CodY of Lactococcus lactis MG1363 is a transcriptional regulator that represses the expression of several genes encoding proteins of the proteolytic system. DNA microarray analysis, comparing the expression profiles of L. lactis MG1363 and an isogenic strain in which codY was mutated, was used to determine the CodY regulon. In peptide-rich medium and exponentially growing cells, where CodY exerts strong repressing activity, the expression of over 30 genes was significantly increased upon removal of codY. The differentially expressed genes included those predominantly involved in amino acid transport and metabolism. In addition, several genes belonging to other functional categories were derepressed, stressing the pleiotropic role of CodY. Scrutinizing the transcriptome data with bioinformatics tools revealed the presence of a novel overrepresented motif in the upstream regions of several of the genes derepressed in L. lactis MG1363⌬codY. Evidence is presented that this 15-bp cis-sequence, AATTTTCWGAAAATT, serves as a high affinity binding site for CodY, as shown by electrophoretic mobility shift assays and DNase I footprinting analyses. The presence of this CodY-box is sufficient to evoke CodY-mediated regulation in vivo. A copy of this motif is also present in the upstream region of codY itself. It is shown that CodY regulates its own synthesis and requires the CodY-box and branched-chain amino acids to interact with its promoter.For the Gram-positive organism Lactococcus lactis, a lactic acid bacterium, auxotrophic for branched-chain amino acids (BCAAs), 2 methionine and histidine (1-3), maintenance of the nitrogen balance is essential. When this bacterium grows in milk, it uses the ubiquitous milk proteins (caseins) for its growth, employing a comprehensive and balanced proteolytic system (4 -6). The extracellular cell wall-bound serine proteinase (PrtP) is an essential part of the proteolytic system, as it hydrolyzes the large caseins into smaller fragments. These peptides of various sizes, and free amino acids, can then be taken up into the cell by various transport systems, e.g. the oligopeptide transport system Opp (4) and the di-and tripeptide transport systems DtpP and DtpT (7,8). Once inside, the peptides are degraded further by either endopeptidases (e.g. PepO and PepF) or aminopeptidases (e.g. PepN, PepX, and PepC) (9).Although the proteolytic system of lactic acid bacteria has been characterized thoroughly over the past 20 years (6), new components are still being identified. For example, upon deletion of the main transport system for oligopeptides (opp), growth on media containing specific oligopeptides was still possible (10), suggesting the presence of at least one additional peptide transport system. Recently, a novel peptide transporter has been identified, encoded by dpp (opt), which is able to take over (part of) the role of opp (10 -12).Previous studies have shown that expression in L. lactis MG1363 of a number of genes of the proteolytic system is repressed in nitrogen-rich media. When L. l...