Microarray analysis of the Bacillus subtilis K‐state: genome‐wide expression changes dependent on ComK

Abstract

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’.

Silencing of natural transformation by an RNA chaperone and a multitarget small RNA

“…The regulon controlled by Lpp0148 (fold change > 2, P < 0.01) consists of 11 genes upregulated in the mutant strain and arranged in seven potential transcriptional units (Table S1). Among those genes, six are homologous to either genes encoding elements of the DNA uptake system (comEA, comEC, and comF) or genes previously found induced in competent bacteria (comM, radC, and mreB) (23)(24)(25). lpp1976 is the last gene of an operon with lpp1977 and lpp1978, both of which are moderately induced (fold change, 1.8 and 1.3, respectively; P < 0.01).…”

The Bacillus subtilis ywkA gene encodes a malic enzyme and its transcription is activated by the YufL/YufM two-component system in response to malate

“…However, we found no drastic transformability defect, if any, of yufL, yufM or ywkA mutant strains (T. Doan & S. Aymerich, unpublished data). The study of the genome-wide expression changes dependent on ComK, recently reported by Berka et al (2002), led these authors to conclude that the ComK regulon defines a growth-arrested state, distinct from sporulation, of which competence for genetic transformation is but one notable feature. They suggest that this is a unique adaptation to stress and that it be termed the 'K-state'.…”

“…The transcriptome analysis performed by Kobayashi et al (2001) has revealed 97 other differentiallly expressed genes in the yufL mutant strain overexpressing yufM compared to the wild-type strain. Because this list included several competence genes, and especially comK and most of the members of the ComK regulon (Berka et al, 2002;Ogura et al, 2002), the authors suggested that the YufL/YufM TCS would be involved in competence development. However, we found no drastic transformability defect, if any, of yufL, yufM or ywkA mutant strains (T. Doan & S. Aymerich, unpublished data).…”

Genomewide transcriptional changes associated with genetic alterations and nutritional supplementation affecting tryptophan metabolism in Bacillus subtilis

“…For the first six experiments listed in Table 1, we constructed DNA microarrays consisting of PCR-amplified B. subtilis 168 ORFs by using a complete set of ORF-specific PCR primers as described (10). Primers were designed based on the ORFs listed on the SubtiList database (http:͞͞genolist.…”

“…The hierarchical cluster of genes coordinately induced with those of the trp operon includes several genes that are associated with competence development, DNA uptake, or recombination (e.g., comP, comQ, mreB, mreC, mreD, mutSB, and radC) (10). It is possible that the apparent induction of these transcripts is a nonspecific consequence of limiting nitrogen conditions that occurs when cells are grown in minimal medium without added amino acids (27).…”