Open Access Research article

Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism

Aurélie Guyet1, Nadia Benaroudj2, Caroline Proux3, Myriam Gominet1, Jean-Yves Coppée3 and Philippe Mazodier1*

Author Affiliations

1 Unité de Biologie des Bactéries Pathogènes à Gram-Positif, Institut Pasteur, CNRS URA 2172, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France

2 Unité Biologie des Spirochètes, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France

3 Plateforme Transcriptome et Epigenome (PF2), 28 rue du Docteur Roux, 75724 Paris Cedex 15, France

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BMC Microbiology 2014, 14:81  doi:10.1186/1471-2180-14-81

Published: 3 April 2014

Additional files

Additional file 1: Table S1:

Oligonucleotides used in this study.

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Additional file 2: Table S2:

Complete set of genes differentially expressed in the S. lividans adpA mutant. S. coelicolor microarrays were used to test for genes differentially expressed in the S. lividans adpA mutant and wild-type 1326, at growth time point T, in liquid YEME medium. Annotated function, Fc, P-values, and classification of the proteins are presented according to the microarray SCO genes, by increasing SCO gene number.

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Additional file 3: Figure S1:

Effect of the mutation of one AdpA-binding site in the S. lividans hyaS promoter on AdpA-binding specificity. Mutation of an AdpA-binding site in the S. lividans hyaS promoter region prevents formation of an AdpA-DNA complex in vitro. Sequence of the mutated AdpA-binding site (at -129 nt) and EMSA performed with the mutated hyaS promoter region are shown.

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Additional file 4: Table S3:

Comparison of gene expression profiles between S. coelicolor bldA-dependent and S. lividans AdpA-dependent genes. Comparison of the gene expression profiles of some S. coelicolor bldA-dependent genes whose S. lividans orthologs are AdpA-dependent (see Additional file 2: Table S2). Putative AdpA-binding sites were identified in silico (see Additional file 5: Table S4), suggesting that in the S. coelicolor bldA mutant, the adpA translation defect leads to bldA-dependence of the genes identified previously [42,47,48].

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Additional file 5: Table S4:

Putative S. coelicolor AdpA-binding sites upstream from the S. lividans AdpA-dependent genes. We identified putative AdpA-binding sites in silico using the S. coelicolor genome and we analysed orthologs of S. lividans AdpA-dependent genes (based on our microarray data); the sequences and positions of the sites with the highest scores according to PREDetector are shown. S. coelicolor, S. lividans and S. griseus ortholog genes are indicated and previously identified direct or probably direct S. griseus AdpA-dependent genes are highlighted.

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