Transcriptomic analysis of Streptomyces clavuligerus ΔccaR::tsr: effects of the cephamycin C‐clavulanic acid cluster regulator CcaR on global regulation

• Published in: Microbial biotechnology Vol. 7; no. 3; pp. 221 - 231
• Main Authors: Álvarez‐Álvarez, R., Rodríguez‐García, A., Santamarta, I., Pérez‐Redondo, R., Prieto‐Domínguez, A., Martínez‐Burgo, Y., Liras, P.
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons Ltd 01.05.2014
• Subjects: Biosynthetic Pathways - genetics; Cephamycins - metabolism; Clavulanic Acid - metabolism; Culture Media - chemistry; Gene Deletion; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genes, Reporter; Luciferases - analysis; Luciferases - genetics; Multigene Family; Real-Time Polymerase Chain Reaction; Streptomyces; Streptomyces - genetics; Streptomyces - growth & development; Streptomyces - metabolism; Streptomyces clavuligerus; Transcription Factors - genetics
• ISSN: 1751-7915; 1751-7915
• DOI: 10.1111/1751-7915.12109

Summary Streptomyces clavuligerus ATCC 27064 and S. clavuligerus ΔccaR::tsr cultures were grown in asparagine‐starch medium, and samples were taken in the exponential and stationary growth phases. Transcriptomic analysis showed that the expression of 186 genes was altered in the ccaR‐deleted mutant. These genes belong to the cephamycin C gene cluster, clavulanic acid gene cluster, clavams, holomycin, differentiation, carbon, nitrogen, amino acids or phosphate metabolism and energy production. All the clavulanic acid biosynthesis genes showed Mc values in the order of −4.23. The blip gene‐encoding a β‐lactamase inhibitory protein was also controlled by the cephamycin C‐clavulanic acid cluster regulator (Mc −2.54). The expression of the cephamycin C biosynthesis genes was greatly reduced in the mutant (Mc values up to −7.1), while the genes involved in putative β‐lactam resistance were less affected (Mc average −0.88). Genes for holomycin biosynthesis were upregulated. In addition, the lack of clavulanic acid and cephamycin production negatively affected the expression of genes for the clavulanic acid precursor arginine and of miscellaneous genes involved in nitrogen metabolism (amtB, glnB, glnA3, glnA2, glnA1). The transcriptomic results were validated by quantative reverse transcription polymerase chain reaction and luciferase assay of luxAB‐coupled promoters. Transcriptomic analysis of the homologous genes of S. coelicolor validated the results obtained for S. clavuligerus primary metabolism genes. Transcriptomic analysis showed that the expression of one hundred and eighty six genes was different in S. clavuligerus ATCC 27064 and S. clavuligerus ∆ccaR::tsr cultures. Expression of all the clavulanic acid biosynthesis genes and cephamycin C biosynthesis genes was greatly reduced in the mutant Genes for holomycin biosynthesis were up‐regulated. The transcriptomic results were validated by RT‐qPCR and luciferase assay of luxAB‐coupled promoters.