A Role for the RNA Polymerase Gene Specificity Factor σ(54) in the Uniform Colony Growth of Uropathogenic Escherichia coli

The canonical function of a bacterial sigma (σ) factor is to determine the gene specificity of the RNA polymerase (RNAP). In several diverse bacterial species, the σ(54) factor uniquely confers distinct functional and regulatory properties on the RNAP. A hallmark feature of the σ(54)-RNAP is the obligatory requirement for an activator ATPase to allow transcription initiation. Different activator ATPases couple diverse environmental cues to the σ(54)-RNAP to mediate adaptive changes in gene expression. Hence, the genes that rely upon σ(54) for their transcription have a wide range of different functions suggesting that the repertoire of functions performed by genes, directly or indirectly affected by σ(54), is not yet exhaustive. By comparing the growth patterns of prototypical enteropathogenic, uropathogenic, and nonpathogenic Escherichia coli strains devoid of σ(54), we uncovered that the absence of σ(54) results in two differently sized colonies that appear at different times specifically in the uropathogenic E. coli (UPEC) strain. Notably, UPEC bacteria devoid of individual activator ATPases of the σ(54)-RNAP do not phenocopy the σ(54) mutant strain. Thus, it seems that σ(54)’s role as a determinant of uniform colony appearance in UPEC bacteria represents a putative non-canonical function of σ(54) in regulating genetic information flow. IMPORTANCE RNA synthesis is the first step of gene expression. The multisubunit RNA polymerase (RNAP) is the central enzyme responsible for RNA synthesis in bacteria. The dissociable sigma (σ) factor subunit directs the RNAP to different sets of genes to allow their expression in response to various cellular needs. Of the seven σ factors in Escherichia coli and related bacteria, σ(54) exists in a class of its own. This study has uncovered that σ(54) is a determinant of the uniform growth of uropathogenic E. coli on solid media. This finding suggests a role for this σ(54) in gene regulation that extends beyond its known function as an RNAP gene specificity factor.