ArticlePLoS genetics2018
Extensive reshaping of bacterial operons by programmed mRNA decay.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 77 citations in OpenAlex.
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- Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning.Nature communications · 2024Article
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- Co-transcriptional gene regulation in eukaryotes and prokaryotes.Nature reviews. Molecular cell biology · 2024Review
- Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species.Microbiology spectrum · 2024Article
- Cross-evaluation of E. coli's operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons.Cell systems · 2024Article
- Selective RNA Processing and Stabilization are Multi-Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Methodologies for bacterial ribonuclease characterization using RNA-seq.FEMS microbiology reviews · 2023Review
- Complex Regulation of Gamma-Hemolysin Expression Impacts Staphylococcus aureus Virulence.Microbiology spectrum · 2023Article
- Improved RNA stability estimation indicates that transcriptional interference is frequent in diverse bacteria.Communications biology · 2023Article
- Envelope Stress Activates Expression of the Twin Arginine Translocation (Tat) System in Salmonella.Microbiology spectrum · 2022Article
- Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome.Nucleic acids research · 2022Article
- Synthetic 3'-UTR valves for optimal metabolic flux control in Escherichia coli.Nucleic acids research · 2022Article
- Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains.PLoS genetics · 2022Article
- Article
- OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data.PLoS computational biology · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.