1
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Schmelling NM, Bross M. What is holding back cyanobacterial research and applications? A survey of the cyanobacterial research community. Nat Commun 2024; 15:6758. [PMID: 39117643 DOI: 10.1038/s41467-024-50828-6] [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: 07/12/2023] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Cyanobacteria are a diverse group of prokaryotic organisms that have been the subject of intense basic research, resulting in a wealth of knowledge about fundamental cellular processes such as photosynthesis. However, the translation of that research towards industry-relevant applications is still limited. To understand the reasons for this contradictory situation, we conducted a quantitative survey among researchers in the cyanobacterial community, a set of individual interviews with established researchers, and a literature analysis. Our results show that the community seems to be committed to embracing cyanobacterial diversity and promoting collaboration. Additionally, participants expressed a strong desire to develop standardized protocols for research and establish larger consortia to accelerate progress. The results of the survey highlight the need for a more integrated approach to cyanobacterial research that encompasses both basic and applied aspects. Based on the survey and interview results as well as our literature analysis, we highlight areas for potential improvement, strategies to enhance cyanobacterial research, and open questions that demand further exploration. Addressing these challenges should accelerate the development of industrial applications based on cyanobacterial research.
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2
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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 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.
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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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3
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Kenkel A, Karande R, Bühler K. Evaluating scaling of capillary photo-biofilm reactors for high cell density cultivation of mixed trophies artificial microbial consortia. Eng Life Sci 2023; 23:e2300014. [PMID: 37664011 PMCID: PMC10472910 DOI: 10.1002/elsc.202300014] [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: 02/23/2023] [Revised: 05/12/2023] [Accepted: 05/27/2023] [Indexed: 09/05/2023] Open
Abstract
Capillary biofilm reactors (CBRs) are attractive for growing photoautotrophic bacteria as they allow high cell-density cultivation. Here, we evaluated the CBR system's suitability to grow an artificial consortium composed of Synechocystis sp. PCC 6803 and Pseudomonas sp. VBL120. The impact of reactor material, flow rate, pH, O2, and medium composition on biomass development and long-term biofilm stability at different reactor scales was studied. Silicone was superior over other materials like glass or PVC due to its excellent O2 permeability. High flow rates of 520 μL min-1 prevented biofilm sloughing in 1 m capillary reactors, leading to a 54% higher biomass dry weight combined with the lowest O2 concentration inside the reactor compared to standard operating conditions. Further increase in reactor length to 5 m revealed a limitation in trace elements. Increasing trace elements by a factor of five allowed for complete surface coverage with a biomass dry weight of 36.8 g m-2 and, thus, a successful CBR scale-up by a factor of 25. Practical application: Cyanobacteria use light energy to upgrade CO2, thereby holding the potential for carbon-neutral production processes. One of the persisting challenges is low cell density due to light limitations and O2 accumulation often occurring in established flat panel or tubular photobioreactors. Compared to planktonic cultures, much higher cell densities (factor 10 to 100) can be obtained in cyanobacterial biofilms. The capillary biofilm reactor (CBR) offers good growth conditions for cyanobacterial biofilms, but its applicability has been shown only on the laboratory scale. Here, a first scale-up study based on sizing up was performed, testing the feasibility of this system for large-scale applications. We demonstrate that by optimizing nutrient supply and flow conditions, the system could be enlarged by factor 25 by enhancing the length of the reactor. This reactor concept, combined with cyanobacterial biofilms and numbering up, holds the potential to be applied as a flexible, carbon-neutral production platform for value-added compounds.
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Affiliation(s)
- Amelie Kenkel
- Department of Solar MaterialsHelmholtz Center for Environmental Research, UFZLeipzigGermany
| | - Rohan Karande
- Research and Transfer Center for bioactive Matter b‐ACT, Institute of BiochemistryLeipzig UniversityLeipzigGermany
| | - Katja Bühler
- Department of Environmental MicrobiologyHelmholtz Center for Environmental Research, UFZLeipzigGermany
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4
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Agustinus B, Gillam EMJ. Solar-powered P450 catalysis: Engineering electron transfer pathways from photosynthesis to P450s. J Inorg Biochem 2023; 245:112242. [PMID: 37187017 DOI: 10.1016/j.jinorgbio.2023.112242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/17/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
With the increasing focus on green chemistry, biocatalysis is becoming more widely used in the pharmaceutical and other chemical industries for sustainable production of high value and structurally complex chemicals. Cytochrome P450 monooxygenases (P450s) are attractive biocatalysts for industrial application due to their ability to transform a huge range of substrates in a stereo- and regiospecific manner. However, despite their appeal, the industrial application of P450s is limited by their dependence on costly reduced nicotinamide adenine dinucleotide phosphate (NADPH) and one or more auxiliary redox partner proteins. Coupling P450s to the photosynthetic machinery of a plant allows photosynthetically-generated electrons to be used to drive catalysis, overcoming this cofactor dependency. Thus, photosynthetic organisms could serve as photobioreactors with the capability to produce value-added chemicals using only light, water, CO2 and an appropriate chemical as substrate for the reaction/s of choice, yielding new opportunities for producing commodity and high-value chemicals in a carbon-negative and sustainable manner. This review will discuss recent progress in using photosynthesis for light-driven P450 biocatalysis and explore the potential for further development of such systems.
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Affiliation(s)
- Bernadius Agustinus
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia.
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5
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Mager M, Pineda Hernandez H, Brandenburg F, López-Maury L, McCormick AJ, Nürnberg DJ, Orthwein T, Russo DA, Victoria AJ, Wang X, Zedler JAZ, Branco dos Santos F, Schmelling NM. Interlaboratory Reproducibility in Growth and Reporter Expression in the Cyanobacterium Synechocystis sp. PCC 6803. ACS Synth Biol 2023; 12:1823-1835. [PMID: 37246820 PMCID: PMC10278186 DOI: 10.1021/acssynbio.3c00150] [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: 03/11/2023] [Indexed: 05/30/2023]
Abstract
In recent years, a plethora of new synthetic biology tools for use in cyanobacteria have been published; however, their reported characterizations often cannot be reproduced, greatly limiting the comparability of results and hindering their applicability. In this interlaboratory study, the reproducibility of a standard microbiological experiment for the cyanobacterial model organism Synechocystis sp. PCC 6803 was assessed. Participants from eight different laboratories quantified the fluorescence intensity of mVENUS as a proxy for the transcription activity of the three promoters PJ23100, PrhaBAD, and PpetE over time. In addition, growth rates were measured to compare growth conditions between laboratories. By establishing strict and standardized laboratory protocols, reflecting frequently reported methods, we aimed to identify issues with state-of-the-art procedures and assess their effect on reproducibility. Significant differences in spectrophotometer measurements across laboratories from identical samples were found, suggesting that commonly used reporting practices of optical density values need to be supplemented by cell count or biomass measurements. Further, despite standardized light intensity in the incubators, significantly different growth rates between incubators used in this study were observed, highlighting the need for additional reporting requirements of growth conditions for phototrophic organisms beyond the light intensity and CO2 supply. Despite the use of a regulatory system orthogonal to Synechocystis sp. PCC 6803, PrhaBAD, and a high level of protocol standardization, ∼32% variation in promoter activity under induced conditions was found across laboratories, suggesting that the reproducibility of other data in the field of cyanobacteria might be affected similarly.
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Affiliation(s)
- Maurice Mager
- Institute
for Synthetic Microbiology, Heinrich Heine
University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| | - Hugo Pineda Hernandez
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Fabian Brandenburg
- Helmholtz
Centre for Environmental Research (UFZ), Permoserstrasse 15, 04318 Leipzig, Germany
| | - Luis López-Maury
- Instituto
de Bioquímica Vegetal y Fotosíntesis, University of Seville − CSIC, Américo Vespucio 49, 41092 Sevilla, Spain
- Departamento
de Bioquímica Vegetal y Biología Molecular, Facultad
de Biología, University of Seville, Avenida Reina Mercedes, 41012 Sevilla, Spain
| | - Alistair J. McCormick
- Institute
of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, 1.04 Daniel Rutherford Building, King’s
Buildings, EH9 3BF Edinburgh, U.K.
| | - Dennis J. Nürnberg
- Department
of Physics, Experimental Biophysics, Freie
University Berlin, Arnimallee
14, 14195 Berlin, Germany
- Dahlem
Centre of Plant Sciences, Freie Universität
Berlin, Albrecht-Thaer-Weg 6, 14195 Berlin, Germany
| | - Tim Orthwein
- Interfaculty
Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - David A. Russo
- Institute
for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich Schiller University Jena, Lessingstrasse 8, 07743 Jena, Germany
| | - Angelo Joshua Victoria
- Institute
of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, 1.04 Daniel Rutherford Building, King’s
Buildings, EH9 3BF Edinburgh, U.K.
| | - Xiaoran Wang
- Department
of Physics, Experimental Biophysics, Freie
University Berlin, Arnimallee
14, 14195 Berlin, Germany
| | - Julie A. Z. Zedler
- Matthias
Schleiden Institute for Genetics, Bioinformatics and Molecular Botany,
Synthetic Biology of Photosynthetic Organisms, Friedrich Schiller University Jena, Dornburgerstrasse 159, 07743 Jena, Germany
| | - 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
| | - Nicolas M. Schmelling
- Institute
for Synthetic Microbiology, Heinrich Heine
University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
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6
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Simultaneous production of γ-linolenic acid and carotenoids by a novel microalgal strain isolated from the underexplored habitat of intermittent streams. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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7
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Cao J, Russo DA, Xie T, Groß GA, Zedler JAZ. A droplet-based microfluidic platform enables high-throughput combinatorial optimization of cyanobacterial cultivation. Sci Rep 2022; 12:15536. [PMID: 36109626 PMCID: PMC9477827 DOI: 10.1038/s41598-022-19773-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/05/2022] [Indexed: 11/09/2022] Open
Abstract
Cyanobacteria are fast-growing, genetically accessible, photoautotrophs. Therefore, they have attracted interest as sustainable production platforms. However, the lack of techniques to systematically optimize cultivation parameters in a high-throughput manner is holding back progress towards industrialization. To overcome this bottleneck, here we introduce a droplet-based microfluidic platform capable of one- (1D) and two-dimension (2D) screening of key parameters in cyanobacterial cultivation. We successfully grew three different unicellular, biotechnologically relevant, cyanobacteria: Synechocystis sp. PCC 6803, Synechococcus elongatus UTEX 2973 and Synechococcus sp. UTEX 3154. This was followed by a highly-resolved 1D screening of nitrate, phosphate, carbonate, and salt concentrations. The 1D screening results suggested that nitrate and/or phosphate may be limiting nutrients in standard cultivation media. Finally, we use 2D screening to determine the optimal N:P ratio of BG-11. Application of the improved medium composition in a high-density cultivation setup led to an increase in biomass yield of up to 15.7%. This study demonstrates that droplet-based microfluidics can decrease the volume required for cyanobacterial cultivation and screening up to a thousand times while significantly increasing the multiplexing capacity. Going forward, microfluidics have the potential to play a significant role in the industrial exploitation of cyanobacteria.
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8
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Heterologous Lactate Synthesis in Synechocystis sp. Strain PCC 6803 Causes a Growth Condition-Dependent Carbon Sink Effect. Appl Environ Microbiol 2022; 88:e0006322. [PMID: 35369703 PMCID: PMC9040622 DOI: 10.1128/aem.00063-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Cyanobacteria are considered promising hosts for product synthesis directly from CO2 via photosynthetic carbon assimilation. The introduction of heterologous carbon sinks in terms of product synthesis has been reported to induce the so-called “carbon sink effect,” described as the release of unused photosynthetic capacity by the introduction of additional carbon. This effect is thought to arise from a limitation of carbon metabolism that represents a bottleneck in carbon and electron flow, thus enforcing a downregulation of photosynthetic efficiency. It is not known so far how the cellular source/sink balance under different growth conditions influences the extent of the carbon sink effect and in turn product formation from CO2, constituting a heterologous carbon sink. We compared the Synechocystis sp. strain PCC 6803 wild type (WT) with an engineered lactate-producing strain (SAA023) in defined metabolic states. Unexpectedly, high-light conditions combined with carbon limitation enabled additional carbon assimilation for lactate production without affecting biomass formation. Thus, a strong carbon sink effect only was observed under carbon and thus sink limitation, but not under high-sink conditions. We show that the carbon sink effect was accompanied by an increased rate of alternative electron flow (AEF). Thus, AEF plays a crucial role in the equilibration of source/sink imbalances, presumably via ATP/NADPH balancing. This study emphasizes that the evaluation of the biotechnological potential of cyanobacteria profits from cultivation approaches enabling the establishment of defined metabolic states and respective quantitative analytics. Factors stimulating photosynthesis and carbon fixation are discussed. IMPORTANCE Previous studies reported various and differing effects of the heterologous production of carbon-based molecules on photosynthetic and growth efficiency of cyanobacteria. The typically applied cultivation in batch mode, with continuously changing growth conditions, however, precludes a clear differentiation between the impact of cultivation conditions on cell physiology and effects related to the specific nature of the product and its synthesis pathway. In this study, we employed a continuous cultivation system to maintain defined source/sink conditions and thus metabolic states. This allowed a systematic and quantitative analysis of the effect of NADPH-consuming lactate production on photosynthetic and growth efficiency. This approach enables a realistic evaluation of the biotechnological potential of engineered cyanobacterial strains. For example, the quantum requirement for carbon production was found to constitute an excellent indicator of the source/sink balance and thus a key parameter for photobioprocess optimization. Such knowledge is fundamental for rational and efficient strain and process development.
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9
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Puzorjov A, Mert Unal S, Wear MA, McCormick AJ. Pilot scale production, extraction and purification of a thermostable phycocyanin from Synechocystis sp. PCC 6803. BIORESOURCE TECHNOLOGY 2022; 345:126459. [PMID: 34863843 PMCID: PMC8811538 DOI: 10.1016/j.biortech.2021.126459] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 06/09/2023]
Abstract
Phycocyanin (PC) is a soluble blue pigment-protein primarily harvested from the cyanobacterium Arthrospira platensis. PC is in high demand from several industries, but its narrow stability range limits potential applications. Here, a pilot scale (120 L total) batch production, extraction and purification process for thermostable PC (Te-PC) from a Synechocystis sp. PCC 6803 'Olive' strain expressing the PC operon cpcBACD from Thermosynechococcus elongatus BP-1 on a self-replicating vector is presented. Batch cultivation without antibiotics had no impact on growth or Te-PC production and optimisation of growth conditions resulted in Te-PC contents of 75.3 ± 1.7 mg g DW-1. Wet biomass was harvested following chitosan-based flocculation with a 97 ± 2% efficiency, and Te-PC was extracted by high pressure homogenisation. Subsequent purification by heat-treatment and two-step ammonium sulfate precipitation removed chlorophyll and allophycocyanin contamination, resulting in Te-PC purities of 2.9 ± 0.7 and a mean Te-PC recovery of 84 ± 12%.
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Affiliation(s)
- Anton Puzorjov
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Suleyman Mert Unal
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Martin A Wear
- The Edinburgh Protein Purification Facility, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Alistair J McCormick
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
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10
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Satta A, Lu Z, Plan MR, Esquirol L, Ebert BE. Microbial Production, Extraction, and Quantitative Analysis of Isoprenoids. Methods Mol Biol 2022; 2469:239-259. [PMID: 35508844 DOI: 10.1007/978-1-0716-2185-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Isoprenoids, also known as terpenes or terpenoids, are compounds made of one or more isoprene (C5H8) moieties and constitute the largest class of natural products. They play diverse roles in biology and have broad industrial uses as flavors, fragrances, biofuels, polymers, agricultural chemicals, and medicines. Most isoprenoids are secondary plant metabolites and only produced in very low amounts. To make these valuable compounds economically accessible, significant efforts in the culture and engineering of microbial cells for isoprenoid biosynthesis have been made in the last decades. The protocols presented here describe lab-scale cultivation of microbes, either naturally producing or engineered, for isoprenoid production, the extraction of products and their quantification by high-performance liquid chromatography. Examples of isoprenoids covered in this chapter include (C10) mono-, (C15) sesqui-, (C20) di-, (C30) tri-, and (C40) tetraterpenoids. We focus on yeast and cyanobacteria as production systems, but the protocols can be adapted for other organisms.
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Affiliation(s)
- Alessandro Satta
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Zeyu Lu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Manuel R Plan
- Metabolomics Australia (Queensland Node), Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
| | - Birgitta E Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia.
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11
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Analysing intracellular isoprenoid metabolites in diverse prokaryotic and eukaryotic microbes. Methods Enzymol 2022; 670:235-284. [DOI: 10.1016/bs.mie.2022.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Battaglino B, Du W, Pagliano C, Jongbloets JA, Re A, Saracco G, Branco dos Santos F. Channeling Anabolic Side Products toward the Production of Nonessential Metabolites: Stable Malate Production in Synechocystis sp. PCC6803. ACS Synth Biol 2021; 10:3518-3526. [PMID: 34808039 PMCID: PMC8689693 DOI: 10.1021/acssynbio.1c00440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Powered by (sun)light to oxidize water, cyanobacteria can directly convert atmospheric CO2 into valuable carbon-based compounds and meanwhile release O2 to the atmosphere. As such, cyanobacteria are promising candidates to be developed as microbial cell factories for the production of chemicals. Nevertheless, similar to other microbial cell factories, engineered cyanobacteria may suffer from production instability. The alignment of product formation with microbial fitness is a valid strategy to tackle this issue. We have described previously the "FRUITS" algorithm for the identification of metabolites suitable to be coupled to growth (i.e., side products in anabolic reactions) in the model cyanobacterium Synechocystis. sp PCC6803. However, the list of candidate metabolites identified using this algorithm can be somewhat limiting, due to the inherent structure of metabolic networks. Here, we aim at broadening the spectrum of candidate compounds beyond the ones predicted by FRUITS, through the conversion of a growth-coupled metabolite to downstream metabolites via thermodynamically favored conversions. We showcase the feasibility of this approach for malate production using fumarate as the growth-coupled substrate in Synechocystis mutants. A final titer of ∼1.2 mM was achieved for malate during photoautotrophic batch cultivations. Under prolonged continuous cultivation, the most efficient malate-producing strain can maintain its productivity for at least 45 generations, sharply contrasting with other producing Synechocystis strains engineered with classical approaches. Our study also opens a new possibility for extending the stable production concept to derivatives of growth-coupled metabolites, increasing the list of suitable target compounds.
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Affiliation(s)
- Beatrice Battaglino
- Applied Science and Technology Department, BioSolar Lab, Politecnico di Torino, Environment
Park, Via Livorno 60, 10144 Torino, Italy
- Centre for Sustainable Future Technologies, Istituto Italiano di Tecnologia, Environment
Park, Via Livorno 60, 10144 Torino, Italy
| | - Wei Du
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Cristina Pagliano
- Applied Science and Technology Department, BioSolar Lab, Politecnico di Torino, Environment
Park, Via Livorno 60, 10144 Torino, Italy
| | - Joeri A. Jongbloets
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Angela Re
- Centre for Sustainable Future Technologies, Istituto Italiano di Tecnologia, Environment
Park, Via Livorno 60, 10144 Torino, Italy
| | - Guido Saracco
- Applied Science and Technology Department, BioSolar Lab, Politecnico di Torino, Environment
Park, Via Livorno 60, 10144 Torino, Italy
| | - 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
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13
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Yu King Hing N, Aryal UK, Morgan JA. Probing Light-Dependent Regulation of the Calvin Cycle Using a Multi-Omics Approach. FRONTIERS IN PLANT SCIENCE 2021; 12:733122. [PMID: 34671374 PMCID: PMC8521058 DOI: 10.3389/fpls.2021.733122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Photoautotrophic microorganisms are increasingly explored for the conversion of atmospheric carbon dioxide into biomass and valuable products. The Calvin-Benson-Bassham (CBB) cycle is the primary metabolic pathway for net CO2 fixation within oxygenic photosynthetic organisms. The cyanobacteria, Synechocystis sp. PCC 6803, is a model organism for the study of photosynthesis and a platform for many metabolic engineering efforts. The CBB cycle is regulated by complex mechanisms including enzymatic abundance, intracellular metabolite concentrations, energetic cofactors and post-translational enzymatic modifications that depend on the external conditions such as the intensity and quality of light. However, the extent to which each of these mechanisms play a role under different light intensities remains unclear. In this work, we conducted non-targeted proteomics in tandem with isotopically non-stationary metabolic flux analysis (INST-MFA) at four different light intensities to determine the extent to which fluxes within the CBB cycle are controlled by enzymatic abundance. The correlation between specific enzyme abundances and their corresponding reaction fluxes is examined, revealing several enzymes with uncorrelated enzyme abundance and their corresponding flux, suggesting flux regulation by mechanisms other than enzyme abundance. Additionally, the kinetics of 13C labeling of CBB cycle intermediates and estimated inactive pool sizes varied significantly as a function of light intensity suggesting the presence of metabolite channeling, an additional method of flux regulation. These results highlight the importance of the diverse methods of regulation of CBB enzyme activity as a function of light intensity, and highlights the importance of considering these effects in future kinetic models.
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Affiliation(s)
- Nathaphon Yu King Hing
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, United States
| | - Uma K. Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN, United States
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, West Lafayette, IN, United States
| | - John A. Morgan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, United States
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
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14
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Karlsen J, Asplund-Samuelsson J, Jahn M, Vitay D, Hudson EP. Slow Protein Turnover Explains Limited Protein-Level Response to Diurnal Transcriptional Oscillations in Cyanobacteria. Front Microbiol 2021; 12:657379. [PMID: 34194405 PMCID: PMC8237939 DOI: 10.3389/fmicb.2021.657379] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/22/2021] [Indexed: 12/31/2022] Open
Abstract
Metabolically engineered cyanobacteria have the potential to mitigate anthropogenic CO2 emissions by converting CO2 into renewable fuels and chemicals. Yet, better understanding of metabolic regulation in cyanobacteria is required to develop more productive strains that can make industrial scale-up economically feasible. The aim of this study was to find the cause for the previously reported inconsistency between oscillating transcription and constant protein levels under day-night growth conditions. To determine whether translational regulation counteracts transcriptional changes, Synechocystis sp. PCC 6803 was cultivated in an artificial day-night setting and the level of transcription, translation and protein was measured across the genome at different time points using mRNA sequencing, ribosome profiling and quantitative proteomics. Furthermore, the effect of protein turnover on the amplitude of protein oscillations was investigated through in silico simulations using a protein mass balance model. Our experimental analysis revealed that protein oscillations were not dampened by translational regulation, as evidenced by high correlation between translational and transcriptional oscillations (r = 0.88) and unchanged protein levels. Instead, model simulations showed that these observations can be attributed to a slow protein turnover, which reduces the effect of protein synthesis oscillations on the protein level. In conclusion, these results suggest that cyanobacteria have evolved to govern diurnal metabolic shifts through allosteric regulatory mechanisms in order to avoid the energy burden of replacing the proteome on a daily basis. Identification and manipulation of such mechanisms could be part of a metabolic engineering strategy for overproduction of chemicals.
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Affiliation(s)
- Jan Karlsen
- Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Johannes Asplund-Samuelsson
- Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Michael Jahn
- Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Dóra Vitay
- Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden.,Biosyntia ApS, Copenhagen, Denmark
| | - Elton P Hudson
- Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
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15
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Liu D, Liberton M, Hendry JI, Aminian-Dehkordi J, Maranas CD, Pakrasi HB. Engineering biology approaches for food and nutrient production by cyanobacteria. Curr Opin Biotechnol 2020; 67:1-6. [PMID: 33129046 DOI: 10.1016/j.copbio.2020.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/13/2020] [Accepted: 09/21/2020] [Indexed: 01/10/2023]
Abstract
As photoautotrophic organisms, cyanobacteria capture and store solar energy in the form of biomass. Cyanobacterial biomass has been an important component of diet and nutrition in several regions for centuries. Synthetic biology strategies are currently being applied to increase the yield and productivity of cyanobacterial biomass by optimizing solar energy utilization and CO2 fixation rates for carbon storage. Likewise, engineering cyanobacteria as cellular factories to synthesize carbohydrates, amino acids, proteins, lipids and fatty acids is providing an attractive way to sustainably produce food and nutrients for human consumption. In this review, we have summarized recent progress in both aspects and prospective trends under development.
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Affiliation(s)
- Deng Liu
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Michelle Liberton
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - John I Hendry
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Javad Aminian-Dehkordi
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, MO 63130, USA.
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16
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Iron limitation – A perspective on a growth-restricted cultivation strategy for a H2 production system using the diazotrophic cyanobacterium Nostoc PCC 7120 ΔhupW. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.biteb.2020.100508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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17
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Xu Y, Wang X, Fu Y, Hu F, Qian G, Liu Q, Sun Y. Interaction energy and detachment of magnetic nanoparticles-algae. ENVIRONMENTAL TECHNOLOGY 2020; 41:2618-2624. [PMID: 30694112 DOI: 10.1080/09593330.2019.1575918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
Magnetic separation, a promising bioseparation technology, is confronted with the challenges in recovery and recycle of magnetic matters during algae harvesting for biofuel extraction. The thermodynamic method was used to characterize the surface interactions between MNPs and algae cells. Three methods were adopted to detach magnetic nanoparticles-algae (Microcystis aeruginosa, Synechocystis sp., Nannochloropsis maritima and Stigeoclonium sp.) and recover magnetic nanoparticles (MNPs) in this study. The thermodynamic method indicated that the greatest adhesion strength was expected for Stigeoclonium sp. on MNPs. High detachment efficiency of MNP-algae was achieved by ultrasonic-extracting, which got above 90% after 5 recycles. Moreover, the harvesting efficiencies of these four algae cells could remain more than 90% after 5 recycles using a mixture of the regenerated and the raw MNPs.
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Affiliation(s)
- Yunfeng Xu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, People's Republic of China
| | - Xin Wang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, People's Republic of China
| | - Yu Fu
- Guizhou Academy of Testing and Analysis, Guiyang, People's Republic of China
| | - Fanglu Hu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, People's Republic of China
| | - Guangren Qian
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, People's Republic of China
| | - Qiang Liu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, People's Republic of China
| | - Ying Sun
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, People's Republic of China
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18
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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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19
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Ng I, Keskin BB, Tan S. A Critical Review of Genome Editing and Synthetic Biology Applications in Metabolic Engineering of Microalgae and Cyanobacteria. Biotechnol J 2020; 15:e1900228. [DOI: 10.1002/biot.201900228] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/07/2020] [Indexed: 12/13/2022]
Affiliation(s)
- I‐Son Ng
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
| | - Batuhan Birol Keskin
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
| | - Shih‐I Tan
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
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20
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Wu W, Du W, Gallego RP, Hellingwerf KJ, van der Woude AD, Branco dos Santos F. Using osmotic stress to stabilize mannitol production in Synechocystis sp. PCC6803. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:117. [PMID: 32636923 PMCID: PMC7331161 DOI: 10.1186/s13068-020-01755-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/23/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Mannitol is a C(6) polyol that is used in the food and medical sector as a sweetener and antioxidant, respectively. The sustainable production of mannitol, especially via the direct conversion of CO2 by photosynthetic cyanobacteria, has become increasingly appealing. However, previous work aiming to achieve mannitol production in the marine Synechococcus sp. PCC7002 via heterologous expression of mannitol-1-phosphate-5-dehydrogenase (mtlD) and mannitol-1-phosphatase (m1p, in short: a 'mannitol cassette'), proved to be genetically unstable. In this study, we aim to overcome this genetic instability by conceiving a strategy to stabilize mannitol production using Synechocystis sp. PCC6803 as a model cyanobacterium. RESULTS Here, we explore the stabilizing effect that mannitol production may have on cells faced with osmotic stress, in the freshwater cyanobacterium Synechocystis sp. PCC6803. We first validated that mannitol can function as a compatible solute in Synechocystis sp. PCC6803, and in derivative strains in which the ability to produce one or both of the native compatible solutes was impaired. Wild-type Synechocystis, complemented with a mannitol cassette, indeed showed increased salt tolerance, which was even more evident in Synechocystis strains in which the ability to synthesize the endogenous compatible solutes was impaired. Next we tested the genetic stability of all these strains with respect to their mannitol productivity, with and without salt stress, during prolonged turbidostat cultivations. The obtained results show that mannitol production under salt stress conditions in the Synechocystis strain that cannot synthesize its endogenous compatible solutes is remarkably stable, while the control strain completely loses this ability in only 6 days. DNA sequencing results of the control groups that lost the ability to synthesize mannitol revealed that multiple types of mutation occurred in the mtlD gene that can explain the disruption of mannitol production. CONCLUSIONS Mannitol production in freshwater Synechocsytis sp. PCC6803 confers it with increased salt tolerance. Under this strategy, genetically instability which was the major challenge for mannitol production in cyanobacteria is tackled. This paper marks the first report of utilization of the response to salt stress as a factor that can increase the stability of mannitol production in a cyanobacterial cell factory.
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Affiliation(s)
- Wenyang Wu
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Wei Du
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Ruth Perez Gallego
- Photanol B.V, Matrix V, Science Park 406, 1098 XH Amsterdam, The Netherlands
- Present Address: NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, P.O. Box 59, Den Burg, Texel, 1790 AB Utrecht, The Netherlands
| | - Klaas J. Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Photanol B.V, Matrix V, Science Park 406, 1098 XH Amsterdam, The Netherlands
| | | | - Filipe Branco dos Santos
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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21
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Pauly M, Gawenda N, Wagner C, Fischbach P, Ramírez V, Axmann IM, Voiniciuc C. The Suitability of Orthogonal Hosts to Study Plant Cell Wall Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2019; 8:E516. [PMID: 31744209 PMCID: PMC6918405 DOI: 10.3390/plants8110516] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 12/20/2022]
Abstract
Plant cells are surrounded by an extracellular matrix that consists mainly of polysaccharides. Many molecular components involved in plant cell wall polymer synthesis have been identified, but it remains largely unknown how these molecular players function together to define the length and decoration pattern of a polysaccharide. Synthetic biology can be applied to answer questions beyond individual glycosyltransferases by reconstructing entire biosynthetic machineries required to produce a complete wall polysaccharide. Recently, this approach was successful in establishing the production of heteromannan from several plant species in an orthogonal host-a yeast-illuminating the role of an auxiliary protein in the biosynthetic process. In this review we evaluate to what extent a selection of organisms from three kingdoms of life (Bacteria, Fungi and Animalia) might be suitable for the synthesis of plant cell wall polysaccharides. By identifying their key attributes for glycoengineering as well as analyzing the glycosidic linkages of their native polymers, we present a valuable comparison of their key advantages and limitations for the production of different classes of plant polysaccharides.
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Affiliation(s)
- Markus Pauly
- Institute for Plant Cell Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.P.); (N.G.); (V.R.)
| | - Niklas Gawenda
- Institute for Plant Cell Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.P.); (N.G.); (V.R.)
| | - Christine Wagner
- Independent Junior Research Group–Designer Glycans, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Patrick Fischbach
- Institute of Synthetic Biology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Vicente Ramírez
- Institute for Plant Cell Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.P.); (N.G.); (V.R.)
| | - Ilka M. Axmann
- Institute for Synthetic Microbiology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Cătălin Voiniciuc
- Independent Junior Research Group–Designer Glycans, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
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22
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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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23
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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.
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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
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24
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Liang Y, Tang J, Luo Y, Kaczmarek MB, Li X, Daroch M. Thermosynechococcus as a thermophilic photosynthetic microbial cell factory for CO 2 utilisation. BIORESOURCE TECHNOLOGY 2019; 278:255-265. [PMID: 30708328 DOI: 10.1016/j.biortech.2019.01.089] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/17/2019] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
Thermophilic unicellular cyanobacterium Thermosynechococcus elongatus PKUAC-SCTE542, has been developed as a thermophilic photosynthetic microbial cell factory for CO2 utilisation. The strain exhibits its highest growth rate around 55 °C, can withstand up to 15% CO2, and up to 0.5 M concentration of sodium bicarbonate. The strain is also capable of resisting a 200 ppm concentration of NO and SO2 in simulated flue gasses, and these compounds have a positive effect on its growth. Whole genome sequencing of the strain revealed the presence of numerous forms of active transport of nutrients and additional chaperones acting as the predominant mechanism of strain adaptation to high temperatures. Based on the sequenced genome, two neutral gene insertion sites have been identified and engineered using modular vectors. Site-specific knock-ins and knock-outs have been performed using the spectinomycin resistance gene and proved functional, enabling future application of the strain to produce biofuels and biochemicals from waste CO2.
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Affiliation(s)
- Yuanmei Liang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jie Tang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, China; Shenzhen Aone Medical Laboratory Co Ltd, Shenzhen 518107, China
| | - Yifan Luo
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Michal B Kaczmarek
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Institute of Technical Biochemistry, Lodz University of Technology, Lodz, Poland
| | - Xingkang Li
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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25
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Zavřel T, Faizi M, Loureiro C, Poschmann G, Stühler K, Sinetova M, Zorina A, Steuer R, Červený J. Quantitative insights into the cyanobacterial cell economy. eLife 2019; 8:42508. [PMID: 30714903 PMCID: PMC6391073 DOI: 10.7554/elife.42508] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/01/2019] [Indexed: 01/27/2023] Open
Abstract
Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological acclimations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial acclimations to different growth rates have implications to understand and optimize photosynthetic productivity.
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Affiliation(s)
- Tomáš Zavřel
- Laboratory of Adaptive BiotechnologiesGlobal Change Research Institute CASBrnoCzech Republic
| | - Marjan Faizi
- Institut für Biologie, Fachinstitut für Theoretische BiologieHumboldt-Universität zu BerlinBerlinGermany
| | - Cristina Loureiro
- Department of Applied PhysicsPolytechnic University of ValenciaValenciaSpain
| | - Gereon Poschmann
- Molecular Proteomics Laboratory, BMFZHeinrich-Heine-Universität DüsseldorfDüsseldorfGermany
| | - Kai Stühler
- Molecular Proteomics Laboratory, BMFZHeinrich-Heine-Universität DüsseldorfDüsseldorfGermany
| | - Maria Sinetova
- Timiryazev Institute of Plant PhysiologyRussian Academy of SciencesMoscowRussian Federation
| | - Anna Zorina
- Timiryazev Institute of Plant PhysiologyRussian Academy of SciencesMoscowRussian Federation
| | - Ralf Steuer
- Institut für Biologie, Fachinstitut für Theoretische BiologieHumboldt-Universität zu BerlinBerlinGermany
| | - Jan Červený
- Laboratory of Adaptive BiotechnologiesGlobal Change Research Institute CASBrnoCzech Republic
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26
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Cordara A, Manfredi M, van Alphen P, Marengo E, Pirone R, Saracco G, Branco Dos Santos F, Hellingwerf KJ, Pagliano C. Response of the thylakoid proteome of Synechocystis sp. PCC 6803 to photohinibitory intensities of orange-red light. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:524-534. [PMID: 30316162 DOI: 10.1016/j.plaphy.2018.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/01/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
Photoautotrophic growth of Synechocystis sp. PCC 6803 in a flat-panel photobioreactor, run in turbidostat mode under increasing intensities of orange-red light (636 nm), showed a maximal growth rate (0.12 h-1) at 300 μmolphotons m-2 s-1, whereas first signs of photoinhibition were detected above 800 μmolphotons m-2 s-1. To investigate the dynamic modulation of the thylakoid proteome in response to photoinhibitory light intensities, quantitative proteomics analyses by SWATH mass spectrometry were performed by comparing thylakoid membranes extracted from Synechocystis grown under low-intensity illumination (i.e. 50 μmolphotons m-2 s-1) with samples isolated from cells subjected to photoinhibitory light regimes (800, 950 and 1460 μmolphotons m-2 s-1). We identified and quantified 126 proteins with altered abundance in all three photoinhibitory illumination regimes. These data reveal the strategies by which Synechocystis responds to photoinibitory growth irradiances of orange-red light. The accumulation of core proteins of Photosystem II and reduction of oxygen-evolving-complex subunits in photoinhibited cells revealed a different turnover and repair rates of the integral and extrinsic Photosystem II subunits with variation of light intensity. Furthermore, Synechocystis displayed a differentiated response to photoinhibitory regimes also regarding Photosystem I: the amount of PsaD, PsaE, PsaJ and PsaM subunits decreased, while there was an increased abundance of the PsaA, PsaB, Psak2 and PsaL proteins. Photoinhibition with 636 nm light also elicited an increased capacity for cyclic electron transport, a lowering of the amount of phycobilisomes and an increase of the orange carotenoid protein content, all presumably as a photoprotective mechanism against the generation of reactive oxygen species.
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Affiliation(s)
- Alessandro Cordara
- Applied Science and Technology Department-BioSolar Lab, Politecnico di Torino, Environment Park, Via Livorno 60, 10144, Torino, Italy; Centre for Sustainable Future Technologies, Istituto Italiano di Tecnologia, Environment Park, Via Livorno 60, 10144, Torino, Italy
| | - Marcello Manfredi
- ISALIT-Department of Science and Technological Innovation, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy; Department of Science and Technological Innovation, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy
| | - Pascal van Alphen
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1090, GE, Amsterdam, Netherlands
| | - Emilio Marengo
- ISALIT-Department of Science and Technological Innovation, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy; Department of Science and Technological Innovation, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy
| | - Raffaele Pirone
- Applied Science and Technology Department, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy
| | - Guido Saracco
- Applied Science and Technology Department, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy
| | - Filipe Branco Dos Santos
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1090, GE, Amsterdam, Netherlands
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1090, GE, Amsterdam, Netherlands
| | - Cristina Pagliano
- Applied Science and Technology Department-BioSolar Lab, Politecnico di Torino, Environment Park, Via Livorno 60, 10144, Torino, Italy.
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