Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Combinatorial Gene Control02:33

Combinatorial Gene Control

8.5K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
8.5K
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

30.7K
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...
30.7K
Global Regulatory Systems01:28

Global Regulatory Systems

99
Global regulatory systems in bacteria enable rapid and coordinated responses to environmental changes by integrating sensory inputs with gene expression, ensuring efficient adaptation to fluctuating conditions. Key global regulatory mechanisms include regulons, two-component systems, sigma factors, and secondary messengers.Regulons and Global RegulatorsA regulon is a collection of genes and operons controlled by a common global regulator. These regulators enable bacteria to prioritize resource...
99
Gene Regulation During Sporulation01:17

Gene Regulation During Sporulation

125
Sporulation is a complex developmental process that allows certain Gram-positive bacteria, such as Bacillus subtilis and Clostridium species, to survive extreme environmental conditions. This process is tightly regulated by a series of signaling cascades and transcriptional controls, ensuring the formation of a highly resistant endospore.Sporulation is triggered by unfavorable conditions, such as nutrient depletion, and is governed by a phosphorelay system. One of the sensor kinases, such as...
125
Coordination of Gene Expression Processes in Bacteria01:29

Coordination of Gene Expression Processes in Bacteria

199
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...
199
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

6.7K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.7K

You might also read

Related Articles

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

Sort by
Same author

Evolutionary trajectories determine feasibility of collateral sensitivity-based antibiotic treatment strategies in critical bacterial pathogens.

Communications biology·2025
Same author

Modeling <math><msup><mrow><mi>σ</mi></mrow> <mrow><mi>E</mi></mrow></msup></math> biochemical network reveals context-dependent feedback control and kinetic constraints in the envelope stress response.

bioRxiv : the preprint server for biology·2025
Same author

Effects of cooling on <i>E. coli</i>'s DNA organization, structure, and gene expression.

Microbiology and molecular biology reviews : MMBR·2025
Same author

Rapid label-free identification of seven bacterial species using microfluidics, single-cell time-lapse phase-contrast microscopy, and deep learning-based image and video classification.

PloS one·2025
Same author

Culture-free detection of bacteria from blood for rapid sepsis diagnosis.

NPJ digital medicine·2025
Same author

Changes in Spo0A~P pulsing frequency control biofilm matrix deactivation.

PLoS computational biology·2025

Related Experiment Video

Updated: Sep 29, 2025

DNA-affinity-purified Chip DAP-chip Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
12:24

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

Published on: July 21, 2014

16.9K

Sequence-dependent model of genes with dual σ factor preference.

Ines S C Baptista1, Vinodh Kandavalli2, Vatsala Chauhan1

  • 1Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland.

Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms
|March 26, 2022
PubMed
Summary
This summary is machine-generated.

Escherichia coli uses dual sigma factors (σ70+38) to regulate gene expression during growth transitions. Promoter sequences quantitatively determine gene response, enabling predictable synthetic circuit design.

Keywords:
Dual σ factor preferenceE. coliFlow cytometryRNA-seqSequence-dependent gene expression model

More Related Videos

A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues
07:10

A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues

Published on: February 19, 2019

9.1K
A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae
10:18

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

Published on: April 25, 2015

10.5K

Related Experiment Videos

Last Updated: Sep 29, 2025

DNA-affinity-purified Chip DAP-chip Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
12:24

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

Published on: July 21, 2014

16.9K
A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues
07:10

A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues

Published on: February 19, 2019

9.1K
A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae
10:18

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

Published on: April 25, 2015

10.5K

Area of Science:

  • Microbiology
  • Molecular Biology
  • Systems Biology

Background:

  • Escherichia coli employs sigma factors to control gene expression during stress and growth phase changes.
  • Most genes respond to a single sigma factor, but ~5% exhibit dual specificity.
  • σ70 regulates housekeeping genes, while σ38 controls stationary phase and stress responses.

Purpose of the Study:

  • Investigate the regulatory mechanisms of genes with dual sigma factor (σ70 and σ38) preference in E. coli.
  • Determine the quantitative relationship between promoter sequences and gene expression levels in response to σ factor availability.
  • Develop a predictive model for dual-σ factor-dependent gene regulation.

Main Methods:

  • RNA sequencing (RNA-seq) to quantify gene expression.
  • Flow cytometry to measure cellular responses.
  • Sequence analysis to correlate promoter elements with gene regulation.
  • Development and validation of a sequence-dependent mathematical model.

Main Results:

  • Genes with dual σ70+38 preference are significantly upregulated during stationary growth, similar to σ38-specific genes.
  • A quantitative, sequence-dependent relationship exists between promoter characteristics and gene response to σ38 levels.
  • A validated model accurately predicts the dual sensitivity of σ70+38 genes across growth phases.

Conclusions:

  • Dual-specificity promoters provide predictable, sequence-dependent control over gene expression during growth phase transitions.
  • These findings offer insights into bacterial stress response and gene regulation.
  • σ70+38 gene regulatory elements can serve as building blocks for synthetic biology circuits with tunable sensitivity.