Reciprocating RNA Polymerase batters through roadblocks
Abstract RNA polymerases must transit through protein roadblocks to produce full-length transcripts. Here we report real-time measurements of Escherichia coli RNA polymerase passing through different barriers. As intuitively expected, assisting forces facilitated, and opposing forces hindered, RNA p...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2024-04-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-47531-x |
| _version_ | 1797209266161975296 |
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| author | Jin Qian Allison Cartee Wenxuan Xu Yan Yan Bing Wang Irina Artsimovitch David Dunlap Laura Finzi |
| author_facet | Jin Qian Allison Cartee Wenxuan Xu Yan Yan Bing Wang Irina Artsimovitch David Dunlap Laura Finzi |
| author_sort | Jin Qian |
| collection | DOAJ |
| description | Abstract RNA polymerases must transit through protein roadblocks to produce full-length transcripts. Here we report real-time measurements of Escherichia coli RNA polymerase passing through different barriers. As intuitively expected, assisting forces facilitated, and opposing forces hindered, RNA polymerase passage through lac repressor protein bound to natural binding sites. Force-dependent differences were significant at magnitudes as low as 0.2 pN and were abolished in the presence of the transcript cleavage factor GreA, which rescues backtracked RNA polymerase. In stark contrast, opposing forces promoted passage when the rate of RNA polymerase backtracking was comparable to, or faster than the rate of dissociation of the roadblock, particularly in the presence of GreA. Our experiments and simulations indicate that RNA polymerase may transit after roadblocks dissociate, or undergo cycles of backtracking, recovery, and ramming into roadblocks to pass through. We propose that such reciprocating motion also enables RNA polymerase to break protein-DNA contacts that hold RNA polymerase back during promoter escape and RNA chain elongation. This may facilitate productive transcription in vivo. |
| first_indexed | 2024-04-24T09:51:58Z |
| format | Article |
| id | doaj.art-2fd007c86b294e6ba3514a48941511de |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-24T09:51:58Z |
| publishDate | 2024-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-2fd007c86b294e6ba3514a48941511de2024-04-14T11:20:34ZengNature PortfolioNature Communications2041-17232024-04-0115111110.1038/s41467-024-47531-xReciprocating RNA Polymerase batters through roadblocksJin Qian0Allison Cartee1Wenxuan Xu2Yan Yan3Bing Wang4Irina Artsimovitch5David Dunlap6Laura Finzi7Physics Department, Emory UniversityPhysics Department, Emory UniversityPhysics Department, Emory UniversityPhysics Department, Emory UniversityThe Center for RNA Biology and Department of Microbiology, The Ohio State UniversityThe Center for RNA Biology and Department of Microbiology, The Ohio State UniversityPhysics Department, Emory UniversityPhysics Department, Emory UniversityAbstract RNA polymerases must transit through protein roadblocks to produce full-length transcripts. Here we report real-time measurements of Escherichia coli RNA polymerase passing through different barriers. As intuitively expected, assisting forces facilitated, and opposing forces hindered, RNA polymerase passage through lac repressor protein bound to natural binding sites. Force-dependent differences were significant at magnitudes as low as 0.2 pN and were abolished in the presence of the transcript cleavage factor GreA, which rescues backtracked RNA polymerase. In stark contrast, opposing forces promoted passage when the rate of RNA polymerase backtracking was comparable to, or faster than the rate of dissociation of the roadblock, particularly in the presence of GreA. Our experiments and simulations indicate that RNA polymerase may transit after roadblocks dissociate, or undergo cycles of backtracking, recovery, and ramming into roadblocks to pass through. We propose that such reciprocating motion also enables RNA polymerase to break protein-DNA contacts that hold RNA polymerase back during promoter escape and RNA chain elongation. This may facilitate productive transcription in vivo.https://doi.org/10.1038/s41467-024-47531-x |
| spellingShingle | Jin Qian Allison Cartee Wenxuan Xu Yan Yan Bing Wang Irina Artsimovitch David Dunlap Laura Finzi Reciprocating RNA Polymerase batters through roadblocks Nature Communications |
| title | Reciprocating RNA Polymerase batters through roadblocks |
| title_full | Reciprocating RNA Polymerase batters through roadblocks |
| title_fullStr | Reciprocating RNA Polymerase batters through roadblocks |
| title_full_unstemmed | Reciprocating RNA Polymerase batters through roadblocks |
| title_short | Reciprocating RNA Polymerase batters through roadblocks |
| title_sort | reciprocating rna polymerase batters through roadblocks |
| url | https://doi.org/10.1038/s41467-024-47531-x |
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