Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.

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 geno...

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Autores principales:	Björn Voss, Henk Bolhuis, David P Fewer, Matthias Kopf, Fred Möke, Fabian Haas, Rehab El-Shehawy, Paul Hayes, Birgitta Bergman, Kaarina Sivonen, Elke Dittmann, Dave J Scanlan, Martin Hagemann, Lucas J Stal, Wolfgang R Hess
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/71564b77acfc4d8ebc9bab1f0b3621c9
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spelling	oai:doaj.org-article:71564b77acfc4d8ebc9bab1f0b3621c92021-11-18T07:51:30ZInsights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.1932-620310.1371/journal.pone.0060224https://doaj.org/article/71564b77acfc4d8ebc9bab1f0b3621c92013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23555932/?tool=EBIhttps://doaj.org/toc/1932-6203Nodularia 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.Björn VossHenk BolhuisDavid P FewerMatthias KopfFred MökeFabian HaasRehab El-ShehawyPaul HayesBirgitta BergmanKaarina SivonenElke DittmannDave J ScanlanMartin HagemannLucas J StalWolfgang R HessPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 3, p e60224 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Björn Voss Henk Bolhuis David P Fewer Matthias Kopf Fred Möke Fabian Haas Rehab El-Shehawy Paul Hayes Birgitta Bergman Kaarina Sivonen Elke Dittmann Dave J Scanlan Martin Hagemann Lucas J Stal Wolfgang R Hess Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.
description	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.
format	article
author	Björn Voss Henk Bolhuis David P Fewer Matthias Kopf Fred Möke Fabian Haas Rehab El-Shehawy Paul Hayes Birgitta Bergman Kaarina Sivonen Elke Dittmann Dave J Scanlan Martin Hagemann Lucas J Stal Wolfgang R Hess
author_facet	Björn Voss Henk Bolhuis David P Fewer Matthias Kopf Fred Möke Fabian Haas Rehab El-Shehawy Paul Hayes Birgitta Bergman Kaarina Sivonen Elke Dittmann Dave J Scanlan Martin Hagemann Lucas J Stal Wolfgang R Hess
author_sort	Björn Voss
title	Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.
title_short	Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.
title_full	Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.
title_fullStr	Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.
title_full_unstemmed	Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.
title_sort	insights into the physiology and ecology of the brackish-water-adapted cyanobacterium nodularia spumigena ccy9414 based on a genome-transcriptome analysis.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/71564b77acfc4d8ebc9bab1f0b3621c9
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Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.

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