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

Proceedings of the National Academy of Sciences of the United States of America
Lingting LiYu Zhang

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. Here, 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'-en...Continue Reading

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Citations

Aug 14, 2020·Nucleic Acids Research·Fulin WangWei Lin
Aug 28, 2020·Frontiers in Microbiology·Rishi Kishore Vishwakarma, Konstantin Brodolin
Oct 13, 2020·Biochemistry. Biokhimii︠a︡·I V Petushkov, A V Kulbachinskiy
Jan 1, 2021·The Journal of Biological Chemistry·Konstantin Brodolin, Zakia Morichaud
Oct 31, 2020·Nature Reviews. Microbiology·James ChenElizabeth A Campbell
Feb 10, 2021·Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms·Sujith PuthiyaveetilIskander M Ibrahim
Jan 12, 2021·The Journal of Biological Chemistry·Konstantin Brodolin, Zakia Morichaud
Jul 23, 2021·Proceedings of the National Academy of Sciences of the United States of America·Dylan M PlaskonM Thomas Record
Jun 22, 2021·Journal of Bacteriology·Kemardo K HenryRichard L Gourse

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