ArticlePLoS genetics2015
Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
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106 citing papers in PubMed, 192 citations in OpenAlex.
- Long-range mRNA folding shapes expression and sequence of bacterial genes.Molecular cell · 2026Article
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- Bacterial gene 5' ends have unusual mutation rates that can mislead tests of selection.PLoS biology · 2025Article
- Long-range mRNA folding shapes expression and sequence of bacterial genes.bioRxiv : the preprint server for biology · 2025Article
- Innovative design and comprehensive characterization of a valine-enhanced lipid nanoparticle-coated mRNA vaccine targeting the SARS-CoV-2 S-RBD antigen.Scientific reports · 2025Article
- m6A modification is incorporated into bacterial mRNA without specific functional benefit.Nucleic acids research · 2025Article
- Increasing recombinant protein production in E. coli via FACS-based selection of N-terminal coding DNA libraries.The FEBS journal · 2025Article
- The human mitochondrial mRNA structurome reveals mechanisms of gene expression.Science (New York, N.Y.) · 2024Article
- RNase E searches for cleavage sites in RNA by linear diffusion: direct evidence from single-molecule FRET.Nucleic acids research · 2024Article
- Direct and indirect control of Rho-dependent transcription termination by theRNA (New York, N.Y.) · 2024Article
- RNA-seq reveals multifaceted gene expression response to Fab production in Escherichia coli fed-batch processes with particular focus on ribosome stalling.Microbial cell factories · 2024Article
- Decoding stoichiometric protein synthesis inBiophysical reports · 2023Article
- Sequence specificity defines the effectiveness of PPMOs targetingAntimicrobial agents and chemotherapy · 2023Article
- Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes inRNA (New York, N.Y.) · 2023Article
- Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.Nucleic acids research · 2023Article
- Role of the 5' end phosphorylation state for small RNA stability and target RNA regulation in bacteria.Nucleic acids research · 2023Article
- RNase Y Autoregulates Its Synthesis inMicroorganisms · 2023Article
- Article
- Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria.Science (New York, N.Y.) · 2022Article
- Precise tuning of bacterial translation initiation by non-equilibrium 5'-UTR unfolding observed in single mRNAs.Nucleic acids research · 2022Article
46 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation.
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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.