Document Type
Article
Version Deposited
Published Version
Publication Date
12-5-2024
Publication Title
Nucleic acids research
DOI
10.1093/nar/gkae1135
Abstract
Antibiotic streptolydigin (Stl) inhibits bacterial transcription by blocking the trigger loop folding in the active center of RNA polymerase (RNAP), which is essential for catalysis. We use acoustic force spectroscopy to characterize the dynamics of transcription elongation in ternary elongation complexes (ECs) of RNAP in the presence of Stl at a single-molecule level. We found that Stl induces long-lived stochastic pauses while the instantaneous velocity of transcription between the pauses is unaffected. Stl enhances the short-lived pauses associated with an off-pathway early paused state intermediates of the RNAP nucleotide addition cycle. Unexpectedly, we found that transcript cleavage factors GreA and GreB, which were thought to be Stl competitors, do not alleviate the Stl-induced pausing; instead, they synergistically increase transcription inhibition by Stl. This is the first known instance of a transcriptional factor enhancing antibiotic activity. We propose a structural model of the EC-Gre-Stl complex that explains the observed Stl activities and provides insight into possible cooperative action of secondary channel factors and other antibiotics binding at the Stl pocket. These results offer a new strategy for high-throughput screening for prospective antibacterial agents.
Recommended Citation
Arseniev, Anatolii; Panfilov, Mikhail; Pobegalov, Georgii; Potyseva, Alina; Pavlinova, Polina; Yakunina, Maria; Lee, Jookyung; Borukhov, Sergei; Severinov, Konstantin; and Khodorkovskii, Mikhail, "Single-Molecule Studies Reveal the Off-Pathway Early Paused State Intermediates as a Target of Streptolydigin Inhibition of RNA Polymerase and Its Dramatic Enhancement by Gre Factors" (2024). Rowan-Virtua School of Osteopathic Medicine Departmental Research. 255.
https://rdw.rowan.edu/som_facpub/255
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License
Published Citation
Anatolii Arseniev, Mikhail Panfilov, Georgii Pobegalov, Alina Potyseva, Polina Pavlinova, Maria Yakunina, Jookyung Lee, Sergei Borukhov, Konstantin Severinov, Mikhail Khodorkovskii, Single-molecule studies reveal the off-pathway early paused state intermediates as a target of streptolydigin inhibition of RNA polymerase and its dramatic enhancement by Gre factors, Nucleic Acids Research, 2024;, gkae1135, https://doi.org/10.1093/nar/gkae1135
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