Genome-wide transcription regulation and chromosome structural arrangement by GalR in E. coli
The regulatory protein, GalR, is known for controlling transcription of genes related to D-galactose metabolism in Escherichia coli. Here, using a combination of experimental and bioinformatic approaches, we identify novel GalR binding sites upstream of several genes whose function is not directly r...
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doaj-f89e3f841dfe4bae9cc06ab9e2174c9c2020-11-24T21:58:55ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2016-11-01310.3389/fmolb.2016.00074224342Genome-wide transcription regulation and chromosome structural arrangement by GalR in E. coliZhong Qian0Andrei Trostel1Dale Eugene Alexis Lewis2Sang Jun Lee3Ximiao He4Anne M Stringer5Joseph T Wade6Joseph T Wade7Thomas D Schneider8Tim Durfee9Sankar Adhya10NIH/NCINIH/NCINIH/NCIKorea Research Institute of Bioscience and BiotechnologyNIH/NCIWadsworth Center, New York State Department of HealthWadsworth Center, New York State Department of HealthSchool of Public Health, University of AlbanyNational Institutes of Health, National Cancer Institute, Center for Cancer Research,DNASTAR, Inc.,NIH/NCIThe regulatory protein, GalR, is known for controlling transcription of genes related to D-galactose metabolism in Escherichia coli. Here, using a combination of experimental and bioinformatic approaches, we identify novel GalR binding sites upstream of several genes whose function is not directly related to D-galactose metabolism. Moreover, we do not observe regulation of these genes by GalR under standard growth conditions. Thus, our data indicate a broader regulatory role for GalR, and suggest that regulation by GalR is modulated by other factors. Surprisingly, we detect regulation of 158 transcripts by GalR, with few regulated genes being associated with a nearby GalR binding site. Based on our earlier observation of long-range interactions between distally bound GalR dimers, we propose that GalR indirectly regulates the transcription of many genes by inducing large-scale restructuring of the chromosome.http://journal.frontiersin.org/Journal/10.3389/fmolb.2016.00074/fullChIP-chipnucleoidMega-loopSuperhelicity.GalR regulon |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Zhong Qian Andrei Trostel Dale Eugene Alexis Lewis Sang Jun Lee Ximiao He Anne M Stringer Joseph T Wade Joseph T Wade Thomas D Schneider Tim Durfee Sankar Adhya |
spellingShingle |
Zhong Qian Andrei Trostel Dale Eugene Alexis Lewis Sang Jun Lee Ximiao He Anne M Stringer Joseph T Wade Joseph T Wade Thomas D Schneider Tim Durfee Sankar Adhya Genome-wide transcription regulation and chromosome structural arrangement by GalR in E. coli Frontiers in Molecular Biosciences ChIP-chip nucleoid Mega-loop Superhelicity. GalR regulon |
author_facet |
Zhong Qian Andrei Trostel Dale Eugene Alexis Lewis Sang Jun Lee Ximiao He Anne M Stringer Joseph T Wade Joseph T Wade Thomas D Schneider Tim Durfee Sankar Adhya |
author_sort |
Zhong Qian |
title |
Genome-wide transcription regulation and chromosome structural arrangement by GalR in E. coli |
title_short |
Genome-wide transcription regulation and chromosome structural arrangement by GalR in E. coli |
title_full |
Genome-wide transcription regulation and chromosome structural arrangement by GalR in E. coli |
title_fullStr |
Genome-wide transcription regulation and chromosome structural arrangement by GalR in E. coli |
title_full_unstemmed |
Genome-wide transcription regulation and chromosome structural arrangement by GalR in E. coli |
title_sort |
genome-wide transcription regulation and chromosome structural arrangement by galr in e. coli |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Molecular Biosciences |
issn |
2296-889X |
publishDate |
2016-11-01 |
description |
The regulatory protein, GalR, is known for controlling transcription of genes related to D-galactose metabolism in Escherichia coli. Here, using a combination of experimental and bioinformatic approaches, we identify novel GalR binding sites upstream of several genes whose function is not directly related to D-galactose metabolism. Moreover, we do not observe regulation of these genes by GalR under standard growth conditions. Thus, our data indicate a broader regulatory role for GalR, and suggest that regulation by GalR is modulated by other factors. Surprisingly, we detect regulation of 158 transcripts by GalR, with few regulated genes being associated with a nearby GalR binding site. Based on our earlier observation of long-range interactions between distally bound GalR dimers, we propose that GalR indirectly regulates the transcription of many genes by inducing large-scale restructuring of the chromosome. |
topic |
ChIP-chip nucleoid Mega-loop Superhelicity. GalR regulon |
url |
http://journal.frontiersin.org/Journal/10.3389/fmolb.2016.00074/full |
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