Related Experiment Video

Updated: Sep 28, 2026

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

Interdomain linkers of homologous response regulators determine their mechanism of action

Don Walthers1, Van K Tran, Linda J Kenney

  • 1Department of Molecular Microbiology & Immunology L220, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97201-3098, USA.

Journal of Bacteriology
|December 18, 2002
PubMed

Insights

OmpR and PhoB response regulators use different mechanisms for gene expression control. Their N-terminal phosphorylation and interdomain linker are crucial for activating the C-terminal DNA binding domain.

Area of Science:

  • Molecular Biology
  • Bacterial Gene Regulation
  • Protein-DNA Interactions

Background:

  • OmpR and PhoB are homologous response regulators controlling gene expression via phosphorylation.
  • Both proteins possess N-terminal phosphorylation domains and C-terminal DNA-binding domains linked by flexible regions.
  • Despite structural similarities, they exhibit distinct activation mechanisms upon N-terminal phosphorylation.

Purpose of the Study:

  • To investigate the mechanistic basis for the differential regulation of OmpR and PhoB effector domains.
  • To determine the role of the interdomain linker in mediating N-terminal phosphorylation effects on DNA binding.
  • To explore the functional requirements for productive interaction with RNA polymerase.

Main Methods:

  • Construction and analysis of OmpR-PhoB chimeras.
  • Comparative studies of phosphorylation-dependent DNA binding affinities.
  • Assessment of chimera interactions with RNA polymerase.

Main Results:

  • The N-terminal phosphorylation domain requires its cognate interdomain linker for effective regulation of the C-terminal effector domain.
  • Phosphorylation of OmpR stimulates C-terminal DNA binding, while PhoB phosphorylation relieves C-terminal inhibition.
  • The isolated C-terminal domain of OmpR alone is insufficient for efficient RNA polymerase interaction.

Conclusions:

  • The interdomain linker is a critical determinant for the distinct activation mechanisms of OmpR and PhoB.
  • Specific interactions between the N-terminus, linker, and C-terminus are essential for proper effector domain function.
  • Efficient gene regulation by OmpR involves coordinated interactions beyond just DNA binding.

More Related Videos

Identification of Post-translational Modifications of Plant Protein Complexes10:07

Identification of Post-translational Modifications of Plant Protein Complexes

Published on: February 22, 2014

Detection of Heterodimerization of Protein Isoforms Using an in Situ Proximity Ligation Assay09:18

Detection of Heterodimerization of Protein Isoforms Using an in Situ Proximity Ligation Assay

Published on: October 20, 2018

Related Concept Videos

Global Regulatory Systems01:28

Global Regulatory Systems

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...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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 dimers that...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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 dimers that...
Transducer Mechanism: Enzyme-Linked Receptors01:27

Transducer Mechanism: Enzyme-Linked Receptors

Enzyme-linked receptors are cell-surface receptors acting as an enzyme or associating with an enzyme intracellularly. They make excellent drug targets. Drugs can bind to the extracellular ligand-binding domain or directly affect their enzymatic domain and alter their activity.
Major types that are helpful drug targets include:
Signal Transduction: Overview01:26

Signal Transduction: Overview

Cells respond to many types of information, often through receptor proteins positioned on the membrane. They respond to chemical signals, such as hormones, neurotransmitters, and other signaling molecules, initiating a series of molecular reactions to produce an appropriate response. This is called signal transduction. Cells also coordinate different responses elicited by the same signaling molecule via mediators, allowing molecular cross-talk.
Typically, signal transduction involves three...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...