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ABSTRACT:
PROVIDER: PRJNA776034 | ENA |
REPOSITORIES: ENA
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Project description:Cotranscriptional Folding of a ZTP Riboswitch
| PRJNA510362 | ENA
Project description:Riboswitches are cis-acting regulating RNA elements mostly found in the 5’-UTR of bacterial mRNAs. The Salmonella enterica mgtA riboswitch controls mgtA expression upon the sensing of intracellular Mg2+ ions. A leader peptide (MgtL) is contained within the mgtA riboswitch and its translation has been previously shown to be affected by Mg2+ concentrations. The current regulatory model suggests that the efficiency of MgtL translation is inversely related to mgtA transcription. Herein we show that the orthologue mgtA riboswitch of Escherichia coli also contains a leader peptide but, unlike S. enterica, that its translation is proportionally related to mgtA expression. Our results also suggest that ribosome stalling at mgtL is crucial for mgtA expression. Together, our results indicate that in E. coli, the expression of the MgtL leader peptide and mgtA are positively coordinated according to the intracellular Mg2+ concentration, a unique mechanism among known riboswitches.
2023-05-01 | GSE203590 | GEO
Project description:Riboswitches are ligand-binding elements contained within the 5M-bM-^@M-^Y untranslated regions of bacterial transcripts, which generally regulate expression of downstream open reading frames. Here we show that in Listeria monocytogenes, a Vitamin B12-binding (B12) riboswitch controls expression of a non-coding regulatory RNA, Rli55. Rli55 in turn controls expression of the eut genes, which enable ethanolamine utilization and require B12 as a cofactor. Defects in ethanolamine utilization, or in its regulation by Rli55, significantly attenuate Listeria virulence in mice. Rli55 functions by sequestering the two-component response regulator, EutV via a EutV binding-site contained within the RNA. Thus Rli55 is a riboswitch-regulated member of the small group of regulatory RNAs that function by sequestering a protein and reveals a unique mechanism of signal integration in bacterial gene regulation. RNA-Seq and CLIP-Seq to investigate the sequestration of EutV by rli55
2014-08-22 | E-GEOD-60363 | biostudies-arrayexpress
Project description:Riboswitches are ligand-binding elements contained within the 5’ untranslated regions of bacterial transcripts, which generally regulate expression of downstream open reading frames. Here we show that in Listeria monocytogenes, a Vitamin B12-binding (B12) riboswitch controls expression of a non-coding regulatory RNA, Rli55. Rli55 in turn controls expression of the eut genes, which enable ethanolamine utilization and require B12 as a cofactor. Defects in ethanolamine utilization, or in its regulation by Rli55, significantly attenuate Listeria virulence in mice. Rli55 functions by sequestering the two-component response regulator, EutV via a EutV binding-site contained within the RNA. Thus Rli55 is a riboswitch-regulated member of the small group of regulatory RNAs that function by sequestering a protein and reveals a unique mechanism of signal integration in bacterial gene regulation.
2014-08-22 | GSE60363 | GEO
Project description:Alignment of fasting and feeding with the sleep/wake cycle is coordinated by hypothalamic neurons, though the underlying molecular programs remain incompletely understood. Here we demonstrate that the clock transcription pathway maximizes eating during wakefulness and glucose production during sleep through transcription pathway maximizes eating during autonomous circadian regulation of NPY/AgRP neurons. Tandem profiling of whole cell and ribosome-bound mRNAs in morning and evening under dynamic fasting and fed conditions identified temporal control of activity-dependent gene repertoires in AgRP neurons central to synaptogenesis, bioenergetics, and neurotransmitter and peptidergic signaling. Synaptic and circadian pathways were specific to whole cell RNA analyses, while bioenergetic pathways were selectively enriched in the ribosome-bound transcriptome. Finally, we demonstrate that the AgRP clock mediates the transcriptional food acquisition with sleep/wake state. response to leptin. Our results reveal that time-of-day restriction in transcriptional control of energy-sensing neurons underlies the alignment of hunger and day restriction in transcriptional control of energy-sensing neurons underlies the alignment of hunger and food acquisition with sleep/wake state.
2019-03-04 | GSE124693 | GEO
Project description:Histone methyltransferase SETD1A is critical for acute myeloid leukemia (AML) cell survival, but the molecular mechanism driving SETD1A gene regulation remains elusive. To delineate the role of SETD1A, we utilize a protein degrader technology to induce rapid SETD1A degradation in AML cell lines. SETD1A degradation results in immediate downregulation of transcripts associated with DNA repair and heme biosynthesis pathways. CRISPR-based functional analyses and metabolomics reveal an essential role of SETD1A to maintain mitochondrial respiration in AML cells. These SETD1A targets are enriched in head-to-head (H2H) genes. SETD1A degradation disrupts a non-enzymatic SETD1A domain-dependent cyclin K function, increases the Ser5P RNA polymerase II (RNAP2) at TSS, and induces the promoter-proximal pausing of RNAP2 in a strand-specific manner. This study reveals a non-enzymatic role for SETD1A in transcriptional pause release and provides insight into the mechanism of RNAP2 pausing and its function in cancer.
2022-10-12 | ST002323 | MetabolomicsWorkbench
Project description:A set of small RNAs was identified in Vancomycin-resistant Enterococcus faecium, a leading cause of MDR infections. We described here the function of srn_2050, acting as a T-box riboswitch to regulate expression of downstream genes encoding the HisRS and AspRS aminoacyl-tRNA synthetases. Comparative RNAseq between Aus0004 and isogenic srn_2050 mutant identified the genes whose expression is impacted by the RNA. srn_2050 structure in its ‘off state’ was deciphered by in-line probing, containing T-box consensus sequences, a pseudoknot, a specifier loop and a terminator. Transcription binding assays between the riboswitch and either tRNAAsp or tRNAHis indicate that each deacylated tRNA interacts with the T-box. Their anticodons bind to a GACAC sequence within the specifier loop (GAC and CAC are Asp and His codons, respectively), whereas tRNATyr (UA/C-U) does not. A pioneering evaluation of E. faecium amino acid auxotrophy, with emphasis on E. faecium strain Aus0004, revealed auxotrophy for Histidine but not for Aspartic acid. Based on comparative growths and RNAseq between Aus004 and Aus004-srn2050, the riboswitch is shown essential for growth under aspartate starvation. This is the first example of a functional riboswitch in E. faecium with two overlapping codons allowing a dual tRNA-dependent regulation at transcriptional level.
2020-11-16 | GSE161499 | GEO
Project description:Short-term adaptation to changing environments relies on regulatory elements translating changing metabolite concentrations into a specifically optimized transcriptome. So far the focus of analyses has been divided between regulatory elements identified in vivo and kinetic studies of small molecules interacting with the regulatory elements in vitro. Here we describe how in vivo Regulatory Kinetics can describe a regulon through the effects of the metabolite controlling it, exemplified by temporal purine exhaustion in Lactococcus lactis. We deduced a causal relation between the pathway precursor 5-phosphoribosyl-1-pyrophosphate (PRPP) and each individual mRNA levels, whereby unambiguous and homogenous relations could be obtained for PurR regulated genes, thus linking a specific regulon to a specific metabolite. As PurR activates gene expression upon binding of PRPP, the pur mRNA curves reflect the in vivo kinetics of PurR PRPP binding and activation. The method singled out the xpt-pbuX operon as kinetically distinct, which was found to be caused by a guanine riboswitch whose regulation was overlaying the PurR regulation. The strategy outlined here can be adapted to analyze the individual effects of members from larger metabolomes in virtually any organism, for elucidating regulatory networks in vivo. Agilent 8x15k custom microarrays Fifteen samples from two cultures were taken in a time-course experiment.
2013-12-01 | E-GEOD-52135 | biostudies-arrayexpress