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Related Concept Videos

Translational Regulation01:29

Translational Regulation

Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
Types of RNA01:23

Types of RNA

Overview
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 the regulation of 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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Leaky Scanning02:28

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
Riboswitches01:56

Riboswitches

Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...

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Related Experiment Video

Updated: Jun 4, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Accessibility and evolutionary conservation mark bacterial small-rna target-binding regions.

Asaf Peer1, Hanah Margalit

  • 1Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel.

Journal of Bacteriology
|February 1, 2011
PubMed
Summary

Bacterial small noncoding RNAs (sRNAs) regulate gene expression by base pairing with mRNA. Their conserved and accessible target-binding regions can now be computationally identified to find sRNA targets.

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MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
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Last Updated: Jun 4, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

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

Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • Bacterial small noncoding RNAs (sRNAs) are key posttranscriptional regulators.
  • sRNAs modulate gene expression by binding to mRNA targets.
  • Understanding sRNA-target interactions is crucial for deciphering bacterial regulatory networks.

Purpose of the Study:

  • To identify conserved and accessible regions in bacterial sRNAs responsible for mRNA binding.
  • To develop a computational method for predicting sRNA target-binding sites.
  • To enhance the discovery of sRNA targets.

Main Methods:

  • Compilation of experimentally validated sRNA target-binding regions.
  • Systematic analysis of evolutionary conservation and accessibility of these regions.
  • Development and validation of a computational prediction tool.

Main Results:

  • sRNA target-binding regions are significantly more conserved and accessible than random sequences.
  • The computational method achieves high specificity and sensitivity in identifying these regions.
  • Predicted regions accurately correspond to known sRNA-mRNA interaction sites.

Conclusions:

  • Evolutionary conservation and accessibility are key features of sRNA target-binding regions.
  • Computational prediction of these regions aids in identifying novel sRNA targets.
  • This approach facilitates a deeper understanding of bacterial gene regulation by sRNAs.