Transcription-coupled DNA supercoiling dictates the chromosomal arrangement of bacterial genes

Nucleic Acids Research
Patrick Sobetzko

Abstract

Over the recent decade, the central importance of DNA supercoiling in chromosome organization and global gene regulation of bacteria became more and more visible. With a regulon comprising more than 2000 genes in Escherichia coli, DNA supercoiling is among the most influential regulators of gene expression found in bacteria so far. However, the mechanism creating thousands of diverse temporal gene expression patterns coordinated by DNA supercoiling remains unclear. In this study we show that a specific chromosomal arrangement of genes modulates the local levels of DNA supercoiling at gene promoters via transcription-coupled DNA supercoiling (TCDS) in the model organism E. coli. Our findings provide a consistent explanation for the strong positive coupling of temporal gene expression patterns of neighboring genes. Using comparative genomics we are furthermore able to provide evidence that TCDS is a driving force for the evolution of chromosomal gene arrangement patterns in other Enterobacteriaceae. With the currently available data of promoter supercoiling sensitivity we prove that the same principle is applicable also for the evolutionary distant gram-positive pathogenic bacterium Streptococcus pneumoniae. Moreover, our finding...Continue Reading

References

Dec 1, 1990·Trends in Genetics : TIG·K Drlica
Feb 20, 1985·Journal of Molecular Biology·J G BrahmsV Vagner
Oct 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·L F Liu, J C Wang
Nov 14, 1972·Journal of Molecular Biology·A Worcel, E Burgi
Jan 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·R R Sinden, D E Pettijohn
Sep 20, 1995·Molecular & General Genetics : MGG·H TanakaF Imamoto
Dec 24, 1997·Molecular Microbiology·R SchneiderG Muskhelishvili
Jan 8, 1999·Journal of Molecular Biology·D Chen, D M Lilley
Nov 29, 2002·Frontiers in Bioscience : a Journal and Virtual Library·Chien-Chung Chen, Hai-Young Wu
Jul 31, 2003·Journal of Molecular Biology·Helge AunerAndrew Travers
Jul 17, 2004·Genes & Development·Lisa PostowNicholas R Cozzarelli
Nov 13, 2004·Genome Biology·Kyeong Soo JeongArkady B Khodursky
Nov 13, 2004·Genome Biology·Brian J PeterNicholas R Cozzarelli
Feb 3, 2005·Nature Reviews. Microbiology·Andrew Travers, Georgi Muskhelishvili
Jan 15, 2008·Nature Structural & Molecular Biology·Fedor KouzineDavid Levens
Feb 21, 2008·BMC Systems Biology·Carsten MarrGeorgi Muskhelishvili
Mar 17, 2011·BMC Systems Biology·Nikolaus SonnenscheinMarc-Thorsten Hütt
Dec 21, 2011·Proceedings of the National Academy of Sciences of the United States of America·Patrick SobetzkoGeorgi Muskhelishvili
Jun 20, 2012·Microbiology and Immunology·Mukesh Kumar YadavJae-Jun Song
Oct 25, 2012·Nucleic Acids Research·Feng GaoChun-Ting Zhang
Jul 19, 2013·Transcription·Catherine NaughtonNick Gilbert
Jul 16, 2014·PloS One·María-José FerrándizAdela G de la Campa
Sep 5, 2014·PLoS Computational Biology·Sam Meyer, Guillaume Beslon
Dec 9, 2014·SpringerPlus·Alejandra Gutiérrez-EstradaMaría Del Carmen Gómez-Eichelmann
Feb 5, 2015·The Journal of Biological Chemistry·Veneta GerganovaGeorgi Muskhelishvili

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Citations

Jul 2, 2016·Trends in Microbiology·Jelle Slager, Jan-Willem Veening
Oct 16, 2016·Biophysics Reviews·Agnes NoySarah A Harris
Sep 3, 2016·PLoS Genetics·Jakob Frimodt-MøllerAnders Løbner-Olesen
Jan 22, 2017·Biophysical Journal·Agnes NoySarah A Harris
Mar 15, 2018·Nucleic Acids Research·Yan YanLaura Finzi
Mar 24, 2018·Annual Review of Biophysics·David L ShisOleg A Igoshin
Nov 1, 2017·Proceedings of the National Academy of Sciences of the United States of America·Zhong QianSankar Adhya
Mar 3, 2017·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Dominic J O' Lee
Jun 3, 2016·Clinical Science·Charles J DormanMatthew J Dorman
Dec 31, 2016·Biophysics Reviews·Agnes NoySarah A Harris
Apr 19, 2017·PloS One·Lucia PannierJulio Collado-Vides
Jun 20, 2019·Nucleic Acids Research·Bilal El HoudaiguiSam Meyer
Jul 12, 2017·The Journal of Biological Chemistry·Xiaoduo ZhiFenfei Leng
May 17, 2017·Biophysics Reviews·Georgi Muskhelishvili, Andrew Travers
May 13, 2018·International Journal of Molecular Sciences·Qingxuan ZhouYuk-Ching Tse-Dinh
Apr 12, 2017·Nucleic Acids Research·Qingxuan ZhouYuk-Ching Tse-Dinh
Dec 1, 2017·Current Genetics·Sam MeyerGeorgi Muskhelishvili
May 17, 2017·Biophysics Reviews·Charles J Dorman, Matthew J Dorman
Mar 20, 2019·Nature Reviews. Genetics·Paul B TalbertSteven Henikoff
Nov 22, 2019·Frontiers in Bioengineering and Biotechnology·Carlo A KleinPatrick Sobetzko
May 17, 2017·Biophysics Reviews·Charles J Dorman, Matthew J Dorman
Nov 3, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Ovidiu PopaOliver Ebenhöh
Aug 28, 2019·Computational and Structural Biotechnology Journal·Shiny Martis BSam Meyer
Mar 9, 2021·ELife·Anna Nagy-StaronCalin C Guet
Aug 11, 2020·Metabolic Engineering Communications·Julie E ChavesJoshua K Michener
Aug 17, 2021·Protein Science : a Publication of the Protein Society·Alexandre Duprey, Eduardo A Groisman
Dec 4, 2021·Physical Review Letters·Purba ChatterjeeSangjin Kim
Dec 25, 2021·Nucleic Acids Research·Shubham TripathiHerbert Levine

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