Interplay of CodY and ScoC in the Regulation of Major Extracellular Protease Genes of Bacillus subtilis

Abstract

AprE and NprE are two major extracellular proteases in Bacillus subtilis whose expression is directly regulated by several pleiotropic transcriptional factors, including AbrB, DegU, ScoC, and SinR. In cells growing in a rich, complex medium, the aprE and nprE genes are strongly expressed only during the post-exponential growth phase; mutations in genes encoding the known regulators affect the level of post-exponential-phase gene expression but do not permit high-level expression during the exponential growth phase. Using DNA-binding assays and expression and mutational analyses, we have shown that the genes for both exoproteases are also under strong, direct, negative control by the global transcriptional regulator CodY. However, because CodY also represses scoC, little or no derepression of aprE and nprE was seen in a codY null mutant due to overexpression of scoC. Thus, CodY is also an indirect positive regulator of these genes by limiting the synthesis of a second repressor. In addition, in cells growing under conditions that activate CodY, a scoC null mutation had little effect on aprE or nprE expression; full effects of scoC or codY null mutations could be seen only in the absence of the other regulator. However, even the codY scoC double mutant did not show high levels of aprE and nprE gene expression during exponential growth phase in a rich, complex medium. Only a third mutation, in abrB, allowed such expression. Thus, three repressors can contribute to reducing exoprotease gene expression during growth in the presence of excess nutrients. IMPORTANCEThe major Bacillus subtilis exoproteases, AprE and NprE, are important metabolic enzymes whose genes are subject to complex regulation by multiple transcription factors. We show here that expression of the aprE and nprE genes is also controlled, both directly and indirectly, by CodY, a global transcriptional regulator that responds to the intracellular pools of amino acids. Direct CodY-mediated repression explains a long-standing puzzle, that is, why exoproteases are not produced when cells are growing exponentially in a medium containing abundant quantities of proteins or their degradation products. Indirect regulation of aprE and nprE through CodY-mediated repression of the scoC gene, encoding another pleiotropic repressor, serves to maintain a significant level of repression of exoprotease genes when CodY loses activity. Bacillus subtilis produces at least eight extracellular or cell wallassociated proteases (1, 2). The alkaline serine protease subtilisin (AprE) and the neutral metalloprotease NprE, commonly referred to as the major exoproteases, account for ϳ95% of the total extracellular protease activity of B. subtilis (3). Even though the major function of AprE and NprE is thought to be supplying amino acids for growth via degradation of extracellular proteins, they have also been ascribed other physiological roles. AprE is involved in the production of two quorum-sensing signaling peptides (PhrA and CSF) (4), processing of the peptide antibiot...

Inactivation of Polymyxin by Hydrolytic Mechanism

“…2). This result is in agreement with several previous reports for other alkaline proteases (35,36). In B. subtilis, the expression of extracellular proteases AprE and NprE is directly or indirectly regulated by multiple transcriptional regulators, including AbrB, DegU, Spo0A, ScoC, SinR, and CodY (36).…”

CodY-Dependent Regulation of Sporulation in Clostridium difficile

“…ScoC directly downregulates opp, app, and sinIR expression (87,88), suggesting that ScoC may inhibit sporulation under high-nutrient conditions by repressing the expression of genes involved in early sporulation events. Further, CodY directly represses scoC transcription, and CodY and ScoC independently coregulate several loci, including opp (89,90). Altogether, these results imply that multiple regulators control B. subtilis sporulation through nutrient-dependent alteration of early sporulation gene expression.…”

Genome‐wide identification of Listeria monocytogenes CodY‐binding sites

“…As a result, at least parts of those genes will be transcribed even when CodY is actively blocking the completion of transcription. Third, binding of CodY to some regions in vivo and the resulting CodY‐mediated regulation of the corresponding genes may be prevented under certain conditions by the presence or absence of other regulators (Barbieri et al, ; Belitsky et al, ).…”

“…Although ChIP‐Seq experiments can reveal extended regions of protein binding, they do not pinpoint the binding sites, that is, exact sequences that directly contribute to protein binding, especially when several binding sites are located in close vicinity of each other. In addition, regulation by CodY and binding of CodY to DNA can be masked by the activities of other gene‐specific or global regulators, some of which are themselves under CodY control (Barbieri, Albertini, Ferrari, Sonenshein, & Belitsky, ; Belitsky et al, ). Regulators that compete with CodY for binding may be active under laboratory conditions but less active during infection allowing CodY‐mediated regulation to dominate.…”