The elemental mechanism of transcriptional pausing
Transcriptional pausing underlies regulation of cellular RNA biogenesis. A consensus pause sequence that acts on RNA polymerases (RNAPs) from bacteria to mammals halts RNAP in an elemental paused state from which longer-lived pauses can arise. Although the structural foundations of pauses prolonged...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2019-01-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/40981 |
| _version_ | 1811253169458511872 |
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| author | Jason Saba Xien Yu Chua Tatiana V Mishanina Dhananjaya Nayak Tricia A Windgassen Rachel Anne Mooney Robert Landick |
| author_facet | Jason Saba Xien Yu Chua Tatiana V Mishanina Dhananjaya Nayak Tricia A Windgassen Rachel Anne Mooney Robert Landick |
| author_sort | Jason Saba |
| collection | DOAJ |
| description | Transcriptional pausing underlies regulation of cellular RNA biogenesis. A consensus pause sequence that acts on RNA polymerases (RNAPs) from bacteria to mammals halts RNAP in an elemental paused state from which longer-lived pauses can arise. Although the structural foundations of pauses prolonged by backtracking or nascent RNA hairpins are recognized, the fundamental mechanism of the elemental pause is less well-defined. Here we report a mechanistic dissection that establishes the elemental pause signal (i) is multipartite; (ii) causes a modest conformational shift that puts γ-proteobacterial RNAP in an off-pathway state in which template base loading but not RNA translocation is inhibited; and (iii) allows RNAP to enter pretranslocated and one-base-pair backtracked states easily even though the half-translocated state observed in paused cryo-EM structures rate-limits pause escape. Our findings provide a mechanistic basis for the elemental pause and a framework to understand how pausing is modulated by sequence, cellular conditions, and regulators. |
| first_indexed | 2024-04-12T16:46:48Z |
| format | Article |
| id | doaj.art-24639bf2d563493da405524c788c5de8 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T16:46:48Z |
| publishDate | 2019-01-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-24639bf2d563493da405524c788c5de82022-12-22T03:24:33ZengeLife Sciences Publications LtdeLife2050-084X2019-01-01810.7554/eLife.40981The elemental mechanism of transcriptional pausingJason Saba0https://orcid.org/0000-0001-7273-2970Xien Yu Chua1https://orcid.org/0000-0003-2455-9493Tatiana V Mishanina2Dhananjaya Nayak3Tricia A Windgassen4Rachel Anne Mooney5Robert Landick6https://orcid.org/0000-0002-5042-0383Department of Biochemistry, University of Wisconsin-Madison, Madison, United StatesDepartment of Biochemistry, University of Wisconsin-Madison, Madison, United StatesDepartment of Biochemistry, University of Wisconsin-Madison, Madison, United StatesDepartment of Biochemistry, University of Wisconsin-Madison, Madison, United StatesDepartment of Biochemistry, University of Wisconsin-Madison, Madison, United StatesDepartment of Biochemistry, University of Wisconsin-Madison, Madison, United StatesDepartment of Biochemistry, University of Wisconsin-Madison, Madison, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, United StatesTranscriptional pausing underlies regulation of cellular RNA biogenesis. A consensus pause sequence that acts on RNA polymerases (RNAPs) from bacteria to mammals halts RNAP in an elemental paused state from which longer-lived pauses can arise. Although the structural foundations of pauses prolonged by backtracking or nascent RNA hairpins are recognized, the fundamental mechanism of the elemental pause is less well-defined. Here we report a mechanistic dissection that establishes the elemental pause signal (i) is multipartite; (ii) causes a modest conformational shift that puts γ-proteobacterial RNAP in an off-pathway state in which template base loading but not RNA translocation is inhibited; and (iii) allows RNAP to enter pretranslocated and one-base-pair backtracked states easily even though the half-translocated state observed in paused cryo-EM structures rate-limits pause escape. Our findings provide a mechanistic basis for the elemental pause and a framework to understand how pausing is modulated by sequence, cellular conditions, and regulators.https://elifesciences.org/articles/40981transcriptionRNA polymerasegene regulation |
| spellingShingle | Jason Saba Xien Yu Chua Tatiana V Mishanina Dhananjaya Nayak Tricia A Windgassen Rachel Anne Mooney Robert Landick The elemental mechanism of transcriptional pausing eLife transcription RNA polymerase gene regulation |
| title | The elemental mechanism of transcriptional pausing |
| title_full | The elemental mechanism of transcriptional pausing |
| title_fullStr | The elemental mechanism of transcriptional pausing |
| title_full_unstemmed | The elemental mechanism of transcriptional pausing |
| title_short | The elemental mechanism of transcriptional pausing |
| title_sort | elemental mechanism of transcriptional pausing |
| topic | transcription RNA polymerase gene regulation |
| url | https://elifesciences.org/articles/40981 |
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