The Small Regulatory RNA SyR1/PsrR1 Controls Photosynthetic Functions in Cyanobacteria

Georg, Jens; Dienst, Dennis; Schürgers, Nils; Wallner, Thomas; Kopp, Dominik; Stazic, Damir; Kuchmina, Ekaterina; Klähn, Stephan; Lokstein, Heiko; Hess, Wolfgang R.; Wilde, Annegret

doi:10.1105/tpc.114.129767

Cited by 104 publications

(148 citation statements)

References 63 publications

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“…In addition to gifA, NsiR4 might regulate additional targets (Table 1), similar to many other sRNAs, e.g., the cyanobacterial sRNA PsrR1, which regulates a set of photosynthesis genes, thereby executing a global regulatory function (28). In the NsiR4oex strain, decreased ssr1528 gene expression was observed, whereas increased ssr1528 gene expression was observed in the ΔnsiR4 KO strain.…”

Section: Distribution Of Nsir4 Among Cyanobacteria and Evolution Of Tmentioning

confidence: 95%

“…Genome-wide mapping of TSSs revealed a high number of potentially regulatory sRNAs in cyanobacteria (19,26,27). One of these sRNAs, the light-regulated and widely conserved PsrR1, is a key regulator of photosynthesis (28).…”

Section: Bacterial Small Rnas With Regulatory Potentialmentioning

confidence: 99%

“…Although the microarray analysis of strains with altered sRNA expression has proven valuable for functional studies of sRNA regulators in enterobacteria (39) and cyanobacteria (28), additional targets might have been missed. This approach is limited when a gene is not expressed under the investigated growth conditions, i.e., some targets might be only expressed in N-depleted cells.…”

Section: Distribution Of Nsir4 Among Cyanobacteria and Evolution Of Tmentioning

confidence: 99%

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The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7

Klähn

Schaal

Georg

et al. 2015

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

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Glutamine synthetase (GS), a key enzyme in biological nitrogen assimilation, is regulated in multiple ways in response to varying nitrogen sources and levels. Here we show a small regulatory RNA, NsiR4 (nitrogen stress-induced RNA 4), which plays an important role in the regulation of GS in cyanobacteria. NsiR4 expression in the unicellular Synechocystis sp. PCC 6803 and in the filamentous, nitrogen-fixing Anabaena sp. PCC 7120 is stimulated through nitrogen limitation via NtcA, the global transcriptional regulator of genes involved in nitrogen metabolism. NsiR4 is widely conserved throughout the cyanobacterial phylum, suggesting a conserved function. In silico target prediction, transcriptome profiling on pulse overexpression, and site-directed mutagenesis experiments using a heterologous reporter system showed that NsiR4 interacts with the 5′UTR of gifA mRNA, which encodes glutamine synthetase inactivating factor (IF)7. In Synechocystis, we observed an inverse relationship between the levels of NsiR4 and the accumulation of IF7 in vivo. This NsiR4-dependent modulation of gifA (IF7) mRNA accumulation influenced the glutamine pool and thus NH + 4 assimilation via GS. As a second target, we identified ssr1528, a hitherto uncharacterized nitrogen-regulated gene. Competition experiments between WT and an ΔnsiR4 KO mutant showed that the lack of NsiR4 led to decreased acclimation capabilities of Synechocystis toward oscillating nitrogen levels. These results suggest a role for NsiR4 in the regulation of nitrogen metabolism in cyanobacteria, especially for the adaptation to rapid changes in available nitrogen sources and concentrations. NsiR4 is, to our knowledge, the first identified bacterial sRNA regulating the primary assimilation of a macronutrient.regulatory RNA | Synechocystis | nitrogen assimilation | glutamine synthetase inactivating factors | NtcA

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Section: Distribution Of Nsir4 Among Cyanobacteria and Evolution Of Tmentioning

confidence: 95%

Section: Bacterial Small Rnas With Regulatory Potentialmentioning

confidence: 99%

Section: Distribution Of Nsir4 Among Cyanobacteria and Evolution Of Tmentioning

confidence: 99%

See 1 more Smart Citation

The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7

Klähn

Schaal

Georg

et al. 2015

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

Self Cite

103

116

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“…These effects are directly related to the conditions required for regulation of crhR expression, namely, the redox potential of the electron transport chain (29). Although CrhR function is not known, the small RNA (sRNA) PsrR1 regulates expression of many photosynthesis-related genes (48). CrhR mutation-mediated disruption of PsrR1 function would be expected to generate similar phenotypic alterations.…”

Section: Figmentioning

confidence: 99%

Cyanobacterial RNA Helicase CrhR Localizes to the Thylakoid Membrane Region and Cosediments with Degradosome and Polysome Complexes in Synechocystis sp. Strain PCC 6803

et al. 2016

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The cyanobacterium Synechocystis sp. strain PCC 6803 encodes a single DEAD box RNA helicase, CrhR, whose expression is tightly autoregulated in response to cold stress. Subcellular localization and proteomic analysis results indicate that CrhR localizes to both the cytoplasmic and thylakoid membrane regions and cosediments with polysome and RNA degradosome components. Evidence is presented that either functional RNA helicase activity or a C-terminal localization signal was required for polysome but not thylakoid membrane localization. Polysome fractionation and runoff translation analysis results indicate that CrhR associates with actively translating polysomes. The data implicate a role for CrhR in translation or RNA degradation in the thylakoid region related to thylakoid biogenesis or stability, a role that is enhanced at low temperature. Furthermore, CrhR cosedimentation with polysome and RNA degradosome complexes links alteration of RNA secondary structure with a potential translation-RNA degradation complex in Synechocystis. IMPORTANCEThe interaction between mRNA translation and degradation is a major determinant controlling gene expression. Regulation of RNA function by alteration of secondary structure by RNA helicases performs crucial roles, not only in both of these processes but also in all aspects of RNA metabolism. Here, we provide evidence that the cyanobacterial RNA helicase CrhR localizes to both the cytoplasmic and thylakoid membrane regions and cosediments with actively translating polysomes and RNA degradosome components. These findings link RNA helicase alteration of RNA secondary structure with translation and RNA degradation in prokaryotic systems and contribute to the data supporting the idea of the existence of a macromolecular machine catalyzing these reactions in prokaryotic systems, an association hitherto recognized only in archaea and eukarya. C ompartmentalization of metabolic processes is crucial for cells to avoid futile cycles. While this is efficiently achieved by lipid bilayers in eukaryotic cells, this solution does not generally apply in prokaryotes. Although prokaryotes have the ability to compartmentalize using invagination of the inner cell membrane, these compartments, for example, magnetosomes, tend to perform one specific function and are not widely used (1). Prokaryotes can also form proteinaceous microcompartments in which specific reactions occur, the primary cyanobacterial example being that of carboxysomes (2). Prokaryotes do not compartmentalize routine, everyday anabolic and catabolic processes such as transcription and translation or protein and RNA decay; however, there is a growing body of evidence indicating that prokaryotes spatially confine these cellular processes (3). A prime example is the localization of the RNA degradation complex, the degradosome, to the cytoplasmic membrane (CM) in Escherichia coli (4) and Bacillus subtilis (5).The E. coli degradosome consists of RNase E, polynucleotide phosphorylase (PNPase), enolase, and the DEAD box RNA he...

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“…Cleavage fragments were separated on 7 M urea-6% polyacrylamide gels and visualized by ethidium bromide staining. RNA was in vitro transcribed ) and full-length RNA was purified by gel extraction (Georg et al 2014). For generation of templates for in vitro synthesis of isiA 59 UTR, intcA and isrR, Synechocystis PCC6803 genomic DNA was used.…”

Section: End-point In Vitro Rnase E Cleavage Assaymentioning

confidence: 99%

A Novel Strategy for Exploitation of Host RNase E Activity by a Marine Cyanophage

et al. 2016

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Previous studies have shown that infection of Prochlorococcus MED4 by the cyanophage P-SSP7 leads to increased transcript levels of host endoribonuclease (RNase) E. However, it has remained enigmatic whether this is part of a host defense mechanism to degrade phage messenger RNA (mRNA) or whether this single-strand RNA-specific RNase is utilized by the phage. Here we describe a hitherto unknown means through which this cyanophage increases expression of RNase E during phage infection and concomitantly protects its own RNA from degradation. We identified two functionally different RNase E mRNA variants, one of which is significantly induced during phage infection. This transcript lacks the 59 UTR, is considerably more stable than the other transcript, and is likely responsible for increased RNase E protein levels during infection. Furthermore, selective enrichment and in vivo analysis of double-stranded RNA (dsRNA) during infection revealed that phage antisense RNAs (asRNAs) sequester complementary mRNAs to form dsRNAs, such that the phage protein-coding transcriptome is nearly completely covered by asRNAs. In contrast, the host protein-coding transcriptome is only partially covered by asRNAs. These data suggest that P-SSP7 orchestrates degradation of host RNA by increasing RNase E expression while masking its own transcriptome from RNase E degradation in dsRNA complexes. We propose that this combination of strategies contributes significantly to phage progeny production.KEYWORDS antisense RNA; T7-like cyanophage P-SSP7; dsRNA fishing; RNase E; Prochlorococcus A common theme of the lifestyle of viruses is the manipulation of host metabolism for the purpose of viral reproduction. However, different virus types have established different regulatory pathways for the takeover and manipulation of their particular hosts. For example, all genes of T4 and the early genes of T7 Escherichia coli bacteriophages are transcribed by the host RNA polymerase (RNAP) (Ueno and Yonesaki 2004;Molineux 2006). However, expression of middle and late T4 genes is mediated by host RNAP that has been modified by T4-encoded factors (Ueno and Yonesaki 2004). In contrast to T4, the subsequent T7 expression program is coordinated by the activity of a phage RNAP (Maniloff and Ackermann 1998). Nevertheless, direct manipulation of host proteins plays a crucial role for the gene expression program of T7.The gene product of the early T7 0.7 gene codes for a protein kinase (Rahmsdorf et al. 1974) and is responsible for phosphorylation and, thus, functional manipulation of .90 host proteins (Robertson et al. 1994). For example, phosphorylation of host RNAP b9-subunit (Zillig et al. 1975) results in reduced processivity, which is believed to assist in the coordinated transition of expression from T7 cluster 1 to cluster 2 genes (Severinova and Severinov 2006). In addition, phosphorylation of translation factors such as IF1, IF2, and IF3 is required for expression of T7 cluster 3 genes (Robertson and Nicholson 1992).Another protein of particul...

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The Small Regulatory RNA SyR1/PsrR1 Controls Photosynthetic Functions in Cyanobacteria

Cited by 104 publications

References 63 publications

The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7

The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7

Cyanobacterial RNA Helicase CrhR Localizes to the Thylakoid Membrane Region and Cosediments with Degradosome and Polysome Complexes in Synechocystis sp. Strain PCC 6803

A Novel Strategy for Exploitation of Host RNase E Activity by a Marine Cyanophage

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