Related Experiment Video

Updated: Jun 24, 2025

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
08:34

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria

Published on: February 23, 2021

6.7K

Cooperation of regulatory RNA and the RNA degradosome in transcript surveillance

Katarzyna J Bandyra1,2, Kathrin S Fröhlich3,4, Jörg Vogel3,5

  • 1Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.

Nucleic Acids Research
|June 6, 2024
PubMed

Insights

Regulatory small RNA (sRNA) MicC targets Salmonella ompD mRNA for degradation by RNase E. This process is facilitated by the 30S translation pre-initiation complex, enabling rapid gene expression control.

Area of Science:

  • Microbiology
  • Molecular Biology
  • RNA Biology

Background:

  • Salmonella outer membrane porin D (OmpD) is crucial for bacterial survival.
  • Small regulatory RNAs (sRNAs) play key roles in bacterial gene regulation.
  • RNase E is a major bacterial ribonuclease involved in mRNA degradation.

Purpose of the Study:

  • To elucidate the mechanism by which the sRNA MicC triggers the degradation of ompD mRNA.
  • To investigate the role of the 30S translation pre-initiation complex (PIC) in sRNA-mediated mRNA cleavage.
  • To understand the involvement of the RNA degradosome in this regulatory pathway.

Main Methods:

  • In vitro biochemical assays to study RNA-RNA interactions and ribonuclease activity.
  • Recruitment of ompD mRNA into the 30S PIC.
  • Analysis of RNase E activity in the presence of degradosome components.

Main Results:

  • MicC sRNA base-pairs with ompD mRNA, creating a target site for RNase E.
  • Cleavage occurs downstream of the pairing site, leading to ompD mRNA destruction.
  • The 30S PIC facilitates access of the cleavage site to RNase E, suggesting a role in mRNA surveillance.
  • Degradosome components, including RNase E, are essential for efficient cleavage, involving substrate capture and handover.

Conclusions:

  • The 30S PIC acts as a platform for sRNA-mediated mRNA degradation by the RNA degradosome.
  • This mechanism allows for rapid and efficient termination of gene expression in response to regulatory signals.
  • Findings reveal a novel layer of post-transcriptional gene regulation in Salmonella.

More Related Videos

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip13:34

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

Published on: September 29, 2012

27.6K
Isolation of Cognate RNA-protein Complexes from Cells Using Oligonucleotide-directed Elution10:53

Isolation of Cognate RNA-protein Complexes from Cells Using Oligonucleotide-directed Elution

Published on: January 16, 2017

9.0K

Related Concept Videos

Nuclear Export of mRNA02:31

Nuclear Export of mRNA

Before mRNAs are exported to the cytoplasm, it is crucial to check each mRNA for structural and functional integrity. Eukaryotic cells use several different mechanisms, collectively known as mRNA surveillance, to look for irregularities in mRNAs. Irregular or aberrant mRNA are rapidly degraded by various enzymes. If a defective mRNA escapes the surveillance, it would be translated into a protein which would either be non-functional or not function properly. One of the primary irregularities in...
7.7K
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
889
Types of RNA01:20

Types of RNA

Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in regulating gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA Performs Diverse...
5.7K
RNA Interference01:23

RNA Interference

RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
26.0K
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
22.6K
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
10.6K