title: GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.
abstract: Using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic GE23077 (GE) binds directly to the bacterial RNA polymerase (RNAP) active-center 'i' and 'i+1' nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. The target-based resistance spectrum for GE is unusually small, reflecting the fact that the GE binding site on RNAP includes residues of the RNAP active center that cannot be substituted without loss of RNAP activity. The GE binding site on RNAP is different from the rifamycin binding site. Accordingly, GE and rifamycins do not exhibit cross-resistance, and GE and a rifamycin can bind simultaneously to RNAP. The GE binding site on RNAP is immediately adjacent to the rifamycin binding site. Accordingly, covalent linkage of GE to a rifamycin provides a bipartite inhibitor having very high potency and very low susceptibility to target-based resistance. DOI: http://dx.doi.org/10.7554/eLife.02450.001.
authors.affiliation: Waksman Institute, Rutgers University, Piscataway, United States.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.forename: David
authors.initials: D
authors.lastname: Degen
authors.forename: Mary X
authors.initials: MX
authors.lastname: Ho
authors.forename: Elena
authors.initials: E
authors.lastname: Sineva
authors.forename: Katherine Y
authors.initials: KY
authors.lastname: Ebright
authors.forename: Yon W
authors.initials: YW
authors.lastname: Ebright
authors.forename: Vladimir
authors.initials: V
authors.lastname: Mekler
authors.forename: Hanif
authors.initials: H
authors.lastname: Vahedian-Movahed
authors.forename: Yu
authors.initials: Y
authors.lastname: Feng
authors.forename: Ruiheng
authors.initials: R
authors.lastname: Yin
authors.forename: Steve
authors.initials: S
authors.lastname: Tuske
authors.forename: Herbert
authors.initials: H
authors.lastname: Irschik
authors.forename: Rolf
authors.initials: R
authors.lastname: Jansen
authors.forename: Sonia
authors.initials: S
authors.lastname: Maffioli
authors.forename: Stefano
authors.initials: S
authors.lastname: Donadio
authors.forename: Eddy
authors.initials: E
authors.lastname: Arnold
authors.forename: Richard H
authors.initials: RH
authors.lastname: Ebright
mesh_terms: D000617:Aminoglycosides / Q000737:chemistry / Q000494:pharmacology; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology; D008958:Models, Molecular; D009711:Nucleotides / Q000378:metabolism*; D010456:Peptides, Cyclic / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D012318:RNA Polymerase I / Q000378:metabolism*; D012294:Rifamycins / Q000494:pharmacology; D016963:Thermus thermophilus / Q000201:enzymology; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D000617:Aminoglycosides; C489256:GE 23077-A; C489257:GE 23077-B; D009711:Nucleotides; D010456:Peptides, Cyclic; D012294:Rifamycins; C051799:sorangicin A; C052000:sorangicin B; D012318:RNA Polymerase I
keywords: RNA polymerase; RNA polymerase-promoter open complex; bipartite inhibitor; inhibitor; transcription; transcription initiation
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