Promoter use by sigma 38 (rpoS) RNA polymerase. Amino acid clusters for DNA binding and isomerization.

Sigma(38) is a non-essential but highly homologous member of the sigma(70) family of transcription factors. In vitro mutagenesis and in vivo screening were used to identify 22 critical amino acids in the promoter interaction domain of Escherichia coli sigma(38). Electrophoretic mobility shift assay studies showed that residues involved in duplex DNA binding largely segregated into distinct regions that coincided with those of sigma(70). However, the majority of these amino acids were in non-conserved positions. Analysis indicates that this region of the two sigma(s) probably has a common overall organization but differs in how its amino acids are used to form functional open complexes. Placement of the mutations on the known sigma(70) holoenzyme structure shows two clusters; one appears to be used for duplex DNA recognition and the other for the subsequent isomerization events. Permanganate assays for DNA melting support this view.