Spore formation by Bacillus subtilis is a primitive form of development. In response to nutrient starvation and high cell density, B. subtilis divides asymmetrically, resulting in two cells with different sizes and cell fates. Immediately after division, the transcription factor sigma(F) becomes active in the smaller prespore, which is followed by the activation of sigma(E) in the larger mother cell. In this report, we examine the role of the mother cell-specific transcription factor sigma(E) in maintaining the compartmentalization of gene expression during development. We have studied a strain with a deletion of the spoIIIE gene, encoding a DNA translocase, that exhibits uncompartmentalized sigma(F) activity. We have determined that the deletion of spoIIIE alone does not substantially impact compartmentalization, but in the spoIIIE mutant, the expression of putative peptidoglycan hydrolases under the control of sigma(E) in the mother cell destroys the integrity of the septum. As a consequence, small proteins can cross the septum, thereby abolishing compartmentalization. In addition, we have found that in a mutant with partially impaired control of sigma(F), the activation of sigma(E) in the mother cell is important to prevent the activation of sigma(F) in this compartment. Therefore, the activity of sigma(E) can either maintain or abolish the compartmentalization Of sigma(F), depending upon the genetic makeup of the strain. We conclude that sigma(E) activity must be carefully regulated in order to maintain compartmentalization of gene expression during development.