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Translational Regulation

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 RNA

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...

Types of RNA

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...

Bacterial RNA Polymerase

Bacterial 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...

Bacterial RNA Polymerase

Bacterial 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...

RNA Interference

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...

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Related Experiment Video

Updated: May 13, 2026

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

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

Published on: February 23, 2021

Computational small RNA prediction in bacteria.

Jayavel Sridhar¹, Paramasamy Gunasekaran

¹UGC-Networking Resource Centre in Biological Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, TN, India.

Bioinformatics and Biology Insights

|March 22, 2013

Summary

Bacterial small RNAs (sRNAs) are crucial gene regulators with diverse roles. Computational methods now efficiently identify these essential molecules in bacteria, aiding research.

Keywords:

base composition comparative genomics ncRNA sRNA prediction structure stability transcriptional signal

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Published on: January 27, 2021

Area of Science:

Microbiology
Genomics
Bioinformatics

Background:

Bacterial small RNAs (sRNAs) are increasingly recognized for their critical regulatory functions beyond gene expression, impacting environmental sensing and pathogenesis.
Historically, detecting noncoding transcripts like sRNAs was challenging using traditional genetic screening methods.
The vast number of publicly available prokaryotic genome sequences has revolutionized the discovery of bacterial sRNAs.

Purpose of the Study:

To comprehensively review and assess small RNA prediction methods and tools developed over the last decade.
To evaluate the attributes, compatibility, and prediction accuracy of various computational approaches for identifying bacterial sRNAs.
To highlight how computational screening has streamlined the process of sRNA identification in bacteria.

Main Methods:

Discussing four major computational strategies for predicting sRNA locations in bacterial genomes: comparative genomics, secondary structure/thermodynamic stability analysis, 'Orphan' transcriptional signals, and ab initio methods.
Detailing the application of these computational tools for locating putative genomic sRNAs.
Emphasizing the subsequent experimental validation of computationally identified transcripts.

Main Results:

Identification of numerous computational methods and tools for bacterial sRNA prediction.
Assessment of these tools based on their predictive performance, compatibility, and specific attributes.
Demonstration of the significant simplification of bacterial sRNA identification through computational screening.

Conclusions:

Computational screening has become an indispensable and efficient approach for identifying bacterial small RNAs.
A variety of computational methods exist, each with unique strengths, for predicting sRNA locations.
The ongoing development and assessment of these tools are crucial for advancing our understanding of bacterial regulatory networks.