Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data
- Authors:
-
- Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Minho, Braga (Portugal)
- Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Paris-Saclay Univ., Jouy-en-Josas (France)
- Univ. of Minho, Braga (Portugal)
- Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
- OSTI Identifier:
- 1337227
- Alternate Identifier(s):
- OSTI ID: 1393150
- Report Number(s):
- PNNL-SA-115053
Journal ID: ISSN 1664-302X; KP1601010
- Grant/Contract Number:
- AC05-76RL01830; AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 7; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Atomic Regulon; regulatory network; stimuli; regulation; Bacillus subtilis
Citation Formats
Faria, Jose P., Overbeek, Ross, Taylor, Ronald C., Conrad, Neal, Vonstein, Veronika, Goelzer, Anne, Fromion, Vincent, Rocha, Miguel, Rocha, Isabel, and Henry, Christopher S. Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data. United States: N. p., 2016.
Web. doi:10.3389/fmicb.2016.00275.
Faria, Jose P., Overbeek, Ross, Taylor, Ronald C., Conrad, Neal, Vonstein, Veronika, Goelzer, Anne, Fromion, Vincent, Rocha, Miguel, Rocha, Isabel, & Henry, Christopher S. Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data. United States. https://doi.org/10.3389/fmicb.2016.00275
Faria, Jose P., Overbeek, Ross, Taylor, Ronald C., Conrad, Neal, Vonstein, Veronika, Goelzer, Anne, Fromion, Vincent, Rocha, Miguel, Rocha, Isabel, and Henry, Christopher S. Fri .
"Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data". United States. https://doi.org/10.3389/fmicb.2016.00275. https://www.osti.gov/servlets/purl/1337227.
@article{osti_1337227,
title = {Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data},
author = {Faria, Jose P. and Overbeek, Ross and Taylor, Ronald C. and Conrad, Neal and Vonstein, Veronika and Goelzer, Anne and Fromion, Vincent and Rocha, Miguel and Rocha, Isabel and Henry, Christopher S.},
abstractNote = {},
doi = {10.3389/fmicb.2016.00275},
journal = {Frontiers in Microbiology},
number = ,
volume = 7,
place = {United States},
year = {Fri Mar 18 00:00:00 EDT 2016},
month = {Fri Mar 18 00:00:00 EDT 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 10 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
CDD: NCBI's conserved domain database
journal, November 2014
- Marchler-Bauer, Aron; Derbyshire, Myra K.; Gonzales, Noreen R.
- Nucleic Acids Research, Vol. 43, Issue D1
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis
journal, January 2008
- Goelzer, Anne; Bekkal Brikci, Fadia; Martin-Verstraete, Isabelle
- BMC Systems Biology, Vol. 2, Issue 1
Sensing Small Molecules by Nascent RNA
journal, November 2002
- Mironov, Alexander S.; Gusarov, Ivan; Rafikov, Ruslan
- Cell, Vol. 111, Issue 5
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
journal, September 2005
- Overbeek, R.
- Nucleic Acids Research, Vol. 33, Issue 17
Prediction of operons in microbial genomes
journal, March 2001
- Ermolaeva, M. D.
- Nucleic Acids Research, Vol. 29, Issue 5
Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis
journal, March 2012
- Nicolas, P.; Mader, U.; Dervyn, E.
- Science, Vol. 335, Issue 6072
Commitment to sporulation in Bacillus subtilis and its relationship to development of actinomycin resistance
journal, June 1969
- Sterlini, Janet M.; Mandelstam, J.
- Biochemical Journal, Vol. 113, Issue 1
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model
journal, October 2012
- Tanaka, Kosei; Henry, Christopher S.; Zinner, Jenifer F.
- Nucleic Acids Research, Vol. 41, Issue 1
Antisense RNA Control in Bacteria, Phages, and Plasmids
journal, October 1994
- Wagner, E. G. H.; Simons, R. W.
- Annual Review of Microbiology, Vol. 48, Issue 1
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes
journal, October 2009
- Novichkov, Pavel S.; Laikova, Olga N.; Novichkova, Elena S.
- Nucleic Acids Research, Vol. 38, Issue suppl_1
The evolution of gene regulation by transcription factors and microRNAs
journal, February 2007
- Chen, Kevin; Rajewsky, Nikolaus
- Nature Reviews Genetics, Vol. 8, Issue 2
Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism
journal, March 2012
- Buescher, J. M.; Liebermeister, W.; Jules, M.
- Science, Vol. 335, Issue 6072
Carbon Catabolite Control of the Metabolic Network in Bacillus subtilis
journal, February 2009
- Fujita, Yasutaro
- Bioscience, Biotechnology, and Biochemistry, Vol. 73, Issue 2
Expression of the tre operon of Bacillus subtilis 168 is regulated by the repressor TreR.
journal, January 1996
- Schöck, F.; Dahl, M. K.
- Journal of bacteriology, Vol. 178, Issue 15
Molecular analysis of the interaction between the Bacillus subtilis trehalose repressor TreR and the tre operator
journal, October 1998
- Bürklen, L.; Schöck, F.; Dahl, M. K.
- Molecular and General Genetics MGG, Vol. 260, Issue 1
The riboswitch control of bacterial metabolism
journal, January 2004
- Nudler, E.
- Trends in Biochemical Sciences, Vol. 29, Issue 1
The role of the CcpA transcriptional regulator in carbon metabolism in Bacillus subtilis
journal, January 1996
- Henkin, Tina M.
- FEMS Microbiology Letters, Vol. 135, Issue 1
yveB, encoding endolevanase LevB, is part of the sacB–yveB–yveA levansucrase tricistronic operon in Bacillus subtilis
journal, December 2001
- Pereira, Yannick; Petit-Glatron, Marie-Françoise; Chambert, Régis
- Microbiology, Vol. 147, Issue 12
Inferring the transcriptional network of Bacillus subtilis
journal, January 2009
- Fadda, Abeer; Fierro, Ana Carolina; Lemmens, Karen
- Molecular BioSystems, Vol. 5, Issue 12
The Bacillus subtilis hemAXCDBL gene cluster, which encodes enzymes of the biosynthetic pathway from glutamate to uroporphyrinogen III.
journal, January 1991
- Hansson, M.; Rutberg, L.; Schröder, I.
- Journal of Bacteriology, Vol. 173, Issue 8
A ribonucleic antiterminator sequence (RAT) and a distant palindrome are both involved in sucrose induction of the Bacillus subtilis sacXY regulatory operon
journal, November 1995
- Tortosa, P.; Le Coq, D.
- Microbiology, Vol. 141, Issue 11
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
journal, October 2007
- Sierro, Nicolas; Makita, Yuko; de Hoon, Michiel
- Nucleic Acids Research, Vol. 36, Issue suppl_1
The sacT gene regulating the sacPA operon in Bacillus subtilis shares strong homology with transcriptional antiterminators.
journal, January 1990
- Debarbouille, M.; Arnaud, M.; Fouet, A.
- Journal of Bacteriology, Vol. 172, Issue 7
Essential Bacillus subtilis genes
journal, April 2003
- Kobayashi, K.; Ehrlich, S. D.; Albertini, A.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 8
SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis
journal, November 2011
- Mader, U.; Schmeisky, A. G.; Florez, L. A.
- Nucleic Acids Research, Vol. 40, Issue D1
The transcription unit architecture of the Escherichia coli genome
journal, November 2009
- Cho, Byung-Kwan; Zengler, Karsten; Qiu, Yu
- Nature Biotechnology, Vol. 27, Issue 11
A novel method for accurate operon predictions in all sequenced prokaryotes
journal, February 2005
- Price, M. N.
- Nucleic Acids Research, Vol. 33, Issue 3
SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis
journal, October 2013
- Eijlander, Robyn T.; de Jong, Anne; Krawczyk, Antonina O.
- Nucleic Acids Research, Vol. 42, Issue D1
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
journal, June 2010
- Novichkov, P. S.; Rodionov, D. A.; Stavrovskaya, E. D.
- Nucleic Acids Research, Vol. 38, Issue Web Server
uvrB gene deletion enhances SOS chromotest sensitivity for nitroreductases that preferentially generate the 4-hydroxylamine metabolite of the anti-cancer prodrug CB1954
journal, October 2010
- Prosser, G. A.; Patterson, A. V.; Ackerley, D. F.
- Journal of Biotechnology, Vol. 150, Issue 1
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
journal, January 2002
- Edgar, R.
- Nucleic Acids Research, Vol. 30, Issue 1
Extracellular signals that define distinct and coexisting cell fates in Bacillus subtilis
journal, March 2010
- López, Daniel; Kolter, Roberto
- FEMS Microbiology Reviews, Vol. 34, Issue 2
Subti Wiki–a database for the model organism Bacillus subtilis that links pathway, interaction and expression information
journal, October 2013
- Michna, Raphael H.; Commichau, Fabian M.; Tödter, Dominik
- Nucleic Acids Research, Vol. 42, Issue D1
Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach
journal, November 2006
- Steggles, L. J.; Banks, R.; Shaw, O.
- Bioinformatics, Vol. 23, Issue 3
Transcriptome Complexity in a Genome-Reduced Bacterium
journal, November 2009
- Güell, Marc; van Noort, Vera; Yus, Eva
- Science, Vol. 326, Issue 5957
iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations
journal, January 2009
- Henry, Christopher S.; Zinner, Jenifer F.; Cohoon, Matthew P.
- Genome Biology, Vol. 10, Issue 6
Reconstruction of microbial transcriptional regulatory networks
journal, February 2004
- Herrgård, Markus J.; Covert, Markus W.; Palsson, Bernhard Ø
- Current Opinion in Biotechnology, Vol. 15, Issue 1
Bacillus subtilis Fur represses one of two paralogous haem-degrading monooxygenases
journal, November 2011
- Gaballa, Ahmed; Helmann, John D.
- Microbiology, Vol. 157, Issue 11
Microbiology in the post-genomic era
journal, May 2008
- Medini, Duccio; Serruto, Davide; Parkhill, Julian
- Nature Reviews Microbiology, Vol. 6, Issue 6
Essential genes in Bacillus subtilis: a re-evaluation after ten years
journal, January 2013
- Commichau, Fabian M.; Pietack, Nico; Stülke, Jörg
- Molecular BioSystems, Vol. 9, Issue 6
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki
journal, January 2009
- Florez, L. A.; Roppel, S. F.; Schmeisky, A. G.
- Database, Vol. 2009, Issue 0
Molecular analysis of the interaction between the Bacillus subtilis trehalose repressor TreR and the tre operator
journal, October 1998
- Bürklen, L.; Schöck, F.; Dahl, M. K.
- Molecular and General Genetics MGG, Vol. 260, Issue 1
Reconstruction of microbial transcriptional regulatory networks
journal, February 2004
- Herrgård, Markus J.; Covert, Markus W.; Palsson, Bernhard Ø
- Current Opinion in Biotechnology, Vol. 15, Issue 1
uvrB gene deletion enhances SOS chromotest sensitivity for nitroreductases that preferentially generate the 4-hydroxylamine metabolite of the anti-cancer prodrug CB1954
journal, October 2010
- Prosser, G. A.; Patterson, A. V.; Ackerley, D. F.
- Journal of Biotechnology, Vol. 150, Issue 1
The riboswitch control of bacterial metabolism
journal, January 2004
- Nudler, E.
- Trends in Biochemical Sciences, Vol. 29, Issue 1
The transcription unit architecture of the Escherichia coli genome
journal, November 2009
- Cho, Byung-Kwan; Zengler, Karsten; Qiu, Yu
- Nature Biotechnology, Vol. 27, Issue 11
The evolution of gene regulation by transcription factors and microRNAs
journal, February 2007
- Chen, Kevin; Rajewsky, Nikolaus
- Nature Reviews Genetics, Vol. 8, Issue 2
Microbiology in the post-genomic era
journal, May 2008
- Medini, Duccio; Serruto, Davide; Parkhill, Julian
- Nature Reviews Microbiology, Vol. 6, Issue 6
Synergism between IL7R and CXCR4 drives BCR-ABL induced transformation in Philadelphia chromosome-positive acute lymphoblastic leukemia
journal, June 2020
- Abdelrasoul, Hend; Vadakumchery, Anila; Werner, Markus
- Nature Communications, Vol. 11, Issue 1
Inferring the transcriptional network of Bacillus subtilis
journal, January 2009
- Fadda, Abeer; Fierro, Ana Carolina; Lemmens, Karen
- Molecular BioSystems, Vol. 5, Issue 12
Essential genes in Bacillus subtilis: a re-evaluation after ten years
journal, January 2013
- Commichau, Fabian M.; Pietack, Nico; Stülke, Jörg
- Molecular BioSystems, Vol. 9, Issue 6
Commitment to sporulation in Bacillus subtilis and its relationship to development of actinomycin resistance
journal, June 1969
- Sterlini, Janet M.; Mandelstam, J.
- Biochemical Journal, Vol. 113, Issue 1
Essential Bacillus subtilis genes
journal, April 2003
- Kobayashi, K.; Ehrlich, S. D.; Albertini, A.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 8
Transcriptional Regulation in Constraints-based Metabolic Models of Escherichia coli
journal, May 2002
- Covert, Markus W.; Palsson, Bernhard Ø.
- Journal of Biological Chemistry, Vol. 277, Issue 31
Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach
journal, November 2006
- Steggles, L. J.; Banks, R.; Shaw, O.
- Bioinformatics, Vol. 23, Issue 3
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki
journal, January 2009
- Florez, L. A.; Roppel, S. F.; Schmeisky, A. G.
- Database, Vol. 2009, Issue 0
Prediction of operons in microbial genomes
journal, March 2001
- Ermolaeva, M. D.
- Nucleic Acids Research, Vol. 29, Issue 5
A novel method for accurate operon predictions in all sequenced prokaryotes
journal, February 2005
- Price, M. N.
- Nucleic Acids Research, Vol. 33, Issue 3
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
journal, September 2005
- Overbeek, R.
- Nucleic Acids Research, Vol. 33, Issue 17
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
journal, October 2007
- Sierro, Nicolas; Makita, Yuko; de Hoon, Michiel
- Nucleic Acids Research, Vol. 36, Issue suppl_1
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes
journal, October 2009
- Novichkov, Pavel S.; Laikova, Olga N.; Novichkova, Elena S.
- Nucleic Acids Research, Vol. 38, Issue suppl_1
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
journal, June 2010
- Novichkov, P. S.; Rodionov, D. A.; Stavrovskaya, E. D.
- Nucleic Acids Research, Vol. 38, Issue Web Server
SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis
journal, November 2011
- Mader, U.; Schmeisky, A. G.; Florez, L. A.
- Nucleic Acids Research, Vol. 40, Issue D1
Subti Wiki–a database for the model organism Bacillus subtilis that links pathway, interaction and expression information
journal, October 2013
- Michna, Raphael H.; Commichau, Fabian M.; Tödter, Dominik
- Nucleic Acids Research, Vol. 42, Issue D1
CDD: NCBI's conserved domain database
journal, November 2014
- Marchler-Bauer, Aron; Derbyshire, Myra K.; Gonzales, Noreen R.
- Nucleic Acids Research, Vol. 43, Issue D1
yveB, encoding endolevanase LevB, is part of the sacB–yveB–yveA levansucrase tricistronic operon in Bacillus subtilis
journal, December 2001
- Pereira, Yannick; Petit-Glatron, Marie-Françoise; Chambert, Régis
- Microbiology, Vol. 147, Issue 12
A ribonucleic antiterminator sequence (RAT) and a distant palindrome are both involved in sucrose induction of the Bacillus subtilis sacXY regulatory operon
journal, November 1995
- Tortosa, P.; Le Coq, D.
- Microbiology, Vol. 141, Issue 11
Bacillus subtilis Fur represses one of two paralogous haem-degrading monooxygenases
journal, November 2011
- Gaballa, Ahmed; Helmann, John D.
- Microbiology, Vol. 157, Issue 11
The role of the CcpA transcriptional regulator in carbon metabolism in Bacillus subtilis
journal, January 1996
- Henkin, Tina M.
- FEMS Microbiology Letters, Vol. 135, Issue 1
Transcriptome Complexity in a Genome-Reduced Bacterium
journal, November 2009
- Güell, Marc; van Noort, Vera; Yus, Eva
- Science, Vol. 326, Issue 5957
Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis
journal, March 2012
- Nicolas, P.; Mader, U.; Dervyn, E.
- Science, Vol. 335, Issue 6072
Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism
journal, March 2012
- Buescher, J. M.; Liebermeister, W.; Jules, M.
- Science, Vol. 335, Issue 6072
Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis
journal, March 2013
- Leyn, S. A.; Kazanov, M. D.; Sernova, N. V.
- Journal of Bacteriology, Vol. 195, Issue 11
The sacT gene regulating the sacPA operon in Bacillus subtilis shares strong homology with transcriptional antiterminators.
journal, January 1990
- Debarbouille, M.; Arnaud, M.; Fouet, A.
- Journal of Bacteriology, Vol. 172, Issue 7
The Bacillus subtilis hemAXCDBL gene cluster, which encodes enzymes of the biosynthetic pathway from glutamate to uroporphyrinogen III.
journal, January 1991
- Hansson, M.; Rutberg, L.; Schröder, I.
- Journal of Bacteriology, Vol. 173, Issue 8
Expression of the tre operon of Bacillus subtilis 168 is regulated by the repressor TreR.
journal, January 1996
- Schöck, F.; Dahl, M. K.
- Journal of bacteriology, Vol. 178, Issue 15
Regulation of the Bacillus subtilis fur and perR Genes by PerR: Not All Members of the PerR Regulon Are Peroxide Inducible
journal, June 2002
- Fuangthong, Mayuree; Herbig, Andrew F.; Bsat, Nada
- Journal of Bacteriology, Vol. 184, Issue 12
Functional Analysis of the Bacillus subtilis Zur Regulon
journal, December 2002
- Gaballa, Ahmed; Wang, Tao; Ye, Rick W.
- Journal of Bacteriology, Vol. 184, Issue 23
Recognition of DNA by Three Ferric Uptake Regulator (Fur) Homologs in Bacillus subtilis
journal, October 2003
- Fuangthong, M.; Helmann, J. D.
- Journal of Bacteriology, Vol. 185, Issue 21
Requirements for Transformation in Bacillus Subtilis1
journal, January 1961
- Anagnostopoulos, C.; Spizizen, John
- Journal of Bacteriology, Vol. 81, Issue 5
Inferring gene Regulatory Networks from Time-Ordered gene Expression data of Bacillus Subtilis Using Differential Equations
conference, December 2002
- De Hoon, Michiel J. L.; Imoto, Seiya; Kobayashi, Kazuo
- Biocomputing 2003
Antisense RNA Control in Bacteria, Phages, and Plasmids
journal, October 1994
- Wagner, E. G. H.; Simons, R. W.
- Annual Review of Microbiology, Vol. 48, Issue 1
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis
journal, January 2008
- Goelzer, Anne; Bekkal Brikci, Fadia; Martin-Verstraete, Isabelle
- BMC Systems Biology, Vol. 2, Issue 1
Carbon Catabolite Control of the Metabolic Network in Bacillus subtilis
journal, February 2009
- Fujita, Yasutaro
- Bioscience, Biotechnology, and Biochemistry, Vol. 73, Issue 2
Works referencing / citing this record:
The Genome-Scale Integrated Networks in Microorganisms
journal, February 2018
- Hao, Tong; Wu, Dan; Zhao, Lingxuan
- Frontiers in Microbiology, Vol. 9
Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation
journal, November 2016
- Faria, José P.; Davis, James J.; Edirisinghe, Janaka N.
- Frontiers in Microbiology, Vol. 7
The Genome-Scale Integrated Networks in Microorganisms
journal, February 2018
- Hao, Tong; Wu, Dan; Zhao, Lingxuan
- Frontiers in Microbiology, Vol. 9