b Streptomyces clavuligerus claR::aph is a claR-defective mutant, but in addition to its claR defect it also carries fewer copies of the resident linear plasmids pSCL2 and pSCL4 (on the order of 4 ؋ 10 5 -fold lower than the wild-type strain), as shown by qPCR. To determine the function of ClaR without potential interference due to plasmid copy number, a new strain, S. clavuligerus ⌬claR:: aac, with claR deleted and carrying the wild-type level of plasmids, was constructed. Transcriptomic analyses were performed in S. clavuligerus ⌬claR::aac and S. clavuligerus ATCC 27064 as the control strain. The new ⌬claR mutant did not produce clavulanic acid (CA) and showed a partial expression of genes for the early steps of the CA biosynthesis pathway and a very poor expression (1 to 8%) of the genes for the late steps of the CA pathway. Genes for cephamycin C biosynthesis were weakly upregulated (1.7-fold at 22.5 h of culture) in the ⌬claR mutant, but genes for holomycin biosynthesis were expressed at levels from 3-to 572-fold higher than in the wild-type strain, supporting the observed overproduction of holomycin by S. clavuligerus ⌬claR:: aac. Interestingly, three secondary metabolites produced by gene clusters SMCp20, SMCp22, and SMCp24, encoding still-cryptic compounds, had partially or totally downregulated their genes in the mutant, suggesting a regulatory role for ClaR wider than previously reported. In addition, the amfR gene was downregulated, and consequently, the mutant did not produce aerial mycelium. Expression levels of about 100 genes in the genome were partially up-or downregulated in the ⌬claR mutant, many of them related to the upregulation of the sigma factor-encoding rpoE gene.
The claR gene, located in the Streptomyces clavuligerus CA gene cluster, encodes a LysR-type regulator (1, 2). LysR-type transcriptional regulators (LTTRs) follow the pattern of the model regulator controlling lysA expression in Enterobacteriaceae (3). The LTTRs act on metabolic pathways but also in quorum sensing, virulence, motility, nitrogen fixation, oxidative stress responses, and other systems (3, 4, 5). These global transcriptional regulators act mostly as activators but also as repressors and control single genes or operons. The LysR proteins are tetramers, have a helix-turn-helix (HTH) motif close to the N terminus, and bind palindromic sequences identified as T-N 11 -A (6). The binding affinity is usually determined by a ligand coinducer molecule (7).The presence of LysR-type regulators in antibiotic biosynthesis gene clusters is relatively frequent (8, 9, 10). In undecylprodigiosin and actinorhodin production, the autoregulated StgR LTTR negatively controls the expression of the redD and actII-orf4 genes encoding pathway-specific activators (11).The claR gene of S. clavuligerus is expressed as a monocistronic transcript that encodes a protein of 431 amino acids (M r , 47,080). ClaR contains HTH motifs in its amino-and carboxyl-terminal regions. The HTH close to the C-terminal end of the protein contains, fully conser...