The Impact of Global Transcriptional Regulation on Bacterial Gene Order.
Mathematical Biosciences
Microbial Genetics
Microbiology
Journal
iScience
ISSN: 2589-0042
Titre abrégé: iScience
Pays: United States
ID NLM: 101724038
Informations de publication
Date de publication:
24 Apr 2020
24 Apr 2020
Historique:
received:
18
08
2019
revised:
15
12
2019
accepted:
27
03
2020
pubmed:
14
4
2020
medline:
14
4
2020
entrez:
14
4
2020
Statut:
ppublish
Résumé
Bacterial gene expression depends on the allocation of limited transcriptional resources provided a particular growth rate and growth condition. Early studies in a few genes suggested this global regulation to generate a unifying hyperbolic expression pattern. Here, we developed a large-scale method that generalizes these experiments to quantify the response to growth of over 700 genes that a priori do not exhibit any specific control. We distinguish a core subset following a promoter-specific hyperbolic response. Within this group, we sort genes with regard to their responsiveness to the global regulatory program to show that those with a particularly sensitive linear response are located near the origin of replication. We then find evidence that this genomic architecture is biologically significant by examining position conservation of E. coli genes in 100 bacteria. The response to the transcriptional resources of the cell results in an additional feature contributing to bacterial genome organization.
Identifiants
pubmed: 32283521
pii: S2589-0042(20)30213-3
doi: 10.1016/j.isci.2020.101029
pmc: PMC7155222
pii:
doi:
Types de publication
Journal Article
Langues
eng
Pagination
101029Informations de copyright
Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of Interests The authors declare no competing interest.
Références
Biophys J. 1974 Feb;14(2):119-23
pubmed: 4591542
Mol Syst Biol. 2013;9:634
pubmed: 23340840
PLoS Comput Biol. 2009 Oct;5(10):e1000545
pubmed: 19851443
Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):E1038-47
pubmed: 25695966
Microbiol Mol Biol Rev. 1998 Jun;62(2):434-64
pubmed: 9618448
J Gen Microbiol. 1958 Dec;19(3):607-16
pubmed: 13611203
J Gen Microbiol. 1958 Dec;19(3):592-606
pubmed: 13611202
BMC Evol Biol. 2007 Sep 23;7:169
pubmed: 17888177
Curr Biol. 2017 May 8;27(9):1278-1287
pubmed: 28416114
Mol Microbiol. 2006 Mar;59(5):1506-18
pubmed: 16468991
Trends Genet. 2005 Aug;21(8):440-3
pubmed: 15978695
Nucleic Acids Res. 2014 Oct;42(18):11383-92
pubmed: 25209233
PLoS One. 2008;3(11):e3657
pubmed: 18987754
Mol Microbiol. 2008 Jun;68(5):1128-48
pubmed: 18430135
Nucleic Acids Res. 2012 Oct;40(18):8979-92
pubmed: 22833608
EMBO J. 2004 Oct 27;23(21):4330-41
pubmed: 15470498
Science. 2010 Nov 19;330(6007):1099-102
pubmed: 21097934
J Mol Biol. 1999 Sep 10;292(1):19-37
pubmed: 10493854
Trends Microbiol. 2016 Oct;24(10):788-800
pubmed: 27364121
Mol Biosyst. 2015 Apr;11(4):1184-93
pubmed: 25712329
Mol Syst Biol. 2013 Apr 16;9:658
pubmed: 23591774
Nat Commun. 2016 Mar 30;7:11055
pubmed: 27025941
Proc Biol Sci. 2018 Jun 13;285(1880):
pubmed: 29899074
Nat Microbiol. 2016 Sep 12;1(11):16160
pubmed: 27617693
J Mol Biol. 1968 Feb 14;31(3):519-40
pubmed: 4866337
Mol Syst Biol. 2017 Jan 3;13(1):903
pubmed: 28049137
Science. 2013 Nov 29;342(6162):1237435
pubmed: 24288338
Cell. 2009 Dec 24;139(7):1366-75
pubmed: 20064380
Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):E42-50
pubmed: 22184251
mBio. 2017 Feb 28;8(1):
pubmed: 28246358
Plasmid. 2004 Jul;52(1):13-30
pubmed: 15212889
Nucleic Acids Res. 2015 Feb 18;43(3):1783-94
pubmed: 25618851
Proc Natl Acad Sci U S A. 1998 Aug 18;95(17):9761-6
pubmed: 9707549
Biophys Rev. 2016 Nov;8(Suppl 1):89-100
pubmed: 28510216
Nat Genet. 2003 Aug;34(4):377-8
pubmed: 12847524
Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20245-50
pubmed: 19073937
Trends Genet. 2016 Nov;32(11):717-723
pubmed: 27575299
Nat Methods. 2006 Aug;3(8):623-8
pubmed: 16862137