<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.1d3 20150301//EN"  "JATS-archivearticle1.dtd"><article xmlns:xlink="http://www.w3.org/1999/xlink" article-type="research-article" dtd-version="1.1d3"><front><journal-meta><journal-id journal-id-type="nlm-ta">elife</journal-id><journal-id journal-id-type="publisher-id">eLife</journal-id><journal-title-group><journal-title>eLife</journal-title></journal-title-group><issn publication-format="electronic">2050-084X</issn><publisher><publisher-name>eLife Sciences Publications, Ltd</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">105545</article-id><article-id pub-id-type="doi">10.7554/eLife.105545</article-id><article-categories><subj-group subj-group-type="display-channel"><subject>Research Article</subject></subj-group><subj-group subj-group-type="heading"><subject>Biochemistry and Chemical Biology</subject></subj-group><subj-group subj-group-type="heading"><subject>Structural Biology and Molecular Biophysics</subject></subj-group></article-categories><title-group><article-title>Pleomorphic effects of three small-molecule inhibitors on transcription elongation by <italic>Mycobacterium tuberculosis</italic> RNA polymerase</article-title></title-group><contrib-group><contrib contrib-type="author" id="author-409340"><name><surname>Herrera-Asmat</surname><given-names>Omar</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-404511"><name><surname>Tong</surname><given-names>Alexander B</given-names></name><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-3793-2533</contrib-id><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-409341"><name><surname>Lin</surname><given-names>Wenxia</given-names></name><xref ref-type="aff" rid="aff2">2</xref><xref ref-type="other" rid="par-3"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-409356"><name><surname>Kong</surname><given-names>Tiantian</given-names></name><xref ref-type="aff" rid="aff3">3</xref><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-158769"><name><surname>Del Valle</surname><given-names>Juan R</given-names></name><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-8315-5264</contrib-id><xref ref-type="aff" rid="aff4">4</xref><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-409357"><name><surname>Guerra</surname><given-names>Daniel G</given-names></name><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-2410-722X</contrib-id><xref ref-type="aff" rid="aff5">5</xref><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-11089"><name><surname>Ebright</surname><given-names>Yon W</given-names></name><xref ref-type="aff" rid="aff6">6</xref><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-109074"><name><surname>Ebridght</surname><given-names>Richard H</given-names></name><xref ref-type="aff" rid="aff6">6</xref><xref ref-type="other" rid="par-1"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" corresp="yes" id="author-35524"><name><surname>Bustamante</surname><given-names>Carlos</given-names></name><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-2970-0073</contrib-id><xref ref-type="aff" rid="aff2">2</xref><xref ref-type="corresp" rid="cor1">*</xref><xref ref-type="other" rid="par-2"/><xref ref-type="other" rid="par-4"/><xref ref-type="fn" rid="conf1"/></contrib><aff id="aff1"><institution content-type="dept">Jason L Choy Laboratory of Single-Molecule Biophysics</institution>, <institution>University of California, Berkeley</institution>, <addr-line><named-content content-type="city">Berkeley</named-content></addr-line>, <country>United States</country></aff><aff id="aff2"><institution content-type="dept">California Institute for Quantitative Biosciences</institution>, <institution>University of California, Berkeley</institution>, <addr-line><named-content content-type="city">Berkeley</named-content></addr-line>, <country>United States</country></aff><aff id="aff3"><institution content-type="dept">Department of Biomedical Engineering</institution>, <institution>Shenzhen University</institution>, <addr-line><named-content content-type="city">Shenzhen</named-content></addr-line>, <country>China</country></aff><aff id="aff4"><institution content-type="dept">Department of Chemistry and Biochemistry</institution>, <institution>University of Notre Dame</institution>, <addr-line><named-content content-type="city">Notre Dame</named-content></addr-line>, <country>United States</country></aff><aff id="aff5"><institution content-type="dept">Laboratorio de Moléculas Individuales</institution>, <institution>Universidad Peruana Cayetano Heredia</institution>, <addr-line><named-content content-type="city">Lima</named-content></addr-line>, <country>Peru</country></aff><aff id="aff6"><institution content-type="dept">Waksman Institute</institution>, <institution>Rutgers, The State University of New Jersey</institution>, <addr-line><named-content content-type="city">Piscataway</named-content></addr-line>, <country>United States</country></aff></contrib-group><contrib-group content-type="section"><contrib contrib-type="editor" id="author-38389"><name><surname>Xiao</surname><given-names>Jie</given-names></name><role>Reviewing editor</role><aff><institution>Johns Hopkins University</institution>, <country>United States</country></aff></contrib></contrib-group><author-notes><corresp id="cor1"><label>*</label>For correspondence: <email>carlosb@berkeley.edu</email> (CB);</corresp></author-notes><pub-date date-type="pub" publication-format="electronic"><day>03</day><month>10</month><year>2025</year></pub-date><volume>14</volume><elocation-id>e105545</elocation-id><history><date date-type="received"><day>09</day><month>12</month><year>2024</year></date><date date-type="accepted"><day>02</day><month>10</month><year>2025</year></date></history><permissions><copyright-statement>© 2025, Herrera-Asmat et al</copyright-statement><copyright-year>2025</copyright-year><copyright-holder>Herrera-Asmat et al</copyright-holder><license xlink:href="https://creativecommons.org/licenses/by/4.0/"><license-p>This article is distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use and redistribution provided that the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="elife-105545-v1.pdf"/><abstract><p>The <italic>Mycobacterium tuberculosis</italic> RNA polymerase (MtbRNAP) is the target of the first-line anti-tuberculosis inhibitor rifampin, however, the emergence of rifampin resistance necessitates the development of new antibiotics. Here, we communicate the first single-molecule characterization of MtbRNAP elongation and its inhibition by three diverse small-molecule inhibitors: N(α)-aroyl-N-aryl-phenylalaninamide (D-IX216), streptolydigin (Stl), and pseudouridimycin (PUM) using high-resolution optical tweezers. Compared to <italic>Escherichia coli</italic> RNA polymerase (EcoRNAP), MtbRNAP transcribes more slowly, has similar mechanical robustness, and only weakly recognizes <italic>E. coli</italic> pause sequences. The three small-molecule inhibitors of MtbRNAP exhibit strikingly different effects on transcription elongation. In the presence of D-IX216, which inhibits RNAP active-center bridge-helix motions required for nucleotide addition, the enzyme exhibits transitions between slowly and super-slowly elongating inhibited states. Stl, which inhibits the RNAP trigger-loop motions also required for nucleotide addition, inhibits RNAP primarily by inducing pausing and backtracking. PUM, a nucleoside analog of UTP, in addition to acting as a competitive inhibitor, induces the formation of slowly elongating RNAP inhibited states. Our results indicate that the three classes of small-molecule inhibitors affect the enzyme in distinct ways and show that the combination of Stl and D-IX216, which both target the RNAP bridge helix, has a strong synergistic effect on the enzyme.</p></abstract><kwd-group kwd-group-type="research-organism"><title>Research organism</title><kwd><italic>E. coli</italic></kwd></kwd-group><funding-group><award-group id="par-1"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000002</institution-id><institution>National Institutes of Health</institution></institution-wrap></funding-source><award-id>GM041376</award-id><principal-award-recipient><name><surname>Ebridght</surname><given-names>Richard H</given-names></name></principal-award-recipient></award-group><award-group id="par-2"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000002</institution-id><institution>National Institutes of Health</institution></institution-wrap></funding-source><award-id>R01GM032543</award-id><principal-award-recipient><name><surname>Bustamante</surname><given-names>Carlos</given-names></name></principal-award-recipient></award-group><award-group id="par-3"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100001809</institution-id><institution>National Natural Science Foundation of China</institution></institution-wrap></funding-source><award-id>31900883</award-id><principal-award-recipient><name><surname>Lin</surname><given-names>Wenxia</given-names></name></principal-award-recipient></award-group><award-group id="par-4"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000011</institution-id><institution>Howard Hughes Medical Institute</institution></institution-wrap></funding-source><principal-award-recipient><name><surname>Bustamante</surname><given-names>Carlos</given-names></name></principal-award-recipient></award-group><funding-statement>The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.</funding-statement></funding-group></article-meta></front><back><sec id="s1" sec-type="additional-information"><title>Additional information</title><fn-group content-type="competing-interest"><title>Competing interest</title><fn fn-type="conflict" id="conf1"><p>The authors declare that no competing interests exist.</p></fn></fn-group></sec><sec id="s2" sec-type="supplementary-material"><title>Additional Files</title><sec id="s3" sec-type="data-availability"><title>Data availability</title><p>All oligos/plasmids used in this study are available upon reasonable request. See Supplementary Tables S1-S3 for a list of materials.Transcription traces are available from Dryad at https://doi.org/10.5061/dryad.2fqz6130m.Matlab code used for analysis is available on Github at https://doi.org/10.5281/zenodo.15232932.</p><p>The following datasets were generated:</p><p><element-citation id="dataset1" publication-type="data" specific-use="isSupplementedBy"><person-group person-group-type="author"><collab>Herrera-Asmat O</collab><collab>Tong AB</collab><collab>Bustamante C</collab></person-group><year iso-8601-date="2025">2025</year><source>Single-molecule optical tweezers data of transcription of M.tuberculosis and E.coli RNAP in the presence of single-molecule inhibitors</source><ext-link ext-link-type="uri" xlink:href="https://doi.org/10.5061/dryad.2fqz6130m">https://doi.org/10.5061/dryad.2fqz6130m</ext-link><comment>Dryad Digital Repository, doi:10.5061/dryad.2fqz6130m</comment></element-citation></p></sec><supplementary-material><ext-link xlink:href="elife-105545-supp-v1.zip">Download zip</ext-link><p>Any figures and tables for this article are included in the PDF. The zip folder contains additional supplemental files.</p></supplementary-material></sec></back></article>