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The effect of macromolecular crowding on single-round transcription by Escherichia coli RNA polymerase.
Chung, SangYoon; Lerner, Eitan; Jin, Yan; Kim, Soohong; Alhadid, Yazan; Grimaud, Logan Wilson; Zhang, Irina X; Knobler, Charles M; Gelbart, William M; Weiss, Shimon.
Afiliación
  • Chung S; Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA.
  • Lerner E; Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA.
  • Jin Y; Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
  • Kim S; Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA.
  • Alhadid Y; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Grimaud LW; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
  • Zhang IX; Interdepartmental Program in Molecular, Cellular, and Integrative Physiology, University of California, Los Angeles, CA 90095, USA.
  • Knobler CM; Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA.
  • Gelbart WM; Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA.
  • Weiss S; Department of Chemistry and Biochemistry, University of California Los Angeles, CA 90095, USA.
Nucleic Acids Res ; 47(3): 1440-1450, 2019 02 20.
Article en En | MEDLINE | ID: mdl-30590739
Previous works have reported significant effects of macromolecular crowding on the structure and behavior of biomolecules. The crowded intracellular environment, in contrast to in vitro buffer solutions, likely imparts similar effects on biomolecules. The enzyme serving as the gatekeeper for the genome, RNA polymerase (RNAP), is among the most regulated enzymes. Although it was previously demonstrated that macromolecular crowding affects association of RNAP to DNA, not much is known about how crowding acts on late initiation and promoter clearance steps, which are considered to be the rate-determining steps for many promoters. Here, we demonstrate that macromolecular crowding enhances the rate of late initiation and promoter clearance using in vitro quenching-based single-molecule kinetics assays. Moreover, the enhancement's dependence on crowder size notably deviates from predictions by the scaled-particle theory, commonly used for description of crowding effects. Our findings shed new light on how enzymatic reactions could be affected by crowded conditions in the cellular milieu.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Transcripción Genética / ARN Polimerasas Dirigidas por ADN / Proteínas de Unión al ADN Tipo de estudio: Prognostic_studies Idioma: En Revista: Nucleic Acids Res Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Transcripción Genética / ARN Polimerasas Dirigidas por ADN / Proteínas de Unión al ADN Tipo de estudio: Prognostic_studies Idioma: En Revista: Nucleic Acids Res Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido