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RyhB-mRNA pairing in absence of the RNA chaperone Hfq in vivo

ABSTRACT: The RNA chaperone Hfq is regarded as a critical effector promoting interaction between small regulatory RNAs (sRNAs) and cognate target mRNAs. While much of this interpretation is based on in vitro assays, no in vivo evidence actually exists to support this model. Here we report that Hfq is typically unnecessary for binding of various sRNA-mRNA complexes in vivo. Data obtained from pull-downs of MS2-tagged RyhB, RybB and DsrA sRNAs followed by RNAseq identification of target mRNAs suggest that absence of Hfq is not essential for sRNA-mRNA complex formation in vivo.

ORGANISM(S): Escherichia coli K-12

PROVIDER: GSE113591 | GEO | 2021/09/22

REPOSITORIES: GEO

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RybB-mRNA pairing in absence of the RNA chaperone Hfq in vivo

Project description:The RNA chaperone Hfq is regarded as a critical effector promoting interaction between small regulatory RNAs (sRNAs) and cognate target mRNAs. While much of this interpretation is based on in vitro assays, no in vivo evidence actually exists to support this model. Here we report that Hfq is typically unnecessary for binding of various sRNA-mRNA complexes in vivo. Data obtained from pull-downs of MS2-tagged RyhB, RybB and DsrA sRNAs followed by RNAseq identification of target mRNAs suggest that absence of Hfq is not essential for sRNA-mRNA complex formation in vivo.

2021-09-22 | GSE113589 | GEO

DsrA-mRNA pairing in absence of the RNA chaperone Hfq in vivo

2021-09-22 | GSE113587 | GEO

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals RprA sRNA targetome.

Project description:Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. Using this technology, we already revealed the targetome of RyhB, RybB and DsrA, three well-characterized sRNAs in Escherichia coli. In this study, we perform MAPS with RprA sRNA.

2018-01-03 | GSE80020 | GEO

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals CyaR sRNA targetome in Escherichia coli.

2018-01-03 | GSE90128 | GEO

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals GcvB sRNA targetome.

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RNA-seq data of Escheirchia coli K12 MG1655 of overexpression of GcvB, MicA, ArcZ, RyhB or CyaR sRNAs

Project description:To study the regulatory outcome of Hfq-mediated sRNA-target interactions, we measured the change in gene expression following overexpression of each of five well-established sRNAs: GcvB, MicA, ArcZ, RyhB and CyaR. For each of the studied sRNAs we applied RNA-seq to two E. coli K-12 MG1655 strains: (1) a WT strain or a strain deleted of the sRNA gene; (2) a strain overexpressing the sRNA, either artificially from a plasmid or from the endogenous sRNA gene by changing the growth condition. For GcvB induction, the E. coli K-12 MG1655 Z1 gcvB::Cm, pZA12-gcvB and the E. coli K-12 MG1655 Z1 gcvB::Cm, pTP-011 strains were used. For MicA overexpression the E. coli K-12 MG1655lacIq pBRplac, pEF21-Hfq and the E. coli K-12 MG1655lacIq pMicA, pEF21-Hfq strains were used. For ArcZ induction the E. coli K-12 MG1655 Z1 arcZ::Cm, pZE12-ArcZ and the E. coli K-12 MG1655 Z1 arcZ::Cm, pJV300 strains were used. For RyhB overexpression the E. coli K-12 MG1655 ryhB::Cm and the E. coli K-12 MG1655 were used. For CyaR induction the E. coli K-12 MG1655 Z1 cyaR::Cm, pZE12-CyaR and the E. coli K-12 MG1655 Z1 cyaR::Cm, pJV300 strains were used. All E. coli strains used in this study were grown overnight in Luria Bertani (LB) medium at 37 °C with shaking (200 r.p.m.), diluted 100-fold in fresh LB medium, and re-grown with shaking at 37 °C to exponential phase, for GcvB (OD600 = 0.3) and for RyhB (OD600 = 0.5), or to stationary phase, for ArcZ WT, ArcZ M1, ArcZ M2 and CyaR (OD600 = 1.0) and for MicA (grown for 6 hr). For induction of ArcZ and GcvB, IPTG was added (1mM, 20 min). MicA was constitutively expressed and further induced at the end of growth with IPTG (1mM, 20 min). For induction of RyhB, the iron chelator 2,2'-Dipyridyl was added (200 μM, 30 min).

2020-03-03 | E-MTAB-8229 | biostudies-arrayexpress

MS2-affinity purification coupled with RNA sequencing (MAPS) reveals RyhB sRNA targetome

Project description:Despite the overwhelming information about sRNAs, one of the biggest challenges in the sRNA field is characterizing sRNA targetomes. Thus, we develop a novel method to identify RNAs that interact with a specific sRNA, regardless of the type of regulation (positive or negative) or targets (mRNA, tRNA, sRNA). This method is called MAPS: MS2 affinity purification coupled with RNA sequencing. As proof of principle, we identified RNAs bound to RyhB, a well-characterized E. coli sRNA. Identification of RNAs co-purified with MS2-RyhB in a rne131 ?ryhB strain. RyhB (without MS2) was used as control

2015-04-16 | E-GEOD-66519 | biostudies-arrayexpress

Identification of RNA interacting with the sRNA sponge 3'ETSleuZ

Project description:During glyW-cysT-leuZ polycistronic tRNA maturation, the 3’external transcribed spacer (3’ETS) sequence is excised and act as a sRNA sponge (Lalaouna et al., 2015). Using MS2-affinity purification coupled with RNA sequencing (MAPS), we demonstrated that 3’ETSleuZ was highly and specifically enriched by co-purification with at least two different small regulatory RNAs (sRNAs), RyhB and RybB. Both sRNAs were shown to base pair with the same region in 3’ETSleuZ. Here, we use MS2-3’ETSleuZ as bait to co-purify all interacting sRNAs and confirm 3’ETSleuZ/RyhB and 3’ETSleuZ/RybB interactions.

2017-11-28 | GSE79278 | GEO

Probing the RyhB-2 regulon in Salmonella Typhimurium

Project description:Typically, the expression of sRNAs is activated in response to environmental stimuli in order to regulate gene expression through post-transcriptional mechanisms. In the present work we show that the Salmonella Typhimurium paralog sRNAs RyhB-1 and RyhB-2 are induced in response to the nitrosating agent S-nitrosoglutathione (GSNO). Inactivation of these sRNAs decreased S. Typhimurium resistance to GSNO and increased the levels of nitrosylated proteins. These results prompted us to evaluate a possible role of these sRNAs in nitrosative stress resistance. RNA profiling was used as a screening to identify novel RyhB-1 and RyhB-2 regulated targets, and a subset of genes was filtered based on their potential role in the response to nitrosative stress. To confirm our observation, expression of the candidate targets was analyzed by quantitative RT-PCR in a wild type, single and double mutant strains (M-NM-^TryhB1, M-NM-^TryhB2 and M-NM-^TryhB1 M-NM-^TryhB2) treated with GSNO. In response to GSNO RyhB-1 and RyhB-2 negatively regulate the expression of the genes cyoABC (cytochrome o oxidase complex), cydB (cytochrome d oxidase complex), cybC (cytochrome b-562), and positively regulate the nirBCD operon (nitrite reductase system). Together, these results suggest that RyhB-1 and RyhB-2 finely tune the expression of genes coding for cytochrome and the nitrate reductase system, allowing the cell to cope with GSNO-induced stress. Total RNA was harvested from two biological replicates of wt S. Typhimurium overexpressing the sRNA RyhB-2 grown in LB medium, in order to identify RhyB-2 targets that might be implicated in reactive nitrogen stress resistance.

2014-06-10 | E-GEOD-58110 | biostudies-arrayexpress

RNA-Seq samples of E. coli K12 MG1655, deletion of ryhB sRNA gene, 2,2’-Dipyridy

Project description:Bacteria adapt to environmental changes by remodeling their gene expression programs. The change in expression of specific genes is due to the combined effects of various regulators, among them small RNAs (sRNAs). Here we present a straightforward RNA-seq-based approach to infer the contribution of a sRNA to the total change in gene expression levels of specific genes in response to shifts in environmental conditions, demonstrated here for the sRNA RyhB in cells growing under iron limitation stress. We show that the contribution of RyhB to changes in expression levels of specific genes upon iron limitation varies between the genes, from relatively mild contribution to the expression change of some genes to ~100% effect on the expression change of other genes. Interestingly, the contribution of RyhB is high for genes undergoing in total mild expression changes and relatively low for genes undergoing in total high expression changes, implying that for almost all affected genes RyhB renders small changes in expression upon iron limitation. Determining the contribution of a sRNA to the total changes in expression levels of genes in response to an environmental change is important for understanding the integration of regulation by sRNAs in the cellular networks regulating cellular physiology.

2022-12-09 | E-MTAB-10502 | biostudies-arrayexpress

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