Structural basis for promoter-10 element recognition by the bacterial RNA polymerase σ subunit

Cell. 2011 Dec 9;147(6):1257-69. doi: 10.1016/j.cell.2011.10.041. Epub 2011 Dec 1.

Abstract

The key step in bacterial promoter opening is recognition of the -10 promoter element (T(-12)A(-11)T(-10)A(-9)A(-8)T(-7) consensus sequence) by the RNA polymerase σ subunit. We determined crystal structures of σ domain 2 bound to single-stranded DNA bearing-10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every -10 element nucleotide. Base-specific interactions occur primarily with A(-11) and T(-7), which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the -10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by σ. These results provide a detailed structural basis for the critical roles of A(-11) and T(-7) in promoter melting and reveal important insights into the initiation of transcription bubble formation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism*
  • Base Pairing
  • Base Sequence
  • Crystallography, X-Ray
  • DNA, Single-Stranded / chemistry
  • DNA, Single-Stranded / metabolism*
  • DNA-Directed RNA Polymerases / chemistry
  • DNA-Directed RNA Polymerases / metabolism
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / metabolism
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular
  • Promoter Regions, Genetic*
  • Sigma Factor / chemistry*
  • Sigma Factor / metabolism*
  • Thermus / metabolism*

Substances

  • Bacterial Proteins
  • DNA, Single-Stranded
  • Escherichia coli Proteins
  • Sigma Factor
  • RNA polymerase sigma 70
  • DNA-Directed RNA Polymerases

Associated data

  • PDB/3UGO
  • PDB/3UGP