Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling.

Nature Communications
Soumya G RemeshMichal Hammel

Abstract

Bacterial nucleoid remodeling dependent on conserved histone-like protein, HU is one of the determining factors in global gene regulation. By imaging of near-native, unlabeled E. coli cells by soft X-ray tomography, we show that HU remodels nucleoids by promoting the formation of a dense condensed core surrounded by less condensed isolated domains. Nucleoid remodeling during cell growth and environmental adaptation correlate with pH and ionic strength controlled molecular switch that regulated HUαα dependent intermolecular DNA bundling. Through crystallographic and solution-based studies we show that these effects mechanistically rely on HUαα promiscuity in forming multiple electrostatically driven multimerization interfaces. Changes in DNA bundling consequently affects gene expression globally, likely by constrained DNA supercoiling. Taken together our findings unveil a critical function of HU-DNA interaction in nucleoid remodeling that may serve as a general microbial mechanism for transcriptional regulation to synchronize genetic responses during the cell cycle and adapt to changing environments.

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Citations

Feb 24, 2021·The EMBO Journal·Marina FericTom Misteli
Feb 19, 2021·Biophysical Journal·Haiqing Zhao
Mar 28, 2021·Trends in Cell Biology·Marina Feric, Tom Misteli
Mar 30, 2021·Frontiers in Microbiology·Monika GlinkowskaLeise Riber
Aug 24, 2021·Molecular Plant Pathology·Qian SuGuang-Tao Lu
Sep 3, 2021·Nature Communications·Marcin J SzafranDagmara Jakimowicz

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Datasets Mentioned

BETA
GSE134667

Methods Mentioned

BETA
X-ray
macromolecular crystallography
fluorescence imaging
RNA-seq
PCR
Assay
electrophoresis
size exclusion chromatography

Software Mentioned

Multi
Bcl2fastq
OriginLab
RSEM
SasView
PHASER
SCÅTTER
Chromosome Conformation Capture Analysis
AREC
Phenix Refine

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