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Sim ZY, Goh KC, He Y, Gin KYH. Present and future potential role of toxin-producing Synechococcus in the tropical region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165230. [PMID: 37400026 DOI: 10.1016/j.scitotenv.2023.165230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
As anthropogenic induced temperature rises and nutrient loadings increase in fresh and brackish environments, the ecological function of the phytoplankton community is expected to favour the picocyanobacteria, of the genus Synechococcus. Synechococcus is already a ubiquitous cyanobacterium found in both freshwater and marine environments, notwithstanding that the toxigenic species still remains unexplored in many freshwaters. Their fast growth rate and their ability to produce toxins make Synechococcus a potential dominant player in harmful algal blooms under climate change scenarios. This study examines the responses of a novel toxin-producing Synechococcus (i.e., one belonging to a freshwater clade; the other belonging to a brackish clade) to environmental changes that reflect climate change effects. We conducted a series of controlled experiments under present and predicted future temperatures, as well as under various N and P nutrients loadings. Our findings highlight how Synechococcus can be altered by the differing reactions to increasing temperature and nutrients, which resulted in considerable variations in cell abundance, growth rate, death rate, cellular stoichiometry and toxin production. Synechococcus had the highest growth observed at 28 °C, and further increases in temperature resulted in a decline for both fresh and brackish waters. Cellular stoichiometry was also altered, where more nitrogen (N) per cell was required, and the plasticity of N:P was more severe for the brackish clade. However, Synechococcus become more toxic under future scenario. Anatoxin-a (ATX) saw the greatest spike when temperature was at 34 °C especially under P-enrichment conditions. In contrast, Cylindrospermopsin (CYN) was promoted at the lowest tested temperature (25 °C) and under N-limitation. Overall, both temperature and external nutrients are the dominant control over Synechococcus toxins production. A model was also created to assess Synechococcus toxicity to zooplankton grazing. Zooplankton grazing was reduced by two folds under nutrient limitation, but temperature accounted for very insignificant change.
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Affiliation(s)
- Zhi Yang Sim
- National University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, Singapore 138602, Singapore
| | - Kwan Chien Goh
- National University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, Singapore 138602, Singapore
| | - Yiliang He
- National University of Singapore Center for Eco-Environment Research, Nanjing Hydraulic Research Institute, Nanjing 210098, China
| | - K Y H Gin
- National University of Singapore Environmental Research Institute, National University of Singapore, 1 Create Way, #15-02, Singapore 138602, Singapore; Department of Civil and Environmental Engineering, National University of Singapore, Blk E1A-07-03, 1 Engineering Drive 2, Singapore 117576, Singapore.
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Noell SE, Hellweger FL, Temperton B, Giovannoni SJ. A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments. Microbiol Mol Biol Rev 2023; 87:e0012422. [PMID: 36995249 PMCID: PMC10304753 DOI: 10.1128/mmbr.00124-22] [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] [Indexed: 03/31/2023] Open
Abstract
In this review, we consider the regulatory strategies of aquatic oligotrophs, microbial cells that are adapted to thrive under low-nutrient concentrations in oceans, lakes, and other aquatic ecosystems. Many reports have concluded that oligotrophs use less transcriptional regulation than copiotrophic cells, which are adapted to high nutrient concentrations and are far more common subjects for laboratory investigations of regulation. It is theorized that oligotrophs have retained alternate mechanisms of regulation, such as riboswitches, that provide shorter response times and smaller amplitude responses and require fewer cellular resources. We examine the accumulated evidence for distinctive regulatory strategies in oligotrophs. We explore differences in the selective pressures copiotrophs and oligotrophs encounter and ask why, although evolutionary history gives copiotrophs and oligotrophs access to the same regulatory mechanisms, they might exhibit distinctly different patterns in how these mechanisms are used. We discuss the implications of these findings for understanding broad patterns in the evolution of microbial regulatory networks and their relationships to environmental niche and life history strategy. We ask whether these observations, which have emerged from a decade of increased investigation of the cell biology of oligotrophs, might be relevant to recent discoveries of many microbial cell lineages in nature that share with oligotrophs the property of reduced genome size.
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Affiliation(s)
- Stephen E. Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, United Kingdom
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3
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The proteome of Chlamydomonas reinhardtii during phosphorus depletion and repletion. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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Tay JW, Cameron JC. Asymmetric survival in single-cell lineages of cyanobacteria in response to photodamage. PHOTOSYNTHESIS RESEARCH 2023; 155:289-297. [PMID: 36581718 DOI: 10.1007/s11120-022-00986-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Oxygenic photosynthesis is driven by the coupled action of the light-dependent pigment-protein complexes, photosystem I and II, located within the internal thylakoid membrane system. However, photosystem II is known to be prone to photooxidative damage. Thus, photosynthetic organisms have evolved a repair cycle to continuously replace the damaged proteins in photosystem II. However, it has remained difficult to deconvolute the damage and repair processes using traditional ensemble approaches. Here, we demonstrate an automated approach using time-lapse fluorescence microscopy and computational image analysis to study the dynamics and effects of photodamage in single cells at subcellular resolution in cyanobacteria. By growing cells in a two-dimensional layer, we avoid shading effects, thereby generating uniform and reproducible growth conditions. Using this platform, we analyzed the growth and physiology of multiple strains simultaneously under defined photoinhibitory conditions stimulated by UV-A light. Our results reveal an asymmetric cellular response to photodamage between sibling cells and the generation of an elusive subcellular structure, here named a 'photoendosome,' derived from the thylakoid which could indicate the presence of a previously unknown photoprotective mechanism. We anticipate these results to be a starting point for further studies to better understand photodamage and repair at the single-cell level.
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Affiliation(s)
- Jian Wei Tay
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO, 80309, USA
| | - Jeffrey C Cameron
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA.
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO, 80309, USA.
- National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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Cheng J, Zhang K, Li J, Hou Y. Using δF IP as a potential biomarker for risk assessment of environmental pollutants in aquatic ecosystem: A case study of marine cyanobacterium Synechococcus sp. PCC7002. CHEMOSPHERE 2023; 313:137621. [PMID: 36566796 DOI: 10.1016/j.chemosphere.2022.137621] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Increased hazardous substances application causes more environmental pollution and risks for human health. Microalgae are the important biological groups in marine ecosystem, and considered to be sensitive to environmental pollutants. Therefore, toxicity test on marine microalgae could provide the most efficient method for aquatic toxicity assessment, and could also be used as the early warning signals in aquatic ecosystem. In view of this, our study aimed at investigating the toxicity potential of two typical organic compounds, and screening out novel photosynthetic indicators for the risk assessment of environmental pollutants. In this study, benzyl alcohol and 2-phenylethanol were chosen as the target organic compounds, and preliminary toxicity mechanism of these organic compounds on marine cyanobacterium Synechococcus sp. PCC7002 was investigated with chlorophyll fluorescence technology. Results showed that PCC7002 could be affected by benzyl alcohol or 2-phenylethanol stress, and the toxicity effect was concentration-dependent. And external benzyl alcohol and 2-phenylethanol stress damaged the oxygen evolving complex, and suppressed electron transport at the donor and receptor sides of photosystem II (PSII), influencing the absorption, transfer, and application of light energy. Furthermore, potential biomarkers were screened by half maximal inhibitory concentration (IC50) on the basis of pearson correlation coefficient analysis, and fluorescence intensity difference between the I-step and P-step of OJIP curve (δFIP) seems to be the most sensitive indicator for external stress. This study would be of significant interest to the biomarker community, and pave the way for the practical resource for marine pollution monitoring and assessment.
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Affiliation(s)
- Jie Cheng
- School of Life Sciences, Liaocheng University, Liaocheng, 252000, China; State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
| | - Kaidian Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan University, Haikou, 570100, China; State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Jiashun Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yuyong Hou
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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Diversity and Evolution of Iron Uptake Pathways in Marine Cyanobacteria from the Perspective of the Coastal Strain Synechococcus sp. Strain PCC 7002. Appl Environ Microbiol 2023; 89:e0173222. [PMID: 36533965 PMCID: PMC9888192 DOI: 10.1128/aem.01732-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Marine cyanobacteria contribute to approximately half of the ocean primary production, and their biomass is limited by low iron (Fe) bioavailability in many regions of the open seas. The mechanisms by which marine cyanobacteria overcome Fe limitation remain unclear. In this study, multiple Fe uptake pathways have been identified in a coastal strain of Synechococcus sp. strain PCC 7002. A total of 49 mutants were obtained by gene knockout methods, and 10 mutants were found to have significantly decreased growth rates compared to the wild type (WT). The genes related to active Fe transport pathways such as TonB-dependent transporters and the synthesis and secretion of siderophores are found to be essential for the adaptation of Fe limitation in Synechococcus sp. PCC 7002. By comparing the Fe uptake pathways of this coastal strain with other open-ocean cyanobacterial strains, it can be concluded that the Fe uptake strategies from different cyanobacteria have a strong relationship with the Fe bioavailability in their habitats. The evolution and adaptation of cyanobacterial iron acquisition strategies with the change of iron environments from ancient oceans to modern oceans are discussed. This study provides new insights into the diversified strategies of marine cyanobacteria in different habitats from temporal and spatial scales. IMPORTANCE Iron (Fe) is an important limiting factor of marine primary productivity. Cyanobacteria, the oldest photosynthetic oxygen-evolving organisms on the earth, play crucial roles in marine primary productivity, especially in the oligotrophic ocean. How they overcome Fe limitation during the long-term evolution process has not been fully revealed. Fe uptake mechanisms of cyanobacteria have been partially studied in freshwater cyanobacteria but are largely unknown in marine cyanobacterial species. In this paper, the characteristics of Fe uptake mechanisms in a coastal model cyanobacterium, Synechococcus sp. PCC 7002, were studied. Furthermore, the relationship between Fe uptake strategies and Fe environments of cyanobacterial habitats has been revealed from temporal and spatial scales, which provides a good case for marine microorganisms adapting to changes in the marine environment.
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Development of shuttle vectors for rapid prototyping of engineered Synechococcus sp. PCC7002. Appl Microbiol Biotechnol 2022; 106:8169-8181. [PMID: 36401644 DOI: 10.1007/s00253-022-12289-z] [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: 04/21/2022] [Revised: 09/18/2022] [Accepted: 11/11/2022] [Indexed: 11/20/2022]
Abstract
Cyanobacteria are of particular interest for chemical production as they can assimilate CO2 and use solar energy to power chemical synthesis. However, unlike the model microorganism of Escherichia coli, the availability of genetic toolboxes for rapid proof-of-concept studies in cyanobacteria is generally lacking. In this study, we first characterized a set of promoters to efficiently drive gene expressions in the marine cyanobacterium Synechococcus sp. PCC7002. We identified that the endogenous cpcBA promoter represented one of the strongest promoters in PCC7002. Next, a set of shuttle vectors was constructed based on the endogenous pAQ1 plasmid to facilitate the rapid pathway assembly. Moreover, we used the shuttle vectors to modularly optimize the amorpha-4,11-diene synthesis in PCC7002. By modularly optimizing the metabolic pathway, we managed to redistribute the central metabolism toward the amorpha-4,11-diene production in PCC7002 with enhanced product titer. Taken together, the plasmid toolbox developed in this study will greatly accelerate the generation of genetically engineered PCC7002. KEY POINTS: • Promoter characterization revealed that the endogenous cpcBA promoter represented one of the strongest promoters in PCC7002 • A set of shuttle vectors with different antibiotic selection markers was constructed based on endogenous pAQ1 plasmid • By modularly optimizing the metabolic pathway, amorpha-4,11-diene production in PCC7002 was improved.
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Distribution and Genomic Variation of Thermophilic Cyanobacteria in Diverse Microbial Mats at the Upper Temperature Limits of Photosynthesis. mSystems 2022; 7:e0031722. [PMID: 35980085 PMCID: PMC9600594 DOI: 10.1128/msystems.00317-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Thermophilic cyanobacteria have been extensively studied in Yellowstone National Park (YNP) hot springs, particularly during decades of work on the thick laminated mats of Octopus and Mushroom springs. However, focused studies of cyanobacteria outside these two hot springs have been lacking, especially regarding how physical and chemical parameters along with community morphology influence the genomic makeup of these organisms. Here, we used a metagenomic approach to examine cyanobacteria existing at the upper temperature limit of photosynthesis. We examined 15 alkaline hot spring samples across six geographic areas of YNP, all with various physical and chemical parameters and community morphology. We recovered 22 metagenome-assembled genomes (MAGs) belonging to thermophilic cyanobacteria, notably an uncultured Synechococcus-like taxon recovered from a setting at the upper temperature limit of photosynthesis, 73°C, in addition to thermophilic Gloeomargarita. Furthermore, we found that three distinct groups of Synechococcus-like MAGs recovered from different temperature ranges vary in their genomic makeup. MAGs from the uncultured very-high-temperature (up to 73°C) Synechococcus-like taxon lack key nitrogen metabolism genes and have genes implicated in cellular stress responses that diverge from other Synechococcus-like MAGs. Across all parameters measured, temperature was the primary determinant of taxonomic makeup of recovered cyanobacterial MAGs. However, total Fe, community morphology, and biogeography played an additional role in the distribution and abundance of upper-temperature-limit-adapted Synechococcus-like MAGs. These findings expand our understanding of cyanobacterial diversity in YNP and provide a basis for interrogation of understudied thermophilic cyanobacteria. IMPORTANCE Oxygenic photosynthesis arose early in microbial evolution-approximately 2.5 to 3.5 billion years ago-and entirely reshaped the biological makeup of Earth. However, despite the span of time in which photosynthesis has been refined, it is strictly limited to temperatures below 73°C, a barrier that many other biological processes have been able to overcome. Furthermore, photosynthesis at temperatures above 56°C is limited to circumneutral and alkaline pH. Hot springs in Yellowstone National Park (YNP), which have a large diversity in temperatures, pH, and geochemistry, provide a natural laboratory to study thermophilic microbial mats and the cyanobacteria within. While cyanobacteria in YNP microbial mats have been studied for decades, a vast majority of the work has focused on two springs within the same geyser basin, both containing similar community morphologies. Thus, the drivers of cyanobacterial adaptations to the upper limits of photosynthesis across a variety of environmental parameters have been understudied. Our findings provide new insights into the influence of these parameters on both taxonomic diversity and genomic content of cyanobacteria across a range of hot spring samples.
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Giordano M, Goodman CA, Huang F, Raven JA, Ruan Z. A mechanistic study of the influence of nitrogen and energy availability on the NH4+ sensitivity of nitrogen assimilation in Synechococcus. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5596-5611. [PMID: 35595516 PMCID: PMC9467657 DOI: 10.1093/jxb/erac219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/19/2022] [Indexed: 05/23/2023]
Abstract
In most algae, NO3- assimilation is tightly controlled and is often inhibited by the presence of NH4+. In the marine, non-colonial, non-diazotrophic cyanobacterium Synechococcus UTEX 2380, NO3- assimilation is sensitive to NH4+ only when N does not limit growth. We sequenced the genome of Synechococcus UTEX 2380, studied the genetic organization of the nitrate assimilation related (NAR) genes, and investigated expression and kinetics of the main NAR enzymes, under N or light limitation. We found that Synechococcus UTEX 2380 is a β-cyanobacterium with a full complement of N uptake and assimilation genes and NAR regulatory elements. The nitrate reductase of our strain showed biphasic kinetics, previously observed only in freshwater or soil diazotrophic Synechococcus strains. Nitrite reductase and glutamine synthetase showed little response to our growth treatments, and their activity was usually much higher than that of nitrate reductase. NH4+ insensitivity of NAR genes may be associated with the stimulation of the binding of the regulator NtcA to NAR gene promoters by the high 2-oxoglutarate concentrations produced under N limitation. NH4+ sensitivity in energy-limited cells fits with the fact that, under these conditions, the use of NH4+ rather than NO3- decreases N-assimilation cost, whereas it would exacerbate N shortage under N limitation.
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Affiliation(s)
- Mario Giordano
- STU-UNIVPM Joint Algal Research Center, Marine Biology Institute, Shantou University, Shantou, Guangdong 515063, China
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona 60131, Italy
- CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA
- Institute of Microbiology ASCR, Algatech, Trebon, Czech Republic
- National Research Council, Institute of Marine Science, Venezia, Italy
| | - Charles A Goodman
- CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA
| | - Fengying Huang
- STU-UNIVPM Joint Algal Research Center, Marine Biology Institute, Shantou University, Shantou, Guangdong 515063, China
| | - John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5 DA, UK
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo NSW 2007, Australia
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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Ma J, Wang P, Hu B, Wang X, Qian J. Synergistic promoting effect of increasing aquatic ammonium and CO 2 on Microcystis aeruginosa. CHEMOSPHERE 2022; 301:134553. [PMID: 35405194 DOI: 10.1016/j.chemosphere.2022.134553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/13/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Owing to climate change and intensive agricultural development, freshwater bodies have been affected by increases in both CO2 levels and chemically-reduced forms of N. However, little is known about how these changes affect cyanobacterial growth and blooms. This study explored a range of light conditions (30, 80, 130, or 200 μmol photons/m2/s) wherein Microcystis aeruginosa, a widespread bloom-forming species, was exposed to different concentrations of CO2 (400 parts per million (ppm) and 1000 ppm) in a medium containing NH4+ or NO3-. The interactive effects of N sources and CO2 levels on the C/N metabolic balance and energy balance were examined to assess changes in the growth of M. aeruginosa. When the light intensity was 80 μmol photons/m2/s, elevated CO2 could reduce intracellular reactive oxygen species (ROS) in NH4+-grown M. aeruginosa. Meanwhile, cell density and chlorophyll a (Chl a) increased with increasing CO2 levels, and the increase in Chl a was significantly greater in NH4+-grown M. aeruginosa than in NO3--grown M. aeruginosa. Under light conditions of 200 μmol photons/m2/s, elevated CO2 concentration caused NO3--grown M. aeruginosa to be affected by a large amount of ROS, and the growth of NO3--grown M. aeruginosa was finally suppressed. However, NH4+-grown M. aeruginosa had a smaller amount of ROS and showed improved growth as CO2 was elevated. This difference can be attributed to the faster metabolic pathways in the NH4+ environment, which manifested in a lower accumulation of 2-oxoglutarate and fatty acids as CO2 was elevated. These findings suggest that the simultaneous increase in ammonium and CO2 in aquatic ecosystems confers cyanobacteria with greater advantages than the combination of nitrate and CO2, which may aggravate cyanobacterial blooms.
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Affiliation(s)
- Jingjie Ma
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China.
| | - Bin Hu
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Jin Qian
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing, 210098, People's Republic of China; College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
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Gilbert NE, LeCleir GR, Strzepek RF, Ellwood MJ, Twining BS, Roux S, Pennacchio C, Boyd PW, Wilhelm SW. Bioavailable iron titrations reveal oceanic Synechococcus ecotypes optimized for different iron availabilities. ISME COMMUNICATIONS 2022; 2:54. [PMID: 37938659 PMCID: PMC9723758 DOI: 10.1038/s43705-022-00132-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/24/2022] [Accepted: 06/09/2022] [Indexed: 04/18/2023]
Abstract
The trace metal iron (Fe) controls the diversity and activity of phytoplankton across the surface oceans, a paradigm established through decades of in situ and mesocosm experimental studies. Despite widespread Fe-limitation within high-nutrient, low chlorophyll (HNLC) waters, significant contributions of the cyanobacterium Synechococcus to the phytoplankton stock can be found. Correlations among differing strains of Synechococcus across different Fe-regimes have suggested the existence of Fe-adapted ecotypes. However, experimental evidence of high- versus low-Fe adapted strains of Synechococcus is lacking, and so we investigated the transcriptional responses of microbial communities inhabiting the HNLC, sub-Antarctic region of the Southern Ocean during the Spring of 2018. Analysis of metatranscriptomes generated from on-deck incubation experiments reflecting a gradient of Fe-availabilities reveal transcriptomic signatures indicative of co-occurring Synechococcus ecotypes adapted to differing Fe-regimes. Functional analyses comparing low-Fe and high-Fe conditions point to various Fe-acquisition mechanisms that may allow persistence of low-Fe adapted Synechococcus under Fe-limitation. Comparison of in situ surface conditions to the Fe-titrations indicate ecological relevance of these mechanisms as well as persistence of both putative ecotypes within this region. This Fe-titration approach, combined with transcriptomics, highlights the short-term responses of the in situ phytoplankton community to Fe-availability that are often overlooked by examining genomic content or bulk physiological responses alone. These findings expand our knowledge about how phytoplankton in HNLC Southern Ocean waters adapt and respond to changing Fe supply.
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Affiliation(s)
- Naomi E Gilbert
- Department of Microbiology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Gary R LeCleir
- Department of Microbiology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert F Strzepek
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7004, Australia
- Australian Antarctic Program Partnership (AAPP), Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Michael J Ellwood
- Research School of Earth Sciences, Australian National University, Canberra, ACT, Australia
| | | | - S Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - C Pennacchio
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, TN, 37996, USA.
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Bantu L, Chauhan S, Srikumar A, Hirakawa Y, Suzuki I, Hagemann M, Prakash JSS. A membrane-bound cAMP receptor protein, SyCRP1 mediates inorganic carbon response in Synechocystis sp. PCC 6803. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194803. [PMID: 35272049 DOI: 10.1016/j.bbagrm.2022.194803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/24/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
The availability of inorganic carbon (Ci) as the source for photosynthesis is fluctuating in aquatic environments. Despite the involvement of transcriptional regulators CmpR and NdhR in regulating genes encoding Ci transporters at limiting CO2, the Ci-sensing mechanism is largely unknown among cyanobacteria. Here we report that a cAMP-dependent transcription factor SyCRP1 mediates Ci response in Synechocystis. The mutant ∆sycrp1 exhibited a slow-growth phenotype and reduced maximum rate of bicarbonate-dependent photosynthetic electron transport (Vmax) compared to wild-type at the scarcity of CO2. The number of carboxysomes was decreased significantly in the ∆sycrp1 at low CO2 consistent with its reduced Vmax. The DNA microarray analysis revealed the upregulation of genes encoding Ci transporters in ∆sycrp1. The membrane-localized SyCRP1 was released into the cytosol in wild-type cells shifted from low to high CO2 or upon cAMP treatment. Soluble His-tagged SyCRP1 was shown to target DNA-binding sites upstream of the Ci-regulated genes sbtA and ccmK3. In addition, cAMP enhanced the binding of SyCRP1 to its target sites. Our data collectively suggest that the Ci is sensed through the second messenger cAMP releasing membrane-bound SyCRP1 into cytoplasm under sufficient CO2 conditions. Hence, SyCRP1 is a possible regulator of carbon concentrating mechanism, and such a regulation might be mediated via sensing Ci levels through cAMP in Synechocystis.
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Affiliation(s)
- Lingaswamy Bantu
- From the Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Suraj Chauhan
- From the Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Afshan Srikumar
- From the Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Yoshihisa Hirakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba 305-8572, Japan
| | - Iwane Suzuki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba 305-8572, Japan
| | - Martin Hagemann
- Plant Physiology Department, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany
| | - Jogadhenu S S Prakash
- From the Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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Vijayakumar S, Angione C. Protocol for hybrid flux balance, statistical, and machine learning analysis of multi-omic data from the cyanobacterium Synechococcus sp. PCC 7002. STAR Protoc 2021; 2:100837. [PMID: 34632416 PMCID: PMC8488602 DOI: 10.1016/j.xpro.2021.100837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Combining a computational framework for flux balance analysis with machine learning improves the accuracy of predicting metabolic activity across conditions, while enabling mechanistic interpretation. This protocol presents a guide to condition-specific metabolic modeling that integrates regularized flux balance analysis with machine learning approaches to extract key features from transcriptomic and fluxomic data. We demonstrate the protocol as applied to Synechococcus sp. PCC 7002; we also outline how it can be adapted to any species or community with available multi-omic data. For complete details on the use and execution of this protocol, please refer to Vijayakumar et al. (2020).
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Affiliation(s)
- Supreeta Vijayakumar
- School of Computing, Engineering & Digital Technologies, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK
| | - Claudio Angione
- School of Computing, Engineering & Digital Technologies, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK
- Centre for Digital Innovation, Teesside University, Middlesbrough TS1 3BX, UK
- Healthcare Innovation Centre, Teesside University, Middlesbrough TS1 3BX, UK
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Yu Q, He J, Zhao Q, Wang X, Zhi Y, Li X, Li X, Li L, Ge B. Regulation of nitrogen source for enhanced photobiological H2 production by co-culture of Chlamydomonas reinhardtii and Mesorhizobium sangaii. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Long-Term Survival of Synechococcus and Heterotrophic Bacteria without External Nutrient Supply after Changes in Their Relationship from Antagonism to Mutualism. mBio 2021; 12:e0161421. [PMID: 34465027 PMCID: PMC8406228 DOI: 10.1128/mbio.01614-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine phytoplankton and heterotrophic bacteria share a very close but usually changeable relationship. However, the ultimate fate of their unstable relationship on a long-term scale is unclear. Here, the relationship between Synechococcus and heterotrophic bacterial communities underwent a dramatic shift from antagonism to commensalism and eventually to mutualism during long-term cocultivation. The relationship change is attributed to the different (even opposite) effects of diverse bacterial members on Synechococcus and the ratio of beneficial to harmful bacteria. Different bacterial members also interact with each other (e.g., quorum-sensing communication, hostility, or mutual promotion) and drive a dynamic succession in the entire community structure that corresponds exactly to the shift in its relationship with Synechococcus. In the final mutualism stage, a self-sufficient nitrogen cycle, including nitrogen fixation, denitrification, and organic nitrogen degradation, contributed to the healthy survival of Synechococcus for 2 years without an exogenous nutrient supply. This natural selective trait of Synechococcus and heterotrophic bacteria toward mutualism under long-term coexistence provides a novel clue for understanding the ubiquity and competitive advantage of Synechococcus in global oceans.
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Stability and bioactivity of carotenoids from Synechococcus sp. PCC 7002 in Zein/NaCas/Gum Arabic composite nanoparticles fabricated by pH adjustment and heat treatment antisolvent precipitation. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.106663] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Kharwar S, Bhattacharjee S, Chakraborty S, Mishra AK. Regulation of sulfur metabolism, homeostasis and adaptive responses to sulfur limitation in cyanobacteria. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00819-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Amino Acid Analog Induces Stress Response in Marine Synechococcus. Appl Environ Microbiol 2021; 87:e0020021. [PMID: 33990310 DOI: 10.1128/aem.00200-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Characterizing the cell-level metabolic trade-offs that phytoplankton exhibit in response to changing environmental conditions is important for predicting the impact of these changes on marine food web dynamics and biogeochemical cycling. The time-selective proteome-labeling approach, bioorthogonal noncanonical amino acid tagging (BONCAT), has potential to provide insight into differential allocation of resources at the cellular level, especially when coupled with proteomics. However, the application of this technique in marine phytoplankton remains limited. We demonstrate that the marine cyanobacteria Synechococcus sp. and two groups of eukaryotic algae take up the modified amino acid l-homopropargylglycine (HPG), suggesting that BONCAT can be used to detect translationally active phytoplankton. However, the impact of HPG addition on growth dynamics varied between groups of phytoplankton. In addition, proteomic analysis of Synechococcus cells grown with HPG revealed a physiological shift in nitrogen metabolism, general protein stress, and energy production, indicating a potential limitation for the use of BONCAT in understanding the cell-level response of Synechococcus sp. to environmental change. Variability in HPG sensitivity between algal groups and the impact of HPG on Synechococcus physiology indicates that particular considerations should be taken when applying this technique to other marine taxa or mixed marine microbial communities. IMPORTANCE Phytoplankton form the base of the marine food web and substantially impact global energy and nutrient flow. Marine picocyanobacteria of the genus Synechococcus comprise a large portion of phytoplankton biomass in the ocean and therefore are important model organisms. The technical challenges of environmental proteomics in mixed microbial communities have limited our ability to detect the cell-level adaptations of phytoplankton communities to a changing environment. The proteome labeling technique, bioorthogonal noncanonical amino acid tagging (BONCAT), has potential to address some of these challenges by simplifying proteomic analyses. This study explores the ability of marine phytoplankton to take up the modified amino acid, l-homopropargylglycine (HPG), required for BONCAT, and investigates the proteomic response of Synechococcus to HPG. We not only demonstrate that cyanobacteria can take up HPG but also highlight the physiological impact of HPG on Synechococcus, which has implications for future applications of this technique in the marine environment.
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Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications. Genes (Basel) 2021; 12:genes12040500. [PMID: 33805386 PMCID: PMC8066212 DOI: 10.3390/genes12040500] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for their genetic and physiological interests summarized in this review. Extensive "omics" data sets have been generated, and genome-scale models (GSM) have been developed for the rational engineering of these cyanobacteria for biotechnological purposes. We presently discuss what should be done to improve our understanding of the genotype-phenotype relationships of these models and generate robust and predictive models of their metabolism. Furthermore, we also emphasize that because Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002 represent only a limited part of the wide biodiversity of cyanobacteria, other species distantly related to these three models, should be studied. Finally, we highlight the need to strengthen the communication between academic researchers, who know well cyanobacteria and can engineer them for biotechnological purposes, but have a limited access to large photobioreactors, and industrial partners who attempt to use natural or engineered cyanobacteria to produce interesting chemicals at reasonable costs, but may lack knowledge on cyanobacterial physiology and metabolism.
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Vijayakumar S, Rahman PKSM, Angione C. A Hybrid Flux Balance Analysis and Machine Learning Pipeline Elucidates Metabolic Adaptation in Cyanobacteria. iScience 2020; 23:101818. [PMID: 33354660 PMCID: PMC7744713 DOI: 10.1016/j.isci.2020.101818] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/23/2020] [Accepted: 11/13/2020] [Indexed: 01/20/2023] Open
Abstract
Machine learning has recently emerged as a promising tool for inferring multi-omic relationships in biological systems. At the same time, genome-scale metabolic models (GSMMs) can be integrated with such multi-omic data to refine phenotypic predictions. In this work, we use a multi-omic machine learning pipeline to analyze a GSMM of Synechococcus sp. PCC 7002, a cyanobacterium with large potential to produce renewable biofuels. We use regularized flux balance analysis to observe flux response between conditions across photosynthesis and energy metabolism. We then incorporate principal-component analysis, k-means clustering, and LASSO regularization to reduce dimensionality and extract key cross-omic features. Our results suggest that combining metabolic modeling with machine learning elucidates mechanisms used by cyanobacteria to cope with fluctuations in light intensity and salinity that cannot be detected using transcriptomics alone. Furthermore, GSMMs introduce critical mechanistic details that improve the performance of omic-based machine learning methods. A pipeline for metabolic modeling in Synechococcus sp. PCC 7002 is presented Metabolic fluxes display clear differences in pathway activity across conditions Omic-informed GSMMs provide critical mechanistic details within machine learning Combining GSMM and machine learning improves methods based on transcriptomics alone
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Affiliation(s)
- Supreeta Vijayakumar
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK
| | - Pattanathu K S M Rahman
- Centre for Enzyme Innovation, Institute of Biological and Biomedical Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2UP, UK.,Tara Biologics, Woking, Surrey GU21 6BP, UK
| | - Claudio Angione
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK.,Centre for Digital Innovation, Teesside University, Middlesbrough TS1 3BX, UK.,Healthcare Innovation Centre, Teesside University, Middlesbrough TS1 3BX, UK
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Bhadra-Lobo S, Kim MK, Lun DS. Assessment of transcriptomic constraint-based methods for central carbon flux inference. PLoS One 2020; 15:e0238689. [PMID: 32903284 PMCID: PMC7480874 DOI: 10.1371/journal.pone.0238689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 08/21/2020] [Indexed: 11/18/2022] Open
Abstract
MOTIVATION Determining intracellular metabolic flux through isotope labeling techniques such as 13C metabolic flux analysis (13C-MFA) incurs significant cost and effort. Previous studies have shown transcriptomic data coupled with constraint-based metabolic modeling can determine intracellular fluxes that correlate highly with 13C-MFA measured fluxes and can achieve higher accuracy than constraint-based metabolic modeling alone. These studies, however, used validation data limited to E. coli and S. cerevisiae grown on glucose, with significantly similar flux distribution for central metabolism. It is unclear whether those results apply to more diverse metabolisms, and therefore further, extensive validation is needed. RESULTS In this paper, we formed a dataset of transcriptomic data coupled with corresponding 13C-MFA flux data for 21 experimental conditions in different unicellular organisms grown on varying carbon substrates and conditions. Three computational flux-balance analysis (FBA) methods were comparatively assessed. The results show when uptake rates of carbon sources and key metabolites are known, transcriptomic data provides no significant advantage over constraint-based metabolic modeling (average correlation coefficients, transcriptomic E-Flux2 0.725 and SPOT 0.650 vs non-transcriptomic pFBA 0.768). When uptake rates are unknown, however, predictions obtained utilizing transcriptomic data are generally good and significantly better than those obtained using constraint-based metabolic modeling alone (E-Flux2 0.385 and SPOT 0.583 vs pFBA 0.237). Thus, transcriptomic data coupled with constraint-based metabolic modeling is a promising method to obtain intracellular flux estimates in microorganisms, particularly in cases where uptake rates of key metabolites cannot be easily determined, such as for growth in complex media or in vivo conditions.
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Affiliation(s)
- Siddharth Bhadra-Lobo
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States of America
- * E-mail:
| | - Min Kyung Kim
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States of America
| | - Desmond S. Lun
- Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States of America
- Department of Computer Science, Rutgers, The State University of New Jersey, Camden, NJ, United States of America
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States of America
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Solovchenko A, Gorelova O, Karpova O, Selyakh I, Semenova L, Chivkunova O, Baulina O, Vinogradova E, Pugacheva T, Scherbakov P, Vasilieva S, Lukyanov A, Lobakova E. Phosphorus Feast and Famine in Cyanobacteria: Is Luxury Uptake of the Nutrient Just a Consequence of Acclimation to Its Shortage? Cells 2020; 9:E1933. [PMID: 32825634 PMCID: PMC7564538 DOI: 10.3390/cells9091933] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/12/2020] [Accepted: 08/20/2020] [Indexed: 01/02/2023] Open
Abstract
To cope with fluctuating phosphorus (P) availability, cyanobacteria developed diverse acclimations, including luxury P uptake (LPU)-taking up P in excess of the current metabolic demand. LPU is underexplored, despite its importance for nutrient-driven rearrangements in aquatic ecosystems. We studied the LPU after the refeeding of P-deprived cyanobacterium Nostoc sp. PCC 7118 with inorganic phosphate (Pi), including the kinetics of Pi uptake, turnover of polyphosphate, cell ultrastructure, and gene expression. The P-deprived cells deployed acclimations to P shortage (reduction of photosynthetic apparatus and mobilization of cell P reserves). The P-starved cells capable of LPU exhibited a biphasic kinetic of the Pi uptake and polyphosphate formation. The first (fast) phase (1-2 h after Pi refeeding) occurred independently of light and temperature. It was accompanied by a transient accumulation of polyphosphate, still upregulated genes encoding high-affinity Pi transporters, and an ATP-dependent polyphosphate kinase. During the second (slow) phase, recovery from P starvation was accompanied by the downregulation of these genes. Our study revealed no specific acclimation to ample P conditions in Nostoc sp. PCC 7118. We conclude that the observed LPU phenomenon does not likely result from the activation of a mechanism specific for ample P conditions. On the contrary, it stems from slow disengagement of the low-P responses after the abrupt transition from low-P to ample P conditions.
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Affiliation(s)
- Alexei Solovchenko
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (O.G.); (O.K.); (I.S.); (L.S.); (O.C.); (O.B.); (E.V.); (T.P.); (P.S.); (S.V.); (A.L.)
- Ecology Research Laboratory, Pskov State University, 180000 Pskov, Russia
- Institute of Natural Sciences, Derzhavin Tambov State University, 392000 Tambov, Russia
| | - Olga Gorelova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (O.G.); (O.K.); (I.S.); (L.S.); (O.C.); (O.B.); (E.V.); (T.P.); (P.S.); (S.V.); (A.L.)
| | - Olga Karpova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (O.G.); (O.K.); (I.S.); (L.S.); (O.C.); (O.B.); (E.V.); (T.P.); (P.S.); (S.V.); (A.L.)
| | - Irina Selyakh
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (O.G.); (O.K.); (I.S.); (L.S.); (O.C.); (O.B.); (E.V.); (T.P.); (P.S.); (S.V.); (A.L.)
| | - Larisa Semenova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (O.G.); (O.K.); (I.S.); (L.S.); (O.C.); (O.B.); (E.V.); (T.P.); (P.S.); (S.V.); (A.L.)
| | - Olga Chivkunova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (O.G.); (O.K.); (I.S.); (L.S.); (O.C.); (O.B.); (E.V.); (T.P.); (P.S.); (S.V.); (A.L.)
| | - Olga Baulina
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (O.G.); (O.K.); (I.S.); (L.S.); (O.C.); (O.B.); (E.V.); (T.P.); (P.S.); (S.V.); (A.L.)
| | - Elizaveta Vinogradova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (O.G.); (O.K.); (I.S.); (L.S.); (O.C.); (O.B.); (E.V.); (T.P.); (P.S.); (S.V.); (A.L.)
| | - Tatiana Pugacheva
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (O.G.); (O.K.); (I.S.); (L.S.); (O.C.); (O.B.); (E.V.); (T.P.); (P.S.); (S.V.); (A.L.)
| | - Pavel Scherbakov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (O.G.); (O.K.); (I.S.); (L.S.); (O.C.); (O.B.); (E.V.); (T.P.); (P.S.); (S.V.); (A.L.)
| | - Svetlana Vasilieva
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (O.G.); (O.K.); (I.S.); (L.S.); (O.C.); (O.B.); (E.V.); (T.P.); (P.S.); (S.V.); (A.L.)
| | - Alexandr Lukyanov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (O.G.); (O.K.); (I.S.); (L.S.); (O.C.); (O.B.); (E.V.); (T.P.); (P.S.); (S.V.); (A.L.)
| | - Elena Lobakova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (O.G.); (O.K.); (I.S.); (L.S.); (O.C.); (O.B.); (E.V.); (T.P.); (P.S.); (S.V.); (A.L.)
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Shilova IN, Magasin JD, Mills MM, Robidart JC, Turk-Kubo KA, Zehr JP. Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system. PLoS One 2020; 15:e0231771. [PMID: 32310982 PMCID: PMC7170224 DOI: 10.1371/journal.pone.0231771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/31/2020] [Indexed: 11/18/2022] Open
Abstract
Marine phytoplankton are responsible for approximately half of photosynthesis on Earth. However, their ability to drive ocean productivity depends on critical nutrients, especially bioavailable nitrogen (N) which is scarce over vast areas of the ocean. Phytoplankton differ in their preferences for N substrates as well as uptake efficiencies and minimal N requirements relative to other critical nutrients, including iron (Fe) and phosphorus. In this study, we used the MicroTOOLs high-resolution environmental microarray to examine transcriptomic responses of phytoplankton communities in the California Current System (CCS) transition zone to added urea, ammonium, nitrate, and also Fe in the late summer when N depletion is common. Transcript level changes of photosynthetic, carbon fixation, and nutrient stress genes indicated relief of N limitation in many strains of Prochlorococcus, Synechococcus, and eukaryotic phytoplankton. The transcriptomic responses helped explain shifts in physiological and growth responses observed later. All three phytoplankton groups had increased transcript levels of photosynthesis and/or carbon fixation genes in response to all N substrates. However, only Prochlorococcus had decreased transcript levels of N stress genes and grew substantially, specifically after urea and ammonium additions, suggesting that Prochlorococcus outcompeted other community members in these treatments. Diatom transcript levels of carbon fixation genes increased in response to Fe but not to Fe with N which might have favored phytoplankton that were co-limited by N and Fe. Moreover, transcription patterns of closely related strains indicated variability in N utilization, including nitrate utilization by some high-light adapted Prochlorococcus. Finally, up-regulation of urea transporter genes by both Prochlorococcus and Synechococcus in response to filtered deep water suggested a regulatory mechanism other than classic control via the global N regulator NtcA. This study indicated that co-existing phytoplankton strains experience distinct nutrient stresses in the transition zone of the CCS, an understudied region where oligotrophic and coastal communities naturally mix.
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Affiliation(s)
- Irina N. Shilova
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (INS); (JPZ)
| | - Jonathan D. Magasin
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Matthew M. Mills
- Department of Earth System Science, Stanford University, Stanford, California, United States of America
| | - Julie C. Robidart
- Ocean Technology and Engineering, National Oceanography Centre, Southampton, England, United Kingdom
| | - Kendra A. Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (INS); (JPZ)
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Nagappan S, Devendran S, Tsai PC, Jayaraman H, Alagarsamy V, Pugazhendhi A, Ponnusamy VK. Metabolomics integrated with transcriptomics and proteomics: Evaluation of systems reaction to nitrogen deficiency stress in microalgae. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.11.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Mechanical regulation of photosynthesis in cyanobacteria. Nat Microbiol 2020; 5:757-767. [PMID: 32203409 DOI: 10.1038/s41564-020-0684-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 02/04/2020] [Indexed: 12/17/2022]
Abstract
Photosynthetic organisms regulate their responses to many diverse stimuli in an effort to balance light harvesting with utilizable light energy for carbon fixation and growth (source-sink regulation). This balance is critical to prevent the formation of reactive oxygen species that can lead to cell death. However, investigating the molecular mechanisms that underlie the regulation of photosynthesis in cyanobacteria using ensemble-based measurements remains a challenge due to population heterogeneity. Here, to address this problem, we used long-term quantitative time-lapse fluorescence microscopy, transmission electron microscopy, mathematical modelling and genetic manipulation to visualize and analyse the growth and subcellular dynamics of individual wild-type and mutant cyanobacterial cells over multiple generations. We reveal that mechanical confinement of actively growing Synechococcus sp. PCC 7002 cells leads to the physical disassociation of phycobilisomes and energetic decoupling from the photosynthetic reaction centres. We suggest that the mechanical regulation of photosynthesis is a critical failsafe that prevents cell expansion when light and nutrients are plentiful, but when space is limiting. These results imply that cyanobacteria must convert a fraction of the available light energy into mechanical energy to overcome frictional forces in the environment, providing insight into the regulation of photosynthesis and how microorganisms navigate their physical environment.
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Ng I, Keskin BB, Tan S. A Critical Review of Genome Editing and Synthetic Biology Applications in Metabolic Engineering of Microalgae and Cyanobacteria. Biotechnol J 2020; 15:e1900228. [DOI: 10.1002/biot.201900228] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/07/2020] [Indexed: 12/13/2022]
Affiliation(s)
- I‐Son Ng
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
| | - Batuhan Birol Keskin
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
| | - Shih‐I Tan
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
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Zhou Y, Li X, Xia Q, Dai R. Transcriptomic survey on the microcystins production and growth of Microcystis aeruginosa under nitrogen starvation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 700:134501. [PMID: 31689655 DOI: 10.1016/j.scitotenv.2019.134501] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/15/2019] [Accepted: 09/15/2019] [Indexed: 06/10/2023]
Abstract
Cyanobacteria are a vital component of freshwater phytoplankton, and many species are recognized for their ability to produce toxins and harmful algal blooms (HABs). Nitrogen is an essential element of all the complex macromolecules in algal cells. However, the underlying molecular mechanism of the changes in transcriptomic patterns and physiological responses in response to N starvation is poorly understood. The transcriptomes were generated via RNA-sequencing (RNA-Seq) technology to study the major metabolic pathway under N starvation. The results shed light on the mechanism of toxin production and physiological adaptations in Microcystis aeruginosa (M. aeruginosa). The cell density gradually increased during the first two days then declined over time and was finally stable at (15.50 ± 0.5) × 105 cell mL-1 after 6 days. The chlorophyll-a content and phycocyanin content of M. aeruginosa increased during the first two days and subsequently decreased markedly over time under N starvation. The variable to maximum chlorophyll fluorescence ratio (Fv/Fm ratio) decreased with time under N starvation. Most photosynthesis genes have similarity decreasing trends with growth physiological changes. The microcystins (MCs) levels generally increased first, reaching a peak value with 1.35 pg cell-1 on the fifth day, and then remained roughly constant. The genes involved in N metabolism-related gene expression were upregulated to maintain normal biological activity, while the genes involved in photosynthesis-related gene expression were downregulated to save energy. All genes encoding algae toxin synthesis were upregulated under N starvation. The observed expression patterns demonstrate that all MCs genes respond similarly to MCs production within the cell. Our results indicate the response mechanism of M. aeruginosa under N starvation and provide a comprehensive understanding of N-controlling cyanobacteria and MCs synthesis.
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Affiliation(s)
- Yanping Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Xuan Li
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Qiongqiong Xia
- North China Municipal Engineering Design & Research Institute Co. Ltd., Tianjin 300074, China
| | - Ruihua Dai
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China.
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Kirilovsky D. Modulating Energy Transfer from Phycobilisomes to Photosystems: State Transitions and OCP-Related Non-Photochemical Quenching. PHOTOSYNTHESIS IN ALGAE: BIOCHEMICAL AND PHYSIOLOGICAL MECHANISMS 2020. [DOI: 10.1007/978-3-030-33397-3_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Hirai K, Nojo M, Sato Y, Tsuzuki M, Sato N. Contribution of protein synthesis depression to poly-β-hydroxybutyrate accumulation in Synechocystis sp. PCC 6803 under nutrient-starved conditions. Sci Rep 2019; 9:19944. [PMID: 31882765 PMCID: PMC6934822 DOI: 10.1038/s41598-019-56520-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 12/11/2019] [Indexed: 12/24/2022] Open
Abstract
Poly-β-hydroxybutyrate (PHB) in cyanobacteria, which accumulates as energy and carbon sources through the action of photosynthesis, is expected to substitute for petroleum-based plastics. This study first demonstrated that PHB accumulation was induced, with the appearance of lipid droplets, in sulfur (S)-starved cells of a cyanobacterium, Synechocystis sp. PCC 6803, however, to a lower level than in nitrogen (N)- or phosphorus (P)-starved cells. Concomitantly found was repression of the accumulation of total cellular proteins in the S-starved cells to a similar level to that in N-starved cells, and a severer level than in P-starved cells. Intriguingly, PHB accumulation was induced in Synechocystis even under nutrient-replete conditions, upon repression of the accumulation of total cellular proteins through treatment of the wild type cells with a protein synthesis inhibitor, chloramphenicol, or through disruption of the argD gene for Arg synthesis. Meanwhile, the expression of the genes for PHB synthesis was hardly induced in S-starved cells, in contrast to their definite up-regulation in N- or P-starved cells. It therefore seemed that PHB accumulation in S-starved cells is achieved through severe repression of protein synthesis, but is smaller than in N- or P-starved cells, owing to little induction of the expression of PHB synthesis genes.
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Affiliation(s)
- Kazuho Hirai
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Miki Nojo
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Yosuke Sato
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Mikio Tsuzuki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Norihiro Sato
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan.
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Maeda SI, Aoba R, Nishino Y, Omata T. A Novel Bacterial Nitrate Transporter Composed of Small Transmembrane Proteins. PLANT & CELL PHYSIOLOGY 2019; 60:2180-2192. [PMID: 31198965 DOI: 10.1093/pcp/pcz112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 05/27/2019] [Indexed: 06/09/2023]
Abstract
A putative silent gene of the freshwater cyanobacterium Synechococcus elongatus strain PCC 7942, encoding a small protein with two transmembrane helices, was named nrtS, since its overexpression from an inducible promoter conferred nitrate uptake activity on the nitrate transport-less NA4 mutant of S. elongatus. Homologs of nrtS, encoding proteins of 67-118 amino acid residues, are present in a limited number of eubacteria including mostly cyanobacteria and proteobacteria, but some others, e.g. the actinobacteria of the Mycobacterium tuberculosis complex, also have the gene. When expressed in NA4, the nrtS homolog of the γ-proteobacterium Marinomonas mediterranea took up nitrate with higher affinity for the substrate as compared with the S. elongatus NrtS (Km of 0.49 mM vs. 2.5 mM). Among the 61 bacterial species carrying the nrtS homolog, the marine cyanobacterium Synechococcus sp. strain PCC 7002 is unique in having two nrtS genes (nrtS1 and nrtS2) located in tandem on the chromosome. Coexpression of the two genes in NA4 resulted in nitrate uptake with a Km (NO3-) of 0.15 mM, while expression of either of the two resulted in low-affinity nitrate uptake activity with Km values of >3 mM, indicating that NrtS1 and NrtS2 form a heteromeric transporter complex. The heteromeric transporter was shown to transport nitrite as well. A Synechococcus sp. strain PCC 7002 mutant defective in the nitrate transporter (NrtP) showed a residual activity of nitrate uptake, which was ascribed to the NrtS proteins. Blue-native PAGE and immunoblotting analysis suggested a hexameric structure for the NrtS proteins.
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Affiliation(s)
- Shin-Ichi Maeda
- Laboratory of Photosynthesis Research, Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Risa Aoba
- Laboratory of Photosynthesis Research, Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Yuma Nishino
- Laboratory of Photosynthesis Research, Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Tatsuo Omata
- Laboratory of Photosynthesis Research, Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
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Veaudor T, Cassier-Chauvat C, Chauvat F. Genomics of Urea Transport and Catabolism in Cyanobacteria: Biotechnological Implications. Front Microbiol 2019; 10:2052. [PMID: 31551986 PMCID: PMC6737895 DOI: 10.3389/fmicb.2019.02052] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/20/2019] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are widely-diverse prokaryotes that colonize our planet. They use solar energy to assimilate huge amounts of atmospheric CO2 and produce a large part of the biomass and oxygen that sustain most life forms. Cyanobacteria are therefore increasingly studied for basic research objectives, as well as for the photosynthetic production of chemicals with industrial interests. One potential approach to reduce the cost of future bioproduction processes is to couple them with wastewater treatment, often polluted with urea, which in any case is cheaper than nitrate. As of yet, however, research has mostly focused on a very small number of model cyanobacteria growing on nitrate. Thus, the genetic inventory of the cyanobacterial phylum is still insufficiently employed to meaningfully select the right host for the right purpose. This review reports what is known about urea transport and catabolism in cyanobacteria, and what can be inferred from the comparative analysis of the publicly available genome sequence of the 308 cyanobacteria. We found that most cyanobacteria mostly harbor the genes encoding the urea catabolytic enzymes urease (ureABCDEFG), but not systematically, together with the urea transport (urtABCDE). These findings are consistent with the capacity of the few tested cyanobacteria that grow on urea as the sole nitrogen source. They also indicate that urease is important for the detoxification of internally generated urea (re-cycling its carbon and nitrogen). In contrast, several cyanobacteria have urtABCDE but not ureABCDEFG, suggesting that urtABCDE could operate in the transport of not only urea but also of other nutrients. Only four cyanobacteria appeared to have the genes encoding the urea carboxylase (uc) and allophanate hydrolase (ah) enzymes that sequentially catabolize urea. Three of these cyanobacteria belongs to the genera Gloeobacter and Gloeomargarita that have likely diverged early from other cyanobacteria, suggesting that the urea carboxylase and allophanate hydrolase enzymes appeared in cyanobacteria before urease.
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Affiliation(s)
- Théo Veaudor
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Corinne Cassier-Chauvat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Franck Chauvat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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33
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Carmichael JR, Zhou H, Butler A. A suite of asymmetric citrate siderophores isolated from a marine Shewanella species. J Inorg Biochem 2019; 198:110736. [DOI: 10.1016/j.jinorgbio.2019.110736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 10/26/2022]
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Årstøl E, Hohmann-Marriott MF. Cyanobacterial Siderophores-Physiology, Structure, Biosynthesis, and Applications. Mar Drugs 2019; 17:E281. [PMID: 31083354 PMCID: PMC6562677 DOI: 10.3390/md17050281] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 11/16/2022] Open
Abstract
Siderophores are low-molecular-weight metal chelators that function in microbial iron uptake. As iron limits primary productivity in many environments, siderophores are of great ecological importance. Additionally, their metal binding properties have attracted interest for uses in medicine and bioremediation. Here, we review the current state of knowledge concerning the siderophores produced by cyanobacteria. We give an overview of all cyanobacterial species with known siderophore production, finding siderophores produced in all but the most basal clades, and in a wide variety of environments. We explore what is known about the structure, biosynthesis, and cycling of the cyanobacterial siderophores that have been characterized: Synechobactin, schizokinen and anachelin. We also highlight alternative siderophore functionality and technological potential, finding allelopathic effects on competing phytoplankton and likely roles in limiting heavy-metal toxicity. Methodological improvements in siderophore characterization and detection are briefly described. Since most known cyanobacterial siderophores have not been structurally characterized, the application of mass spectrometry techniques will likely reveal a breadth of variation within these important molecules.
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Affiliation(s)
- Erland Årstøl
- Department of Biotechnology, PhotoSynLab, Norwegian University of Science and Technology, 7491 Trondheim, Norway.
| | - Martin F Hohmann-Marriott
- Department of Biotechnology, PhotoSynLab, Norwegian University of Science and Technology, 7491 Trondheim, Norway.
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Zhou Y, Zhang X, Li X, Jia P, Dai R. Evaluation of changes in Microcystis aeruginosa growth and microcystin production by urea via transcriptomic surveys. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 655:181-187. [PMID: 30469064 DOI: 10.1016/j.scitotenv.2018.11.100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
The freshwater cyanobacteria, Microcystis aeruginosa (M. aeruginosa), is well known to produce microcystins (MCs) and induce the formation of harmful algal blooms (HABs) in aquatic environments, but the effects that urea fertilizer has on cyanobacterial growth and toxin production from a molecular biology perspective remain poorly understood. We evaluated changes in the growth and toxicity of M. aeruginosa cultured under different conditions of nitrogen (N) starvation (NN), low nitrogen (LN), and high nitrogen (HN). Cell density and chlorophyll-a concentrations decreased in cyanobacteria exposed to N starvation and increased following the addition of urea, whereas MCs content increased to a peak and then decreased after urea addition. Transcriptomic analysis confirmed that most genes encoding MCs and genes involved in N metabolic pathways were upregulated under N starvation and LN conditions, whereas these genes were downregulated under HN conditions. Our results offer important insights into the exploring N in controlling the formation of HABs and toxin production based on both physiological and molecular response.
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Affiliation(s)
- Yanping Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Xufeng Zhang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Xuan Li
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Peili Jia
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Ruihua Dai
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China.
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36
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Selão TT, Jebarani J, Ismail NA, Norling B, Nixon PJ. Enhanced Production of D-Lactate in Cyanobacteria by Re-Routing Photosynthetic Cyclic and Pseudo-Cyclic Electron Flow. FRONTIERS IN PLANT SCIENCE 2019; 10:1700. [PMID: 32117327 PMCID: PMC7025493 DOI: 10.3389/fpls.2019.01700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/03/2019] [Indexed: 05/22/2023]
Abstract
Cyanobacteria are promising chassis strains for the photosynthetic production of platform and specialty chemicals from carbon dioxide. Their efficient light harvesting and metabolic flexibility abilities have allowed a wide range of biomolecules, such as the bioplastic polylactate precursor D-lactate, to be produced, though usually at relatively low yields. In order to increase photosynthetic electron flow towards the production of D-lactate, we have generated several strains of the marine cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) with deletions in genes involved in cyclic or pseudo-cyclic electron flow around photosystem I. Using a variant of the Chlamydomonas reinhardtii D-lactate dehydrogenase (LDHSRT, engineered to efficiently utilize NADPH in vivo), we have shown that deletion of either of the two flavodiiron flv homologs (involved in pseudo-cyclic electron transport) or the Syn7002 pgr5 homolog (proposed to be a vital part of the cyclic electron transport pathway) is able to increase D-lactate production in Syn7002 strains expressing LDHSRT and the Escherichia coli LldP (lactate permease), especially at low temperature (25°C) and 0.04% (v/v) CO2, though at elevated temperatures (38°C) and/or high (1%) CO2 concentrations, the effect was less obvious. The Δpgr5 background seemed to be particularly beneficial at 25°C and 0.04% (v/v) CO2, with a nearly 7-fold increase in D-lactate accumulation in comparison to the wild-type background (≈1000 vs ≈150 mg/L) and decreased side effects in comparison to the flv deletion strains. Overall, our results show that manipulation of photosynthetic electron flow is a viable strategy to increase production of platform chemicals in cyanobacteria under ambient conditions.
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Affiliation(s)
- Tiago Toscano Selão
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jasmin Jebarani
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nurul Aina Ismail
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Birgitta Norling
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Peter Julian Nixon
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Life Sciences, Imperial College London, London, United Kingdom
- *Correspondence: Peter Julian Nixon,
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37
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Grund M, Jakob T, Wilhelm C, Bühler B, Schmid A. Electron balancing under different sink conditions reveals positive effects on photon efficiency and metabolic activity of Synechocystis sp. PCC 6803. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:43. [PMID: 30858880 PMCID: PMC6391784 DOI: 10.1186/s13068-019-1378-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/14/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Cyanobacteria are ideal model organisms to exploit photosynthetically derived electrons or fixed carbon for the biotechnological synthesis of high value compounds and energy carriers. Much effort is spent on the rational design of heterologous pathways to produce value-added chemicals. Much less focus is drawn on the basic physiological responses and potentials of phototrophs to deal with natural or artificial electron and carbon sinks. However, an understanding of how electron sinks influence or regulate cellular physiology is essential for the efficient application of phototrophic organisms in an industrial setting, i.e., to achieve high productivities and product yields. RESULTS The physiological responses of the cyanobacterium Synechocystis sp. PCC 6803 to electron sink variation were investigated in a systematic and quantitative manner. A variation in electron demand was achieved by providing two N sources with different degrees of reduction. By additionally varying light and CO2 availabilities, steady state conditions with strongly differing source-sink ratios were established. Balancing absorbed photons and electrons used for different metabolic processes revealed physiological responses to sink/source ratio variation. Surprisingly, an additional electron sink under light and thus energy limitation was found not to hamper growth, but was compensated by improved photosynthetic efficiency and activity. In the absence of carbon and light limitation, an increase in electron demand even stimulated carbon assimilation and growth. CONCLUSION The metabolism of Synechocystis sp. PCC 6803 is highly flexible regarding the compensation of additional electron demands. Under light limitation, photosynthesis obviously does not necessarily run at its maximal capacity, possibly for the sake of robustness. Increased electron demands can even boost photosynthetic activity and growth.
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Affiliation(s)
- Marcel Grund
- Department of Solar Materials, Helmholtz Center for Environmental Research GmbH–UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Torsten Jakob
- Plant Physiology Group, Institute for Biology, University of Leipzig, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Christian Wilhelm
- Plant Physiology Group, Institute for Biology, University of Leipzig, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Center for Environmental Research GmbH–UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Andreas Schmid
- Department of Solar Materials, Helmholtz Center for Environmental Research GmbH–UFZ, Permoserstraße 15, 04318 Leipzig, Germany
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38
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Forchhammer K, Schwarz R. Nitrogen chlorosis in unicellular cyanobacteria – a developmental program for surviving nitrogen deprivation. Environ Microbiol 2018; 21:1173-1184. [DOI: 10.1111/1462-2920.14447] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/04/2018] [Accepted: 10/09/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, University Tübingen Auf der Morgenstelle 28, 72076 Tübingen Germany
| | - Rakefet Schwarz
- The Mina & Everard Goodman Faculty of Life SciencesBar‐Ilan University Ramat‐Gan 5290002 Israel
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39
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Bolay P, Muro-Pastor MI, Florencio FJ, Klähn S. The Distinctive Regulation of Cyanobacterial Glutamine Synthetase. Life (Basel) 2018; 8:E52. [PMID: 30373240 PMCID: PMC6316151 DOI: 10.3390/life8040052] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/23/2018] [Accepted: 10/25/2018] [Indexed: 12/02/2022] Open
Abstract
Glutamine synthetase (GS) features prominently in bacterial nitrogen assimilation as it catalyzes the entry of bioavailable nitrogen in form of ammonium into cellular metabolism. The classic example, the comprehensively characterized GS of enterobacteria, is subject to exquisite regulation at multiple levels, among them gene expression regulation to control GS abundance, as well as feedback inhibition and covalent modifications to control enzyme activity. Intriguingly, the GS of the ecologically important clade of cyanobacteria features fundamentally different regulatory systems to those of most prokaryotes. These include the interaction with small proteins, the so-called inactivating factors (IFs) that inhibit GS linearly with their abundance. In addition to this protein interaction-based regulation of GS activity, cyanobacteria use alternative elements to control the synthesis of GS and IFs at the transcriptional level. Moreover, cyanobacteria evolved unique RNA-based regulatory mechanisms such as glutamine riboswitches to tightly tune IF abundance. In this review, we aim to outline the current knowledge on the distinctive features of the cyanobacterial GS encompassing the overall control of its activity, sensing the nitrogen status, transcriptional and post-transcriptional regulation, as well as strain-specific differences.
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Affiliation(s)
- Paul Bolay
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Permoserstrasse 15, D-04318 Leipzig, Germany.
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Américo Vespucio 49, E-41092 Seville, Spain.
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Américo Vespucio 49, E-41092 Seville, Spain.
| | - Stephan Klähn
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Permoserstrasse 15, D-04318 Leipzig, Germany.
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40
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Biogenic Polyphosphate Nanoparticles from a Marine Cyanobacterium Synechococcus sp. PCC 7002: Production, Characterization, and Anti-Inflammatory Properties In Vitro. Mar Drugs 2018; 16:md16090322. [PMID: 30201855 PMCID: PMC6163655 DOI: 10.3390/md16090322] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/05/2018] [Accepted: 09/05/2018] [Indexed: 11/25/2022] Open
Abstract
Probiotic-derived polyphosphates have attracted interest as potential therapeutic agents to improve intestinal health. The current study discovered the intracellular accumulation of polyphosphates in a marine cyanobacterium Synechococcus sp. PCC 7002 as nano-sized granules. The maximum accumulation of polyphosphates in Synechococcus sp. PCC 7002 was found at the late logarithmic growth phase when the medium contained 0.74 mM of KH2PO4, 11.76 mM of NaNO3, and 30.42 mM of Na2SO4. Biogenic polyphosphate nanoparticles (BPNPs) were obtained intact from the algae cells by hot water extraction, and were purified to remove the organic impurities by Sephadex G-100 gel filtration. By using 100 kDa ultrafiltration, BPNPs were fractionated into the larger and smaller populations with diameters ranging between 30–70 nm and 10–30 nm, respectively. 4′,6-diamidino-2-phenylindole fluorescence and orthophosphate production revealed that a minor portion of BPNPs (about 14–18%) were degraded during simulated gastrointestinal digestion. In vitro studies using lipopolysaccharide-activated RAW264.7 cells showed that BPNPs inhibited cyclooxygenase-2, inducible nitric oxide (NO) synthase expression, and the production of proinflammatory mediators, including NO, tumor necrosis factor-α, interleukin-6, and interleukin-1β through suppressing the Toll-like receptor 4/NF-κB signaling pathway. Overall, there is promise in the use of the marine cyanobacterium Synechococcus sp. PCC 7002 to produce BPNPs, an anti-inflammatory postbiotic.
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Blanco-Ameijeiras S, Moisset SAM, Trimborn S, Campbell DA, Heiden JP, Hassler CS. Elemental Stoichiometry and Photophysiology Regulation of Synechococcus sp. PCC7002 Under Increasing Severity of Chronic Iron Limitation. PLANT & CELL PHYSIOLOGY 2018; 59:1803-1816. [PMID: 29860486 DOI: 10.1093/pcp/pcy097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
Iron (Fe) is an essential cofactor for many metabolic enzymes of photoautotrophs. Although Fe limits phytoplankton productivity in broad areas of the ocean, phytoplankton have adapted their metabolism and growth to survive in these conditions. Using the euryhaline cyanobacterium Synechococcus sp. PCC7002, we investigated the physiological responses to long-term acclimation to four levels of Fe availability representative of the contemporary ocean (36.7, 3.83, 0.47 and 0.047 pM Fe'). With increasing severity of Fe limitation, Synechococcus sp. cells gradually decreased their volume and growth while increasing their energy allocation into organic carbon and nitrogen cellular pools. Furthermore, the total cellular content of pigments decreased. Additionally, with increasing severity of Fe limitation, intertwined responses of PSII functional cross-section (σPSII), re-oxidation time of the plastoquinone primary acceptor QA (τ) and non-photochemical quenching revealed a shift in the photophysiological response between mild to strong Fe limitation compared with severe limitation. Under mild and strong Fe limitation, there was a decrease in linear electron transport accompanied by progressive loss of state transitions. Under severe Fe limitation, state transitions seemed to be largely supplanted by alternative electron pathways. In addition, mechanisms to dissipate energy excess and minimize oxidative stress associated with high irradiances increased with increasing severity of Fe limitation. Overall, our results establish the sequence of physiological strategies adopted by the cells under increasing severity of chronic Fe limitation, within a range of Fe concentrations relevant to modern ocean biogeochemistry.
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Affiliation(s)
- Sonia Blanco-Ameijeiras
- Department F.-A. Forel for Environmental and Aquatic Sciences, Faculty of Science, University of Geneva, Boulevard Carl-Vogt 66, Geneva 4, Switzerland
| | - Sophie A M Moisset
- Department F.-A. Forel for Environmental and Aquatic Sciences, Faculty of Science, University of Geneva, Boulevard Carl-Vogt 66, Geneva 4, Switzerland
| | - Scarlett Trimborn
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, Germany
- Marine Botany, University of Bremen, Leobener Strasse NW2-A, Bremen, Germany
| | - Douglas A Campbell
- Biology, Faculty of Science, Mount Allison University, Sackville, NB, Canada
| | - Jasmin P Heiden
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, Germany
- Marine Botany, University of Bremen, Leobener Strasse NW2-A, Bremen, Germany
| | - Christel S Hassler
- Department F.-A. Forel for Environmental and Aquatic Sciences, Faculty of Science, University of Geneva, Boulevard Carl-Vogt 66, Geneva 4, Switzerland
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42
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Liu X, Yang M, Wang Y, Chen Z, Zhang J, Lin X, Ge F, Zhao J. Effects of PSII Manganese-Stabilizing Protein Succinylation on Photosynthesis in the Model Cyanobacterium Synechococcus sp. PCC 7002. PLANT & CELL PHYSIOLOGY 2018; 59:1466-1482. [PMID: 29912468 DOI: 10.1093/pcp/pcy080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 04/14/2018] [Indexed: 06/08/2023]
Abstract
Lysine succinylation is a newly identified protein post-translational modification and plays important roles in various biological pathways in both prokaryotes and eukaryotes, but its extent and function in photosynthetic organisms remain largely unknown. Here, we performed the first systematic studies of lysine succinylation in cyanobacteria, which are the only prokaryotes capable of oxygenic photosynthesis and the established model organisms for studying photosynthetic mechanisms. By using mass spectrometry analysis in combination with the enrichment of succinylated peptides from digested cell lysates, we identified 1,704 lysine succinylation sites on 691 proteins in a model cyanobacterium Synechococcus sp. PCC 7002. Bioinformatic analysis revealed that a large proportion of the succinylation sites were present on proteins in photosynthesis and metabolism. Among all identified succinylated proteins involved in photosynthesis, the PSII manganese-stabilizing protein (PsbO) was found to be succinylated on Lys99 and Lys234. Functional studies of PsbO were performed by site-directed mutagenesis, and mutants mimicking either constitutively succinylated (K99E and K234E) or non-succinylated states (K99R and K234R) were constructed. The succinylation-mimicking K234E mutant exhibited a decreased oxygen evolution rate of the PSII center and the efficiency of energy transfer during the photosynthetic reaction. Molecular dynamics simulations suggested a mechanism that may allow succinylation to influence the efficiency of photosynthesis by altering the conformation of PsbO, thereby hindering the interaction between PsbO and the PSII core. Our findings suggest that reversible succinylation may be an important regulatory mechanism during photosynthesis in Synechococcus, as well as in other photosynthetic organisms.
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Affiliation(s)
- Xin Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingkun Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yan Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhuo Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jia Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaohuang Lin
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jindong Zhao
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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43
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Shimmori Y, Kanesaki Y, Nozawa M, Yoshikawa H, Ehira S. Transcriptional Activation of Glycogen Catabolism and the Oxidative Pentose Phosphate Pathway by NrrA Facilitates Cell Survival Under Nitrogen Starvation in the Cyanobacterium Synechococcus sp. Strain PCC 7002. PLANT & CELL PHYSIOLOGY 2018; 59:1225-1233. [PMID: 29566230 DOI: 10.1093/pcp/pcy059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/14/2018] [Indexed: 06/08/2023]
Abstract
Cyanobacteria respond to nitrogen deprivation by changing cellular metabolism. Glycogen is accumulated within cells to assimilate excess carbon and energy during nitrogen starvation, and inhibition of glycogen synthesis results in impaired nitrogen response and decreased ability to survive. In spite of glycogen accumulation, genes related to glycogen catabolism are up-regulated by nitrogen deprivation. In this study, we found that glycogen catabolism was also involved in acclimation to nitrogen deprivation in the cyanobacterium Synechococcus sp. PCC 7002. The glgP2 gene, encoding glycogen phosphorylase, was induced by nitrogen deprivation, and its expression was regulated by the nitrogen-regulated response regulator A (NrrA), which is a highly conserved transcriptional regulator in cyanobacteria. Activation of glycogen phosphorylase under nitrogen-deprived conditions was abolished by disruption of the nrrA gene, and survival of the nrrA mutant declined. In addition, a glgP2 mutant was highly susceptible to nitrogen starvation. NrrA also regulated expression of the tal-zwf-opcA operon, encoding enzymes of the oxidative pentose phosphate (OPP) pathway, and inactivation of glucose-6-phosphate dehydrogenase, the first enzyme of the OPP pathway, decreased the ability to survive under nitrogen starvation. It was concluded that NrrA facilitates cell survival by activating glycogen degradation and the OPP pathway under nitrogen-deprived conditions.
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Affiliation(s)
- Yuka Shimmori
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Masafumi Nozawa
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan
| | | | - Shigeki Ehira
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
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Qian X, Zhang Y, Lun DS, Dismukes GC. Rerouting of Metabolism into Desired Cellular Products by Nutrient Stress: Fluxes Reveal the Selected Pathways in Cyanobacterial Photosynthesis. ACS Synth Biol 2018; 7:1465-1476. [PMID: 29617123 DOI: 10.1021/acssynbio.8b00116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Boosting cellular growth rates while redirecting metabolism to make desired products are the preeminent goals of gene engineering of photoautotrophs, yet so far these goals have been hardly achieved owing to lack of understanding of the functional pathways and their choke points. Here we apply a 13C mass isotopic method (INST-MFA) to quantify instantaneous fluxes of metabolites during photoautotrophic growth. INST-MFA determines the globally most accurate set of absolute fluxes for each metabolite from a finite set of measured 13C-isotopomer fluxes by minimizing the sum of squared residuals between experimental and predicted mass isotopomers. We show that the widely observed shift in biomass composition in cyanobacteria, demonstrated here with Synechococcus sp. PCC 7002, favoring glycogen synthesis during nitrogen starvation is caused by (1) increased flux through a bottleneck step in gluconeogenesis (3PG → GAP/DHAP), and (2) flux overflow through a previously unrecognized hybrid gluconeogenesis-pentose phosphate (hGPP) pathway. Our data suggest the slower growth rate and biomass accumulation under N starvation is due to a reduced carbon fixation rate and a reduced flux of carbon into amino acid precursors. Additionally, 13C flux from α-ketoglutarate to succinate is demonstrated to occur via succinic semialdehyde, an alternative to the conventional TCA cycle, in Synechococcus 7002 under photoautotrophic conditions. We found that pyruvate and oxaloacetate are synthesized mainly by malate dehydrogenase with minimal flux into acetyl coenzyme-A via pyruvate dehydrogenase. Nutrient stress induces major shifts in fluxes into new pathways that deviate from historical metabolic pathways derived from model bacteria.
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Affiliation(s)
- Xiao Qian
- Waksman Institute, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Yuan Zhang
- Waksman Institute, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Desmond S. Lun
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, United States
- Department of Computer Science, Rutgers University, Camden, New Jersey 08102, United States
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - G. Charles Dismukes
- Waksman Institute, Rutgers University, New Brunswick, New Jersey 08854, United States
- Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
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Clark RL, McGinley LL, Purdy HM, Korosh TC, Reed JL, Root TW, Pfleger BF. Light-optimized growth of cyanobacterial cultures: Growth phases and productivity of biomass and secreted molecules in light-limited batch growth. Metab Eng 2018; 47:230-242. [PMID: 29601856 PMCID: PMC5984190 DOI: 10.1016/j.ymben.2018.03.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/23/2018] [Accepted: 03/25/2018] [Indexed: 11/22/2022]
Abstract
Cyanobacteria are photosynthetic microorganisms whose metabolism can be modified through genetic engineering for production of a wide variety of molecules directly from CO2, light, and nutrients. Diverse molecules have been produced in small quantities by engineered cyanobacteria to demonstrate the feasibility of photosynthetic biorefineries. Consequently, there is interest in engineering these microorganisms to increase titer and productivity to meet industrial metrics. Unfortunately, differing experimental conditions and cultivation techniques confound comparisons of strains and metabolic engineering strategies. In this work, we discuss the factors governing photoautotrophic growth and demonstrate nutritionally replete conditions in which a model cyanobacterium can be grown to stationary phase with light as the sole limiting substrate. We introduce a mathematical framework for understanding the dynamics of growth and product secretion in light-limited cyanobacterial cultures. Using this framework, we demonstrate how cyanobacterial growth in differing experimental systems can be easily scaled by the volumetric photon delivery rate using the model organisms Synechococcus sp. strain PCC7002 and Synechococcus elongatus strain UTEX2973. We use this framework to predict scaled up growth and product secretion in 1L photobioreactors of two strains of Synechococcus PCC7002 engineered for production of l-lactate or L-lysine. The analytical framework developed in this work serves as a guide for future metabolic engineering studies of cyanobacteria to allow better comparison of experiments performed in different experimental systems and to further investigate the dynamics of growth and product secretion.
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Affiliation(s)
- Ryan L Clark
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States.
| | - Laura L McGinley
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States.
| | - Hugh M Purdy
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States.
| | - Travis C Korosh
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States; Department of Environmental Chemistry and Technology, University of Wisconsin - Madison, 660 N Park St., Madison, WI 53706, United States.
| | - Jennifer L Reed
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States.
| | - Thatcher W Root
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States.
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, 1415 Engineering Dr., Madison, WI 53706, United States.
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Pérez AA, Ferlez BH, Applegate AM, Walters K, He Z, Shen G, Golbeck JH, Bryant DA. Presence of a [3Fe-4S] cluster in a PsaC variant as a functional component of the photosystem I electron transfer chain in Synechococcus sp. PCC 7002. PHOTOSYNTHESIS RESEARCH 2018; 136:31-48. [PMID: 28916964 DOI: 10.1007/s11120-017-0437-0] [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: 06/29/2017] [Accepted: 08/23/2017] [Indexed: 06/07/2023]
Abstract
A site-directed C14G mutation was introduced into the stromal PsaC subunit of Synechococcus sp. strain PCC 7002 in vivo in order to introduce an exchangeable coordination site into the terminal FB [4Fe-4S] cluster of Photosystem I (PSI). Using an engineered PSI-less strain (psaAB deletion), psaC was deleted and replaced with recombinant versions controlled by a strong promoter, and the psaAB deletion was complemented. Modified PSI accumulated at lower levels in this strain and supported slower photoautotrophic growth than wild type. As-isolated PSI complexes containing PsaCC14G showed resonances with g values of 2.038 and 2.007 characteristic of a [3Fe-4S]1+ cluster. When the PSI complexes were illuminated at 15 K, these resonances partially disappeared and two new sets of resonances appeared. The majority set had g values of 2.05, 1.95, and 1.85, characteristic of FA-, and the minority set had g values of 2.11, 1.90, and 1.88 from FB' in the modified site. The S = 1/2 spin state of the latter implied the presence of a thiolate as the terminal ligand. The [3Fe-4S] clusters could be partially reconstituted with iron, producing a larger population of [4Fe-4S] clusters. Rates of flavodoxin reduction were identical in PSI complexes isolated from wild type and the PsaCC14G variant strain; this implied equivalent capacity for forward electron transfer in PSI complexes that contained [3Fe-4S] and [4Fe-4S] clusters. The development of this cyanobacterial strain is a first step toward translation of in vitro PSI-based biosolar molecular wire systems in vivo and provides new insights into the formation of Fe/S clusters.
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Affiliation(s)
- Adam A Pérez
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Bryan H Ferlez
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 28824, USA
| | - Amanda M Applegate
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
- Musculoskeletal Transplant Foundation, Jessup, PA, 18434, USA
| | - Karim Walters
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Zhihui He
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA.
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Chrismas NAM, Anesio AM, Sánchez-Baracaldo P. The future of genomics in polar and alpine cyanobacteria. FEMS Microbiol Ecol 2018; 94:4904125. [PMID: 29506259 PMCID: PMC5939894 DOI: 10.1093/femsec/fiy032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/23/2018] [Indexed: 01/01/2023] Open
Abstract
In recent years, genomic analyses have arisen as an exciting way of investigating the functional capacity and environmental adaptations of numerous micro-organisms of global relevance, including cyanobacteria. In the extreme cold of Arctic, Antarctic and alpine environments, cyanobacteria are of fundamental ecological importance as primary producers and ecosystem engineers. While their role in biogeochemical cycles is well appreciated, little is known about the genomic makeup of polar and alpine cyanobacteria. In this article, we present ways that genomic techniques might be used to further our understanding of cyanobacteria in cold environments in terms of their evolution and ecology. Existing examples from other environments (e.g. marine/hot springs) are used to discuss how methods developed there might be used to investigate specific questions in the cryosphere. Phylogenomics, comparative genomics and population genomics are identified as methods for understanding the evolution and biogeography of polar and alpine cyanobacteria. Transcriptomics will allow us to investigate gene expression under extreme environmental conditions, and metagenomics can be used to complement tradition amplicon-based methods of community profiling. Finally, new techniques such as single cell genomics and metagenome assembled genomes will also help to expand our understanding of polar and alpine cyanobacteria that cannot readily be cultured.
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Affiliation(s)
- Nathan A M Chrismas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
| | - Alexandre M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
| | - Patricia Sánchez-Baracaldo
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
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Badary A, Takamatsu S, Nakajima M, Ferri S, Lindblad P, Sode K. Glycogen Production in Marine Cyanobacterial Strain Synechococcus sp. NKBG 15041c. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:109-117. [PMID: 29330710 DOI: 10.1007/s10126-017-9792-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/15/2017] [Indexed: 06/07/2023]
Abstract
An important feature offered by marine cyanobacterial strains over freshwater strains is the capacity to grow in seawater, replacing the need for often-limited freshwater. However, there are only limited numbers of marine cyanobacteria that are available for genetic manipulation and bioprocess applications. The marine unicellular cyanobacteria Synechococcus sp. strain NKBG 15041c (NKBG15041c) has been extensively studied. Recombinant DNA technologies are available for this strain, and its genomic information has been elucidated. However, an investigation of carbohydrate production, such as glycogen production, would provide information for inevitable biofuel-related compound production, but it has not been conducted. In this study, glycogen production by marine cyanobacterium NKBG15041c was investigated under different cultivation conditions. NKBG15041c yielded up to 399 μg/ml/OD730 when cells were cultivated for 168 h in nitrogen-depleted medium (marine BG11ΔN) after medium replacement (336 h after inoculation). Cultivation under nitrogen-limited conditions also yielded an accumulation of glycogen in NKBG15041c cells (1 mM NaNO3, 301 μg/ml/OD730; 3 mM NaNO3, 393 μg/ml/OD730; and 5 mM NaNO3, 328 μg/ml/OD730) under ambient conditions. Transcriptional analyses were carried out for 13 putative genes responsible for glycogen synthesis and catabolism that were predicted based on homology analyses with Synechocystis sp. PCC 6803 (PCC6803) and Synechococcus sp. PCC7002 (PCC7002). The transcriptional analyses revealed that glycogen production in NKBG15041c under nitrogen-depleted conditions can be explained by the contribution of both increased carbon flux towards glycogen synthesis, similar to PCC6803 and PCC7002, and increased transcriptional levels of genes responsible for glycogen synthesis, which is different from the conventionally reported phenomenon, resulting in a relatively high amount of glycogen under ambient conditions compared to PCC6803 and PCC7002.
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Affiliation(s)
- Amr Badary
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
- JST, CREST, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Shouhei Takamatsu
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
- JST, CREST, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Mitsuharu Nakajima
- JST, CREST, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo, 183-8538, Japan
| | - Stefano Ferri
- JST, CREST, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
- Department of Applied Chemistry and Biochemical Engineering, Shizuoka University, 3-5-1 Johoku, Naka-Ku, Hamamatsu, Shizuoka, 432-8561, Japan
| | - Peter Lindblad
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, SE-751 20, Uppsala, Sweden
| | - Koji Sode
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
- JST, CREST, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo, 183-8538, Japan.
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49
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Esteves-Ferreira AA, Inaba M, Fort A, Araújo WL, Sulpice R. Nitrogen metabolism in cyanobacteria: metabolic and molecular control, growth consequences and biotechnological applications. Crit Rev Microbiol 2018. [DOI: 10.1080/1040841x.2018.1446902] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Alberto A. Esteves-Ferreira
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, Brazil
| | - Masami Inaba
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
| | - Antoine Fort
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
| | - Wagner L. Araújo
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Ronan Sulpice
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
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50
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Shimakawa G, Watanabe S, Miyake C. A Carbon Dioxide Limitation-Inducible Protein, ColA, Supports the Growth of Synechococcus sp. PCC 7002. Mar Drugs 2017; 15:md15120390. [PMID: 29244744 PMCID: PMC5742850 DOI: 10.3390/md15120390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/30/2017] [Accepted: 12/09/2017] [Indexed: 11/16/2022] Open
Abstract
A limitation in carbon dioxide (CO₂), which occurs as a result of natural environmental variation, suppresses photosynthesis and has the potential to cause photo-oxidative damage to photosynthetic cells. Oxygenic phototrophs have strategies to alleviate photo-oxidative damage to allow life in present atmospheric CO₂ conditions. However, the mechanisms for CO₂ limitation acclimation are diverse among the various oxygenic phototrophs, and many mechanisms remain to be discovered. In this study, we found that the gene encoding a CO₂ limitation-inducible protein, ColA, is required for the cyanobacterium Synechococcus sp. PCC 7002 (S. 7002) to acclimate to limited CO₂ conditions. An S. 7002 mutant deficient in ColA (ΔcolA) showed lower chlorophyll content, based on the amount of nitrogen, than that in S. 7002 wild-type (WT) under ambient air but not high CO₂ conditions. Both thermoluminescence and protein carbonylation detected in the ambient air grown cells indicated that the lack of ColA promotes oxidative stress in S. 7002. Alterations in the photosynthetic O₂ evolution rate and relative electron transport rate in the short-term response, within an hour, to CO₂ limitation were the same between the WT and ΔcolA. Conversely, these photosynthetic parameters were mostly lower in the long-term response of a few days in ΔcolA than in the WT. These data suggest that ColA is required to sustain photosynthetic activity for living under ambient air in S. 7002. The unique phylogeny of ColA revealed diverse strategies to acclimate to CO₂ limitation among cyanobacteria.
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Affiliation(s)
- Ginga Shimakawa
- Department of Biological and Environmental Science, Faculty of Agriculture, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan.
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan.
| | - Chikahiro Miyake
- Department of Biological and Environmental Science, Faculty of Agriculture, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan.
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