title: High-resolution detection of DNA binding sites of the global transcriptional regulator GlxR in Corynebacterium glutamicum.
abstract: The transcriptional regulator GlxR has been characterized as a global hub within the gene-regulatory network of Corynebacterium glutamicum. Chromatin immunoprecipitation with a specific anti-GlxR antibody and subsequent high-throughput sequencing (ChIP-seq) was applied to C. glutamicum to get new in vivo insights into the gene composition of the GlxR regulon. In a comparative approach, C. glutamicum cells were grown with either glucose or acetate as the sole carbon source prior to immunoprecipitation. High-throughput sequencing resulted in 69 million reads and 2.6 Gb of genomic information. After mapping of these data on the genome sequence of C. glutamicum, 107 enriched DNA fragments were detected from cells grown with glucose as carbon source. GlxR binding sites were identified in the sequence of 79 enriched DNA fragments, of which 21 sites were not previously reported. Electrophoretic mobility shift assays with 40-mer oligomers covering the GlxR binding sites were performed for validation of the in vivo results. The detection of new binding sites confirmed the role of GlxR as a regulator of carbon source metabolism and energy conversion, but additionally revealed binding of GlxR in front of the 6C non-coding RNA gene and to non-canonical DNA binding sites within protein-coding regions. The present study underlines the dynamics within the GlxR regulon by identifying in vivo targets during growth on glucose and contributes to the expansion of knowledge of this important transcriptional regulator.
authors.affiliation: Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany.
authors.forename: Britta
authors.initials: B
authors.lastname: Jungwirth
authors.affiliation: Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors.forename: Claudia
authors.initials: C
authors.lastname: Sala
authors.affiliation: Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany.
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Kohl
authors.affiliation: Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors.forename: Swapna
authors.initials: S
authors.lastname: Uplekar
authors.affiliation: Computational Systems Biology, Max-Planck-Institut für Informatik, Saarbrücken, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Baumbach
authors.affiliation: Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors.forename: Stewart T
authors.initials: ST
authors.lastname: Cole
authors.affiliation: Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany.
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
authors.affiliation: Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Tauch
mesh_terms: D019342:Acetic Acid / Q000378:metabolism; D001665:Binding Sites; D002244:Carbon / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D048230:Corynebacterium glutamicum / Q000235:genetics* / Q000378:metabolism; D004269:DNA, Bacterial / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D015964:Gene Expression Regulation, Bacterial; D005947:Glucose / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D011485:Protein Binding; D018085:Regulon; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004269:DNA, Bacterial; D014157:Transcription Factors; D002244:Carbon; D005947:Glucose; D019342:Acetic Acid