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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.<\/jats:p>","DOI":"10.1093\/nar\/gkae1135","type":"journal-article","created":{"date-parts":[[2024,12,10]],"date-time":"2024-12-10T20:15:04Z","timestamp":1733861704000},"source":"Crossref","is-referenced-by-count":1,"title":["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"],"prefix":"10.1093","volume":"53","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0901-4188","authenticated-orcid":false,"given":"Anatolii","family":"Arseniev","sequence":"first","affiliation":[{"name":"Peter the Great St. Petersburg Polytechnic University ,\u00a0Research Center of Nanobiotechnologies,\u00a0Polytechnicheskaya, 29 B,\u00a0 Saint Petersburg , 195251,","place":["Russia"]},{"name":"Institute of Molecular Genetics, Russian Academy of Sciences ,\u00a0Kurchatov Sq., 2,\u00a0 Moscow ,\u00a0123182,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikhail","family":"Panfilov","sequence":"additional","affiliation":[{"name":"Peter the Great St. Petersburg Polytechnic University ,\u00a0Research Center of Nanobiotechnologies,\u00a0Polytechnicheskaya, 29 B,\u00a0 Saint Petersburg , 195251,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0836-0732","authenticated-orcid":false,"given":"Georgii","family":"Pobegalov","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy, University College London , Gower street,\u00a0 London ,\u00a0WC1E 6BT,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alina","family":"Potyseva","sequence":"additional","affiliation":[{"name":"Peter the Great St. Petersburg Polytechnic University ,\u00a0Research Center of Nanobiotechnologies,\u00a0Polytechnicheskaya, 29 B,\u00a0 Saint Petersburg , 195251,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Polina","family":"Pavlinova","sequence":"additional","affiliation":[{"name":"Peter the Great St. Petersburg Polytechnic University ,\u00a0Research Center of Nanobiotechnologies,\u00a0Polytechnicheskaya, 29 B,\u00a0 Saint Petersburg , 195251,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2083-3643","authenticated-orcid":false,"given":"Maria","family":"Yakunina","sequence":"additional","affiliation":[{"name":"Peter the Great St. Petersburg Polytechnic University ,\u00a0Research Center of Nanobiotechnologies,\u00a0Polytechnicheskaya, 29 B,\u00a0 Saint Petersburg , 195251,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jookyung","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine ,\u00a02 Medical Center Drive,\u00a0 Stratford , NJ 08084-1489 ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sergei","family":"Borukhov","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine ,\u00a02 Medical Center Drive,\u00a0 Stratford , NJ 08084-1489 ,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9706-450X","authenticated-orcid":false,"given":"Konstantin","family":"Severinov","sequence":"additional","affiliation":[{"name":"Institute of Gene Biology, Russian Academy of Sciences , 34\/5 Vavilova Street,\u00a0 Moscow , 119334,\u00a0","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikhail","family":"Khodorkovskii","sequence":"additional","affiliation":[{"name":"Peter the Great St. Petersburg Polytechnic University ,\u00a0Research Center of 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