The forespore line of gene expression during sporulation in Bacillus subtilis

The dynamic of transcription regulatory networks governs the biological function of cellular systems. One of the most significant and common network motifs is the feedforward loop (FFL), in which one transcription factor regulates the synthesis of the second transcription factor, and both then jointly control the expression of target genes. Using the Gram-positive bacterium Bacillus subtilis as a model system, I show that the forespore program of gene transcription during sporulation is driven forward by a linked series of FFLs.; B. subtilis integrates a variety of environmental and physiological signals in the decision to sporulate. Asymmetric division during sporulation generates a germ cell, the forespore, which ultimately becomes the spore. Gene expression in the forespore is governed by a hierarchical cascade consisting of transcription factors sigmaF, sigma G, RsfA, and SpoVT. Using transcriptional profiling and bioinformatics, I show that 44 genes (grouped into 36 transcription units) are expressed under the control of sigmaF, 4 of which are additionally regulated by the DNA-binding protein RsfA; and 88 genes (grouped into 67 transcription units) are transcribed under the control of sigmaG, 46 of which are further regulated by SpoVT. Promoters for many of the newly identified sigma F- and sigmaG-controlled genes were located by a computer algorithm and/or by transcription start site mapping. In total, 120 genes (grouped into 94 transcription units) are activated in the forespore during sporulation. Among these, 57 genes are new members of the sigma F and sigmaG regulons identified in this study.; Comparative genomics analysis was performed, and 65 of the 120 forespore-specific genes were present in at least five of the Gram-positive endospore-forming bacteria and absent in the closely-related but non-endospore-forming bacteria of the genus Listeria. To determine the function of the newly identified sigmaF- and sigmaG-controlled genes, systematic gene inactivation was performed to generate null mutations in 56 genes. My collaborators and I characterized two of the resulting mutants (ykoVUDelta and yyaCDelta). We discovered the role of YkoVU in DNA double-strand break repair via the Ku-based nonhomologous end joining pathway during germination, and explored the function of YyaC in the degradation of small, acid-soluble proteins.; The transcriptional profiling, bioinformatics, and functional analysis of the forespore line of gene expression during sporulation in B. subtilis allows us to understand cellular differentiation in terms of its underlying regulatory circuit. Together with the identification of the mother cell line of gene expression, we now have a comprehensive understanding of the program of gene expression in each cell compartment during sporulation.