The Impact of Global Transcriptional Regulation on Bacterial Gene Order

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...

Full description

Saved in:

Bibliographic Details
Published in	iScience Vol. 23; no. 4; p. 101029
Main Authors	Yubero, Pablo, Poyatos, Juan F.
Format	Journal Article
Language	English
Published	United States Elsevier Inc 24.04.2020 Elsevier
Subjects	Mathematical Biosciences Microbial Genetics Microbiology Microbiology Mathematical Biosciences Microbial Genetics
Online Access	Get full text
ISSN	2589-0042 2589-0042
DOI	10.1016/j.isci.2020.101029

Cover

Abstract	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. [Display omitted] •Cell physiology determines a global transcriptional regulatory program•Constitutive genes show a differential response to this global regulation•The most responsive constitutive genes are located near the origin of replication•Global transcriptional regulation acts as a gene position conservation force Microbiology; Microbial Genetics; Mathematical Biosciences
AbstractList	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. [Display omitted] •Cell physiology determines a global transcriptional regulatory program•Constitutive genes show a differential response to this global regulation•The most responsive constitutive genes are located near the origin of replication•Global transcriptional regulation acts as a gene position conservation force Microbiology; Microbial Genetics; Mathematical Biosciences 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. • Cell physiology determines a global transcriptional regulatory program • Constitutive genes show a differential response to this global regulation • The most responsive constitutive genes are located near the origin of replication • Global transcriptional regulation acts as a gene position conservation force Microbiology; Microbial Genetics; Mathematical Biosciences 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. : Microbiology; Microbial Genetics; Mathematical Biosciences Subject Areas: Microbiology, Microbial Genetics, Mathematical Biosciences 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.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. 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.
ArticleNumber	101029
Author	Yubero, Pablo Poyatos, Juan F.
AuthorAffiliation	1 Logic of Genomic Systems Laboratory, CNB - CSIC, Madrid 28049, Spain
AuthorAffiliation_xml	– name: 1 Logic of Genomic Systems Laboratory, CNB - CSIC, Madrid 28049, Spain
Author_xml	– sequence: 1 givenname: Pablo surname: Yubero fullname: Yubero, Pablo organization: Logic of Genomic Systems Laboratory, CNB - CSIC, Madrid 28049, Spain – sequence: 2 givenname: Juan F. surname: Poyatos fullname: Poyatos, Juan F. email: jpoyatos@cnb.csic.es organization: Logic of Genomic Systems Laboratory, CNB - CSIC, Madrid 28049, Spain
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/32283521$$D View this record in MEDLINE/PubMed
BookMark	eNqNUVtrFDEUHqRia-0f8EHm0ZddTy4zk4AIWnRdKBRkfQ6Z5Mw2SzYZMzOV_nuzO7W0PhQh5HLyXc7ldXESYsCieEtgSYDUH3ZLNxi3pECPAaDyRXFGKyEXAJyePLqfFhfDsAPISKBc1q-KU0apYBUlZ8Vqc4Plet9rM5axK1c-ttqXm6TDYJLrRxdDfv_A7eT14VHm9SWDMbkcX2HA8jpZTG-Kl532A17cn-fFz29fN5ffF1fXq_Xl56uFyXbjggFSMF3dCMIMBybzXklmQROobcsEMR1vKtlJLWlta6g7zHfLkaNtgLPzYj3r2qh3qk9ur9OditqpYyCmrdJpdMajko1umayZqdqKC6wEcINEg22EaEwtsxabtabQ67vf2vsHQQLq0GW1U4cuq0OX1dzlzPo0s_qp3aM1GMak_ZNUnv4Ed6O28VY1pKoopVng_b1Air8mHEa1zybovQ4Yp0FRJmTOjgNk6LvHXg8mf-eXAWIGmBSHIWGnjBuPg8rWzj9fB_2H-l_Ff5xJmGd86zCpjMBg0LqEZsxDcM_R_wARJtU9
CitedBy_id	crossref_primary_10_3389_fmicb_2023_1119878 crossref_primary_10_1007_s11270_023_06829_0 crossref_primary_10_1016_j_amc_2020_125914 crossref_primary_10_1021_acssynbio_3c00009 crossref_primary_10_1093_molbev_msab193 crossref_primary_10_1128_mbio_03432_22
Cites_doi	10.1111/j.1365-2958.2008.06229.x 10.1073/pnas.1108229109 10.1038/msb.2013.14 10.1126/science.1192588 10.1111/j.1365-2958.2006.05046.x 10.1371/journal.pcbi.1000545 10.1038/sj.emboj.7600434 10.1128/MMBR.62.2.434-464.1998 10.1099/00221287-19-3-607 10.1073/pnas.95.17.9761 10.1126/science.1237435 10.1186/1471-2148-7-169 10.1093/nar/gks694 10.1006/jmbi.1999.3056 10.1016/j.tig.2005.06.002 10.1016/j.cell.2009.12.001 10.1016/0022-2836(68)90425-7 10.1038/nmeth895 10.1039/C4MB00721B 10.1016/S0006-3495(74)70003-0 10.1098/rspb.2018.0789 10.1371/journal.pone.0003657 10.1073/pnas.0804953105 10.1016/j.cub.2017.03.022 10.1128/mBio.00097-17 10.1073/pnas.1416533112 10.1093/nar/gkv040 10.1038/nmicrobiol.2016.160 10.1038/msb.2012.70 10.15252/msb.20167402 10.1016/j.plasmid.2004.04.001 10.1038/ng1209 10.1007/s12551-016-0238-2 10.1016/j.tim.2016.06.003 10.1016/j.tig.2016.08.006 10.1099/00221287-19-3-592 10.1093/nar/gku828 10.1038/ncomms11055
ContentType	Journal Article
Copyright	2020 The Author(s) Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved. 2020 The Author(s) 2020
Copyright_xml	– notice: 2020 The Author(s) – notice: Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved. – notice: 2020 The Author(s) 2020
DBID	6I. AAFTH AAYXX CITATION NPM 7X8 5PM ADTOC UNPAY DOA
DOI	10.1016/j.isci.2020.101029
DatabaseName	ScienceDirect Open Access Titles Elsevier:ScienceDirect:Open Access CrossRef PubMed MEDLINE - Academic PubMed Central (Full Participant titles) Unpaywall for CDI: Periodical Content Unpaywall DOAJ Directory of Open Access Journals
DatabaseTitle	CrossRef PubMed MEDLINE - Academic
DatabaseTitleList	MEDLINE - Academic PubMed
Database_xml	– sequence: 1 dbid: DOA name: Directory of Open Access Journals url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 3 dbid: UNPAY name: Unpaywall url: https://proxy.k.utb.cz/login?url=https://unpaywall.org/ sourceTypes: Open Access Repository
DeliveryMethod	fulltext_linktorsrc
EISSN	2589-0042
ExternalDocumentID	oai_doaj_org_article_97ab3963c5b548e5804ce1a0d7887c69 10.1016/j.isci.2020.101029 PMC7155222 32283521 10_1016_j_isci_2020_101029 S2589004220302133
Genre	Journal Article
GroupedDBID	0R~ 53G 6I. AACTN AAEDW AAFTH AALRI AAMRU AAXUO ABMAC ADBBV ADVLN AEXQZ AFTJW AITUG ALMA_UNASSIGNED_HOLDINGS AMRAJ AOIJS BCNDV EBS FDB GROUPED_DOAJ HYE M41 OK1 ROL RPM SSZ AAYWO AAYXX ACVFH ADCNI AEUPX AFPUW AIGII AKBMS AKYEP APXCP CITATION EJD NCXOZ NPM 7X8 5PM ADTOC UNPAY
ID	FETCH-LOGICAL-c521t-30e20cf67813c40393c4593d0a106db381cf4759f9a926d606fef9ad4e4ed7043
IEDL.DBID	UNPAY
ISSN	2589-0042
IngestDate	Fri Oct 03 12:45:00 EDT 2025 Sun Oct 26 03:39:28 EDT 2025 Tue Sep 30 16:34:48 EDT 2025 Thu Oct 02 06:18:13 EDT 2025 Thu Jan 02 22:57:40 EST 2025 Tue Jul 01 01:03:29 EDT 2025 Thu Apr 24 22:52:08 EDT 2025 Sun Apr 06 06:53:08 EDT 2025
IsDoiOpenAccess	true
IsOpenAccess	true
IsPeerReviewed	true
IsScholarly	true
Issue	4
Keywords	Microbiology Mathematical Biosciences Microbial Genetics
Language	English
License	This is an open access article under the CC BY license. Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). cc-by
LinkModel	DirectLink
MergedId	FETCHMERGED-LOGICAL-c521t-30e20cf67813c40393c4593d0a106db381cf4759f9a926d606fef9ad4e4ed7043
Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Lead Contact
OpenAccessLink	https://proxy.k.utb.cz/login?url=http://www.cell.com/article/S2589004220302133/pdf
PMID	32283521
PQID	2389693400
PQPubID	23479
ParticipantIDs	doaj_primary_oai_doaj_org_article_97ab3963c5b548e5804ce1a0d7887c69 unpaywall_primary_10_1016_j_isci_2020_101029 pubmedcentral_primary_oai_pubmedcentral_nih_gov_7155222 proquest_miscellaneous_2389693400 pubmed_primary_32283521 crossref_citationtrail_10_1016_j_isci_2020_101029 crossref_primary_10_1016_j_isci_2020_101029 elsevier_sciencedirect_doi_10_1016_j_isci_2020_101029
ProviderPackageCode	CITATION AAYXX
PublicationCentury	2000
PublicationDate	2020-04-24
PublicationDateYYYYMMDD	2020-04-24
PublicationDate_xml	– month: 04 year: 2020 text: 2020-04-24 day: 24
PublicationDecade	2020
PublicationPlace	United States
PublicationPlace_xml	– name: United States
PublicationTitle	iScience
PublicationTitleAlternate	iScience
PublicationYear	2020
Publisher	Elsevier Inc Elsevier
Publisher_xml	– name: Elsevier Inc – name: Elsevier
References	Couturier, Rocha (bib8) 2006; 59 Si, Li, Cox, Sauls, Azizi, Sou, Schwartz, Erickstad, Jun, Li, Jun (bib33) 2017; 27 del Solar, Giraldo, Ruiz-Echevarría, Espinosa, Díaz-Orejas (bib9) 1998; 62 Gibson, Wilson, Feil, Eyre-Walker (bib15) 2018; 285 Liang, Bipatnath, Xu, Chen, Dennis, Ehrenberg, Bremer (bib23) 1999; 292 Block, Hussein, Liang, Lim (bib3) 2012; 40 Camas, Poyatos (bib6) 2008; 3 Gerosa, Kochanowski, Heinemann, Sauer (bib14) 2013; 9 Gyorfy, Draskovits, Vernyik, Blattner, Gaal, Posfai (bib16) 2015; 43 Morrison, Chattoraj (bib25) 2004; 52 Slager, Veening (bib34) 2016; 24 Berthoumieux, de Jong, Baptist, Pinel, Ranquet, Ropers, Geiselmann (bib2) 2013; 9 Kubitschek (bib21) 1974; 14 Deris, Kim, Zhang, Okano, Hermsen, Groisman, Hwa (bib10) 2013; 342 Lal, Dhar, Trostel, Kouzine, Seshasayee, Adhya (bib22) 2016; 7 Zaslaver, Bren, Ronen, Itzkovitz, Kikoin, Shavit, Liebermeister, Surette, Alon (bib40) 2006; 3 Schaechter, Maaloe, Kjeldgaard (bib31) 1958; 19 Kjeldgaard, Maaloe, Schaechter (bib17) 1958; 19 Klumpp, Zhang, Hwa (bib19) 2009; 139 Estrem, Gaal, Ross, Gourse (bib13) 1998; 95 Parter, Kashtan, Alon (bib27) 2007; 7 Weiße, Oyarzún, Danos, Swain (bib39) 2015; 112 Kochanowski, Gerosa, Brunner, Christodoulou, Nikolaev, Sauer (bib20) 2017; 13 Roller, Stoddard, Schmidt (bib30) 2016; 1 Sobetzko, Travers, Muskhelishvili (bib35) 2012; 109 Traxler, Summers, Nguyen, Zacharia, Hightower, Smith, Conway (bib37) 2008; 68 Peebo, Valgepea, Maser, Nahku, Adamberg, Vilu (bib28) 2015; 11 Zaslaver, Kaplan, Bren, Jinich, Mayo, Dekel, Alon, Itzkovitz (bib41) 2009; 5 Donachie, Robinson (bib11) 1987 Valens, Penaud, Rossignol, Cornet, Boccard (bib38) 2004; 23 Dorman, Dorman (bib12) 2016; 8 Scott, Gunderson, Mateescu, Zhang, Hwa (bib32) 2010; 330 Bremer, Dennis (bib4) 1996; 2 Nanninga, Woldringh (bib26) 1985 Bar-Ziv, Voichek, Barkai (bib1) 2016; 32 Cooper, Helmstetter (bib7) 1968; 31 Klumpp, Hwa (bib18) 2008; 105 Mitchison (bib24) 2005; 21 Bryant, Sellars, Busby, Lee (bib5) 2014; 42 Rocha, Danchin (bib29) 2003; 34 Soler-Bistué, Timmermans, Mazel (bib36) 2017; 8 del Solar (10.1016/j.isci.2020.101029_bib9) 1998; 62 Kochanowski (10.1016/j.isci.2020.101029_bib20) 2017; 13 Liang (10.1016/j.isci.2020.101029_bib23) 1999; 292 Klumpp (10.1016/j.isci.2020.101029_bib18) 2008; 105 Rocha (10.1016/j.isci.2020.101029_bib29) 2003; 34 Scott (10.1016/j.isci.2020.101029_bib32) 2010; 330 Valens (10.1016/j.isci.2020.101029_bib38) 2004; 23 Gyorfy (10.1016/j.isci.2020.101029_bib16) 2015; 43 Nanninga (10.1016/j.isci.2020.101029_bib26) 1985 Mitchison (10.1016/j.isci.2020.101029_bib24) 2005; 21 Peebo (10.1016/j.isci.2020.101029_bib28) 2015; 11 Zaslaver (10.1016/j.isci.2020.101029_bib41) 2009; 5 Lal (10.1016/j.isci.2020.101029_bib22) 2016; 7 Sobetzko (10.1016/j.isci.2020.101029_bib35) 2012; 109 Gerosa (10.1016/j.isci.2020.101029_bib14) 2013; 9 Gibson (10.1016/j.isci.2020.101029_bib15) 2018; 285 Schaechter (10.1016/j.isci.2020.101029_bib31) 1958; 19 Camas (10.1016/j.isci.2020.101029_bib6) 2008; 3 Dorman (10.1016/j.isci.2020.101029_bib12) 2016; 8 Traxler (10.1016/j.isci.2020.101029_bib37) 2008; 68 Bar-Ziv (10.1016/j.isci.2020.101029_bib1) 2016; 32 Block (10.1016/j.isci.2020.101029_bib3) 2012; 40 Soler-Bistué (10.1016/j.isci.2020.101029_bib36) 2017; 8 Roller (10.1016/j.isci.2020.101029_bib30) 2016; 1 Cooper (10.1016/j.isci.2020.101029_bib7) 1968; 31 Deris (10.1016/j.isci.2020.101029_bib10) 2013; 342 Kjeldgaard (10.1016/j.isci.2020.101029_bib17) 1958; 19 Morrison (10.1016/j.isci.2020.101029_bib25) 2004; 52 Kubitschek (10.1016/j.isci.2020.101029_bib21) 1974; 14 Si (10.1016/j.isci.2020.101029_bib33) 2017; 27 Zaslaver (10.1016/j.isci.2020.101029_bib40) 2006; 3 Klumpp (10.1016/j.isci.2020.101029_bib19) 2009; 139 Berthoumieux (10.1016/j.isci.2020.101029_bib2) 2013; 9 Weiße (10.1016/j.isci.2020.101029_bib39) 2015; 112 Bryant (10.1016/j.isci.2020.101029_bib5) 2014; 42 Parter (10.1016/j.isci.2020.101029_bib27) 2007; 7 Donachie (10.1016/j.isci.2020.101029_bib11) 1987 Estrem (10.1016/j.isci.2020.101029_bib13) 1998; 95 Couturier (10.1016/j.isci.2020.101029_bib8) 2006; 59 Slager (10.1016/j.isci.2020.101029_bib34) 2016; 24 Bremer (10.1016/j.isci.2020.101029_bib4) 1996; 2
References_xml	– volume: 342 start-page: 1237435 year: 2013 ident: bib10 article-title: The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria publication-title: Science – volume: 14 start-page: 119 year: 1974 end-page: 123 ident: bib21 article-title: Constancy of the ratio of DNA to cell volume in steady-state cultures of Escherichia coli B-r publication-title: Biophys. J. – volume: 7 start-page: 169 year: 2007 ident: bib27 article-title: Environmental variability and modularity of bacterial metabolic networks publication-title: BMC Evol. Biol. – volume: 62 start-page: 434 year: 1998 end-page: 464 ident: bib9 article-title: Replication and control of circular bacterial plasmids publication-title: Microbiol. Mol. Biol. Rev. – volume: 34 start-page: 377 year: 2003 end-page: 378 ident: bib29 article-title: Essentiality, not expressiveness, drives gene-strand bias in bacteria publication-title: Nat. Genet. – volume: 27 start-page: 1278 year: 2017 end-page: 1287 ident: bib33 article-title: Invariance of initiation mass and predictability of cell size in Escherichia coli publication-title: Curr. Biol. – volume: 109 start-page: E42 year: 2012 end-page: E50 ident: bib35 article-title: Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle publication-title: Proc. Natl. Acad. Sci. U S A. – volume: 3 start-page: 623 year: 2006 end-page: 628 ident: bib40 article-title: A comprehensive library of fluorescent transcriptional reporters for publication-title: Nat. Methods – volume: 13 start-page: 903 year: 2017 ident: bib20 article-title: Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli publication-title: Mol. Syst. Biol. – start-page: 259 year: 1985 end-page: 318 ident: bib26 article-title: Cell Growth, Genome Duplication, and Cell Division. Molecular Cytology of Escherichia coli – volume: 330 start-page: 1099 year: 2010 end-page: 1102 ident: bib32 article-title: Interdependence of cell growth and gene expression: origins and consequences publication-title: Science – volume: 105 start-page: 20245 year: 2008 end-page: 20250 ident: bib18 article-title: Growth-rate-dependent partitioning of RNA polymerases in bacteria publication-title: Proc. Natl. Acad. Sci. U S A – volume: 8 start-page: 89 year: 2016 end-page: 100 ident: bib12 article-title: DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression publication-title: Biophys. Rev. – volume: 285 start-page: 20180789 year: 2018 ident: bib15 article-title: The distribution of bacterial doubling times in the wild publication-title: Proc. R. Soc. B – volume: 11 start-page: 1184 year: 2015 end-page: 1193 ident: bib28 article-title: Proteome reallocation in Escherichia coli with increasing specific growth rate publication-title: Mol. Biosyst. – volume: 32 start-page: 717 year: 2016 end-page: 723 ident: bib1 article-title: Dealing with gene-dosage imbalance during S phase publication-title: Trends Genet. – volume: 95 start-page: 9761 year: 1998 end-page: 9766 ident: bib13 article-title: Identification of an UP element consensus sequence for bacterial promoters publication-title: Proc. Natl. Acad. Sci. U S A – volume: 9 start-page: 658 year: 2013 ident: bib14 article-title: Dissecting specific and global transcriptional regulation of bacterial gene expression publication-title: Mol. Syst. Biol. – volume: 19 start-page: 607 year: 1958 end-page: 616 ident: bib17 article-title: The transition between different physiological states during balanced growth of Salmonella typhimurium publication-title: J. Gen. Microbiol. – volume: 5 start-page: e1000545 year: 2009 ident: bib41 article-title: Invariant distribution of promoter activities in Escherichia coli publication-title: PLoS Comput. Biol. – volume: 42 start-page: 11383 year: 2014 end-page: 11392 ident: bib5 article-title: Chromosome position effects on gene expression in Escherichia coli K-12 publication-title: Nucleic Acids Res. – volume: 8 start-page: e00097-17 year: 2017 ident: bib36 article-title: The proximity of ribosomal protein genes to oriC enhances Vibrio cholerae fitness in the absence of multifork replication publication-title: mBio – volume: 43 start-page: 1783 year: 2015 end-page: 1794 ident: bib16 article-title: Engineered ribosomal RNA operon copy-number variants of E. coli reveal the evolutionary trade-offs shaping rRNA operon number publication-title: Nucleic Acids Res. – volume: 1 start-page: 16160 year: 2016 ident: bib30 article-title: Exploiting rRNA operon copy number to investigate bacterial reproductive strategies publication-title: Nat. Microbiol. – volume: 7 start-page: 11055 year: 2016 ident: bib22 article-title: Genome scale patterns of supercoiling in a bacterial chromosome publication-title: Nat. Commun. – volume: 40 start-page: 8979 year: 2012 end-page: 8992 ident: bib3 article-title: Regulatory consequences of gene translocation in bacteria publication-title: Nucleic Acids Res. – volume: 59 start-page: 1506 year: 2006 end-page: 1518 ident: bib8 article-title: Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes publication-title: Mol. Microbiol. – volume: 19 start-page: 592 year: 1958 end-page: 606 ident: bib31 article-title: Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium publication-title: J. Gen. Microbiol. – start-page: 1578 year: 1987 end-page: 1593 ident: bib11 article-title: Cell Division: Parameter Values and the Process. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology – volume: 139 start-page: 1366 year: 2009 end-page: 1375 ident: bib19 article-title: Growth rate-dependent global effects on gene expression in bacteria publication-title: Cell – volume: 2 start-page: 1553 year: 1996 end-page: 1569 ident: bib4 article-title: Modulation of chemical composition and other parameters of the cell by growth rate. E coli Salmonella publication-title: Cell. Mol Biol. – volume: 68 start-page: 1128 year: 2008 end-page: 1148 ident: bib37 article-title: The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli publication-title: Mol. Microbiol. – volume: 21 start-page: 440 year: 2005 end-page: 443 ident: bib24 article-title: The regional rule for bacterial base composition publication-title: Trends Genet. – volume: 52 start-page: 13 year: 2004 end-page: 30 ident: bib25 article-title: Replication of a unit-copy plasmid F in the bacterial cell cycle: a replication rate function analysis publication-title: Plasmid – volume: 9 year: 2013 ident: bib2 article-title: Shared control of gene expression in bacteria by transcription factors and global physiology of the cell publication-title: Mol. Syst. Biol. – volume: 23 start-page: 4330 year: 2004 end-page: 4341 ident: bib38 article-title: Macrodomain organization of the Escherichia coli chromosome publication-title: EMBO J. – volume: 112 start-page: E1038 year: 2015 end-page: E1047 ident: bib39 article-title: Mechanistic links between cellular trade-offs, gene expression, and growth publication-title: Proc. Natl. Acad. Sci. U S A – volume: 292 start-page: 19 year: 1999 end-page: 37 ident: bib23 article-title: Activities of constitutive promoters in Escherichia coli publication-title: J. Mol. Biol. – volume: 3 start-page: e3657 year: 2008 ident: bib6 article-title: What determines the assembly of transcriptional network Motifs in Escherichia coli? publication-title: PLoS One – volume: 31 start-page: 519 year: 1968 end-page: 540 ident: bib7 article-title: Chromosome replication and the division cycle of Escherichia coli Br publication-title: J. Mol. Biol. – volume: 24 start-page: 788 year: 2016 end-page: 800 ident: bib34 article-title: Hard-wired control of bacterial processes by chromosomal gene location publication-title: Trends Microbiol. – volume: 68 start-page: 1128 year: 2008 ident: 10.1016/j.isci.2020.101029_bib37 article-title: The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli publication-title: Mol. Microbiol. doi: 10.1111/j.1365-2958.2008.06229.x – volume: 109 start-page: E42 year: 2012 ident: 10.1016/j.isci.2020.101029_bib35 article-title: Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle publication-title: Proc. Natl. Acad. Sci. U S A. doi: 10.1073/pnas.1108229109 – volume: 9 start-page: 658 year: 2013 ident: 10.1016/j.isci.2020.101029_bib14 article-title: Dissecting specific and global transcriptional regulation of bacterial gene expression publication-title: Mol. Syst. Biol. doi: 10.1038/msb.2013.14 – volume: 330 start-page: 1099 year: 2010 ident: 10.1016/j.isci.2020.101029_bib32 article-title: Interdependence of cell growth and gene expression: origins and consequences publication-title: Science doi: 10.1126/science.1192588 – volume: 59 start-page: 1506 year: 2006 ident: 10.1016/j.isci.2020.101029_bib8 article-title: Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes publication-title: Mol. Microbiol. doi: 10.1111/j.1365-2958.2006.05046.x – volume: 5 start-page: e1000545 year: 2009 ident: 10.1016/j.isci.2020.101029_bib41 article-title: Invariant distribution of promoter activities in Escherichia coli publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.1000545 – volume: 23 start-page: 4330 year: 2004 ident: 10.1016/j.isci.2020.101029_bib38 article-title: Macrodomain organization of the Escherichia coli chromosome publication-title: EMBO J. doi: 10.1038/sj.emboj.7600434 – volume: 62 start-page: 434 year: 1998 ident: 10.1016/j.isci.2020.101029_bib9 article-title: Replication and control of circular bacterial plasmids publication-title: Microbiol. Mol. Biol. Rev. doi: 10.1128/MMBR.62.2.434-464.1998 – volume: 19 start-page: 607 year: 1958 ident: 10.1016/j.isci.2020.101029_bib17 article-title: The transition between different physiological states during balanced growth of Salmonella typhimurium publication-title: J. Gen. Microbiol. doi: 10.1099/00221287-19-3-607 – start-page: 259 year: 1985 ident: 10.1016/j.isci.2020.101029_bib26 – start-page: 1578 year: 1987 ident: 10.1016/j.isci.2020.101029_bib11 – volume: 2 start-page: 1553 year: 1996 ident: 10.1016/j.isci.2020.101029_bib4 article-title: Modulation of chemical composition and other parameters of the cell by growth rate. E coli Salmonella publication-title: Cell. Mol Biol. – volume: 95 start-page: 9761 year: 1998 ident: 10.1016/j.isci.2020.101029_bib13 article-title: Identification of an UP element consensus sequence for bacterial promoters publication-title: Proc. Natl. Acad. Sci. U S A doi: 10.1073/pnas.95.17.9761 – volume: 342 start-page: 1237435 year: 2013 ident: 10.1016/j.isci.2020.101029_bib10 article-title: The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria publication-title: Science doi: 10.1126/science.1237435 – volume: 7 start-page: 169 year: 2007 ident: 10.1016/j.isci.2020.101029_bib27 article-title: Environmental variability and modularity of bacterial metabolic networks publication-title: BMC Evol. Biol. doi: 10.1186/1471-2148-7-169 – volume: 40 start-page: 8979 year: 2012 ident: 10.1016/j.isci.2020.101029_bib3 article-title: Regulatory consequences of gene translocation in bacteria publication-title: Nucleic Acids Res. doi: 10.1093/nar/gks694 – volume: 292 start-page: 19 year: 1999 ident: 10.1016/j.isci.2020.101029_bib23 article-title: Activities of constitutive promoters in Escherichia coli publication-title: J. Mol. Biol. doi: 10.1006/jmbi.1999.3056 – volume: 21 start-page: 440 year: 2005 ident: 10.1016/j.isci.2020.101029_bib24 article-title: The regional rule for bacterial base composition publication-title: Trends Genet. doi: 10.1016/j.tig.2005.06.002 – volume: 139 start-page: 1366 year: 2009 ident: 10.1016/j.isci.2020.101029_bib19 article-title: Growth rate-dependent global effects on gene expression in bacteria publication-title: Cell doi: 10.1016/j.cell.2009.12.001 – volume: 31 start-page: 519 year: 1968 ident: 10.1016/j.isci.2020.101029_bib7 article-title: Chromosome replication and the division cycle of Escherichia coli Br publication-title: J. Mol. Biol. doi: 10.1016/0022-2836(68)90425-7 – volume: 3 start-page: 623 year: 2006 ident: 10.1016/j.isci.2020.101029_bib40 article-title: A comprehensive library of fluorescent transcriptional reporters for Escherichia coli publication-title: Nat. Methods doi: 10.1038/nmeth895 – volume: 11 start-page: 1184 year: 2015 ident: 10.1016/j.isci.2020.101029_bib28 article-title: Proteome reallocation in Escherichia coli with increasing specific growth rate publication-title: Mol. Biosyst. doi: 10.1039/C4MB00721B – volume: 14 start-page: 119 year: 1974 ident: 10.1016/j.isci.2020.101029_bib21 article-title: Constancy of the ratio of DNA to cell volume in steady-state cultures of Escherichia coli B-r publication-title: Biophys. J. doi: 10.1016/S0006-3495(74)70003-0 – volume: 285 start-page: 20180789 year: 2018 ident: 10.1016/j.isci.2020.101029_bib15 article-title: The distribution of bacterial doubling times in the wild publication-title: Proc. R. Soc. B doi: 10.1098/rspb.2018.0789 – volume: 3 start-page: e3657 year: 2008 ident: 10.1016/j.isci.2020.101029_bib6 article-title: What determines the assembly of transcriptional network Motifs in Escherichia coli? publication-title: PLoS One doi: 10.1371/journal.pone.0003657 – volume: 105 start-page: 20245 year: 2008 ident: 10.1016/j.isci.2020.101029_bib18 article-title: Growth-rate-dependent partitioning of RNA polymerases in bacteria publication-title: Proc. Natl. Acad. Sci. U S A doi: 10.1073/pnas.0804953105 – volume: 27 start-page: 1278 year: 2017 ident: 10.1016/j.isci.2020.101029_bib33 article-title: Invariance of initiation mass and predictability of cell size in Escherichia coli publication-title: Curr. Biol. doi: 10.1016/j.cub.2017.03.022 – volume: 8 start-page: e00097-17 year: 2017 ident: 10.1016/j.isci.2020.101029_bib36 article-title: The proximity of ribosomal protein genes to oriC enhances Vibrio cholerae fitness in the absence of multifork replication publication-title: mBio doi: 10.1128/mBio.00097-17 – volume: 112 start-page: E1038 year: 2015 ident: 10.1016/j.isci.2020.101029_bib39 article-title: Mechanistic links between cellular trade-offs, gene expression, and growth publication-title: Proc. Natl. Acad. Sci. U S A doi: 10.1073/pnas.1416533112 – volume: 43 start-page: 1783 year: 2015 ident: 10.1016/j.isci.2020.101029_bib16 article-title: Engineered ribosomal RNA operon copy-number variants of E. coli reveal the evolutionary trade-offs shaping rRNA operon number publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkv040 – volume: 1 start-page: 16160 year: 2016 ident: 10.1016/j.isci.2020.101029_bib30 article-title: Exploiting rRNA operon copy number to investigate bacterial reproductive strategies publication-title: Nat. Microbiol. doi: 10.1038/nmicrobiol.2016.160 – volume: 9 year: 2013 ident: 10.1016/j.isci.2020.101029_bib2 article-title: Shared control of gene expression in bacteria by transcription factors and global physiology of the cell publication-title: Mol. Syst. Biol. doi: 10.1038/msb.2012.70 – volume: 13 start-page: 903 year: 2017 ident: 10.1016/j.isci.2020.101029_bib20 article-title: Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli publication-title: Mol. Syst. Biol. doi: 10.15252/msb.20167402 – volume: 52 start-page: 13 year: 2004 ident: 10.1016/j.isci.2020.101029_bib25 article-title: Replication of a unit-copy plasmid F in the bacterial cell cycle: a replication rate function analysis publication-title: Plasmid doi: 10.1016/j.plasmid.2004.04.001 – volume: 34 start-page: 377 year: 2003 ident: 10.1016/j.isci.2020.101029_bib29 article-title: Essentiality, not expressiveness, drives gene-strand bias in bacteria publication-title: Nat. Genet. doi: 10.1038/ng1209 – volume: 8 start-page: 89 year: 2016 ident: 10.1016/j.isci.2020.101029_bib12 article-title: DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression publication-title: Biophys. Rev. doi: 10.1007/s12551-016-0238-2 – volume: 24 start-page: 788 year: 2016 ident: 10.1016/j.isci.2020.101029_bib34 article-title: Hard-wired control of bacterial processes by chromosomal gene location publication-title: Trends Microbiol. doi: 10.1016/j.tim.2016.06.003 – volume: 32 start-page: 717 year: 2016 ident: 10.1016/j.isci.2020.101029_bib1 article-title: Dealing with gene-dosage imbalance during S phase publication-title: Trends Genet. doi: 10.1016/j.tig.2016.08.006 – volume: 19 start-page: 592 year: 1958 ident: 10.1016/j.isci.2020.101029_bib31 article-title: Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium publication-title: J. Gen. Microbiol. doi: 10.1099/00221287-19-3-592 – volume: 42 start-page: 11383 year: 2014 ident: 10.1016/j.isci.2020.101029_bib5 article-title: Chromosome position effects on gene expression in Escherichia coli K-12 publication-title: Nucleic Acids Res. doi: 10.1093/nar/gku828 – volume: 7 start-page: 11055 year: 2016 ident: 10.1016/j.isci.2020.101029_bib22 article-title: Genome scale patterns of supercoiling in a bacterial chromosome publication-title: Nat. Commun. doi: 10.1038/ncomms11055
SSID	ssj0002002496
Score	2.1561108
Snippet	Bacterial gene expression depends on the allocation of limited transcriptional resources provided a particular growth rate and growth condition. Early studies...
SourceID	doaj unpaywall pubmedcentral proquest pubmed crossref elsevier
SourceType	Open Website Open Access Repository Aggregation Database Index Database Enrichment Source Publisher
StartPage	101029
SubjectTerms	Mathematical Biosciences Microbial Genetics Microbiology
SummonAdditionalLinks	– databaseName: DOAJ Directory of Open Access Journals dbid: DOA link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1LS8NAEF6kF72I4iu-iOBNg0k2u-keVXweFETB27LZB7aUtKhF_PfO7Ca1paAehB6abZo2s99mvmFnviHkMO9WgjMKYYliLAH-b5IqK3nieCVKkTnUHMNsizt-_VTcPrPnqVZfmBMW5IGD4U5EqSoKKNGsAnJtWTcttM1UajANTnNfupd2xVQw1ffbayiF5zvLMcwJAmg2FTMhuQsrXiE4zP1A6vnlt1fy4v0zzmmefM7nUC6O65H6_FCDwZSDulwhyw2zjE_DHa2SBVuvkSuAQXzjKyHjoYuDwn_sHVT7uIDjh9CQHg5ieJ0FAWcYR03q-B7FOdfJ0-XF4_l10vROSDS2KEhoavNUO3BFGdUFFuDqgglqUgUxoKnAT2uHUn9OKJFzA2GMs_DeFLawpkwLukE69bC2WyRWjnFrwdiZxeVuBKO5E7yi1JVdUZqIZK3tpG6ExbG_xUC2GWR9ifaWaG8Z7B2Ro8l3RkFW48ezz3BKJmeiJLYfAKDIBijyN6BEhLUTKht2EVgDXKr3448ftLMvYenhfoqq7XD8JoHtCC4oPAUjshnQMPmLFGWFYCYiUs7gZOYeZj-pey9e3rtEVbw8j8jxBFF_sNH2f9hohyzhJXG3LC92Sef9dWz3gHS9V_t-fX0BAF0kdA priority: 102 providerName: Directory of Open Access Journals
Title	The Impact of Global Transcriptional Regulation on Bacterial Gene Order
URI	https://dx.doi.org/10.1016/j.isci.2020.101029 https://www.ncbi.nlm.nih.gov/pubmed/32283521 https://www.proquest.com/docview/2389693400 https://pubmed.ncbi.nlm.nih.gov/PMC7155222 http://www.cell.com/article/S2589004220302133/pdf https://doaj.org/article/97ab3963c5b548e5804ce1a0d7887c69
UnpaywallVersion	publishedVersion
Volume	23
hasFullText	1
inHoldings	1
isFullTextHit
isPrint
journalDatabaseRights	– providerCode: PRVAON databaseName: Directory of Open Access Journals customDbUrl: eissn: 2589-0042 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0002002496 issn: 2589-0042 databaseCode: DOA dateStart: 20180101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVAQN databaseName: PubMed Central customDbUrl: eissn: 2589-0042 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0002002496 issn: 2589-0042 databaseCode: RPM dateStart: 20180101 isFulltext: true titleUrlDefault: https://www.ncbi.nlm.nih.gov/pmc/ providerName: National Library of Medicine
link	http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV3db9MwED-N7gFeYIiPZbApSLxBtsSOnfhxQ4zBw0CDSuPJSvwBG1Vaba0Q_PXc2UmhqjQNqQ-xc3Ua3-U-0rvfAbxkdauk4BiWNEJk6P_brC0qmXnZqkoVnjDHKNviVJ6Myw_n4nwDhsaFlFVJb6yDju737uAzE7UKYFUokQyDqoOZ9XdgUwp0v0ewOT79dPiVmsgJSv9Bur44JuZxUXErxoEsTOTBlfxrgAJO_4odWvcz19Ml7y66WfPrZzOZ_GOLjh_A2VDRE1NQfuwv5u2--b0O8Hj729yC-71nmh5Guoew4bpH8A7FKH0fKinTqU9jh4A0GLhB3eD4LDa0x0GKn6MIAI3zhGmdfiRwz8cwPn775c1J1vdeyAy1OMh47lhuPJqygpuSCnhNKRS3eYMxpG3RzhtPUIFeNYpJi2GQd3hsS1c6W-UlfwKjbtq5bUgbL6RzdWUKR-rCKsGZV7Ll3Fe1qmwCxcAQbXpgcuqPMdFDBtqlJiZqYqKOTEzg1fI7swjLcSP1EfF5SUmQ2mFievVN99uvVdW0HNWRES1GcU7UeWlc0eSW8i2NxEXEICW6906i14FLXdx48ReDSGl8dIntTeemi2uN3pKSiqMWTeBpFLHlT-QES4ScSKBaEb6Ve1g90118D_DgFaHqMZbA66WY3mKPdv6P_BncoxH9r8bK5zCaXy3cLrpn83YvvNbY6x_LP9-fNT8
linkProvider	Unpaywall
linkToUnpaywall	http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1Lb9QwEB6V7QEupYhXCkVB4gZpEzu242NbtRQOBRVWKicr8aMUVtlV2RWCX89MnCysVqqKlEPsTLKJZzKPzcw3AK9Y1WgpOIYltRAZ-v8uawolsyAbrXQRCHOMsi3O5Om4fH8hLjZgaFxIWZX0j3Wno_u12__ERKU7sCqUSIZB1f7MhTuwKQW63yPYHJ99PPhCTeQEpf8gXV8cE_O4qLgV40DWTeSdK_nXAHU4_St2aN3PXE-XvLtoZ_Wvn_Vk8o8tOrkP50NFT0xB-b63mDd79vc6wOPtH3MbtnrPND2IdA9gw7cP4S2KUfquq6RMpyGNHQLSzsAN6gbH57GhPQ5S3A4jADTOE6Z1-oHAPR_B-OT489Fp1vdeyCy1OMh47lluA5qygtuSCnhtKTR3eY0xpGvQzttAUIFB15pJh2FQ8LjvSl96p_KSP4ZRO239U0jrIKT3lbKFJ3XhtOAsaNlwHlSllUugGBhibA9MTv0xJmbIQPtmiImGmGgiExN4vTxnFmE5bqQ-JD4vKQlSu5uYXl-afvmNVnXDUR1Z0WAU50WVl9YXde4o39JKvIgYpMT03kn0OvBSVzf--MtBpAy-usT2uvXTxQ-D3pKWmqMWTeBJFLHlLXKCJUJOJKBWhG_lGVaPtFdfO3hwRah6jCXwZimmt1ijnf8jfwb3aETf1Vj5HEbz64XfRfds3rzoX8g_peE0Sg
openUrl	ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=The+Impact+of+Global+Transcriptional+Regulation+on+Bacterial+Gene+Order&rft.jtitle=iScience&rft.au=Yubero%2C+Pablo&rft.au=Poyatos%2C+Juan+F.&rft.date=2020-04-24&rft.pub=Elsevier&rft.eissn=2589-0042&rft.volume=23&rft.issue=4&rft_id=info:doi/10.1016%2Fj.isci.2020.101029&rft_id=info%3Apmid%2F32283521&rft.externalDocID=PMC7155222
thumbnail_l	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2589-0042&client=summon
thumbnail_m	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2589-0042&client=summon
thumbnail_s	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2589-0042&client=summon