H-NS can facilitate specific DNA-binding by RNA polymerase in AT-rich gene regulatory regions.

Shivani S Singh,David C Grainger,William F Burkholder

doi:10.1371/journal.pgen.1003589

Shivani S Singh, David C Grainger + Show 1 more

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https://doi.org/10.1371/journal.pgen.1003589

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Journal: PLoS Genetics	Publication Date: Jun 20, 2013
Citations: 41	License type: CC BY 4.0

Affiliation: University of Birmingham

Abstract

Extremely AT-rich DNA sequences present a challenging template for specific recognition by RNA polymerase. In bacteria, this is because the promoter −10 hexamer, the major DNA element recognised by RNA polymerase, is itself AT-rich. We show that Histone-like Nucleoid Structuring (H-NS) protein can facilitate correct recognition of a promoter by RNA polymerase in AT-rich gene regulatory regions. Thus, at the Escherichia coli ehxCABD operon, RNA polymerase is unable to distinguish between the promoter −10 element and similar overlapping sequences. This problem is resolved in native nucleoprotein because the overlapping sequences are masked by H-NS. Our work provides mechanistic insight into nucleoprotein structure and its effect on protein-DNA interactions in prokaryotic cells.

Highlights

Transcription is initiated by binding of RNA polymerase to specific DNA sequences known as promoters [1]
We show that Histone-like Nucleoid Structuring (H-NS) protein can facilitate correct recognition of a promoter by RNA polymerase in AT-rich gene regulatory regions
In the context of native nucleoprotein this self-competition is negated. This is because RNA polymerase has instead to compete with H-NS (Figure 6)

Summary

Introduction

Transcription is initiated by binding of RNA polymerase to specific DNA sequences known as promoters [1]. Following promoter recognition the resulting complex undergoes a process of isomerisation. 14 base pairs (bp) of DNA, close to the transcription start site, are unwound [2]. It has long been known that promoter unwinding is facilitated by the weak base stacking interactions associated with AT-rich DNA. The eukaryotic TATA box (59-TATAAA-39) is unwound during transcription initiation [4]. Because DNA elements recognised by RNA polymerase are AT-rich, chromosomal regions, where DNA AT-content is unusually high, prove challenging templates for recognition. RNA polymerase may bind cryptic promoters [6] or initiate transcription promiscuously [7]

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