Related Experiment Video
Updated: Dec 30, 2025
10:42
RNA Purification from Intracellularly Grown Listeria monocytogenes in Macrophage Cells
Published on: June 4, 2016
9.7K
Genome-wide identification of Listeria monocytogenes CodY-binding sites
Rajesh Biswas1, Abraham L Sonenshein1, Boris R Belitsky1
1Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
Molecular Microbiology
|January 17, 2020
Summary
CodY, a global regulator in Listeria monocytogenes, binds to thousands of DNA regions, primarily within genes. This study maps these binding sites to understand CodY
Area of Science:
- Microbiology
- Genetics
- Molecular Biology
Background:
- CodY acts as a global transcriptional regulator in Listeria monocytogenes, influencing numerous genes and operons.
- Understanding CodY's DNA-binding landscape is crucial for deciphering gene regulation in this pathogen.
Purpose of the Study:
- To identify genome-wide DNA regions bound by CodY in Listeria monocytogenes in vitro.
- To characterize the binding sites and propose a model for CodY-DNA interaction.
Main Methods:
- In vitro DNA affinity purification combined with massively parallel sequencing (IDAP-Seq).
- Strand-specific analysis for single-nucleotide resolution of binding sites.
- Gel shift and DNase I footprinting assays for validation.
Main Results:
- Over 2,000 CodY-binding regions identified, with 388 strongest sites selected for analysis.
- Most CodY-binding sites were located within the coding regions of genes.
- A previously noted binding site in the prfA gene was found to be weaker than many others.
Conclusions:
- CodY exhibits extensive DNA binding across the Listeria monocytogenes genome, with a preference for intragenic regions.
- The findings provide insights into CodY's regulatory mechanisms and its interaction with DNA, including potential roles in virulence gene regulation.
Related Concept Videos
01:49Conserved Binding Sites
5.0K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.0K
01:03Single-Strand DNA Binding Proteins
16.4K
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
16.4K
01:29Modern Molecular Taxonomy
513
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
513