Upstream sequence elements required for NarL-mediated activation of transcription from the narGHJI promoter of Escherichia coli

Abstract

Transcription of the narGHJI operon (encoding nitrate reductase) in Escherichia coli is primarily dependent on the activation of the pleiotropic transacting factor Fnr, which interacts with the promoter through a cis element (Fnr box) located near the transcription start site. Further stimulation of transcription occurs in the presence of nitrate and is dependent on activation of the transacting factor NarL and a cis-acting sequence (NarL box) located approximately 200 base pairs upstream from the transcription start site. To define the structure of the NarL box, alterations in the NarL box region, generated by saturation mutagenesis of the sequence from positions -184 to -202 in the narGHJI promoter of a narG::lacZ fusion-bearing plasmid, were analyzed for their effects on NarL-mediated stimulation of transcription. Single base substitutions that significantly reduced the NarL-mediated stimulation were restricted to a 6-base sequence, TACTCC, located at positions -193 to -198 in the narGHJI promoter. When 2 bases were modified, NarL-mediated stimulation was severely reduced when one or both alterations were located within the 6-base sequence. Attempts to restore NarL-mediated stimulation with an inverted NarL box were not successful. Although previous studies suggested that NarL-mediated stimulation of transcription may occur by a DNA looping mechanism, the results presented here demonstrate that it does not involve the passive formation of a simple DNA loop. Replacement of 94 or 108 bases of the approximately 150 base sequence between the Fnr box and the NarL box with an unrelated sequence resulted in elimination of NarL-mediated stimulation of transcription. Furthermore, shifting of most of the intervening sequence or defined segments of the sequence by 4 bases while maintaining the position of the NarL box relative to sequences required for Fnr-dependent, anaerobic transcription also eliminated the NarL-mediated stimulation. We conclude that in addition to the 6-base NarL box located on a specific face of the promoter DNA, the stimulation of transcription by NarL requires some specific sequences and/or higher order structure specified by the DNA that separates the NarL box from the Fnr box.