Cryo-EM structure of Escherichia coli 70 RNA polymerase and promoter DNA complex revealed a role of non-conserved region during the open complex formation

Anoop Narayanan, Frank S. Vago, Kunpeng Li, M. Zuhaib Qayyum, Dinesh Yernool, Wen Jiang, Katsuhiko Murakami

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In Escherichia coli, a primary70 factor forms the RNAP holoenzyme to express housekeeping genes. The 70 contains a large insertion between the conserved regions 1.2 and 2.1, the non-conserved region (NCR), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the E. coli RNAP70 holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 Å resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between theNCR and promoter DNA just upstream of the 10 element, which was not observed in a previously determined E. coli RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography because of restraint of crystal packing effects. Disruption of theNCR and DNA interaction by the amino acid substitutions (R157A/R157E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the NCR and DNA interaction is conserved in proteobacteria, and RNAP in other bacteria replaces its role with a transcription factor.

Original languageEnglish (US)
Pages (from-to)7367-7375
Number of pages9
JournalJournal of Biological Chemistry
Volume293
Issue number19
DOIs
StatePublished - Jan 1 2018

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DNA-Directed RNA Polymerases
Escherichia coli
DNA
Transcription
Holoenzymes
RNA
Nucleic Acid Conformation
Proteobacteria
Transcription Initiation Site
X Ray Crystallography
Essential Genes
Amino Acid Substitution
X ray crystallography
Gene expression
Transcription Factors
Machinery
Conformations
Bacteria
Substitution reactions
Genes

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

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title = "Cryo-EM structure of Escherichia coli 70 RNA polymerase and promoter DNA complex revealed a role of non-conserved region during the open complex formation",
abstract = "First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In Escherichia coli, a primary70 factor forms the RNAP holoenzyme to express housekeeping genes. The 70 contains a large insertion between the conserved regions 1.2 and 2.1, the non-conserved region (NCR), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the E. coli RNAP70 holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 {\AA} resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between theNCR and promoter DNA just upstream of the 10 element, which was not observed in a previously determined E. coli RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography because of restraint of crystal packing effects. Disruption of theNCR and DNA interaction by the amino acid substitutions (R157A/R157E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the NCR and DNA interaction is conserved in proteobacteria, and RNAP in other bacteria replaces its role with a transcription factor.",
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Cryo-EM structure of Escherichia coli 70 RNA polymerase and promoter DNA complex revealed a role of non-conserved region during the open complex formation. / Narayanan, Anoop; Vago, Frank S.; Li, Kunpeng; Qayyum, M. Zuhaib; Yernool, Dinesh; Jiang, Wen; Murakami, Katsuhiko.

In: Journal of Biological Chemistry, Vol. 293, No. 19, 01.01.2018, p. 7367-7375.

Research output: Contribution to journalArticle

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T1 - Cryo-EM structure of Escherichia coli 70 RNA polymerase and promoter DNA complex revealed a role of non-conserved region during the open complex formation

AU - Narayanan, Anoop

AU - Vago, Frank S.

AU - Li, Kunpeng

AU - Qayyum, M. Zuhaib

AU - Yernool, Dinesh

AU - Jiang, Wen

AU - Murakami, Katsuhiko

PY - 2018/1/1

Y1 - 2018/1/1

N2 - First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In Escherichia coli, a primary70 factor forms the RNAP holoenzyme to express housekeeping genes. The 70 contains a large insertion between the conserved regions 1.2 and 2.1, the non-conserved region (NCR), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the E. coli RNAP70 holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 Å resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between theNCR and promoter DNA just upstream of the 10 element, which was not observed in a previously determined E. coli RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography because of restraint of crystal packing effects. Disruption of theNCR and DNA interaction by the amino acid substitutions (R157A/R157E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the NCR and DNA interaction is conserved in proteobacteria, and RNAP in other bacteria replaces its role with a transcription factor.

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