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Srivastava R, Singh N, Kanda T, Yadav S, Yadav S, Atri N. Cyanobacterial Proteomics: Diversity and Dynamics. J Proteome Res 2024. [PMID: 38470568 DOI: 10.1021/acs.jproteome.3c00779] [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: 03/14/2024]
Abstract
Cyanobacteria (oxygenic photoautrophs) comprise a diverse group holding significance both environmentally and for biotechnological applications. The utilization of proteomic techniques has significantly influenced investigations concerning cyanobacteria. Application of proteomics allows for large-scale analysis of protein expression and function within cyanobacterial systems. The cyanobacterial proteome exhibits tremendous functional, spatial, and temporal diversity regulated by multiple factors that continuously modify protein abundance, post-translational modifications, interactions, localization, and activity to meet the dynamic needs of these tiny blue greens. Modern mass spectrometry-based proteomics techniques enable system-wide examination of proteome complexity through global identification and high-throughput quantification of proteins. These powerful approaches have revolutionized our understanding of proteome dynamics and promise to provide novel insights into integrated cellular behavior at an unprecedented scale. In this Review, we present modern methods and cutting-edge technologies employed for unraveling the spatiotemporal diversity and dynamics of cyanobacterial proteomics with a specific focus on the methods used to analyze post-translational modifications (PTMs) and examples of dynamic changes in the cyanobacterial proteome investigated by proteomic approaches.
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Affiliation(s)
| | - Nidhi Singh
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Tripti Kanda
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Sadhana Yadav
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Shivam Yadav
- Department of Botany, University of Allahabad, Allahabad 211002, India
| | - Neelam Atri
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
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Muth-Pawlak D, Kreula S, Gollan PJ, Huokko T, Allahverdiyeva Y, Aro EM. Patterning of the Autotrophic, Mixotrophic, and Heterotrophic Proteomes of Oxygen-Evolving Cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 2022; 13:891895. [PMID: 35694301 PMCID: PMC9175036 DOI: 10.3389/fmicb.2022.891895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Proteomes of an oxygenic photosynthetic cyanobacterium, Synechocystis sp. PCC 6803, were analyzed under photoautotrophic (low and high CO2, assigned as ATLC and ATHC), photomixotrophic (MT), and light-activated heterotrophic (LAH) conditions. Allocation of proteome mass fraction to seven sub-proteomes and differential expression of individual proteins were analyzed, paying particular attention to photosynthesis and carbon metabolism–centered sub-proteomes affected by the quality and quantity of the carbon source and light regime upon growth. A distinct common feature of the ATHC, MT, and LAH cultures was low abundance of inducible carbon-concentrating mechanisms and photorespiration-related enzymes, independent of the inorganic or organic carbon source. On the other hand, these cells accumulated a respiratory NAD(P)H dehydrogenase I (NDH-11) complex in the thylakoid membrane (TM). Additionally, in glucose-supplemented cultures, a distinct NDH-2 protein, NdbA, accumulated in the TM, while the plasma membrane-localized NdbC and terminal oxidase decreased in abundance in comparison to both AT conditions. Photosynthetic complexes were uniquely depleted under the LAH condition but accumulated under the ATHC condition. The MT proteome displayed several heterotrophic features typical of the LAH proteome, particularly including the high abundance of ribosome as well as amino acid and protein biosynthesis machinery-related components. It is also noteworthy that the two equally light-exposed ATHC and MT cultures allocated similar mass fractions of the total proteome to the seven distinct sub-proteomes. Unique trophic condition-specific expression patterns were likewise observed among individual proteins, including the accumulation of phosphate transporters and polyphosphate polymers storing energy surplus in highly energetic bonds under the MT condition and accumulation under the LAH condition of an enzyme catalyzing cyanophycin biosynthesis. It is concluded that the rigor of cell growth in the MT condition results, to a great extent, by combining photosynthetic activity with high intracellular inorganic carbon conditions created upon glucose breakdown and release of CO2, besides the direct utilization of glucose-derived carbon skeletons for growth. This combination provides the MT cultures with excellent conditions for growth that often exceeds that of mere ATHC.
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Yu King Hing N, Aryal UK, Morgan JA. Probing Light-Dependent Regulation of the Calvin Cycle Using a Multi-Omics Approach. FRONTIERS IN PLANT SCIENCE 2021; 12:733122. [PMID: 34671374 PMCID: PMC8521058 DOI: 10.3389/fpls.2021.733122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Photoautotrophic microorganisms are increasingly explored for the conversion of atmospheric carbon dioxide into biomass and valuable products. The Calvin-Benson-Bassham (CBB) cycle is the primary metabolic pathway for net CO2 fixation within oxygenic photosynthetic organisms. The cyanobacteria, Synechocystis sp. PCC 6803, is a model organism for the study of photosynthesis and a platform for many metabolic engineering efforts. The CBB cycle is regulated by complex mechanisms including enzymatic abundance, intracellular metabolite concentrations, energetic cofactors and post-translational enzymatic modifications that depend on the external conditions such as the intensity and quality of light. However, the extent to which each of these mechanisms play a role under different light intensities remains unclear. In this work, we conducted non-targeted proteomics in tandem with isotopically non-stationary metabolic flux analysis (INST-MFA) at four different light intensities to determine the extent to which fluxes within the CBB cycle are controlled by enzymatic abundance. The correlation between specific enzyme abundances and their corresponding reaction fluxes is examined, revealing several enzymes with uncorrelated enzyme abundance and their corresponding flux, suggesting flux regulation by mechanisms other than enzyme abundance. Additionally, the kinetics of 13C labeling of CBB cycle intermediates and estimated inactive pool sizes varied significantly as a function of light intensity suggesting the presence of metabolite channeling, an additional method of flux regulation. These results highlight the importance of the diverse methods of regulation of CBB enzyme activity as a function of light intensity, and highlights the importance of considering these effects in future kinetic models.
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Affiliation(s)
- Nathaphon Yu King Hing
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, United States
| | - Uma K. Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN, United States
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, West Lafayette, IN, United States
| | - John A. Morgan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, United States
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
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Spät P, Barske T, Maček B, Hagemann M. Alterations in the CO 2 availability induce alterations in the phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803. THE NEW PHYTOLOGIST 2021; 231:1123-1137. [PMID: 34058021 DOI: 10.1111/nph.17423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Cyanobacteria are the only prokaryotes that perform plant-like oxygenic photosynthesis. They evolved an inorganic carbon-concentrating mechanism to adapt to low CO2 conditions. Quantitative phosphoproteomics was applied to analyze regulatory features during the acclimation to low CO2 conditions in the model cyanobacterium Synechocystis sp. PCC 6803. Overall, more than 2500 proteins were quantified, equivalent to c. 70% of the Synechocystis theoretical proteome. Proteins with changing abundances correlated largely with mRNA expression levels. Functional annotation of the noncorrelating proteins revealed an enrichment of key metabolic processes fundamental for maintaining cellular homeostasis. Furthermore, 105 phosphoproteins harboring over 200 site-specific phosphorylation events were identified. Subunits of the bicarbonate transporter BCT1 and the redox switch protein CP12 were among phosphoproteins with reduced phosphorylation levels at lower CO2 , whereas the serine/threonine protein kinase SpkC revealed increased phosphorylation levels. The corresponding ΔspkC mutant was characterized and showed decreased ability to acclimate to low CO2 conditions. Possible phosphorylation targets of SpkC including a BCT1 subunit were identified by phosphoproteomics. Collectively, our study highlights the importance of posttranscriptional regulation of protein abundances as well as posttranslational regulation by protein phosphorylation for the successful acclimation towards low CO2 conditions in Synechocystis and possibly among cyanobacteria.
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Affiliation(s)
- Philipp Spät
- Department of Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, D-72076, Germany
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, D-72076, Germany
| | - Thomas Barske
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, D-18059, Germany
| | - Boris Maček
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, D-72076, Germany
| | - Martin Hagemann
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, D-18059, Germany
- Department Life, Light and Matter, Interdisciplinary Faculty, University of Rostock, Rostock, D-18059, Germany
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Toyoshima M, Sakata M, Ueno Y, Toya Y, Matsuda F, Akimoto S, Shimizu H. Proteome analysis of response to different spectral light irradiation in Synechocystis sp. PCC 6803. J Proteomics 2021; 246:104306. [PMID: 34157441 DOI: 10.1016/j.jprot.2021.104306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 11/27/2022]
Abstract
In cyanobacteria, it is known that the excitation ratios of photosystem (PS) I and PSII changes with the wavelength of irradiated light due to mobile phycobilisome (PBS) and spillover, affecting the photosynthetic ATP/NADPH synthesis ratio and metabolic flux state. However, the mechanisms by which these changes are controlled have not been well studied. In this study, we performed a targeted proteomic analysis of Synechocystis sp. PCC 6803 under different spectral light conditions to clarify the regulation mechanisms of mobile PBS, spillover and metabolisms under different light qualities at the protein level. The results showed an increase in the amount of proteins mainly involved in CO2 fixation under Red1 light conditions with a high specific growth rate, suggesting that the rate of intracellular metabolism is controlled by the rate of carbon uptake, not by changes in the amount of each enzyme. Correlation analysis between protein levels and PSI/PSII excitation ratios revealed that PsbQUY showed high correlations and significantly increased under Blue and Red2 light conditions, where the PSI/PSII excitation ratio was higher due to spillover. In the strains lacking the genes encoding these proteins, a decrease in the PSI/PSII excitation ratio was observed, suggesting that PsbQUY contribute to spillover occurrence. SIGNIFICANCE: In cyanobacteria, the photosynthetic apparatus's responses, such as state transition [mobile PBS and spillover], occur due to the intensity and wavelength of irradiated light, resulting in changes in photosynthetic electron transport and metabolic flux states. Previous studies have analyzed the response of Synechocystis sp. PCC 6803 to light intensity from various directions, but only spectroscopic analysis of the photosynthetic apparatus has been done on the response to changes in the wavelength of irradiated light. This study analyzed the response mechanisms of mobile PBS, spillover, photosynthetic, and metabolic systems in Synechocystis sp. PCC 6803 under six different spectral light conditions by a targeted proteomic analysis. As a result, many proteins were successfully quantified, and the metabolic enzymes and photosynthetic apparatus were analyzed using an integrated approach. Principal component and correlation analyses and volcano plots revealed that the PSII subunits PsbQ, PsbU, and PsbY have a strong correlation with the PSI/PSII excitation ratio and contribute to spillover occurrence. Thus, statistical analysis based on proteome data revealed that PsbQ, PsbU, and PsbY are involved in spillover, as revealed by spectroscopic analysis.
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Affiliation(s)
- Masakazu Toyoshima
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masumi Sakata
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshifumi Ueno
- Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Seiji Akimoto
- Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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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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Bolay P, Rozbeh R, Muro-Pastor MI, Timm S, Hagemann M, Florencio FJ, Forchhammer K, Klähn S. The Novel P II-Interacting Protein PirA Controls Flux into the Cyanobacterial Ornithine-Ammonia Cycle. mBio 2021; 12:e00229-21. [PMID: 33758091 PMCID: PMC8092223 DOI: 10.1128/mbio.00229-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/16/2021] [Indexed: 12/11/2022] Open
Abstract
Among prokaryotes, cyanobacteria have an exclusive position as they perform oxygenic photosynthesis. Cyanobacteria substantially differ from other bacteria in further aspects, e.g., they evolved a plethora of unique regulatory mechanisms to control primary metabolism. This is exemplified by the regulation of glutamine synthetase (GS) via small proteins termed inactivating factors (IFs). Here, we reveal another small protein, encoded by the ssr0692 gene in the model strain Synechocystis sp. PCC 6803, that regulates flux into the ornithine-ammonia cycle (OAC), the key hub of cyanobacterial nitrogen stockpiling and remobilization. This regulation is achieved by the interaction with the central carbon/nitrogen control protein PII, which commonly controls entry into the OAC by activating the key enzyme of arginine synthesis, N-acetyl-l-glutamate kinase (NAGK). In particular, the Ssr0692 protein competes with NAGK for PII binding and thereby prevents NAGK activation, which in turn lowers arginine synthesis. Accordingly, we termed it PII-interacting regulator of arginine synthesis (PirA). Similar to the GS IFs, PirA accumulates in response to ammonium upshift due to relief from repression by the global nitrogen control transcription factor NtcA. Consistent with this, the deletion of pirA affects the balance of metabolite pools of the OAC in response to ammonium shocks. Moreover, the PirA-PII interaction requires ADP and is prevented by PII mutations affecting the T-loop conformation, the major protein interaction surface of this signal processing protein. Thus, we propose that PirA is an integrator determining flux into N storage compounds not only depending on the N availability but also the energy state of the cell.IMPORTANCE Cyanobacteria contribute a significant portion to the annual oxygen yield and play important roles in biogeochemical cycles, e.g., as major primary producers. Due to their photosynthetic lifestyle, cyanobacteria also arouse interest as hosts for the sustainable production of fuel components and high-value chemicals. However, their broad application as microbial cell factories is hampered by limited knowledge about the regulation of metabolic fluxes in these organisms. Our research identified a novel regulatory protein that controls nitrogen flux, in particular arginine synthesis. Besides its role as a proteinogenic amino acid, arginine is a precursor for the cyanobacterial storage compound cyanophycin, which is of potential interest to biotechnology. Therefore, the obtained results will not only enhance our understanding of flux control in these organisms but also help to provide a scientific basis for targeted metabolic engineering and, hence, the design of photosynthesis-driven biotechnological applications.
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Affiliation(s)
- Paul Bolay
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Leipzig, Germany
| | - Rokhsareh Rozbeh
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Tübingen University, Tübingen, Germany
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Stefan Timm
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Martin Hagemann
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Tübingen University, Tübingen, Germany
| | - Stephan Klähn
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Leipzig, Germany
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8
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D'Agostino PM, Yeung ACY, Poljak A, David Waite T, Neilan BA. Comparative proteomics of the toxigenic diazotroph Raphidiopsis raciborskii (cyanobacteria) in response to iron. Environ Microbiol 2020; 23:405-414. [PMID: 33200490 DOI: 10.1111/1462-2920.15328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/13/2020] [Indexed: 11/30/2022]
Abstract
Raphidiopsis raciborskii is an invasive bloom-forming cyanobacteria with the flexibility to utilize atmospheric and fixed nitrogen. Since nitrogen-fixation has a high requirement for iron as an ezyme cofactor, we hypothesize that iron availability would determine the success of the species under nitrogen-fixing conditions. This study compares the proteomic response of cylindrospermopsin-producing and non-toxic strains of R. racibroskii to reduced iron concentrations, under nitrogen-fixing conditions, to examine any strain-specific adaptations that might increase fitness under these conditions. We also compared their proteomic responses at exponential and stationary growth phases to capture the changes throughout the growth cycle. Overall, the toxic strain was more competitive under Fe-starved conditions during exponential phase, with upregulated growth and transport-related proteins. The non-toxic strain showed reduced protein expression across multiple primary metabolism pathways. We propose that the increased expression of porin proteins during the exponential growth phase enables toxic strains to persist under Fe-starved conditions with this ability providing a potential explanation for the increased fitness of cylindrospermoipsin-producing strains during unfavourable environmental conditions.
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Affiliation(s)
- Paul M D'Agostino
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.,Chair of Technical Biochemistry, Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Anna C Y Yeung
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.,School of Civil and Environmental Engineering, UNSW, Sydney, NSW, Australia
| | - Anne Poljak
- Bioanalytical Mass Spectrometry Facility, UNSW, Sydney, NSW, Australia
| | - Trevor David Waite
- School of Civil and Environmental Engineering, UNSW, Sydney, NSW, Australia
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.,School of Environmental and Life Sciences, University of Newcastle, Newcastle, NSW, Australia
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Rapid Transcriptional Reprogramming Triggered by Alteration of the Carbon/Nitrogen Balance Has an Impact on Energy Metabolism in Nostoc sp. PCC 7120. Life (Basel) 2020; 10:life10110297. [PMID: 33233741 PMCID: PMC7699953 DOI: 10.3390/life10110297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
Nostoc (Anabaena) sp. PCC 7120 is a filamentous cyanobacterial species that fixes N2 to nitrogenous compounds using specialised heterocyst cells. Changes in the intracellular ratio of carbon to nitrogen (C/N balance) is known to trigger major transcriptional reprogramming of the cell, including initiating the differentiation of vegetative cells to heterocysts. Substantial transcriptional analysis has been performed on Nostoc sp. PCC 7120 during N stepdown (low to high C/N), but not during C stepdown (high to low C/N). In the current study, we shifted the metabolic balance of Nostoc sp. PCC 7120 cultures grown at 3% CO2 by introducing them to atmospheric conditions containing 0.04% CO2 for 1 h, after which the changes in gene expression were measured using RNAseq transcriptomics. This analysis revealed strong upregulation of carbon uptake, while nitrogen uptake and metabolism and early stages of heterocyst development were downregulated in response to the shift to low CO2. Furthermore, gene expression changes revealed a decrease in photosynthetic electron transport and increased photoprotection and reactive oxygen metabolism, as well a decrease in iron uptake and metabolism. Differential gene expression was largely attributed to change in the abundances of the metabolites 2-phosphoglycolate and 2-oxoglutarate, which signal a rapid shift from fluent photoassimilation to glycolytic metabolism of carbon after transition to low CO2. This work shows that the C/N balance in Nostoc sp. PCC 7120 rapidly adjusts the metabolic strategy through transcriptional reprogramming, enabling survival in the fluctuating environment.
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Andersson B, Godhe A, Filipsson HL, Rengefors K, Berglund O. Differences in metal tolerance among strains, populations, and species of marine diatoms - Importance of exponential growth for quantification. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 226:105551. [PMID: 32707232 DOI: 10.1016/j.aquatox.2020.105551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/20/2020] [Accepted: 06/16/2020] [Indexed: 05/21/2023]
Abstract
Strains of microalgae vary in traits between species and populations due to adaptation or stochastic processes. Traits of individual strains may also vary depending on the acclimatization state and external forces, such as abiotic stress. In this study we tested how metal tolerance differs among marine diatoms at three organizational levels: species, populations, and strains. At the species level we compared two pelagic Baltic Sea diatoms (Skeletonema marinoi and Thalassiosira baltica). We found that the between-species differences in tolerance (EC50) to the biologically active metals (Cu, Co, Ni, and Zn) was similar to that within-species. In contrast, the two species differed significantly in tolerance towards the non-essential metals, Ag (three-fold higher in T. baltica), Pb and Cd (two and three-fold higher in S. marinoi). At the population level, we found evidence that increased tolerance against Cu and Co (17 and 41 % higher EC50 on average, respectively) had evolved in a S. marinoi population subjected to historical mining activity. On a strain level we demonstrate how the growth phase of cultures (i.e., cellular densities above exponential growth) modulated dose-response relationships to Ag, Cd, Co, Cu, and Zn. Specifically, the EC50's were reduced by 10-60 % in non-exponentially growing S. marinoi (strain RO5AC), depending on metal. For the essential metals these differences were often larger than the average differences between the two species and populations. Consequently, without careful experimental design, interactions between nutrient limitation and metal stress may interfere with detection of small, but evolutionary and ecologically important, differences in tolerance between microalgae. To avoid such artifacts, we outline a semi-continuous cultivation approach that maintains, and empirically tests, that exponential growth is achieved. We argue that such an approach is essential to enable comparison of population or strain differences in tolerance using dose-response tests on cultures of microalgae.
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Affiliation(s)
- Björn Andersson
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden.
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | | | | | - Olof Berglund
- Department of Biology, Lund University, Lund, Sweden
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11
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Eladel H, Battah M, Dawa A, Abd-Elhay R, Anees D. Effect of rice straw extracts on growth of two phytoplankton isolated from a fish pond. JOURNAL OF APPLIED PHYCOLOGY 2019; 31:3557-3563. [DOI: 10.1007/s10811-019-01766-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 09/02/2023]
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12
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Santana-Sanchez A, Solymosi D, Mustila H, Bersanini L, Aro EM, Allahverdiyeva Y. Flavodiiron proteins 1-to-4 function in versatile combinations in O 2 photoreduction in cyanobacteria. eLife 2019; 8:e45766. [PMID: 31294693 PMCID: PMC6658166 DOI: 10.7554/elife.45766] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/10/2019] [Indexed: 12/15/2022] Open
Abstract
Flavodiiron proteins (FDPs) constitute a group of modular enzymes widespread in Bacteria, Archaea and Eukarya. Synechocystis sp. PCC 6803 has four FDPs (Flv1-4), which are essential for the photoprotection of photosynthesis. A direct comparison of light-induced O2 reduction (Mehler-like reaction) under high (3% CO2, HC) and low (air level CO2, LC) inorganic carbon conditions demonstrated that the Flv1/Flv3 heterodimer is solely responsible for an efficient steady-state O2 photoreduction under HC, with flv2 and flv4 expression strongly down-regulated. Conversely, under LC conditions, Flv1/Flv3 acts only as a transient electron sink, due to the competing withdrawal of electrons by the highly induced NDH-1 complex. Further, in vivo evidence is provided indicating that Flv2/Flv4 contributes to the Mehler-like reaction when naturally expressed under LC conditions, or, when artificially overexpressed under HC. The O2 photoreduction driven by Flv2/Flv4 occurs down-stream of PSI in a coordinated manner with Flv1/Flv3 and supports slow and steady-state O2 photoreduction.
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Affiliation(s)
| | - Daniel Solymosi
- Molecular Plant Biology, Department of BiochemistryUniversity of TurkuTurkuFinland
| | - Henna Mustila
- Molecular Plant Biology, Department of BiochemistryUniversity of TurkuTurkuFinland
| | - Luca Bersanini
- Molecular Plant Biology, Department of BiochemistryUniversity of TurkuTurkuFinland
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of BiochemistryUniversity of TurkuTurkuFinland
| | - Yagut Allahverdiyeva
- Molecular Plant Biology, Department of BiochemistryUniversity of TurkuTurkuFinland
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13
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Watzer B, Spät P, Neumann N, Koch M, Sobotka R, Macek B, Hennrich O, Forchhammer K. The Signal Transduction Protein P II Controls Ammonium, Nitrate and Urea Uptake in Cyanobacteria. Front Microbiol 2019; 10:1428. [PMID: 31293555 PMCID: PMC6603209 DOI: 10.3389/fmicb.2019.01428] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/05/2019] [Indexed: 11/22/2022] Open
Abstract
PII signal transduction proteins are widely spread among all domains of life where they regulate a multitude of carbon and nitrogen metabolism related processes. Non-diazotrophic cyanobacteria can utilize a high variety of organic and inorganic nitrogen sources. In recent years, several physiological studies indicated an involvement of the cyanobacterial PII protein in regulation of ammonium, nitrate/nitrite, and cyanate uptake. However, direct interaction of PII has not been demonstrated so far. In this study, we used biochemical, molecular genetic and physiological approaches to demonstrate that PII regulates all relevant nitrogen uptake systems in Synechocystis sp. strain PCC 6803: PII controls ammonium uptake by interacting with the Amt1 ammonium permease, probably similar to the known regulation of E. coli ammonium permease AmtB by the PII homolog GlnK. We could further clarify that PII mediates the ammonium- and dark-induced inhibition of nitrate uptake by interacting with the NrtC and NrtD subunits of the nitrate/nitrite transporter NrtABCD. We further identified the ABC-type urea transporter UrtABCDE as novel PII target. PII interacts with the UrtE subunit without involving the standard interaction surface of PII interactions. The deregulation of urea uptake in a PII deletion mutant causes ammonium excretion when urea is provided as nitrogen source. Furthermore, the urea hydrolyzing urease enzyme complex appears to be coupled to urea uptake. Overall, this study underlines the great importance of the PII signal transduction protein in the regulation of nitrogen utilization in cyanobacteria.
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Affiliation(s)
- Björn Watzer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Philipp Spät
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Organismic Interactions, University of Tübingen, Tübingen, Germany.,Interfaculty Institute for Cell Biology, Department of Quantitative Proteomics, University of Tübingen, Tübingen, Germany
| | - Niels Neumann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Moritz Koch
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Roman Sobotka
- Centre Algatech, Institute of Microbiology, Academy of Sciences of the Czech Republic, Třeboň, Czechia
| | - Boris Macek
- Interfaculty Institute for Cell Biology, Department of Quantitative Proteomics, University of Tübingen, Tübingen, Germany
| | - Oliver Hennrich
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Organismic Interactions, University of Tübingen, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Department of Organismic Interactions, University of Tübingen, Tübingen, Germany
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14
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Mehta K, Jaiswal D, Nayak M, Prasannan CB, Wangikar PP, Srivastava S. Elevated carbon dioxide levels lead to proteome-wide alterations for optimal growth of a fast-growing cyanobacterium, Synechococcus elongatus PCC 11801. Sci Rep 2019; 9:6257. [PMID: 31000743 PMCID: PMC6472392 DOI: 10.1038/s41598-019-42576-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/29/2019] [Indexed: 12/21/2022] Open
Abstract
The environmental considerations attributing to the escalation of carbon dioxide emissions have raised alarmingly. Consequently, the concept of sequestration and biological conversion of CO2 by photosynthetic microorganisms is gaining enormous recognition. In this study, in an attempt to discern the synergistic CO2 tolerance mechanisms, metabolic responses to increasing CO2 concentrations were determined for Synechococcus elongatus PCC 11801, a fast-growing, novel freshwater strain, using quantitative proteomics. The protein expression data revealed that the organism responded to elevated CO2 by not only regulating the cellular transporters involved in carbon-nitrogen uptake and assimilation but also by inducing photosynthesis, carbon fixation and glycolysis. Several components of photosynthetic machinery like photosystem reaction centers, phycobilisomes, cytochromes, etc. showed a marked up-regulation with a concomitant downshift in proteins involved in photoprotection and redox maintenance. Additionally, enzymes belonging to the TCA cycle and oxidative pentose phosphate pathway exhibited a decline in their expression, further highlighting that the demand for reduced cofactors was fulfilled primarily through photosynthesis. The present study brings the first-ever comprehensive assessment of intricate molecular changes in this novel strain while shifting from carbon-limited to carbon-sufficient conditions and may pave the path for future host and pathway engineering for production of sustainable fuels through efficient CO2 capture.
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Affiliation(s)
- Kanika Mehta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Damini Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Monalisha Nayak
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Charulata B Prasannan
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India. .,DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India. .,Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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15
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Toyoshima M, Sakata M, Ohnishi K, Tokumaru Y, Kato Y, Tokutsu R, Sakamoto W, Minagawa J, Matsuda F, Shimizu H. Targeted proteome analysis of microalgae under high-light conditions by optimized protein extraction of photosynthetic organisms. J Biosci Bioeng 2019; 127:394-402. [DOI: 10.1016/j.jbiosc.2018.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/23/2018] [Accepted: 09/02/2018] [Indexed: 12/14/2022]
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16
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Abstract
Ribosome profiling accesses the translational step of gene expression via deep sequencing of ribosome-protected mRNA footprints. Pairing of ribosome profiling and transcriptomics data provides a translational efficiency for each gene. Here, the translatome and transcriptome of the model cyanobacterium
Synechocystis
were compared under carbon-replete and carbon starvation conditions. The latter may be experienced when cyanobacteria are cultivated in poorly mixed bioreactors or engineered to be product-secreting cell factories. A small fraction of genes (<200), including stress response genes, showed changes in translational efficiency during carbon starvation, indicating condition-dependent translation-level regulation. We observed ribosome occupancy in untranslated regions, possibly due to an alternative translation initiation mechanism in
Synechocystis.
The higher proportion of ribosomes residing in untranslated regions during carbon starvation may be a mechanism to quickly inactivate superfluous ribosomes. This work provides the first ribosome profiling data for cyanobacteria and reveals new regulation strategies for coping with nutrient limitation.
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17
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Giner-Lamia J, Robles-Rengel R, Hernández-Prieto MA, Muro-Pastor MI, Florencio FJ, Futschik ME. Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803. Nucleic Acids Res 2017; 45:11800-11820. [PMID: 29036481 PMCID: PMC5714215 DOI: 10.1093/nar/gkx860] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022] Open
Abstract
In cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA. In addition to genes associated with nitrogen and carbon metabolism, a considerable number of genes without current functional annotation were among direct targets providing a rich reservoir for further studies. The NtcA regulon also included eight non-coding RNAs, of which Ncr1071, Syr6 and NsiR7 were experimentally validated, and their putative targets were computationally predicted. Surprisingly, we found substantial NtcA binding associated with delayed expression changes indicating that NtcA can reside in a poised state controlled by other factors. Indeed, a role of PipX as modulating factor in nitrogen regulation was confirmed for selected NtcA-targets. We suggest that the indicated poised state of NtcA enables a more differentiated response to nitrogen limitation and can be advantageous in native habitats of Synechocystis.
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Affiliation(s)
- Joaquín Giner-Lamia
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,Laboratory of Intracellular Bacterial Pathogens, Department of Microbial Biotechnology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Rocío Robles-Rengel
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Miguel A Hernández-Prieto
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,ARC Centre of Excellence for Translational Photosynthesis and School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Matthias E Futschik
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal.,School of Biomedical & Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth PL6 8BU, UK
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18
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Carvalho LL, Salminen TA, Dahlström KM. Slr0006-like proteins: A TsaC/TsaC2/YciO subfamily exclusive to cyanobacteria. Mol Phylogenet Evol 2017; 109:1-10. [DOI: 10.1016/j.ympev.2016.12.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/15/2016] [Accepted: 12/28/2016] [Indexed: 12/01/2022]
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19
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Responses of the marine diatom Thalassiosira pseudonana to changes in CO 2 concentration: a proteomic approach. Sci Rep 2017; 7:42333. [PMID: 28181560 PMCID: PMC5299434 DOI: 10.1038/srep42333] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 01/10/2017] [Indexed: 12/18/2022] Open
Abstract
The concentration of CO2 in many aquatic systems is variable, often lower than the KM of the primary carboxylating enzyme Rubisco, and in order to photosynthesize efficiently, many algae operate a facultative CO2 concentrating mechanism (CCM). Here we measured the responses of a marine diatom, Thalassiosira pseudonana, to high and low concentrations of CO2 at the level of transcripts, proteins and enzyme activity. Low CO2 caused many metabolic pathways to be remodeled. Carbon acquisition enzymes, primarily carbonic anhydrase, stress, degradation and signaling proteins were more abundant while proteins associated with nitrogen metabolism, energy production and chaperones were less abundant. A protein with similarities to the Ca2+/ calmodulin dependent protein kinase II_association domain, having a chloroplast targeting sequence, was only present at low CO2. This protein might be a specific response to CO2 limitation since a previous study showed that other stresses caused its reduction. The protein sequence was found in other marine diatoms and may play an important role in their response to low CO2 concentration.
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20
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Veit S, Takeda K, Tsunoyama Y, Baymann F, Nevo R, Reich Z, Rögner M, Miki K, Rexroth S. Structural and functional characterisation of the cyanobacterial PetC3 Rieske protein family. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1879-1891. [DOI: 10.1016/j.bbabio.2016.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/12/2016] [Accepted: 09/17/2016] [Indexed: 11/30/2022]
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21
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Kupriyanova EV, Cho SM, Park YI, Pronina NA, Los DA. The complete genome of a cyanobacterium from a soda lake reveals the presence of the components of CO 2-concentrating mechanism. PHOTOSYNTHESIS RESEARCH 2016; 130:151-165. [PMID: 26908147 DOI: 10.1007/s11120-016-0235-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Abstract
At present geological epoch, the carbon concentrating mechanism (CCM) of cyanobacteria represents the obligatory tool for adaptation to low content of CO2 in the atmosphere and for the maintenance of sufficient photosynthetic activity. Functional CCM was found in modern cyanobacteria from different ecological niches. However, the presence of such mechanism in species that inhabit soda lakes is not obvious due to high content of inorganic carbon (C i) in the environment. Here we analyze CCM components that have been identified by sequencing of the whole genome of the alkaliphilic cyanobacterium Microcoleus sp. IPPAS B-353. The composition of the CCM components of Microcoleus is similar to that of 'model' β-cyanobacteria, freshwater and marine Synechococcus or Synechocystis spp. However, CahB1 protein of Microcoleus, which is the homolog of CcaA, the carboxysomal β-type carbonic anhydrase (CA) of β-cyanobacteria, appeared to be the only active CA located in cell envelopes. The conservative regions of CcmM, CahG (a homolog of archeal γ-CAs, Cam/CamH), and ChpX of Microcoleus possess single amino acid substitutions that may cause a lack of CA activities. Unlike model cyanobacteria, Microcoleus induces only one BicA-type bicarbonate transporter in response to C i limitation. The differences in the appearance of CCM components and in their characteristics between alkaliphilic Microcoleus and freshwater or marine cyanobacteria are described. The possible reasons for the maintenance of CCM components in cyanobacteria, which permanently live at high concentrations of C i in soda lakes, are discussed.
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Affiliation(s)
- Elena V Kupriyanova
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, Moscow, Russia, 127276.
| | - Sung Mi Cho
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, Korea
| | - Natalia A Pronina
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, Moscow, Russia, 127276
| | - Dmitry A Los
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, Moscow, Russia, 127276
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22
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Angeleri M, Muth-Pawlak D, Aro EM, Battchikova N. Study of O-Phosphorylation Sites in Proteins Involved in Photosynthesis-Related Processes in Synechocystis sp. Strain PCC 6803: Application of the SRM Approach. J Proteome Res 2016; 15:4638-4652. [DOI: 10.1021/acs.jproteome.6b00732] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Martina Angeleri
- Molecular Plant Biology,
Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Dorota Muth-Pawlak
- Molecular Plant Biology,
Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Eva-Mari Aro
- Molecular Plant Biology,
Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Natalia Battchikova
- Molecular Plant Biology,
Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
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23
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Physiological and Proteomic Responses of Continuous Cultures of Microcystis aeruginosa PCC 7806 to Changes in Iron Bioavailability and Growth Rate. Appl Environ Microbiol 2016; 82:5918-29. [PMID: 27474713 DOI: 10.1128/aem.01207-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/24/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The hepatotoxin microcystin (MCYST) is produced by a variety of freshwater cyanobacterial species, including Microcystis aeruginosa Interestingly, MCYST-producing M. aeruginosa strains have been shown to outcompete their nontoxic counterparts under iron-limiting conditions. However, the reasons for this are unclear. Here we examined the proteomic response of M. aeruginosa PCC 7806 continuous cultures under different iron and growth regimes. Iron limitation was correlated with a global reduction in levels of proteins associated with energy metabolism and photosynthesis. These proteomic changes were consistent with physiological observations, including reduced chlorophyll a content and reduced cell size. While levels of MCYST biosynthesis proteins did not fluctuate during the study period, both intra- and extracellular toxin quotas were significantly higher under iron-limiting conditions. Our results support the hypothesis that intracellular MCYST plays a role in protecting the cell against oxidative stress. Further, we propose that extracellular MCYST may act as a signaling molecule, stimulating MCYST production under conditions of iron limitation and enhancing the fitness of bloom populations. IMPORTANCE Microcystin production in water supply reservoirs is a global public health problem. Understanding the ecophysiology of hepatotoxic cyanobacteria, including their responses to the presence of key micronutrient metals such as iron, is central to managing harmful blooms. To our knowledge, this was the first study to examine proteomic and physiological changes occurring in M. aeruginosa continuous cultures under conditions of iron limitation at different growth rates.
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24
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Orf I, Timm S, Bauwe H, Fernie AR, Hagemann M, Kopka J, Nikoloski Z. Can cyanobacteria serve as a model of plant photorespiration? - a comparative meta-analysis of metabolite profiles. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2941-2952. [PMID: 26969741 DOI: 10.1093/jxb/erw068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Photorespiration is a process that is crucial for the survival of oxygenic phototrophs in environments that favour the oxygenation reaction of Rubisco. While photorespiration is conserved among cyanobacteria, algae, and embryophytes, it evolved to different levels of complexity in these phyla. The highest complexity is found in embryophytes, where the pathway involves four cellular compartments and respective transport processes. The complexity of photorespiration in embryophytes raises the question whether a simpler system, such as cyanobacteria, may serve as a model to facilitate our understanding of the common key aspects of photorespiration. In this study, we conducted a meta-analysis of publicly available metabolite profiles from the embryophyte Arabidopsis thaliana and the cyanobacterium Synechocystis sp. PCC 6803 grown under conditions that either activate or suppress photorespiration. The comparative meta-analysis evaluated the similarity of metabolite profiles, the variability of metabolite pools, and the patterns of metabolite ratios. Our results show that the metabolic signature of photorespiration is in part conserved between the compared model organisms under conditions that favour the oxygenation reaction. Therefore, our findings support the claim that cyanobacteria can serve as prokaryotic models of photorespiration in embryophytes.
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Affiliation(s)
- Isabel Orf
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam OT Golm, Germany
| | - Stefan Timm
- Universität Rostock, Abteilung Pflanzenphysiologie, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Hermann Bauwe
- Universität Rostock, Abteilung Pflanzenphysiologie, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam OT Golm, Germany
| | - Martin Hagemann
- Universität Rostock, Abteilung Pflanzenphysiologie, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Joachim Kopka
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam OT Golm, Germany
| | - Zoran Nikoloski
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam OT Golm, Germany
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25
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Peltier G, Aro EM, Shikanai T. NDH-1 and NDH-2 Plastoquinone Reductases in Oxygenic Photosynthesis. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:55-80. [PMID: 26735062 DOI: 10.1146/annurev-arplant-043014-114752] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Oxygenic photosynthesis converts solar energy into chemical energy in the chloroplasts of plants and microalgae as well as in prokaryotic cyanobacteria using a complex machinery composed of two photosystems and both membrane-bound and soluble electron carriers. In addition to the major photosynthetic complexes photosystem II (PSII), cytochrome b6f, and photosystem I (PSI), chloroplasts also contain minor components, including a well-conserved type I NADH dehydrogenase (NDH-1) complex that functions in close relationship with photosynthesis and likewise originated from the endosymbiotic cyanobacterial ancestor. Some plants and many microalgal species have lost plastidial ndh genes and a functional NDH-1 complex during evolution, and studies have suggested that a plastidial type II NADH dehydrogenase (NDH-2) complex substitutes for the electron transport activity of NDH-1. However, although NDH-1 was initially thought to use NAD(P)H as an electron donor, recent research has demonstrated that both chloroplast and cyanobacterial NDH-1s oxidize reduced ferredoxin. We discuss more recent findings related to the biochemical composition and activity of NDH-1 and NDH-2 in relation to the physiology and regulation of photosynthesis, particularly focusing on their roles in cyclic electron flow around PSI, chlororespiration, and acclimation to changing environments.
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Affiliation(s)
- Gilles Peltier
- Institute of Environmental Biology and Biotechnology, CEA, CNRS, Aix-Marseille University, CEA Cadarache, 13018 Saint-Paul-lès-Durance, France;
| | - Eva-Mari Aro
- Department of Biochemistry, University of Turku, 20014 Turku, Finland;
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26
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Vuorijoki L, Isojärvi J, Kallio P, Kouvonen P, Aro EM, Corthals GL, Jones PR, Muth-Pawlak D. Development of a Quantitative SRM-Based Proteomics Method to Study Iron Metabolism of Synechocystis sp. PCC 6803. J Proteome Res 2015; 15:266-79. [DOI: 10.1021/acs.jproteome.5b00800] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Linda Vuorijoki
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Janne Isojärvi
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Pauli Kallio
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Petri Kouvonen
- Turku
Proteomics Facility, Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland
| | - Eva-Mari Aro
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Garry L. Corthals
- Turku
Proteomics Facility, Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland
- Van’t
Hoff Institute for Molecular Sciences, University of Amsterdam, 1018 WV Amsterdam, The Netherlands
| | - Patrik R. Jones
- Department
of Life Sciences, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
| | - Dorota Muth-Pawlak
- Molecular
Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
- Turku
Proteomics Facility, Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland
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27
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Xiong W, Lee TC, Rommelfanger S, Gjersing E, Cano M, Maness PC, Ghirardi M, Yu J. Phosphoketolase pathway contributes to carbon metabolism in cyanobacteria. NATURE PLANTS 2015; 2:15187. [PMID: 27250745 DOI: 10.1038/nplants.2015.187] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/30/2015] [Indexed: 05/20/2023]
Abstract
Central carbon metabolism in cyanobacteria comprises the Calvin-Benson-Bassham (CBB) cycle, glycolysis, the pentose phosphate (PP) pathway and the tricarboxylic acid (TCA) cycle. Redundancy in this complex metabolic network renders the rational engineering of cyanobacterial metabolism for the generation of biomass, biofuels and chemicals a challenge. Here we report the presence of a functional phosphoketolase pathway, which splits xylulose-5-phosphate (or fructose-6-phosphate) to acetate precursor acetyl phosphate, in an engineered strain of the model cyanobacterium Synechocystis (ΔglgC/xylAB), in which glycogen synthesis is blocked, and xylose catabolism enabled through the introduction of xylose isomerase and xylulokinase. We show that this mutant strain is able to metabolise xylose to acetate on nitrogen starvation. To see whether acetate production in the mutant is linked to the activity of phosphoketolase, we disrupted a putative phosphoketolase gene (slr0453) in the ΔglgC/xylAB strain, and monitored metabolic flux using (13)C labelling; acetate and 2-oxoglutarate production was reduced in the light. A metabolic flux analysis, based on isotopic data, suggests that the phosphoketolase pathway metabolises over 30% of the carbon consumed by ΔglgC/xylAB during photomixotrophic growth on xylose and CO2. Disruption of the putative phosphoketolase gene in wild-type Synechocystis also led to a deficiency in acetate production in the dark, indicative of a contribution of the phosphoketolase pathway to heterotrophic metabolism. We suggest that the phosphoketolase pathway, previously uncharacterized in photosynthetic organisms, confers flexibility in energy and carbon metabolism in cyanobacteria, and could be exploited to increase the efficiency of cyanobacterial carbon metabolism and photosynthetic productivity.
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Affiliation(s)
- Wei Xiong
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, USA
| | - Tai-Chi Lee
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, USA
| | - Sarah Rommelfanger
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, USA
| | - Erica Gjersing
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, USA
| | - Melissa Cano
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, USA
| | - Pin-Ching Maness
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, USA
| | - Maria Ghirardi
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, USA
| | - Jianping Yu
- National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, USA
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Gao L, Wang J, Ge H, Fang L, Zhang Y, Huang X, Wang Y. Toward the complete proteome of Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2015; 126:203-219. [PMID: 25862646 DOI: 10.1007/s11120-015-0140-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 04/02/2015] [Indexed: 06/04/2023]
Abstract
The proteome of the photosynthetic model organism Synechocystis sp. PCC 6803 has been extensively analyzed in the last 15 years for the purpose of identifying proteins specifically expressed in subcellular compartments or differentially expressed in different environmental or internal conditions. This review summarizes the progress achieved so far with the emphasis on the impact of different techniques, both in sample preparation and protein identification, on the increasing coverage of proteome identification. In addition, this review evaluates the current completeness of proteome identification, and provides insights on the potential factors that could affect the complete identification of the Synechocystis proteome.
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Affiliation(s)
- Liyan Gao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Jinlong Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Haitao Ge
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Longfa Fang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China.
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Touloupakis E, Cicchi B, Benavides AMS, Torzillo G. Effect of high pH on growth of Synechocystis sp. PCC 6803 cultures and their contamination by golden algae (Poterioochromonas sp.). Appl Microbiol Biotechnol 2015; 100:1333-1341. [PMID: 26541331 PMCID: PMC4717179 DOI: 10.1007/s00253-015-7024-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/31/2015] [Accepted: 09/08/2015] [Indexed: 11/29/2022]
Abstract
Culturing cyanobacteria in a highly alkaline environment is a possible strategy for controlling contamination by other organisms. Synechocystis PCC 6803 cells were grown in continuous cultures to assess their growth performance at different pH values. Light conversion efficiency linearly decreased with the increase in pH and ranged between 12.5 % (PAR) at pH 7.5 (optimal) and decreased to 8.9 % at pH 11.0. Photosynthetic activity, assessed by measuring both chlorophyll fluorescence and photosynthesis rate, was not much affected going from pH 7.5 to 11.0, while productivity, growth yield, and biomass yield on light energy declined by 32, 28, and 26 % respectively at pH 11.0. Biochemical composition of the biomass did not change much within pH 7 and 10, while when grown at pH 11.0, carbohydrate content increased by 33 % while lipid content decreased by about the same amount. Protein content remained almost constant (average 65.8 % of dry weight). Cultures maintained at pH above 11.0 could grow free of contaminants (protozoa and other competing microalgae belonging to the species of Poterioochromonas).
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Affiliation(s)
- Eleftherios Touloupakis
- Istituto per lo Studio degli Ecosistemi, CNR, Via Madonna del Piano 10, I-50019, Sesto Fiorentino, Italy
| | - Bernardo Cicchi
- Istituto per lo Studio degli Ecosistemi, CNR, Via Madonna del Piano 10, I-50019, Sesto Fiorentino, Italy
| | - Ana Margarita Silva Benavides
- Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, 2060, Costa Rica
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, San Pedro, San José, 2060, Costa Rica
| | - Giuseppe Torzillo
- Istituto per lo Studio degli Ecosistemi, CNR, Via Madonna del Piano 10, I-50019, Sesto Fiorentino, Italy.
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Battchikova N, Angeleri M, Aro EM. Proteomic approaches in research of cyanobacterial photosynthesis. PHOTOSYNTHESIS RESEARCH 2015; 126:47-70. [PMID: 25359503 DOI: 10.1007/s11120-014-0050-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 10/18/2014] [Indexed: 05/03/2023]
Abstract
Oxygenic photosynthesis in cyanobacteria, algae, and plants is carried out by a fabulous pigment-protein machinery that is amazingly complicated in structure and function. Many different approaches have been undertaken to characterize the most important aspects of photosynthesis, and proteomics has become the essential component in this research. Here we describe various methods which have been used in proteomic research of cyanobacteria, and demonstrate how proteomics is implemented into on-going studies of photosynthesis in cyanobacterial cells.
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Affiliation(s)
- Natalia Battchikova
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland.
| | - Martina Angeleri
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
| | - Eva-Mari Aro
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
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31
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[NiFe]-hydrogenase is essential for cyanobacterium Synechocystis sp. PCC 6803 aerobic growth in the dark. Sci Rep 2015. [PMID: 26215212 PMCID: PMC4517062 DOI: 10.1038/srep12424] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The cyanobacterium Synechocystis sp. PCC 6803 has a bidirectional [NiFe]-hydrogenase (Hox hydrogenase) which reversibly reduces protons to H2. This enzyme is composed of a hydrogenase domain and a diaphorase moiety, which is distinctly homologous to the NADH input module of mitochondrial respiratory Complex I. Hox hydrogenase physiological function is still unclear, since it is not required for Synechocystis fitness under standard growth conditions. We analyzed the phenotype under prolonged darkness of three Synechocystis knock-out strains, lacking either Hox hydrogenase (ΔHoxE-H) or one of the proteins responsible for the assembly of its NiFe active site (ΔHypA1 and ΔHypB1). We found that Hox hydrogenase is required for Synechocystis growth under this condition, regardless of the functional status of its catalytic site, suggesting an additional role beside hydrogen metabolism. Moreover, quantitative proteomic analyses revealed that the expression levels of several subunits of the respiratory NADPH/plastoquinone oxidoreductase (NDH-1) are reduced when Synechocystis is grown in the dark. Our findings suggest that the Hox hydrogenase could contribute to electron transport regulation when both photosynthetic and respiratory pathways are down-regulated, and provide a possible explanation for the close evolutionary relationship between mitochondrial respiratory Complex I and cyanobacterial [NiFe]-hydrogenases.
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Allahverdiyeva Y, Isojärvi J, Zhang P, Aro EM. Cyanobacterial Oxygenic Photosynthesis is Protected by Flavodiiron Proteins. Life (Basel) 2015; 5:716-43. [PMID: 25761262 PMCID: PMC4390876 DOI: 10.3390/life5010716] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/04/2015] [Accepted: 02/25/2015] [Indexed: 12/13/2022] Open
Abstract
Flavodiiron proteins (FDPs, also called flavoproteins, Flvs) are modular enzymes widely present in Bacteria and Archaea. The evolution of cyanobacteria and oxygenic photosynthesis occurred in concert with the modulation of typical bacterial FDPs. Present cyanobacterial FDPs are composed of three domains, the β-lactamase-like, flavodoxin-like and flavin-reductase like domains. Cyanobacterial FDPs function as hetero- and homodimers and are involved in the regulation of photosynthetic electron transport. Whilst Flv2 and Flv4 proteins are limited to specific cyanobacterial species (β-cyanobacteria) and function in photoprotection of Photosystem II, Flv1 and Flv3 proteins, functioning in the "Mehler-like" reaction and safeguarding Photosystem I under fluctuating light conditions, occur in nearly all cyanobacteria and additionally in green algae, mosses and lycophytes. Filamentous cyanobacteria have additional FDPs in heterocyst cells, ensuring a microaerobic environment for the function of the nitrogenase enzyme under the light. Here, the evolution, occurrence and functional mechanisms of various FDPs in oxygenic photosynthetic organisms are discussed.
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Affiliation(s)
- Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Janne Isojärvi
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Pengpeng Zhang
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
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33
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Plohnke N, Seidel T, Kahmann U, Rögner M, Schneider D, Rexroth S. The proteome and lipidome of Synechocystis sp. PCC 6803 cells grown under light-activated heterotrophic conditions. Mol Cell Proteomics 2015; 14:572-84. [PMID: 25561504 PMCID: PMC4349978 DOI: 10.1074/mcp.m114.042382] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/10/2014] [Indexed: 12/31/2022] Open
Abstract
Cyanobacteria are photoautotrophic prokaryotes with a plant-like photosynthetic machinery. Because of their short generation times, the ease of their genetic manipulation, and the limited size of their genome and proteome, cyanobacteria are popular model organisms for photosynthetic research. Although the principal mechanisms of photosynthesis are well-known, much less is known about the biogenesis of the thylakoid membrane, hosting the components of the photosynthetic, and respiratory electron transport chain in cyanobacteria. Here we present a detailed proteome analysis of the important model and host organism Synechocystis sp. PCC 6803 under light-activated heterotrophic growth conditions. Because of the mechanistic importance and severe changes in thylakoid membrane morphology under light-activated heterotrophic growth conditions, a focus was put on the analysis of the membrane proteome, which was supported by a targeted lipidome analysis. In total, 1528 proteins (24.5% membrane integral) were identified in our analysis. For 641 of these proteins quantitative information was obtained by spectral counting. Prominent changes were observed for proteins associated with oxidative stress response and protein folding. Because of the heterotrophic growth conditions, also proteins involved in carbon metabolism and C/N-balance were severely affected. Although intracellular thylakoid membranes were significantly reduced, only minor changes were observed in their protein composition. The increased proportion of the membrane-stabilizing sulfoqinovosyl diacyl lipids found in the lipidome analysis, as well as the increased content of lipids with more saturated acyl chains, are clear indications for a coordinated synthesis of proteins and lipids, resulting in stabilization of intracellular thylakoid membranes under stress conditions.
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Affiliation(s)
- Nicole Plohnke
- From the ‡Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Tobias Seidel
- §Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Uwe Kahmann
- ¶Department of Molecular Cell Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Matthias Rögner
- From the ‡Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Dirk Schneider
- §Department of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany;
| | - Sascha Rexroth
- From the ‡Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr-University Bochum, 44780 Bochum, Germany;
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Multi-level kinetic model explaining diverse roles of isozymes in prokaryotes. PLoS One 2014; 9:e105292. [PMID: 25127487 PMCID: PMC4138046 DOI: 10.1371/journal.pone.0105292] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 07/22/2014] [Indexed: 12/23/2022] Open
Abstract
Current standard methods for kinetic and genomic modeling cannot provide deep insight into metabolic regulation. Here, we developed and evaluated a multi-scale kinetic modeling approach applicable to any prokaryote. Specifically, we highlight the primary metabolism of the cyanobacterium Synechococcus elongatus PCC 7942. The model bridges metabolic data sets from cells grown at different CO2 conditions by integrating transcriptomic data and isozymes. Identification of the regulatory roles of isozymes allowed the calculation and explanation of the absolute metabolic concentration of 3-phosphoglycerate. To demonstrate that this method can characterize any isozyme, we determined the function of two glycolytic glyceraldehyde-3-phosphate dehydrogenases: one co-regulates high concentrations of the 3-phosphoglycerate, the other shifts the bifurcation point in hexose regulation, and both improve biomass production. Moreover, the regulatory roles of multiple phosphoglycolate phosphatases were defined for varying (non-steady) CO2 conditions, suggesting their protective role against toxic photorespiratory intermediates.
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35
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Proteomic analysis of Synechocystis sp. PCC6803 responses to low-temperature and high light conditions. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-013-0563-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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36
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Kopf M, Klähn S, Scholz I, Matthiessen JKF, Hess WR, Voß B. Comparative analysis of the primary transcriptome of Synechocystis sp. PCC 6803. DNA Res 2014; 21:527-39. [PMID: 24935866 PMCID: PMC4195498 DOI: 10.1093/dnares/dsu018] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
RNA-seq and especially differential RNA-seq-type transcriptomic analyses (dRNA-seq) are powerful analytical tools, as they not only provide insights into gene expression changes but also provide detailed information about all promoters active at a given moment, effectively giving a deep insight into the transcriptional landscape. Synechocystis sp. PCC 6803 (Synechocystis 6803) is a unicellular model cyanobacterium that is widely used in research fields from ecology, photophysiology to systems biology, modelling and biotechnology. Here, we analysed the response of the Synechocystis 6803 primary transcriptome to different, environmentally relevant stimuli. We established genome-wide maps of the transcriptional start sites active under 10 different conditions relevant for photosynthetic growth and identified 4,091 transcriptional units, which provide information about operons, 5′ and 3′ untranslated regions (UTRs). Based on a unique expression factor, we describe regulons and relevant promoter sequences at single-nucleotide resolution. Finally, we report several sRNAs with an intriguing expression pattern and therefore likely function, specific for carbon depletion (CsiR1), nitrogen depletion (NsiR4), phosphate depletion (PsiR1), iron stress (IsaR1) or photosynthesis (PsrR1). This dataset is accompanied by comprehensive information providing extensive visualization and data access to allow an easy-to-use approach for the design of experiments, the incorporation into modelling studies of the regulatory system and for comparative analyses.
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Affiliation(s)
- Matthias Kopf
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany
| | - Stephan Klähn
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany
| | - Ingeborg Scholz
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany
| | - Jasper K F Matthiessen
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany
| | - Björn Voß
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany
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37
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Bharti RK, Srivastava S, Thakur IS. Proteomic analysis of carbon concentrating chemolithotrophic bacteria Serratia sp. for sequestration of carbon dioxide. PLoS One 2014; 9:e91300. [PMID: 24619032 PMCID: PMC3949746 DOI: 10.1371/journal.pone.0091300] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/08/2014] [Indexed: 11/19/2022] Open
Abstract
A chemolithotrophic bacterium enriched in the chemostat in presence of sodium bicarbonate as sole carbon source was identified as Serratia sp. by 16S rRNA sequencing. Carbon dioxide sequestering capacity of bacterium was detected by carbonic anhydrase enzyme and ribulose-1, 5- bisphosphate carboxylase/oxygenase (RuBisCO). The purified carbonic anhydrase showed molecular weight of 29 kDa. Molecular weight of RuBisCO was 550 kDa as determined by fast protein liquid chromatography (FPLC), however, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed presence of two subunits whose molecular weights were 56 and 14 kDa. The Western blot analysis of the crude protein and purified sample cross reacted with RuBisCO large-subunit polypeptides antibodies showed strong band pattern at molecular weight around 56 kDa regions. Whole cell soluble proteins of Serratia sp. grown under autotrophic and heterotrophic conditions were resolved by two-dimensional gel electrophoresis and MALDI-TOF/MS for differential expression of proteins. In proteomic analysis of 63 protein spots, 48 spots were significantly up-regulated in the autotrophically grown cells; seven enzymes showed its utilization in autotrophic carbon fixation pathways and other metabolic activities of bacterium including lipid metabolisms indicated sequestration potency of carbon dioxide and production of biomaterials.
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Affiliation(s)
- Randhir K. Bharti
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shaili Srivastava
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
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38
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Anfelt J, Hallström B, Nielsen J, Uhlén M, Hudson EP. Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803. Appl Environ Microbiol 2013; 79:7419-27. [PMID: 24056459 PMCID: PMC3837751 DOI: 10.1128/aem.02694-13] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 09/16/2013] [Indexed: 01/28/2023] Open
Abstract
Cyanobacteria are emerging as promising hosts for production of advanced biofuels such as n-butanol and alkanes. However, cyanobacteria suffer from the same product inhibition problems as those that plague other microbial biofuel hosts. High concentrations of butanol severely reduce growth, and even small amounts can negatively affect metabolic processes. An understanding of how cyanobacteria are affected by their biofuel product can enable identification of engineering strategies for improving their tolerance. Here we used transcriptome sequencing (RNA-Seq) to assess the transcriptome response of Synechocystis sp. strain PCC 6803 to two concentrations of exogenous n-butanol. Approximately 80 transcripts were differentially expressed at 40 mg/liter butanol, and 280 transcripts were different at 1 g/liter butanol. Our results suggest a compromised cell membrane, impaired photosynthetic electron transport, and reduced biosynthesis. Accumulation of intracellular reactive oxygen species (ROS) scaled with butanol concentration. Using the physiology and transcriptomics data, we selected several genes for overexpression in an attempt to improve butanol tolerance. We found that overexpression of several proteins, notably, the small heat shock protein HspA, improved tolerance to butanol. Transcriptomics-guided engineering created more solvent-tolerant cyanobacteria strains that could be the foundation for a more productive biofuel host.
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Affiliation(s)
- Josefine Anfelt
- School of Biotechnology, KTH—Royal Institute of Technology, Stockholm, Sweden
| | - Björn Hallström
- Novo Nordisk Foundation Center for Biosustainability, Science for Life Laboratory, Stockholm, Sweden
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Science for Life Laboratory, Stockholm, Sweden
- Department of Chemical and Biological Engineering, Chalmers Institute of Technology, Gothenburg, Sweden
| | - Mathias Uhlén
- School of Biotechnology, KTH—Royal Institute of Technology, Stockholm, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Science for Life Laboratory, Stockholm, Sweden
| | - Elton P. Hudson
- School of Biotechnology, KTH—Royal Institute of Technology, Stockholm, Sweden
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39
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Savakis PE, Angermayr SA, Hellingwerf KJ. Synthesis of 2,3-butanediol by Synechocystis sp. PCC6803 via heterologous expression of a catabolic pathway from lactic acid- and enterobacteria. Metab Eng 2013; 20:121-30. [DOI: 10.1016/j.ymben.2013.09.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 09/25/2013] [Accepted: 09/26/2013] [Indexed: 02/08/2023]
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40
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Gao L, Shen C, Liao L, Huang X, Liu K, Wang W, Guo L, Jin W, Huang F, Xu W, Wang Y. Functional proteomic discovery of Slr0110 as a central regulator of carbohydrate metabolism in Synechocystis species PCC6803. Mol Cell Proteomics 2013; 13:204-19. [PMID: 24169622 DOI: 10.1074/mcp.m113.033803] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The unicellular photosynthetic model-organism cyanobacterium Synechocystis sp. PCC6803 can grow photoautotrophically using CO2 or heterotrophically using glucose as the sole carbon source. Several pathways are involved in carbon metabolism in Synechocystis, and the concerted regulation of these pathways by numerous known and unknown genes is critical for the survival and growth of the organism. Here, we report that a hypothetical protein encoded by the open reading frame slr0110 is necessary for heterotrophic growth of Synechocystis. The slr0110-deletion mutant is defective in glucose uptake, heterotrophic growth, and dark viability without detectable defects in autotrophic growth, whereas the level of photosystem II and the rate of oxygen evolution are increased in the mutant. Quantitative proteomic analysis revealed that several proteins in glycolysis and the oxidative pentose phosphate pathway are down-regulated, whereas proteins in photosystem II and phycobilisome are significantly up-regulated, in the mutant. Among the down-regulated proteins are glucose transporter, glucokinase, glucose-6-phosphate isomerase, and glucose-6-phosphate dehydrogenase and its assembly protein OpcA, suggesting that glycolysis, oxidative pentose phosphate, and glycogen synthesis pathways are significantly inhibited in the mutant, which was further confirmed by enzymatic assays and quantification of glycogen content. These findings establish Slr0110 as a novel central regulator of carbon metabolism in Synechocystis, and shed light on an intricate mechanism whereby photosynthesis and carbon metabolism are well concerted to survive the crisis when one or more pathways of the system are impaired.
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Affiliation(s)
- Liyan Gao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Rd., Beijing 100101, China
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Carmel D, Dahlström KM, Holmström M, Allahverdiyeva Y, Battchikova N, Aro EM, Salminen TA, Mulo P. Structural model, physiology and regulation of Slr0006 in Synechocystis PCC 6803. Arch Microbiol 2013; 195:727-36. [PMID: 24043215 DOI: 10.1007/s00203-013-0924-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 08/27/2013] [Accepted: 09/02/2013] [Indexed: 11/29/2022]
Abstract
The slr0006 gene of Synechocystis sp. PCC 6803 is upregulated at mRNA and protein level under carbon limitation. The T(N11)A motif in the upstream region of slr0006 is a binding site for transcriptional regulator NdhR, and accumulation of the Slr0006 protein in ndhR deletion mutant grown in high CO2 suggests that NdhR may be a negative regulator of slr0006. Accumulation requires photosynthetic electron transfer, because no Slr0006 was detected in darkness or in the presence of electron transfer inhibitors DCMU and DBMIB. Structural modeling of the Slr0006 protein suggests that it adopts Sua5/YciO/YrdC family fold, which is an α/β twisted open-sheet structure. Similar to the structurally known members of this protein family, the surface of Slr0006 contains positively charged cavity indicating a possible binding site for RNA or nucleotides. Moreover, Slr0006 was co-localized with 30S ribosomal proteins and rRNA, suggesting involvement in processes linked to protein synthesis.
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Affiliation(s)
- Dalton Carmel
- Department of Biochemistry, Molecular Plant Biology, University of Turku, 20014, Turku, Finland
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42
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Development of Synechocystis sp. PCC 6803 as a phototrophic cell factory. Mar Drugs 2013; 11:2894-916. [PMID: 23945601 PMCID: PMC3766872 DOI: 10.3390/md11082894] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 06/14/2013] [Accepted: 07/15/2013] [Indexed: 01/08/2023] Open
Abstract
Cyanobacteria (blue-green algae) play profound roles in ecology and biogeochemistry. One model cyanobacterial species is the unicellular cyanobacterium Synechocystis sp. PCC 6803. This species is highly amenable to genetic modification. Its genome has been sequenced and many systems biology and molecular biology tools are available to study this bacterium. Recently, researchers have put significant efforts into understanding and engineering this bacterium to produce chemicals and biofuels from sunlight and CO2. To demonstrate our perspective on the application of this cyanobacterium as a photosynthesis-based chassis, we summarize the recent research on Synechocystis 6803 by focusing on five topics: rate-limiting factors for cell cultivation; molecular tools for genetic modifications; high-throughput system biology for genome wide analysis; metabolic modeling for physiological prediction and rational metabolic engineering; and applications in producing diverse chemicals. We also discuss the particular challenges for systems analysis and engineering applications of this microorganism, including precise characterization of versatile cell metabolism, improvement of product rates and titers, bioprocess scale-up, and product recovery. Although much progress has been achieved in the development of Synechocystis 6803 as a phototrophic cell factory, the biotechnology for “Compounds from Synechocystis” is still significantly lagging behind those for heterotrophic microbes (e.g., Escherichia coli).
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Fuszard MA, Ow SY, Gan CS, Noirel J, Ternan NG, McMullan G, Biggs CA, Reardon KF, Wright PC. The quantitative proteomic response of Synechocystis sp. PCC6803 to phosphate acclimation. AQUATIC BIOSYSTEMS 2013; 9:5. [PMID: 23442353 PMCID: PMC3600050 DOI: 10.1186/2046-9063-9-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 01/28/2013] [Indexed: 05/11/2023]
Abstract
BACKGROUND Inorganic phosphate (Pi) is a critical nutrient for all life and is periodically limiting in marine and freshwater provinces, yet little is understood how organisms acclimate to fluctuations in Pi within their environment. To investigate whole cell adaptation, we grew Synechocystis sp. PCC6803, a model freshwater cyanobacterium, in 3%, and 0.3% inorganic phosphate (Pi) media. The cells were allowed to acclimate over 60 days, and cells were harvested for quantitative high throughput mass spectrometry-based proteomics using the iTRAQ™ labelling technology. RESULTS In total, 120 proteins were identified, and 52 proteins were considered differentially abundant compared to the control. Alkaline phosphatase (APase) activities correlated significantly (p < 0.05) with observed relative PhoA abundances. PstS1 and PstS2 were both observed, yet PstS1 was not differentially more abundant than the control. Phycobilisome protein abundances appeared to be coordinated, and are significantly less abundant in 0.3% Pi than 3% Pi cultures. Also, the central metabolic cell function appears to have shifted towards the production of (NADPH) reducing energy and nucleotide sugars. CONCLUSIONS This acclimation response bears strong similarity to the previously reported response to nitrogen deprivation within Synechocystis sp. PCC 6803. However, it also demonstrates some characteristics of desiccation stress, such as the regulation of fatty acids and increased abundance of rehydrin in the 3% Pi culture.
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Affiliation(s)
- Matthew A Fuszard
- BSRC Mass Spectrometry and Proteomics Facility, Department of Chemistry, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Saw Yen Ow
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | | | - Josseilin Noirel
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - Nigel G Ternan
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry, BT52 1SA, UK
| | - Geoff McMullan
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry, BT52 1SA, UK
| | - Catherine A Biggs
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - Kenneth F Reardon
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523-1370, USA
| | - Phillip C Wright
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
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Carbon availability affects diurnally controlled processes and cell morphology of Cyanothece 51142. PLoS One 2013; 8:e56887. [PMID: 23457634 PMCID: PMC3574086 DOI: 10.1371/journal.pone.0056887] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 01/17/2013] [Indexed: 11/25/2022] Open
Abstract
Cyanobacteria are oxygenic photoautotrophs notable for their ability to utilize atmospheric CO2 as the major source of carbon. The prospect of using cyanobacteria to convert solar energy and high concentrations of CO2 efficiently into biomass and renewable energy sources has sparked substantial interest in using flue gas from coal-burning power plants as a source of inorganic carbon. However, in order to guide further advances in this area, a better understanding of the metabolic changes that occur under conditions of high CO2 is needed. To determine the effect of high CO2 on cell physiology and growth, we analyzed the global transcriptional changes in the unicellular diazotrophic cyanobacterium Cyanothece 51142 grown in 8% CO2-enriched air. We found a concerted response of genes related to photosynthesis, carbon metabolism, respiration, nitrogen fixation, ribosome biosynthesis, and the synthesis of nucleotides and structural cell wall polysaccharides. The overall response to 8% CO2 in Cyanothece 51142 involves different strategies, to compensate for the high C/N ratio during both phases of the diurnal cycle. Our analyses show that high CO2 conditions trigger the production of carbon-rich compounds and stimulate processes such as respiration and nitrogen fixation. In addition, we observed that high levels of CO2 affect fundamental cellular processes such as cell growth and dramatically alter the intracellular morphology. This study provides novel insights on how diurnal and developmental rhythms are integrated to facilitate adaptation to high CO2 in Cyanothece 51142.
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Schwarz D, Orf I, Kopka J, Hagemann M. Recent applications of metabolomics toward cyanobacteria. Metabolites 2013; 3:72-100. [PMID: 24957891 PMCID: PMC3901253 DOI: 10.3390/metabo3010072] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/23/2013] [Accepted: 01/23/2013] [Indexed: 11/16/2022] Open
Abstract
Our knowledge on cyanobacterial molecular biology increased tremendously by the application of the "omics" techniques. Only recently, metabolomics was applied systematically to model cyanobacteria. Metabolomics, the quantitative estimation of ideally the complete set of cellular metabolites, is particularly well suited to mirror cellular metabolism and its flexibility under diverse conditions. Traditionally, small sets of metabolites are quantified in targeted metabolome approaches. The development of separation technologies coupled to mass-spectroscopy- or nuclear-magnetic-resonance-based identification of low molecular mass molecules presently allows the profiling of hundreds of metabolites of diverse chemical nature. Metabolome analysis was applied to characterize changes in the cyanobacterial primary metabolism under diverse environmental conditions or in defined mutants. The resulting lists of metabolites and their steady state concentrations in combination with transcriptomics can be used in system biology approaches. The application of stable isotopes in fluxomics, i.e. the quantitative estimation of carbon and nitrogen fluxes through the biochemical network, has only rarely been applied to cyanobacteria, but particularly this technique will allow the making of kinetic models of cyanobacterial systems. The further application of metabolomics in the concert of other "omics" technologies will not only broaden our knowledge, but will also certainly strengthen the base for the biotechnological application of cyanobacteria.
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Affiliation(s)
- Doreen Schwarz
- Institut Biowissenschaften, Pflanzenphysiologie, Universität Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Isabel Orf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany.
| | - Joachim Kopka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Golm, Germany.
| | - Martin Hagemann
- Institut Biowissenschaften, Pflanzenphysiologie, Universität Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany.
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Zhang L, Selão TT, Pisareva T, Qian J, Sze SK, Carlberg I, Norling B. Deletion of Synechocystis sp. PCC 6803 leader peptidase LepB1 affects photosynthetic complexes and respiration. Mol Cell Proteomics 2013; 12:1192-203. [PMID: 23358502 DOI: 10.1074/mcp.m112.022145] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The cyanobacterium Synechocystis sp. PCC 6803 possesses two leader peptidases, LepB1 (Sll0716) and LepB2 (Slr1377), responsible for the processing of signal peptide-containing proteins. Deletion of the gene for LepB1 results in an inability to grow photoautotrophically and an extreme light sensitivity. Here we show, using a combination of Blue Native/SDS-PAGE, Western blotting and iTRAQ analysis, that lack of LepB1 strongly affects the cell's ability to accumulate wild-type levels of both photosystem I (PSI) and cytochrome (Cyt) b6f complexes. The impaired assembly of PSI and Cyt b6f is considered to be caused by the no or slow processing of the integral subunits PsaF and Cyt f respectively. In particular, PsaF, one of the PSI subunits, was found incorporated into PSI in its unprocessed form, which could influence the assembly and/or stability of PSI. In contrast to these results, we found the amount of assembled photosystem II (PSII) unchanged, despite a slower processing of PsbO. Thus, imbalance in the ratios of PSI and Cyt b6f to photosystem II leads to an imbalanced photosynthetic electron flow up- and down-stream of the plastoquinone pool, resulting in the observed light sensitivity of the mutant. We conclude that LepB1 is the natural leader peptidase for PsaF, PsbO, and Cyt f. The maturation of PsbO and Cyt f can be partially performed by LepB2, whereas PsaF processing is completely dependent on LepB1. iTRAQ analysis also revealed a number of indirect effects accompanying the mutation, primarily a strong induction of the CydAB oxidase as well as a significant decrease in phycobiliproteins and chlorophyll/heme biosynthesis enzymes.
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Affiliation(s)
- Lifang Zhang
- Nanyang Technological University, School of Biological Sciences, 637551 Singapore
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Knock-out of Low CO2-Induced slr0006 Gene in Synechocystis sp. PCC 6803: Consequences on Growth and Proteome. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/978-3-642-32034-7_142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Wang H, Sivonen K, Rouhiainen L, Fewer DP, Lyra C, Rantala-Ylinen A, Vestola J, Jokela J, Rantasärkkä K, Li Z, Liu B. Genome-derived insights into the biology of the hepatotoxic bloom-forming cyanobacterium Anabaena sp. strain 90. BMC Genomics 2012; 13:613. [PMID: 23148582 PMCID: PMC3542288 DOI: 10.1186/1471-2164-13-613] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 11/05/2012] [Indexed: 11/15/2022] Open
Abstract
Background Cyanobacteria can form massive toxic blooms in fresh and brackish bodies of water and are frequently responsible for the poisoning of animals and pose a health risk for humans. Anabaena is a genus of filamentous diazotrophic cyanobacteria commonly implicated as a toxin producer in blooms in aquatic ecosystems throughout the world. The biology of bloom-forming cyanobacteria is poorly understood at the genome level. Results Here, we report the complete sequence and comprehensive annotation of the bloom-forming Anabaena sp. strain 90 genome. It comprises two circular chromosomes and three plasmids with a total size of 5.3 Mb, encoding a total of 4,738 genes. The genome is replete with mobile genetic elements. Detailed manual annotation demonstrated that almost 5% of the gene repertoire consists of pseudogenes. A further 5% of the genome is dedicated to the synthesis of small peptides that are the products of both ribosomal and nonribosomal biosynthetic pathways. Inactivation of the hassallidin (an antifungal cyclic peptide) biosynthetic gene cluster through a deletion event and a natural mutation of the buoyancy-permitting gvpG gas vesicle gene were documented. The genome contains a large number of genes encoding restriction-modification systems. Two novel excision elements were found in the nifH gene that is required for nitrogen fixation. Conclusions Genome analysis demonstrated that this strain invests heavily in the production of bioactive compounds and restriction-modification systems. This well-annotated genome provides a platform for future studies on the ecology and biology of these important bloom-forming cyanobacteria.
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Affiliation(s)
- Hao Wang
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, FIN-00014, Finland
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Eisenhut M, Georg J, Klähn S, Sakurai I, Mustila H, Zhang P, Hess WR, Aro EM. The antisense RNA As1_flv4 in the Cyanobacterium Synechocystis sp. PCC 6803 prevents premature expression of the flv4-2 operon upon shift in inorganic carbon supply. J Biol Chem 2012; 287:33153-62. [PMID: 22854963 PMCID: PMC3460422 DOI: 10.1074/jbc.m112.391755] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The functional relevance of natural cis-antisense transcripts is mostly unknown. Here we have characterized the association of three antisense RNAs and one intergenically encoded noncoding RNA with an operon that plays a crucial role in photoprotection of photosystem II under low carbon conditions in the cyanobacterium Synechocystis sp. PCC 6803. Cyanobacteria show strong gene expression dynamics in response to a shift of cells from high carbon to low levels of inorganic carbon (Ci), but the regulatory mechanisms are poorly understood. Among the most up-regulated genes in Synechocystis are flv4, sll0218, and flv2, which are organized in the flv4-2 operon. The flavodiiron proteins encoded by this operon open up an alternative electron transfer route, likely starting from the QB site in photosystem II, under photooxidative stress conditions. Our expression analysis of cells shifted from high carbon to low carbon demonstrated an inversely correlated transcript accumulation of the flv4-2 operon mRNA and one antisense RNA to flv4, designated as As1_flv4. Overexpression of As1_flv4 led to a decrease in flv4-2 mRNA. The promoter activity of as1_flv4 was transiently stimulated by Ci limitation and negatively regulated by the AbrB-like transcription regulator Sll0822, whereas the flv4-2 operon was positively regulated by the transcription factor NdhR. The results indicate that the tightly regulated antisense RNA As1_flv4 establishes a transient threshold for flv4-2 expression in the early phase after a change in Ci conditions. Thus, it prevents unfavorable synthesis of the proteins from the flv4-2 operon.
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Affiliation(s)
- Marion Eisenhut
- Department of Biochemistry and Food Science, Plant Physiology and Molecular Biology, University of Turku, Turku FI-20014, Finland
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Muramatsu M, Hihara Y. Acclimation to high-light conditions in cyanobacteria: from gene expression to physiological responses. JOURNAL OF PLANT RESEARCH 2012; 125:11-39. [PMID: 22006212 DOI: 10.1007/s10265-011-0454-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 08/23/2011] [Indexed: 05/04/2023]
Abstract
Photosynthetic organisms have evolved various acclimatory responses to high-light (HL) conditions to maintain a balance between energy supply (light harvesting and electron transport) and consumption (cellular metabolism) and to protect the photosynthetic apparatus from photodamage. The molecular mechanism of HL acclimation has been extensively studied in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Whole genome DNA microarray analyses have revealed that the change in gene expression profile under HL is closely correlated with subsequent acclimatory responses such as (1) acceleration in the rate of photosystem II turnover, (2) downregulation of light harvesting capacity, (3) development of a protection mechanism for the photosystems against excess light energy, (4) upregulation of general protection mechanism components, and (5) regulation of carbon and nitrogen assimilation. In this review article, we survey recent progress in the understanding of the molecular mechanisms of these acclimatory responses in Synechocystis sp. PCC 6803. We also briefly describe attempts to understand HL acclimation in various cyanobacterial species in their natural environments.
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Affiliation(s)
- Masayuki Muramatsu
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Ibaraki, 305-8602, Japan
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