Gene silencing by H-NS from distal DNA site

• Published in: Molecular microbiology Vol. 86; no. 3; pp. 707 - 719
• Main Authors: Shin, Minsang, Lagda, Arvin Cesar, Lee, Jae Woong, Bhat, Abhay, Rhee, Joon Haeng, Kim, Jeong-Sun, Takeyasu, Kunio, Choy, Hyon E.
• Format: Journal Article
• Language: English
• Published: Oxford Blackwell Publishing Ltd 01-11-2012; Blackwell
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Binding Sites; Biological and medical sciences; Deoxyribonucleic acid; DNA; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; E coli; Escherichia coli; Escherichia coli - chemistry; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Fundamental and applied biological sciences. Psychology; Gene Expression Regulation, Bacterial; Gene Silencing; Genes; Microbiology; Molecules; Phosphoproteins - chemistry; Phosphoproteins - genetics; Phosphoproteins - metabolism; Promoter Regions, Genetic; Protein Binding; Proteins; RNA polymerase; Transcription, Genetic; Gene silencing
• ISSN: 0950-382X; 1365-2958
• DOI: 10.1111/mmi.12012

Summary
In the modern concept of gene regulation, ‘DNA looping’ is the most common underlying mechanism in the interaction between RNA polymerase (RNAP) and transcription factors acting at a distance. This study demonstrates an additional mechanism by which DNA‐bound proteins communicate with each other, by analysing the bacterial histone‐like nucleoid‐structuring protein (H‐NS), a general transcriptional silencer. The LEE5 promoter (LEE5p) of enteropathogenic Escherichia coli was used as a model system to investigate the mechanism of H‐NS‐mediated transcription repression. We found that H‐NS represses LEE5p by binding to a cluster of A tracks upstream of −114, followed by spreading to a site at the promoter through the oligomerization of H‐NS molecules. At the promoter, the H‐NS makes a specific contact with the carboxy terminal domain of the α subunit of RNAP, which prevents the processing of RNAP–promoter complexes into initiation‐competent open promoter complexes, thereby regulating LEE5p from distance.