Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling

Sangjin Kim; Bruno Beltran; Irnov Irnov; Christine Jacobs-Wagner

doi:10.1016/j.cell.2019.08.033

Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling

Cell. 2019 Sep 19;179(1):106-119.e16. doi: 10.1016/j.cell.2019.08.033.

Authors

Sangjin Kim¹, Bruno Beltran², Irnov Irnov³, Christine Jacobs-Wagner⁴

Affiliations

¹ Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA. Electronic address: sangjin@illinois.edu.
² Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA.
³ Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA.
⁴ Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA. Electronic address: christine.jacobs-wagner@yale.edu.

PMID: 31539491
DOI: 10.1016/j.cell.2019.08.033

Abstract

Genes are often transcribed by multiple RNA polymerases (RNAPs) at densities that can vary widely across genes and environmental conditions. Here, we provide in vitro and in vivo evidence for a built-in mechanism by which co-transcribing RNAPs display either collaborative or antagonistic dynamics over long distances (>2 kb) through transcription-induced DNA supercoiling. In Escherichia coli, when the promoter is active, co-transcribing RNAPs translocate faster than a single RNAP, but their average speed is not altered by large variations in promoter strength and thus RNAP density. Environmentally induced promoter repression reduces the elongation efficiency of already-loaded RNAPs, causing premature termination and quick synthesis arrest of no-longer-needed proteins. This negative effect appears independent of RNAP convoy formation and is abrogated by topoisomerase I activity. Antagonistic dynamics can also occur between RNAPs from divergently transcribed gene pairs. Our findings may be broadly applicable given that transcription on topologically constrained DNA is the norm across organisms.

Keywords: DNA supercoiling; RNA polymerase; gene regulation; group dynamics; premature termination; transcription elongation.

MeSH terms

DNA, Bacterial / genetics*
DNA, Superhelical / genetics*
DNA-Directed RNA Polymerases / chemistry
DNA-Directed RNA Polymerases / genetics*
Escherichia coli / genetics*
Gene Expression Regulation, Bacterial / genetics
Glucose / pharmacology
Glycosides / pharmacology
Isopropyl Thiogalactoside / pharmacology
Kinetics
Lac Operon / drug effects
Lac Operon / genetics
Plasmids / genetics
Promoter Regions, Genetic / genetics
RNA, Bacterial / genetics
Real-Time Polymerase Chain Reaction
Rifampin / pharmacology
Transcription, Genetic*

Substances

DNA, Bacterial
DNA, Superhelical
Glycosides
RNA, Bacterial
2-nitrophenyl-beta-fucoside
Isopropyl Thiogalactoside
DNA-Directed RNA Polymerases
Glucose
Rifampin