Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis
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ABSTRACT:
ORGANISM(S): Bacillus subtilis
PROVIDER: GSE148936 | GEO | 2020/07/24
REPOSITORIES: GEO
Similar Datasets
Project description:RNA structure influences numerous processes in all organisms. In bacteria, these processes include transcription termination and attenuation, small RNA and protein binding, translation initiation, and mRNA stability, and can be regulated via metabolite availability and other stresses. Here we use Structure-seq2 to probe the in vivo RNA structurome of Bacillus subtilis grown in the presence and absence of amino acids. Our results reveal that amino acid starvation results in lower overall dimethyl sulfate (DMS) reactivity of the transcriptome, indicating enhanced protection owing to protein binding or RNA structure. Starvation-induced changes in DMS reactivity correlated inversely with transcript abundance changes. This correlation was particularly pronounced in genes associated with the stringent response and CodY regulons, which are involved in adaptation to nutritional stress, suggesting that RNA structure contributes to transcript abundance change in regulons involved in amino acid metabolism. Structure-seq2 accurately reported on four known amino acid-responsive riboswitches: T-box, SAM, glycine, and lysine riboswitches. Additionally, we discovered a transcription attenuation mechanism that reduces yfmG expression when amino acids are added to the growth medium. We also found that translation of a leader peptide (YfmH) encoded just upstream of yfmG regulates yfmG expression. Our results are consistent with a model in which a slow rate of yfmH translation caused by limitation of the amino acids encoded in YfmH prevents transcription termination in the yfmG leader region by favoring formation of an overlapping antiterminator structure. This novel RNA switch offers a way to simultaneously monitor the levels of multiple amino acids.
| S-EPMC7491331 | biostudies-literature
Project description:Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis
| PRJNA626579 | ENA
Project description:Here we use Structure-seq2 to probe the in vivo RNA structurome of B. subtilis grown at four different temperatures. We show that increases in reactivity with increasing temperature follow non-monotonic trends. Focusing on subregions of the transcriptome led to the discovery of two novel RNA thermometers that control expression of glpF and glpT.
2023-05-23 | GSE224126 | GEO
Project description:CodY is a nutritional regulator mainly involved in amino acid metabolism. It has been extensively studied in Bacillis subtilis and Lactococcus lactis. We investigated the role of CodY in gene regulation and virulence of the human pathogen Streptococcus pneumoniae. We constructed a codY-mutant and examined the effect on gene and protein expression by microarray and 2D DIGE analysis. The pneumococcal CodY-regulon was found to consist predominantly of genes involved in amino acid metabolism, but also several other cellular processes, such as carbon metabolism and iron uptake. By means of electrophoretic mobility shift assays and DNA footprinting, we showed that most targets identified are under direct control of CodY. By mutating DNA predicted to represent the CodY-box based on the L. lactis consensus, we demonstrated that this sequence is indeed required for in vitro DNA-binding to target promoters. Similar to L. lactis, DNA-binding of CodY was enhanced in the presence of the branched chain amino acids isoleucine, leucine, and valine, and not by GTP. We observed in experimental mouse models that CodY is transcribed in the murine nasopharynx and lungs, and is specifically required for colonization. This finding was underscored by the diminished ability of the codY-mutant to adhere to nasopharyngeal cells in vitro. In conclusion, pneumococcal CodY predominantly regulates genes involved in amino acid metabolism and contributes to the early stages of infection, i.e. colonization of the nasopharynx. Keywords: codY CodY of Streptococcus pneumoniae: link between nutritional gene regulation and virulence
2010-05-25 | E-GEOD-7350 | biostudies-arrayexpress
Project description:CodY is a conserved broad acting transcriptional factor that regulates the expression of genes related to amino acid metabolism and virulence in Staphylococcus aureus. CodY target genes have been studied by using in vitro DNA affinity purification and deep sequencing (IDAP-Seq). In this study we performed the first in vivo determination of CodY target genes using a novel CodY monoclonal antibody in established ChIP-exo protocols. Our results showed, 1) The same 165 CodY target genes in both strains; 2) That the differential binding intensity for the same target genes under the same conditions were due to sequence differences in the same CodY binding site in the two strains; 3) Based on transcriptomic data, a CodY regulon comprising 72 target genes that revealed that CodY is mainly involved in amino acid transport and metabolism, inorganic ion transport and metabolism, and cellular transcription and translation; and 4) CodY systematically regulated central metabolic flux to generate branched-chain amino acids (BCAAs) by mapping the CodY regulon onto a genome-scale metabolic model of S. aureus. Our study performed the first system-level analysis of CodY in two closely related dominant USA300 TCH1516 and LAC strains, thus expanding the size of the known CodY regulon, and giving new insights into the similarities and differences of CodY regulatory roles between closely related strains.
2022-08-29 | GSE163312 | GEO
Project description:CodY is a nutritional regulator mainly involved in amino acid metabolism. It has been extensively studied in Bacillis subtilis and Lactococcus lactis. We investigated the role of CodY in gene regulation and virulence of the human pathogen Streptococcus pneumoniae. We constructed a codY-mutant and examined the effect on gene and protein expression by microarray and 2D DIGE analysis. The pneumococcal CodY-regulon was found to consist predominantly of genes involved in amino acid metabolism, but also several other cellular processes, such as carbon metabolism and iron uptake. By means of electrophoretic mobility shift assays and DNA footprinting, we showed that most targets identified are under direct control of CodY. By mutating DNA predicted to represent the CodY-box based on the L. lactis consensus, we demonstrated that this sequence is indeed required for in vitro DNA-binding to target promoters. Similar to L. lactis, DNA-binding of CodY was enhanced in the presence of the branched chain amino acids isoleucine, leucine, and valine, and not by GTP. We observed in experimental mouse models that CodY is transcribed in the murine nasopharynx and lungs, and is specifically required for colonization. This finding was underscored by the diminished ability of the codY-mutant to adhere to nasopharyngeal cells in vitro. In conclusion, pneumococcal CodY predominantly regulates genes involved in amino acid metabolism and contributes to the early stages of infection, i.e. colonization of the nasopharynx. Keywords: codY
2007-11-20 | GSE7350 | GEO
Project description:More than 200 direct CodY target genes in Staphylococcus aureus were identified by genome-wide analysis of in vitro DNA binding. This analysis, which was confirmed for some genes by DNase I footprinting assays, revealed that CodY is a direct regulator of numerous transcription units associated with amino acid biosynthesis, transport of macromolecules and virulence. The virulence genes regulated by CodY fell into three groups. One group was dependent on the Agr system for its expression; these genes were indirectly regulated by CodY through its repression of the agr locus. A second group was regulated directly by CodY. The third group, which includes genes for alpha-toxin and capsule synthesis, was regulated by CodY in two ways, i.e., by direct repression and by repression of the agr locus. Since S. aureus CodY was activated in vitro by the branched chain amino acids and GTP, CodY appears to link changes in intracellular metabolite pools with the induction of numerous adaptive responses, including virulence.
2010-04-01 | GSE20973 | GEO
Project description:CodY of Lactococcus lactis MG1363 is a transcriptional regulator that represses the expression of several genes encoding proteins of the proteolytic system. DNA microarray analysis, comparing the expression profiles of L. lactis MG1363 and an isogenic strain in which codY was mutated, was used to determine the CodY regulon. In peptide-rich medium and exponentially growing cells, where CodY exerts strong repressing activity, the expression of over 30 genes was significantly increased upon removal of codY. The differentially expressed genes included those predominantly involved in amino acid transport and metabolism. In addition, several genes belonging to other functional categories were derepressed, stressing the pleiotropic role of CodY. Scrutinizing the transcriptome data with bioinformatics tools revealed the presence of a novel overrepresented motif in the upstream regions of several of the genes derepressed in L. lactis MG1363codY. Evidence is presented that this 15-bps cis-sequence, AATTTTCWGAAAATT, serves as a high-affinity binding site for CodY, as shown by electrophoretic mobility shift assays and DNaseI footprinting analyses. The presence of this CodY-box is sufficient to evoke CodY-mediated regulation in vivo. A copy of this motif is also present in the upstream region of codY itself. It is shown that CodY regulates its own synthesis and requires the CodY-box and branched-chain amino acids to interact with its promoter. Keywords: genetic modification
2005-07-22 | GSE2823 | GEO
Project description:More than 200 direct CodY target genes in Staphylococcus aureus were identified by genome-wide analysis of in vitro DNA binding. This analysis, which was confirmed for some genes by DNase I footprinting assays, revealed that CodY is a direct regulator of numerous transcription units associated with amino acid biosynthesis, transport of macromolecules and virulence. The virulence genes regulated by CodY fell into three groups. One group was dependent on the Agr system for its expression; these genes were indirectly regulated by CodY through its repression of the agr locus. A second group was regulated directly by CodY. The third group, which includes genes for alpha-toxin and capsule synthesis, was regulated by CodY in two ways, i.e., by direct repression and by repression of the agr locus. Since S. aureus CodY was activated in vitro by the branched chain amino acids and GTP, CodY appears to link changes in intracellular metabolite pools with the induction of numerous adaptive responses, including virulence. Affymetrix GeneChips were used to compare the transcript titers of S. aureus strains UAMS-1 (wild type) and corresponding agr- (strain CM18), codY- (strain MS1), and agr- codY- (strain CM19) isogenic mutant strains during exponential and stationary phase growth. At least two biological replicates were assessed for each strain and each growth phase.
2010-04-13 | E-GEOD-20973 | biostudies-arrayexpress
Project description:CodY is a widely conserved global regulator, regulating nitrogen metabolism, virulence, and stress response in Gram-positive bacteria. Here, we performed ChIP-seq to define the CodY regulon in L. lactis, and found that CodY served either as an activator or as a repressor of hundreds of genes. The genes involved in amino acid biosynthesis and transport, cell wall synthesis, nisin synthesis and immunity, and several transcription regulators were identified regulated by CodY for the first time. Intriguingly, CodY could directly bind to the downstream of codY. This study gives new insights into the function of CodY controlling cell wall synthesis, nisin synthesis and immunity, as well as self-regulation in L. lactis.
2022-01-28 | GSE139902 | GEO