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Kraus A, Spät P, Timm S, Wilson A, Schumann R, Hagemann M, Maček B, Hess WR. Protein NirP1 regulates nitrite reductase and nitrite excretion in cyanobacteria. Nat Commun 2024; 15:1911. [PMID: 38429292 PMCID: PMC10907346 DOI: 10.1038/s41467-024-46253-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/19/2024] [Indexed: 03/03/2024] Open
Abstract
When the supply of inorganic carbon is limiting, photosynthetic cyanobacteria excrete nitrite, a toxic intermediate in the ammonia assimilation pathway from nitrate. It has been hypothesized that the excreted nitrite represents excess nitrogen that cannot be further assimilated due to the missing carbon, but the underlying molecular mechanisms are unclear. Here, we identified a protein that interacts with nitrite reductase, regulates nitrogen metabolism and promotes nitrite excretion. The protein, which we named NirP1, is encoded by an unannotated gene that is upregulated under low carbon conditions and controlled by transcription factor NtcA, a central regulator of nitrogen homeostasis. Ectopic overexpression of nirP1 in Synechocystis sp. PCC 6803 resulted in a chlorotic phenotype, delayed growth, severe changes in amino acid pools, and nitrite excretion. Coimmunoprecipitation experiments indicated that NirP1 interacts with nitrite reductase, a central enzyme in the assimilation of ammonia from nitrate/nitrite. Our results reveal that NirP1 is widely conserved in cyanobacteria and plays a crucial role in the coordination of C/N primary metabolism by targeting nitrite reductase.
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Affiliation(s)
- Alexander Kraus
- Genetics and Experimental Bioinformatics, Faculty of Biology, Freiburg University, D-79104, Freiburg, Germany
| | - Philipp Spät
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, D-72076, Tübingen, Germany
| | - Stefan Timm
- Plant Physiology Department, Institute of Biosciences, University of Rostock, D-18059, Rostock, Germany
| | - Amy Wilson
- Genetics and Experimental Bioinformatics, Faculty of Biology, Freiburg University, D-79104, Freiburg, Germany
| | - Rhena Schumann
- Biological Station Zingst, University of Rostock, D-18374, Zingst, Germany
| | - Martin Hagemann
- Plant Physiology Department, Institute of Biosciences, University of Rostock, D-18059, Rostock, Germany
| | - Boris Maček
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, D-72076, Tübingen, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, Freiburg University, D-79104, Freiburg, Germany.
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2
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Moulin SLY, Frail S, Braukmann T, Doenier J, Steele-Ogus M, Marks JC, Mills MM, Yeh E. The endosymbiont of Epithemia clementina is specialized for nitrogen fixation within a photosynthetic eukaryote. ISME COMMUNICATIONS 2024; 4:ycae055. [PMID: 38707843 PMCID: PMC11070190 DOI: 10.1093/ismeco/ycae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 05/07/2024]
Abstract
Epithemia spp. diatoms contain obligate, nitrogen-fixing endosymbionts, or diazoplasts, derived from cyanobacteria. These algae are a rare example of photosynthetic eukaryotes that have successfully coupled oxygenic photosynthesis with oxygen-sensitive nitrogenase activity. Here, we report a newly-isolated species, E. clementina, as a model to investigate endosymbiotic acquisition of nitrogen fixation. We demonstrate that the diazoplast, which has lost photosynthesis, provides fixed nitrogen to the diatom host in exchange for fixed carbon. To identify the metabolic changes associated with this endosymbiotic specialization, we compared the Epithemia diazoplast with its close, free-living cyanobacterial relative, Crocosphaera subtropica. Unlike C. subtropica, in which nitrogenase activity is temporally separated from photosynthesis, we show that nitrogenase activity in the diazoplast is continuous through the day (concurrent with host photosynthesis) and night. Host and diazoplast metabolism are tightly coupled to support nitrogenase activity: Inhibition of photosynthesis abolishes daytime nitrogenase activity, while nighttime nitrogenase activity no longer requires cyanobacterial glycogen storage pathways. Instead, import of host-derived carbohydrates supports nitrogenase activity throughout the day-night cycle. Carbohydrate metabolism is streamlined in the diazoplast compared to C. subtropica with retention of the oxidative pentose phosphate pathway and oxidative phosphorylation. Similar to heterocysts, these pathways may be optimized to support nitrogenase activity, providing reducing equivalents and ATP and consuming oxygen. Our results demonstrate that the diazoplast is specialized for endosymbiotic nitrogen fixation. Altogether, we establish a new model for studying endosymbiosis, perform a functional characterization of this diazotroph endosymbiosis, and identify metabolic adaptations for endosymbiotic acquisition of a critical biological function.
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Affiliation(s)
- Solène L Y Moulin
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305, United States
| | - Sarah Frail
- Department of Biochemistry, Stanford School of Medicine, Stanford, CA 94305, United States
| | - Thomas Braukmann
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305, United States
- Department of Biochemistry, Stanford School of Medicine, Stanford, CA 94305, United States
| | - Jon Doenier
- Department of Biochemistry, Stanford School of Medicine, Stanford, CA 94305, United States
| | - Melissa Steele-Ogus
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305, United States
| | - Jane C Marks
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AR 86011, United States
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, United States
| | - Matthew M Mills
- Department of Earth System Science, Stanford Doerr School of Sustainability, Stanford, CA 94305, United States
| | - Ellen Yeh
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305, United States
- Department of Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, United States
- Chan Zuckerberg Biohub, San Francisco, CA 94158, United States
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3
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Moulin SL, Frail S, Doenier J, Braukmann T, Yeh E. The endosymbiont of Epithemia clementina is specialized for nitrogen fixation within a photosynthetic eukaryote. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531752. [PMID: 37066385 PMCID: PMC10103950 DOI: 10.1101/2023.03.08.531752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Epithemia spp. diatoms contain obligate, nitrogen-fixing endosymbionts, or "diazoplasts", derived from cyanobacteria. These algae are a rare example of photosynthetic eukaryotes that have successfully coupled oxygenic photosynthesis with oxygen-sensitive nitrogenase activity. Here, we report a newly-isolated species, E. clementina, as a model to investigate endosymbiotic acquisition of nitrogen fixation. To detect the metabolic changes associated with endosymbiotic specialization, we compared nitrogen fixation, associated carbon and nitrogen metabolism, and their regulatory pathways in the Epithemia diazoplast with its close, free-living cyanobacterial relative, Crocosphaera subtropica. Unlike C. subtropica, we show that nitrogenase activity in the diazoplast is concurrent with, and even dependent on, host photosynthesis and no longer associated with cyanobacterial glycogen storage suggesting carbohydrates are imported from the host diatom. Carbohydrate catabolism in the diazoplast indicates that the oxidative pentose pathway and oxidative phosphorylation, in concert, generates reducing equivalents and ATP and consumes oxygen to support nitrogenase activity. In contrast to expanded nitrogenase activity, the diazoplast has diminished ability to utilize alternative nitrogen sources. Upon ammonium repletion, negative feedback regulation of nitrogen fixation was conserved, however ammonia assimilation showed paradoxical responses in the diazoplast compared with C. subtropica. The altered nitrogen regulation likely favors nitrogen transfer to the host. Our results suggest that the diazoplast is specialized for endosymbiotic nitrogen fixation. Altogether, we establish a new model for studying endosymbiosis, perform the first functional characterization of this diazotroph endosymbiosis, and identify metabolic adaptations for endosymbiotic acquisition of a critical biological function.
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Affiliation(s)
- Solène L.Y. Moulin
- Department of Pathology, Stanford School of Medicine, Stanford, California, USA
| | - Sarah Frail
- Department of Biochemistry, Stanford School of Medicine, Stanford, California, USA
| | - Jon Doenier
- Department of Biochemistry, Stanford School of Medicine, Stanford, California, USA
| | - Thomas Braukmann
- Department of Pathology, Stanford School of Medicine, Stanford, California, USA
- Department of Biochemistry, Stanford School of Medicine, Stanford, California, USA
| | - Ellen Yeh
- Department of Pathology, Stanford School of Medicine, Stanford, California, USA
- Department of Microbiology & Immunology, Stanford School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA 94158
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4
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Díez J, López-Lozano A, Domínguez-Martín MA, Gómez-Baena G, Muñoz-Marín MC, Melero-Rubio Y, García-Fernández JM. Regulatory and metabolic adaptations in the nitrogen assimilation of marine picocyanobacteria. FEMS Microbiol Rev 2023; 47:6794272. [PMID: 36323406 DOI: 10.1093/femsre/fuac043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/17/2022] Open
Abstract
Prochlorococcus and Synechococcus are the two most abundant photosynthetic organisms on Earth, with a strong influence on the biogeochemical carbon and nitrogen cycles. Early reports demonstrated the streamlining of regulatory mechanisms in nitrogen metabolism and the removal of genes not strictly essential. The availability of a large series of genomes, and the utilization of latest generation molecular techniques have allowed elucidating the main mechanisms developed by marine picocyanobacteria to adapt to the environments where they thrive, with a particular interest in the strains inhabiting oligotrophic oceans. Given that nitrogen is often limited in those environments, a series of studies have explored the strategies utilized by Prochlorococcus and Synechococcus to exploit the low concentrations of nitrogen-containing molecules available in large areas of the oceans. These strategies include the reduction in the GC and the cellular protein contents; the utilization of truncated proteins; a reduced average amount of N in the proteome; the development of metabolic mechanisms to perceive and utilize nanomolar nitrate concentrations; and the reduced responsiveness of key molecular regulatory systems such as NtcA to 2-oxoglutarate. These findings are in sharp contrast with the large body of knowledge obtained in freshwater cyanobacteria. We will outline the main discoveries, stressing their relevance to the ecological success of these important microorganisms.
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Affiliation(s)
- J Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - A López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - M A Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - G Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - M C Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - Y Melero-Rubio
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - J M García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
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5
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Casanova-Ferrer P, Muñoz-García J, Ares S. Mathematical models of nitrogen-fixing cell patterns in filamentous cyanobacteria. Front Cell Dev Biol 2022; 10:959468. [PMID: 36187490 PMCID: PMC9523125 DOI: 10.3389/fcell.2022.959468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
The Anabaena genus is a model organism of filamentous cyanobacteria whose vegetative cells can differentiate under nitrogen-limited conditions into a type of cell called a heterocyst. These heterocysts lose the possibility to divide and are necessary for the filament because they can fix and share environmental nitrogen. In order to distribute the nitrogen efficiently, heterocysts are arranged to form a quasi-regular pattern whose features are maintained as the filament grows. Recent efforts have allowed advances in the understanding of the interactions and genetic mechanisms underlying this dynamic pattern. Here, we present a systematic review of the existing theoretical models of nitrogen-fixing cell differentiation in filamentous cyanobacteria. These filaments constitute one of the simplest forms of multicellular organization, and this allows for several modeling scales of this emergent pattern. The system has been approached at three different levels. From bigger to smaller scale, the system has been considered as follows: at the population level, by defining a mean-field simplified system to study the ratio of heterocysts and vegetative cells; at the filament level, with a continuous simplification as a reaction-diffusion system; and at the cellular level, by studying the genetic regulation that produces the patterning for each cell. In this review, we compare these different approaches noting both the virtues and shortcomings of each one of them.
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Affiliation(s)
- Pau Casanova-Ferrer
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain
- Centro Nacional de Biotecnologia (CNB), CSIC, Madrid, Spain
| | - Javier Muñoz-García
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain
| | - Saúl Ares
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Centro Nacional de Biotecnologia (CNB), CSIC, Madrid, Spain
- *Correspondence: Saúl Ares,
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6
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Domínguez-Martín MA, López-Lozano A, Melero-Rubio Y, Gómez-Baena G, Jiménez-Estrada JA, Kukil K, Diez J, García-Fernández JM. Marine Synechococcus sp. Strain WH7803 Shows Specific Adaptative Responses to Assimilate Nanomolar Concentrations of Nitrate. Microbiol Spectr 2022; 10:e0018722. [PMID: 35852322 PMCID: PMC9430850 DOI: 10.1128/spectrum.00187-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/24/2022] [Indexed: 11/20/2022] Open
Abstract
Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrient availability and temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to micromolar ammonium or nitrogen starvation. We found that Synechococcus has a specific response to a nanomolar nitrate concentration that differs from the response shown under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentrations of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural environment. IMPORTANCE Marine Synechococcus are a very abundant group of photosynthetic organisms on our planet. Previous studies have shown blooms of these organisms when nanomolar concentrations of nitrate become available. We have assessed the effect of nanomolar nitrate concentrations by studying the transcriptome and proteome of Synechococcus sp. WH7803, together with some physiological parameters. We found evidence that Synechococcus sp. strain WH7803 does sense and react to nanomolar concentrations of nitrate, suggesting the occurrence of specific adaptive mechanisms to allow their utilization. Thus, very low concentrations of nitrate in the ocean seem to be a significant nitrogen source for marine picocyanobacteria.
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Grants
- Ministerio de Ciencia e Innovacion, Government of Spain (cofunded by the FEDER program, European Union)
- Consejeria de Conocimiento, Investigacion y Universidad, Junta de Andalucia (Spain), cofunded by the FEDER program (European Union)
- Universidad de Cordoba (Spain), Programa Propio de Investigacion
- Junta de Andalucia (Spain), Programa Operativo de Empleo Juvenil, cofunded by the FEDER programme (European Union)
- Consejería de Transformación Económica, Industria, Conocimiento y Universidades, Junta de Andalucia (Spain), cofunded by the FEDER program (European Union)
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Affiliation(s)
- María Agustina Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Yesica Melero-Rubio
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Guadalupe Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Juan Andrés Jiménez-Estrada
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Kateryna Kukil
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Jesús Diez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
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7
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Krysenko S, Wohlleben W. Polyamine and Ethanolamine Metabolism in Bacteria as an Important Component of Nitrogen Assimilation for Survival and Pathogenicity. Med Sci (Basel) 2022; 10:40. [PMID: 35997332 PMCID: PMC9397018 DOI: 10.3390/medsci10030040] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Nitrogen is an essential element required for bacterial growth. It serves as a building block for the biosynthesis of macromolecules and provides precursors for secondary metabolites. Bacteria have developed the ability to use various nitrogen sources and possess two enzyme systems for nitrogen assimilation involving glutamine synthetase/glutamate synthase and glutamate dehydrogenase. Microorganisms living in habitats with changeable availability of nutrients have developed strategies to survive under nitrogen limitation. One adaptation is the ability to acquire nitrogen from alternative sources including the polyamines putrescine, cadaverine, spermidine and spermine, as well as the monoamine ethanolamine. Bacterial polyamine and monoamine metabolism is not only important under low nitrogen availability, but it is also required to survive under high concentrations of these compounds. Such conditions can occur in diverse habitats such as soil, plant tissues and human cells. Strategies of pathogenic and non-pathogenic bacteria to survive in the presence of poly- and monoamines offer the possibility to combat pathogens by using their capability to metabolize polyamines as an antibiotic drug target. This work aims to summarize the knowledge on poly- and monoamine metabolism in bacteria and its role in nitrogen metabolism.
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Affiliation(s)
- Sergii Krysenko
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
| | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
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8
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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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9
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Brenes-Álvarez M, Olmedo-Verd E, Vioque A, Muro-Pastor AM. A nitrogen stress-inducible small RNA regulates CO2 fixation in Nostoc. PLANT PHYSIOLOGY 2021; 187:787-798. [PMID: 34608966 PMCID: PMC8491059 DOI: 10.1093/plphys/kiab309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/09/2021] [Indexed: 05/09/2023]
Abstract
In the absence of fixed nitrogen, some filamentous cyanobacteria differentiate heterocysts, specialized cells devoted to fixing atmospheric nitrogen (N2). This differentiation process is controlled by the global nitrogen regulator NtcA and involves extensive metabolic reprogramming, including shutdown of photosynthetic CO2 fixation in heterocysts, to provide a microaerobic environment suitable for N2 fixation. Small regulatory RNAs (sRNAs) are major post-transcriptional regulators of gene expression in bacteria. In cyanobacteria, responding to nitrogen deficiency involves transcribing several nitrogen-regulated sRNAs. Here, we describe the participation of nitrogen stress-inducible RNA 4 (NsiR4) in post-transcriptionally regulating the expression of two genes involved in CO2 fixation via the Calvin cycle: glpX, which encodes bifunctional sedoheptulose-1,7-bisphosphatase/fructose-1,6-bisphosphatase (SBPase), and pgk, which encodes phosphoglycerate kinase (PGK). Using a heterologous reporter assay in Escherichia coli, we show that NsiR4 interacts with the 5'-untranslated region (5'-UTR) of glpX and pgk mRNAs. Overexpressing NsiR4 in Nostoc sp. PCC 7120 resulted in a reduced amount of SBPase protein and reduced PGK activity, as well as reduced levels of both glpX and pgk mRNAs, further supporting that NsiR4 negatively regulates these two enzymes. In addition, using a gfp fusion to the nsiR4 promoter, we show stronger expression of NsiR4 in heterocysts than in vegetative cells, which could contribute to the heterocyst-specific shutdown of Calvin cycle flux. Post-transcriptional regulation of two Calvin cycle enzymes by NsiR4, a nitrogen-regulated sRNA, represents an additional link between nitrogen control and CO2 assimilation.
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Affiliation(s)
- Manuel Brenes-Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville E-41092, Spain
| | - Elvira Olmedo-Verd
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville E-41092, Spain
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville E-41092, Spain
| | - Alicia M. Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville E-41092, Spain
- Author for communication:
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10
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Discovery of a small protein factor involved in the coordinated degradation of phycobilisomes in cyanobacteria. Proc Natl Acad Sci U S A 2021; 118:2012277118. [PMID: 33509926 PMCID: PMC7865187 DOI: 10.1073/pnas.2012277118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
During genome analysis, genes encoding small proteins are frequently neglected. Accordingly, small proteins have remained underinvestigated in all domains of life. Based on a previous systematic search for such genes, we present the functional analysis of the 66 amino acids protein NblD in a photosynthetic cyanobacterium. We show that NblD plays a crucial role during the coordinated dismantling of phycobilisome light-harvesting complexes. This disassembly is triggered when the cells become starved for nitrogen, a condition that frequently occurs in nature. Similar to NblA that tags phycobiliproteins for proteolysis, NblD binds to phycocyanin polypeptides but has a different function. The results show that, even in a well-investigated process, crucial new players can be discovered if small proteins are taken into consideration. Phycobilisomes are the major pigment–protein antenna complexes that perform photosynthetic light harvesting in cyanobacteria, rhodophyte, and glaucophyte algae. Up to 50% of the cellular nitrogen can be stored in their giant structures. Accordingly, upon nitrogen depletion, phycobilisomes are rapidly degraded following an intricate genetic program. Here, we describe the role of NblD, a cysteine-rich, small protein in this process in cyanobacteria. Deletion of the nblD gene in the cyanobacterium Synechocystis sp. PCC 6803 prevented the degradation of phycobilisomes, leading to a nonbleaching (nbl) phenotype, which could be complemented by a plasmid-localized gene copy. Competitive growth experiments between the ΔnblD and the wild-type strain provided direct evidence for the physiological importance of NblD under nitrogen-limited conditions. Ectopic expression of NblD under nitrogen-replete conditions showed no effect, in contrast to the unrelated proteolysis adaptors NblA1 and NblA2, which can trigger phycobilisome degradation. Transcriptome analysis indicated increased nblA1/2 transcript levels in the ΔnblD strain during nitrogen starvation, implying that NblD does not act as a transcriptional (co)regulator. However, immunoprecipitation and far-western experiments identified the chromophorylated (holo form) of the phycocyanin β-subunit (CpcB) as its target, while apo-CpcB was not bound. The addition of recombinant NblD to isolated phycobilisomes caused a reduction in phycocyanin absorbance and a broadening and shifting of the peak to lower wavelengths, indicating the occurrence of structural changes. These data demonstrate that NblD plays a crucial role in the coordinated dismantling of phycobilisomes and add it as a factor to the genetically programmed response to nitrogen starvation.
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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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12
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Phycobilisome breakdown effector NblD is required to maintain the cellular amino acid composition during nitrogen starvation. J Bacteriol 2021; 204:JB0015821. [PMID: 34228497 PMCID: PMC8765419 DOI: 10.1128/jb.00158-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small proteins are critically involved in the acclimation response of photosynthetic cyanobacteria to nitrogen starvation. NblD is the 66-amino-acid effector of nitrogen-limitation-induced phycobilisome breakdown, which is believed to replenish the cellular amino acid pools. To address the physiological functions of NblD, the concentrations of amino acids, intermediates of the arginine catabolism pathway and several organic acids were measured during the response to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 wild type and in an nblD deletion strain. A characteristic signature of metabolite pool composition was identified, which shows that NblD-mediated phycobilisome degradation is required to maintain the cellular amino acid and organic acid pools during nitrogen starvation. Specific deviations from the wild type suggest wider-reaching effects that also affect such processes as redox homeostasis via glutathione and tetrapyrrole biosynthesis, both of which are linked to the strongly decreased glutamate pool, and transcriptional reprogramming via an enhanced concentration of 2-oxoglutarate, the metabolite co-regulator of the NtcA transcription factor. The essential role played by NblD in metabolic homeostasis is consistent with the widespread occurrence of NblD throughout the cyanobacterial radiation and the previously observed strong positive selection for the nblD gene under fluctuating nitrogen supply. Importance Cyanobacteria play important roles in the global carbon and nitrogen cycles. In their natural environment, these organisms are exposed to fluctuating nutrient conditions. Nitrogen starvation induces a coordinated nitrogen-saving program that includes the breakdown of nitrogen-rich photosynthetic pigments, particularly phycobiliproteins. The small protein NblD was recently identified as an effector of phycobilisome breakdown in cyanobacteria. In this study, we demonstrate that the NblD-mediated degradation of phycobiliproteins is needed to sustain cellular pools of soluble amino acids and other crucial metabolites. The essential role played by NblD in metabolic homeostasis explains why genes encoding this small protein are conserved in almost all members of cyanobacterial radiation.
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Inactivation of Three RG(S/T)GR Pentapeptide-Containing Negative Regulators of HetR Results in Lethal Differentiation of Anabaena PCC 7120. Life (Basel) 2020; 10:life10120326. [PMID: 33291589 PMCID: PMC7761841 DOI: 10.3390/life10120326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 12/19/2022] Open
Abstract
The filamentous cyanobacterium Anabaena sp. PCC 7120 produces, during the differentiation of heterocysts, a short peptide PatS and a protein HetN, both containing an RGSGR pentapeptide essential for activity. Both act on the master regulator HetR to guide heterocyst pattern formation by controlling the binding of HetR to DNA and its turnover. A third small protein, PatX, with an RG(S/T)GR motif is present in all HetR-containing cyanobacteria. In a nitrogen-depleted medium, inactivation of patX does not produce a discernible change in phenotype, but its overexpression blocks heterocyst formation. Mutational analysis revealed that PatX is not required for normal intercellular signaling, but it nonetheless is required when PatS is absent to prevent rapid ectopic differentiation. Deprivation of all three negative regulators—PatS, PatX, and HetN—resulted in synchronous differentiation. However, in a nitrogen-containing medium, such deprivation leads to extensive fragmentation, cell lysis, and aberrant differentiation, while either PatX or PatS as the sole HetR regulator can establish and maintain a semiregular heterocyst pattern. These results suggest that tight control over HetR by PatS and PatX is needed to sustain vegetative growth and regulated development. The mutational analysis has been interpreted in light of the opposing roles of negative regulators of HetR and the positive regulator HetL.
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Rachedi R, Foglino M, Latifi A. Stress Signaling in Cyanobacteria: A Mechanistic Overview. Life (Basel) 2020; 10:life10120312. [PMID: 33256109 PMCID: PMC7760821 DOI: 10.3390/life10120312] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/22/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
Cyanobacteria are highly diverse, widely distributed photosynthetic bacteria inhabiting various environments ranging from deserts to the cryosphere. Throughout this range of niches, they have to cope with various stresses and kinds of deprivation which threaten their growth and viability. In order to adapt to these stresses and survive, they have developed several global adaptive responses which modulate the patterns of gene expression and the cellular functions at work. Sigma factors, two-component systems, transcriptional regulators and small regulatory RNAs acting either separately or collectively, for example, induce appropriate cyanobacterial stress responses. The aim of this review is to summarize our current knowledge about the diversity of the sensors and regulators involved in the perception and transduction of light, oxidative and thermal stresses, and nutrient starvation responses. The studies discussed here point to the fact that various stresses affecting the photosynthetic capacity are transduced by common mechanisms.
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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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Forchhammer K, Selim KA. Carbon/nitrogen homeostasis control in cyanobacteria. FEMS Microbiol Rev 2020; 44:33-53. [PMID: 31617886 PMCID: PMC8042125 DOI: 10.1093/femsre/fuz025] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/14/2019] [Indexed: 02/06/2023] Open
Abstract
Carbon/nitrogen (C/N) balance sensing is a key requirement for the maintenance of cellular homeostasis. Therefore, cyanobacteria have evolved a sophisticated signal transduction network targeting the metabolite 2-oxoglutarate (2-OG), the carbon skeleton for nitrogen assimilation. It serves as a status reporter for the cellular C/N balance that is sensed by transcription factors NtcA and NdhR and the versatile PII-signaling protein. The PII protein acts as a multitasking signal-integrating regulator, combining the 2-OG signal with the energy state of the cell through adenyl-nucleotide binding. Depending on these integrated signals, PII orchestrates metabolic activities in response to environmental changes through binding to various targets. In addition to 2-OG, other status reporter metabolites have recently been discovered, mainly indicating the carbon status of the cells. One of them is cAMP, which is sensed by the PII-like protein SbtB. The present review focuses, with a main emphasis on unicellular model strains Synechoccus elongatus and Synechocystis sp. PCC 6803, on the physiological framework of these complex regulatory loops, the tight linkage to metabolism and the molecular mechanisms governing the signaling processes.
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Affiliation(s)
- Karl Forchhammer
- Lehrstuhl für Mikrobiologie, Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
| | - Khaled A Selim
- Lehrstuhl für Mikrobiologie, Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
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Kurio Y, Koike Y, Kanesaki Y, Watanabe S, Ehira S. The CRP-family transcriptional regulator DevH regulates expression of heterocyst-specific genes at the later stage of differentiation in the cyanobacterium Anabaena sp. strain PCC 7120. Mol Microbiol 2020; 114:553-562. [PMID: 32564445 DOI: 10.1111/mmi.14558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 12/16/2022]
Abstract
Heterocysts are terminally differentiated cells of filamentous cyanobacteria, which are specialized for nitrogen fixation. Because nitrogenase is easily inactivated by oxygen, the intracellular environment of heterocysts is kept microoxic. In heterocysts, the oxygen-evolving photosystem II is inactivated, a heterocyst-specific envelope with an outer polysaccharide layer and an inner glycolipid layer is formed to limit oxygen entry, and oxygen consumption is activated. Heterocyst differentiation, which is accompanied by drastic morphological and physiological changes, requires strictly controlled gene expression systems. Here, we investigated the functions of a CRP-family transcriptional regulator, DevH, in the process of heterocyst differentiation. A devH-knockdown strain, devH-kd, was created by replacing the original promoter with the gifA promoter, which is repressed during heterocyst differentiation. Although devH-kd formed morphologically distinct cells with the heterocyst envelope polysaccharide layer, it was unable to grow diazotrophically. Genes involved in construction of the microoxic environment, such as cox operons and the hgl island, were not upregulated in devH-kd. Moreover, expression of the nif gene cluster was completely abolished. Although CnfR was expressed in devH-kd, the nif gene cluster was not induced even under microoxic conditions. Thus, DevH is necessary for the establishment of a microoxic environment and induction of nitrogenase in heterocysts.
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Affiliation(s)
- Yohei Kurio
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Yosuke Koike
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Shigeki Ehira
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
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18
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Labella JI, Cantos R, Salinas P, Espinosa J, Contreras A. Distinctive Features of PipX, a Unique Signaling Protein of Cyanobacteria. Life (Basel) 2020; 10:life10060079. [PMID: 32481703 PMCID: PMC7344720 DOI: 10.3390/life10060079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 05/23/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022] Open
Abstract
PipX is a unique cyanobacterial protein identified by its ability to bind to PII and NtcA, two key regulators involved in the integration of signals of the nitrogen/carbon and energy status, with a tremendous impact on nitrogen assimilation and gene expression in cyanobacteria. PipX provides a mechanistic link between PII, the most widely distributed signaling protein, and NtcA, a global transcriptional regulator of cyanobacteria. PII, required for cell survival unless PipX is inactivated or down-regulated, functions by protein–protein interactions with transcriptional regulators, transporters, and enzymes. In addition, PipX appears to be involved in a wider signaling network, supported by the following observations: (i) PII–PipX complexes interact with PlmA, an as yet poorly characterized transcriptional regulator also restricted to cyanobacteria; (ii) the pipX gene is functionally connected with pipY, a gene encoding a universally conserved pyridoxal phosphate binding protein (PLPBP) involved in vitamin B6 and amino acid homeostasis, whose loss-of-function mutations cause B6-dependent epilepsy in humans, and (iii) pipX is part of a relatively robust, six-node synteny network that includes pipY and four additional genes that might also be functionally connected with pipX. In this overview, we propose that the study of the protein–protein interaction and synteny networks involving PipX would contribute to understanding the peculiarities and idiosyncrasy of signaling pathways that are conserved in cyanobacteria.
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19
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Scholl J, Dengler L, Bader L, Forchhammer K. Phosphoenolpyruvate carboxylase from the cyanobacterium Synechocystis sp. PCC 6803 is under global metabolic control by P II signaling. Mol Microbiol 2020; 114:292-307. [PMID: 32274833 DOI: 10.1111/mmi.14512] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/20/2022]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is the second major carbon-fixing enzyme in photoautotrophic organisms. PEPC is required for the synthesis of amino acids of the glutamate and aspartate family by replenishing the TCA cycle. Furthermore, in cyanobacteria, PEPC, together with malate dehydrogenase and malic enzyme, forms a metabolic shunt for the synthesis of pyruvate from PEP. During this process, CO2 is first fixed and later released again. Due to its central metabolic position, it is crucial to fully understand the regulation of PEPC. Here, we identify PEPC from the cyanobacterium Synechocystis sp. PCC 6803 (PEPC) as a novel interaction partner for the global signal transduction protein PII . In addition to an extensive characterization of PEPC, we demonstrate specific PII -PEPC complex formation and its enzymatic consequences. PEPC activity is tuned by the metabolite-sensing properties of PII : Whereas in the absence of PII, PEPC is subjected to ATP inhibition, it is activated beyond its basal activity in the presence of PII . Furthermore, PII -PEPC complex formation is inhibited by ADP and PEPC activation by PII -ATP is mitigated in the presence of 2-OG, linking PEPC regulation to the cell's global carbon/nitrogen status. Finally, physiological relevance of the in vitro measurements was proven by metabolomic analyses of Synechocystis wild-type and PII -deficient cells.
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Affiliation(s)
- Jörg Scholl
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University, Tübingen, Germany
| | - Lisa Dengler
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University, Tübingen, Germany
| | - Laura Bader
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls University, Tübingen, Germany
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20
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Muro-Pastor AM, Hess WR. Regulatory RNA at the crossroads of carbon and nitrogen metabolism in photosynthetic cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194477. [PMID: 31884117 DOI: 10.1016/j.bbagrm.2019.194477] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are photosynthetic bacteria that populate widely different habitats. Accordingly, cyanobacteria exhibit a wide spectrum of lifestyles, physiologies, and morphologies and possess genome sizes and gene numbers which may vary by up to a factor of ten within the phylum. Consequently, large differences exist between individual species in the size and complexity of their regulatory networks. Several non-coding RNAs have been identified that play crucial roles in the acclimation responses of cyanobacteria to changes in the environment. Some of these regulatory RNAs are conserved throughout the cyanobacterial phylum, while others exist only in a few taxa. Here we give an overview on characterized regulatory RNAs in cyanobacteria, with a focus on regulators of photosynthesis, carbon and nitrogen metabolism. However, chances are high that these regulators represent just the tip of the iceberg.
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Affiliation(s)
- Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, E-41092 Sevilla, Spain
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104 Freiburg, Germany; University of Freiburg, Freiburg Institute for Advanced Studies, Albertstr. 19, D-79104 Freiburg, Germany.
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21
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Mock M, Schmid A, Bühler K. Photoautotrophic production of succinate via the oxidative branch of the tricarboxylic acid cycle influences glycogen accumulation in Synechocystis sp. PCC 6803. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Robles-Rengel R, Florencio FJ, Muro-Pastor MI. Redox interference in nitrogen status via oxidative stress is mediated by 2-oxoglutarate in cyanobacteria. THE NEW PHYTOLOGIST 2019; 224:216-228. [PMID: 31168850 DOI: 10.1111/nph.15979] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/30/2019] [Indexed: 05/10/2023]
Abstract
Reactive oxygen species (ROS) are generated naturally in photosynthetic organisms by respiration and photosynthesis. Therefore, detoxification of these compounds, avoiding oxidative stress, is essential for proper cell function. In cyanobacteria, some observations point to a crosstalk between ROS homeostasis, in particular hydrogen peroxide, and nitrogen metabolism by a mechanism independent of known redox regulators. Using glutamine synthetase (GS), a finely regulated enzyme essential for nitrogen assimilation, as a tool, we were able to monitor nitrogen metabolism in relation to oxidative stress. We show that hydrogen peroxide clearly alters the expression of different genes related to nitrogen metabolism, both in the wild-type strain of the cyanobacterium Synechocystis sp. PCC 6803 and in a mutant strain lacking the catalase-peroxidase encoded by the katG gene and therefore highly sensitive to oxidative stress. As cyanobacteria perceive nitrogen status by sensing intracellular 2-oxoglutarate (2-OG) concentrations, the hydrogen peroxide effect was analysed under different nitrogen conditions in the wild-type, the ∆katG strain and in a strain able to transport 2-OG. The results obtained demonstrate that hydrogen peroxide interferes with signalling of cellular carbon : nitrogen status by decreasing the intracellular concentrations of 2-OG and hence altering the function of the 2-OG-sensing global nitrogen regulator NtcA.
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Affiliation(s)
- Rocío Robles-Rengel
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, 41092, Spain
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, 41092, Spain
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, 41092, Spain
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Cantos R, Labella JI, Espinosa J, Contreras A. The nitrogen regulator PipX acts in cis to prevent operon polarity. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:495-507. [PMID: 30126050 DOI: 10.1111/1758-2229.12688] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/10/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Abstract
Cyanobacteria, phototrophic organisms performing oxygenic photosynthesis, must adapt their metabolic processes to important environmental challenges, like those imposed by the succession of days and nights. Not surprisingly, certain regulatory proteins are found exclusively in this phylum. One of these unique factors, PipX, provides a mechanistic link between signals of carbon/nitrogen and of energy, transduced by the signalling protein PII, and the control of gene expression by the global nitrogen regulator NtcA. Here we report a new regulatory function of PipX: enhancement in cis of pipY expression, a gene encoding a universally conserved protein involved in amino/keto acid and Pyridoxal phosphate homeostasis. In Synechococcus elongatus and many other cyanobacteria these genes are expressed as a bicistronic pipXY operon. Despite being cis-acting, polarity suppression by PipX is nevertheless reminiscent of the function of NusG paralogues typified by RfaH, which are non-essential operon-specific bacterial factors acting in trans to upregulate horizontally-acquired genes. Furthermore, PipX and members of the NusG superfamily share a TLD/KOW structural domain, suggesting regulatory interactions of PipX with the translation machinery. Our results also suggest that the cis-acting function of PipX is a sophisticated regulatory strategy for maintaining appropriate PipX-PipY stoichiometry.
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Affiliation(s)
- Raquel Cantos
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Jose I Labella
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Javier Espinosa
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
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Flores E, Picossi S, Valladares A, Herrero A. Transcriptional regulation of development in heterocyst-forming cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:673-684. [DOI: 10.1016/j.bbagrm.2018.04.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 01/02/2023]
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25
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Klähn S, Bolay P, Wright PR, Atilho RM, Brewer KI, Hagemann M, Breaker RR, Hess WR. A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria. Nucleic Acids Res 2019; 46:10082-10094. [PMID: 30085248 PMCID: PMC6212724 DOI: 10.1093/nar/gky709] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/25/2018] [Indexed: 12/19/2022] Open
Abstract
As the key enzyme of bacterial nitrogen assimilation, glutamine synthetase (GS) is tightly regulated. In cyanobacteria, GS activity is controlled by the interaction with inactivating protein factors IF7 and IF17 encoded by the genes gifA and gifB, respectively. We show that a glutamine-binding aptamer within the gifB 5′ UTR of Synechocystis sp. PCC 6803 is critical for the expression of IF17. Binding of glutamine induced structural re-arrangements in this RNA element leading to enhanced protein synthesis in vivo and characterizing it as a riboswitch. Mutagenesis showed the riboswitch mechanism to contribute at least as much to the control of gene expression as the promoter-mediated transcriptional regulation. We suggest this and a structurally related but distinct element, to be designated type 1 and type 2 glutamine riboswitches. Extended biocomputational searches revealed that glutamine riboswitches are exclusively but frequently found in cyanobacterial genomes, where they are primarily associated with gifB homologs. Hence, this RNA-based sensing mechanism is common in cyanobacteria and establishes a regulatory feedback loop that couples the IF17-mediated GS inactivation to the intracellular glutamine levels. Together with the previously described sRNA NsiR4, these results show that non-coding RNA is an indispensable component in the control of nitrogen assimilation in cyanobacteria.
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Affiliation(s)
- Stephan Klähn
- Genetics & Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Department of Solar Materials, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Paul Bolay
- Genetics & Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Patrick R Wright
- Bioinformatics, Technical Faculty, University of Freiburg, Freiburg, Germany
| | - Ruben M Atilho
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kenneth I Brewer
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Martin Hagemann
- Department of Plant Physiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Ronald R Breaker
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Freiburg Institute for Advanced Studies, University of Freiburg, Germany
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26
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Forcada-Nadal A, Llácer JL, Contreras A, Marco-Marín C, Rubio V. The P II-NAGK-PipX-NtcA Regulatory Axis of Cyanobacteria: A Tale of Changing Partners, Allosteric Effectors and Non-covalent Interactions. Front Mol Biosci 2018; 5:91. [PMID: 30483512 PMCID: PMC6243067 DOI: 10.3389/fmolb.2018.00091] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 10/18/2018] [Indexed: 11/13/2022] Open
Abstract
PII, a homotrimeric very ancient and highly widespread (bacteria, archaea, plants) key sensor-transducer protein, conveys signals of abundance or poorness of carbon, energy and usable nitrogen, converting these signals into changes in the activities of channels, enzymes, or of gene expression. PII sensing is mediated by the PII allosteric effectors ATP, ADP (and, in some organisms, AMP), 2-oxoglutarate (2OG; it reflects carbon abundance and nitrogen scarcity) and, in many plants, L-glutamine. Cyanobacteria have been crucial for clarification of the structural bases of PII function and regulation. They are the subject of this review because the information gathered on them provides an overall structure-based view of a PII regulatory network. Studies on these organisms yielded a first structure of a PII complex with an enzyme, (N-acetyl-Lglutamate kinase, NAGK), deciphering how PII can cause enzyme activation, and how it promotes nitrogen stockpiling as arginine in cyanobacteria and plants. They have also revealed the first clear-cut mechanism by which PII can control gene expression. A small adaptor protein, PipX, is sequestered by PII when nitrogen is abundant and is released when is scarce, swapping partner by binding to the 2OG-activated transcriptional regulator NtcA, co-activating it. The structures of PII-NAGK, PII-PipX, PipX alone, of NtcA in inactive and 2OG-activated forms and as NtcA-2OG-PipX complex, explain structurally PII regulatory functions and reveal the changing shapes and interactions of the T-loops of PII depending on the partner and on the allosteric effectors bound to PII. Cyanobacterial studies have also revealed that in the PII-PipX complex PipX binds an additional transcriptional factor, PlmA, thus possibly expanding PipX roles beyond NtcA-dependency. Further exploration of these roles has revealed a functional interaction of PipX with PipY, a pyridoxal-phosphate (PLP) protein involved in PLP homeostasis whose mutations in the human ortholog cause epilepsy. Knowledge of cellular levels of the different components of this PII-PipX regulatory network and of KD values for some of the complexes provides the basic background for gross modeling of the system at high and low nitrogen abundance. The cyanobacterial network can guide searches for analogous components in other organisms, particularly of PipX functional analogs.
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Affiliation(s)
- Alicia Forcada-Nadal
- Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas, Valencia, Spain.,Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - José Luis Llácer
- Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas, Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras - Instituto de Salud Carlos III, Valencia, Spain
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Clara Marco-Marín
- Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas, Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras - Instituto de Salud Carlos III, Valencia, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas, Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras - Instituto de Salud Carlos III, Valencia, Spain
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27
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Bolay P, Muro-Pastor MI, Florencio FJ, Klähn S. The Distinctive Regulation of Cyanobacterial Glutamine Synthetase. Life (Basel) 2018; 8:E52. [PMID: 30373240 PMCID: PMC6316151 DOI: 10.3390/life8040052] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/23/2018] [Accepted: 10/25/2018] [Indexed: 12/02/2022] Open
Abstract
Glutamine synthetase (GS) features prominently in bacterial nitrogen assimilation as it catalyzes the entry of bioavailable nitrogen in form of ammonium into cellular metabolism. The classic example, the comprehensively characterized GS of enterobacteria, is subject to exquisite regulation at multiple levels, among them gene expression regulation to control GS abundance, as well as feedback inhibition and covalent modifications to control enzyme activity. Intriguingly, the GS of the ecologically important clade of cyanobacteria features fundamentally different regulatory systems to those of most prokaryotes. These include the interaction with small proteins, the so-called inactivating factors (IFs) that inhibit GS linearly with their abundance. In addition to this protein interaction-based regulation of GS activity, cyanobacteria use alternative elements to control the synthesis of GS and IFs at the transcriptional level. Moreover, cyanobacteria evolved unique RNA-based regulatory mechanisms such as glutamine riboswitches to tightly tune IF abundance. In this review, we aim to outline the current knowledge on the distinctive features of the cyanobacterial GS encompassing the overall control of its activity, sensing the nitrogen status, transcriptional and post-transcriptional regulation, as well as strain-specific differences.
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Affiliation(s)
- Paul Bolay
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Permoserstrasse 15, D-04318 Leipzig, Germany.
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Américo Vespucio 49, E-41092 Seville, Spain.
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Américo Vespucio 49, E-41092 Seville, Spain.
| | - Stephan Klähn
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Permoserstrasse 15, D-04318 Leipzig, Germany.
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28
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Cyanophycin Synthesis Optimizes Nitrogen Utilization in the Unicellular Cyanobacterium Synechocystis sp. Strain PCC 6803. Appl Environ Microbiol 2018; 84:AEM.01298-18. [PMID: 30120117 DOI: 10.1128/aem.01298-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/09/2018] [Indexed: 11/20/2022] Open
Abstract
Cyanophycin is a carbon/nitrogen storage polymer widely distributed in most cyanobacterial strains and in a few heterotrophic bacteria. It is a nonribosomal polypeptide consisting of equimolar amounts of aspartate and arginine. Here, we focused on the physiological function and cell biology of cyanophycin in the unicellular nondiazotrophic cyanobacterium Synechocystis sp. strain PCC 6803. To study the cellular localization of the cyanophycin-synthesizing enzyme CphA during cyanophycin synthesis and degradation, we fused it to green fluorescent protein. When CphA was inactive, it localized diffusely in the cytoplasm. When cyanophycin synthesis was triggered, CphA first aggregated into foci and later localized on the surface of cyanophycin granules. In the corresponding cell extracts, localization of CphA on the cyanophycin granule surface required Mg2+ During cyanophycin degradation, CphA dissociated from the granule surface and returned to its inactive form in the cytoplasm. To investigate the physiological role of cyanophycin, we compared wild-type cells with a CphA-deficient mutant. Under standard laboratory conditions, the ability to synthesize cyanophycin did not confer a growth advantage. To mimic the situation in natural habitats, cells were cultured with a fluctuating and limiting nitrogen supplementation and/or day/night cycles. Under all of these conditions, cyanophycin provided a fitness advantage to the wild type over the mutant lacking cyanophycin. During resuscitation from nitrogen starvation, wild-type cells accumulated cyanophycin during the night and used it as an internal nitrogen source during the day. This demonstrates that cyanophycin can be used as a temporary nitrogen storage to uncouple nitrogen assimilation from photosynthesis.IMPORTANCE We clarified the elusive biological function of cyanophycin in the nondiazotrophic cyanobacterium Synechocystis sp. PCC 6803. Cyanophycin is a dynamic carbon/nitrogen storage polymer (multi-arginyl-l-polyaspartate) that is conditionally present in most cyanobacteria and a few heterotrophic bacteria as cellular inclusion granules. Here, we show that the cyanophycin-synthesizing enzyme CphA in the nonactive state localizes diffusely in the cytoplasm. When cyanophycin synthesis is triggered, active CphA first aggregates into foci and then covers the surface of mature cyanophycin granules, which in vitro requires Mg2+ as a cofactor. Cyanophycin accumulation enables Synechocystis sp. to optimize nitrogen assimilation under nitrogen-poor conditions, in particular when the nitrogen supply fluctuates and during day/night cycles, by allowing continuous nitrogen assimilation and storage. Therefore, cyanophycin provides the wild-type cyanobacterium with a clear fitness advantage over non-cyanophycin-producing cells in natural environments with fluctuating nitrogen supply.
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29
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Popova AA, Rasmussen U, Semashko TA, Govorun VM, Koksharova OA. Stress effects of cyanotoxin β-methylamino-L-alanine (BMAA) on cyanobacterial heterocyst formation and functionality. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:369-377. [PMID: 29624906 DOI: 10.1111/1758-2229.12647] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/28/2018] [Accepted: 04/01/2018] [Indexed: 06/08/2023]
Abstract
Various species of cyanobacteria, diatoms and dinoflagellates are capable of synthesizing the non-proteinogenic neurotoxic amino acid β-N-methylamino-L-alanine (BMAA), which is known to be a causative agent of human neurodegeneration. Similar to most cyanotoxins, the biological and ecological functions of BMAA in cyanobacteria are unknown. In this study, we show for the first time that BMAA, in micromolar amounts, inhibits the formation of heterocysts (specialized nitrogen-fixing cells) in heterocystous, diazotrophic cyanobacteria [Anabaena sp. PCC 7120, Nostoc punctiforme PCC 73102 (ATCC 29133), Nostoc sp. strain 8963] under conditions of nitrogen starvation. The inhibitory effect of BMAA is abolished by the addition of glutamate. To understand the genetic reason for the observed phenomenon, we used qPCR to study the expression of key genes involved in cell differentiation and nitrogen metabolism in the model cyanobacterium Anabaena sp. PCC 7120. We observed that in the presence of BMAA, Anabaena sp. PCC 7120 does not express two essential genes associated with heterocyst differentiation, namely, hetR and hepA. We also found that addition of BMAA to cyanobacterial cultures with mature heterocysts inhibits nifH gene expression and nitrogenase activity.
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Affiliation(s)
- Alexandra A Popova
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square, 2, 123182 Moscow, Russia
| | - Ulla Rasmussen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Tatiana A Semashko
- Scientific-Research Institute of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Vadim M Govorun
- Scientific-Research Institute of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Olga A Koksharova
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square, 2, 123182 Moscow, Russia
- Lomonosov Moscow State University, Belozersky Institute of Physical-Chemical Biology, Leninskie Gory, 1, 40, Moscow, 119992, Russia
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30
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Kóbori TO, Uzumaki T, Kis M, Kovács L, Domonkos I, Itoh S, Krynická V, Kuppusamy SG, Zakar T, Dean J, Szilák L, Komenda J, Gombos Z, Ughy B. Phosphatidylglycerol is implicated in divisome formation and metabolic processes of cyanobacteria. JOURNAL OF PLANT PHYSIOLOGY 2018; 223:96-104. [PMID: 29558689 DOI: 10.1016/j.jplph.2018.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 06/08/2023]
Abstract
Phosphatidylglycerol is an essential phospholipid for photosynthesis and other cellular processes. We investigated the role of phosphatidylglycerol in cell division and metabolism in a phophatidylglycerol-auxotrophic strain of Synechococcus PCC7942. Here we show that phosphatidylglycerol is essential for the photosynthetic electron transfer and for the oligomerisation of the photosynthetic complexes, notably, we revealed that this lipid is important for non-linear electron transport. Furthermore, we demonstrate that phosphatidylglycerol starvation elevated the expressions of proteins of nitrogen and carbon metabolism. Moreover, we show that phosphatidylglycerol-deficient cells changed the morphology, became elongated, the FtsZ ring did not assemble correctly, and subsequently the division was hindered. However, supplementation with phosphatidylglycerol restored the ring-like structure at the mid-cell region and the normal cell size, demonstrating the phosphatidylglycerol is needed for normal septum formation. Taken together, central roles of phosphatidylglycerol were revealed; it is implicated in the photosynthetic activity, the metabolism and the fission of bacteria.
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Affiliation(s)
- Tímea O Kóbori
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary; Doctoral School of Biology, University of Szeged, H-6726 Szeged, Hungary
| | - Tatsuya Uzumaki
- Center for Gene Research, Nagoya University, Furocyo, Chikusa, Nagoya 464-8607, Japan
| | - Mihály Kis
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary
| | - László Kovács
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary
| | - Ildikó Domonkos
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary
| | - Shigeru Itoh
- Center for Gene Research, Nagoya University, Furocyo, Chikusa, Nagoya 464-8607, Japan
| | - Vendula Krynická
- Institute of Microbiology, Center Algatech, Czech Academy of Sciences, Opatovický mlýn, 37981 Třeboň, Czech Republic
| | - Saravanan G Kuppusamy
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary
| | - Tomas Zakar
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary
| | - Jason Dean
- Institute of Microbiology, Center Algatech, Czech Academy of Sciences, Opatovický mlýn, 37981 Třeboň, Czech Republic
| | - László Szilák
- Institute of Biology, Savaria Campus, Eötvös Lorand University, Szombathely, H-9700, Hungary
| | - Josef Komenda
- Institute of Microbiology, Center Algatech, Czech Academy of Sciences, Opatovický mlýn, 37981 Třeboň, Czech Republic
| | - Zoltán Gombos
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary
| | - Bettina Ughy
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary.
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31
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Espinosa J, Labella JI, Cantos R, Contreras A. Energy drives the dynamic localization of cyanobacterial nitrogen regulators during diurnal cycles. Environ Microbiol 2018; 20:1240-1252. [PMID: 29441670 DOI: 10.1111/1462-2920.14071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 12/31/2022]
Abstract
Cyanobacteria, phototrophic organisms performing oxygenic photosynthesis, must adapt their metabolic processes to the challenges imposed by the succession of days and nights. Two conserved cyanobacterial proteins, PII and PipX, function as hubs of the nitrogen interaction network, forming complexes with a variety of diverse targets. While PII proteins are found in all three domains of life as integrators of signals of the nitrogen and carbon balance, PipX proteins are unique to cyanobacteria, where they provide a mechanistic link between PII signalling and the control of gene expression by the global nitrogen regulator NtcA. Here we demonstrate that PII and PipX display distinct localization patterns during diurnal cycles, co-localizing into the same foci at the periphery and poles of the cells during dark periods, a circadian-independent process requiring a low ATP/ADP ratio. Genetic, cellular biology and biochemical approaches used here provide new insights into the nitrogen regulatory network, calling attention to the roles of PII as energy sensors and its interactions with PipX in the context of essential signalling pathways. This study expands the contribution of the nitrogen regulators PII and PipX to integrate and transduce key environmental signals that allow cyanobacteria to thrive in our planet.
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Affiliation(s)
- Javier Espinosa
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - José I Labella
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Raquel Cantos
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
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32
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Esteves-Ferreira AA, Inaba M, Fort A, Araújo WL, Sulpice R. Nitrogen metabolism in cyanobacteria: metabolic and molecular control, growth consequences and biotechnological applications. Crit Rev Microbiol 2018. [DOI: 10.1080/1040841x.2018.1446902] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Alberto A. Esteves-Ferreira
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, Brazil
| | - Masami Inaba
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
| | - Antoine Fort
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
| | - Wagner L. Araújo
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Ronan Sulpice
- National University of Ireland – Galway, Plant Systems Biology Lab, School of Natural Sciences, Plant and AgriBiosciences Research Centre, Galway, Ireland
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33
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Domínguez-Martín MA, López-Lozano A, Clavería-Gimeno R, Velázquez-Campoy A, Seidel G, Burkovski A, Díez J, García-Fernández JM. Differential NtcA Responsiveness to 2-Oxoglutarate Underlies the Diversity of C/N Balance Regulation in Prochlorococcus. Front Microbiol 2018; 8:2641. [PMID: 29375510 PMCID: PMC5767323 DOI: 10.3389/fmicb.2017.02641] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/19/2017] [Indexed: 11/29/2022] Open
Abstract
Previous studies showed differences in the regulatory response to C/N balance in Prochlorococcus with respect to other cyanobacteria, but no information was available about its causes, or the ecological advantages conferred to thrive in oligotrophic environments. We addressed the changes in key enzymes (glutamine synthetase, isocitrate dehydrogenase) and the ntcA gene (the global nitrogen regulator) involved in C/N metabolism and its regulation, in three model Prochlorococcus strains: MED4, SS120, and MIT9313. We observed a remarkable level of diversity in their response to azaserine, a glutamate synthase inhibitor which increases the concentration of the key metabolite 2-oxoglutarate, used to sense the C/N balance by cyanobacteria. Besides, we studied the binding between the global nitrogen regulator (NtcA) and the promoter of the glnA gene in the same Prochlorococcus strains, and its dependence on the 2-oxoglutarate concentration, by using isothermal titration calorimetry, surface plasmon resonance, and electrophoretic mobility shift. Our results show a reduction in the responsiveness of NtcA to 2-oxoglutarate in Prochlorococcus, especially in the MED4 and SS120 strains. This suggests a trend to streamline the regulation of C/N metabolism in late-branching Prochlorococcus strains (MED4 and SS120), in adaptation to the rather stable conditions found in the oligotrophic ocean gyres where this microorganism is most abundant.
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Affiliation(s)
- María A Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Rafael Clavería-Gimeno
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units BIFI-IQFR-CSIC and GBsC-BIFI-CSIC, Universidad de Zaragoza, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units BIFI-IQFR-CSIC and GBsC-BIFI-CSIC, Universidad de Zaragoza, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas, Barcelona, Spain.,Fundación ARAID, Gobierno de Aragón, Zaragoza, Spain
| | - Gerald Seidel
- Professur für Mikrobiologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Burkovski
- Professur für Mikrobiologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - José M García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
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34
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Ehira S, Shimmori Y, Watanabe S, Kato H, Yoshikawa H, Ohmori M. The nitrogen-regulated response regulator NrrA is a conserved regulator of glycogen catabolism in β-cyanobacteria. Microbiology (Reading) 2017; 163:1711-1719. [DOI: 10.1099/mic.0.000549] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shigeki Ehira
- Department of Biological Science, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Yuka Shimmori
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Hiroaki Kato
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masayuki Ohmori
- Department of Biological Science, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
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35
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Muro-Pastor AM, Brenes-Álvarez M, Vioque A. A combinatorial strategy of alternative promoter use during differentiation of a heterocystous cyanobacterium. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:449-458. [PMID: 28585763 DOI: 10.1111/1758-2229.12555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/24/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Heterocystous cyanobacteria such as Nostoc sp. are filamentous photosynthetic organisms that, in response to nitrogen deficiency, undergo a differentiation process transforming certain, semi-regularly spaced cells into heterocysts, devoted to nitrogen fixation. During transition to a nitrogen-fixing regime, growth of most vegetative cells in the filament is temporarily arrested due to nutritional deprivation, but developing heterocysts require intense transcriptional activity. Therefore, the coexistence of arrested vegetative cells and actively developing prospective heterocysts relies on the simultaneous operation of somewhat opposite transcriptional programs. We have identified genes with multiple nitrogen-responsive transcriptional starts appearing in seemingly paradoxical combinations. For instance, sigA, encoding the RNA polymerase housekeeping sigma factor, is transcribed from one major nitrogen stress-repressed promoter and from a second, nitrogen stress-induced promoter. Here, we show that both promoters are expressed with complementary temporal dynamics. Using a gfp reporter we also show that transcription from the inducible promoter takes place exclusively in differentiating heterocysts and is already detected before any morphological or fluorescence signature of differentiation is observed. Tandem promoters with opposite dynamics could operate a compensatory mechanism in which repression of transcription from the major promoter operative in vegetative cells is offset by transcription from a new promoter only in developing heterocyst.
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Affiliation(s)
- Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, E-41092, Spain
| | - Manuel Brenes-Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, E-41092, Spain
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, E-41092, Spain
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Labella JI, Cantos R, Espinosa J, Forcada-Nadal A, Rubio V, Contreras A. PipY, a Member of the Conserved COG0325 Family of PLP-Binding Proteins, Expands the Cyanobacterial Nitrogen Regulatory Network. Front Microbiol 2017; 8:1244. [PMID: 28744260 PMCID: PMC5504682 DOI: 10.3389/fmicb.2017.01244] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 06/20/2017] [Indexed: 11/13/2022] Open
Abstract
Synechococcus elongatus PCC 7942 is a paradigmatic model organism for nitrogen regulation in cyanobacteria. Expression of genes involved in nitrogen assimilation is positively regulated by the 2-oxoglutarate receptor and global transcriptional regulator NtcA. Maximal activation requires the subsequent binding of the co-activator PipX. PII, a protein found in all three domains of life as an integrator of signals of the nitrogen and carbon balance, binds to PipX to counteract NtcA activity at low 2-oxoglutarate levels. PII-PipX complexes can also bind to the transcriptional regulator PlmA, whose regulon remains unknown. Here we expand the nitrogen regulatory network to PipY, encoded by the bicistronic operon pipXY in S. elongatus. Work with PipY, the cyanobacterial member of the widespread family of COG0325 proteins, confirms the conserved roles in vitamin B6 and amino/keto acid homeostasis and reveals new PLP-related phenotypes, including sensitivity to antibiotics targeting essential PLP-holoenzymes or synthetic lethality with cysK. In addition, the related phenotypes of pipY and pipX mutants are consistent with genetic interactions in the contexts of survival to PLP-targeting antibiotics and transcriptional regulation. We also showed that PipY overexpression increased the length of S. elongatus cells. Taken together, our results support a universal regulatory role for COG0325 proteins, paving the way to a better understanding of these proteins and of their connections with other biological processes.
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Affiliation(s)
- José I Labella
- Departamento de Fisiología, Genética y Microbiología, Universidad de AlicanteAlicante, Spain
| | - Raquel Cantos
- Departamento de Fisiología, Genética y Microbiología, Universidad de AlicanteAlicante, Spain
| | - Javier Espinosa
- Departamento de Fisiología, Genética y Microbiología, Universidad de AlicanteAlicante, Spain
| | - Alicia Forcada-Nadal
- Departamento de Fisiología, Genética y Microbiología, Universidad de AlicanteAlicante, Spain.,Instituto de Biomedicina de Valencia - Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia - Consejo Superior de Investigaciones CientíficasValencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras - Instituto de Salud Carlos IIIValencia, Spain
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de AlicanteAlicante, Spain
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Quantitative Proteomics Shows Extensive Remodeling Induced by Nitrogen Limitation in Prochlorococcusmarinus SS120. mSystems 2017; 2:mSystems00008-17. [PMID: 28593196 PMCID: PMC5451487 DOI: 10.1128/msystems.00008-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/26/2017] [Indexed: 12/27/2022] Open
Abstract
Prochlorococcus requires the capability to accommodate to environmental changes in order to proliferate in oligotrophic oceans, in particular regarding nitrogen availability. A precise knowledge of the composition and changes in the proteome can yield fundamental insights into such a response. Here we report a detailed proteome analysis of the important model cyanobacterium Prochlorococcus marinus SS120 after treatment with azaserine, an inhibitor of ferredoxin-dependent glutamate synthase (GOGAT), to simulate extreme nitrogen starvation. In total, 1,072 proteins, corresponding to 57% of the theoretical proteome, were identified-the maximum proteome coverage obtained for any Prochlorococcus strain thus far. Spectral intensity, calibrated quantification by the Hi3 method, was obtained for 1,007 proteins. Statistically significant changes (P value of <0.05) were observed for 408 proteins, with the majority of proteins (92.4%) downregulated after 8 h of treatment. There was a strong decrease in ribosomal proteins upon azaserine addition, while many transporters were increased. The regulatory proteins PII and PipX were decreased, and the global nitrogen regulator NtcA was upregulated. Furthermore, our data for Prochlorococcus indicate that NtcA also participates in the regulation of photosynthesis. Prochlorococcus responds to the lack of nitrogen by slowing down translation, while inducing photosynthetic cyclic electron flow and biosynthesis of proteins involved in nitrogen uptake and assimilation. IMPORTANCEProchlorococcus is the most abundant photosynthetic organism on Earth, contributing significantly to global primary production and playing a prominent role in biogeochemical cycles. Here we study the effects of extreme nitrogen limitation, a feature of the oligotrophic oceans inhabited by this organism. Quantitative proteomics allowed an accurate quantification of the Prochlorococcus proteome, finding three main responses to nitrogen limitation: upregulation of nitrogen assimilation-related proteins, including transporters; downregulation of ribosome proteins; and induction of the photosystem II cyclic electron flow. This suggests that nitrogen limitation affects a range of metabolic processes far wider than initially believed, with the ultimate goal of saving nitrogen and maximizing the nitrogen uptake and assimilation capabilities of the cell.
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Esteves-Ferreira AA, Cavalcanti JHF, Vaz MGMV, Alvarenga LV, Nunes-Nesi A, Araújo WL. Cyanobacterial nitrogenases: phylogenetic diversity, regulation and functional predictions. Genet Mol Biol 2017; 40:261-275. [PMID: 28323299 PMCID: PMC5452144 DOI: 10.1590/1678-4685-gmb-2016-0050] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 12/21/2016] [Indexed: 12/21/2022] Open
Abstract
Cyanobacteria is a remarkable group of prokaryotic photosynthetic microorganisms, with several genera capable of fixing atmospheric nitrogen (N2) and presenting a wide range of morphologies. Although the nitrogenase complex is not present in all cyanobacterial taxa, it is spread across several cyanobacterial strains. The nitrogenase complex has also a high theoretical potential for biofuel production, since H2 is a by-product produced during N2 fixation. In this review we discuss the significance of a relatively wide variety of cell morphologies and metabolic strategies that allow spatial and temporal separation of N2 fixation from photosynthesis in cyanobacteria. Phylogenetic reconstructions based on 16S rRNA and nifD gene sequences shed light on the evolutionary history of the two genes. Our results demonstrated that (i) sequences of genes involved in nitrogen fixation (nifD) from several morphologically distinct strains of cyanobacteria are grouped in similarity with their morphology classification and phylogeny, and (ii) nifD genes from heterocytous strains share a common ancestor. By using this data we also discuss the evolutionary importance of processes such as horizontal gene transfer and genetic duplication for nitrogenase evolution and diversification. Finally, we discuss the importance of H2 synthesis in cyanobacteria, as well as strategies and challenges to improve cyanobacterial H2 production.
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Affiliation(s)
- Alberto A Esteves-Ferreira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - João Henrique Frota Cavalcanti
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcelo Gomes Marçal Vieira Vaz
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Luna V Alvarenga
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Max-Planck-partner group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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Labella JI, Obrebska A, Espinosa J, Salinas P, Forcada-Nadal A, Tremiño L, Rubio V, Contreras A. Expanding the Cyanobacterial Nitrogen Regulatory Network: The GntR-Like Regulator PlmA Interacts with the PII-PipX Complex. Front Microbiol 2016; 7:1677. [PMID: 27840625 PMCID: PMC5083789 DOI: 10.3389/fmicb.2016.01677] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/06/2016] [Indexed: 11/17/2022] Open
Abstract
Cyanobacteria, phototrophic organisms that perform oxygenic photosynthesis, perceive nitrogen status by sensing 2-oxoglutarate levels. PII, a widespread signaling protein, senses and transduces nitrogen and energy status to target proteins, regulating metabolism and gene expression. In cyanobacteria, under conditions of low 2-oxoglutarate, PII forms complexes with the enzyme N-acetyl glutamate kinase, increasing arginine biosynthesis, and with PII-interacting protein X (PipX), making PipX unavailable for binding and co-activation of the nitrogen regulator NtcA. Both the PII-PipX complex structure and in vivo functional data suggested that this complex, as such, could have regulatory functions in addition to PipX sequestration. To investigate this possibility we performed yeast three-hybrid screening of genomic libraries from Synechococcus elongatus PCC7942, searching for proteins interacting simultaneously with PII and PipX. The only prey clone found in the search expressed PlmA, a member of the GntR family of transcriptional regulators proven here by gel filtration to be homodimeric. Interactions analyses further confirmed the simultaneous requirement of PII and PipX, and showed that the PlmA contacts involve PipX elements exposed in the PII-PipX complex, specifically the C-terminal helices and one residue of the tudor-like body. In contrast, PII appears not to interact directly with PlmA, possibly being needed indirectly, to induce an extended conformation of the C-terminal helices of PipX and for modulating the surface polarity at the PII-PipX boundary, two elements that appear crucial for PlmA binding. Attempts to inactive plmA confirmed that this gene is essential in S. elongatus. Western blot assays revealed that S. elongatus PlmA, irrespective of the nitrogen regime, is a relatively abundant transcriptional regulator, suggesting the existence of a large PlmA regulon. In silico studies showed that PlmA is universally and exclusively found in cyanobacteria. Based on interaction data, on the relative amounts of the proteins involved in PII-PipX-PlmA complexes, determined in western assays, and on the restrictions imposed by the symmetries of trimeric PII and dimeric PlmA molecules, a structural and regulatory model for PlmA function is discussed in the context of the cyanobacterial nitrogen interaction network.
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Affiliation(s)
- Jose I Labella
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | - Anna Obrebska
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | - Javier Espinosa
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | - Paloma Salinas
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | | | - Lorena Tremiño
- Instituto de Biomedicina de Valencia of the CSIC Valencia, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia of the CSICValencia, Spain; Group 739, CIBER de Enfermedades Raras (CIBERER-ISCIII)Valencia, Spain
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
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40
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Wheatley NM, Eden KD, Ngo J, Rosinski JS, Sawaya MR, Cascio D, Collazo M, Hoveida H, Hubbell WL, Yeates TO. A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein. J Mol Biol 2016; 428:4013-4030. [PMID: 27464895 PMCID: PMC5048545 DOI: 10.1016/j.jmb.2016.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/11/2016] [Accepted: 07/18/2016] [Indexed: 11/18/2022]
Abstract
Autotrophic bacteria rely on various mechanisms to increase intracellular concentrations of inorganic forms of carbon (i.e., bicarbonate and CO2) in order to improve the efficiency with which they can be converted to organic forms. Transmembrane bicarbonate transporters and carboxysomes play key roles in accumulating bicarbonate and CO2, but other regulatory elements of carbon concentration mechanisms in bacteria are less understood. In this study, after analyzing the genomic regions around α-type carboxysome operons, we characterize a protein that is conserved across these operons but has not been previously studied. On the basis of a series of apo- and ligand-bound crystal structures and supporting biochemical data, we show that this protein, which we refer to as the carboxysome-associated PII protein (CPII), represents a new and distinct subfamily within the broad superfamily of previously studied PII regulatory proteins, which are generally involved in regulating nitrogen metabolism in bacteria. CPII undergoes dramatic conformational changes in response to ADP binding, and the affinity for nucleotide binding is strongly enhanced by the presence of bicarbonate. CPII therefore appears to be a unique type of PII protein that senses bicarbonate availability, consistent with its apparent genomic association with the carboxysome and its constituents.
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Affiliation(s)
- Nicole M Wheatley
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Kevin D Eden
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Joanna Ngo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Justin S Rosinski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Michael Collazo
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Hamidreza Hoveida
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Wayne L Hubbell
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; Jules Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - Todd O Yeates
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
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41
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Abstract
The metabolite 2-oxoglutarate (also known as α-ketoglutarate, 2-ketoglutaric acid, or oxoglutaric acid) lies at the intersection between the carbon and nitrogen metabolic pathways. This compound is a key intermediate of one of the most fundamental biochemical pathways in carbon metabolism, the tricarboxylic acid (TCA) cycle. In addition, 2-oxoglutarate also acts as the major carbon skeleton for nitrogen-assimilatory reactions. Experimental data support the conclusion that intracellular levels of 2-oxoglutarate fluctuate according to nitrogen and carbon availability. This review summarizes how nature has capitalized on the ability of 2-oxoglutarate to reflect cellular nutritional status through evolution of a variety of 2-oxoglutarate-sensing regulatory proteins. The number of metabolic pathways known to be regulated by 2-oxoglutarate levels has increased significantly in recent years. The signaling properties of 2-oxoglutarate are highlighted by the fact that this metabolite regulates the synthesis of the well-established master signaling molecule, cyclic AMP (cAMP), in Escherichia coli.
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42
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The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7. Proc Natl Acad Sci U S A 2015; 112:E6243-52. [PMID: 26494284 DOI: 10.1073/pnas.1508412112] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Glutamine synthetase (GS), a key enzyme in biological nitrogen assimilation, is regulated in multiple ways in response to varying nitrogen sources and levels. Here we show a small regulatory RNA, NsiR4 (nitrogen stress-induced RNA 4), which plays an important role in the regulation of GS in cyanobacteria. NsiR4 expression in the unicellular Synechocystis sp. PCC 6803 and in the filamentous, nitrogen-fixing Anabaena sp. PCC 7120 is stimulated through nitrogen limitation via NtcA, the global transcriptional regulator of genes involved in nitrogen metabolism. NsiR4 is widely conserved throughout the cyanobacterial phylum, suggesting a conserved function. In silico target prediction, transcriptome profiling on pulse overexpression, and site-directed mutagenesis experiments using a heterologous reporter system showed that NsiR4 interacts with the 5'UTR of gifA mRNA, which encodes glutamine synthetase inactivating factor (IF)7. In Synechocystis, we observed an inverse relationship between the levels of NsiR4 and the accumulation of IF7 in vivo. This NsiR4-dependent modulation of gifA (IF7) mRNA accumulation influenced the glutamine pool and thus [Formula: see text] assimilation via GS. As a second target, we identified ssr1528, a hitherto uncharacterized nitrogen-regulated gene. Competition experiments between WT and an ΔnsiR4 KO mutant showed that the lack of NsiR4 led to decreased acclimation capabilities of Synechocystis toward oscillating nitrogen levels. These results suggest a role for NsiR4 in the regulation of nitrogen metabolism in cyanobacteria, especially for the adaptation to rapid changes in available nitrogen sources and concentrations. NsiR4 is, to our knowledge, the first identified bacterial sRNA regulating the primary assimilation of a macronutrient.
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Wang Y, Liu X, Laurini E, Posocco P, Ziarelli F, Fermeglia M, Qu F, Pricl S, Zhang CC, Peng L. Mimicking the 2-oxoglutaric acid signalling function using molecular probes: insights from structural and functional investigations. Org Biomol Chem 2015; 12:4723-9. [PMID: 24869624 DOI: 10.1039/c4ob00630e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
2-Oxoglutaric acid (2-OG) has gained considerable attention because of its newly discovered signalling role in addition to its established metabolic functions. With the aim of further exploring the signalling function of 2-OG, here we present a structure-activity relationship study using 2-OG probes bearing different carbon chain lengths and terminal groups. Our results highlight the importance of the five-membered carbon molecular skeleton and of the two carboxylic terminals in maintaining the signalling functions of the parent molecule 2-OG. These findings provide valuable information for designing new, effective molecular probes able to dissect and discriminate the newly discovered, complex signalling role of 2-OG from its canonical activity in metabolism.
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Affiliation(s)
- Yang Wang
- Aix-Marseille Université, CNRS, CINaM UMR 7325, 13288, Marseille, France.
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Regulation of the scp Genes in the Cyanobacterium Synechocystis sp. PCC 6803--What is New? Molecules 2015; 20:14621-37. [PMID: 26274949 PMCID: PMC6331805 DOI: 10.3390/molecules200814621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 08/05/2015] [Accepted: 08/07/2015] [Indexed: 11/18/2022] Open
Abstract
In the cyanobacterium Synechocystis sp. PCC 6803 there are five genes encoding small CAB-like (SCP) proteins, which have been shown to be up-regulated under stress. Analyses of the promoter sequences of the scp genes revealed the existence of an NtcA binding motif in two scp genes, scpB and scpE. Binding of NtcA, the key transcriptional regulator during nitrogen stress, to the promoter regions was shown by electrophoretic mobility shift assay. The metabolite 2-oxoglutarate did not increase the affinity of NtcA for binding to the promoters of scpB and scpE. A second motif, the HIP1 palindrome 5ʹ GGCGATCGCC 3ʹ, was detected in the upstream regions of scpB and scpC. The transcription factor encoded by sll1130 has been suggested to recognize this motif to regulate heat-responsive genes. Our data suggest that HIP1 is not a regulatory element within the scp genes. Further, the presence of the high light regulatory (HLR1) motif was confirmed in scpB-E, in accordance to their induced transcriptions in cells exposed to high light. The HLR1 motif was newly discovered in eight additional genes.
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45
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One day of nitrogen starvation reveals the effect of sigE and rre37 overexpression on the expression of genes related to carbon and nitrogen metabolism in Synechocystis sp. PCC 6803. J Biosci Bioeng 2015; 120:128-34. [DOI: 10.1016/j.jbiosc.2014.12.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/19/2014] [Accepted: 12/20/2014] [Indexed: 01/08/2023]
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46
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Yingping F, Lemeille S, González A, Risoul V, Denis Y, Richaud P, Lamrabet O, Fillat MF, Zhang CC, Latifi A. The Pkn22 Ser/Thr kinase in Nostoc PCC 7120: role of FurA and NtcA regulators and transcript profiling under nitrogen starvation and oxidative stress. BMC Genomics 2015. [PMID: 26220092 PMCID: PMC4518582 DOI: 10.1186/s12864-015-1703-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background The filamentous cyanobacterium Nostoc sp. strain PCC 7120 can fix N2 when combined nitrogen is not available. Furthermore, it has to cope with reactive oxygen species generated as byproducts of photosynthesis and respiration. We have previously demonstrated the synthesis of Ser/Thr kinase Pkn22 as an important survival response of Nostoc to oxidative damage. In this study we wished to investigate the possible involvement of this kinase in signalling peroxide stress and nitrogen deprivation. Results Quantitative RT-PCR experiments revealed that the pkn22 gene is induced in response to peroxide stress and to combined nitrogen starvation. Electrophoretic motility assays indicated that the pkn22 promoter is recognized by the global transcriptional regulators FurA and NtcA. Transcriptomic analysis comparing a pkn22-insertion mutant and the wild type strain indicated that this kinase regulates genes involved in important cellular functions such as photosynthesis, carbon metabolism and iron acquisition. Since metabolic changes may lead to oxidative stress, we investigated whether this is the case with nitrogen starvation. Our results rather invalidate this hypothesis thereby suggesting that the function of Pkn22 under nitrogen starvation is independent of its role in response to peroxide stress. Conclusions Our analyses have permitted a more complete functional description of Ser/Thr kinase in Nostoc. We have decrypted the transcriptional regulation of the pkn22 gene, and analysed the whole set of genes under the control of this kinase in response to the two environmental changes often encountered by cyanobacteria in their natural habitat: oxidative stress and nitrogen deprivation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1703-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fan Yingping
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
| | - Sylvain Lemeille
- Department of Microbiology and Molecular Medicine, CMU, Medical Faculty, University of Geneva, Genève, 1211, Switzerland.
| | - Andrés González
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009, Zaragoza, Spain.
| | - Véronique Risoul
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
| | - Yann Denis
- Plate-forme Transcriptome FR3479, IMM-CNRS, Marseille, France.
| | - Pierre Richaud
- CEA, DSV, IBEB, SBVME, Saint-Paul-lez-Durance, F-13108, France. .,CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France. .,Aix Marseille Université, BVME UMR7265, Marseille, F-13284, France.
| | - Otmane Lamrabet
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
| | - Maria F Fillat
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009, Zaragoza, Spain.
| | - Cheng-Cai Zhang
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
| | - Amel Latifi
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
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47
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Beversdorf LJ, Miller TR, McMahon KD. Long-term monitoring reveals carbon-nitrogen metabolism key to microcystin production in eutrophic lakes. Front Microbiol 2015; 6:456. [PMID: 26029192 PMCID: PMC4428211 DOI: 10.3389/fmicb.2015.00456] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/27/2015] [Indexed: 02/04/2023] Open
Abstract
The environmental drivers contributing to cyanobacterial dominance in aquatic systems have been extensively studied. However, understanding of toxic vs. non-toxic cyanobacterial population dynamics and the mechanisms regulating cyanotoxin production remain elusive, both physiologically and ecologically. One reason is the disconnect between laboratory and field-based studies. Here, we combined 3 years of temporal data, including microcystin (MC) concentrations, 16 years of long-term ecological research, and 10 years of molecular data to investigate the potential factors leading to the selection of toxic Microcystis and MC production. Our analysis revealed that nitrogen (N) speciation and inorganic carbon (C) availability might be important drivers of Microcystis population dynamics and that an imbalance in cellular C: N ratios may trigger MC production. More specifically, precipitous declines in ammonium concentrations lead to a transitional period of N stress, even in the presence of high nitrate concentrations, that we call the “toxic phase.” Following the toxic phase, temperature and cyanobacterial abundance remained elevated but MC concentrations drastically declined. Increases in ammonium due to lake turnover may have led to down regulation of MC synthesis or a shift in the community from toxic to non-toxic species. While total phosphorus (P) to total N ratios were relatively low over the time-series, MC concentrations were highest when total N to total P ratios were also highest. Similarly, high C: N ratios were also strongly correlated to the toxic phase. We propose a metabolic model that corroborates molecular studies and reflects our ecological observations that C and N metabolism may regulate MC production physiologically and ecologically. In particular, we hypothesize that an imbalance between 2-oxoglutarate and ammonium in the cell regulates MC synthesis in the environment.
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Affiliation(s)
- Lucas J Beversdorf
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison Madison, WI, USA ; Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee Milwaukee, WI, USA
| | - Todd R Miller
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee Milwaukee, WI, USA
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison Madison, WI, USA ; Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
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Induction of the Nitrate Assimilation nirA Operon and Protein-Protein Interactions in the Maturation of Nitrate and Nitrite Reductases in the Cyanobacterium Anabaena sp. Strain PCC 7120. J Bacteriol 2015; 197:2442-52. [PMID: 25962912 DOI: 10.1128/jb.00198-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/05/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Nitrate is widely used as a nitrogen source by cyanobacteria, in which the nitrate assimilation structural genes frequently constitute the so-called nirA operon. This operon contains the genes encoding nitrite reductase (nirA), a nitrate/nitrite transporter (frequently an ABC-type transporter; nrtABCD), and nitrate reductase (narB). In the model filamentous cyanobacterium Anabaena sp. strain PCC 7120, which can fix N2 in specialized cells termed heterocysts, the nirA operon is expressed at high levels only in media containing nitrate or nitrite and lacking ammonium, a preferred nitrogen source. Here we examined the genes downstream of the nirA operon in Anabaena and found that a small open reading frame of unknown function, alr0613, can be cotranscribed with the operon. The next gene in the genome, alr0614 (narM), showed an expression pattern similar to that of the nirA operon, implying correlated expression of narM and the operon. A mutant of narM with an insertion mutation failed to produce nitrate reductase activity, consistent with the idea that NarM is required for the maturation of NarB. Both narM and narB mutants were impaired in the nitrate-dependent induction of the nirA operon, suggesting that nitrite is an inducer of the operon in Anabaena. It has previously been shown that the nitrite reductase protein NirA requires NirB, a protein likely involved in protein-protein interactions, to attain maximum activity. Bacterial two-hybrid analysis confirmed possible NirA-NirB and NarB-NarM interactions, suggesting that the development of both nitrite reductase and nitrate reductase activities in cyanobacteria involves physical interaction of the corresponding enzymes with their cognate partners, NirB and NarM, respectively. IMPORTANCE Nitrate is an important source of nitrogen for many microorganisms that is utilized through the nitrate assimilation system, which includes nitrate/nitrite membrane transporters and the nitrate and nitrite reductases. Many cyanobacteria assimilate nitrate, but regulation of the nitrate assimilation system varies in different cyanobacterial groups. In the N2-fixing, heterocyst-forming cyanobacteria, the nirA operon, which includes the structural genes for the nitrate assimilation system, is expressed in the presence of nitrate or nitrite if ammonium is not available to the cells. Here we studied the genes required for production of an active nitrate reductase, providing information on the nitrate-dependent induction of the operon, and found evidence for possible protein-protein interactions in the maturation of nitrate reductase and nitrite reductase.
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Work VH, Melnicki MR, Hill EA, Davies FK, Kucek LA, Beliaev AS, Posewitz MC. Lauric Acid Production in a Glycogen-Less Strain of Synechococcus sp. PCC 7002. Front Bioeng Biotechnol 2015; 3:48. [PMID: 25964950 PMCID: PMC4408914 DOI: 10.3389/fbioe.2015.00048] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 03/25/2015] [Indexed: 12/04/2022] Open
Abstract
The cyanobacterium Synechococcus sp. Pasteur culture collection 7002 was genetically engineered to synthesize biofuel-compatible medium-chain fatty acids (FAs) during photoautotrophic growth. Expression of a heterologous lauroyl-acyl carrier protein (C12:0-ACP) thioesterase with concurrent deletion of the endogenous putative acyl-ACP synthetase led to secretion of transesterifiable C12:0 FA in CO2-supplemented batch cultures. When grown at steady state over a range of light intensities in a light-emitting diode turbidostat photobioreactor, the C12-secreting mutant exhibited a modest reduction in growth rate and increased O2 evolution relative to the wild-type (WT). Inhibition of (i) glycogen synthesis by deletion of the glgC-encoded ADP-glucose pyrophosphorylase (AGPase) and (ii) protein synthesis by nitrogen deprivation were investigated as potential mechanisms for metabolite redistribution to increase FA synthesis. Deletion of AGPase led to a 10-fold decrease in reducing carbohydrates and secretion of organic acids during nitrogen deprivation consistent with an energy spilling phenotype. When the carbohydrate-deficient background (ΔglgC) was modified for C12 secretion, no increase in C12 was achieved during nutrient replete growth, and no C12 was recovered from any strain upon nitrogen deprivation under the conditions used. At steady state, the growth rate of the ΔglgC strain saturated at a lower light intensity than the WT, but O2 evolution was not compromised and became increasingly decoupled from growth rate with rising irradiance. Photophysiological properties of the ΔglgC strain suggest energy dissipation from photosystem II and reconfiguration of electron flow at the level of the plastoquinone pool.
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Affiliation(s)
- Victoria H. Work
- Civil and Environmental Engineering Division, Colorado School of Mines, Golden, CO, USA
| | - Matthew R. Melnicki
- Microbiology Group, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Eric A. Hill
- Microbiology Group, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Fiona K. Davies
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO, USA
| | - Leo A. Kucek
- Microbiology Group, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Matthew C. Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO, USA
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Torres-Sánchez A, Gómez-Gardeñes J, Falo F. An integrative approach for modeling and simulation of heterocyst pattern formation in cyanobacteria filaments. PLoS Comput Biol 2015; 11:e1004129. [PMID: 25816286 PMCID: PMC4376521 DOI: 10.1371/journal.pcbi.1004129] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 01/14/2015] [Indexed: 11/18/2022] Open
Abstract
Heterocyst differentiation in cyanobacteria filaments is one of the simplest examples of cellular differentiation and pattern formation in multicellular organisms. Despite of the many experimental studies addressing the evolution and sustainment of heterocyst patterns and the knowledge of the genetic circuit underlying the behavior of single cyanobacterium under nitrogen deprivation, there is still a theoretical gap connecting these two macroscopic and microscopic processes. As an attempt to shed light on this issue, here we explore heterocyst differentiation under the paradigm of systems biology. This framework allows us to formulate the essential dynamical ingredients of the genetic circuit of a single cyanobacterium into a set of differential equations describing the time evolution of the concentrations of the relevant molecular products. As a result, we are able to study the behavior of a single cyanobacterium under different external conditions, emulating nitrogen deprivation, and simulate the dynamics of cyanobacteria filaments by coupling their respective genetic circuits via molecular diffusion. These two ingredients allow us to understand the principles by which heterocyst patterns can be generated and sustained. In particular, our results point out that, by including both diffusion and noisy external conditions in the computational model, it is possible to reproduce the main features of the formation and sustainment of heterocyst patterns in cyanobacteria filaments as observed experimentally. Finally, we discuss the validity and possible improvements of the model.
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Affiliation(s)
- Alejandro Torres-Sánchez
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, Zaragoza, Spain
- Laboratori de Càlcul Numèric, Universitat de Politècnica de Catalunya, Barcelona, Spain
| | - Jesús Gómez-Gardeñes
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
| | - Fernando Falo
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
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