title: A high-throughput method to examine protein-nucleotide interactions identifies targets of the bacterial transcriptional regulatory protein fur.
abstract: The Ferric uptake regulatory protein (Fur) is a transcriptional regulatory protein that functions to control gene transcription in response to iron in a number of pathogenic bacteria. In this study, we applied a label-free, quantitative and high-throughput analysis method, Interferometric Reflectance Imaging Sensor (IRIS), to rapidly characterize Fur-DNA interactions in vitro with predicted Fur binding sequences in the genome of Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhea. IRIS can easily be applied to examine multiple protein-protein, protein-nucleotide and nucleotide-nucleotide complexes simultaneously and demonstrated here that seventy percent of the predicted Fur boxes in promoter regions of iron-induced genes bound to Fur in vitro with a range of affinities as observed using this microarray screening technology. Combining binding data with mRNA expression levels in a gonococcal fur mutant strain allowed us to identify five new gonococcal genes under Fur-mediated direct regulation.
authors.affiliation: Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston University, Boston, Massachusetts, United States of America.
authors.forename: Chunxiao
authors.initials: C
authors.lastname: Yu
authors.affiliation: Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America.
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Lopez
authors.affiliation: Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, United States of America.
authors.forename: Han
authors.initials: H
authors.lastname: Hu
authors.affiliation: Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, United States of America.
authors.forename: Yu
authors.initials: Y
authors.lastname: Xia
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America.
authors.forename: David S
authors.initials: DS
authors.lastname: Freedman
authors.affiliation: Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America.
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Reddington
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America.
authors.forename: George G
authors.initials: GG
authors.lastname: Daaboul
authors.affiliation: Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America; Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America; Physics Department, Boston University, Boston, Massachusetts, United States of America.
authors.forename: M Selim
authors.initials: MS
authors.lastname: Unlü
authors.affiliation: Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston University, Boston, Massachusetts, United States of America; Department of Microbiology, Boston University School of Medicine, Boston University, Boston, Massachusetts, United States of America.
authors.forename: Caroline Attardo
authors.initials: CA
authors.lastname: Genco
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D015374:Biosensing Techniques / Q000379:methods*; D016384:Consensus Sequence; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D016680:Genome, Bacterial / Q000235:genetics; D009344:Neisseria gonorrhoeae / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D018085:Regulon / Q000235:genetics; D012097:Repressor Proteins / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012097:Repressor Proteins