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Alcamán ME, Alcorta J, Bergman B, Vásquez M, Polz M, Díez B. Physiological and gene expression responses to nitrogen regimes and temperatures in Mastigocladus sp. strain CHP1, a predominant thermotolerant cyanobacterium of hot springs. Syst Appl Microbiol 2016; 40:102-113. [PMID: 28081924 DOI: 10.1016/j.syapm.2016.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/16/2016] [Accepted: 11/21/2016] [Indexed: 11/26/2022]
Abstract
Cyanobacteria are widely distributed primary producers with significant implications for the global biogeochemical cycles of carbon and nitrogen. Diazotrophic cyanobacteria of subsection V (Order Stigonematales) are particularly ubiquitous in photoautotrophic microbial mats of hot springs. The Stigonematal cyanobacterium strain CHP1 isolated from the Porcelana hot spring (Chile) was one of the major contributors of the new nitrogen through nitrogen fixation. Further morphological and genetic characterization verified that the strain CHP1 belongs to Stigonematales, and it formed a separate clade together with other thermophiles of the genera Fischerella and Mastigocladus. Strain CHP1 fixed maximum N2 in the light, independent of the temperature range. At 50°C nifH gene transcripts showed high expression during the light period, whereas the nifH gene expression at 45°C was arrhythmic. The strain displayed a high affinity for nitrate and a low tolerance for high ammonium concentrations, whereas the narB and glnA genes showed higher expression in light and at the beginning of the dark phase. It is proposed that Mastigocladus sp. strain CHP1 would represent a good model for the study of subsection V thermophilic cyanobacteria, and for understanding the adaptations of these photoautotrophic organisms inhabiting microbial mats in hot springs globally.
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Affiliation(s)
- M Estrella Alcamán
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, Casilla 144-D, C.P. 651 3677 Santiago, Chile.
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, Casilla 144-D, C.P. 651 3677 Santiago, Chile
| | - Birgitta Bergman
- Department of Ecology, Environment and Plant Sciences and Science for Life Laboratory, Stockholm University, S-10691 Stockholm, Sweden
| | - Mónica Vásquez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, Casilla 144-D, C.P. 651 3677 Santiago, Chile
| | - Martin Polz
- Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), 15 Vassar Street, Cambridge, MA 02139, USA
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Libertador Bernardo O'Higgins 340, Casilla 144-D, C.P. 651 3677 Santiago, Chile; Center for Climate and Resilience Research (CR)2, Chile.
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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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3
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Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont. Nat Commun 2013; 4:1767. [PMID: 23612308 PMCID: PMC3667715 DOI: 10.1038/ncomms2748] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 03/15/2013] [Indexed: 11/26/2022] Open
Abstract
Diatoms with symbiotic N2-fixing cyanobacteria are often abundant in the oligotrophic
open ocean gyres. The most abundant cyanobacterial symbionts form heterocysts (specialized
cells for N2 fixation) and provide nitrogen (N) to their hosts, but their
morphology, cellular locations and abundances differ depending on the host. Here we show
that the location of the symbiont and its dependency on the host are linked to the evolution
of the symbiont genome. The genome of Richelia (found inside the siliceous frustule
of Hemiaulus) is reduced and lacks ammonium transporters, nitrate/nitrite reductases
and glutamine:2-oxoglutarate aminotransferase. In contrast, the genome of the closely
related Calothrix (found outside the frustule of Chaetoceros) is more similar
to those of free-living heterocyst-forming cyanobacteria. The genome of Richelia is
an example of metabolic streamlining that has implications for the evolution of
N2-fixing symbiosis and
potentially for manipulating plant–cyanobacterial interactions. Cyanobacterial symbionts of marine diatoms can localize intracellularly or
externally to their host partners. Here Hilton et al. describe the genomes of two
diazotroph cyanobacterial symbionts of diatoms and show that the location of the symbiont
affects expression of nitrogen assimilation genes.
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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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Huergo LF, Pedrosa FO, Muller-Santos M, Chubatsu LS, Monteiro RA, Merrick M, Souza EM. PII signal transduction proteins: pivotal players in post-translational control of nitrogenase activity. MICROBIOLOGY-SGM 2012; 158:176-190. [PMID: 22210804 DOI: 10.1099/mic.0.049783-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The fixation of atmospheric nitrogen by the prokaryotic enzyme nitrogenase is an energy- expensive process and consequently it is tightly regulated at a variety of levels. In many diazotrophs this includes post-translational regulation of the enzyme's activity, which has been reported in both bacteria and archaea. The best understood response is the short-term inactivation of nitrogenase in response to a transient rise in ammonium levels in the environment. A number of proteobacteria species effect this regulation through reversible ADP-ribosylation of the enzyme, but other prokaryotes have evolved different mechanisms. Here we review current knowledge of post-translational control of nitrogenase and show that, for the response to ammonium, the P(II) signal transduction proteins act as key players.
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Affiliation(s)
- Luciano F Huergo
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Fábio O Pedrosa
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Marcelo Muller-Santos
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Leda S Chubatsu
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Rose A Monteiro
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
| | - Mike Merrick
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, UK
| | - Emanuel M Souza
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, UFPR Curitiba, PR, Brazil
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