Global Analysis of the Expression of Salmonella RyhB regulon
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ABSTRACT:
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
SUBMITTER: Jeong Nam Kim
PROVIDER: E-GEOD-19813 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Purpose:To investigate the effect of small RNA RyhB-1and RyhB-2 deletion of Salmonella enteritidis on genes expression of genome under simulated intestinal conditions Methods:S. Enteritidis wild type (WT) strain 50336 and mutants △ryhB-1, △ryhB-2, and △ryhB-1/ryhB-2 were grown overnight in 50 mL of the LB medium with 160 rpm shaking at 37°C under aerobic condition, washed thrice, and re-suspended with iron-limited and nutrient-limited medium. The above prepared bacterial cells were cultured for 2 h at 37°C in the anaerobic workstation. Each sample was analysed in triplicate. Total RNA of the above stains was extracted using TRIzol reagentwith DNase digestion according to the manufacturer’s instruction. Ribosome RNA was removed using a Ribo-Zero rRNA removal kit (Illumina) that leaves the mRNA. Sequencing libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), sequenced on an Illumina Hiseq 2000 platform at Beijing Novogene Bioinformatics Technology。 Results: Analysis of the RNA-Seq data identified 496, 250, and 553 DEGs in △ryhB-1, △ryhB-2, and △ryhB-1△ryhB-2, respectively, compared to the WT strain.A total of 213 genes changed in △ryhB-1, △ryhB-2, and △ryhB-1△ryhB-2 mutants. The transcriptional levels of 176 genes changed in △ryhB-1 and △ryhB-1△ryhB-2 but not in △ryhB-2. Furthermore, 14 genes were only changed in RyhB-2, 96 DEGs were only identified in △ryhB-1, and 12 DEGs were only identified in △ryhB-2 but not in △ryhB-1△ryhB-2. Moreover, 150 DEGs were only identified in △ryhB-1△ryhB-2 but neither in △ryhB-1 nor in △ryhB-2. Conclusions: A total of 213 genes could be regulated by △ryhB-1, △ryhB-2, and △ryhB-1△ryhB-2 mutants, 176 genes are regulated only by RyhB-1, 14 genes were regulated only by RyhB-2.
2022-04-23 | GSE201112 | GEO
Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type 、 ryhB-1、 ryhB-2、 ryhB-1/ryhB-2 Mutant Strains Transcriptomes
| PRJNA828446 | ENA
Project description:Analysis of the Expression Change of RyhB Regulon in RyhB-deleted Mutant Strains.
2010-01-08 | GSE19813 | GEO
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 (ΔryhB1, ΔryhB2 and ΔryhB1 ΔryhB2) 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.
2014-06-10 | GSE58110 | GEO
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
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
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
Project description:The effects of RyhB expression were examined by Ribo-seq and RNA-seq after 10 min to avoid indirect effects. Expression of RyhB was induced by arabinose from cells carrying pBAD-ryhB plasmid. The RyhB expression was confirmed by real-time PCR. As a control, cells with vector pNM12 were grown and induced. The cells were pulverized and total mRNAs were extracted from the pulverized cells and processed for Ribo-seq and RNA-seq.
2014-11-01 | E-MTAB-2903 | biostudies-arrayexpress
Project description:RyhB is a non-coding RNA regulated by the Fur repressor. It has previously been shown to cause the rapid degradation of a number of mRNAs that encode proteins that utilize iron. Here we examine the effect of ectopic RyhB production on global gene expression by microarray analysis. Many of the previously identified targets were found, as well as other mRNAs encoding iron-binding proteins, bringing the total number of regulated operons to at least 18, encoding 56 genes. The two major operons involved in Fe-S cluster assembly showed different behavior; the isc operon appears to be a direct target of RyhB action, while the suf operon does not. This is consistent with previous findings suggesting that the suf genes but not the isc genes are important for Fe-S cluster synthesis under iron-limiting conditions, presumably for essential iron-binding proteins. In addition, we observed repression of Fur-regulated genes upon RyhB expression, interpreted as due to intracellular iron-sparing resulting from reduced synthesis of iron-binding proteins. Our results demonstrate the broad effects of a single non-coding RNA on iron homeostasis. Keywords: RNA degradation, iron stavation, RyhB small RNA, iron-using proteins
2005-08-31 | GSE3105 | GEO
Project description:Study of the roles played by Fur and RyhB in Shewanella oneidensis
2018-01-01 | GSE104952 | GEO