1
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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 PMCID: PMC11326710 DOI: 10.1371/journal.pcbi.1012280] [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: 01/12/2024] [Revised: 08/15/2024] [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.
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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
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2
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Tiwari D, Kumar N, Bongirwar R, Shukla P. Nutraceutical prospects of genetically engineered cyanobacteria- technological updates and significance. World J Microbiol Biotechnol 2024; 40:263. [PMID: 38980547 DOI: 10.1007/s11274-024-04064-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/23/2024] [Indexed: 07/10/2024]
Abstract
Genetically engineered cyanobacterial strains that have improved growth rate, biomass productivity, and metabolite productivity could be a better option for sustainable bio-metabolite production. The global demand for biobased metabolites with nutraceuticals and health benefits has increased due to their safety and plausible therapeutic and nutritional utility. Cyanobacteria are solar-powered green cellular factories that can be genetically tuned to produce metabolites with nutraceutical and pharmaceutical benefits. The present review discusses biotechnological endeavors for producing bioprospective compounds from genetically engineered cyanobacteria and discusses the challenges and troubleshooting faced during metabolite production. This review explores the cyanobacterial versatility, the use of engineered strains, and the techno-economic challenges associated with scaling up metabolite production from cyanobacteria. Challenges to produce cyanobacterial bioactive compounds with remarkable nutraceutical values have been discussed. Additionally, this review also summarises the challenges and future prospects of metabolite production from genetically engineered cyanobacteria as a sustainable approach.
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Affiliation(s)
- Deepali Tiwari
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Niwas Kumar
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Riya Bongirwar
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India.
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3
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Cho BA, Moreno-Cabezuelo JÁ, Mills LA, del Río Chanona EA, Lea-Smith DJ, Zhang D. Integrated experimental and photo-mechanistic modelling of biomass and optical density production of fast versus slow growing model cyanobacteria. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.102997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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4
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Lindberg P, Kenkel A, Bühler K. Introduction to Cyanobacteria. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 183:1-24. [PMID: 37009973 DOI: 10.1007/10_2023_217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Cyanobacteria are highly interesting microbes with the capacity for oxygenic photosynthesis. They fulfill an important purpose in nature but are also potent biocatalysts. This chapter gives a brief overview of this diverse phylum and shortly addresses the functions these organisms have in the natural ecosystems. Further, it introduces the main topics covered in this volume, which is dealing with the development and application of cyanobacteria as solar cell factories for the production of chemicals including potential fuels. We discuss cyanobacteria as industrial workhorses, present established chassis strains, and give an overview of the current target products. Genetic engineering strategies aiming at the photosynthetic efficiency as well as approaches to optimize carbon fluxes are summarized. Finally, main cultivation strategies are sketched.
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Affiliation(s)
- Pia Lindberg
- Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
| | - Amelie Kenkel
- Helmholtzcenter for Environmental Research, Leipzig, Germany
| | - Katja Bühler
- Helmholtzcenter for Environmental Research, Leipzig, Germany.
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5
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A miniaturized bionic ocean-battery mimicking the structure of marine microbial ecosystems. Nat Commun 2022; 13:5608. [PMID: 36153325 PMCID: PMC9509365 DOI: 10.1038/s41467-022-33358-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 09/14/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractMarine microbial ecosystems can be viewed as a huge ocean-battery charged by solar energy. It provides a model for fabricating bio-solar cell, a bioelectrochemical system that converts light into electricity. Here, we fabricate a bio-solar cell consisting of a four-species microbial community by mimicking the ecological structure of marine microbial ecosystems. We demonstrate such ecological structure consisting of primary producer, primary degrader, and ultimate consumers is essential for achieving high power density and stability. Furthermore, the four-species microbial community is assembled into a spatial-temporally compacted cell using conductive hydrogel as a sediment-like anaerobic matrix, forming a miniaturized bionic ocean-battery. This battery directly converts light into electricity with a maximum power of 380 μW and stably operates for over one month. Reproducing the photoelectric conversion function of marine microbial ecosystems in this bionic battery overcomes the sluggish and network-like electron transfer, showing the biotechnological potential of synthetic microbial ecology.
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6
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A Ubiquitously Conserved Cyanobacterial Protein Phosphatase Essential for High Light Tolerance in a Fast-Growing Cyanobacterium. Microbiol Spectr 2022; 10:e0100822. [PMID: 35727069 PMCID: PMC9430166 DOI: 10.1128/spectrum.01008-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synechococcus elongatus UTEX 2973, the fastest-growing cyanobacterial strain known, optimally grows under extreme high light (HL) intensities of 1,500-2,500 μmol photons m-2 s-1, which is lethal to most other photosynthetic microbes. We leveraged the few genetic differences between Synechococcus 2973 and the HL sensitive strain Synechococcus elongatus PCC 7942 to unravel factors essential for the high light tolerance. We identified a novel protein in Synechococcus 2973 that we have termed HltA for High light tolerance protein A. Using bioinformatic tools, we determined that HltA contains a functional PP2C-type protein phosphatase domain. Phylogenetic analysis showed that the PP2C domain belongs to the bacterial-specific Group II family and is closely related to the environmental stress response phosphatase RsbU. Additionally, we showed that unlike any previously described phosphatases, HltA contains a single N-terminal regulatory GAF domain. We found hltA to be ubiquitous throughout cyanobacteria, indicative of its potentially important role in the photosynthetic lifestyle of these oxygenic phototrophs. Mutations in the hltA gene resulted in severe defects specific to high light growth. These results provide evidence that hltA is a key factor in the tolerance of Synechococcus 2973 to high light and will open new insights into the mechanisms of cyanobacterial light stress response. IMPORTANCE Cyanobacteria are a diverse group of photosynthetic prokaryotes. The cyanobacterium Synechococcus 2973 is a high light tolerant strain with industrial promise due to its fast growth under high light conditions and the availability of genetic modification tools. Currently, little is known about the high light tolerance mechanisms of Synechococcus 2973, and there are many unknowns overall regarding high light tolerance of cyanobacteria. In this study, a comparative genomic analysis of Synechococcus 2973 identified a single nucleotide polymorphism in a locus encoding a serine phosphatase as a key factor for high light tolerance. This novel GAF-containing phosphatase was found to be the sole Group II metal-dependent protein phosphatase that is evolutionarily conserved throughout cyanobacteria. These results shed new light on the light response mechanisms of Synechococcus 2973, improving our understanding of environmental stress response. Additionally, this work will help facilitate the development of Synechococcus 2973 as an industrially useful organism.
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7
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Benner P, Meier L, Pfeffer A, Krüger K, Oropeza Vargas JE, Weuster-Botz D. Lab-scale photobioreactor systems: principles, applications, and scalability. Bioprocess Biosyst Eng 2022; 45:791-813. [PMID: 35303143 PMCID: PMC9033726 DOI: 10.1007/s00449-022-02711-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/14/2022] [Indexed: 12/20/2022]
Abstract
Phototrophic microorganisms that convert carbon dioxide are being explored for their capacity to solve different environmental issues and produce bioactive compounds for human therapeutics and as food additives. Full-scale phototrophic cultivation of microalgae and cyanobacteria can be done in open ponds or closed photobioreactor systems, which have a broad range of volumes. This review focuses on laboratory-scale photobioreactors and their different designs. Illuminated microtiter plates and microfluidic devices offer an option for automated high-throughput studies with microalgae. Illuminated shake flasks are used for simple uncontrolled batch studies. The application of illuminated bubble column reactors strongly emphasizes homogenous gas distribution, while illuminated flat plate bioreactors offer high and uniform light input. Illuminated stirred-tank bioreactors facilitate the application of very well-defined reaction conditions. Closed tubular photobioreactors as well as open photobioreactors like small-scale raceway ponds and thin-layer cascades are applied as scale-down models of the respective large-scale bioreactors. A few other less common designs such as illuminated plastic bags or aquarium tanks are also used mainly because of their relatively low cost, but up-scaling of these designs is challenging with additional light-driven issues. Finally, this review covers recommendations on the criteria for photobioreactor selection and operation while up-scaling of phototrophic bioprocesses with microalgae or cyanobacteria.
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Affiliation(s)
- Philipp Benner
- Department of Energy and Process Engineering, Chair of Biochemical Engineering, Technical University of Munich, TUM School of Engineering and Design, Boltzmannstraße 15, 85748, Garching, Germany
| | - Lisa Meier
- Technical University of Munich, TUM School of Engineering and Design, Boltzmannstraße 15, 85748, Garching, Germany
| | - Annika Pfeffer
- Technical University of Munich, TUM School of Engineering and Design, Boltzmannstraße 15, 85748, Garching, Germany
| | - Konstantin Krüger
- Technical University of Munich, TUM School of Engineering and Design, Boltzmannstraße 15, 85748, Garching, Germany
| | - José Enrique Oropeza Vargas
- Technical University of Munich, TUM School of Engineering and Design, Boltzmannstraße 15, 85748, Garching, Germany
| | - Dirk Weuster-Botz
- Department of Energy and Process Engineering, Chair of Biochemical Engineering, Technical University of Munich, TUM School of Engineering and Design, Boltzmannstraße 15, 85748, Garching, Germany.
- Technical University of Munich, TUM-AlgaeTec Center, 85521, Taufkirchen, Germany.
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8
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Steuer R. Fast-growing phototrophic microorganisms and the productivity of phototrophic cultures (revision). Biotechnol Bioeng 2022; 119:2261-2267. [PMID: 35475579 DOI: 10.1002/bit.28123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/06/2022] [Accepted: 04/18/2022] [Indexed: 11/06/2022]
Abstract
Fast-growing cyanobacterial and microalgal strains are considered to be a promising resource to overcome current productivity barriers of phototrophic cultivation. The purpose of this communication, however, is to argue that a high maximal growth rate itself is not a sufficient or necessary property for high phototrophic productivity. Rather, the light-limited specific growth rate of a phototrophic microorganism is a product of several factors, including the rate of light absorption, the photosynthetic efficiency and the maximal biomass yield per mol photons. It is suggested that, in addition to the maximal growth rate, reports on fast-growing strains should also assess photosynthetic efficiency and maximal biomass yield as predictors of culture productivity. The arguments within the communication are underpinned by a theoretical analysis of a light-limited chemostat, compared to its heterotrophic counterpart. It is shown that for the light-limited chemostat maximal productivity occurs at low dilution rates. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ralf Steuer
- Humboldt-University of Berlin, Institute for Biology, Theoretical Biology (ITB), Invalidenstr. 110, 10115, Berlin, Germany
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9
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Long B, Fischer B, Zeng Y, Amerigian Z, Li Q, Bryant H, Li M, Dai SY, Yuan JS. Machine learning-informed and synthetic biology-enabled semi-continuous algal cultivation to unleash renewable fuel productivity. Nat Commun 2022; 13:541. [PMID: 35087023 PMCID: PMC8795378 DOI: 10.1038/s41467-021-27665-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 12/01/2021] [Indexed: 11/29/2022] Open
Abstract
Algal biofuel is regarded as one of the ultimate solutions for renewable energy, but its commercialization is hindered by growth limitations caused by mutual shading and high harvest costs. We overcome these challenges by advancing machine learning to inform the design of a semi-continuous algal cultivation (SAC) to sustain optimal cell growth and minimize mutual shading. An aggregation-based sedimentation (ABS) strategy is then designed to achieve low-cost biomass harvesting and economical SAC. The ABS is achieved by engineering a fast-growing strain, Synechococcus elongatus UTEX 2973, to produce limonene, which increases cyanobacterial cell surface hydrophobicity and enables efficient cell aggregation and sedimentation. SAC unleashes cyanobacterial growth potential with 0.1 g/L/hour biomass productivity and 0.2 mg/L/hour limonene productivity over a sustained period in photobioreactors. Scaling-up the SAC with an outdoor pond system achieves a biomass yield of 43.3 g/m2/day, bringing the minimum biomass selling price down to approximately $281 per ton. Growth limitation caused by mutual shading and the high harvest cost hamper algal biofuel production. Here, the authors overcome these two problems by designing a semi-continuous algal cultivation system and an aggregation-based sedimentation strategy to achieve high levels production of biomass and limonene.
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Affiliation(s)
- Bin Long
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Bart Fischer
- Department of Agricultural Economics, Texas A&M University, College Station, TX, 77843, USA
| | - Yining Zeng
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Zoe Amerigian
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Qiang Li
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Henry Bryant
- Department of Agricultural Economics, Texas A&M University, College Station, TX, 77843, USA
| | - Man Li
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA.,Synthetic and Systems Biology Innovation Hub (SSBiH), Texas A&M University, College Station, TX, 77843, USA
| | - Susie Y Dai
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA.,Synthetic and Systems Biology Innovation Hub (SSBiH), Texas A&M University, College Station, TX, 77843, USA
| | - Joshua S Yuan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA. .,Synthetic and Systems Biology Innovation Hub (SSBiH), Texas A&M University, College Station, TX, 77843, USA.
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10
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Purdy HM, Pfleger BF, Reed JL. 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] [MESH Headings] [Grants] [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.
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Affiliation(s)
- Hugh M Purdy
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI, 53706, USA.
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI, 53706, USA.
| | - Jennifer L Reed
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI, 53706, USA.
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11
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Jones CM, Parrish S, Nielsen DR. Exploiting Polyploidy for Markerless and Plasmid-Free Genome Engineering in Cyanobacteria. ACS Synth Biol 2021; 10:2371-2382. [PMID: 34530614 DOI: 10.1021/acssynbio.1c00269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Here we describe a universal approach for plasmid-free genome engineering in cyanobacteria that exploits the polyploidy of their chromosomes as a natural counterselection system. Rather than being delivered via replicating plasmids, genes encoding for DNA modifying enzymes are instead integrated into essential genes on the chromosome by allelic exchange, as facilitated by antibiotic selection, a process that occurs readily and with only minor fitness defects. By virtue of the essentiality of these integration sites, full segregation is never achieved, with the strain instead remaining as a merodiploid so long as antibiotic selection is maintained. As a result, once the desired genome modification is complete, removal of antibiotic selection results in the gene encoding for the DNA modifying enzyme to then be promptly eliminated from the population. Proof of concept of this new and generalizable strategy is provided using two different site-specific recombination systems, CRE-lox and DRE-rox, in the fast-growing cyanobacterium Synechococcus sp. PCC 7002, as well as CRE-lox in the model cyanobacterium Synechocystis sp. PCC 6803. Reusability of the method, meanwhile, is demonstrated by constructing a high-CO2 requiring and markerless Δndh3 Δndh4 ΔbicA ΔsbtA mutant of Synechococcus sp. PCC 7002. Overall, this method enables the simple and efficient construction of stable and unmarked mutants in cyanobacteria without the need to develop additional shuttle vectors nor counterselection systems.
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Affiliation(s)
- Christopher M. Jones
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Sydney Parrish
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
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12
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Yunus IS, Wang Z, Sattayawat P, Muller J, Zemichael FW, Hellgardt K, Jones PR. Improved Bioproduction of 1-Octanol Using Engineered Synechocystis sp. PCC 6803. ACS Synth Biol 2021; 10:1417-1428. [PMID: 34003632 DOI: 10.1021/acssynbio.1c00029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
1-Octanol has gained interest as a chemical precursor for both high and low value commodities including fuel, solvents, surfactants, and fragrances. By harnessing the power from sunlight and CO2 as carbon source, cyanobacteria has recently been engineered for renewable production of 1-octanol. The productivity, however, remained low. In the present work, we report efforts to further improve the 1-octanol productivity. Different N-terminal truncations were evaluated on three thioesterases from different plant species, resulting in several candidate thioesterases with improved activity and selectivity toward octanoyl-ACP. The structure/function trials suggest that current knowledge and/or state-of-the art computational tools are insufficient to determine the most appropriate cleavage site for thioesterases in Synechocystis. Additionally, by tuning the inducer concentration and light intensity, we further improved the 1-octanol productivity, reaching up to 35% (w/w) carbon partitioning and a titer of 526 ± 5 mg/L 1-octanol in 12 days. Long-term cultivation experiments demonstrated that the improved strain can be stably maintained for at least 30 days and/or over ten times serial dilution. Surprisingly, the improved strain was genetically stable in contrast to earlier strains having lower productivity (and hence a reduced chance of reaching toxic product concentrations). Altogether, improved enzymes and environmental conditions (e.g., inducer concentration and light intensity) substantially increased the 1-octanol productivity. When cultured under continuous conditions, the bioproduction system reached an accumulative titer of >3.5 g/L 1-octanol over close to 180 days.
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Affiliation(s)
- Ian Sofian Yunus
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Zhixuan Wang
- Department of Chemical Engineering, Imperial College London, SW7 2AZ London, United Kingdom
| | - Pachara Sattayawat
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Jonathan Muller
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Fessehaye W. Zemichael
- Department of Chemical Engineering, Imperial College London, SW7 2AZ London, United Kingdom
| | - Klaus Hellgardt
- Department of Chemical Engineering, Imperial College London, SW7 2AZ London, United Kingdom
| | - Patrik R. Jones
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
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13
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Madsen MA, Hamilton G, Herzyk P, Amtmann A. Environmental Regulation of PndbA600, an Auto-Inducible Promoter for Two-Stage Industrial Biotechnology in Cyanobacteria. Front Bioeng Biotechnol 2021; 8:619055. [PMID: 33542914 PMCID: PMC7853294 DOI: 10.3389/fbioe.2020.619055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/09/2020] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are photosynthetic prokaryotes being developed as sustainable platforms that use renewable resources (light, water, and air) for diverse applications in energy, food, environment, and medicine. Despite the attractive promise that cyanobacteria offer to industrial biotechnology, slow growth rates pose a major challenge in processes which typically require large amounts of biomass and are often toxic to the cells. Two-stage cultivation strategies are an attractive solution to prevent any undesired growth inhibition by de-coupling biomass accumulation (stage I) and the industrial process (stage II). In cyanobacteria, two-stage strategies involve costly transfer methods between stages I and II, and little work has been focussed on using the distinct growth and stationary phases of batch cultures to autoregulate stage transition. In the present study, we identified and characterised a growth phase-specific promoter, which can serve as an auto-inducible switch to regulate two-stage bioprocesses in cyanobacteria. First, growth phase-specific genes were identified from a new RNAseq dataset comparing two growth phases and six nutrient conditions in Synechocystis sp. PCC 6803, including two new transcriptomes for low Mg and low K. A type II NADH dehydrogenase (ndbA) showed robust induction when the cultures transitioned from exponential to stationary phase growth. Behaviour of a 600-bp promoter sequence (PndbA600) was then characterised in detail following the expression of PndbA600:GFP in Synechococcus sp. PCC 7002. Culture density and growth media analyses showed that PndbA600 activation was not dependent on increases in culture density per se but on N availability and on another activating factor present in the spent media of stationary phase cultures (Factor X). PndbA600 deactivation was dependent on the changes in culture density and in either N availability or Factor X. Electron transport inhibition studies revealed a photosynthesis-specific enhancement of active PndbA600 levels. Our findings are summarised in a model describing the environmental regulation of PndbA600, which can now inform the rational design of two-stage industrial processes in cyanobacteria.
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Affiliation(s)
- Mary Ann Madsen
- College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Graham Hamilton
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Pawel Herzyk
- College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom.,Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Anna Amtmann
- College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
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14
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Jones CM, Korosh TC, Nielsen DR, Pfleger BF. Optimization of a T7-RNA polymerase system in Synechococcus sp. PCC 7002 mirrors the protein overproduction phenotype from E. coli BL21(DE3). Appl Microbiol Biotechnol 2021; 105:1147-1158. [PMID: 33443634 DOI: 10.1007/s00253-020-11085-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/14/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023]
Abstract
With the goal of expanding the diversity of tools available for controlling gene expression in cyanobacteria, the T7-RNA polymerase gene expression system from E. coli BL21(DE3) was adapted and systematically engineered for robust function Synechococcus sp. PCC 7002, a fast-growing saltwater strain. Expression of T7-RNA polymerase was controlled via LacI regulation, while functionality was optimized by both further tuning its expression level along with optimizing the translation initiation region of the expressed gene, in this case an enhanced YFP reporter. Under high CO2 conditions, the resulting system displayed a 60-fold dynamic range in expression levels. Furthermore, when maximally induced, T7-RNA polymerase-dependent protein production constituted up to two-thirds of total cellular protein content in Synechococcus sp. PCC 7002. Ultimately, however, this came at the cost of 40% reductions in both biomass and pigmentation levels. Taken together, the developed T7-RNA polymerase gene expression system is effective for controlling and achieving high-level expression of heterologous genes in Synechococcus sp. PCC 7002, making it a valuable tool for cyanobacterial research. KEY POINTS: • Promoter driving T7-RNA polymerase was optimized. • Up to 60-fold dynamic range in expression, depending on CO2 conditions. • Two-thirds of total protein is T7-RNA polymerase dependent.
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Affiliation(s)
- Christopher M Jones
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, AZ, 85287, USA
| | - Travis C Korosh
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - David R Nielsen
- Chemical Engineering, School for Engineering Matter, Transport, and Energy, Arizona State University, Tempe, AZ, 85287, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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15
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Vijayakumar S, Rahman PK, Angione C. A Hybrid Flux Balance Analysis and Machine Learning Pipeline Elucidates Metabolic Adaptation in Cyanobacteria. iScience 2020; 23:101818. [PMID: 33354660 PMCID: PMC7744713 DOI: 10.1016/j.isci.2020.101818] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/23/2020] [Accepted: 11/13/2020] [Indexed: 01/20/2023] Open
Abstract
Machine learning has recently emerged as a promising tool for inferring multi-omic relationships in biological systems. At the same time, genome-scale metabolic models (GSMMs) can be integrated with such multi-omic data to refine phenotypic predictions. In this work, we use a multi-omic machine learning pipeline to analyze a GSMM of Synechococcus sp. PCC 7002, a cyanobacterium with large potential to produce renewable biofuels. We use regularized flux balance analysis to observe flux response between conditions across photosynthesis and energy metabolism. We then incorporate principal-component analysis, k-means clustering, and LASSO regularization to reduce dimensionality and extract key cross-omic features. Our results suggest that combining metabolic modeling with machine learning elucidates mechanisms used by cyanobacteria to cope with fluctuations in light intensity and salinity that cannot be detected using transcriptomics alone. Furthermore, GSMMs introduce critical mechanistic details that improve the performance of omic-based machine learning methods.
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Affiliation(s)
- Supreeta Vijayakumar
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK
| | - Pattanathu K.S.M. Rahman
- Centre for Enzyme Innovation, Institute of Biological and Biomedical Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2UP, UK
- Tara Biologics, Woking, Surrey GU21 6BP, UK
| | - Claudio Angione
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK
- Centre for Digital Innovation, Teesside University, Middlesbrough TS1 3BX, UK
- Healthcare Innovation Centre, Teesside University, Middlesbrough TS1 3BX, UK
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16
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Sebesta J, Peebles CAM. Improving heterologous protein expression in Synechocystis sp. PCC 6803 for alpha-bisabolene production. Metab Eng Commun 2020; 10:e00117. [PMID: 31908923 PMCID: PMC6940699 DOI: 10.1016/j.mec.2019.e00117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 11/10/2019] [Accepted: 12/03/2019] [Indexed: 12/15/2022] Open
Abstract
Cyanobacterial biofuels have the potential to reduce the cost and climate impacts of biofuel production because primary carbon fixation and conversion to fuel are completed together in the cultivation of the cyanobacteria. Cyanobacterial biofuels, therefore, do not rely on costly organic carbon feedstocks that heterotrophs require, which reduces competition for agricultural resources such as arable land and freshwater. However, the published product titer achieved for most molecules of interest using cyanobacteria lag behind what has been achieved using yeast and Escherichia coli (E. coli) cultures. In Synechocystis sp. PCC 6803 (S. 6803), we attempted to increase the product titer of the sesquiterpene, bisabolene, which may be converted to bisabolane, a possible diesel replacement. We tested 19 strains of genetically modified S. 6803 with five different codon usage sequences of the bisabolene synthase from the grand fir tree (Abies grandis). At least three ribosome binding sites (most designed using the RBS Calculator) were tested for each codon usage sequence. We also tested strains with and without the farnesyl pyrophosphate synthase gene from E. coli. Bisabolene titers after five days of growth in continuous light ranged from un-detected to 7.8 mg/L. Bisabolene synthase abundance was measured and found to be well correlated with titer. Select strains were also tested in 12:12 light:dark cycles, where similar titers were reached after the same amount of light exposure time. One engineered strain was also tested in photobioreactors exposed to a simulated outdoor light pattern with maximum light intensity of 1600 μmol photons m-2 s-1. Here, the bisabolene titer reached 22.2 mg/L after 36 days of growth. Dramatic improvements in our ability to control gene expression in cyanobacteria such as S. 6803, and the co-utilization of additional metabolic engineering methods, are needed in order for these titers to improve to the levels reported for engineered E. coli.
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Affiliation(s)
- Jacob Sebesta
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA
| | - Christie AM. Peebles
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA
- Department of Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
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17
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Newly discovered Synechococcus sp. PCC 11901 is a robust cyanobacterial strain for high biomass production. Commun Biol 2020; 3:215. [PMID: 32382027 PMCID: PMC7205611 DOI: 10.1038/s42003-020-0910-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 03/16/2020] [Indexed: 12/31/2022] Open
Abstract
Cyanobacteria, which use solar energy to convert carbon dioxide into biomass, are potential solar biorefineries for the sustainable production of chemicals and biofuels. However, yields obtained with current strains are still uncompetitive compared to existing heterotrophic production systems. Here we report the discovery and characterization of a new cyanobacterial strain, Synechococcus sp. PCC 11901, with promising features for green biotechnology. It is naturally transformable, has a short doubling time of ≈2 hours, grows at high light intensities and in a wide range of salinities and accumulates up to ≈33 g dry cell weight per litre when cultured in a shake-flask system using a modified growth medium − 1.7 to 3 times more than other strains tested under similar conditions. As a proof of principle, PCC 11901 engineered to produce free fatty acids yielded over 6 mM (1.5 g L−1), an amount comparable to that achieved by similarly engineered heterotrophic organisms. Włodarczyk et al. discover that cyanobacterium Synechococcus sp. PCC 11901 accumulates three times more biomass than other cyanobacterial strains in the same conditions. An engineered version of this strain also produces as much free fatty acid as other commonly used heterotrophic microorganisms, suggesting its utility for the sustainable production of carbon-based molecules.
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18
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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.
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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.
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19
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Mechanical regulation of photosynthesis in cyanobacteria. Nat Microbiol 2020; 5:757-767. [PMID: 32203409 DOI: 10.1038/s41564-020-0684-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 02/04/2020] [Indexed: 12/17/2022]
Abstract
Photosynthetic organisms regulate their responses to many diverse stimuli in an effort to balance light harvesting with utilizable light energy for carbon fixation and growth (source-sink regulation). This balance is critical to prevent the formation of reactive oxygen species that can lead to cell death. However, investigating the molecular mechanisms that underlie the regulation of photosynthesis in cyanobacteria using ensemble-based measurements remains a challenge due to population heterogeneity. Here, to address this problem, we used long-term quantitative time-lapse fluorescence microscopy, transmission electron microscopy, mathematical modelling and genetic manipulation to visualize and analyse the growth and subcellular dynamics of individual wild-type and mutant cyanobacterial cells over multiple generations. We reveal that mechanical confinement of actively growing Synechococcus sp. PCC 7002 cells leads to the physical disassociation of phycobilisomes and energetic decoupling from the photosynthetic reaction centres. We suggest that the mechanical regulation of photosynthesis is a critical failsafe that prevents cell expansion when light and nutrients are plentiful, but when space is limiting. These results imply that cyanobacteria must convert a fraction of the available light energy into mechanical energy to overcome frictional forces in the environment, providing insight into the regulation of photosynthesis and how microorganisms navigate their physical environment.
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20
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Sengupta S, Jaiswal D, Sengupta A, Shah S, Gadagkar S, Wangikar PP. Metabolic engineering of a fast-growing cyanobacterium Synechococcus elongatus PCC 11801 for photoautotrophic production of succinic acid. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:89. [PMID: 32467730 PMCID: PMC7236211 DOI: 10.1186/s13068-020-01727-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/09/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Cyanobacteria, a group of photosynthetic prokaryotes, are being increasingly explored for direct conversion of carbon dioxide to useful chemicals. However, efforts to engineer these photoautotrophs have resulted in low product titers. This may be ascribed to the bottlenecks in metabolic pathways, which need to be identified for rational engineering. We engineered the recently reported, fast-growing and robust cyanobacterium, Synechococcus elongatus PCC 11801 to produce succinate, an important platform chemical. Previously, engineering of the model cyanobacterium S. elongatus PCC 7942 has resulted in succinate titer of 0.43 g l-1 in 8 days. RESULTS Building on the previous report, expression of α-ketoglutarate decarboxylase, succinate semialdehyde dehydrogenase and phosphoenolpyruvate carboxylase yielded a succinate titer of 0.6 g l-1 in 5 days suggesting that PCC 11801 is better suited as host for production. Profiling of the engineered strains for 57 intermediate metabolites, a number of enzymes and qualitative analysis of key transcripts revealed potential flux control points. Based on this, we evaluated the effects of overexpression of sedoheptulose-1,7-bisphosphatase, citrate synthase and succinate transporters and knockout of succinate dehydrogenase and glycogen synthase A. The final construct with seven genes overexpressed and two genes knocked out resulted in photoautotrophic production of 0.93 g l-1 succinate in 5 days. CONCLUSION While the fast-growing strain PCC 11801 yielded a much higher titer than the model strain, the efficient photoautotrophy of this novel isolate needs to be harnessed further for the production of desired chemicals. Engineered strains of S. elongatus PCC 11801 showed dramatic alterations in the levels of several metabolites suggesting far reaching effects of pathway engineering. Attempts to overexpress enzymes deemed to be flux controlling led to the emergence of other potential rate-limiting steps. Thus, this process of debottlenecking of the pathway needs to be repeated several times to obtain a significantly superior succinate titer.
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Affiliation(s)
- Shinjinee Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
- DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
| | - Damini Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
| | - Annesha Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
| | - Shikha Shah
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
- DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
| | - Shruti Gadagkar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
| | - Pramod P. Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
- DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 India
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21
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Faizi M, Steuer R. Optimal proteome allocation strategies for phototrophic growth in a light-limited chemostat. Microb Cell Fact 2019; 18:165. [PMID: 31601201 PMCID: PMC6785936 DOI: 10.1186/s12934-019-1209-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/06/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cyanobacteria and other phototrophic microorganisms allow to couple the light-driven assimilation of atmospheric [Formula: see text] directly to the synthesis of carbon-based products, and are therefore attractive platforms for microbial cell factories. While most current engineering efforts are performed using small-scale laboratory cultivation, the economic viability of phototrophic cultivation also crucially depends on photobioreactor design and culture parameters, such as the maximal areal and volumetric productivities. Based on recent insights into the cyanobacterial cell physiology and the resulting computational models of cyanobacterial growth, the aim of this study is to investigate the limits of cyanobacterial productivity in continuous culture with light as the limiting nutrient. RESULTS We integrate a coarse-grained model of cyanobacterial growth into a light-limited chemostat and its heterogeneous light gradient induced by self-shading of cells. We show that phototrophic growth in the light-limited chemostat can be described using the concept of an average light intensity. Different from previous models based on phenomenological growth equations, our model provides a mechanistic link between intracellular protein allocation, population growth and the resulting reactor productivity. Our computational framework thereby provides a novel approach to investigate and predict the maximal productivity of phototrophic cultivation, and identifies optimal proteome allocation strategies for developing maximally productive strains. CONCLUSIONS Our results have implications for efficient phototrophic cultivation and the design of maximally productive phototrophic cell factories. The model predicts that the use of dense cultures in well-mixed photobioreactors with short light-paths acts as an effective light dilution mechanism and alleviates the detrimental effects of photoinhibition even under very high light intensities. We recover the well-known trade-offs between a reduced light-harvesting apparatus and increased population density. Our results are discussed in the context of recent experimental efforts to increase the yield of phototrophic cultivation.
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Affiliation(s)
- Marjan Faizi
- Institut für Biologie, Fachinstitut für Theoretische Biologie, Humboldt-Universität zu Berlin, Invalidenstr. 110, 10115, Berlin, Germany
| | - Ralf Steuer
- Institut für Biologie, Fachinstitut für Theoretische Biologie, Humboldt-Universität zu Berlin, Invalidenstr. 110, 10115, Berlin, Germany.
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22
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Development of a longevous two-species biophotovoltaics with constrained electron flow. Nat Commun 2019; 10:4282. [PMID: 31537786 PMCID: PMC6753107 DOI: 10.1038/s41467-019-12190-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 08/27/2019] [Indexed: 01/07/2023] Open
Abstract
Microbial biophotovoltaics (BPV) offers a biological solution for renewable energy production by using photosynthetic microorganisms as light absorbers. Although abiotic engineering approaches, e.g., electrode modification and device optimization, can enhance the electrochemical communication between living cells and electrodes, the power densities of BPV are still low due to the weak exoelectrogenic activity of photosynthetic microorganisms. Here, we develop a BPV based on a D-lactate mediated microbial consortium consisting of photosynthetic cyanobacteria and exoelectrogenic Shewanella. By directing solar energy from photons to D-lactate, then to electricity, this BPV generates a power density of over 150 mW·m-2 in a temporal separation setup. Furthermore, a spatial-temporal separation setup with medium replenishment enables stable operation for over 40 days with an average power density of 135 mW·m-2. These results demonstrate the electron flow constrained microbial consortium can facilitate electron export from photosynthetic cells and achieve an efficient and durable power output.
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23
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Gorain PC, Paul I, Bhadoria PS, Pal R. An integrated approach towards agricultural wastewater remediation with fatty acid production by two cyanobacteria in bubble column photobioreactors. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101594] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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Selão TT, Włodarczyk A, Nixon PJ, Norling B. Growth and selection of the cyanobacterium Synechococcus sp. PCC 7002 using alternative nitrogen and phosphorus sources. Metab Eng 2019; 54:255-263. [PMID: 31063791 DOI: 10.1016/j.ymben.2019.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/08/2019] [Accepted: 04/29/2019] [Indexed: 12/14/2022]
Abstract
Cyanobacteria, such as Synechococcus sp. PCC 7002 (Syn7002), are promising chassis strains for "green" biotechnological applications as they can be grown in seawater using oxygenic photosynthesis to fix carbon dioxide into biomass. Their other major nutritional requirements for efficient growth are sources of nitrogen (N) and phosphorus (P). As these organisms are more economically cultivated in outdoor open systems, there is a need to develop cost-effective approaches to prevent the growth of contaminating organisms, especially as the use of antibiotic selection markers is neither economically feasible nor ecologically desirable due to the risk of horizontal gene transfer. Here we have introduced a synthetic melamine degradation pathway into Syn7002 and evolved the resulting strain to efficiently use the nitrogen-rich xenobiotic compound melamine as the sole N source. We also show that expression of phosphite dehydrogenase in the absence of its cognate phosphite transporter permits growth of Syn7002 on phosphite and can be used as a selectable marker in Syn7002. We combined these two strategies to generate a strain that can grow on melamine and phosphite as sole N and P sources, respectively. This strain is able to resist deliberate contamination in large excess and should be a useful chassis for metabolic engineering and biotechnological applications using cyanobacteria.
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Affiliation(s)
| | - Artur Włodarczyk
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Peter J Nixon
- School of Biological Sciences, Nanyang Technological University, Singapore; Sir Ernst Chain Building- Wolfson Laboratories, Department of Life Sciences, Imperial College London, S. Kensington Campus, London, SW7 2AZ, UK
| | - Birgitta Norling
- School of Biological Sciences, Nanyang Technological University, Singapore.
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25
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Clark RL, Gordon GC, Bennett NR, Lyu H, Root TW, Pfleger BF. High-CO 2 Requirement as a Mechanism for the Containment of Genetically Modified Cyanobacteria. ACS Synth Biol 2018; 7:384-391. [PMID: 29320853 DOI: 10.1021/acssynbio.7b00377] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
As researchers engineer cyanobacteria for biotechnological applications, we must consider potential environmental release of these organisms. Previous theoretical work has considered cyanobacterial containment through elimination of the CO2-concentrating mechanism (CCM) to impose a high-CO2 requirement (HCR), which could be provided in the cultivation environment but not in the surroundings. In this work, we experimentally implemented an HCR containment mechanism in Synechococcus sp. strain PCC7002 (PCC7002) through deletion of carboxysome shell proteins and showed that this mechanism contained cyanobacteria in a 5% CO2 environment. We considered escape through horizontal gene transfer (HGT) and reduced the risk of HGT escape by deleting competence genes. We showed that the HCR containment mechanism did not negatively impact the performance of a strain of PCC7002 engineered for L-lactate production. We showed through coculture experiments of HCR strains with ccm-containing strains that this HCR mechanism reduced the frequency of escape below the NIH recommended limit for recombinant organisms of one escape event in 108 CFU.
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Affiliation(s)
- Ryan L. Clark
- Department
of Chemical and Biological Engineering, University of Wisconsin − Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Gina C. Gordon
- Department
of Chemical and Biological Engineering, University of Wisconsin − Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
- Microbiology
Doctoral Training Program, University of Wisconsin − Madison, 1550 Linden Drive, Madison, Wisconsin 53706, United States
| | - Nathaniel R. Bennett
- Department
of Chemical and Biological Engineering, University of Wisconsin − Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Haoxiang Lyu
- Department
of Chemical and Biological Engineering, University of Wisconsin − Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Thatcher W. Root
- Department
of Chemical and Biological Engineering, University of Wisconsin − Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Brian F. Pfleger
- Department
of Chemical and Biological Engineering, University of Wisconsin − Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
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