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. 2002 May;184(9):2344-51.
doi: 10.1128/jb.184.9.2344-2351.2002.

Whole-genome Analysis of Genes Regulated by the Bacillus Subtilis Competence Transcription Factor ComK

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Whole-genome Analysis of Genes Regulated by the Bacillus Subtilis Competence Transcription Factor ComK

Mitsuo Ogura et al. J Bacteriol. .
Free PMC article


The Bacillus subtilis competence transcription factor ComK is required for establishment of competence for genetic transformation. In an attempt to study the ComK factor further, we explored the genes regulated by ComK using the DNA microarray technique. In addition to the genes known to be dependent on ComK for expression, we found many genes or operons whose ComK dependence was not known previously. Among these genes, we confirmed the ComK dependence of 16 genes by using lacZ fusions, and three genes were partially dependent on ComK. Transformation efficiency was significantly reduced in an smf disruption mutant, although disruption of the other ComK-dependent genes did not result in significant decreases in transformation efficiency. Nucleotide sequences similar to that of the ComK box were found for most of the newly discovered genes regulated by ComK.


FIG. 1.
FIG. 1.
Expression of fusions between ComK target candidates and lacZ in comK disruption mutants. Each strain contains a pMutin-based transcriptional lacZ fusion (41). Cells were grown in MC medium, and β-galactosidase activities were determined as described previously (29). For lacZ fusions of thdF, yhjB, yhcH, yhcF, and yhcE, the assay was performed two or three times, and representative results of these experiments are shown. The numbers on the x axis indicate the growth time (in hours) relative to the end of vegetative growth (T0). Symbols: •, β-galactosidase activity in wild-type cells; ○, β-galactosidase activity in comK mutant cells.
FIG. 2.
FIG. 2.
Putative ComK boxes found in the upstream regions of the ComK-regulated genes. (A and B) Putative ComK boxes of the genes or operons whose expression was ComK dependent, as shown by both microarray analysis and lacZ fusion experiments and by microarray analysis alone, respectively. (C) Known ComK boxes. Lowercase letters indicate nucleotides that differed from the nucleotides in the ComK consensus sequence. N and dashes indicate nucleotides, and the numbers indicate the spaces between the T and A clusters. The negative numbers on the right indicate the positions of the last nucleotides of the putative ComK boxes relative to the translational start site. The numbers in parentheses are reference numbers.

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