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Marques LCB, Lima JE, Pimentel JDSM, Giani A. Heterocyte production, gene expression and phylogeography in Raphidiopsis ( = Cylindrospermopsis) Raciborskii. FEMS Microbiol Ecol 2022; 98:6576327. [PMID: 35488867 DOI: 10.1093/femsec/fiac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/03/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Raphidiopsis ( = Cylindrospermopsis) raciborskii was described as a subtropical-tropical cyanobacterium, later reported expanding into temperate regions. Heterocyte presence used to distinguish Cylindrospermopsis from the very similar Raphidiopsis, but recently the two genera were recognized as one and unified. This study aimed to investigate how heterocyte production is related to nitrogen (N) limitation in heterocytous and non-heterocytous strains of R.raciborskii. High N-concentrations did not inhibit heterocyte development in some strains, while prolonged N-starvation periods never stimulated production in others. RT-qPCR was used to examine the genetic background, through the expression patterns of nifH, ntcA and hetR. While gene expression increased under N-restriction, N-sufficiency did not suppress nifH transcripts as previously observed in other diazotrophyc cyanobacteria, suggesting that heterocyte production in R. raciborskii is not regulated by N-availability. Heterocytous and non-heterocytous strains were genotypically characterized to assess their phylogenetic relationships,. In the phylogenetic tree, clusters were intermixed and confirmed Raphidiopsis and Cylindrospermopsis as the same genus. The tree supported previous findings of earlier splitting of American strains, while contesting the African origin hypothesis. The existence of two lines of Chinese strains, with distinct evolutionary patterns, is a significant addition that could lead to new hypotheses of the species biogeography.
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Affiliation(s)
- Laísa Corrêa Braga Marques
- Department of Botany, Phycology Laboratory, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Joni Esrom Lima
- Department of Botany, Plant Physiology Laboratory, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | | | - Alessandra Giani
- Department of Botany, Phycology Laboratory, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
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Zhan J, Steglich C, Scholz I, Hess WR, Kirilovsky D. Inverse regulation of light harvesting and photoprotection is mediated by a 3'-end-derived sRNA in cyanobacteria. THE PLANT CELL 2021; 33:358-380. [PMID: 33793852 PMCID: PMC8136909 DOI: 10.1093/plcell/koaa030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Phycobilisomes (PBSs), the principal cyanobacterial antenna, are among the most efficient macromolecular structures in nature, and are used for both light harvesting and directed energy transfer to the photosynthetic reaction center. However, under unfavorable conditions, excess excitation energy needs to be rapidly dissipated to avoid photodamage. The orange carotenoid protein (OCP) senses light intensity and induces thermal energy dissipation under stress conditions. Hence, its expression must be tightly controlled; however, the molecular mechanism of this regulation remains to be elucidated. Here, we describe the discovery of a posttranscriptional regulatory mechanism in Synechocystis sp. PCC 6803 in which the expression of the operon encoding the allophycocyanin subunits of the PBS is directly and in an inverse fashion linked to the expression of OCP. This regulation is mediated by ApcZ, a small regulatory RNA that is derived from the 3'-end of the tetracistronic apcABC-apcZ operon. ApcZ inhibits ocp translation under stress-free conditions. Under most stress conditions, apc operon transcription decreases and ocp translation increases. Thus, a key operon involved in the collection of light energy is functionally connected to the expression of a protein involved in energy dissipation. Our findings support the view that regulatory RNA networks in bacteria evolve through the functionalization of mRNA 3'-UTRs.
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Affiliation(s)
- Jiao Zhan
- Université Paris-Saclay, Commissariat à l’Énergie Atomiques et aux Énergies Alternatives, Centre National de la Recherche Scientifique (CEA, CNRS), Institute for Integrative Biology of the Cell (I2BC), 91198 Gif sur Yvette, France
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Claudia Steglich
- Faculty of Biology, Institute of Biology III, University of Freiburg, D-79104 Freiburg im Breisgau, Germany
| | - Ingeborg Scholz
- Faculty of Biology, Institute of Biology III, University of Freiburg, D-79104 Freiburg im Breisgau, Germany
| | - Wolfgang R Hess
- Faculty of Biology, Institute of Biology III, University of Freiburg, D-79104 Freiburg im Breisgau, Germany
| | - Diana Kirilovsky
- Université Paris-Saclay, Commissariat à l’Énergie Atomiques et aux Énergies Alternatives, Centre National de la Recherche Scientifique (CEA, CNRS), Institute for Integrative Biology of the Cell (I2BC), 91198 Gif sur Yvette, France
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patD, a Gene Regulated by NtcA, Is Involved in the Optimization of Heterocyst Frequency in the Cyanobacterium Anabaena sp. Strain PCC 7120. J Bacteriol 2019; 201:JB.00457-19. [PMID: 31405917 DOI: 10.1128/jb.00457-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/04/2019] [Indexed: 11/20/2022] Open
Abstract
In the filamentous multicellular cyanobacterium Anabaena sp. strain PCC 7120, 5 to 10% of the cells differentiate into heterocysts, which are specialized in N2 fixation. Heterocysts and vegetative cells are mutually dependent for filament growth through nutrient exchange. Thus, the heterocyst frequency should be optimized to maintain the cellular carbon and nitrogen (C/N) balance for filament fitness in the environment. Here, we report the identification of patD, whose expression is directly activated in developing cells by the transcription factor NtcA. The inactivation of patD increases heterocyst frequency and promotes the upregulation of the positive regulator of heterocyst development hetR, whereas its overexpression decreases the heterocyst frequency. The change in heterocyst frequency resulting from the inactivation of patD leads to the reduction in competitiveness of the filaments under combined-nitrogen-depleted conditions. These results indicate that patD regulates heterocyst frequency in Anabaena sp. PCC 7120, ensuring its optimal filament growth.IMPORTANCE Microorganisms have evolved various strategies in order to adapt to the environment and compete with other organisms. Heterocyst differentiation is a prokaryotic model for studying complex cellular regulation. The NtcA-regulated gene patD controls the ratio of heterocysts relative to vegetative cells on the filaments of Anabaena sp. strain PCC 7120. Such a regulation provides a mechanism through which carbon fixation by vegetative cells and nitrogen fixation by heterocysts are properly balanced to ensure optimal growth and keep a competitive edge for long-term survival.
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Zhou Y, Zhang X, Li X, Jia P, Dai R. Evaluation of changes in Microcystis aeruginosa growth and microcystin production by urea via transcriptomic surveys. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 655:181-187. [PMID: 30469064 DOI: 10.1016/j.scitotenv.2018.11.100] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
The freshwater cyanobacteria, Microcystis aeruginosa (M. aeruginosa), is well known to produce microcystins (MCs) and induce the formation of harmful algal blooms (HABs) in aquatic environments, but the effects that urea fertilizer has on cyanobacterial growth and toxin production from a molecular biology perspective remain poorly understood. We evaluated changes in the growth and toxicity of M. aeruginosa cultured under different conditions of nitrogen (N) starvation (NN), low nitrogen (LN), and high nitrogen (HN). Cell density and chlorophyll-a concentrations decreased in cyanobacteria exposed to N starvation and increased following the addition of urea, whereas MCs content increased to a peak and then decreased after urea addition. Transcriptomic analysis confirmed that most genes encoding MCs and genes involved in N metabolic pathways were upregulated under N starvation and LN conditions, whereas these genes were downregulated under HN conditions. Our results offer important insights into the exploring N in controlling the formation of HABs and toxin production based on both physiological and molecular response.
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Affiliation(s)
- Yanping Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Xufeng Zhang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Xuan Li
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Peili Jia
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Ruihua Dai
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China.
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5
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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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Santamarï A-Gï Mez J, Mariscal V, Luque I. Mechanisms for Protein Redistribution in Thylakoids of Anabaena During Cell Differentiation. PLANT & CELL PHYSIOLOGY 2018; 59:1860-1873. [PMID: 29878163 DOI: 10.1093/pcp/pcy103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/25/2018] [Indexed: 06/08/2023]
Abstract
Thylakoid membranes are far from being homogeneous in composition. On the contrary, compositional heterogeneity of lipid and protein content is well known to exist in these membranes. The mechanisms for the confinement of proteins at a particular membrane domain have started to be unveiled, but we are far from a thorough understanding, and many issues remain to be elucidated. During the differentiation of heterocysts in filamentous cyanobacteria of the Anabaena and Nostoc genera, thylakoids undergo a complete reorganization, separating into two membrane domains of different appearance and subcellular localization. Evidence also indicates different functionality and protein composition for these two membrane domains. In this work, we have addressed the mechanisms that govern the specific localization of proteins at a particular membrane domain. Two classes of proteins were distinguished according to their distribution in the thylakoids. Our results indicate that the specific accumulation of proteins of the CURVATURE THYLAKOID 1 (CURT1) family and proteins containing the homologous CAAD domain at subpolar honeycomb thylakoids is mediated by multiple mechanisms including a previously unnoticed phenomenon of thylakoid membrane migration.
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Affiliation(s)
- Javier Santamarï A-Gï Mez
- Instituto de Bioqu�mica Vegetal y Fotos�ntesis, CSIC and Universidad de Sevilla, Avda Am�rico Vespucio 49, Seville E-41092, Spain
| | - Vicente Mariscal
- Instituto de Bioqu�mica Vegetal y Fotos�ntesis, CSIC and Universidad de Sevilla, Avda Am�rico Vespucio 49, Seville E-41092, Spain
| | - Ignacio Luque
- Instituto de Bioqu�mica Vegetal y Fotos�ntesis, CSIC and Universidad de Sevilla, Avda Am�rico Vespucio 49, Seville E-41092, Spain
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Hilton JA, Meeks JC, Zehr JP. Surveying DNA Elements within Functional Genes of Heterocyst-Forming Cyanobacteria. PLoS One 2016; 11:e0156034. [PMID: 27206019 PMCID: PMC4874684 DOI: 10.1371/journal.pone.0156034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 04/14/2016] [Indexed: 01/13/2023] Open
Abstract
Some cyanobacteria are capable of differentiating a variety of cell types in response to environmental factors. For instance, in low nitrogen conditions, some cyanobacteria form heterocysts, which are specialized for N2 fixation. Many heterocyst-forming cyanobacteria have DNA elements interrupting key N2 fixation genes, elements that are excised during heterocyst differentiation. While the mechanism for the excision of the element has been well-studied, many questions remain regarding the introduction of the elements into the cyanobacterial lineage and whether they have been retained ever since or have been lost and reintroduced. To examine the evolutionary relationships and possible function of DNA sequences that interrupt genes of heterocyst-forming cyanobacteria, we identified and compared 101 interruption element sequences within genes from 38 heterocyst-forming cyanobacterial genomes. The interruption element lengths ranged from about 1 kb (the minimum able to encode the recombinase responsible for element excision), up to nearly 1 Mb. The recombinase gene sequences served as genetic markers that were common across the interruption elements and were used to track element evolution. Elements were found that interrupted 22 different orthologs, only five of which had been previously observed to be interrupted by an element. Most of the newly identified interrupted orthologs encode proteins that have been shown to have heterocyst-specific activity. However, the presence of interruption elements within genes with no known role in N2 fixation, as well as in three non-heterocyst-forming cyanobacteria, indicates that the processes that trigger the excision of elements may not be limited to heterocyst development or that the elements move randomly within genomes. This comprehensive analysis provides the framework to study the history and behavior of these unique sequences, and offers new insight regarding the frequency and persistence of interruption elements in heterocyst-forming cyanobacteria.
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Affiliation(s)
- Jason A. Hilton
- University of California Department of Ocean Sciences, Santa Cruz, California, United States of America
- * E-mail:
| | - John C. Meeks
- University of California Department of Microbiology and Molecular Genetics, Davis, California, United States of America
| | - Jonathan P. Zehr
- University of California Department of Ocean Sciences, Santa Cruz, California, United States of America
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8
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Singh S, Mishra AK. Unraveling of cross talk between Ca(2+) and ROS regulating enzymes in Anabaena 7120 and ntcA mutant. J Basic Microbiol 2015; 56:762-78. [PMID: 26374944 DOI: 10.1002/jobm.201500326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/09/2015] [Indexed: 01/25/2023]
Abstract
In order to understand a cross talk between Ca(2+) and ROS regulating enzymes and the possible involvement of ntcA gene, Anabaena sp. PCC 7120 and its derivative ntcA mutant grown in varied levels of calcium chloride (0, 1, 10, and 100 mM) have been investigated. Scanning Electron Microscopy showed abnormal structure formation at high calcium concentration (100 mM) both in wild type and mutant. Fv /Fm values suggested that 100 mM calcium concentration was detrimental for photosynthetic apparatus. SOD, catalase, APX, GR, and peroxidase activity were found to be maximum for 100 mM and minimum for 1 mM of exogenously supplied calcium salt. NADPH contents were higher for wild type than mutant. RAPD-PCR and SDS-PAGE analysis revealed a difference in DNA as well as proteome pattern with changes in calcium chloride regime. Prominent bands of approximately 70, 33, 21, and 14 kDa expressed in the wild type served as the marker polypeptide bands under calcium supplementation. Results suggest that higher levels of calcium ion disturb the cellular homeostasis generating ROS, thereby inducing enhanced levels of antioxidative enzymes. Further, data also suggests possible involvement of ntcA gene in cross talk between calcium ion and ROS regulating enzymes.
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Affiliation(s)
- Savita Singh
- Department of Botany, Laboratory of Microbial Genetics, Banaras Hindu University, Varanasi, India
| | - Arun Kumar Mishra
- Department of Botany, Laboratory of Microbial Genetics, Banaras Hindu University, Varanasi, India
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9
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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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Picossi S, Flores E, Herrero A. The LysR-type transcription factor PacR is a global regulator of photosynthetic carbon assimilation inAnabaena. Environ Microbiol 2015; 17:3341-51. [DOI: 10.1111/1462-2920.12800] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/22/2015] [Accepted: 01/31/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Silvia Picossi
- Instituto de Bioquímica Vegetal y Fotosíntesis; Consejo Superior de Investigaciones Científicas; Universidad de Sevilla; Américo Vespucio 49 Seville E-41092 Spain
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis; Consejo Superior de Investigaciones Científicas; Universidad de Sevilla; Américo Vespucio 49 Seville E-41092 Spain
| | - Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis; Consejo Superior de Investigaciones Científicas; Universidad de Sevilla; Américo Vespucio 49 Seville E-41092 Spain
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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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Role of RNA secondary structure and processing in stability of the nifH1 transcript in the cyanobacterium Anabaena variabilis. J Bacteriol 2015; 197:1408-22. [PMID: 25666132 DOI: 10.1128/jb.02609-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED In the cyanobacterium Anabaena variabilis ATCC 29413, aerobic nitrogen fixation occurs in micro-oxic cells called heterocysts. Synthesis of nitrogenase in heterocysts requires expression of the large nif1 gene cluster, which is primarily under the control of the promoter for the first gene, nifB1. Strong expression of nifH1 requires the nifB1 promoter but is also controlled by RNA processing, which leads to increased nifH1 transcript stability. The processing of the primary nifH1 transcript occurs at the base of a predicted stem-loop structure that is conserved in many heterocystous cyanobacteria. Mutations that changed the predicted secondary structure or changed the sequence of the stem-loop had detrimental effects on the amount of nifH1 transcript, with mutations that altered or destabilized the structure having the strongest effect. Just upstream from the transcriptional processing site for nifH1 was the promoter for a small antisense RNA, sava4870.1. This RNA was more strongly expressed in cells grown in the presence of fixed nitrogen and was downregulated in cells 24 h after nitrogen step down. A mutant strain lacking the promoter for sava4870.1 showed delayed nitrogen fixation; however, that phenotype might have resulted from an effect of the mutation on the processing of the nifH1 transcript. The nifH1 transcript was the most abundant and most stable nif1 transcript, while nifD1 and nifK1, just downstream of nifH1, were present in much smaller amounts and were less stable. The nifD1 and nifK1 transcripts were also processed at sites just upstream of nifD1 and nifK1. IMPORTANCE In the filamentous cyanobacterium Anabaena variabilis, the nif1 cluster, encoding the primary Mo nitrogenase, functions under aerobic growth conditions in specialized cells called heterocysts that develop in response to starvation for fixed nitrogen. The large cluster comprising more than a dozen nif1 genes is transcribed primarily from the promoter for the first gene, nifB1; however, this does not explain the large amount of transcript for the structural genes nifH1, nifD1, and nifK1, which are also under the control of the distant nifB1 promoter. Here, we demonstrate the importance of a predicted stem-loop structure upstream of nifH1 that controls the abundance of nifH1 transcript through transcript processing and stabilization and show that nifD1 and nifK1 transcripts are also controlled by transcript processing.
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Thiel T, Pratte BS. Regulation of Three Nitrogenase Gene Clusters in the Cyanobacterium Anabaena variabilis ATCC 29413. Life (Basel) 2014; 4:944-67. [PMID: 25513762 PMCID: PMC4284476 DOI: 10.3390/life4040944] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/21/2014] [Accepted: 12/04/2014] [Indexed: 11/16/2022] Open
Abstract
The filamentous cyanobacterium Anabaena variabilis ATCC 29413 fixes nitrogen under aerobic conditions in specialized cells called heterocysts that form in response to an environmental deficiency in combined nitrogen. Nitrogen fixation is mediated by the enzyme nitrogenase, which is very sensitive to oxygen. Heterocysts are microxic cells that allow nitrogenase to function in a filament comprised primarily of vegetative cells that produce oxygen by photosynthesis. A. variabilis is unique among well-characterized cyanobacteria in that it has three nitrogenase gene clusters that encode different nitrogenases, which function under different environmental conditions. The nif1 genes encode a Mo-nitrogenase that functions only in heterocysts, even in filaments grown anaerobically. The nif2 genes encode a different Mo-nitrogenase that functions in vegetative cells, but only in filaments grown under anoxic conditions. An alternative V-nitrogenase is encoded by vnf genes that are expressed only in heterocysts in an environment that is deficient in Mo. Thus, these three nitrogenases are expressed differentially in response to environmental conditions. The entire nif1 gene cluster, comprising at least 15 genes, is primarily under the control of the promoter for the first gene, nifB1. Transcriptional control of many of the downstream nif1 genes occurs by a combination of weak promoters within the coding regions of some downstream genes and by RNA processing, which is associated with increased transcript stability. The vnf genes show a similar pattern of transcriptional and post-transcriptional control of expression suggesting that the complex pattern of regulation of the nif1 cluster is conserved in other cyanobacterial nitrogenase gene clusters.
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Affiliation(s)
- Teresa Thiel
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA.
| | - Brenda S Pratte
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA.
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14
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Abstract
To modulate the expression of genes involved in nitrogen assimilation, the cyanobacterial PII-interacting protein X (PipX) interacts with the global transcriptional regulator NtcA and the signal transduction protein PII, a protein found in all three domains of life as an integrator of signals of the nitrogen and carbon balance. PipX can form alternate complexes with NtcA and PII, and these interactions are stimulated and inhibited, respectively, by 2-oxoglutarate, providing a mechanistic link between PII signaling and NtcA-regulated gene expression. Here, we demonstrate that PipX is involved in a much wider interaction network. The effect of pipX alleles on transcript levels was studied by RNA sequencing of S. elongatus strains grown in the presence of either nitrate or ammonium, followed by multivariate analyses of relevant mutant/control comparisons. As a result of this process, 222 genes were classified into six coherent groups of differentially regulated genes, two of which, containing either NtcA-activated or NtcA-repressed genes, provided further insights into the function of NtcA-PipX complexes. The remaining four groups suggest the involvement of PipX in at least three NtcA-independent regulatory pathways. Our results pave the way to uncover new regulatory interactions and mechanisms in the control of gene expression in cyanobacteria.
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Vaishampayan A, Sinha RP, Häder DP. Use of Genetically Improved Nitrogen-Fixing Cyanobacteria in Rice Paddy Fields: Prospects as a Source Material for Engineering Herbicide Sensitivity and Resistance in Plants. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1998.tb00693.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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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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17
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Post AF, Rihtman B, Wang Q. Decoupling of ammonium regulation and ntcA transcription in the diazotrophic marine cyanobacterium Trichodesmium sp. IMS101. THE ISME JOURNAL 2012; 6:629-37. [PMID: 21938021 PMCID: PMC3280139 DOI: 10.1038/ismej.2011.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 08/03/2011] [Accepted: 08/03/2011] [Indexed: 11/09/2022]
Abstract
Nitrogen (N) physiology in the marine cyanobacterium Trichodesmium IMS101 was studied along with transcript accumulation of the N-regulatory gene ntcA and of two of its target genes: napA (nitrate assimilation) and nifH (N(2) fixation). N(2) fixation was impaired in the presence of nitrite, nitrate and urea. Strain IMS101 was capable of growth on these combined N sources at <2 μM but growth rates declined at elevated concentrations. Assimilation of nitrate and urea was impaired in the presence of ammonium. Whereas ecologically relevant N concentrations (2-20 μM) suppressed growth and assimilation, much higher concentrations were required to affect transcript levels. Transcripts of nifH accumulated under nitrogen-fixing conditions; these transcript levels were maintained in the presence of nitrate (100 μM) and ammonium (20 μM). However, nifH transcript levels were below detection at ammonium concentrations >20 μM. napA mRNA was found at low levels in both N(2)-fixing and ammonium-utilizing filaments, and it accumulated in filaments grown with nitrate. The positive effect of nitrate on napA transcription was abolished by ammonium additions of >200 μM. This effect was restored upon addition of the glutamine synthetase inhibitor L-methionin-DL-sulfoximine. Surprisingly, ntcA transcript levels remained high in the presence of ammonium, even at elevated concentrations. These findings indicate that ammonium repression is decoupled from transcriptional activation of ntcA in Trichodesmium IMS101.
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Affiliation(s)
- Anton F Post
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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18
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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: 203] [Impact Index Per Article: 15.6] [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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19
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Kuniyoshi TM, Gonzalez A, Lopez-Gomollon S, Valladares A, Bes MT, Fillat MF, Peleato ML. 2-oxoglutarate enhances NtcA binding activity to promoter regions of the microcystin synthesis gene cluster. FEBS Lett 2011; 585:3921-6. [PMID: 22062155 DOI: 10.1016/j.febslet.2011.10.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 10/19/2011] [Accepted: 10/20/2011] [Indexed: 10/15/2022]
Abstract
The binding affinity of NtcA towards promoter regions of the microcystin gene cluster from Microcystis aeruginosa PCC 7806 has been analyzed by band-shift assay (EMSA). The key nitrogen transcriptional regulator exhibits affinity for two fragments of the bidirectional mcyDA promoter, as well as for promoter regions of mcyE and mcyH. The presence of 2-oxoglutarate increased by 2.5 fold the affinity of NtcA for the mcyA promoter region. The 2-oxoglutarate effect peaked at 0.8 mM, a physiological concentration for this compound under nitrogen-limiting conditions. The results suggest that the 2-oxoglutarate level, as a signal of the C to N balance of the cells, regulates the microcystin gene cluster.
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Affiliation(s)
- Taís M Kuniyoshi
- Departamento de Bioquimica y Biologia Molecular y Celular, Facultad de Ciencias and BIFI, Unidad Asociada Rocasolano (CSIC), Universidad de Zaragoza, Zaragoza, Spain
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20
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Chen YF, Motteux O, Bédu S, Li YZ, Zhang CC. Characterization of Two Critical Residues in the Effector-Binding Domain of NtcA in the Cyanobacterium Anabaena sp. Strain PCC 7120. Curr Microbiol 2011; 63:32-8. [DOI: 10.1007/s00284-011-9936-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 04/09/2011] [Indexed: 11/24/2022]
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21
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Mella-Herrera RA, Neunuebel MR, Kumar K, Saha SK, Golden JW. The sigE gene is required for normal expression of heterocyst-specific genes in Anabaena sp. strain PCC 7120. J Bacteriol 2011; 193:1823-32. [PMID: 21317330 PMCID: PMC3133031 DOI: 10.1128/jb.01472-10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 01/31/2011] [Indexed: 11/20/2022] Open
Abstract
The filamentous cyanobacterium Anabaena (Nostoc) sp. strain PCC 7120 produces specialized cells for nitrogen fixation called heterocysts. Previous work showed that the group 2 sigma factor sigE (alr4249; previously called sigF) is upregulated in differentiating heterocysts 16 h after nitrogen step-down. We now show that the sigE gene is required for normal heterocyst development and normal expression levels of several heterocyst-specific genes. Mobility shift assays showed that the transcription factor NtcA binds to sites in the upstream region of sigE and that this binding is enhanced by 2-oxoglutarate (2-OG). Deletions of the region containing the NtcA binding sites in P(sigE)-gfp reporter plasmids showed that the sites contribute to normal developmental regulation but are not essential for upregulation in heterocysts. Northern RNA blot analysis of nifH mRNA revealed delayed and reduced transcript levels during heterocyst differentiation in a sigE mutant background. Quantitative reverse transcription-PCR (qRT-PCR) analyses of the sigE mutant showed lower levels of transcripts for nifH, fdxH, and hglE2 but normal levels for hupL. We developed a P(nifHD)-gfp reporter construct that showed strong heterocyst-specific expression. Time-lapse microscopy of the P(nifHD)-gfp reporter in a sigE mutant background showed delayed development and undetectable green fluorescent protein (GFP) fluorescence. Overexpression of sigE caused accelerated heterocyst development, an increased heterocyst frequency, and premature expression of GFP fluorescence from the P(nifHD)-gfp reporter.
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Affiliation(s)
- Rodrigo A. Mella-Herrera
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
- Division of Biological Sciences, University of California—San Diego, La Jolla, California 92093-0116
| | - M. Ramona Neunuebel
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
| | - Krithika Kumar
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
| | - Sushanta K. Saha
- Division of Biological Sciences, University of California—San Diego, La Jolla, California 92093-0116
| | - James W. Golden
- Division of Biological Sciences, University of California—San Diego, La Jolla, California 92093-0116
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22
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Overexpression of pknE blocks heterocyst development in Anabaena sp. strain PCC 7120. J Bacteriol 2011; 193:2619-29. [PMID: 21421755 DOI: 10.1128/jb.00120-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The upstream intergenic regions for each of four genes encoding Ser/Thr kinases, all2334, pknE (alr3732), all4668, and all4838, were fused to a gfpmut2 reporter gene to determine their expression during heterocyst development in the cyanobacterium Anabaena (Nostoc) sp. strain PCC 7120. P(pknE)-gfp was upregulated after nitrogen step-down and showed strong expression in differentiating cells. Developmental regulation of pknE required a 118-bp upstream region and was abolished in a hetR mutant. A pknE mutant strain had shorter filaments with slightly higher heterocyst frequency than did the wild type. Overexpression of pknE from its native promoter inhibited heterocyst development in the wild type and in four mutant backgrounds that overproduce heterocysts. Overexpression of pknE from the copper-inducible petE promoter did not completely inhibit heterocyst development but caused a 24-h delay in heterocyst differentiation and cell bleaching 4 to 5 days after nitrogen step-down. Strains overexpressing pknE and containing P(hetR)-gfp or P(patS)-gfp reporters failed to show developmental regulation of the reporters and had undetectable levels of HetR protein. Genetic epistasis experiments suggest that overexpression of pknE blocks HetR activity or downstream regulation.
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23
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Henson BJ, Hartman L, Watson LE, Barnum SR. Evolution and variation of the nifD and hupL elements in the heterocystous cyanobacteria. Int J Syst Evol Microbiol 2011; 61:2938-2949. [PMID: 21278412 DOI: 10.1099/ijs.0.028340-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In heterocystous cyanobacteria, heterocyst differentiation is accompanied by developmentally regulated DNA rearrangements that occur within the nifD and hupL genes, referred to as the nifD and hupL elements. These elements are segments of DNA that are embedded within the coding region of each gene and range from 4 to 24 kb in length. The nifD and hupL elements are independently excised from the genome during the later stages of differentiation by the site-specific recombinases, XisA and XisC, respectively, which are encoded within the elements themselves. Here we examine the variation and evolution of the nifD and hupL elements by comparing full-length nifD and hupL element sequences and by phylogenetic analysis of xisA and xisC gene sequences. There is considerable variation in the size and composition of the nifD and hupL elements, however, conserved regions are also present within representatives of each element. The data suggest that the nifD and hupL elements have undergone a complex pattern of insertions, deletions, translocations and sequence divergence over the course of evolution, but that conserved regions remain.
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Affiliation(s)
- Brian J Henson
- Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, USA
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24
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Structural basis for the allosteric control of the global transcription factor NtcA by the nitrogen starvation signal 2-oxoglutarate. Proc Natl Acad Sci U S A 2010; 107:12487-92. [PMID: 20616047 DOI: 10.1073/pnas.1001556107] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
2-oxogluatarate (2-OG), a metabolite of the highly conserved Krebs cycle, not only plays a critical role in metabolism, but also constitutes a signaling molecule in a variety of organisms ranging from bacteria to plants and animals. In cyanobacteria, the accumulation of 2-OG constitutes the signal of nitrogen starvation and NtcA, a global transcription factor, has been proposed as a putative receptor for 2-OG. Here we present three crystal structures of NtcA from the cyanobacterium Anabaena: the apoform, and two ligand-bound forms in complex with either 2-OG or its analogue 2,2-difluoropentanedioic acid. All structures assemble as homodimers, with each subunit composed of an N-terminal effector-binding domain and a C-terminal DNA-binding domain connected by a long helix (C-helix). The 2-OG binds to the effector-binding domain at a pocket similar to that used by cAMP in catabolite activator protein, but with a different pattern. Comparative structural analysis reveals a putative signal transmission route upon 2-OG binding. A tighter coiled-coil conformation of the two C-helices induced by 2-OG is crucial to maintain the proper distance between the two F-helices for DNA recognition. Whereas catabolite activator protein adopts a transition from off-to-on state upon cAMP binding, our structural analysis explains well why NtcA can bind to DNA even in its apoform, and how 2-OG just enhances the DNA-binding activity of NtcA. These findings provided the structural insights into the function of a global transcription factor regulated by 2-OG, a metabolite standing at a crossroad between carbon and nitrogen metabolisms.
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25
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RNA processing of nitrogenase transcripts in the cyanobacterium Anabaena variabilis. J Bacteriol 2010; 192:3311-20. [PMID: 20435734 DOI: 10.1128/jb.00278-10] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Little is known about the regulation of nitrogenase genes in cyanobacteria. Transcription of the nifH1 and vnfH genes, encoding dinitrogenase reductases for the heterocyst-specific Mo-nitrogenase and the alternative V-nitrogenase, respectively, was studied by using a lacZ reporter. Despite evidence for a transcription start site just upstream of nifH1 and vnfH, promoter fragments that included these start sites did not drive the transcription of lacZ and, for nifH1, did not drive the expression of nifHDK1. Further analysis using larger regions upstream of nifH1 indicated that a promoter within nifU1 and a promoter upstream of nifB1 both contributed to expression of nifHDK1, with the nifB1 promoter contributing to most of the expression. Similarly, while the region upstream of vnfH, containing the putative transcription start site, did not drive expression of lacZ, the region that included the promoter for the upstream gene, ava4055, did. Characterization of the previously reported nifH1 and vnfH transcriptional start sites by 5'RACE (5' rapid amplification of cDNA ends) revealed that these 5' ends resulted from processing of larger transcripts rather than by de novo transcription initiation. The 5' positions of both the vnfH and nifH1 transcripts lie at the base of a stem-loop structure that may serve to stabilize the nifHDK1 and vnfH specific transcripts compared to the transcripts for other genes in the operons providing the proper stoichiometry for the Nif proteins for nitrogenase synthesis.
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26
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Abstract
Many multicellular cyanobacteria produce specialized nitrogen-fixing heterocysts. During diazotrophic growth of the model organism Anabaena (Nostoc) sp. strain PCC 7120, a regulated developmental pattern of single heterocysts separated by about 10 to 20 photosynthetic vegetative cells is maintained along filaments. Heterocyst structure and metabolic activity function together to accommodate the oxygen-sensitive process of nitrogen fixation. This article focuses on recent research on heterocyst development, including morphogenesis, transport of molecules between cells in a filament, differential gene expression, and pattern formation.
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Affiliation(s)
- Krithika Kumar
- Department of Biology, Texas A&M University, College Station, 77843, USA
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27
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Nicolaisen K, Hahn A, Schleiff E. The cell wall in heterocyst formation byAnabaenasp. PCC 7120. J Basic Microbiol 2009; 49:5-24. [DOI: 10.1002/jobm.200800300] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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28
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Role of NtcA, a cyanobacterial global nitrogen regulator, in the regulation of sucrose metabolism gene expression in Anabaena sp. PCC 7120. Arch Microbiol 2008; 191:255-63. [PMID: 19082579 DOI: 10.1007/s00203-008-0450-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 11/09/2008] [Accepted: 11/21/2008] [Indexed: 10/21/2022]
Abstract
In the heterocyst-forming cyanobacterium Anabaena sp. PCC 7120 (also known as Nostoc sp. PCC 7120), it has been shown that spsB and susA, the genes coding for proteins related to sucrose synthesis and cleavage, respectively, exhibit converse expression regarding the nitrogen source. In the nitrogen-fixing filament, spsB expression is mostly localized to the heterocysts and susA is only expressed in vegetative cells. The aim of this work was to investigate the participation of NtcA, a global nitrogen regulator that operates in cyanobacteria, in the regulation of sucrose metabolism genes in Anabaena sp. PCC 7120. The induction of spsB expression observed in the filaments upon combined-nitrogen depletion was abolished in an NtcA-deficient mutant. In vitro experiments showed that NtcA binds specifically but with different affinities to two sites in the spsB promoter region. When susA expression was analyzed after a combined-nitrogen starvation, the levels of mRNA, polypeptide and activity increased in the mutant in comparison with the wild-type strain. Also, NtcA interacted with one site in the promoter region of susA. We conclude that sucrose metabolism is coordinated at the transcriptional level with nitrogen metabolism, suggesting a global metabolism regulating role for NtcA.
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Role of two NtcA-binding sites in the complex ntcA gene promoter of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. J Bacteriol 2008; 190:7584-90. [PMID: 18805988 DOI: 10.1128/jb.00856-08] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that fixes N(2) in specialized cells called heterocysts, which differentiate from vegetative cells in a process that requires the nitrogen control transcription factor NtcA. 2-Oxoglutarate-stimulated binding of purified NtcA to wild-type and modified versions of the ntcA gene promoter from Anabaena sp. was analyzed by mobility shift and DNase I footprinting assays, and the role of NtcA-binding sites in the expression of the ntcA gene during heterocyst differentiation was studied in vivo by using an ntcA-gfp translational fusion and primer extension analysis. Mutation of neither of the two identified NtcA-binding sites eliminated localized expression of ntcA in proheterocysts, but mutation of both sites led to very low, nonlocalized expression.
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30
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Fujita K, Tanaka K, Sadaie Y, Ohta N. Functional analysis of the plastid and nuclear encoded CbbX proteins of Cyanidioschyzon merolae. Genes Genet Syst 2008; 83:135-42. [PMID: 18506097 DOI: 10.1266/ggs.83.135] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
CbbX is believed to be a transcriptional regulator of the subunit genes (rbcL and rbcS) of RuBisCO (Ribulose 1,5-bisphosphate carboxylase/oxygenase) as well as possibly a molecular chaperon of RuBisCO subunit assembly. The unicellular red alga Cyanidioschyzon merolae strain 10D possesses two distinct cbbX genes; one is part of the plastid genome and the other is found in the cell nucleus, whereas the RuBisCO operon (rbcL-rbcS-cbbX) is located only on the plastid genome. We examined the role of CbbX proteins of C. merolae in the expression of the RuBisCO operon. First, His-tagged nuclear and plastid CbbX proteins were produced in Escherichia coli and purified by affinity column chromatography. Both proteins showed binding activity to upstream of the coding region of rbcL. Yeast two hybrid analysis showed direct interaction between nuclear and plastid CbbX proteins but no interaction were found among CbbX, RbcL and RbcS. Then the transcription initiation site of the RuBisCO operon of C. merolae was determined. Next, in order to examine the role of CbbX in vivo, we constructed a plasmid carrying the promoter region of the RuBisCO operon fused to Escherichia coli lacZ, and introduced it into E. coli cells into which a cloned nuclear or plastid cbbX gene under IPTG inducible promoter control was also introduced. Expression of LacZ in the transformed E.coli was observed. Enforced expression of either one of the cbbX genes resulted in a remarkable reduction of lacZ expression suggesting that CbbXs are rather transcriptional regulators than the molecular chaperon of RuBisCO. We discuss the mechanism by which the nuclear and plastid CbbX proteins regulate the RuBisCO operon of C. merolae.
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Affiliation(s)
- Kiyohito Fujita
- Department of Molecular Biology, Faculty of Science, Saitama University, Saitama-City, Saitama, Japan
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31
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Agervald Å, Stensjö K, Holmqvist M, Lindblad P. Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120. BMC Microbiol 2008; 8:69. [PMID: 18442387 PMCID: PMC2408588 DOI: 10.1186/1471-2180-8-69] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Accepted: 04/28/2008] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The maturation of hydrogenases into active enzymes is a complex process and e.g. a correctly assembled active site requires the involvement of at least seven proteins, encoded by hypABCDEF and a hydrogenase specific protease, encoded either by hupW or hoxW. The N2-fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain both an uptake and a bidirectional hydrogenase. The present study addresses the presence and expression of hyp-genes in Nostoc sp. strain PCC 7120. RESULTS RT-PCRs demonstrated that the six hyp-genes together with one ORF may be transcribed as a single operon. Transcriptional start points (TSPs) were identified 280 bp upstream from hypF and 445 bp upstream of hypC, respectively, demonstrating the existence of several transcripts. In addition, five upstream ORFs located in between hupSL, encoding the small and large subunits of the uptake hydrogenase, and the hyp-operon, and two downstream ORFs from the hyp-genes were shown to be part of the same transcript unit. A third TSP was identified 45 bp upstream of asr0689, the first of five ORFs in this operon. The ORFs are annotated as encoding unknown proteins, with the exception of alr0692 which is identified as a NifU-like protein. Orthologues of the four ORFs asr0689-alr0692, with a highly conserved genomic arrangement positioned between hupSL, and the hyp genes are found in several other N2-fixing cyanobacteria, but are absent in non N2-fixing cyanobacteria with only the bidirectional hydrogenase. Short conserved sequences were found in six intergenic regions of the extended hyp-operon, appearing between 11 and 79 times in the genome. CONCLUSION This study demonstrated that five ORFs upstream of the hyp-gene cluster are co-transcribed with the hyp-genes, and identified three TSPs in the extended hyp-gene cluster in Nostoc sp. strain PCC 7120. This may indicate a function related to the assembly of a functional uptake hydrogenase, hypothetically in the assembly of the small subunit of the enzyme.
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Affiliation(s)
- Åsa Agervald
- Department of Photochemistry and Molecular Science, The Ångström Laboratories, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Karin Stensjö
- Department of Photochemistry and Molecular Science, The Ångström Laboratories, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Marie Holmqvist
- Department of Photochemistry and Molecular Science, The Ångström Laboratories, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Peter Lindblad
- Department of Photochemistry and Molecular Science, The Ångström Laboratories, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
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32
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Transcription of hupSL in Anabaena variabilis ATCC 29413 is regulated by NtcA and not by hydrogen. Appl Environ Microbiol 2008; 74:2103-10. [PMID: 18281430 DOI: 10.1128/aem.02855-07] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrogen-fixing cyanobacteria such as Anabaena variabilis ATCC 29413 use an uptake hydrogenase, encoded by hupSL, to recycle hydrogen gas that is produced as an obligate by-product of nitrogen fixation. The regulation of hupSL in A. variabilis is likely to differ from that of the closely related Anabaena sp. strain PCC 7120 because A. variabilis lacks the excision element-mediated regulation that characterizes hupSL regulation in strain PCC 7120. An analysis of the hupSL transcript in a nitrogenase mutant of A. variabilis that does not produce any detectable hydrogen indicated that neither nitrogen fixation nor hydrogen gas was required for the induction of hupSL. Furthermore, exogenous addition of hydrogen gas did not stimulate hupSL transcription. Transcriptional reporter constructs indicated that the accumulation of hupSL transcript after nitrogen step-down was restricted primarily to the microaerobic heterocysts. Anoxic conditions were not sufficient to induce hupSL transcription. The induction of hupSL after nitrogen step-down was reduced in a mutant in the global nitrogen regulator NtcA, but was not reduced in a mutant unable to form heterocysts. A consensus NtcA-binding site was identified upstream of hupSL, and NtcA was found to bind to this region. Thus, while neither hydrogen gas nor anoxia controlled the expression of hupSL, its expression was controlled by NtcA. Heterocyst differentiation was not required for hupSL induction in response to nitrogen step-down, but heterocyst-localized cues may add an additional level of regulation to hupSL.
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Cross-talk Between Iron and Nitrogen Regulatory Networks in Anabaena (Nostoc) sp. PCC 7120: Identification of Overlapping Genes in FurA and NtcA Regulons. J Mol Biol 2007; 374:267-81. [DOI: 10.1016/j.jmb.2007.09.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Revised: 08/30/2007] [Accepted: 09/04/2007] [Indexed: 01/26/2023]
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López-Gomollón S, Hernández JA, Wolk CP, Peleato ML, Fillat MF. Expression of furA is modulated by NtcA and strongly enhanced in heterocysts of Anabaena sp. PCC 7120. MICROBIOLOGY-SGM 2007; 153:42-50. [PMID: 17185533 DOI: 10.1099/mic.0.2006/000091-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fur (ferric uptake regulator) proteins are principally responsible for maintaining iron homeostasis in prokaryotes. Iron is usually a scarce resource. Its limitation reduces photosynthetic rates and cell growth in cyanobacteria in general and especially in cyanobacteria that are fixing dinitrogen, a process that requires the synthesis of numerous proteins with a high content of iron. This paper shows that in the diazotrophic cyanobacterium Anabaena sp. strain PCC 7120, levels of furA mRNA and FurA protein increase significantly in response to nitrogen deprivation, and that furA up-regulation takes place specifically in proheterocysts and mature heterocysts. Great differences in a Northern blot, probed with furA, of RNA from an ntcA mutant relative to wild-type Anabaena sp. were attributable to binding of NtcA, a global regulator of nitrogen metabolism, to the promoter of furA and to the promoter of the furA antisense transcript alr1690-alpha-furA.
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Affiliation(s)
- S López-Gomollón
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
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Tolonen AC, Aach J, Lindell D, Johnson ZI, Rector T, Steen R, Church GM, Chisholm SW. Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Mol Syst Biol 2006; 2:53. [PMID: 17016519 PMCID: PMC1682016 DOI: 10.1038/msb4100087] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Accepted: 07/03/2006] [Indexed: 11/08/2022] Open
Abstract
Nitrogen (N) often limits biological productivity in the oceanic gyres where Prochlorococcus is the most abundant photosynthetic organism. The Prochlorococcus community is composed of strains, such as MED4 and MIT9313, that have different N utilization capabilities and that belong to ecotypes with different depth distributions. An interstrain comparison of how Prochlorococcus responds to changes in ambient nitrogen is thus central to understanding its ecology. We quantified changes in MED4 and MIT9313 global mRNA expression, chlorophyll fluorescence, and photosystem II photochemical efficiency (Fv/Fm) along a time series of increasing N starvation. In addition, the global expression of both strains growing in ammonium-replete medium was compared to expression during growth on alternative N sources. There were interstrain similarities in N regulation such as the activation of a putative NtcA regulon during N stress. There were also important differences between the strains such as in the expression patterns of carbon metabolism genes, suggesting that the two strains integrate N and C metabolism in fundamentally different ways.
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Affiliation(s)
- Andrew C Tolonen
- Department of Biology, MIT/WHOI Joint Program in Oceanography, Cambridge, MA, USA
| | - John Aach
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Debbie Lindell
- Department of Civil and Environmental Engineering, MIT, Cambridge, MA, USA
| | | | - Trent Rector
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Robert Steen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, MIT, Cambridge, MA, USA
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Cheng Y, Li JH, Shi L, Wang L, Latifi A, Zhang CC. A pair of iron-responsive genes encoding protein kinases with a Ser/Thr kinase domain and a His kinase domain are regulated by NtcA in the Cyanobacterium Anabaena sp. strain PCC 7120. J Bacteriol 2006; 188:4822-9. [PMID: 16788191 PMCID: PMC1482992 DOI: 10.1128/jb.00258-06] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The filamentous cyanobacterium Anabaena sp. strain PCC 7120 can fix N(2) when combined nitrogen is not available in the growth medium. It has a family of 13 genes encoding proteins with both a Ser/Thr kinase domain and a His kinase domain. The function of these enzymes is unknown. Two of them are encoded by pkn41 (alr0709) and pkn42 (alr0710). These two genes are separated by only 72 bp on the chromosome, and our results indicate that they are cotranscribed. The expression of pkn41 and pkn42 is induced by iron deprivation irrespective of the nature of the nitrogen source. Mutants inactivating either pkn41, pkn42, or both grow similarly to the wild type under normal conditions, but their growth is impaired either in the presence of an iron chelator or under conditions of nitrogen fixation and iron limitation, two situations where the demand for iron is particularly strong. Consistent with these results, these mutants display lower iron content than the wild type and a higher level of expression for nifJ1 and nifJ2, which encode pyruvate:ferredoxin oxidoreductases. Both nifJ1 and nifJ2 are known to be induced by iron limitation. NtcA, a global regulatory factor for different metabolic pathways, binds to the putative promoter region of pkn41, and the induction of pkn41 in response to iron limitation no longer occurs in an ntcA mutant. Our results suggest that ntcA not only regulates the expression of genes involved in nitrogen and carbon metabolism but also coordinates iron acquisition and nitrogen metabolism by activating the expression of pkn41 and pkn42.
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Affiliation(s)
- Yong Cheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China
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Shi Y, Zhao W, Zhang W, Ye Z, Zhao J. Regulation of intracellular free calcium concentration during heterocyst differentiation by HetR and NtcA in Anabaena sp. PCC 7120. Proc Natl Acad Sci U S A 2006; 103:11334-9. [PMID: 16849429 PMCID: PMC1544087 DOI: 10.1073/pnas.0602839103] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Calcium ions are important to some prokaryotic cellular processes, such as heterocyst differentiation of cyanobacteria. Intracellular free Ca(2+)concentration, [Ca(2+)](i), increases several fold in heterocysts and is regulated by CcbP, a Ca(2+)-binding protein found in heterocyst-forming cyanobacteria. We demonstrate here that CcbP is degraded by HetR, a serine-type protease that controls heterocyst differentiation. The degradation depends on Ca(2+) and appears to be specific because HetR did not digest other tested proteins. CcbP was found to bind two Ca(2+) per molecule with K(D) values of 200 nM and 12.8 microM. Degradation of CcbP releases bound Ca(2+) that contributes significantly to the increase of [Ca(2+)](i) during the process of heterocyst differentiation in Anabaena sp. strain PCC 7120. We suggest that degradation of CcbP is a mechanism of positive autoregulation of HetR. The down-regulation of ccbP in differentiating cells and mature heterocysts, which also is critical to the regulation of [Ca(2+)](i), depends on NtcA. Coexpression of ntcA and a ccbP promoter-controlled gfp in Escherichia coli diminished production of GFP, and the decrease is enhanced by alpha-ketoglutarate. It was also found that NtcA could bind a fragment of the ccbP promoter containing an NtcA-binding sequence in a alpha-ketoglutarate-dependent fashion. Therefore, [Ca(2+)](i) is regulated by a collaboration of HetR and NtcA in heterocyst differentiation in Anabaena sp. strain PCC 7120.
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Affiliation(s)
- Yunming Shi
- State Key Lab of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
| | - Weixing Zhao
- State Key Lab of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
| | - Wei Zhang
- State Key Lab of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
| | - Zi Ye
- State Key Lab of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jindong Zhao
- State Key Lab of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- To whom correspondence should be addressed. E-mail:
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Curatti L, Giarrocco L, Salerno GL. Sucrose synthase and RuBisCo expression is similarly regulated by the nitrogen source in the nitrogen-fixing cyanobacterium Anabaena sp. PLANTA 2006; 223:891-900. [PMID: 16261375 DOI: 10.1007/s00425-005-0142-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2005] [Accepted: 09/26/2005] [Indexed: 05/05/2023]
Abstract
In higher plants and cyanobacteria, sucrose (Suc) metabolism is carried out by a similar set of enzymes. The function and regulation of Suc metabolism in cyanobacteria has begun to be elucidated. In strains of Anabaena sp., filamentous nitrogen-fixing cyanobacteria, Suc synthase (SuS, EC 2.4.1.13) controls Suc cell level through the cleavage of the disaccharide. The present work shows that there are two sus genes in Anabaena (Nostoc) sp. that are co-regulated regarding the nitrogen source; however, only susA accounts for the extractable SuS activity and for the control of the Suc level. Primer extension analysis has uncovered the sequence of the Anabaena susA and susB ammonium-activated putative promoters, which share a high sequence similarity with that of rbcLS encoding ribulose bisphosphate carboxylase/oxygenase (EC 4.1.1.39) and other ammonium up-regulated genes. Moreover, susA and rbcLS expression is developmentally co-localized to the vegetative cells of the nitrogen-fixing cyanobacterial filaments. Our results strongly suggest the existence of a regulatory network that would coordinate the expression of key genes for Suc and nitrogen metabolism, carbon fixation, and development in Anabaena sp.
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Affiliation(s)
- Leonardo Curatti
- Centro de Investigaciones Biológicas, Fundación para Investigaciones Biológicas Aplicadas, FIBA, CC 1348, 7600, Mar del Plata, Argentina
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Su Z, Mao F, Dam P, Wu H, Olman V, Paulsen IT, Palenik B, Xu Y. Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102. Nucleic Acids Res 2006; 34:1050-65. [PMID: 16473855 PMCID: PMC1363776 DOI: 10.1093/nar/gkj496] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Deciphering the regulatory networks encoded in the genome of an organism represents one of the most interesting and challenging tasks in the post-genome sequencing era. As an example of this problem, we have predicted a detailed model for the nitrogen assimilation network in cyanobacterium Synechococcus sp. WH 8102 (WH8102) using a computational protocol based on comparative genomics analysis and mining experimental data from related organisms that are relatively well studied. This computational model is in excellent agreement with the microarray gene expression data collected under ammonium-rich versus nitrate-rich growth conditions, suggesting that our computational protocol is capable of predicting biological pathways/networks with high accuracy. We then refined the computational model using the microarray data, and proposed a new model for the nitrogen assimilation network in WH8102. An intriguing discovery from this study is that nitrogen assimilation affects the expression of many genes involved in photosynthesis, suggesting a tight coordination between nitrogen assimilation and photosynthesis processes. Moreover, for some of these genes, this coordination is probably mediated by NtcA through the canonical NtcA promoters in their regulatory regions.
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Affiliation(s)
- Zhengchang Su
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA 30602, USA
- Computational Biology Institute, Oak Ridge National LaboratoryOak Ridge, TN 37831, USA
| | - Fenglou Mao
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA 30602, USA
| | - Phuongan Dam
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA 30602, USA
- Computational Biology Institute, Oak Ridge National LaboratoryOak Ridge, TN 37831, USA
| | - Hongwei Wu
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA 30602, USA
- Computational Biology Institute, Oak Ridge National LaboratoryOak Ridge, TN 37831, USA
| | - Victor Olman
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA 30602, USA
| | - Ian T. Paulsen
- The Institute of Genome ResearchRockville, MD 20850, USA
| | - Brian Palenik
- Scripps Institution of Oceanography, University of California at San DiegoSan Diego, CA 92093, USA
| | - Ying Xu
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA 30602, USA
- Computational Biology Institute, Oak Ridge National LaboratoryOak Ridge, TN 37831, USA
- To whom correspondence should be addressed at Department of Biochemistry and Molecular Biology, A110 Life Sciences Building, 120 Green Street, University of Georgia, Athens, GA, 30602. Tel: +1 706 542 9779; Fax: +1 706 542 9751;
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Su Z, Olman V, Mao F, Xu Y. Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis. Nucleic Acids Res 2005; 33:5156-71. [PMID: 16157864 PMCID: PMC1214546 DOI: 10.1093/nar/gki817] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We have developed a new method for prediction of cis-regulatory binding sites and applied it to predicting NtcA regulated genes in cyanobacteria. The algorithm rigorously utilizes concurrence information of multiple binding sites in the upstream region of a gene and that in the upstream regions of its orthologues in related genomes. A probabilistic model was developed for the evaluation of prediction reliability so that the prediction false positive rate could be well controlled. Using this method, we have predicted multiple new members of the NtcA regulons in nine sequenced cyanobacterial genomes, and showed that the false positive rates of the predictions have been reduced on an average of 40-fold compared to the conventional methods. A detailed analysis of the predictions in each genome showed that a significant portion of our predictions are consistent with previously published results about individual genes. Intriguingly, NtcA promoters are found for many genes involved in various stages of photosynthesis. Although photosynthesis is known to be tightly coordinated with nitrogen assimilation, very little is known about the underlying mechanism. We postulate for the fist time that these genes serve as the regulatory points to orchestrate these two important processes in a cyanobacterial cell.
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Affiliation(s)
| | | | | | - Ying Xu
- To whom correspondence should be addressed. Tel: 706 542 9779; Fax: 706 542 9751;
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Olmedo-Verd E, Flores E, Herrero A, Muro-Pastor AM. HetR-dependent and -independent expression of heterocyst-related genes in an Anabaena strain overproducing the NtcA transcription factor. J Bacteriol 2005; 187:1985-91. [PMID: 15743946 PMCID: PMC1064053 DOI: 10.1128/jb.187.6.1985-1991.2005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heterocyst development in the cyanobacterium Anabaena sp. strain PCC 7120 depends on both the global nitrogen control transcription factor NtcA and the cell differentiation regulatory protein HetR, with expression of ntcA and hetR being dependent on each other. In this study we constructed strains that constitutively express the ntcA gene leading to high levels of NtcA protein irrespective of the nitrogen source, and we analyzed the effects of such NtcA levels on heterocyst differentiation. In the NtcA-overproducing strain, heterocyst differentiation, induction of NtcA-dependent heterocyst development genes or operons such as devBCA or the cox2 operon, and NtcA-dependent excision of the 11-kb nifD-intervening element only took place under nitrogen deficiency. Although functional heterocysts were produced in response to nitrogen step-down, the NtcA overproducing strain could not grow diazotrophically. Overexpression of ntcA in a hetR background promoted expression of devBCA in response to ammonium withdrawal and excision of the 11-kb element even in the presence of combined nitrogen. Our results show that some NtcA-dependent heterocyst-related genes can be expressed independently of HetR.
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Affiliation(s)
- Elvira Olmedo-Verd
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain
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Muro-Pastor MI, Reyes JC, Florencio FJ. Ammonium assimilation in cyanobacteria. PHOTOSYNTHESIS RESEARCH 2005; 83:135-50. [PMID: 16143848 DOI: 10.1007/s11120-004-2082-7] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Accepted: 07/17/2004] [Indexed: 05/04/2023]
Abstract
In cyanobacteria, after transport by specific permeases, ammonium is incorporated into carbon skeletons by the sequential action of glutamine synthetase (GS) and glutamate synthase (GOGAT). Two types of GS (GSI and GSIII) and two types of GOGAT (ferredoxin-GOGAT and NADH-GOGAT) have been characterized in cyanobacteria. The carbon skeleton substrate of the GS-GOGAT pathway is 2-oxoglutarate that is synthesized by the isocitrate dehydrogenase (IDH). In order to maintain the C-N balance and the amino acid pools homeostasis, ammonium assimilation is tightly regulated. The key regulatory point is the GS, which is controlled at transcriptional and posttranscriptional levels. The transcription factor NtcA plays a critical role regulating the expression of the GS and the IDH encoding genes. In the unicellular cyanobacterium Synechocystis sp. PCC 6803, NtcA controls also the expression of two small proteins (IF7 and IF17) that inhibit the activity of GS by direct protein-protein interaction. Cyanobacteria perceive nitrogen status by sensing the intracellular concentration of 2-oxoglutarate, a signaling metabolite that is able to modulate allosterically the function of NtcA, in vitro. In vivo, a functional dependence between NtcA and the signal transduction protein PII in controlling NtcA-dependent genes has been also shown.
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Affiliation(s)
- M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Isla de la Cartuja, Universidad de Sevilla-CSIC, Av. Américo Vespucio s/n, Seville 41092, Spain. imuro@ ibvf.csic.es
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Herrero A, Muro-Pastor AM, Valladares A, Flores E. Cellular differentiation and the NtcA transcription factor in filamentous cyanobacteria. FEMS Microbiol Rev 2004; 28:469-87. [PMID: 15374662 DOI: 10.1016/j.femsre.2004.04.003] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2003] [Revised: 12/31/2003] [Accepted: 04/04/2004] [Indexed: 10/26/2022] Open
Abstract
Some filamentous cyanobacteria can undergo a variety of cellular differentiation processes that permit their better adaptation to certain environmental conditions. These processes include the differentiation of hormogonia, short filaments aimed at the dispersal of the organism in the environment, of akinetes, cells resistant to various stress conditions, and of heterocysts, cells specialized in the fixation of atmospheric nitrogen in oxic environments. NtcA is a transcriptional regulator that operates global nitrogen control in cyanobacteria by activating (and in some cases repressing) many genes involved in nitrogen assimilation. NtcA is required for the triggering of heterocyst differentiation and for subsequent steps of its development and function. This requirement is based on the role of NtcA as an activator of the expression of hetR and other multiple genes at specific steps of the differentiation process. The products of these genes effect development as well as the distinct metabolism of the mature heterocyst. The different features found in the NtcA-dependent promoters, together with the cellular level of active NtcA protein, should have a role in the determination of the hierarchy of gene activation during the process of heterocyst differentiation.
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Affiliation(s)
- Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Avda. Américo Vespucio s/n, E-41092 Seville, Spain.
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Valladares A, Muro-Pastor AM, Herrero A, Flores E. The NtcA-dependent P1 promoter is utilized for glnA expression in N2-fixing heterocysts of Anabaena sp. strain PCC 7120. J Bacteriol 2004; 186:7337-43. [PMID: 15489445 PMCID: PMC523192 DOI: 10.1128/jb.186.21.7337-7343.2004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression of the glnA gene encoding glutamine synthetase, a key enzyme in nitrogen metabolism, is subject to a variety of regulatory mechanisms in different organisms. In the filamentous, N(2)-fixing cyanobacterium Anabaena sp. strain PCC 7120, glnA is expressed from multiple promoters that generate several transcripts whose abundance is influenced by NtcA, the transcription factor exerting global nitrogen control in cyanobacteria. Whereas RNA(I) originates from a canonical NtcA-dependent promoter (P(1)) and RNA(II) originates from a sigma(70)-type promoter (P(2)), RNA(IV) is influenced by NtcA but the corresponding promoter (P(3)) does not have the structure of NtcA-activated promoters. Using RNA isolated from Anabaena filaments grown under different nitrogen regimens, we observed, in addition to these transcripts, RNA(V), which has previously been detected only in in vitro transcription assays and should originate from P(4). However, in heterocysts, which are differentiated cells specialized in N(2) fixation, RNA(I) was the almost exclusive glnA transcript. Analysis of P(glnA)::lacZ fusions containing different fragments of the glnA upstream region confirmed that fragments carrying P(1), P(2), or P(3) and P(4) have the ability to promote transcription. Mutation of the NtcA-binding site in P(1) eliminated P(1)-directed transcription and allowed increased use of P(2). The NtcA-binding site in the P(1) promoter and binding of NtcA to this site appear to be key factors in determining glnA gene expression in vegetative cells and heterocysts.
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Affiliation(s)
- Ana Valladares
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Científicas Isla de la Cartuja, Avda. Américo Vespucio s/n, E-41092 Seville, Spain
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Oliveira P, Leitão E, Tamagnini P, Moradas-Ferreira P, Oxelfelt F. Characterization and transcriptional analysis of hupSLW in Gloeothece sp. ATCC 27152: an uptake hydrogenase from a unicellular cyanobacterium. Microbiology (Reading) 2004; 150:3647-3655. [PMID: 15528652 DOI: 10.1099/mic.0.27248-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structural genes (hupSL) encoding an uptake hydrogenase in the unicellular cyanobacterium Gloeothece sp. ATCC 27152, a strain capable of aerobic N(2) fixation, were identified and sequenced. 3'-RACE experiments uncovered the presence of an additional ORF 184 bp downstream of hupL, showing a high degree of sequence identity with a gene encoding an uptake-hydrogenase-specific endopeptidase (hupW) in other cyanobacteria. In addition, the transcription start point was identified 238 bp upstream of the hupS translational start. RT-PCR experiments revealed that hupW is co-transcribed with the uptake hydrogenase structural genes in Gloeothece sp. ATCC 27152. In addition, Northern hybridizations clearly showed that hupSLW are transcribed under nitrogen fixing conditions, but not in the presence of combined nitrogen. A putative NtcA binding site was identified in the promoter region upstream of hupS, centred at -41.5 bp with respect to the transcription start point. Electrophoretic retardation of a labelled DNA fragment (harbouring the putative NtcA-binding motif) was significantly affected by an Escherichia coli cell-free extract containing overexpressed NtcA, suggesting that NtcA is involved in the transcriptional regulation of hupSLW.
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Affiliation(s)
- Paulo Oliveira
- Department of Botany, Faculty of Sciences, University of Porto, Rua do Campo Alegre 1191, 4150-181 Porto, Portugal
| | - Elsa Leitão
- Institute for Molecular and Cell Biology - Cellular and Applied Microbiology Unit, University of Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Paula Tamagnini
- Institute for Molecular and Cell Biology - Cellular and Applied Microbiology Unit, University of Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- Department of Botany, Faculty of Sciences, University of Porto, Rua do Campo Alegre 1191, 4150-181 Porto, Portugal
| | - Pedro Moradas-Ferreira
- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Largo Abel Salazar 2, 4099-003 Porto, Portugal
- Institute for Molecular and Cell Biology - Cellular and Applied Microbiology Unit, University of Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Fredrik Oxelfelt
- Institute for Molecular and Cell Biology - Cellular and Applied Microbiology Unit, University of Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
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Wisén S, Bergman B, Mannervik B. Mutagenesis of the cysteine residues in the transcription factor NtcA from Anabaena PCC 7120 and its effects on DNA binding in vitro. ACTA ACUST UNITED AC 2004; 1679:156-63. [PMID: 15297148 DOI: 10.1016/j.bbaexp.2004.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Revised: 06/08/2004] [Accepted: 06/11/2004] [Indexed: 11/19/2022]
Abstract
NtcA is a transcription factor found in a wide variety of cyanobacteria. It is a key component in the control of the nitrogen metabolism, and regulates genes involved in ammonia assimilation, heterocyst differentiation and nitrogen fixation. NtcA expression is subject to nitrogen control, but there is also evidence that the binding of NtcA to DNA can be regulated by a redox mechanism involving the two cysteine residues in the NtcA protein from Anabaena PCC 7120. In order to investigate this further, the two cysteine residues in NtcA were mutated into alanine to give four variants of the protein: wild-type NtcA, the point-mutated variants Cys157Ala and Cys164Ala, as well as the double mutant Cys157Ala/Cys164Ala. The binding of a DNA probe containing a palindromic NtcA-binding motif was investigated by gel mobility shift analysis under non-reducing and reducing conditions. The experiments show that the DNA binding in vitro is stronger in the presence of the reducing agent DTT than in its absence. However, this effect is not due to breaking of a disulfide bond between the cysteine residues, since the double mutant containing no cysteines was also affected by DTT. A molecular model of a monomer of NtcA, based on the homologous cAMP receptor protein structure, was created in order to locate the positions of the cysteine residues. The NtcA model suggested that the positions of the sulfur atoms are not compatible with formation of a bond between them.
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Affiliation(s)
- Susanne Wisén
- Department of Biochemistry, Uppsala University, Biomedical Center, Box 576, SE-751 23 Uppsala, Sweden
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Abstract
The cyanobacterium Anabaena sp. strain PCC 7120 forms single heterocysts about every 10 to 15 vegetative cells along filaments. PatS is thought to be a peptide intercellular signal made by developing heterocysts that prevents neighboring cells from differentiating. Overexpression of the patS gene suppresses heterocyst formation. The hetL gene (all3740) was isolated in a genetic screen to identify genes involved in PatS signaling. Extracopy hetL allowed heterocyst formation in a patS overexpression strain. hetL overexpression from a heterologous promoter in wild-type Anabaena PCC 7120 induced multiple-contiguous heterocysts (Mch) in nitrate-containing medium. The predicted HetL protein is composed almost entirely of pentapeptide repeats with a consensus of A(D/N)L*X, where * is a polar amino acid. Thirty Anabaena PCC 7120 genes contain this repeat motif. A synthetic pentapeptide corresponding to the last 5 amino acids of PatS, which suppresses heterocyst formation in the wild type, did not suppress heterocyst formation in a hetL overexpression strain, indicating that HetL overexpression is affecting heterocyst regulation downstream of PatS production. The transcription regulator NtcA is required for the initiation of heterocyst formation. hetL overexpression allowed the initiation of heterocyst development in an ntcA-null mutant, but differentiation was incomplete. hetR and hetC mutations that block heterocyst development are epistatic to hetL overexpression. A hetL-null mutant showed normal heterocyst development and diazotrophic growth, which could indicate that it is not normally involved in regulating development, that it normally plays a nonessential accessory role, or perhaps that its loss is compensated by cross talk or redundancy with other pentapeptide repeat proteins.
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Affiliation(s)
- Duan Liu
- Department of Biology, Texas A&M University, College Station 77843-3258, USA
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Mori S, Castoreno A, Lammers PJ. Transcript levels of rbcR1, ntcA, and rbcL/S genes in cyanobacterium Anabaena sp. PCC 7120 are downregulated in response to cold and osmotic stress. FEMS Microbiol Lett 2002; 213:167-73. [PMID: 12167533 DOI: 10.1111/j.1574-6968.2002.tb11301.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Using differential display, we identified the Anabaena sp. PCC 7120 ribulose 1,5-bisphosphate carboxylase transcriptional regulator (rbcR1) gene, a member of the LysR family of positive transcription factors. The rbcR1 transcript and its putative target gene ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL/S) were repressed by cold (20 degrees C) and osmotic (sucrose and salt) stress. Cold stress also induced a transient downregulation of the Anabaena 7120 ntcA transcriptional regulator. Expression of the ntcA gene, however, returned to normal levels 2 h after initiation of cold stress and increased significantly above normal levels 24 h after growth at 20 degrees C. The early decline in the expression of the ntcA, rbcR1, and rbcL/S transcripts appears to be part of the Anabaena 7120 global adaptation response to stress. The substantial increase in the ntcA gene expression 24 h following cold stress suggests that Anabaena 7120 experiences substantial nitrogen limitation under these conditions. These data suggest that in response to stress, Anabaena 7120 decreases its metabolic activity through regulation of the CO(2) fixation machinery while enhancing its nitrogen assimilation by inducing the expression of the nitrogen global transcriptional regulator, NtcA.
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Affiliation(s)
- Shahram Mori
- Department of Chemistry and Biochemistry, Box 3C, New Mexico State University, Las Cruces 88003, USA.
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Tanigawa R, Shirokane M, Maeda Si SI, Omata T, Tanaka K, Takahashi H. Transcriptional activation of NtcA-dependent promoters of Synechococcus sp. PCC 7942 by 2-oxoglutarate in vitro. Proc Natl Acad Sci U S A 2002; 99:4251-5. [PMID: 11917135 PMCID: PMC123634 DOI: 10.1073/pnas.072587199] [Citation(s) in RCA: 163] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2001] [Indexed: 11/18/2022] Open
Abstract
The transcription factor NtcA is a global regulator of nitrogen homeostasis in cyanobacteria. It thus positively regulates the expression of genes related to nitrogen assimilation such as glnA (which encodes glutamine synthetase) and ntcA itself in response to nitrogen shortage or depletion. The binding of NtcA to the glnA and ntcA promoters of Synechococcus sp. PCC 7942 in vitro now has been shown to be enhanced by 2-oxoglutarate. In vitro analysis of gene transcription also revealed that the interaction of NtcA with its promoter element was not sufficient for activation of transcription, and 2-oxoglutarate was required for transcriptional initiation by NtcA. Given that the intracellular concentration of 2-oxoglutarate is inversely related to nitrogen availability, it is proposed that this metabolite functions as a signaling molecule that transmits information on cellular nitrogen status to NtcA and thereby regulates the transcription of genes related to nitrogen assimilation in cyanobacteria.
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Affiliation(s)
- Ryohei Tanigawa
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-0032, Japan
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Meeks JC, Elhai J. Regulation of cellular differentiation in filamentous cyanobacteria in free-living and plant-associated symbiotic growth states. Microbiol Mol Biol Rev 2002; 66:94-121; table of contents. [PMID: 11875129 PMCID: PMC120779 DOI: 10.1128/mmbr.66.1.94-121.2002] [Citation(s) in RCA: 313] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Certain filamentous nitrogen-fixing cyanobacteria generate signals that direct their own multicellular development. They also respond to signals from plants that initiate or modulate differentiation, leading to the establishment of a symbiotic association. An objective of this review is to describe the mechanisms by which free-living cyanobacteria regulate their development and then to consider how plants may exploit cyanobacterial physiology to achieve stable symbioses. Cyanobacteria that are capable of forming plant symbioses can differentiate into motile filaments called hormogonia and into specialized nitrogen-fixing cells called heterocysts. Plant signals exert both positive and negative regulatory control on hormogonium differentiation. Heterocyst differentiation is a highly regulated process, resulting in a regularly spaced pattern of heterocysts in the filament. The evidence is most consistent with the pattern arising in two stages. First, nitrogen limitation triggers a nonrandomly spaced cluster of cells (perhaps at a critical stage of their cell cycle) to initiate differentiation. Interactions between an inhibitory peptide exported by the differentiating cells and an activator protein within them causes one cell within each cluster to fully differentiate, yielding a single mature heterocyst. In symbiosis with plants, heterocyst frequencies are increased 3- to 10-fold because, we propose, either differentiation is initiated at an increased number of sites or resolution of differentiating clusters is incomplete. The physiology of symbiotically associated cyanobacteria raises the prospect that heterocyst differentiation proceeds independently of the nitrogen status of a cell and depends instead on signals produced by the plant partner.
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Affiliation(s)
- John C Meeks
- Section of Microbiology, University of California, Davis, California 95616, USA.
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