Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

The Eukaryotic Promoter Region

The Eukaryotic Promoter Region

The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...

The Eukaryotic Promoter Region

The Eukaryotic Promoter Region

The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...

Prokaryotic Transcriptional Activators and Repressors

Prokaryotic Transcriptional Activators and Repressors

The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
Transcription of prokaryotic...

Prokaryotic Transcriptional Activators and Repressors

Prokaryotic Transcriptional Activators and Repressors

The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
Transcription of prokaryotic...

Prokaryotic Gene Structure and Organization

Prokaryotic Gene Structure and Organization

Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...

Coordination of Gene Expression Processes in Bacteria

Coordination of Gene Expression Processes in Bacteria

The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Biocatalytic potential of Ensifer adhaerens S-5 D-Carbamoylase: Insights from in silico and in vitro analyses.

Journal, genetic engineering & biotechnology·2026

Same author

Is the NHS ready for a four day week?

BMJ (Clinical research ed.)·2025

Same author

Reactive Molecules in Cigarette Smoke: Rethinking Cancer Therapy.

Biotech (Basel (Switzerland))·2025

Same author

The green algae CO<sub>2</sub> concentrating mechanism and photorespiration jointly operate during acclimation to low CO<sub>2</sub>.

Nature communications·2025

Same author

Structural Analysis and Substrate Specificity of D-Carbamoylase from <i>Pseudomonas</i>.

Biotech (Basel (Switzerland))·2024

Same author

Alternative electron pathways of photosynthesis power green algal CO2 capture.

The Plant cell·2024

Search research articles

Related Experiment Video

Updated: Jul 5, 2026

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

Published on: July 21, 2014

Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes.

Michael Dekhtyar¹, Amelie Morin, Vehary Sakanyan

¹University of Tver, 33 Jelyabova, 170000 Tver, Russia. Michael.Dekhtyar@tversu.ru

BMC Bioinformatics

|May 13, 2008

Summary

A new algorithm identifies strong bacterial promoter candidates using specific DNA patterns. This computational tool aids in analyzing bacterial genomes, particularly those with lower A+T content, for enhanced gene expression studies.

More Related Videos

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Published on: June 28, 2018

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

Related Experiment Videos

Last Updated: Jul 5, 2026

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

Published on: July 21, 2014

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Published on: June 28, 2018

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

Area of Science:

Bioinformatics
Genomics
Molecular Biology

Background:

Bacterial promoters exhibit unique characteristics distinct from other promoters.
These differences present an opportunity for developing computational tools for promoter identification.
Bioinformatics has not fully exploited these unique promoter features.

Purpose of the Study:

To develop a computational tool for identifying strong bacterial promoter candidates.
To exploit unique bacterial promoter characteristics for improved gene expression analysis.
To validate the predictive accuracy of the developed algorithm.

Main Methods:

Developed a triad pattern algorithm for predicting strong promoter candidates.
Algorithm matches UP-element, -35, and -10 boxes specific to sigma70 factors.
Analyzed 43 bacterial genomes and validated predictions using cell-free expression assays in *Thermotoga maritima*.

Main Results:

The triad pattern algorithm successfully predicts strong promoter candidates in bacterial genomes.
Promoter candidate frequency correlates with the A+T content of the DNA.
Experimental validation confirmed the accuracy of in silico predictions for *Thermotoga maritima*.
Identified strong promoters associated with various cellular functions, including translation and energy metabolism.

Conclusions:

The triad pattern algorithm is effective for bacterial genomes with <62% A+T content.
This tool enhances the investigation of global gene expression in bacteria.
Opens new avenues for studying medically and economically significant bacterial promoters.