1
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Santin A, Collura F, Singh G, Morlino MS, Bizzotto E, Bellan A, Gupte AP, Favaro L, Campanaro S, Treu L, Morosinotto T. Deciphering the genetic landscape of enhanced poly-3-hydroxybutyrate production in Synechocystis sp. B12. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:101. [PMID: 39014484 PMCID: PMC11253406 DOI: 10.1186/s13068-024-02548-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
BACKGROUND Microbial biopolymers such as poly-3-hydroxybutyrate (PHB) are emerging as promising alternatives for sustainable production of biodegradable bioplastics. Their promise is heightened by the potential utilisation of photosynthetic organisms, thus exploiting sunlight and carbon dioxide as source of energy and carbon, respectively. The cyanobacterium Synechocystis sp. B12 is an attractive candidate for its superior ability to accumulate high amounts of PHB as well as for its high-light tolerance, which makes it extremely suitable for large-scale cultivation. Beyond its practical applications, B12 serves as an intriguing model for unravelling the molecular mechanisms behind PHB accumulation. RESULTS Through a multifaceted approach, integrating physiological, genomic and transcriptomic analyses, this work identified genes involved in the upregulation of chlorophyll biosynthesis and phycobilisome degradation as the possible candidates providing Synechocystis sp. B12 an advantage in growth under high-light conditions. Gene expression differences in pentose phosphate pathway and acetyl-CoA metabolism were instead recognised as mainly responsible for the increased Synechocystis sp. B12 PHB production during nitrogen starvation. In both response to strong illumination and PHB accumulation, Synechocystis sp. B12 showed a metabolic modulation similar but more pronounced than the reference strain, yielding in better performances. CONCLUSIONS Our findings shed light on the molecular mechanisms of PHB biosynthesis, providing valuable insights for optimising the use of Synechocystis in economically viable and sustainable PHB production. In addition, this work supplies crucial knowledge about the metabolic processes involved in production and accumulation of these molecules, which can be seminal for the application to other microorganisms as well.
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Grants
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 691712 Horizon 2020 Framework Programme
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- 327331 Ministero dell'Istruzione, dell'Università e della Ricerca
- Ministero dell’Istruzione, dell’Università e della Ricerca
- Università degli Studi di Padova
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Affiliation(s)
- Anna Santin
- Department of Biology, University of Padova, 35131, Padua, Italy.
| | - Flavio Collura
- Department of Biology, University of Padova, 35131, Padua, Italy
| | - Garima Singh
- Department of Biology, University of Padova, 35131, Padua, Italy
| | | | - Edoardo Bizzotto
- Department of Biology, University of Padova, 35131, Padua, Italy
| | | | - Ameya Pankaj Gupte
- Waste to Bioproducts Lab, Department of Agronomy Food Natural Resources Animals and Environment, University of Padova - Agripolis, 35020, Legnaro, PD, Italy
| | - Lorenzo Favaro
- Waste to Bioproducts Lab, Department of Agronomy Food Natural Resources Animals and Environment, University of Padova - Agripolis, 35020, Legnaro, PD, Italy
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | | | - Laura Treu
- Department of Biology, University of Padova, 35131, Padua, Italy
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2
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Dou B, Li Y, Wang F, Chen L, Zhang W. Chassis engineering for high light tolerance in microalgae and cyanobacteria. Crit Rev Biotechnol 2024:1-19. [PMID: 38987975 DOI: 10.1080/07388551.2024.2357368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/05/2024] [Indexed: 07/12/2024]
Abstract
Oxygenic photosynthesis in microalgae and cyanobacteria is considered an important chassis to accelerate energy transition and mitigate global warming. Currently, cultivation systems for photosynthetic microbes for large-scale applications encountered excessive light exposure stress. High light stress can: affect photosynthetic efficiency, reduce productivity, limit cell growth, and even cause cell death. Deciphering photoprotection mechanisms and constructing high-light tolerant chassis have been recent research focuses. In this review, we first briefly introduce the self-protection mechanisms of common microalgae and cyanobacteria in response to high light stress. These mechanisms mainly include: avoiding excess light absorption, dissipating excess excitation energy, quenching excessive high-energy electrons, ROS detoxification, and PSII repair. We focus on the species-specific differences in these mechanisms as well as recent advancements. Then, we review engineering strategies for creating high-light tolerant chassis, such as: reducing the size of the light-harvesting antenna, optimizing non-photochemical quenching, optimizing photosynthetic electron transport, and enhancing PSII repair. Finally, we propose a comprehensive exploration of mechanisms: underlying identified high light tolerant chassis, identification of new genes pertinent to high light tolerance using innovative methodologies, harnessing CRISPR systems and artificial intelligence for chassis engineering modification, and introducing plant photoprotection mechanisms as future research directions.
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Affiliation(s)
- Biyun Dou
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, P.R. China
| | - Yang Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, P.R. China
| | - Fangzhong Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, P.R. China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, P.R. China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, P.R. China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, P.R. China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, P.R. China
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3
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Moore V, Vermaas W. Functional consequences of modification of the photosystem I/photosystem II ratio in the cyanobacterium Synechocystis sp. PCC 6803. J Bacteriol 2024; 206:e0045423. [PMID: 38695523 PMCID: PMC11112997 DOI: 10.1128/jb.00454-23] [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: 12/27/2023] [Accepted: 03/16/2024] [Indexed: 05/24/2024] Open
Abstract
The stoichiometry of photosystem II (PSII) and photosystem I (PSI) varies between photoautotrophic organisms. The cyanobacterium Synechocystis sp. PCC 6803 maintains two- to fivefold more PSI than PSII reaction center complexes, and we sought to modify this stoichiometry by changing the promoter region of the psaAB operon. We thus generated mutants with varied psaAB expression, ranging from ~3% to almost 200% of the wild-type transcript level, but all showing a reduction in PSI levels, relative to wild type, suggesting a role of the psaAB promoter region in translational regulation. Mutants with 25%-70% of wild-type PSI levels were photoautotrophic, with whole-chain oxygen evolution rates on a per-cell basis comparable to that of wild type. In contrast, mutant strains with <10% of the wild-type level of PSI were obligate photoheterotrophs. Variable fluorescence yields of all mutants were much higher than those of wild type, indicating that the PSI content is localized differently than in wild type, with less transfer of PSII-absorbed energy to PSI. Strains with less PSI saturate at a higher light intensity, enhancing productivity at higher light intensities. This is similar to what is found in mutants with reduced antennae. With 3-(3,4-dichlorophenyl)-1,1-dimethylurea present, P700+ re-reduction kinetics in the mutants were slower than in wild type, consistent with the notion that there is less cyclic electron transport if less PSI is present. Overall, strains with a reduction in PSI content displayed surprisingly vigorous growth and linear electron transport. IMPORTANCE Consequences of reduction in photosystem I content were investigated in the cyanobacterium Synechocystis sp. PCC 6803 where photosystem I far exceeds the number of photosystem II complexes. Strains with less photosystem I displayed less cyclic electron transport, grew more slowly at lower light intensity and needed more light for saturation but were surprisingly normal in their whole-chain electron transport rates, implying that a significant fraction of photosystem I is dispensable for linear electron transport in cyanobacteria. These strains with reduced photosystem I levels may have biotechnological relevance as they grow well at higher light intensities.
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Affiliation(s)
- Vicki Moore
- School of Life Sciences and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona, USA
| | - Wim Vermaas
- School of Life Sciences and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, Arizona, USA
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4
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Bolay P, Dodge N, Janssen K, Jensen PE, Lindberg P. Tailoring regulatory components for metabolic engineering in cyanobacteria. PHYSIOLOGIA PLANTARUM 2024; 176:e14316. [PMID: 38686633 DOI: 10.1111/ppl.14316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
The looming climate crisis has prompted an ever-growing interest in cyanobacteria due to their potential as sustainable production platforms for the synthesis of energy carriers and value-added chemicals from CO2 and sunlight. Nonetheless, cyanobacteria are yet to compete with heterotrophic systems in terms of space-time yields and consequently production costs. One major drawback leading to the low production performance observed in cyanobacteria is the limited ability to utilize the full capacity of the photosynthetic apparatus and its associated systems, i.e. CO2 fixation and the directly connected metabolism. In this review, novel insights into various levels of metabolic regulation of cyanobacteria are discussed, including the potential of targeting these regulatory mechanisms to create a chassis with a phenotype favorable for photoautotrophic production. Compared to conventional metabolic engineering approaches, minor perturbations of regulatory mechanisms can have wide-ranging effects.
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Affiliation(s)
- Paul Bolay
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Uppsala, SE, Sweden
| | - Nadia Dodge
- Plant Based Foods and Biochemistry, Food Analytics and Biotechnology, Department of Food Science, University of Copenhagen, Denmark
| | - Kim Janssen
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Uppsala, SE, Sweden
| | - Poul Erik Jensen
- Plant Based Foods and Biochemistry, Food Analytics and Biotechnology, Department of Food Science, University of Copenhagen, Denmark
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Uppsala, SE, Sweden
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5
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Haavisto V, Landry Z, Pontrelli S. High-throughput profiling of metabolic responses to exogenous nutrients in Synechocystis sp. PCC 6803. mSystems 2024; 9:e0022724. [PMID: 38534128 PMCID: PMC11019784 DOI: 10.1128/msystems.00227-24] [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: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/28/2024] Open
Abstract
Cyanobacteria fix carbon dioxide and release carbon-containing compounds into the wider ecosystem, yet they are sensitive to small metabolites that may impact their growth and physiology. Several cyanobacteria can grow mixotrophically, but we currently lack a molecular understanding of how specific nutrients may alter the compounds they release, limiting our knowledge of how environmental factors might impact primary producers and the ecosystems they support. In this study, we develop a high-throughput phytoplankton culturing platform and identify how the model cyanobacterium Synechocystis sp. PCC 6803 responds to nutrient supplementation. We assess growth responses to 32 nutrients at two concentrations, identifying 15 that are utilized mixotrophically. Seven nutrient sources significantly enhance growth, while 19 elicit negative growth responses at one or both concentrations. High-throughput exometabolomics indicates that oxidative stress limits Synechocystis' growth but may be alleviated by antioxidant metabolites. Furthermore, glucose and valine induce strong changes in metabolite exudation in a possible effort to correct pathway imbalances or maintain intracellular elemental ratios. This study sheds light on the flexibility and limits of cyanobacterial physiology and metabolism, as well as how primary production and trophic food webs may be modulated by exogenous nutrients.IMPORTANCECyanobacteria capture and release carbon compounds to fuel microbial food webs, yet we lack a comprehensive understanding of how external nutrients modify their behavior and what they produce. We developed a high throughput culturing platform to evaluate how the model cyanobacterium Synechocystis sp. PCC 6803 responds to a broad panel of externally supplied nutrients. We found that growth may be enhanced by metabolites that protect against oxidative stress, and growth and exudate profiles are altered by metabolites that interfere with central carbon metabolism and elemental ratios. This work contributes a holistic perspective of the versatile response of Synechocystis to externally supplied nutrients, which may alter carbon flux into the wider ecosystem.
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Affiliation(s)
- Vilhelmiina Haavisto
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Zachary Landry
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zürich, Zürich, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
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6
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Miao R, Jahn M, Shabestary K, Peltier G, Hudson EP. CRISPR interference screens reveal growth-robustness tradeoffs in Synechocystis sp. PCC 6803 across growth conditions. THE PLANT CELL 2023; 35:3937-3956. [PMID: 37494719 PMCID: PMC10615215 DOI: 10.1093/plcell/koad208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/01/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023]
Abstract
Barcoded mutant libraries are a powerful tool for elucidating gene function in microbes, particularly when screened in multiple growth conditions. Here, we screened a pooled CRISPR interference library of the model cyanobacterium Synechocystis sp. PCC 6803 in 11 bioreactor-controlled conditions, spanning multiple light regimes and carbon sources. This gene repression library contained 21,705 individual mutants with high redundancy over all open reading frames and noncoding RNAs. Comparison of the derived gene fitness scores revealed multiple instances of gene repression being beneficial in 1 condition while generally detrimental in others, particularly for genes within light harvesting and conversion, such as antennae components at high light and PSII subunits during photoheterotrophy. Suboptimal regulation of such genes likely represents a tradeoff of reduced growth speed for enhanced robustness to perturbation. The extensive data set assigns condition-specific importance to many previously unannotated genes and suggests additional functions for central metabolic enzymes. Phosphoribulokinase, glyceraldehyde-3-phosphate dehydrogenase, and the small protein CP12 were critical for mixotrophy and photoheterotrophy, which implicates the ternary complex as important for redirecting metabolic flux in these conditions in addition to inactivation of the Calvin cycle in the dark. To predict the potency of sgRNA sequences, we applied machine learning on sgRNA sequences and gene repression data, which showed the importance of C enrichment and T depletion proximal to the PAM site. Fitness data for all genes in all conditions are compiled in an interactive web application.
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Affiliation(s)
- Rui Miao
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
| | - Michael Jahn
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
- Max Planck Unit for the Science of Pathogens, 10117 Berlin,Germany
| | - Kiyan Shabestary
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ,UK
| | - Gilles Peltier
- Aix Marseille Univ, CEA, CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13108 Saint Paul-Lez-Durance,France
| | - Elton P Hudson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, SE-17165,Sweden
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7
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Balakrishnan R, Cremer J. Conditionally unutilized proteins and their profound effects on growth and adaptation across microbial species. Curr Opin Microbiol 2023; 75:102366. [PMID: 37625262 DOI: 10.1016/j.mib.2023.102366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/12/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023]
Abstract
Protein synthesis is an important determinant of microbial growth and response that demands a high amount of metabolic and biosynthetic resources. Despite these costs, microbial species from different taxa and habitats massively synthesize proteins that are not utilized in the conditions they currently experience. Based on resource allocation models, recent studies have begun to reconcile the costs and benefits of these conditionally unutilized proteins (CUPs) in the context of varying environmental conditions. Such massive synthesis of CUPs is crucial to consider in different areas of modern microbiology, from the systematic investigation of cell physiology, via the prediction of evolution in laboratory and natural environments, to the rational design of strains in biotechnology applications.
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Affiliation(s)
- Rohan Balakrishnan
- Department of Physics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Jonas Cremer
- Department of Biology, Stanford University, 318 Campus Drive, Stanford, CA 93105, USA.
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8
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Sengupta A, Bandyopadhyay A, Schubert MG, Church GM, Pakrasi HB. Antenna Modification in a Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973 Leads to Improved Efficiency and Carbon-Neutral Productivity. Microbiol Spectr 2023; 11:e0050023. [PMID: 37318337 PMCID: PMC10433846 DOI: 10.1128/spectrum.00500-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023] Open
Abstract
Our planet is sustained by sunlight, the primary energy source made accessible to all life forms by photoautotrophs. Photoautotrophs are equipped with light-harvesting complexes (LHCs) that enable efficient capture of solar energy, particularly when light is limiting. However, under high light, LHCs can harvest photons in excess of the utilization capacity of cells, causing photodamage. This damaging effect is most evident when there is a disparity between the amount of light harvested and carbon available. Cells strive to circumvent this problem by dynamically adjusting the antenna structure in response to the changing light signals, a process known to be energetically expensive. Much emphasis has been laid on elucidating the relationship between antenna size and photosynthetic efficiency and identifying strategies to synthetically modify antennae for optimal light capture. Our study is an effort in this direction and investigates the possibility of modifying phycobilisomes, the LHCs present in cyanobacteria, the simplest of photoautotrophs. We systematically truncate the phycobilisomes of Synechococcus elongatus UTEX 2973, a widely studied, fast-growing model cyanobacterium and demonstrate that partial truncation of its antenna can lead to a growth advantage of up to 36% compared to the wild type and an increase in sucrose titer of up to 22%. In contrast, targeted deletion of the linker protein which connects the first phycocyanin rod to the core proved detrimental, indicating that the core alone is not enough, and it is essential to maintain a minimal rod-core structure for efficient light harvest and strain fitness. IMPORTANCE Light energy is essential for the existence of life on this planet, and only photosynthetic organisms, equipped with light-harvesting antenna protein complexes, can capture this energy, making it readily accessible to all other life forms. However, these light-harvesting antennae are not designed to function optimally under extreme high light, a condition which can cause photodamage and significantly reduce photosynthetic productivity. In this study, we attempt to assess the optimal antenna structure for a fast-growing, high-light tolerant photosynthetic microbe with the goal of improving its productivity. Our findings provide concrete evidence that although the antenna complex is essential, antenna modification is a viable strategy to maximize strain performance under controlled growth conditions. This understanding can also be translated into identifying avenues to improve light harvesting efficiency in higher photoautotrophs.
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Affiliation(s)
- Annesha Sengupta
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | | | - Max G. Schubert
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
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9
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Ge-Zhang S, Cai T, Song M. Life in biophotovoltaics systems. FRONTIERS IN PLANT SCIENCE 2023; 14:1151131. [PMID: 37615025 PMCID: PMC10444202 DOI: 10.3389/fpls.2023.1151131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/03/2023] [Indexed: 08/25/2023]
Abstract
As the most suitable potential clean energy power generation technology, biophotovoltaics (BPV) not only inherits the advantages of traditional photovoltaics, such as safety, reliability and no noise, but also solves the disadvantages of high pollution and high energy consumption in the manufacturing process, providing new functions of self-repair and natural degradation. The basic idea of BPV is to collect light energy and generate electric energy by using photosynthetic autotrophs or their parts, and the core is how these biological materials can quickly and low-loss transfer electrons to the anode through mediators after absorbing light energy and generating electrons. In this mini-review, we summarized the biological materials widely used in BPV at present, mainly cyanobacteria, green algae, biological combinations (using multiple microorganisms in the same BPV system) and isolated products (purified thylakoids, chloroplasts, photosystem I, photosystem II), introduced how researchers overcome the shortcomings of low photocurrent output of BPV, pointed out the limitations that affected the development of BPV' biological materials, and put forward reasonable assumptions accordingly.
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Affiliation(s)
| | - Taoyang Cai
- Aulin College, Northeast Forestry University, Harbin, China
| | - Mingbo Song
- College of Forestry, Northeast Forestry University, Harbin, China
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10
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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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11
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Schumann C, Fernández Méndez J, Berggren G, Lindblad P. Novel concepts and engineering strategies for heterologous expression of efficient hydrogenases in photosynthetic microorganisms. Front Microbiol 2023; 14:1179607. [PMID: 37502399 PMCID: PMC10369191 DOI: 10.3389/fmicb.2023.1179607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/09/2023] [Indexed: 07/29/2023] Open
Abstract
Hydrogen is considered one of the key enablers of the transition towards a sustainable and net-zero carbon economy. When produced from renewable sources, hydrogen can be used as a clean and carbon-free energy carrier, as well as improve the sustainability of a wide range of industrial processes. Photobiological hydrogen production is considered one of the most promising technologies, avoiding the need for renewable electricity and rare earth metal elements, the demands for which are greatly increasing due to the current simultaneous electrification and decarbonization goals. Photobiological hydrogen production employs photosynthetic microorganisms to harvest solar energy and split water into molecular oxygen and hydrogen gas, unlocking the long-pursued target of solar energy storage. However, photobiological hydrogen production has to-date been constrained by several limitations. This review aims to discuss the current state-of-the art regarding hydrogenase-driven photobiological hydrogen production. Emphasis is placed on engineering strategies for the expression of improved, non-native, hydrogenases or photosynthesis re-engineering, as well as their combination as one of the most promising pathways to develop viable large-scale hydrogen green cell factories. Herein we provide an overview of the current knowledge and technological gaps curbing the development of photobiological hydrogenase-driven hydrogen production, as well as summarizing the recent advances and future prospects regarding the expression of non-native hydrogenases in cyanobacteria and green algae with an emphasis on [FeFe] hydrogenases.
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Affiliation(s)
- Conrad Schumann
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Jorge Fernández Méndez
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Gustav Berggren
- Molecular Biomimetics, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Uppsala, Sweden
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12
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Baikie TK, Wey LT, Lawrence JM, Medipally H, Reisner E, Nowaczyk MM, Friend RH, Howe CJ, Schnedermann C, Rao A, Zhang JZ. Photosynthesis re-wired on the pico-second timescale. Nature 2023; 615:836-840. [PMID: 36949188 DOI: 10.1038/s41586-023-05763-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 01/26/2023] [Indexed: 03/24/2023]
Abstract
Photosystems II and I (PSII, PSI) are the reaction centre-containing complexes driving the light reactions of photosynthesis; PSII performs light-driven water oxidation and PSI further photo-energizes harvested electrons. The impressive efficiencies of the photosystems have motivated extensive biological, artificial and biohybrid approaches to 're-wire' photosynthesis for higher biomass-conversion efficiencies and new reaction pathways, such as H2 evolution or CO2 fixation1,2. Previous approaches focused on charge extraction at terminal electron acceptors of the photosystems3. Electron extraction at earlier steps, perhaps immediately from photoexcited reaction centres, would enable greater thermodynamic gains; however, this was believed impossible with reaction centres buried at least 4 nm within the photosystems4,5. Here, we demonstrate, using in vivo ultrafast transient absorption (TA) spectroscopy, extraction of electrons directly from photoexcited PSI and PSII at early points (several picoseconds post-photo-excitation) with live cyanobacterial cells or isolated photosystems, and exogenous electron mediators such as 2,6-dichloro-1,4-benzoquinone (DCBQ) and methyl viologen. We postulate that these mediators oxidize peripheral chlorophyll pigments participating in highly delocalized charge-transfer states after initial photo-excitation. Our results challenge previous models that the photoexcited reaction centres are insulated within the photosystem protein scaffold, opening new avenues to study and re-wire photosynthesis for biotechnologies and semi-artificial photosynthesis.
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Affiliation(s)
- Tomi K Baikie
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Laura T Wey
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Joshua M Lawrence
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Erwin Reisner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Marc M Nowaczyk
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- Department of Biochemistry, University of Rostock, Rostock, Germany
| | | | | | | | - Akshay Rao
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - Jenny Z Zhang
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
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13
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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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14
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Jackson PJ, Hitchcock A, Brindley AA, Dickman MJ, Hunter CN. Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2023; 155:219-245. [PMID: 36542271 PMCID: PMC9958174 DOI: 10.1007/s11120-022-00990-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Quantifying cellular components is a basic and important step for understanding how a cell works, how it responds to environmental changes, and for re-engineering cells to produce valuable metabolites and increased biomass. We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. Components of biosynthetic pathways, such as those for chlorophyll or for photosystem II assembly, range between 1000 and 10,000 copies per cell, but can be tenfold higher for CO2 fixation enzymes. The most abundant subunits are those for photosystem I, with around 100,000 copies per cell, approximately 2 to fivefold higher than for photosystem II and ATP synthase, and 5-20 fold more than for the cytochrome b6f complex. Disparities between numbers of pathway enzymes, between components of electron transfer chains, and between subunits within complexes indicate possible control points for biosynthetic processes, bioenergetic reactions and for the assembly of multisubunit complexes.
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Affiliation(s)
- Philip J Jackson
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK.
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Amanda A Brindley
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - C Neil Hunter
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
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15
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Liu H. AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome. J Mol Biol 2022; 434:167831. [PMID: 36116541 DOI: 10.1016/j.jmb.2022.167831] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022]
Abstract
Intrinsically disordered proteins/regions (IDPRs) are a very large and functionally important class of proteins that participate in weak multivalent interactions in protein complexes. They are recalcitrant for interrogations using X-ray crystallography and cryo-EM. The IDPRs observed at the interface of the photosynthetic pigment protein complexes (PPCs) remain much less clear, e.g., the major cyanobacterial light-harvesting complex (PBS) contains an unstructured PB-loop insertion in the phycocyanobilin domain (PB domain) of ApcE (the largest polypeptide in PBS). Here, a joint platform is built to probe such structural domains. This platform is characterized by two-round progressive justifications of in silico models by using the structural mass spectrometry data. First, the AlphaFold-generated 3D structure of the PB domain (containing PB-loop) was justified in the context of PBS. Second, docking the AlphaFold-generated ApcG (a ligand) into the first-step justified structure (a receptor). The final ligand-receptor complex was then subjected to a second-round justification, again, by using unequivocal isotopically-encoded cross-links identified in LC-MS/MS. This work reveals a full-length PB-loop structure modelled in the PBS basal cylinder, free from any spatial conflicts against the other subunits in PBS. The structure of PB domain highlights the close associations of the intrinsically disordered PB-loop with its binding partners in PBS, including ApcG, another IDPR. The PB-loop region involved in the binding of photosystem II (PSII) is also discussed in the context of excitation energy transfer regulation. This work calls attention to the highly disordered, yet interrogatable interface between the light-harvesting antenna complexes and the reaction centers.
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Affiliation(s)
- Haijun Liu
- Department of Biology Washington University in St. Louis, St. Louis, MO 63130, USA.
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16
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Mills LA, Moreno-Cabezuelo JÁ, Włodarczyk A, Victoria AJ, Mejías R, Nenninger A, Moxon S, Bombelli P, Selão TT, McCormick AJ, Lea-Smith DJ. Development of a Biotechnology Platform for the Fast-Growing Cyanobacterium Synechococcus sp. PCC 11901. Biomolecules 2022; 12:biom12070872. [PMID: 35883428 PMCID: PMC9313322 DOI: 10.3390/biom12070872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 02/07/2023] Open
Abstract
Synechococcus sp. PCC 11901 reportedly demonstrates the highest, most sustained growth of any known cyanobacterium under optimized conditions. Due to its recent discovery, our knowledge of its biology, including the factors underlying sustained, fast growth, is limited. Furthermore, tools specific for genetic manipulation of PCC 11901 are not established. Here, we demonstrate that PCC 11901 shows faster growth than other model cyanobacteria, including the fast-growing species Synechococcuselongatus UTEX 2973, under optimal growth conditions for UTEX 2973. Comparative genomics between PCC 11901 and Synechocystis sp. PCC 6803 reveal conservation of most metabolic pathways but PCC 11901 has a simplified electron transport chain and reduced light harvesting complex. This may underlie its superior light use, reduced photoinhibition, and higher photosynthetic and respiratory rates. To aid biotechnology applications, we developed a vitamin B12 auxotrophic mutant but were unable to generate unmarked knockouts using two negative selectable markers, suggesting that recombinase- or CRISPR-based approaches may be required for repeated genetic manipulation. Overall, this study establishes PCC 11901 as one of the most promising species currently available for cyanobacterial biotechnology and provides a useful set of bioinformatics tools and strains for advancing this field, in addition to insights into the factors underlying its fast growth phenotype.
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Affiliation(s)
- Lauren A. Mills
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - José Ángel Moreno-Cabezuelo
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Artur Włodarczyk
- Bondi Bio Pty Ltd., c/o Climate Change Cluster, University of Technology Sydney, 745 Harris Street, Ultimo, NSW 2007, Australia;
| | - Angelo J. Victoria
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - Rebeca Mejías
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Anja Nenninger
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Paolo Bombelli
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK;
| | - Tiago T. Selão
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - David J. Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
- Correspondence:
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17
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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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18
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Hervey JRD, Bombelli P, Lea-Smith DJ, Hulme AK, Hulme NR, Rullay AK, Keighley R, Howe CJ. A dual compartment cuvette system for correcting scattering in whole-cell absorbance spectroscopy of photosynthetic microorganisms. PHOTOSYNTHESIS RESEARCH 2022; 151:61-69. [PMID: 34390453 PMCID: PMC8795073 DOI: 10.1007/s11120-021-00866-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Absorption spectroscopy is widely used to determine absorption and transmission spectra of chromophores in solution, in addition to suspensions of particles, including micro-organisms. Light scattering, caused by photons deflected from part or all of the cells or other particles in suspension, results in distortions to the absorption spectra, lost information and poor resolution. A spectrophotometer with an integrating sphere may be used to alleviate this problem. However, these instruments are not universally available in biology laboratories, for reasons such as cost. Here, we describe a novel, rapid, and inexpensive technique that minimises the effect of light scattering when performing whole-cell spectroscopy. This method involves using a custom made dual compartment cuvette containing titanium dioxide in one chamber as a scattering agent. Measurements were conducted of a range of different photosynthetic micro-organisms of varying cell size and morphology, including cyanobacteria, eukaryotic microalgae and a purple non-sulphur bacterium. A concentration of 1 mg ml-1 titanium dioxide, using a spectrophotometer with a slit width of 5 nm, produced spectra for cyanobacteria and microalgae similar (1-4% difference) to those obtained using an integrating sphere. The spectrum > 520 nm was similar to that with an integrating sphere with the purple non-sulphur bacterium. This system produced superior results to those obtained using a recently reported method, the application of the diffusing agent, Scotch™ Magic tape, to the side of the cuvette. The protocol can be completed in an equivalent period of time to standard whole-cell absorbance spectroscopy techniques, and is, in principle, suitable for any dual-beam spectrophotometer.
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Affiliation(s)
- John R D Hervey
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Paolo Bombelli
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - David J Lea-Smith
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Alan K Hulme
- Starna Scientific Ltd, Hainault Business Park, 52/54 Fowler Rd, Ilford, IG6 3UT, UK
| | - Nathan R Hulme
- Starna Scientific Ltd, Hainault Business Park, 52/54 Fowler Rd, Ilford, IG6 3UT, UK
| | | | - Robert Keighley
- Shimadzu UK Limited, Unit 1, Mill Crt, Featherstone, MK12 5RD, UK
| | - Christopher J Howe
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, CB2 1QW, UK.
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19
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Carrieri D, Jurista T, Yazvenko N, Schafer Medina A, Strickland D, Roberts JM. Overexpression of NblA decreases phycobilisome content and enhances photosynthetic growth of the cyanobacterium Synechococcus elongatus PCC 7942. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Puzorjov A, Dunn KE, McCormick AJ. Production of thermostable phycocyanin in a mesophilic cyanobacterium. Metab Eng Commun 2021; 13:e00175. [PMID: 34168957 PMCID: PMC8209669 DOI: 10.1016/j.mec.2021.e00175] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/12/2021] [Accepted: 05/28/2021] [Indexed: 11/01/2022] Open
Abstract
Phycocyanin (PC) is a soluble phycobiliprotein found within the light-harvesting phycobilisome complex of cyanobacteria and red algae, and is considered a high-value product due to its brilliant blue colour and fluorescent properties. However, commercially available PC has a relatively low temperature stability. Thermophilic species produce more thermostable variants of PC, but are challenging and energetically expensive to cultivate. Here, we show that the PC operon from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (cpcBACD) is functional in the mesophile Synechocystis sp. PCC 6803. Expression of cpcBACD in an 'Olive' mutant strain of Synechocystis lacking endogenous PC resulted in high yields of thermostable PC (112 ± 1 mg g-1 DW) comparable to that of endogenous PC in wild-type cells. Heterologous PC also improved the growth of the Olive mutant, which was further supported by evidence of a functional interaction with the endogenous allophycocyanin core of the phycobilisome complex. The thermostability properties of the heterologous PC were comparable to those of PC from T. elongatus, and could be purified from the Olive mutant using a low-cost heat treatment method. Finally, we developed a scalable model to calculate the energetic benefits of producing PC from T. elongatus in Synechocystis cultures. Our model showed that the higher yields and lower cultivation temperatures of Synechocystis resulted in a 3.5-fold increase in energy efficiency compared to T. elongatus, indicating that producing thermostable PC in non-native hosts is a cost-effective strategy for scaling to commercial production.
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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
| | - Katherine E. Dunn
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, EH9 3DW, 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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21
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Scorza LC, Simon U, Wear M, Zouliatis A, Dimartino S, McCormick AJ. Evaluation of novel 3D-printed monolithic adsorbers against conventional chromatography columns for the purification of c-phycocyanin from Spirulina. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Xie Y, Chen L, Sun T, Zhang W. Deciphering and engineering high-light tolerant cyanobacteria for efficient photosynthetic cell factories. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Karemore A, Yuan Y, Porubsky W, Chance R. Biomass and pigment production for
Arthrospira platensis
via semi‐continuous cultivation in photobioreactors: Temperature effects. Biotechnol Bioeng 2020; 117:3081-3093. [DOI: 10.1002/bit.27480] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/07/2020] [Accepted: 06/26/2020] [Indexed: 01/12/2023]
Affiliation(s)
- Ankush Karemore
- School of Industrial and Systems Engineering Georgia Institute of Technology Atlanta Georgia
- School of Chemical and Biomolecular Engineering Georgia Institute of Technology Atlanta Georgia
| | | | | | - Ronald Chance
- School of Chemical and Biomolecular Engineering Georgia Institute of Technology Atlanta Georgia
- Algenol Biotech LLC Fort Myers Florida
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24
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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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25
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Luimstra VM, Schuurmans JM, de Carvalho CFM, Matthijs HCP, Hellingwerf KJ, Huisman J. Exploring the low photosynthetic efficiency of cyanobacteria in blue light using a mutant lacking phycobilisomes. PHOTOSYNTHESIS RESEARCH 2019; 141:291-301. [PMID: 30820745 PMCID: PMC6718569 DOI: 10.1007/s11120-019-00630-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/19/2019] [Indexed: 05/28/2023]
Abstract
The ubiquitous chlorophyll a (Chl a) pigment absorbs both blue and red light. Yet, in contrast to green algae and higher plants, most cyanobacteria have much lower photosynthetic rates in blue than in red light. A plausible but not yet well-supported hypothesis is that blue light results in limited energy transfer to photosystem II (PSII), because cyanobacteria invest most Chl a in photosystem I (PSI), whereas their phycobilisomes (PBS) are mostly associated with PSII but do not absorb blue photons. In this paper, we compare the photosynthetic performance in blue and orange-red light of wildtype Synechocystis sp. PCC 6803 and a PBS-deficient mutant. Our results show that the wildtype had much lower biomass, Chl a content, PSI:PSII ratio and O2 production rate per PSII in blue light than in orange-red light, whereas the PBS-deficient mutant had a low biomass, Chl a content, PSI:PSII ratio, and O2 production rate per PSII in both light colors. More specifically, the wildtype displayed a similar low photosynthetic efficiency in blue light as the PBS-deficient mutant in both light colors. Our results demonstrate that the absorption of light energy by PBS and subsequent transfer to PSII are crucial for efficient photosynthesis in cyanobacteria, which may explain both the low photosynthetic efficiency of PBS-containing cyanobacteria and the evolutionary success of chlorophyll-based light-harvesting antennae in environments dominated by blue light.
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Affiliation(s)
- Veerle M Luimstra
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, The Netherlands
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, The Netherlands
| | - J Merijn Schuurmans
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, The Netherlands
| | - Carolina F M de Carvalho
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, The Netherlands
| | - Hans C P Matthijs
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Swammerdam Institute for Life Sciences, University of Amsterdam, PO Box 94248, 1090 GE, Amsterdam, The Netherlands
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, The Netherlands.
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26
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CyanoFactory, a European consortium to develop technologies needed to advance cyanobacteria as chassis for production of chemicals and fuels. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101510] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Vasudevan R, Gale GAR, Schiavon AA, Puzorjov A, Malin J, Gillespie MD, Vavitsas K, Zulkower V, Wang B, Howe CJ, Lea-Smith DJ, McCormick AJ. CyanoGate: A Modular Cloning Suite for Engineering Cyanobacteria Based on the Plant MoClo Syntax. PLANT PHYSIOLOGY 2019; 180:39-55. [PMID: 30819783 PMCID: PMC6501082 DOI: 10.1104/pp.18.01401] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/16/2019] [Indexed: 05/10/2023]
Abstract
Recent advances in synthetic biology research have been underpinned by an exponential increase in available genomic information and a proliferation of advanced DNA assembly tools. The adoption of plasmid vector assembly standards and parts libraries has greatly enhanced the reproducibility of research and the exchange of parts between different labs and biological systems. However, a standardized modular cloning (MoClo) system is not yet available for cyanobacteria, which lag behind other prokaryotes in synthetic biology despite their huge potential regarding biotechnological applications. By building on the assembly library and syntax of the Plant Golden Gate MoClo kit, we have developed a versatile system called CyanoGate that unites cyanobacteria with plant and algal systems. Here, we describe the generation of a suite of parts and acceptor vectors for making (1) marked/unmarked knock-outs or integrations using an integrative acceptor vector, and (2) transient multigene expression and repression systems using known and previously undescribed replicative vectors. We tested and compared the CyanoGate system in the established model cyanobacterium Synechocystis sp. PCC 6803 and the more recently described fast-growing strain Synechococcus elongatus UTEX 2973. The UTEX 2973 fast-growth phenotype was only evident under specific growth conditions; however, UTEX 2973 accumulated high levels of proteins with strong native or synthetic promoters. The system is publicly available and can be readily expanded to accommodate other standardized MoClo parts to accelerate the development of reliable synthetic biology tools for the cyanobacterial community.
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Affiliation(s)
- Ravendran Vasudevan
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Grant A R Gale
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Alejandra A Schiavon
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Anton Puzorjov
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - John Malin
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Michael D Gillespie
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Konstantinos Vavitsas
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
- CSIRO, Synthetic Biology Future Science Platform, Brisbane, Queensland 4001, Australia
| | - Valentin Zulkower
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Christopher J Howe
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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Zlenko DV, Elanskaya IV, Lukashev EP, Bolychevtseva YV, Suzina NE, Pojidaeva ES, Kononova IA, Loktyushkin AV, Stadnichuk IN. Role of the PB-loop in ApcE and phycobilisome core function in cyanobacterium Synechocystis sp. PCC 6803. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:155-166. [DOI: 10.1016/j.bbabio.2018.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/04/2018] [Accepted: 10/29/2018] [Indexed: 11/30/2022]
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Growth of Cyanobacteria Is Constrained by the Abundance of Light and Carbon Assimilation Proteins. Cell Rep 2018; 25:478-486.e8. [DOI: 10.1016/j.celrep.2018.09.040] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/13/2018] [Accepted: 09/11/2018] [Indexed: 11/20/2022] Open
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Zavřel T, Chmelík D, Sinetova MA, Červený J. Spectrophotometric Determination of Phycobiliprotein Content in Cyanobacterium Synechocystis. J Vis Exp 2018. [PMID: 30272659 DOI: 10.3791/58076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
This is a simple protocol for the quantitative determination of phycobiliprotein content in the model cyanobacterium Synechocystis. Phycobiliproteins are the most important components of phycobilisomes, the major light-harvesting antennae in cyanobacteria and several algae taxa. The phycobilisomes of Synechocystis contain two phycobiliproteins: phycocyanin and allophycocyanin. This protocol describes a simple, efficient, and reliable method for the quantitative determination of both phycocyanin and allophycocyanin in this model cyanobacterium. We compared several methods of phycobiliprotein extraction and spectrophotometric quantification. The extraction procedure as described in this protocol was also successfully applied to other cyanobacteria strains such as Cyanothece sp., Synechococcuselongatus, Spirulina sp., Arthrospira sp., and Nostoc sp., as well as to red algae Porphyridium cruentum. However, the extinction coefficients of specific phycobiliproteins from various taxa can differ and it is, therefore, recommended to validate the spectrophotometric quantification method for every single strain individually. The protocol requires little time and can be performed in any standard life science laboratory since it requires only standard equipment.
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Affiliation(s)
- Tomáš Zavřel
- Department of Adaptive Biotechnologies, Global Change Research Institute, Czech Academy of Sciences;
| | - Dominik Chmelík
- Department of Adaptive Biotechnologies, Global Change Research Institute, Czech Academy of Sciences; Department of Plant Physiology, Faculty of Science, Masaryk University
| | - Maria A Sinetova
- Laboratory of Intracellular Regulation, Institute of Plant Physiology, Russian Academy of Sciences
| | - Jan Červený
- Department of Adaptive Biotechnologies, Global Change Research Institute, Czech Academy of Sciences
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Kirst H, Shen Y, Vamvaka E, Betterle N, Xu D, Warek U, Strickland JA, Melis A. Downregulation of the CpSRP43 gene expression confers a truncated light-harvesting antenna (TLA) and enhances biomass and leaf-to-stem ratio in Nicotiana tabacum canopies. PLANTA 2018; 248:139-154. [PMID: 29623472 DOI: 10.1007/s00425-018-2889-7] [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: 01/08/2018] [Accepted: 03/29/2018] [Indexed: 05/13/2023]
Abstract
MAIN CONCLUSION Downregulation in the expression of the signal recognition particle 43 (SRP43) gene in tobacco conferred a truncated photosynthetic light-harvesting antenna (TLA property), and resulted in plants with a greater leaf-to-stem ratio, improved photosynthetic productivity and canopy biomass accumulation under high-density cultivation conditions. Evolution of sizable arrays of light-harvesting antennae in all photosynthetic systems confers a survival advantage for the organism in the wild, where sunlight is often the growth-limiting factor. In crop monocultures, however, this property is strongly counterproductive, when growth takes place under direct and excess sunlight. The large arrays of light-harvesting antennae in crop plants cause the surface of the canopies to over-absorb solar irradiance, far in excess of what is needed to saturate photosynthesis and forcing them to engage in wasteful dissipation of the excess energy. Evidence in this work showed that downregulation by RNA-interference approaches of the Nicotiana tabacum signal recognition particle 43 (SRP43), a nuclear gene encoding a chloroplast-localized component of the photosynthetic light-harvesting assembly pathway, caused a decrease in the light-harvesting antenna size of the photosystems, a corresponding increase in the photosynthetic productivity of chlorophyll in the leaves, and improved tobacco plant canopy biomass accumulation under high-density cultivation conditions. Importantly, the resulting TLA transgenic plants had a substantially greater leaf-to-stem biomass ratio, compared to those of the wild type, grown under identical agronomic conditions. The results are discussed in terms of the potential benefit that could accrue to agriculture upon application of the TLA-technology to crop plants, entailing higher density planting with plants having a greater biomass and leaf-to-stem ratio, translating into greater crop yields per plant with canopies in a novel agronomic configuration.
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Affiliation(s)
- Henning Kirst
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Yanxin Shen
- Biotechnology Division, Altria Client Services, Richmond, VA, 23219, USA
| | - Evangelia Vamvaka
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Nico Betterle
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Dongmei Xu
- Biotechnology Division, Altria Client Services, Richmond, VA, 23219, USA
| | - Ujwala Warek
- Biotechnology Division, Altria Client Services, Richmond, VA, 23219, USA
| | - James A Strickland
- Biotechnology Division, Altria Client Services, Richmond, VA, 23219, USA
| | - Anastasios Melis
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA.
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Magdaong NCM, Blankenship RE. Photoprotective, excited-state quenching mechanisms in diverse photosynthetic organisms. J Biol Chem 2018; 293:5018-5025. [PMID: 29298897 DOI: 10.1074/jbc.tm117.000233] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Light-harvesting complexes (LHCs) serve a dual role in photosynthesis, depending on the prevailing light conditions. In low light, they ensure photosynthetic efficiency by maximizing the light absorption cross-section and subsequent energy storage. Under excess light conditions, LHCs perform photoprotective quenching functions to prevent harmful chemical species such as triplet chlorophyll and singlet oxygen from forming and damaging the photosynthetic apparatus. In this Minireview, various photoprotective quenching mechanisms that have been identified in different photosynthetic organisms are surveyed and summarized, and implications for improving photosynthetic productivity are briefly discussed.
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Affiliation(s)
- Nikki Cecil M Magdaong
- From the Departments of Biology and Chemistry and.,the Photosynthetic Antenna Research Center, Washington University in Saint Louis, St. Louis, Missouri 63130
| | - Robert E Blankenship
- From the Departments of Biology and Chemistry and .,the Photosynthetic Antenna Research Center, Washington University in Saint Louis, St. Louis, Missouri 63130
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Tan X, Hou S, Song K, Georg J, Klähn S, Lu X, Hess WR. The primary transcriptome of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:218. [PMID: 30127850 PMCID: PMC6091082 DOI: 10.1186/s13068-018-1215-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/25/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Cyanobacteria have shown promising potential for the production of various biofuels and chemical feedstocks. Synechococcus elongatus UTEX 2973 is a fast-growing strain with pronounced tolerance to high temperatures and illumination. Hence, this strain appears to be ideal for the development of photosynthetic biotechnology. However, molecular insights on how this strain can rapidly accumulate biomass and carbohydrates under high-light and high-temperature conditions are lacking. RESULTS Differential RNA-Sequencing (dRNA-Seq) enabled the genome-wide identification of 4808 transcription start sites (TSSs) in S. elongatus UTEX 2973 using a background reduction algorithm. High light promoted the transcription of genes associated with central metabolic pathways, whereas the highly induced small RNA (sRNA) PsrR1 likely contributed to the repression of phycobilisome genes and the accelerated glycogen accumulation rates measured under this condition. Darkness caused transcriptome remodeling with a decline in the expression of genes for carbon fixation and other major metabolic pathways and an increase in the expression of genes for glycogen catabolism and Calvin cycle inhibitor CP12. Two of the identified TSSs drive the transcription of highly abundant sRNAs in darkness. One of them is widely conserved throughout the cyanobacterial phylum. Its gene is fused to a protein-coding gene in some species, illustrating the evolutionary origin of sRNAs from an mRNA 3'-end. CONCLUSIONS Our comprehensive set of genome-wide mapped TSSs, sRNAs and promoter activities will be valuable for projects requiring precise information about the control of transcription aimed at metabolic engineering and the elucidation of stress acclimation mechanisms in this promising strain.
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Affiliation(s)
- Xiaoming Tan
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Present Address: College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062 China
| | - Shengwei Hou
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Kuo Song
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Jens Georg
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Stephan Klähn
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No. 1 Wenhai Road, Qingdao, 266237 China
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Freiburg Institute for Advanced Studies, University of Freiburg, Albertstraße 19, 79104 Freiburg, Germany
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Perin G, Simionato D, Bellan A, Carone M, Occhipinti A, Maffei ME, Morosinotto T. Cultivation in industrially relevant conditions has a strong influence on biological properties and performances of Nannochloropsis gaditana genetically modified strains. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Sharon-Gojman R, Leu S, Zarka A. Antenna size reduction and altered division cycles in self-cloned, marker-free genetically modified strains of Haematococcus pluvialis. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.09.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Esteves-Ferreira AA, Inaba M, Obata T, Fort A, Fleming GTA, Araújo WL, Fernie AR, Sulpice R. A Novel Mechanism, Linked to Cell Density, Largely Controls Cell Division in Synechocystis. PLANT PHYSIOLOGY 2017; 174:2166-2182. [PMID: 28646084 PMCID: PMC5543973 DOI: 10.1104/pp.17.00729] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 06/20/2017] [Indexed: 05/28/2023]
Abstract
Many studies have investigated the various genetic and environmental factors regulating cyanobacterial growth. Here, we investigated the growth and metabolism of Synechocystis sp. PCC 6803 under different nitrogen sources, light intensities, and CO2 concentrations. Cells grown on urea showed the highest growth rates. However, for all conditions tested, the daily growth rates in batch cultures decreased steadily over time, and stationary phase was obtained with similar cell densities. Unexpectedly, metabolic and physiological analyses showed that growth rates during log phase were not controlled primarily by the availability of photoassimilates. Further physiological investigations indicated that nutrient limitation, quorum sensing, light quality, and light intensity (self-shading) were not the main factors responsible for the decrease in the growth rate and the onset of the stationary phase. Moreover, cell division rates in fed-batch cultures were positively correlated with the dilution rates. Hence, not only light, CO2, and nutrients can affect growth but also a cell-cell interaction. Accordingly, we propose that cell-cell interaction may be a factor responsible for the gradual decrease of growth rates in batch cultures during log phase, culminating with the onset of stationary phase.
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Affiliation(s)
- Alberto A Esteves-Ferreira
- National University of Ireland-Galway, Plant Systems Biology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, Galway, Ireland
- CAPES Foundation, Ministry of Education of Brazil, Brasilia DF 70040 020, Brazil
| | - Masami Inaba
- National University of Ireland-Galway, Plant Systems Biology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, Galway, Ireland
| | - Toshihiro Obata
- Central Metabolism Laboratory, Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, 14476 Potsdam-Golm, Germany
| | - Antoine Fort
- National University of Ireland-Galway, Genetics and Biotechnology Research Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, Galway, Ireland
| | - Gerard T A Fleming
- National University of Ireland-Galway, Microbiology, School of Natural Sciences, Galway, Ireland
| | - Wagner L Araújo
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Vicosa, Minas Gerais, Brazil
| | - Alisdair R Fernie
- Central Metabolism Laboratory, Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, 14476 Potsdam-Golm, Germany
| | - Ronan Sulpice
- National University of Ireland-Galway, Plant Systems Biology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, Galway, Ireland
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Sarnaik A, Pandit R, Lali A. Growth engineering ofSynechococcus elongatusPCC 7942 for mixotrophy under natural light conditions for improved feedstock production. Biotechnol Prog 2017; 33:1182-1192. [DOI: 10.1002/btpr.2490] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/22/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Aditya Sarnaik
- DBT-ICT Centre for Energy Biosciences, Inst. of Chemical Technology; Mumbai Maharashtra 400019 India
| | - Reena Pandit
- DBT-ICT Centre for Energy Biosciences, Inst. of Chemical Technology; Mumbai Maharashtra 400019 India
| | - Arvind Lali
- DBT-ICT Centre for Energy Biosciences, Inst. of Chemical Technology; Mumbai Maharashtra 400019 India
- Department of Chemical Engineering; Inst. of Chemical Technology; Mumbai Maharashtra 400019 India
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Fuente D, Keller J, Conejero JA, Rögner M, Rexroth S, Urchueguía JF. Light distribution and spectral composition within cultures of micro-algae: Quantitative modelling of the light field in photobioreactors. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.01.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Liberton M, Chrisler WB, Nicora CD, Moore RJ, Smith RD, Koppenaal DW, Pakrasi HB, Jacobs JM. Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803. PLoS One 2017; 12:e0173251. [PMID: 28253354 PMCID: PMC5333879 DOI: 10.1371/journal.pone.0173251] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/17/2017] [Indexed: 11/18/2022] Open
Abstract
In cyanobacteria such as Synechocystis sp. PCC 6803, large antenna complexes called phycobilisomes (PBS) harvest light and transfer the energy to the photosynthetic reaction centers. Modification of the light harvesting machinery in cyanobacteria has widespread consequences, causing changes in cell morphology and physiology. In the current study, we investigated the effects of PBS truncation on the proteomes of three Synechocystis 6803 PBS antenna mutants. These range from the progressive truncation of phycocyanin rods in the CB and CK strains, to full removal of PBS in the PAL mutant. Comparative quantitative protein results revealed surprising changes in protein abundances in the mutant strains. Our results showed that PBS truncation in Synechocystis 6803 broadly impacted core cellular mechanisms beyond light harvesting and photosynthesis. Specifically, we observed dramatic alterations in membrane transport mechanisms, where the most severe PBS truncation in the PAL strain appeared to suppress the cellular utilization and regulation of bicarbonate and iron. These changes point to the role of PBS as a component critical to cell function, and demonstrate the continuing need to assess systems-wide protein based abundances to understand potential indirect phenotypic effects.
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Affiliation(s)
- Michelle Liberton
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - William B. Chrisler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Carrie D. Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Ronald J. Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - David W. Koppenaal
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Himadri B. Pakrasi
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Jon M. Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail:
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40
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Du W, Jongbloets JA, Pineda Hernández H, Bruggeman FJ, Hellingwerf KJ, Branco dos Santos F. Photonfluxostat: A method for light-limited batch cultivation of cyanobacteria at different, yet constant, growth rates. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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41
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Holland SC, Artier J, Miller NT, Cano M, Yu J, Ghirardi ML, Burnap RL. Impacts of genetically engineered alterations in carbon sink pathways on photosynthetic performance. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.09.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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43
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Lea-Smith DJ, Ortiz-Suarez ML, Lenn T, Nürnberg DJ, Baers LL, Davey MP, Parolini L, Huber RG, Cotton CAR, Mastroianni G, Bombelli P, Ungerer P, Stevens TJ, Smith AG, Bond PJ, Mullineaux CW, Howe CJ. Hydrocarbons Are Essential for Optimal Cell Size, Division, and Growth of Cyanobacteria. PLANT PHYSIOLOGY 2016; 172:1928-1940. [PMID: 27707888 PMCID: PMC5100757 DOI: 10.1104/pp.16.01205] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/03/2016] [Indexed: 05/04/2023]
Abstract
Cyanobacteria are intricately organized, incorporating an array of internal thylakoid membranes, the site of photosynthesis, into cells no larger than other bacteria. They also synthesize C15-C19 alkanes and alkenes, which results in substantial production of hydrocarbons in the environment. All sequenced cyanobacteria encode hydrocarbon biosynthesis pathways, suggesting an important, undefined physiological role for these compounds. Here, we demonstrate that hydrocarbon-deficient mutants of Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803 exhibit significant phenotypic differences from wild type, including enlarged cell size, reduced growth, and increased division defects. Photosynthetic rates were similar between strains, although a minor reduction in energy transfer between the soluble light harvesting phycobilisome complex and membrane-bound photosystems was observed. Hydrocarbons were shown to accumulate in thylakoid and cytoplasmic membranes. Modeling of membranes suggests these compounds aggregate in the center of the lipid bilayer, potentially promoting membrane flexibility and facilitating curvature. In vivo measurements confirmed that Synechococcus sp. PCC 7002 mutants lacking hydrocarbons exhibit reduced thylakoid membrane curvature compared to wild type. We propose that hydrocarbons may have a role in inducing the flexibility in membranes required for optimal cell division, size, and growth, and efficient association of soluble and membrane bound proteins. The recent identification of C15-C17 alkanes and alkenes in microalgal species suggests hydrocarbons may serve a similar function in a broad range of photosynthetic organisms.
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Affiliation(s)
- David J Lea-Smith
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.);
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.);
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.);
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.);
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.);
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.);
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Maite L Ortiz-Suarez
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Tchern Lenn
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Dennis J Nürnberg
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Laura L Baers
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Matthew P Davey
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Lucia Parolini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Roland G Huber
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Charles A R Cotton
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Giulia Mastroianni
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Paolo Bombelli
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Petra Ungerer
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Tim J Stevens
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Alison G Smith
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Peter J Bond
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Conrad W Mullineaux
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
| | - Christopher J Howe
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (D.J.L.-S., L.L.B., C.A.R.C., P.B., C.J.H.)
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom (M.L.O.-S., P.J.B.)
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom (T.L., D.J.N., G.M., P.U., C.W.M.)
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (M.P.D., A.G.S.)
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom (L.P.)
- Bioinformatics Institute, A*STAR, Singapore 138671 (R.G.H., P.J.B.)
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom (T.J.S.); and
- National University of Singapore, Department of Biological Sciences, Singapore 117543 (P.J.B.)
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CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002. Metab Eng 2016; 38:170-179. [PMID: 27481676 DOI: 10.1016/j.ymben.2016.07.007] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/18/2016] [Accepted: 07/21/2016] [Indexed: 11/22/2022]
Abstract
Trans-acting regulators provide novel opportunities to study essential genes and regulate metabolic pathways. We have adapted the clustered regularly interspersed palindromic repeats (CRISPR) system from Streptococcus pyogenes to repress genes in trans in the cyanobacterium Synechococcus sp. strain PCC 7002 (hereafter PCC 7002). With this approach, termed CRISPR interference (CRISPRi), transcription of a specific target sequence is repressed by a catalytically inactive Cas9 protein recruited to the target DNA by base-pair interactions with a single guide RNA that is complementary to the target sequence. We adapted this system for PCC 7002 and achieved conditional and titratable repression of a heterologous reporter gene, yellow fluorescent protein. Next, we demonstrated the utility of finely tuning native gene expression by downregulating the abundance of phycobillisomes. In addition, we created a conditional auxotroph by repressing synthesis of the carboxysome, an essential component of the carbon concentrating mechanism cyanobacteria use to fix atmospheric CO2. Lastly, we demonstrated a novel strategy for increasing central carbon flux by conditionally downregulating a key node in nitrogen assimilation. The resulting cells produced 2-fold more lactate than a baseline engineered cell line, representing the highest photosynthetically generated productivity to date. This work is the first example of titratable repression in cyanobacteria using CRISPRi, enabling dynamic regulation of essential processes and manipulation of flux through central carbon metabolism. This tool facilitates the study of essential genes of unknown function and enables groundbreaking metabolic engineering capability, by providing a straightforward approach to redirect metabolism and carbon flux in the production of high-value chemicals.
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Lea-Smith DJ, Vasudevan R, Howe CJ. Generation of Marked and Markerless Mutants in Model Cyanobacterial Species. J Vis Exp 2016. [PMID: 27286310 DOI: 10.3791/54001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Cyanobacteria are ecologically important organisms and potential platforms for production of biofuels and useful industrial products. Genetic manipulation of cyanobacteria, especially model organisms such as Synechocystis sp. PCC6803 and Synechococcus sp. PCC7002, is a key tool for both basic and applied research. Generation of unmarked mutants, whereby chromosomal alterations are introduced into a strain via insertion of an antibiotic resistance cassette (a manipulatable fragment of DNA containing one or more genes), followed by subsequent removal of this cassette using a negative selectable marker, is a particularly powerful technique. Unmarked mutants can be repeatedly genetically manipulated, allowing as many alterations to be introduced into a strain as desired. In addition, the absence of genes encoding antibiotic resistance proteins in the mutated strain is desirable, as it avoids the possibility of 'escape' of antibiotic resistant organisms into the environment. However, detailed methods for repeated rounds of genetic manipulation of cyanobacteria are not well described in the scientific literature. Here we provide a comprehensive description of this technique, which we have successfully used to generate mutants with multiple deletions, single point mutations within a gene of interest and insertion of novel gene cassettes.
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Agostoni M, Lucker BF, Smith MA, Kanazawa A, Blanchard GJ, Kramer DM, Montgomery BL. Competition-based phenotyping reveals a fitness cost for maintaining phycobilisomes under fluctuating light in the cyanobacterium Fremyella diplosiphon. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Photosynthetic, respiratory and extracellular electron transport pathways in cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:247-55. [PMID: 26498190 DOI: 10.1016/j.bbabio.2015.10.007] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 10/09/2015] [Accepted: 10/14/2015] [Indexed: 01/05/2023]
Abstract
Cyanobacteria have evolved elaborate electron transport pathways to carry out photosynthesis and respiration, and to dissipate excess energy in order to limit cellular damage. Our understanding of the complexity of these systems and their role in allowing cyanobacteria to cope with varying environmental conditions is rapidly improving, but many questions remain. We summarize current knowledge of cyanobacterial electron transport pathways, including the possible roles of alternative pathways in photoprotection. We describe extracellular electron transport, which is as yet poorly understood. Biological photovoltaic devices, which measure electron output from cells, and which have been proposed as possible means of renewable energy generation, may be valuable tools in understanding cyanobacterial electron transfer pathways, and enhanced understanding of electron transfer may allow improvements in the efficiency of power output. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux.
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Schuurmans RM, van Alphen P, Schuurmans JM, Matthijs HCP, Hellingwerf KJ. Comparison of the Photosynthetic Yield of Cyanobacteria and Green Algae: Different Methods Give Different Answers. PLoS One 2015; 10:e0139061. [PMID: 26394153 PMCID: PMC4578884 DOI: 10.1371/journal.pone.0139061] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/07/2015] [Indexed: 11/18/2022] Open
Abstract
The societal importance of renewable carbon-based commodities and energy carriers has elicited a particular interest for high performance phototrophic microorganisms. Selection of optimal strains is often based on direct comparison under laboratory conditions of maximal growth rate or additional valued features such as lipid content. Instead of reporting growth rate in culture, estimation of photosynthetic efficiency (quantum yield of PSII) by pulse-amplitude modulated (PAM) fluorimetry is an often applied alternative method. Here we compared the quantum yield of PSII and the photonic yield on biomass for the green alga Chlorella sorokiniana 211-8K and the cyanobacterium Synechocystis sp. PCC 6803. Our data demonstrate that the PAM technique inherently underestimates the photosynthetic efficiency of cyanobacteria by rendering a high F0 and a low FM, specifically after the commonly practiced dark pre-incubation before a yield measurement. Yet when comparing the calculated biomass yield on light in continuous culture experiments, we obtained nearly equal values for both species. Using mutants of Synechocystis sp. PCC 6803, we analyzed the factors that compromise its PAM-based quantum yield measurements. We will discuss the role of dark respiratory activity, fluorescence emission from the phycobilisomes, and the Mehler-like reaction. Based on the above observations we recommend that PAM measurements in cyanobacteria are interpreted only qualitatively.
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Affiliation(s)
- R. Milou Schuurmans
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Pascal van Alphen
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - J. Merijn Schuurmans
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans C. P. Matthijs
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Klaas J. Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Photanol BV, Amsterdam, The Netherlands
- * E-mail:
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49
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The chromosome copy number of the hyperthermophilic archaeon Thermococcus kodakarensis KOD1. Extremophiles 2015; 19:741-50. [PMID: 25952670 PMCID: PMC4502288 DOI: 10.1007/s00792-015-0750-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/12/2015] [Indexed: 01/08/2023]
Abstract
The euryarchaeon Thermococcus kodakarensis is a well-characterized anaerobic hyperthermophilic heterotroph and due to the availability of genetic engineering systems it has become one of the model organisms for studying Archaea. Despite this prominent role among the Euryarchaeota, no data about the ploidy level of this species is available. While polyploidy has been shown to exist in various Euryarchaeota, especially Halobacteria, the chromosome copy number of species belonging to one of the major orders within that phylum, i.e., the Thermococcales (including Thermococcus spp. and Pyrococcus spp.), has never been determined. This prompted us to investigate the chromosome copy number of T. kodakarensis. In this study, we demonstrate that T. kodakarensis is polyploid with a chromosome copy number that varies between 7 and 19 copies, depending on the growth phase. An apparent correlation between the presence of histones and polyploidy in Archaea is observed.
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50
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Cotton CAR, Douglass JS, De Causmaecker S, Brinkert K, Cardona T, Fantuzzi A, Rutherford AW, Murray JW. Photosynthetic constraints on fuel from microbes. Front Bioeng Biotechnol 2015; 3:36. [PMID: 25853129 PMCID: PMC4364286 DOI: 10.3389/fbioe.2015.00036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/04/2015] [Indexed: 01/12/2023] Open
Affiliation(s)
| | | | | | | | - Tanai Cardona
- Department of Life Sciences, Imperial College London , London , UK
| | - Andrea Fantuzzi
- Department of Life Sciences, Imperial College London , London , UK
| | | | - James W Murray
- Department of Life Sciences, Imperial College London , London , UK
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