title: A variable DNA recognition site organization establishes the LiaR-mediated cell envelope stress response of enterococci to daptomycin.
abstract: LiaR is a 'master regulator' of the cell envelope stress response in enterococci and many other Gram-positive organisms. Mutations to liaR can lead to antibiotic resistance to a variety of antibiotics including the cyclic lipopeptide daptomycin. LiaR is phosphorylated in response to membrane stress to regulate downstream target operons. Using DNA footprinting of the regions upstream of the liaXYZ and liaFSR operons we show that LiaR binds an extended stretch of DNA that extends beyond the proposed canonical consensus sequence suggesting a more complex level of regulatory control of target operons. We go on to determine the biochemical and structural basis for increased resistance to daptomycin by the adaptive mutation to LiaR (D191N) first identified from the pathogen Enterococcus faecalis S613. LiaR(D191N) increases oligomerization of LiaR to form a constitutively activated tetramer that has high affinity for DNA even in the absence of phosphorylation leading to increased resistance. Crystal structures of the LiaR DNA binding domain complexed to the putative consensus sequence as well as an adjoining secondary sequence show that upon binding, LiaR induces DNA bending that is consistent with increased recruitment of RNA polymerase to the transcription start site and upregulation of target operons.
authors.affiliation: Department of BioSciences, Rice University, Houston, TX 77005, USA.
authors.forename: Milya
authors.initials: M
authors.lastname: Davlieva
authors.affiliation: Department of BioSciences, Rice University, Houston, TX 77005, USA.
authors.forename: Yiwen
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Center for Biomolecular Structure and Function, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
authors.forename: Paul G
authors.initials: PG
authors.lastname: Leonard
authors.affiliation: Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Center for Biomolecular Structure and Function, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
authors.forename: Troy A
authors.initials: TA
authors.lastname: Johnson
authors.affiliation: Plant-Microbe Genomics Facility, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Zianni
authors.affiliation: Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, 110121, Colombia.
authors.forename: Cesar A
authors.initials: CA
authors.lastname: Arias
authors.affiliation: Center for Biomolecular Structure and Function, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
authors.forename: John E
authors.initials: JE
authors.lastname: Ladbury
authors.affiliation: Department of BioSciences, Rice University, Houston, TX 77005, USA shamoo@rice.edu.
authors.forename: Yousif
authors.initials: Y
authors.lastname: Shamoo
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D016384:Consensus Sequence; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017576:Daptomycin / Q000494:pharmacology*; D024881:Drug Resistance, Bacterial; D013293:Enterococcus faecalis / Q000187:drug effects / Q000235:genetics; D008958:Models, Molecular; D009154:Mutation; D009876:Operon; D011485:Protein Binding; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D017576:Daptomycin