title: The quorum-sensing regulator ComA from Bacillus subtilis activates transcription using topologically distinct DNA motifs.
abstract: ComA-like transcription factors regulate the quorum response in numerous Gram-positive bacteria. ComA proteins belong to the tetrahelical helix-turn-helix superfamily of transcriptional activators, which bind as homodimers to inverted sequence repeats in the DNA. Here, we report that ComA from Bacillus subtilis recognizes a topologically distinct motif, in which the binding elements form a direct repeat. We provide in vitro and in vivo evidence that the canonical and non-canonical site play an important role in facilitating type I and type II promoter activation, respectively, by interacting with different subunits of RNA polymerase. We furthermore show that there is a variety of contexts in which the non-canonical site can occur and identify new direct target genes that are located within the integrative and conjugative element ICEBs1. We therefore suggest that ComA acts as a multifunctional transcriptional activator and provides a striking example for complexity in protein-DNA interactions that evolved in the context of quorum sensing.
authors.affiliation: Center for Molecular Biology (ZMBH) and Center for the Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
authors.forename: Diana
authors.initials: D
authors.lastname: Wolf
authors.affiliation: Center for Molecular Biology (ZMBH) and Center for the Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
authors.forename: Valentina
authors.initials: V
authors.lastname: Rippa
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Mobarec
authors.affiliation: Center for Molecular Biology (ZMBH) and Center for the Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
authors.forename: Patricia
authors.initials: P
authors.lastname: Sauer
authors.affiliation: Center for Molecular Biology (ZMBH) and Center for the Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
authors.forename: Lorenz
authors.initials: L
authors.lastname: Adlung
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Kolb
authors.affiliation: Center for Molecular Biology (ZMBH) and Center for the Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany ilka.bischofs@bioquant.uni-heidelberg.de.
authors.forename: Ilka B
authors.initials: IB
authors.lastname: Bischofs
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D003001:Cloning, Molecular; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000235:genetics* / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D055029:Inverted Repeat Sequences; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D055503:Protein Multimerization; D021122:Protein Subunits / Q000235:genetics* / Q000378:metabolism; D053038:Quorum Sensing / Q000235:genetics*; D011994:Recombinant Proteins / Q000235:genetics / Q000378:metabolism; D015533:Transcriptional Activation
chemical_list: D001426:Bacterial Proteins; C061262:ComA protein, Bacteria; D004268:DNA-Binding Proteins; D021122:Protein Subunits; D011994:Recombinant Proteins; D012321:DNA-Directed RNA Polymerases