Different organization of upstream regulatory region between <i>E. coli</i> and <i>K. pneumoniae</i>.

<p>(A) Venn diagram showing orthologous genes and species-specific genes between <i>E. coli</i> and <i>K. pneumoniae</i>. (B) 4 different types of promoter regions, and their numbers identified in two species. (C) Schematic drawing of annotated TSSs and sequence comparison of regulatory region upstream of <i>lpd</i>. (D) Length difference between the pairs of comparable 5′ UTR. (E) Comparison of sequence conservation of promoter, 5′ UTR, and ORF regions. (F) Sequence conservation of genomic regions surrounding translation start sites.</p

Comparison analysis of orthologous sRNAs.

<p>(A) Expression of RNA-binding protein <i>hfq</i> (B) Sequence conservation of regulatory region upstream of <i>hfq</i> ORF, including promoter, TSS and 5′ UTR. (C) Conservation and expression of non-coding regulatory sRNAs, <i>rprA</i>, <i>arcZ</i> and <i>sgrS</i>. (D) Sequence comparison analysis of <i>rprA</i> and <i>arcZ</i> regulating translation of <i>rpoS</i>. (E) Sequence comparison analysis of <i>sgrS</i> regulating translation of <i>ptsG</i> and <i>manX</i>.</p

TSS annotation and structure of promoter region and 5′ UTR.

<p>(A) Number of TSSs assigned per annotated genes. (B) Distribution of 5′ UTR lengths for <i>E. coli</i> and <i>K. pneumoniae</i>, and the Shine-Dalgarno sequence motif. (C) Sequence motif of promoter region containing −10 and −35 boxes. (D) Conservation of RpoD amino acid sequences of 5 species in gammaproteobacteria and 3 other species belonging to proteobacteria. (E) Di-nucleotide preference near the TSS site.</p

Experimentally determined TSSs and their association with annotated genes.

<p>(A) Genome-wide TSS mapped onto <i>E. coli</i> and <i>K. pneumoniae</i> genome annotation. (B) Number of <i>E. coli</i> sRNAs detected with 5 TSS datasets generated by different methods. (C) Number of sRNAs detected from <i>E. coli</i> and <i>K. pneumoniae</i> during the exponential growth. (D) Schematic drawing of annotated TSSs assigned to orthologous <i>micF</i> sRNA and coding genes surrounding <i>micF</i> in <i>E. coli</i> and <i>K. pneumoniae</i>. (E) Schematic drawing of annotated TSSs assigned to <i>K. pneumoniae</i> sRNA, <i>rnai</i>, and coding genes near <i>rnai</i>.</p