Related Experiment Video
Updated: Jul 14, 2026
08:34
MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
Published on: February 23, 2021
Target identification of small noncoding RNAs in bacteria.
Jörg Vogel1, E Gerhart H Wagner
1Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany. vogel@mpiib-berlin.mpg.de
Current Opinion in Microbiology
|June 19, 2007
Summary
Identifying bacterial small noncoding RNA (sRNA) targets is crucial. This review covers diverse strategies, including transcriptomics, computational predictions, and reporter gene fusions, for finding and validating sRNA targets in bacteria.
Area of Science:
- Microbiology
- Molecular Biology
- Genetics
Background:
- Small noncoding RNAs (sRNAs) are abundant in bacteria like Escherichia coli.
- Known sRNAs regulate gene expression by interacting with messenger RNAs (mRNAs) or proteins.
- Numerous bacterial sRNAs with unknown functions necessitate urgent target identification.
Purpose of the Study:
- To review diverse strategies for identifying and validating bacterial sRNA targets.
- To highlight methods for understanding the regulatory roles of uncharacterized sRNAs.
Main Methods:
- Pulse-expression of sRNAs followed by global transcriptome analysis (microarrays).
- Application of novel biocomputational prediction algorithms.
- Utilizing green fluorescent protein (GFP) reporter gene fusions for target validation.
Main Results:
- The review consolidates various experimental and computational approaches.
- It emphasizes the importance of validation for identified targets.
- Strategies discussed enable the characterization of sRNA regulatory networks.
Conclusions:
- Effective strategies are available for identifying and validating bacterial sRNA targets.
- These methods are essential for elucidating the functions of numerous uncharacterized sRNAs.
- Understanding sRNA targets advances knowledge of bacterial gene regulation.
Related Concept Videos
01:23Types 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...
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...
02:24Ribosome Profiling
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
01:29Translational 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,...
00:43Bacterial RNA Polymerase
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
01:23RNA 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...
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...
02:15Experimental RNAi
RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...