Mechanism for De Novo RNA Synthesis and Initiating Nucleotide Specificity by T7 RNA Polymerase

William P. Kennedy, Jamila R. Momand, Yuhui Yin

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

DNA-directed RNA polymerases are capable of initiating synthesis of RNA without primers, the first catalytic stage of initiation is referred to as de novo RNA synthesis. De novo synthesis is a unique phase in the transcription cycle where the RNA polymerase binds two nucleotides rather than a nascent RNA polymer and a single nucleotide. For bacteriophage T7 RNA polymerase, transcription begins with a marked preference for GTP at the + 1 and + 2 positions. We determined the crystal structures of T7 RNA polymerase complexes captured during the de novo RNA synthesis. The DNA substrates in the structures in the complexes contain a common Φ10 duplex promoter followed by a unique five base single-stranded extension of template DNA whose sequences varied at positions + 1 and + 2, thereby allowing for different pairs of initiating nucleotides GTP, ATP, CTP or UTP to bind. The structures show that the initiating nucleotides bind RNA polymerase in locations distinct from those described previously for elongation complexes. Selection bias in favor of GTP as an initiating nucleotide is accomplished by shape complementarity, extensive protein side-chain and strong base-stacking interactions for the guanine moiety in the enzyme active site. Consequently, an initiating GTP provides the largest stabilization force for the open promoter conformation.

Original languageEnglish (US)
Pages (from-to)256-268
Number of pages13
JournalJournal of Molecular Biology
Volume370
Issue number2
DOIs
StatePublished - Jul 6 2007
Externally publishedYes

Fingerprint

Guanosine Triphosphate
Nucleotides
RNA
DNA-Directed RNA Polymerases
Cytidine Triphosphate
Uridine Triphosphate
Selection Bias
Guanine
Catalytic Domain
Polymers
Adenosine Triphosphate
bacteriophage T7 RNA polymerase
DNA
Enzymes
Proteins

Keywords

  • de novo RVA synthesis
  • GTP specificity
  • T7 RNA polymerase

ASJC Scopus subject areas

  • Virology

Cite this

Mechanism for De Novo RNA Synthesis and Initiating Nucleotide Specificity by T7 RNA Polymerase. / Kennedy, William P.; Momand, Jamila R.; Yin, Yuhui.

In: Journal of Molecular Biology, Vol. 370, No. 2, 06.07.2007, p. 256-268.

Research output: Contribution to journalArticle

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