The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli

Nature Communications, vol. 14, pp. 7478

Abstract

Nucleoid associated proteins (NAPs) maintain the architecture of bacterial chromosomes and regulate gene expression. Thus, their role as transcription factors may involve three-dimensional chromosome re-organisation. While this model is supported by in vitro studies, direct in vivo evidence is lacking. Here, we use RT-qPCR and 3C-qPCR to study the transcriptional and architectural profiles of the H-NS (histone-like nucleoid structuring protein)-regulated, osmoresponsive proVWX operon of Escherichia coli at different osmolarities and provide in vivo evidence for transcription regulation by NAP-mediated chromosome re-modelling in bacteria. By consolidating our in vivo investigations with earlier in vitro and in silico studies that provide mechanistic details of how H-NS re-models DNA in response to osmolarity, we report that activation of proVWX in response to a hyperosmotic shock involves the destabilization of H-NS-mediated bridges anchored between the proVWX downstream and upstream regulatory elements (DRE and URE), and between the DRE and ygaY that lies immediately downstream of proVWX. The re-establishment of these bridges upon adaptation to hyperosmolarity represses the operon. Our results also reveal additional structural features associated with changes in proVWX transcript levels such as the decompaction of local chromatin upstream of the operon, highlighting that further complexity underlies the regulation of this model operon. H-NS and H-NS-like proteins are wide-spread amongst bacteria, suggesting that chromosome re-modelling may be a typical feature of transcriptional control in bacteria.

Authors 7

1. Fatema‐Zahra M. Rashid Aachen Centre for Interdisciplinary Genome Research Centre for Microbial Cell Biology Macromolecular Biochemistry

   Leiden University

   Affiliation as printed

   Centre for Interdisciplinary Genome Research, Leiden University, Leiden, 2333CC, The Netherlands

   Centre for Microbial Cell Biology, Leiden University, Leiden, 2333CC, The Netherlands

   Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands

   Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands

   Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands

   Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands

2. Frédéric G. E. Crémazy Aachen Macromolecular Biochemistry

   Leiden University · Inserm · Université de Versailles Saint-Quentin-en-Yvelines · Université Paris-Saclay · Infection et inflammation

   Affiliation as printed

   Laboratoire Infection et Inflammation, INSERM, UVSQ, Université Paris-Saclay, Versailles, 78180, France

   Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands

   Laboratoire Infection et Inflammation, INSERM, UVSQ, Université Paris-Saclay, Versailles, France

   Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands

3. Andreas Hofmann

   Heidelberg University

   Affiliation as printed

   Statistical Physics and Theoretical Biophysics, Heidelberg University, Heidelberg, D-69120, Germany

   Statistical Physics and Theoretical Biophysics, Heidelberg University, Heidelberg, Germany

4. David Forrest

   University of Birmingham

   Affiliation as printed

   School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK

   School of Biosciences, University of Birmingham, Edgbaston, UK

5. David C. Grainger

   University of Birmingham

   Affiliation as printed

   School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK

   School of Biosciences, University of Birmingham, Edgbaston, UK

6. Dieter W. Heermann

   Heidelberg University

   Affiliation as printed

   Statistical Physics and Theoretical Biophysics, Heidelberg University, Heidelberg, D-69120, Germany

   Statistical Physics and Theoretical Biophysics, Heidelberg University, Heidelberg, Germany

7. Remus Thei Dame corresponding Aachen Centre for Interdisciplinary Genome Research Centre for Microbial Cell Biology Macromolecular Biochemistry

   Leiden University

   Affiliation as printed

   Centre for Interdisciplinary Genome Research, Leiden University, Leiden, 2333CC, The Netherlands. rtdame@chem.leidenuniv.nl

   Centre for Microbial Cell Biology, Leiden University, Leiden, 2333CC, The Netherlands. rtdame@chem.leidenuniv.nl

   Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands. rtdame@chem.leidenuniv.nl

   Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands

   Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands

   Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands