Summary In Bacillus subtilis, the competence transcription factor ComK activates its own transcription as well as the transcription of genes that encode DNA transport proteins. ComK is expressed in about 10% of the cells in a culture grown to competence. Using DNA microarrays representing ≈ 95% of the protein‐coding open reading frames in B. subtilis, we compared the expression profiles of wild‐type and comK strains, as well as of a mecA mutant (which produces active ComK in all the cells of the population) and a comK mecA double mutant. In these comparisons, we identified at least 165 genes that are upregulated by ComK and relatively few that are downregulated. The use of reporter fusions has confirmed these results for several genes. Many of the ComK‐regulated genes are organized in clusters or operons, and 23 of these clusters are preceded by apparent ComK‐box promoter motifs. In addition to those required for DNA uptake, other genes that are upregulated in the presence of ComK are probably involved in DNA repair and in the uptake and utilization of nutritional sources. From this and previous work, we conclude that the ComK regulon defines a growth‐arrested state, distinct from sporulation, of which competence for genetic transformation is but one notable feature. We suggest that this is a unique adaptation to stress and that it be termed the ‘K‐state’.

DNA microarrays comprising Ϸ95% of the Bacillus subtilis annotated protein coding ORFs were deployed to generate a series of snapshots of genomewide transcriptional changes that occur when cells are grown under various conditions that are expected to increase or decrease transcription of the trp operon segment of the aromatic supraoperon. Comparisons of global expression patterns were made between cells grown in the presence of indole acrylic acid, a specific inhibitor of tRNA Trp charging; cells deficient in expression of the mtrB gene, which encodes the tryptophanactivated negative regulatory protein, TRAP; WT cells grown in the presence or absence of two or three of the aromatic amino acids; and cells harboring a tryptophanyl tRNA synthetase mutation conferring temperature-sensitive tryptophan-dependent growth. Our findings validate expected responses of the tryptophan biosynthetic genes and presumed regulatory interrelationships between genes in the different aromatic amino acid pathways and the histidine biosynthetic pathway. Using a combination of supervised and unsupervised statistical methods we identified Ϸ100 genes whose expression profiles were closely correlated with those of the genes in the trp operon. This finding suggests that expression of these genes is influenced directly or indirectly by regulatory events that affect or are a consequence of altered tryptophan metabolism.H omologous protein domains are used by Bacillus subtilis and Escherichia coli to catalyze the same reactions in the biosynthesis of the aromatic amino acids (1). Despite this similarity, very different regulatory proteins and mechanisms are used by these bacteria to regulate aromatic amino acid synthesis. These differences must be partly caused by the different evolutionary histories and experiences of these microorganisms. Operon organization also is somewhat different in the two species, reflecting regulatory interrelationships described as cross-pathway control, that exist between genes for different pathways in B. subtilis that are not evident in E. coli. Thus, the six-gene trp operon of B. subtilis resides within an aromatic supraoperon that contains six additional genes, three upstream and three downstream, concerned with the common aromatic pathway and with phenylalanine, tyrosine, and histidine biosynthesis (Fig. 1). The seventh trp gene, trpG (pabA), is in the folate operon. This gene specifies a protein that functions both in tryptophan and folate biosynthesis; presumably because of this, it is subject to regulation by both metabolites. In E. coli the five-gene trp operon encodes all seven protein domains needed for tryptophan biosynthesis; two of these genes encode fused protein domains that engender bifunctional polypeptides (2).The B. subtilis aromatic supraoperon has three promoters as shown in Fig. 1 (1, 3). One promoter is located before the three genes upstream of the six-gene trp operon. A second promoter immediately precedes the trp operon segment. These two promoters provide trp operon transcripts. The thi...