
- CEIT and Tecnun, University of Navarra, San Sebastián 20018, Spain
| | | |
Collapse
|
45
|
Chen Q, van der Steen JB, Dekker HL, Ganapathy S, de Grip WJ, Hellingwerf KJ. Expression of holo-proteorhodopsin in Synechocystis sp. PCC 6803. Metab Eng 2016; 35:83-94. [PMID: 26869136 DOI: 10.1016/j.ymben.2016.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 01/11/2016] [Accepted: 02/01/2016] [Indexed: 01/15/2023]
Abstract
Retinal-based photosynthesis may contribute to the free energy conversion needed for growth of an organism carrying out oxygenic photosynthesis, like a cyanobacterium. After optimization, this may even enhance the overall efficiency of phototrophic growth of such organisms in sustainability applications. As a first step towards this, we here report on functional expression of the archetype proteorhodopsin in Synechocystis sp. PCC 6803. Upon use of the moderate-strength psbA2 promoter, holo-proteorhodopsin is expressed in this cyanobacterium, at a level of up to 10(5) molecules per cell, presumably in a hexameric quaternary structure, and with approximately equal distribution (on a protein-content basis) over the thylakoid and the cytoplasmic membrane fraction. These results also demonstrate that Synechocystis sp. PCC 6803 has the capacity to synthesize all-trans-retinal. Expressing a substantial amount of a heterologous opsin membrane protein causes a substantial growth retardation Synechocystis, as is clear from a strain expressing PROPS, a non-pumping mutant derivative of proteorhodopsin. Relative to this latter strain, proteorhodopsin expression, however, measurably stimulates its growth.
Collapse
Affiliation(s)
- Que Chen
- Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeroen B van der Steen
- Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Henk L Dekker
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Srividya Ganapathy
- Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Willem J de Grip
- Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
46
|
Zhou J, Zhu T, Cai Z, Li Y. From cyanochemicals to cyanofactories: a review and perspective. Microb Cell Fact 2016; 15:2. [PMID: 26743222 PMCID: PMC4705643 DOI: 10.1186/s12934-015-0405-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/25/2015] [Indexed: 11/18/2022] Open
Abstract
Engineering cyanobacteria for production of chemicals from solar energy, CO2 and water is a potential approach to address global energy and environment issues such as greenhouse effect. To date, more than 20 chemicals have been synthesized by engineered cyanobacteria using CO2 as raw materials, and these studies have been well reviewed. However, unlike heterotrophic microorganisms, the low CO2 fixation rate makes it a long way to go from cyanochemicals to cyanofactories. Here we review recent progresses on improvement of carbon fixation and redistribution of intercellular carbon flux, and discuss the challenges for developing cyanofactories in the future.
Collapse
Affiliation(s)
- Jie Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No 1, West Beichen Road, Chaoyang District, 100101, Beijing, China.
| | - Taicheng Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No 1, West Beichen Road, Chaoyang District, 100101, Beijing, China.
| | - Zhen Cai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No 1, West Beichen Road, Chaoyang District, 100101, Beijing, China.
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, No 1, West Beichen Road, Chaoyang District, 100101, Beijing, China.
| |
Collapse
|
47
|
Klanchui A, Raethong N, Prommeenate P, Vongsangnak W, Meechai A. Cyanobacterial Biofuels: Strategies and Developments on Network and Modeling. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 160:75-102. [PMID: 27783135 DOI: 10.1007/10_2016_42] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cyanobacteria, the phototrophic microorganisms, have attracted much attention recently as a promising source for environmentally sustainable biofuels production. However, barriers for commercial markets of cyanobacteria-based biofuels concern the economic feasibility. Miscellaneous strategies for improving the production performance of cyanobacteria have thus been developed. Among these, the simple ad hoc strategies resulting in failure to optimize fully cell growth coupled with desired product yield are explored. With the advancement of genomics and systems biology, a new paradigm toward systems metabolic engineering has been recognized. In particular, a genome-scale metabolic network reconstruction and modeling is a crucial systems-based tool for whole-cell-wide investigation and prediction. In this review, the cyanobacterial genome-scale metabolic models, which offer a system-level understanding of cyanobacterial metabolism, are described. The main process of metabolic network reconstruction and modeling of cyanobacteria are summarized. Strategies and developments on genome-scale network and modeling through the systems metabolic engineering approach are advanced and employed for efficient cyanobacterial-based biofuels production.
Collapse
Affiliation(s)
- Amornpan Klanchui
- Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Nachon Raethong
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Peerada Prommeenate
- Biochemical Engineering and Pilot Plant Research and Development (BEC) Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.,Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Asawin Meechai
- Department of Chemical Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand.
| |
Collapse
|
48
|
Mohammadi R, Fallah-Mehrabadi J, Bidkhori G, Zahiri J, Javad Niroomand M, Masoudi-Nejad A. A systems biology approach to reconcile metabolic network models with application to Synechocystis sp. PCC 6803 for biofuel production. MOLECULAR BIOSYSTEMS 2016; 12:2552-61. [DOI: 10.1039/c6mb00119j] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Metabolic network models can be optimized for the production of desired materials like biofuels.
Collapse
Affiliation(s)
- Reza Mohammadi
- Laboratory of Systems Biology and Bioinformatics (LBB)
- Institute of Biochemistry and Biophysics
- University of Tehran
- Tehran
- Iran
| | | | | | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL)
- Department of Biophysics
- Faculty of Biological Sciences
- Tarbiat Modares University
- Tehran
| | - Mohammad Javad Niroomand
- Learning Intelligent Systems Lab
- School of Electrical and Computer Engineering
- University of Tehran
- Tehran
- Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB)
- Institute of Biochemistry and Biophysics
- University of Tehran
- Tehran
- Iran
| |
Collapse
|
49
|
Hara KY, Kondo A. ATP regulation in bioproduction. Microb Cell Fact 2015; 14:198. [PMID: 26655598 PMCID: PMC4676173 DOI: 10.1186/s12934-015-0390-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/25/2015] [Indexed: 01/06/2023] Open
Abstract
Adenosine-5'-triphosphate (ATP) is consumed as a biological energy source by many intracellular reactions. Thus, the intracellular ATP supply is required to maintain cellular homeostasis. The dependence on the intracellular ATP supply is a critical factor in bioproduction by cell factories. Recent studies have shown that changing the ATP supply is critical for improving product yields. In this review, we summarize the recent challenges faced by researchers engaged in the development of engineered cell factories, including the maintenance of a large ATP supply and the production of cell factories. The strategies used to enhance ATP supply are categorized as follows: addition of energy substrates, controlling pH, metabolic engineering of ATP-generating or ATP-consuming pathways, and controlling reactions of the respiratory chain. An enhanced ATP supply generated using these strategies improves target production through increases in resource uptake, cell growth, biosynthesis, export of products, and tolerance to toxic compounds.
Collapse
Affiliation(s)
- Kiyotaka Y Hara
- Department of Environmental Sciences, Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan.
| |
Collapse
|
50
|
An algorithm for the reduction of genome-scale metabolic network models to meaningful core models. BMC SYSTEMS BIOLOGY 2015; 9:48. [PMID: 26286864 PMCID: PMC4545695 DOI: 10.1186/s12918-015-0191-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/30/2015] [Indexed: 11/20/2022]
Abstract
Background Constraint-based analysis of genome-scale metabolic models has become a key methodology to gain insights into functions, capabilities, and properties of cellular metabolism. Since their inception, the size and complexity of genome-scale metabolic reconstructions has significantly increased, with a concomitant increase in computational effort required for their analysis. Many stoichiometric methods cannot be applied to large networks comprising several thousand reactions. Furthermore, basic principles of an organism’s metabolism can sometimes be easier studied in smaller models focusing on central metabolism. Therefore, an automated and unbiased reduction procedure delivering meaningful core networks from well-curated genome-scale reconstructions is highly desirable. Results Here we present NetworkReducer, a new algorithm for an automated reduction of metabolic reconstructions to obtain smaller models capturing the central metabolism or other metabolic modules of interest. The algorithm takes as input a network model and a list of protected elements and functions (phenotypes) and applies a pruning step followed by an optional compression step. Network pruning removes elements of the network that are dispensable for the protected functions and delivers a subnetwork of the full system. Loss-free network compression further reduces the network size but not the complexity (dimension) of the solution space. As a proof of concept, we applied NetworkReducer to the iAF1260 genome-scale model of Escherichia coli (2384 reactions, 1669 internal metabolites) to obtain a reduced model that (i) allows the same maximal growth rates under aerobic and anaerobic conditions as in the full model, and (ii) preserves a protected set of reactions representing the central carbon metabolism. The reduced representation comprises 85 metabolites and 105 reactions which we compare to a manually derived E. coli core model. As one particular strength of our approach, NetworkReducer derives a condensed biomass synthesis reaction that is consistent with the full genome-scale model. In a second case study, we reduced a genome-scale model of the cyanobacterium Synechocystis sp. PCC 6803 to obtain a small metabolic module comprising photosynthetic core reactions and the Calvin-Benson cycle allowing synthesis of both biomass and a biofuel (ethanol). Conclusion Although only genome-scale models provide a complete description of an organism’s metabolic capabilities, an unbiased stoichiometric reduction of large-scale metabolic models is highly useful. We are confident that the NetworkReducer algorithm provides a valuable tool for the application of computationally expensive analyses, for educational purposes, as well to identify core models for kinetic modeling and isotopic tracer experiments. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0191-x) contains supplementary material, which is available to authorized users.
Collapse
|