Extensive reshaping of bacterial operons by programmed mRNA decay
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ABSTRACT:
PROVIDER: PRJEB21982 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2433510_1.fastq.gz | Fastqsanger.gz | |||
| ERR2433510_2.fastq.gz | Fastqsanger.gz | |||
| ERR2433520_1.fastq.gz | Fastqsanger.gz | |||
| ERR2433520_2.fastq.gz | Fastqsanger.gz | |||
| ERR2433530_1.fastq.gz | Fastqsanger.gz |
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Project description:Bacterial operons synchronize the expression of multiple genes by placing them under the control of a shared promoter. It was previously shown that polycistronic transcripts can undergo differential RNA decay, leaving some genes within the polycistron more stable than others, but the extent of regulation by differential mRNA decay or its evolutionary conservation remains unknown. Here, we find that a substantial fraction of E. coli genes display non-uniform mRNA stoichiometries despite being coded from the same operon. We further show that these altered operon stoichiometries are shaped post-transcriptionally by differential mRNA decay, which is regulated by RNA structures that protect specific regions in the transcript from degradation. These protective RNA structures are generally coded within the protein-coding regions of the regulated genes and are frequently evolutionarily conserved. Furthermore, we provide evidence that differences in ribosome densities across polycistronic transcript segments, together with the conserved structural RNA elements, play a major role in the differential decay process. Our results highlight a major role for differential mRNA decay in shaping bacterial transcriptomes.
| S-EPMC5927463 | biostudies-literature
Project description:Caenorhabditis elegans and its relatives are unique among animals, possibly even among eukaryotes, in having operons. In these regulated multigene transcription units, a polycistronic pre-mRNA is processed to monocistronic mRNAs by 3' end formation and trans-splicing utilizing a special snRNP, the SL2 snRNP, for downstream mRNAs1. Previously, the correlation between downstream location in an operon and SL2 trans-splicing has been strong, but anecdotal. Although only 28 operons have been reported previously, the complete sequence of the genome reveals numerous gene clusters. To determine how many represent operons, we probed full-genome microarrays for SL2-containing mRNAs. We found significant enrichment for about 1200 genes including most of a group of several hundred genes represented by cDNAs that contain SL2 sequence. Analysis of their genomic arrangements indicates that >90% are downstream genes, falling in 790 distinct operons. We conclude that the genome contains at least 1000 operons, 2- 8 genes in length, that contain ~15% of C. elegans genes. Most of the operons have not been reported previously, and numerous examples of co-transcription of genes encoding functionally related proteins are evident. Inspection of the operon list should reveal heretofore unknown functional relationships. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-07-22 | GSE2975 | GEO
Project description:Genes clustered into polycistronic operons was thought a characteristic of bacteria and many other species. More than half protein-coding genes are organized in polycistronic operons composed of two or more than ten genes in bacterial genomes. Although the structure of operons have been studied precisely, how the member genes within operon maintain their stoichiometry expression is remain unknown. Using a highly accurate label-free absolute quantification method DIA (data-independent acquisition), we present a global analysis of Escherichia coli proteome, quantified 1607 proteins, including 59.1% of the known polycistronic operons. We found shorter operons tend to be more tightly controlled than longer operons, and those operons for metabolic pathways are less controlled for stoichiometry balance than those operons for protein complexes. Our results thus reveal the two-level regulation mode involving transcription and translation of operons would balance the stoichiometry expression of genes in polycistronic operons in different time-scale.
2019-11-12 | PXD010126 | Pride
Project description:Caenorhabditis elegans and its relatives are unique among animals, possibly even among eukaryotes, in having operons. In these regulated multigene transcription units, a polycistronic pre-mRNA is processed to monocistronic mRNAs by 3' end formation and trans-splicing utilizing a special snRNP, the SL2 snRNP, for downstream mRNAs1. Previously, the correlation between downstream location in an operon and SL2 trans-splicing has been strong, but anecdotal. Although only 28 operons have been reported previously, the complete sequence of the genome reveals numerous gene clusters. To determine how many represent operons, we probed full-genome microarrays for SL2-containing mRNAs. We found significant enrichment for about 1200 genes including most of a group of several hundred genes represented by cDNAs that contain SL2 sequence. Analysis of their genomic arrangements indicates that >90% are downstream genes, falling in 790 distinct operons. We conclude that the genome contains at least 1000 operons, 2- 8 genes in length, that contain ~15% of C. elegans genes. Most of the operons have not been reported previously, and numerous examples of co-transcription of genes encoding functionally related proteins are evident. Inspection of the operon list should reveal heretofore unknown functional relationships. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set Computed
2005-07-22 | E-GEOD-2975 | biostudies-arrayexpress
Project description:Despite knowledge of complex prokaryotic transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have played a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of ~64% of all genes including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein-DNA interaction datasets revealed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3' ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes - events usually considered spurious or non-functional. With experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements This SuperSeries is composed of the SubSeries listed below.
2009-06-25 | GSE13150 | GEO
Project description:Caenorhabditis elegans and its relatives are unique among animals, possibly even among eukaryotes, in having operons1. In these regulated multigene transcription units, a polycistronic pre-mRNA is processed to monocistronic mRNAs by 3' end formation and trans-splicing utilizing a special snRNP, the SL2 snRNP2, for downstream mRNAs1. Previously, the correlation between downstream location in an operon and SL2 trans-splicing has been strong, but anecdotal3. Although only 28 operons have been reported previously, the complete sequence of the genome reveals numerous gene clusters4. To determine how many represent operons, we probed full-genome microarrays for SL2-containing mRNAs. We found significant enrichment for about 1200 genes including most of a group of several hundred genes represented by cDNAs that contain SL2 sequence. Analysis of their genomic arrangements indicates that >90% are downstream genes, falling in 790 distinct operons. We conclude that the genome contains at least 1000 operons, 2- 8 genes in length, that contain ~15% of C. elegans genes. Most of the operons have not been reported previously, and numerous examples of co-transcription of genes encoding functionally related proteins are evident. Inspection of the operon list should reveal heretofore unknown functional relationships.
2005-07-13 | E-SMDB-1388 | biostudies-arrayexpress
Project description:Magnetosomes are complex membrane organelles synthesized by magnetotactic bacteria (MTB) for navigation in the magnetic field. Their formation is tightly controlled by ˃30 specific magnetosome genes arranged in operons. The transcriptional organization of these operons in the model MTB Magnetospirillum gryphiswaldense MSR-1 has been long viewed to be simple, having each a convenient promoter that enable transcription of the operon as a single transcriptional unit. Here, by applying Cappable-seq and whole transcriptome shotgun RNA sequencing, we revealed multiple additional transcription starting sites (TSS) within the magnetosome operons mamABop, mms6op and mamXYop. Using experimental validation by bioluminescence reporter, we demonstrated that most of the new TSS are generated by biologically meaningful promoters. Furthermore, the knockout of the primary promoters in mamABop and mms6op resulted only in mild impairments of the magnetosome formation, suggesting that additional transcripts are indeed generated within these operons. Besides, we identified a strong promoter in the intergenic region within mamXYop, which transcript likely represents a non-coding RNA important for proper expression of the genes in this operon. The promoter sequences from MSR-1 are conservative in most magnetotactic Magnetospirillum spp., but not in other MTB, suggesting the functional conservation in magnetospirilla but independent evolution of the transcription circuits within the magnetosome operons in different phylogenetic groups. Taken together, our data suggest much more complex transcriptional architecture of the magnetosome operons in MSR-1 than deemed before and contribute to unraveling the fundamentals of magnetosome biosynthesis at transcriptional level.
2021-08-20 | GSE168986 | GEO
Project description:More than half of the protein-coding genes in bacteria are organized in polycistronic operons composed of two or more genes. Whether the operon organization maintains the stoichiometric expression of the genes within an operon remain under debate. In this study, we performed a label-free data-independent acquisition hyper reaction monitoring mass-spectrometry (HRM-MS) experiment to quantify the Escherichia coli proteome in exponential phase and quantified 93.6% of the cytosolic proteins, covering 67.9% and 56.0% of the translating polycistronic operons in BW25113 and MG1655 strains, respectively. We found the shorter operons tend to be more tightly controlled for stoichiometry than longer operons, and those operons for metabolic pathways are less controlled for stoichiometry compared with operons for protein complexes, illustrating the multifaceted nature of the operon-wise regulation: the operon-wise unified transcriptional level and gene-specific translational level. This multi-level regulation benefits the host by optimizing the efficiency of the productivity of metabolic pathways and maintenance of different types of protein complexes.
2019-07-01 | GSE122971 | GEO
Project description:KSRP knock-down and BMP2 treatment produce a largely overlapping reshape of the transcriptome in C2C12 cells. microRNAs (miRNAs) are essential regulators of development, physiology, and evolution with miRNA biogenesis being strictly controlled at multiple levels. Regulatory proteins, such as KH-type splicing regulatory protein (KSRP), modulate rates and timing of the enzymatic reactions responsible for maturation of select miRNAs from their primary transcripts in response to specific stimuli. Induction of myogenic miRNAs (myomiRs) is essential for muscle differentiation with KSRP phosphorylation being required to convey myogenic signals to enhanced myomiR maturation. Here we show that either KSRP silencing or Bone Morphogenetic Protein (BMP)2-signaling activation in mesenchimal C2C12 cells prevented myogenic differentiation while induced osteoblastic differentiation as revealed by the reshaping of the whole transcriptome analyzed by RNA deep-sequencing. The most striking feature common to both BMP2 signaling activation and KSRP silencing was a blockade of myomiR maturation. Our results demonstrate that phosphorylated SMAD proteins, the transducers of BMP signaling, associate with KSRP and block its interaction with primary-myomiRs. This, in turn, abrogates KSRP-dependent myomiR maturation with the knock-down of SMAD4, 5, and 9 being able to rescue KSRP function. SMAD-induced blockade of KSRP-dependent myomiR maturation, in parallel to the well known SMAD function on gene transcription, inhibits C2C12 cell differentiation into myofibers and contributes to orient cells towards osteoblast lineage. We propose that remodeling of co-regulatory complexes affecting primary-miRNA processing is a mechanism well suited to guide cell fate determination in eukaryotes. Total RNA was prepared from 1. untreated mock-transfected C2C12 cells; 2. BMP2-treated mock-transfected C2C12 cells; 3. untreated shKSRP-transfected C2C12 cells and analyzed by RNA-seq
2013-06-25 | E-GEOD-38907 | biostudies-arrayexpress
Project description:An operon is a set of adjacent genes which are transcribed into a single messenger RNA. Operons allow prokaryotes to efficiently circumvent environmental stresses. It is estimated that about 60% of the Mycobacterium tuberculosis genome is arranged into operons, which makes them interesting drug targets in the face of emerging drug resistance. We therefore developed COSMO - a tool for operon prediction in M. tuberculosis using RNA-seq data. We analyzed four algorithmic parameters and benchmarked COSMO against two top performing operon predictors. COSMO outperformed both predictors in its accuracy and in its ability to distinguish operons activated under distinct conditions.
2022-05-14 | GSE203032 | GEO