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

Authors

  • R. Álvarez-Álvarez,

    1. Área de Microbiología, Departamento de Biología Molecular, Facultad de CC, Biológicas y Ambientales, Universidad de León, León, Spain
    2. Instituto de Biotecnología de Léon (INBIOTEC), Parque Científico de León, León, Spain
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  • A. Rodríguez-García,

    1. Área de Microbiología, Departamento de Biología Molecular, Facultad de CC, Biológicas y Ambientales, Universidad de León, León, Spain
    2. Instituto de Biotecnología de Léon (INBIOTEC), Parque Científico de León, León, Spain
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  • I. Santamarta,

    1. Instituto de Biotecnología de Léon (INBIOTEC), Parque Científico de León, León, Spain
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  • R. Pérez-Redondo,

    1. Instituto de Biotecnología de Léon (INBIOTEC), Parque Científico de León, León, Spain
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  • A. Prieto-Domínguez,

    1. Área de Microbiología, Departamento de Biología Molecular, Facultad de CC, Biológicas y Ambientales, Universidad de León, León, Spain
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  • Y. Martínez-Burgo,

    1. Área de Microbiología, Departamento de Biología Molecular, Facultad de CC, Biológicas y Ambientales, Universidad de León, León, Spain
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  • P. Liras

    Corresponding author
    1. Área de Microbiología, Departamento de Biología Molecular, Facultad de CC, Biológicas y Ambientales, Universidad de León, León, Spain
    2. Instituto de Biotecnología de Léon (INBIOTEC), Parque Científico de León, León, Spain
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  • Funding Information This work was financed by Grants BIO2012–34723 from the Ministry of Science and Innovation and LE046-A11-2 from the Junta de Castilla y León.
  • Correction added on 10 February 2014, after first online publication: The unnecessary second letter “C” in “cephamycin C-clavulanic acid C cluster” has been removed from the article title.

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.

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