Identification of cyanobacterial non-coding RNAs by comparative genome analysis

Axmann, Ilka M.; Kensche, Philip; Vogel, Jörg; Kohl, Stefan; Herzel, Hanspeter; Hess, Wolfgang R.

doi:10.1186/gb-2005-6-9-r73

Cited by 122 publications

(68 citation statements)

References 66 publications

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“…Intergenic regions may give rise to sRNAs, another type of important regulatory factors with an important role in physiological adaption and as a driver of interstrain divergence in bacteria, including cyanobacteria (33,34,(49)(50)(51). Studies of the filamentous and nitrogen-fixing cyanobacterium Nodularia spumigena CCY9414 genome and its acclimation to stress conditions point further sRNAs crucial role in cell functioning, especially in gene expression regulation (13,52).…”

Section: Resultsmentioning

confidence: 99%

Transcriptomic and Proteomic Profiling of Anabaena sp. Strain 90 under Inorganic Phosphorus Stress

Teikari

Österholm

Kopf

et al. 2015

Appl Environ Microbiol

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cInorganic phosphorus (P i ) is one of the main growth-limiting factors of diazotrophic cyanobacteria. Due to human activity, the availability of P i has increased in water bodies, resulting in eutrophication and the formation of massive cyanobacterial blooms. In this study, we examined the molecular responses of the cyanobacterium Anabaena sp. strain 90 to phosphorus deprivation, aiming at the identification of candidate genes to monitor the P i status in cyanobacteria. Furthermore, this study increased the basic understanding of how phosphorus affects diazotrophic and bloom-forming cyanobacteria as a major growth-limiting factor. Based on RNA sequencing data, we identified 246 differentially expressed genes after phosphorus starvation and 823 differentially expressed genes after prolonged P i limitation, most of them related to central metabolism and cellular growth. The transcripts of the genes related to phosphorus transport and assimilation (pho regulon) were most upregulated during phosphorus depletion. One of the most increased transcripts encodes a giant protein of 1,869 amino acid residues, which contains, among others, a phytase-like domain. Our findings predict its crucial role in phosphorus starvation, but future studies are still needed. Using twodimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), we found 43 proteins that were differentially expressed after prolonged phosphorus stress. However, correlation analysis unraveled an association only to some extent between the transcriptomic and proteomic abundances. Based on the present results, we suggest that the method used for monitoring the P i status in cyanobacterial bloom should contain wider combinations of pho regulon genes (e.g., PstABCS transport systems) in addition to the commonly used alkaline phosphatase gene alone. N itrogen and phosphorus loading into aquatic ecosystems is a global problem causing enhanced primary production of photoautotrophic organisms (1-3). Among them, cyanobacteria are major beneficiaries of turbid and eutrophic water. They employ numerous ecophysiological strategies such as the capability for using various nutrient sources, gas vacuoles, photoprotective pigments, and UV-absorbing compounds, which enable them to survive and grow under eutrophic conditions and may lead to the formation of harmful and toxic blooms (1, 4). The theory that nutrient loading is a crucial factor causing harmful cyanobacterial blooms is supported by numerous field and laboratory studies showing that toxin production and growth rate both increase under nutrient-replete conditions (2, 5-8).The diazotrophic Anabaena is one of the most common bloomforming cyanobacterial genera in freshwater and brackish-water ecosystems, alongside Microcystis and Nodularia, respectively (4, 9), and some strains are capable of producing the following toxins: microcystins, anatoxin-a, anatoxin-a(S), and saxitoxins (4, 10). The ecology of these cyanobacteria thus deserves more attention. The abil...

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Section: Resultsmentioning

confidence: 99%

Transcriptomic and Proteomic Profiling of Anabaena sp. Strain 90 under Inorganic Phosphorus Stress

Teikari

Österholm

Kopf

et al. 2015

Appl Environ Microbiol

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“…Alternatively, the vast majority of data on bacterial riboregulators stem from the analysis of enterobacteria, whereas a single systematic search exists for noncoding RNAs in cyanobacteria (23). It is very likely that cyanobacteria, which grow under extremely diverse environmental conditions and have an evolutionary history of Ͼ3 billion years, have developed a complex RNA-based regulatory mechanism to deal with changes in their environment.…”

Section: Discussionmentioning

confidence: 99%

“…Northern blots and hybridizations were performed as described in ref. 23. Verification of equal loading was achieved by measurement of RNA concentrations, direct comparison of rRNA band intensities after staining by ethidium bromide, or hybridization with a 16S rRNA probe.…”

Section: Methodsmentioning

confidence: 99%

An internal antisense RNA regulates expression of the photosynthesis gene isiA

Dühring

Axmann²,

Hess³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

228

241

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Small regulatory noncoding RNAs exist in both eukaryotic and prokaryotic organisms. Most of these RNA transcripts are transencoded RNAs with short and only partial antisense complementarity to their target RNAs, which regulate gene expression by modifying mRNA stability and translation. In contrast, reports on the function of cis-encoded, perfectly complementary antisense RNAs in eubacteria are rare. Cyanobacteria respond to iron deficiency by expressing IsiA (iron stress-induced protein A), which forms a giant ring structure around photosystem I. Here, we show that this process is controlled by IsrR (iron stress-repressed RNA), a cis-encoded antisense RNA transcribed from the isiA noncoding strand. Artificial overexpression of IsrR under iron stress causes a strongly diminished number of IsiA-photosystem I supercomplexes, whereas IsrR depletion results in premature expression of IsiA. The coupled degradation of IsrR͞isiA mRNA duplexes appears to be a reversible switch that can respond to environmental changes. IsrR is the only RNA known so far to regulate a photosynthesis component.cyanobacteria ͉ iron stress ͉ redox stress ͉ regulation of gene expression ͉ light harvesting

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“…These processes include regulating the expression of outer membrane proteins (Guillier and Gottesman 2006;Valentin-Hansen et al 2007), iron homeostasis (Massé et al 2005Vecerek et al 2007), quorum sensing (Lenz et al 2005;Tu and Bassler 2007), and bacterial virulence (Romby et al 2006;ToledoArana et al 2007). For example, it has been found that MicF, a 93-nt sRNA, can inhibit the expression of OmpF, an outer membrane protein (Axmann et al 2005;Vogel and Papenfort 2006;Prévost et al 2007;Urban et al 2007;Song et al 2008;Desnoyers et al 2009;Papenfort et al 2009). Although the functions of some sRNAs have been obtained, there are still many sRNAs with functions waiting to be elucidated.…”

Section: Introductionmentioning

confidence: 99%

sRNATarBase: A comprehensive database of bacterial sRNA targets verified by experiments

Cao¹,

Wu²,

Liu³

et al. 2010

RNA

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Bacterial sRNAs are an emerging class of small regulatory RNAs, 40-500 nt in length, which play a variety of important roles in many biological processes through binding to their mRNA or protein targets. A comprehensive database of experimentally confirmed sRNA targets would be helpful in understanding sRNA functions systematically and provide support for developing prediction models. Here we report on such a database-sRNATarBase. The database holds 138 sRNA-target interactions and 252 noninteraction entries, which were manually collected from peer-reviewed papers. The detailed information for each entry, such as supporting experimental protocols, BLAST-based phylogenetic analysis of sRNA-mRNA target interaction in closely related bacteria, predicted secondary structures for both sRNAs and their targets, and available binding regions, is provided as accurately as possible. This database also provides hyperlinks to other databases including GenBank, SWISS-PROT, and MPIDB. The database is available from the web page http://ccb.bmi.ac.cn/srnatarbase/.

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Identification of cyanobacterial non-coding RNAs by comparative genome analysis

Cited by 122 publications

References 66 publications

Transcriptomic and Proteomic Profiling of Anabaena sp. Strain 90 under Inorganic Phosphorus Stress

Transcriptomic and Proteomic Profiling of Anabaena sp. Strain 90 under Inorganic Phosphorus Stress

An internal antisense RNA regulates expression of the photosynthesis gene isiA

sRNATarBase: A comprehensive database of bacterial sRNA targets verified by experiments

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