No Cover Image

Journal article 399 views 185 downloads

How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting?

Xiaobo Jing, Pavel Loskot Orcid Logo, Jin Yu

Physical Biology, Volume: 15, Issue: 6, Start page: 066007

Swansea University Author: Pavel Loskot Orcid Logo

Check full text

DOI (Published version): 10.1088/1478-3975/aad933

Abstract

Transcription plays an essential role in gene expression. The transcription bursting in bacteria has been suggested to be regulated by positive supercoiling accumulation in front of a transcribing RNA polymerase (RNAP) together with gyrase binding on DNA to release the supercoiling. In this work, we...

Full description

Published in: Physical Biology
ISSN: 1478-3975
Published: 2018
Online Access: Check full text

URI: https://cronfa.swan.ac.uk/Record/cronfa43257
Tags: Add Tag
No Tags, Be the first to tag this record!
first_indexed 2018-08-13T18:15:56Z
last_indexed 2019-09-23T14:05:29Z
id cronfa43257
recordtype SURis
fullrecord <?xml version="1.0"?><rfc1807><datestamp>2019-09-23T04:31:51.2502664</datestamp><bib-version>v2</bib-version><id>43257</id><entry>2018-08-13</entry><title>How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting?</title><swanseaauthors><author><sid>bc7cba9ef306864239b9348c3aea4c3e</sid><ORCID>0000-0002-2773-2186</ORCID><firstname>Pavel</firstname><surname>Loskot</surname><name>Pavel Loskot</name><active>true</active><ethesisStudent>false</ethesisStudent></author></swanseaauthors><date>2018-08-13</date><deptcode>EEN</deptcode><abstract>Transcription plays an essential role in gene expression. The transcription bursting in bacteria has been suggested to be regulated by positive supercoiling accumulation in front of a transcribing RNA polymerase (RNAP) together with gyrase binding on DNA to release the supercoiling. In this work, we study the supercoiling regulation in the case of a battery of RNAPs working together on DNA by constructing a multi-state quantitative model, which allows gradual and stepwise supercoiling accumulation and release in the RNAP transcription. We solved for transcription characteristics under the multi-state bursting model for a single RNAP transcription, and then simulated for a battery of RNAPs on DNA with T7 and E. coli RNAP types of traffic, respectively, probing both the average and fluctuation impacts of the supercoiling regulation. Our studies show that due to the supercoiling accumulation and release, the number of RNAP molecules loaded onto the DNA vary significantly along time in the traffic condition. Though multiple RNAPs in transcription promote the mRNA production, they also enhance the supercoiling accumulation to suppress the production. In particular, the fluctuations of the mRNA transcripts become highly pronounced for a battery of RNAPs transcribing together under the supercoiling regulation, especially for a long process of transcription elongation. In such an elongation process, though a single RNAP can work at a high duty ratio, multiple RNAPs are hardly able to do so. Our multi-state model thus provides a systematical characterization of the quantitative features of the bacterial transcription bursting; it also supports improved physical examinations on top of this general modeling framework.</abstract><type>Journal Article</type><journal>Physical Biology</journal><volume>15</volume><journalNumber>6</journalNumber><paginationStart>066007</paginationStart><publisher/><issnElectronic>1478-3975</issnElectronic><keywords/><publishedDay>31</publishedDay><publishedMonth>12</publishedMonth><publishedYear>2018</publishedYear><publishedDate>2018-12-31</publishedDate><doi>10.1088/1478-3975/aad933</doi><url/><notes/><college>COLLEGE NANME</college><department>Engineering</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>EEN</DepartmentCode><institution>Swansea University</institution><apcterm/><lastEdited>2019-09-23T04:31:51.2502664</lastEdited><Created>2018-08-13T09:29:35.5668276</Created><path><level id="1">Faculty of Science and Engineering</level><level id="2">School of Engineering and Applied Sciences - Uncategorised</level></path><authors><author><firstname>Xiaobo</firstname><surname>Jing</surname><order>1</order></author><author><firstname>Pavel</firstname><surname>Loskot</surname><orcid>0000-0002-2773-2186</orcid><order>2</order></author><author><firstname>Jin</firstname><surname>Yu</surname><order>3</order></author></authors><documents><document><filename>0043257-31082018162744.pdf</filename><originalFilename>jing2018(2).pdf</originalFilename><uploaded>2018-08-31T16:27:44.0500000</uploaded><type>Output</type><contentLength>3550357</contentLength><contentType>application/pdf</contentType><version>Accepted Manuscript</version><cronfaStatus>true</cronfaStatus><embargoDate>2019-08-09T00:00:00.0000000</embargoDate><copyrightCorrect>true</copyrightCorrect><language>eng</language></document></documents><OutputDurs/></rfc1807>
spelling 2019-09-23T04:31:51.2502664 v2 43257 2018-08-13 How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting? bc7cba9ef306864239b9348c3aea4c3e 0000-0002-2773-2186 Pavel Loskot Pavel Loskot true false 2018-08-13 EEN Transcription plays an essential role in gene expression. The transcription bursting in bacteria has been suggested to be regulated by positive supercoiling accumulation in front of a transcribing RNA polymerase (RNAP) together with gyrase binding on DNA to release the supercoiling. In this work, we study the supercoiling regulation in the case of a battery of RNAPs working together on DNA by constructing a multi-state quantitative model, which allows gradual and stepwise supercoiling accumulation and release in the RNAP transcription. We solved for transcription characteristics under the multi-state bursting model for a single RNAP transcription, and then simulated for a battery of RNAPs on DNA with T7 and E. coli RNAP types of traffic, respectively, probing both the average and fluctuation impacts of the supercoiling regulation. Our studies show that due to the supercoiling accumulation and release, the number of RNAP molecules loaded onto the DNA vary significantly along time in the traffic condition. Though multiple RNAPs in transcription promote the mRNA production, they also enhance the supercoiling accumulation to suppress the production. In particular, the fluctuations of the mRNA transcripts become highly pronounced for a battery of RNAPs transcribing together under the supercoiling regulation, especially for a long process of transcription elongation. In such an elongation process, though a single RNAP can work at a high duty ratio, multiple RNAPs are hardly able to do so. Our multi-state model thus provides a systematical characterization of the quantitative features of the bacterial transcription bursting; it also supports improved physical examinations on top of this general modeling framework. Journal Article Physical Biology 15 6 066007 1478-3975 31 12 2018 2018-12-31 10.1088/1478-3975/aad933 COLLEGE NANME Engineering COLLEGE CODE EEN Swansea University 2019-09-23T04:31:51.2502664 2018-08-13T09:29:35.5668276 Faculty of Science and Engineering School of Engineering and Applied Sciences - Uncategorised Xiaobo Jing 1 Pavel Loskot 0000-0002-2773-2186 2 Jin Yu 3 0043257-31082018162744.pdf jing2018(2).pdf 2018-08-31T16:27:44.0500000 Output 3550357 application/pdf Accepted Manuscript true 2019-08-09T00:00:00.0000000 true eng
title How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting?
spellingShingle How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting?
Pavel Loskot
title_short How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting?
title_full How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting?
title_fullStr How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting?
title_full_unstemmed How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting?
title_sort How does supercoiling regulation on a battery of RNA polymerases impact on bacterial transcription bursting?
author_id_str_mv bc7cba9ef306864239b9348c3aea4c3e
author_id_fullname_str_mv bc7cba9ef306864239b9348c3aea4c3e_***_Pavel Loskot
author Pavel Loskot
author2 Xiaobo Jing
Pavel Loskot
Jin Yu
format Journal article
container_title Physical Biology
container_volume 15
container_issue 6
container_start_page 066007
publishDate 2018
institution Swansea University
issn 1478-3975
doi_str_mv 10.1088/1478-3975/aad933
college_str Faculty of Science and Engineering
hierarchytype
hierarchy_top_id facultyofscienceandengineering
hierarchy_top_title Faculty of Science and Engineering
hierarchy_parent_id facultyofscienceandengineering
hierarchy_parent_title Faculty of Science and Engineering
department_str School of Engineering and Applied Sciences - Uncategorised{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Engineering and Applied Sciences - Uncategorised
document_store_str 1
active_str 0
description Transcription plays an essential role in gene expression. The transcription bursting in bacteria has been suggested to be regulated by positive supercoiling accumulation in front of a transcribing RNA polymerase (RNAP) together with gyrase binding on DNA to release the supercoiling. In this work, we study the supercoiling regulation in the case of a battery of RNAPs working together on DNA by constructing a multi-state quantitative model, which allows gradual and stepwise supercoiling accumulation and release in the RNAP transcription. We solved for transcription characteristics under the multi-state bursting model for a single RNAP transcription, and then simulated for a battery of RNAPs on DNA with T7 and E. coli RNAP types of traffic, respectively, probing both the average and fluctuation impacts of the supercoiling regulation. Our studies show that due to the supercoiling accumulation and release, the number of RNAP molecules loaded onto the DNA vary significantly along time in the traffic condition. Though multiple RNAPs in transcription promote the mRNA production, they also enhance the supercoiling accumulation to suppress the production. In particular, the fluctuations of the mRNA transcripts become highly pronounced for a battery of RNAPs transcribing together under the supercoiling regulation, especially for a long process of transcription elongation. In such an elongation process, though a single RNAP can work at a high duty ratio, multiple RNAPs are hardly able to do so. Our multi-state model thus provides a systematical characterization of the quantitative features of the bacterial transcription bursting; it also supports improved physical examinations on top of this general modeling framework.
published_date 2018-12-31T03:54:31Z
_version_ 1763752722336579584
score 11.012678

Similar Items