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Title: RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription

Abstract

All organisms—bacteria, archaea, and eukaryotes—have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. In this paper, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the “σ-finger” of the bacterial transcription initiation factor σ. The structures reveal that—for both the primary σ-factor and extracytoplasmic (ECF) σ-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA—the “σ-finger” is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from ~5 nt to ~10 nt.

Authors:
 [1];  [2];  [2]; ORCiD logo [2]; ORCiD logo [3]
  1. Chinese Academy of Sciences (CAS), Shanghai (China); Univ. of Chinese Academy of Sciences, Beijing (China)
  2. Rutgers Univ., Piscataway, NJ (United States)
  3. Chinese Academy of Sciences (CAS), Shanghai (China); Rutgers Univ., Piscataway, NJ (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
Chinese Academy of Sciences (CAS); National Natural Science Foundation of China (NNSFC); National Institutes of Health (NIH)
OSTI Identifier:
1608866
Grant/Contract Number:  
31670067; 31822001; QYZDB-SSWSMC005; GM041376
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 117; Journal Issue: 11; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; transcription initiation; initial transcription; promoter escape; sigma factor; initiation factor

Citation Formats

Li, Lingting, Molodtsov, Vadim, Lin, Wei, Ebright, Richard H., and Zhang, Yu. RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription. United States: N. p., 2020. Web. https://doi.org/10.1073/pnas.1920747117.
Li, Lingting, Molodtsov, Vadim, Lin, Wei, Ebright, Richard H., & Zhang, Yu. RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription. United States. https://doi.org/10.1073/pnas.1920747117
Li, Lingting, Molodtsov, Vadim, Lin, Wei, Ebright, Richard H., and Zhang, Yu. Tue . "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription". United States. https://doi.org/10.1073/pnas.1920747117. https://www.osti.gov/servlets/purl/1608866.
@article{osti_1608866,
title = {RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription},
author = {Li, Lingting and Molodtsov, Vadim and Lin, Wei and Ebright, Richard H. and Zhang, Yu},
abstractNote = {All organisms—bacteria, archaea, and eukaryotes—have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. In this paper, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the “σ-finger” of the bacterial transcription initiation factor σ. The structures reveal that—for both the primary σ-factor and extracytoplasmic (ECF) σ-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA—the “σ-finger” is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from ~5 nt to ~10 nt.},
doi = {10.1073/pnas.1920747117},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 11,
volume = 117,
place = {United States},
year = {2020},
month = {3}
}

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