1
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Álvarez-Escribano I, Suárez-Murillo B, Brenes-Álvarez M, Vioque A, Muro-Pastor AM. Antisense RNA regulates glutamine synthetase in a heterocyst-forming cyanobacterium. PLANT PHYSIOLOGY 2024; 195:2911-2920. [PMID: 38708585 PMCID: PMC11288750 DOI: 10.1093/plphys/kiae263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 05/07/2024]
Abstract
Glutamine synthetase (GS) is a key enzyme involved in nitrogen assimilation and the maintenance of C/N balance, and it is strictly regulated in all bacteria. In cyanobacteria, GS expression is controlled by nitrogen control A (NtcA) transcription factor, which operates global nitrogen regulation in these photosynthetic organisms. Furthermore, posttranslational regulation of GS is operated by protein-protein interaction with GS inactivating factors (IFs). In this study, we describe an additional regulatory mechanism involving an antisense RNA. In Nostoc sp. PCC 7120, the gifA gene (encoding GS inactivating factor IF7) is transcribed downstream of the GS (glnA) gene, from the opposite strand, and the gifA mRNA extends into the glnA coding sequence in antisense orientation. Therefore, the dual RNA transcript that encodes gifA constitutes two functional regions: a 5' protein-coding region, encoding IF7, and a 3' untranslated region that acts as an antisense to glnA. By increasing the levels of such antisense RNA either in cis or in trans, we demonstrate that the amount of GS activity can be modulated by the presence of the antisense RNA. The tail-to-tail disposition of the glnA and gifA genes observed in many cyanobacterial strains from the Nostocales clade suggests the prevalence of such antisense RNA-mediated regulation of GS in this group of cyanobacteria.
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Affiliation(s)
- Isidro Álvarez-Escribano
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
| | - Belén Suárez-Murillo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
| | - Manuel Brenes-Álvarez
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
| | - Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
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2
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Perin G, Fletcher T, Sagi-Kiss V, Gaboriau DCA, Carey MR, Bundy JG, Jones PR. Calm on the surface, dynamic on the inside. Molecular homeostasis of Anabaena sp. PCC 7120 nitrogen metabolism. PLANT, CELL & ENVIRONMENT 2021; 44:1885-1907. [PMID: 33608943 DOI: 10.1111/pce.14034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen sources are all converted into ammonium/ia as a first step of assimilation. It is reasonable to expect that molecular components involved in the transport of ammonium/ia across biological membranes connect with the regulation of both nitrogen and central metabolism. We applied both genetic (i.e., Δamt mutation) and environmental treatments to a target biological system, the cyanobacterium Anabaena sp PCC 7120. The aim was to both perturb nitrogen metabolism and induce multiple inner nitrogen states, respectively, followed by targeted quantification of key proteins, metabolites and enzyme activities. The absence of AMT transporters triggered a substantial whole-system response, affecting enzyme activities and quantity of proteins and metabolites, spanning nitrogen and carbon metabolisms. Moreover, the Δamt strain displayed a molecular fingerprint indicating nitrogen deficiency even under nitrogen replete conditions. Contrasting with such dynamic adaptations was the striking near-complete lack of an externally measurable altered phenotype. We conclude that this species evolved a highly robust and adaptable molecular network to maintain homeostasis, resulting in substantial internal but minimal external perturbations. This analysis provides evidence for a potential role of AMT transporters in the regulatory/signalling network of nitrogen metabolism and the existence of a novel fourth regulatory mechanism controlling glutamine synthetase activity.
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Affiliation(s)
- Giorgio Perin
- Department of Life Sciences, Imperial College London, London, UK
| | - Tyler Fletcher
- Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Virag Sagi-Kiss
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - David C A Gaboriau
- Facility for Imaging by Light Microscopy, NHLI, Imperial College London, London, UK
| | - Mathew R Carey
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jacob G Bundy
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Patrik R Jones
- Department of Life Sciences, Imperial College London, London, UK
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3
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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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4
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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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5
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Neira JL, Ortore MG, Florencio FJ, Muro-Pastor MI, Rizzuti B. Dynamics of the intrinsically disordered inhibitor IF7 of glutamine synthetase in isolation and in complex with its partner. Arch Biochem Biophys 2020; 683:108303. [PMID: 32074499 DOI: 10.1016/j.abb.2020.108303] [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] [Received: 12/14/2019] [Revised: 02/09/2020] [Accepted: 02/11/2020] [Indexed: 11/26/2022]
Abstract
Glutamine synthetase (GS) catalyzes the ATP-dependent formation of glutamine from glutamate and ammonia. The activity of Synechocystis sp. PCC 6803 GS is regulated, among other mechanisms, by protein-protein interactions with a 65-residue-long, intrinsically disordered protein (IDP), named IF7. IDPs explore diverse conformations in their free states and, in some cases, in their molecular complexes. We used both nuclear magnetic resonance (NMR) at 11.7 T and small angle X-ray scattering (SAXS) to study the size and the dynamics in the picoseconds-to-nanosecond (ps-ns) timescale of: (i) isolated IF7; and (ii) the IF7/GS complex. Our SAXS findings, together with MD results, show: (i) some of the possible IF7 structures in solution; and, (ii) that the presence of IF7 affected the structure of GS in solution. The joint use of SAXS and NMR shows that movements of each amino acid of IF7 were uncorrelated with those of its neighbors. Residues of IF7 with the largest values of the relaxation rates (R1, R2 and ηxy), in the free and bound species, were mainly clustered around: (i) the C terminus of the protein; and (ii) Ala30. These residues, together with Arg8 (which is a hot-spot residue in the interaction with GS), had a restricted mobility in the presence of GS. The C-terminal region, which appeared more compact in our MD simulations of isolated IF7, seemed to be involved in non-native contacts with GS that help in the binding between the two macromolecules.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain.
| | - Maria Grazia Ortore
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy.
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, 87036, Arcavacata di Rende, Cosenza, Italy
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6
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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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7
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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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8
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Brenes‐Álvarez M, Mitschke J, Olmedo‐Verd E, Georg J, Hess WR, Vioque A, Muro‐Pastor AM. Elements of the heterocyst‐specific transcriptome unravelled by co‐expression analysis inNostocsp. PCC 7120. Environ Microbiol 2019; 21:2544-2558. [DOI: 10.1111/1462-2920.14647] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/06/2019] [Accepted: 05/01/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Manuel Brenes‐Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla E‐41092 Sevilla Spain
| | - Jan Mitschke
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of Freiburg D‐79104 Freiburg Germany
| | - Elvira Olmedo‐Verd
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla E‐41092 Sevilla Spain
| | - Jens Georg
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of Freiburg D‐79104 Freiburg Germany
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of Freiburg D‐79104 Freiburg Germany
- Freiburg Institute for Advanced Studies, University of Freiburg D‐79104 Freiburg Germany
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla E‐41092 Sevilla Spain
| | - Alicia M. Muro‐Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla E‐41092 Sevilla Spain
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9
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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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10
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Herrero A, Flores E. Genetic responses to carbon and nitrogen availability in Anabaena. Environ Microbiol 2018; 21:1-17. [PMID: 30066380 DOI: 10.1111/1462-2920.14370] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/27/2018] [Accepted: 07/29/2018] [Indexed: 11/27/2022]
Abstract
Heterocyst-forming cyanobacteria are filamentous organisms that perform oxygenic photosynthesis and CO2 fixation in vegetative cells and nitrogen fixation in heterocysts, which are formed under deprivation of combined nitrogen. These organisms can acclimate to use different sources of nitrogen and respond to different levels of CO2 . Following work mainly done with the best studied heterocyst-forming cyanobacterium, Anabaena, here we summarize the mechanisms of assimilation of ammonium, nitrate, urea and N2 , the latter involving heterocyst differentiation, and describe aspects of CO2 assimilation that involves a carbon concentration mechanism. These processes are subjected to regulation establishing a hierarchy in the assimilation of nitrogen sources -with preference for the most reduced nitrogen forms- and a dependence on sufficient carbon. This regulation largely takes place at the level of gene expression and is exerted by a variety of transcription factors, including global and pathway-specific transcriptional regulators. NtcA is a CRP-family protein that adjusts global gene expression in response to the C-to-N balance in the cells, and PacR is a LysR-family transcriptional regulator (LTTR) that extensively acclimates the cells to oxygenic phototrophy. A cyanobacterial-specific transcription factor, HetR, is involved in heterocyst differentiation, and other LTTR factors are specifically involved in nitrate and CO2 assimilation.
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Affiliation(s)
- Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Américo Vespucio 49, E-41092, Seville, Spain
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Américo Vespucio 49, E-41092, Seville, Spain
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11
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Neira JL, Florencio FJ, Muro-Pastor MI. The isolated, twenty-three-residue-long, N-terminal region of the glutamine synthetase inactivating factor binds to its target. Biophys Chem 2017; 228:1-9. [DOI: 10.1016/j.bpc.2017.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 05/31/2017] [Accepted: 05/31/2017] [Indexed: 01/31/2023]
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12
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Cozza C, Neira JL, Florencio FJ, Muro-Pastor MI, Rizzuti B. Intrinsically disordered inhibitor of glutamine synthetase is a functional protein with random-coil-like pK a values. Protein Sci 2017; 26:1105-1115. [PMID: 28295918 DOI: 10.1002/pro.3157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 01/22/2023]
Abstract
The sequential action of glutamine synthetase (GS) and glutamate synthase (GOGAT) in cyanobacteria allows the incorporation of ammonium into carbon skeletons. In the cyanobacterium Synechocystis sp. PCC 6803, the activity of GS is modulated by the interaction with proteins, which include a 65-residue-long intrinsically disordered protein (IDP), the inactivating factor IF7. This interaction is regulated by the presence of charged residues in both IF7 and GS. To understand how charged amino acids can affect the binding of an IDP with its target and to provide clues on electrostatic interactions in disordered states of proteins, we measured the pKa values of all IF7 acidic groups (Glu32, Glu36, Glu38, Asp40, Asp58, and Ser65, the backbone C-terminus) at 100 mM NaCl concentration, by using NMR spectroscopy. We also obtained solution structures of IF7 through molecular dynamics simulation, validated them on the basis of previous experiments, and used them to obtain theoretical estimates of the pKa values. Titration values for the two Asp and three Glu residues of IF7 were similar to those reported for random-coil models, suggesting the lack of electrostatic interactions around these residues. Furthermore, our results suggest the presence of helical structure at the N-terminus of the protein and of conformational changes at acidic pH values. The overall experimental and in silico findings suggest that local interactions and conformational equilibria do not play a role in determining the electrostatic features of the acidic residues of IF7.
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Affiliation(s)
- Concetta Cozza
- Molecular Biophysics Laboratory, Department of Physics, University of Calabria, Rende, Italy
| | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Unidad Asociada IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Rende, Italy
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13
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Galmozzi CV, Florencio FJ, Muro-Pastor MI. The Cyanobacterial Ribosomal-Associated Protein LrtA Is Involved in Post-Stress Survival in Synechocystis sp. PCC 6803. PLoS One 2016; 11:e0159346. [PMID: 27442126 PMCID: PMC4956104 DOI: 10.1371/journal.pone.0159346] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/30/2016] [Indexed: 02/06/2023] Open
Abstract
A light-repressed transcript encodes the LrtA protein in cyanobacteria. We show that half-life of lrtA transcript from Synechocystis sp. PCC 6803 is higher in dark-treated cells as compared to light-grown cells, suggesting post-transcriptional control of lrtA expression. The lrtA 5´ untranslated leader region is involved in that darkness-dependent regulation. We also found that Synechocystis sp. PCC 6803 LrtA is a ribosome-associated protein present in both 30S and 70S ribosomal particles. In order to investigate the function of this protein we have constructed a deletion mutant of the lrtA gene. Cells lacking LrtA (∆lrtA) had significantly lower amount of 70S particles and a greater amount of 30S and 50S particles, suggesting a role of LrtA in stabilizing 70S particles. Synechocystis strains with different amounts of LrtA protein: wild-type, ∆lrtA, and LrtAS (overexpressing lrtA) showed no differences in their growth rate under standard laboratory conditions. However, a clear LrtA dose-dependent effect was observed in the presence of the antibiotic tylosin, being the LrtAS strains the most sensitive. Similar results were obtained under hyperosmotic stress caused by sorbitol. Conversely, after prolonged periods of starvation, ∆lrtA strains were delayed in their growth with respect to the wild-type and the LrtAS strains. A positive role of LrtA protein in post-stress survival is proposed.
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Affiliation(s)
- Carla V. Galmozzi
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Francisco J. Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - M. Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
- * E-mail:
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14
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Pantoja-Uceda D, Neira JL, Saelices L, Robles-Rengel R, Florencio FJ, Muro-Pastor MI, Santoro J. Dissecting the Binding between Glutamine Synthetase and Its Two Natively Unfolded Protein Inhibitors. Biochemistry 2016; 55:3370-82. [DOI: 10.1021/acs.biochem.6b00072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - José L. Neira
- Instituto
de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
- Instituto
de Biocomputación y Física de Sistemas Complejos (BIFI),
Unidad Asociada IQFR-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Lorena Saelices
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Rocío Robles-Rengel
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Francisco J. Florencio
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - M. Isabel Muro-Pastor
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain
| | - Jorge Santoro
- Instituto
de Química Física Rocasolano (IQFR), CSIC, 28006 Madrid, Spain
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15
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Saelices L, Robles-Rengel R, Florencio FJ, Muro-Pastor MI. A core of three amino acids at the carboxyl-terminal region of glutamine synthetase defines its regulation in cyanobacteria. Mol Microbiol 2015; 96:483-96. [PMID: 25626767 DOI: 10.1111/mmi.12950] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2015] [Indexed: 11/28/2022]
Abstract
Glutamine synthetase (GS) type I is a key enzyme in nitrogen metabolism, and its activity is finely controlled by cellular carbon/nitrogen balance. In cyanobacteria, a reversible process that involves protein-protein interaction with two proteins, the inactivating factors IF7 and IF17, regulates GS. Previously, we showed that three arginine residues of IFs are critical for binding and inhibition of GS. In this work, taking advantage of the specificity of GS/IFs interaction in the model cyanobacteria Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, we have constructed a different chimeric GSs from these two cyanobacteria. Analysis of these proteins, together with a site-directed mutagenesis approach, indicates that a core of three residues (E419, N456 and R459) is essential for the inactivation process. The three residues belong to the last 56 amino acids of the C-terminus of Synechocystis GS. A protein-protein docking modeling of Synechocystis GS in complex with IF7 supports the role of the identified core for GS/IF interaction.
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Affiliation(s)
- Lorena Saelices
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Seville, 41092, Spain
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16
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Muñoz-Martín MA, Mateo P, Leganés F, Fernández-Piñas F. A battery of bioreporters of nitrogen bioavailability in aquatic ecosystems based on cyanobacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 475:169-179. [PMID: 23910393 DOI: 10.1016/j.scitotenv.2013.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 07/02/2013] [Accepted: 07/03/2013] [Indexed: 06/02/2023]
Abstract
Cyanobacteria are the main primary producers and are responsible for the blooms and eutrophication processes caused by excess nutrients in surface waters. The aim of this paper is to use cyanobacteria to monitor the presence and bioavailability of different chemical species of nitrogen in freshwater. Cyanobacteria have mechanisms which can detect the presence of nutrients in their environment and can activate or repress specific genes, or operons, depending on nutrient bioavailability. Therefore, monitoring the expression of these genes can facilitate measurement of the availability of nutrients. To achieve this we have constructed self-bioluminescent reporter strains of the filamentous nitrogen-fixing cyanobacterium Nostoc sp. PCC 7120 expressing promoters of genes responsive to nitrogen fused to the luxCDABE operon. Three promoters were selected to direct the expression of luxCDABE: The first, the glnA promoter, is activated in the absence of combined nitrogen. We found that it responded linearly to the addition of known amounts of combined N in the range 50-500 μM NH₄(+) or NO₃(-). The second, the nirA operon promoter, turns on in the presence of nitrate being inhibited by ammonium. The bioreporter responded linearly in the range of 10-100 μM NO₃. The third, the gifA promoter, is activated in the presence of ammonium, responding linearly in the range 100-600 μM NH4(+). We also used a previously described strain of Synechococcus elongatus PCC 7942 expressing glnN (glutamine synthetase type III) fused to luxAB. We found that the glnN promoter responded linearly to the addition of known amounts of N in the range 50-500 μM NH₄(+) or NO₃(-). These cyanobacterial bioreporters were tested in real environmental samples (i.e. river waters) which confirmed their validity and showed a broad spectrum response. They are therefore useful in the detection of both total N-bioavailability and specific nitrogen species.
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Affiliation(s)
- M Angeles Muñoz-Martín
- Department of Biology, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
| | - Pilar Mateo
- Department of Biology, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
| | - Francisco Leganés
- Department of Biology, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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17
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Picossi S, Flores E, Herrero A. ChIP analysis unravels an exceptionally wide distribution of DNA binding sites for the NtcA transcription factor in a heterocyst-forming cyanobacterium. BMC Genomics 2014; 15:22. [PMID: 24417914 PMCID: PMC3898017 DOI: 10.1186/1471-2164-15-22] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 12/26/2013] [Indexed: 11/20/2022] Open
Abstract
Background The CRP-family transcription factor NtcA, universally found in cyanobacteria, was initially discovered as a regulator operating N control. It responds to the N regime signaled by the internal 2-oxoglutarate levels, an indicator of the C to N balance of the cells. Canonical NtcA-activated promoters bear an NtcA-consensus binding site (GTAN8TAC) centered at about 41.5 nucleotides upstream from the transcription start point. In strains of the Anabaena/Nostoc genera NtcA is pivotal for the differentiation of heterocysts in response to N stress. Results In this study, we have used chromatin immunoprecipitation followed by high-throughput sequencing to identify the whole catalog of NtcA-binding sites in cells of the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120 three hours after the withdrawal of combined N. NtcA has been found to bind to 2,424 DNA regions in the genome of Anabaena, which have been ascribed to 2,153 genes. Interestingly, only a small proportion of those genes are involved in N assimilation and metabolism, and 65% of the binding regions were located intragenically. Conclusions The distribution of NtcA-binding sites identified here reveals the largest bacterial regulon described to date. Our results show that NtcA has a much wider role in the physiology of the cell than it has been previously thought, acting both as a global transcriptional regulator and possibly also as a factor influencing the superstructure of the chromosome (and plasmids).
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Affiliation(s)
- Silvia Picossi
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, Seville E-41092, Spain.
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18
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Park JJ, Lechno-Yossef S, Wolk CP, Vieille C. Cell-specific gene expression in Anabaena variabilis grown phototrophically, mixotrophically, and heterotrophically. BMC Genomics 2013; 14:759. [PMID: 24191963 PMCID: PMC4046671 DOI: 10.1186/1471-2164-14-759] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 10/26/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND When the filamentous cyanobacterium Anabaena variabilis grows aerobically without combined nitrogen, some vegetative cells differentiate into N2-fixing heterocysts, while the other vegetative cells perform photosynthesis. Microarrays of sequences within protein-encoding genes were probed with RNA purified from extracts of vegetative cells, from isolated heterocysts, and from whole filaments to investigate transcript levels, and carbon and energy metabolism, in vegetative cells and heterocysts in phototrophic, mixotrophic, and heterotrophic cultures. RESULTS Heterocysts represent only 5% to 10% of cells in the filaments. Accordingly, levels of specific transcripts in vegetative cells were with few exceptions very close to those in whole filaments and, also with few exceptions (e.g., nif1 transcripts), levels of specific transcripts in heterocysts had little effect on the overall level of those transcripts in filaments. In phototrophic, mixotrophic, and heterotrophic growth conditions, respectively, 845, 649, and 846 genes showed more than 2-fold difference (p < 0.01) in transcript levels between vegetative cells and heterocysts. Principal component analysis showed that the culture conditions tested affected transcript patterns strongly in vegetative cells but much less in heterocysts. Transcript levels of the genes involved in phycobilisome assembly, photosynthesis, and CO2 assimilation were high in vegetative cells in phototrophic conditions, and decreased when fructose was provided. Our results suggest that Gln, Glu, Ser, Gly, Cys, Thr, and Pro can be actively produced in heterocysts. Whether other protein amino acids are synthesized in heterocysts is unclear. Two possible components of a sucrose transporter were identified that were upregulated in heterocysts in two growth conditions. We consider it likely that genes with unknown function represent a larger fraction of total transcripts in heterocysts than in vegetative cells across growth conditions. CONCLUSIONS This study provides the first comparison of transcript levels in heterocysts and vegetative cells from heterocyst-bearing filaments of Anabaena. Although the data presented do not give a complete picture of metabolism in either type of cell, they provide a metabolic scaffold on which to build future analyses of cell-specific processes and of the interactions of the two types of cells.
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Affiliation(s)
- Jeong-Jin Park
- />Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- />Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824 USA
- />Present address: Institute of Biological Chemistry, Washington State University, Pullman, WA 99164 USA
| | - Sigal Lechno-Yossef
- />Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- />MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
| | - Coleman Peter Wolk
- />Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- />MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
- />Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
| | - Claire Vieille
- />Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- />Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824 USA
- />Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
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19
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Voß B, Bolhuis H, Fewer DP, Kopf M, Möke F, Haas F, El-Shehawy R, Hayes P, Bergman B, Sivonen K, Dittmann E, Scanlan DJ, Hagemann M, Stal LJ, Hess WR. Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis. PLoS One 2013; 8:e60224. [PMID: 23555932 PMCID: PMC3610870 DOI: 10.1371/journal.pone.0060224] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 02/23/2013] [Indexed: 11/18/2022] Open
Abstract
Nodularia spumigena is a filamentous diazotrophic cyanobacterium that dominates the annual late summer cyanobacterial blooms in the Baltic Sea. But N. spumigena also is common in brackish water bodies worldwide, suggesting special adaptation allowing it to thrive at moderate salinities. A draft genome analysis of N. spumigena sp. CCY9414 yielded a single scaffold of 5,462,271 nucleotides in length on which genes for 5,294 proteins were annotated. A subsequent strand-specific transcriptome analysis identified more than 6,000 putative transcriptional start sites (TSS). Orphan TSSs located in intergenic regions led us to predict 764 non-coding RNAs, among them 70 copies of a possible retrotransposon and several potential RNA regulators, some of which are also present in other N2-fixing cyanobacteria. Approximately 4% of the total coding capacity is devoted to the production of secondary metabolites, among them the potent hepatotoxin nodularin, the linear spumigin and the cyclic nodulapeptin. The transcriptional complexity associated with genes involved in nitrogen fixation and heterocyst differentiation is considerably smaller compared to other Nostocales. In contrast, sophisticated systems exist for the uptake and assimilation of iron and phosphorus compounds, for the synthesis of compatible solutes, and for the formation of gas vesicles, required for the active control of buoyancy. Hence, the annotation and interpretation of this sequence provides a vast array of clues into the genomic underpinnings of the physiology of this cyanobacterium and indicates in particular a competitive edge of N. spumigena in nutrient-limited brackish water ecosystems.
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Affiliation(s)
- Björn Voß
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Henk Bolhuis
- Department of Marine Microbiology, Royal Netherlands Institute of Sea Research, Yerseke, The Netherlands
| | - David P. Fewer
- Food and Environmental Sciences, Division of Microbiology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Matthias Kopf
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Fred Möke
- Plant Physiology, Institute Biosciences, University of Rostock, Rostock, Germany
| | - Fabian Haas
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Paul Hayes
- Faculty of Science, University of Portsmouth, Portsmouth, United Kingdom
| | | | - Kaarina Sivonen
- Food and Environmental Sciences, Division of Microbiology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Elke Dittmann
- Institute for Biochemistry and Biology, University of Potsdam, Golm, Germany
| | - Dave J. Scanlan
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Martin Hagemann
- Plant Physiology, Institute Biosciences, University of Rostock, Rostock, Germany
| | - Lucas J. Stal
- Department of Marine Microbiology, Royal Netherlands Institute of Sea Research, Yerseke, The Netherlands
- Department of Aquatic Microbiology, University of Amsterdam, Amsterdam, The Netherlands
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
- * E-mail:
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20
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Abstract
RNA helicases are associated with every aspect of RNA metabolism and function. A diverse range of RNA helicases are encoded by essentially every organism. While RNA helicases alter gene expression, RNA helicase expression is itself regulated, frequently in response to abiotic stress. Photosynthetic cyanobacteria present a unique model system to investigate RNA helicase expression and function. This chapter describes methodology to study the expression and cellular localization of RNA helicases, providing insights into the metabolic pathway(s) in which these enzymes function in cyanobacteria. The approaches are applicable to other systems as well.
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Affiliation(s)
- George W Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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21
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Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc Natl Acad Sci U S A 2011; 108:20130-5. [PMID: 22135468 DOI: 10.1073/pnas.1112724108] [Citation(s) in RCA: 199] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The fixation of atmospheric N(2) by cyanobacteria is a major source of nitrogen in the biosphere. In Nostocales, such as Anabaena, this process is spatially separated from oxygenic photosynthesis and occurs in heterocysts. Upon nitrogen step-down, these specialized cells differentiate from vegetative cells in a process controlled by two major regulators: NtcA and HetR. However, the regulon controlled by these two factors is only partially defined, and several aspects of the differentiation process have remained enigmatic. Using differential RNA-seq, we experimentally define a genome-wide map of >10,000 transcriptional start sites (TSS) of Anabaena sp. PCC7120, a model organism for the study of prokaryotic cell differentiation and N(2) fixation. By analyzing the adaptation to nitrogen stress, our global TSS map provides insight into the dynamic changes that modify the transcriptional organization at a critical step of the differentiation process. We identify >900 TSS with minimum fold change in response to nitrogen deficiency of eight. From these TSS, at least 209 were under control of HetR, whereas at least 158 other TSS were potentially directly controlled by NtcA. Our analysis of the promoters activated during the switch to N(2) fixation adds hundreds of protein-coding genes and noncoding transcripts to the list of potentially involved factors. These data experimentally define the NtcA regulon and the DIF(+) motif, a palindrome at or close to position -35 that seems essential for heterocyst-specific expression of certain genes.
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22
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Saelices L, Galmozzi CV, Florencio FJ, Muro-Pastor MI. Mutational analysis of the inactivating factors, IF7 and IF17 from Synechocystis sp. PCC 6803: critical role of arginine amino acid residues for glutamine synthetase inactivation. Mol Microbiol 2011; 82:964-75. [PMID: 22023175 DOI: 10.1111/j.1365-2958.2011.07865.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Synechocystis sp. PCC 6803 glutamine synthetase type I (GS) activity is controlled by a process that involves protein-protein interaction with two inactivating factors (IF7 and IF17). IF7 is a natively unfolded, 65-residue-long protein, homologous to the carboxy-terminal region of IF17. Both proteins have abundance of positively charged amino acid residues and a high isoelectric point. In this study, we analyse the IF amino acid residues involved in GS inactivation by a mutational approach, both in vitro and in vivo. The results clearly indicate that the GS-IF complex formation must be determined mainly by electrostatic interactions. We have identified three conserved arginine residues of IF7 and IF17 that are essential for the interaction of these proteins with GS. All these residues map in the homologous region of IFs. Furthermore, in vitro analysis of a truncated IF17 protein without the 82-residue-long amino-terminal part, together with the analysis of a Synechocystis strain expressing a chimeric protein, containing this amino-terminal part of IF17 fused to IF7, demonstrates that amino-terminal region of IF17 mostly confers a higher stability to this protein.
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Affiliation(s)
- Lorena Saelices
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Américo Vespucio 49, E-41092 Sevilla, Spain
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23
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Saelices L, Galmozzi CV, Florencio FJ, Muro-Pastor MI, Neira JL. The Inactivating Factor of Glutamine Synthetase IF17 Is an Intrinsically Disordered Protein, Which Folds upon Binding to Its Target. Biochemistry 2011; 50:9767-78. [DOI: 10.1021/bi2009272] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lorena Saelices
- Instituto de Bioquı́mica
Vegetal y Fotosı́ntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - Carla V. Galmozzi
- Instituto de Bioquı́mica
Vegetal y Fotosı́ntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - Francisco J. Florencio
- Instituto de Bioquı́mica
Vegetal y Fotosı́ntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - M. Isabel Muro-Pastor
- Instituto de Bioquı́mica
Vegetal y Fotosı́ntesis, CSIC-Universidad de Sevilla, Seville, Spain
| | - José L. Neira
- Instituto de Biologı́a
Molecular y Celular, Universidad Miguel Hernández, Elche (Alicante), Spain
- Instituto de Biocomputación y Fı́sica de Sistemas Complejos, Zaragoza,
Spain
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