Characterization of a σ54-dependent promoter in the glnA gene. (A). Genomic context of glnA gene in the X. fastidiosa chromosome indicating other genes associated with nitrogen metabolism. (B). Determination of the transcription start site of glnA by primer extension assay. Reactions were performed using total RNA from J1a12 and rpoN strains and the [γ-32P]ATP-labeled primer XF1842EXT. A DNA sequencing ladder of phage M13mp18 was used as molecular size marker. The arrow indicates the band corresponding to the extended fragment. (C). Nucleotide sequence of X. fastidiosa glnA promoter region. The transcriptional start site determined by primer extension analysis and the -12 and -24 conserved sequence elements of the σ54-dependent promoter are boxed. The re-annotated initiation codon (ATG) and the putative IHF binding site are underlined. The predicted Shine-Dalgarno sequence is double underlined. The putative NtrC binding sites are indicated by dashed lines.