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Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding.


ABSTRACT: A key regulated step of transcription is promoter melting by RNA polymerase (RNAP) to form the open promoter complex1-3. To generate the open complex, the conserved catalytic core of the RNAP combines with initiation factors to locate promoter DNA, unwind 12-14 base pairs of the DNA duplex and load the template-strand DNA into the RNAP active site. Formation of the open complex is a multi-step process during which transient intermediates of unknown structure are formed4-6. Here we present cryo-electron microscopy structures of bacterial RNAP-promoter DNA complexes, including structures of partially melted intermediates. The structures show that late steps of promoter melting occur within the RNAP cleft, delineate key roles for fork-loop 2 and switch 2-universal structural features of RNAP-in restricting access of DNA to the RNAP active site, and explain why clamp opening is required to allow entry of single-stranded template DNA into the active site. The key roles of fork-loop 2 and switch 2 suggest a common mechanism for late steps in promoter DNA opening to enable gene expression across all domains of life.

SUBMITTER: Boyaci H 

PROVIDER: S-EPMC6399747 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding.

Boyaci Hande H   Chen James J   Jansen Rolf R   Darst Seth A SA   Campbell Elizabeth A EA  

Nature 20190109 7739


A key regulated step of transcription is promoter melting by RNA polymerase (RNAP) to form the open promoter complex<sup>1-3</sup>. To generate the open complex, the conserved catalytic core of the RNAP combines with initiation factors to locate promoter DNA, unwind 12-14 base pairs of the DNA duplex and load the template-strand DNA into the RNAP active site. Formation of the open complex is a multi-step process during which transient intermediates of unknown structure are formed<sup>4-6</sup>.  ...[more]

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