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Utilization of variably spaced promoter‐like elements by the bacterial RNA polymerase holoenzyme during early elongation
Author(s) -
Devi Pukhrambam Grihanjali,
Campbell Elizabeth A.,
Darst Seth A.,
Nickels Bryce E.
Publication year - 2010
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1111/j.1365-2958.2009.07021.x
Subject(s) - biology , elongation , rna polymerase ii , rna polymerase , rna processing , polymerase , promoter , rna , genetics , gene , gene expression , materials science , metallurgy , ultimate tensile strength
Summary The bacterial RNA polymeras holoenzyme consists of a catalytic core enzyme in complex with a σ factor that is required for promoter‐specific transcription initiation. During initiation, members of the σ 70 family of σ factors contact two conserved promoter elements, the −10 and −35 elements, which are separated by ∼17 base pairs (bp). σ 70 family members contain four flexibly linked domains. Two of these domains, σ 2 and σ 4 , contain determinants for interactions with the promoter −10 and −35 elements respectively. σ 2 and σ 4 also contain core‐binding determinants. When bound to core the inter‐domain distance between σ 2 and σ 4 matches the distance between promoter elements separated by ∼17 bp. Prior work indicates that during early elongation the nascent RNA‐assisted displacement of σ 4 from core can enable the holoenzyme to adopt a configuration in which σ 2 and σ 4 are bound to ‘promoter‐like’ DNA elements separated by a single base pair. Here we demonstrate that holoenzyme can also adopt configurations in which σ 2 and σ 4 are bound to ‘promoter‐like’ DNA elements separated by 0, 2 or 3 bp. Thus, our findings suggest that displacement of σ 4 from core enables the RNA polymerase holoenzyme to adopt a broad range of ‘elongation‐specific’ configurations.