Bacterial promoter repression by DNA looping without protein-protein binding competition

Nicole A. Becker, Alexander M. Greiner, Justin P. Peters, L James Maher III

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

The Escherichia coli lactose operon provides a paradigm for understanding gene control by DNA looping where the lac repressor (LacI) protein competes with RNA polymerase for DNA binding. Not all promoter loops involve direct competition between repressor and RNA polymerase. This raises the possibility that positioning a promoter within a tightly constrained DNA loop is repressive per se, an idea that has previously only been considered in vitro. Here, we engineer living E. coli bacteria to measure repression due to promoter positioning within such a tightly constrained DNA loop in the absence of protein-protein binding competition. We show that promoters held within such DNA loops are repressed ∼100-fold, with up to an additional ∼10-fold repression (∼1000-fold total) dependent on topological positioning of the promoter on the inner or outer face of the DNA loop. Chromatin immunoprecipitation data suggest that repression involves inhibition of both RNA polymerase initiation and elongation. These in vivo results show that gene repression can result from tightly looping promoter DNA even in the absence of direct competition between repressor and RNA polymerase binding.

Original languageEnglish (US)
Pages (from-to)5495-5504
Number of pages10
JournalNucleic Acids Research
Volume42
Issue number9
DOIs
StatePublished - 2014

Fingerprint

Protein Binding
DNA-Directed RNA Polymerases
DNA
Lac Repressors
Proteins
Escherichia coli
Repressor Proteins
Lac Operon
Chromatin Immunoprecipitation
Genes
Bacteria

ASJC Scopus subject areas

  • Genetics

Cite this

Bacterial promoter repression by DNA looping without protein-protein binding competition. / Becker, Nicole A.; Greiner, Alexander M.; Peters, Justin P.; Maher III, L James.

In: Nucleic Acids Research, Vol. 42, No. 9, 2014, p. 5495-5504.

Research output: Contribution to journalArticle

Becker, Nicole A. ; Greiner, Alexander M. ; Peters, Justin P. ; Maher III, L James. / Bacterial promoter repression by DNA looping without protein-protein binding competition. In: Nucleic Acids Research. 2014 ; Vol. 42, No. 9. pp. 5495-5504.
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