Conservation and divergence in transcriptional regulation by σ-factors. (a) Clustering σ-factor binding patterns revealed conserved and divergent transcriptional regulation of 2,876 orthologous genes. (b) crp is regulated by σ70 and σ38 in both species, showing regulation conservation. (c) In Esherichia coli, cutA is a part of the dcuA-cutA-dipZ transcription unit (TU) and is regulated by σ70 and σ38, while cutA in Klebsiella pneumoniae is the first gene in its TU, and is directly bound by σ70. (d) In K. pneumoniae, panD is a part of the panBCD TU, which is regulated by σ70. However, in E. coli, panD is separated from panBC by yadD, making another distinct TU. These two TUs are both regulated by σ70. (e) A genomic region containing ydeA and marC in both species was inverted, and this genomic inversion was accompanied by a transcription regulation switch between σ70 and σ38.