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Volumn 5, Issue , 2014, Pages

Deciphering fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; FERRIC UPTAKE REGULATOR; IRON; RNA POLYMERASE; BACTERIAL PROTEIN; FERRIC UPTAKE REGULATING PROTEINS, BACTERIAL; PROTEIN BINDING; REPRESSOR PROTEIN;

EID: 84920906247     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms5910     Document Type: Article
Times cited : (225)

References (50)
  • 1
    • 67650094768 scopus 로고    scopus 로고
    • This is not your mother's repressor: The complex role of fur in pathogenesis
    • Carpenter, B. M., Whitmire, J. M. & Merrell, D. S. This is not your mother's repressor: the complex role of fur in pathogenesis. Infect. Immun. 77, 2590-2601 (2009).
    • (2009) Infect. Immun. , vol.77 , pp. 2590-2601
    • Carpenter, B.M.1    Whitmire, J.M.2    Merrell, D.S.3
  • 3
    • 3042816068 scopus 로고    scopus 로고
    • Fur functions as an activator and as a repressor of putative virulence genes in Neisseria meningitidis
    • Delany, I., Rappuoli, R. & Scarlato, V. Fur functions as an activator and as a repressor of putative virulence genes in Neisseria meningitidis. Mol. Microbiol. 52, 1081-1090 (2004).
    • (2004) Mol. Microbiol. , vol.52 , pp. 1081-1090
    • Delany, I.1    Rappuoli, R.2    Scarlato, V.3
  • 4
    • 75149173382 scopus 로고    scopus 로고
    • Induction of the ferritin gene (ftnA) of Escherichia coli by Fe(2+)-Fur is mediated by reversal of H-NS silencing and is RyhB independent
    • Nandal, A. et al. Induction of the ferritin gene (ftnA) of Escherichia coli by Fe(2+)-Fur is mediated by reversal of H-NS silencing and is RyhB independent. Mol. Microbiol. 75, 637-657 (2010).
    • (2010) Mol. Microbiol. , vol.75 , pp. 637-657
    • Nandal, A.1
  • 5
    • 84890135354 scopus 로고    scopus 로고
    • Identification and characterization of novel Helicobacter pylori apo-Fur-regulated target genes
    • Carpenter, B. M. et al. Identification and characterization of novel Helicobacter pylori apo-Fur-regulated target genes. J. Bacteriol. 195, 5526-5539 (2013).
    • (2013) J. Bacteriol. , vol.195 , pp. 5526-5539
    • Carpenter, B.M.1
  • 6
    • 84862548944 scopus 로고    scopus 로고
    • Structure and regulon of Campylobacter jejuni ferric uptake regulator fur define apo-Fur regulation
    • Butcher, J. et al. Structure and regulon of Campylobacter jejuni ferric uptake regulator Fur define apo-Fur regulation. Proc. Natl Acad. Sci. USA 109, 10047-10052 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 10047-10052
    • Butcher, J.1
  • 7
    • 84860330705 scopus 로고    scopus 로고
    • Expression of multidrug resistance efflux pump gene norA is iron responsive in Staphylococcus aureus
    • Deng, X. et al. Expression of multidrug resistance efflux pump gene norA is iron responsive in Staphylococcus aureus. J. Bacteriol. 194, 1753-1762 (2012).
    • (2012) J. Bacteriol. , vol.194 , pp. 1753-1762
    • Deng, X.1
  • 8
    • 78651281217 scopus 로고    scopus 로고
    • EcoCyc: A comprehensive database of Escherichia coli biology
    • Keseler, I. M. et al. EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 39, D583-D590 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. D583-D590
    • Keseler, I.M.1
  • 9
    • 0043032822 scopus 로고    scopus 로고
    • Global iron-dependent gene regulation in Escherichia coli. A new mechanism for iron homeostasis
    • McHugh, J. P. et al. Global iron-dependent gene regulation in Escherichia coli. A new mechanism for iron homeostasis. J. Biol. Chem. 278, 29478-29486 (2003).
    • (2003) J. Biol. Chem. , vol.278 , pp. 29478-29486
    • McHugh, J.P.1
  • 10
    • 0037007078 scopus 로고    scopus 로고
    • A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli
    • Masse, E. & Gottesman, S. A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc. Natl Acad. Sci. USA 99, 4620-4625 (2002).
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 4620-4625
    • Masse, E.1    Gottesman, S.2
  • 11
    • 84876543942 scopus 로고    scopus 로고
    • RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
    • Salgado, H. et al. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 41, D203-D213 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. D203-D213
    • Salgado, H.1
  • 12
    • 77950219265 scopus 로고    scopus 로고
    • Staphylococcus aureus fur regulates the expression of virulence factors that contribute to the pathogenesis of pneumonia
    • Torres, V. J. et al. Staphylococcus aureus fur regulates the expression of virulence factors that contribute to the pathogenesis of pneumonia. Infect. Immun. 78, 1618-1628 (2010).
    • (2010) Infect. Immun. , vol.78 , pp. 1618-1628
    • Torres, V.J.1
  • 13
    • 77954016214 scopus 로고    scopus 로고
    • Helicobacter pylori apo-Fur regulation appears unconserved across species
    • Miles, S., Carpenter, B. M., Gancz, H. & Merrell, D. S. Helicobacter pylori apo-Fur regulation appears unconserved across species. J. Microbiol. 48, 378-386 (2010).
    • (2010) J. Microbiol. , vol.48 , pp. 378-386
    • Miles, S.1    Carpenter, B.M.2    Gancz, H.3    Merrell, D.S.4
  • 14
    • 57349087129 scopus 로고    scopus 로고
    • Oxidant-responsive induction of the suf operon, encoding a Fe-S assembly system, through fur and IscR in Escherichia coli
    • Lee, K. C., Yeo, W. S. & Roe, J. H. Oxidant-responsive induction of the suf operon, encoding a Fe-S assembly system, through Fur and IscR in Escherichia coli. J. Bacteriol. 190, 8244-8247 (2008).
    • (2008) J. Bacteriol. , vol.190 , pp. 8244-8247
    • Lee, K.C.1    Yeo, W.S.2    Roe, J.H.3
  • 15
    • 44849093465 scopus 로고    scopus 로고
    • Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts
    • Cho, B. K., Knight, E. M., Barrett, C. L. & Palsson, B. O. Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res. 18, 900-910 (2008).
    • (2008) Genome Res. , vol.18 , pp. 900-910
    • Cho, B.K.1    Knight, E.M.2    Barrett, C.L.3    Palsson, B.O.4
  • 16
    • 58049200606 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli
    • Cho, B. K. et al. Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli. Proc. Natl Acad. Sci. USA 105, 19462-19467 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 19462-19467
    • Cho, B.K.1
  • 17
    • 84887308033 scopus 로고    scopus 로고
    • The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally
    • Park, D. M. et al. The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally. PLoS Genet. 9, e1003839 (2013).
    • (2013) PLoS Genet. , vol.9 , pp. e1003839
    • Park, D.M.1
  • 18
    • 84879620270 scopus 로고    scopus 로고
    • Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding
    • Myers, K. S. et al. Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. PLoS Genet. 9, e1003565 (2013).
    • (2013) PLoS Genet. , vol.9 , pp. e1003565
    • Myers, K.S.1
  • 20
    • 34547653116 scopus 로고    scopus 로고
    • EfeUOB (YcdNOB) is a tripartite acid-induced and CpxAR-regulated low-pH Fe2 + transporter that is cryptic in Escherichia coli K-12 but functional in E. Coli O157:H7
    • Cao, J. et al. EfeUOB (YcdNOB) is a tripartite, acid-induced and CpxAR-regulated, low-pH Fe2 + transporter that is cryptic in Escherichia coli K-12 but functional in E. coli O157:H7. Mol. Microbiol. 65, 857-875 (2007).
    • (2007) Mol. Microbiol. , vol.65 , pp. 857-875
    • Cao, J.1
  • 21
    • 84866160409 scopus 로고    scopus 로고
    • Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling
    • Kim, D. et al. Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. PLoS Genet. 8, e1002867 (2012).
    • (2012) PLoS Genet. , vol.8 , pp. e1002867
    • Kim, D.1
  • 22
    • 84860321923 scopus 로고    scopus 로고
    • Fur-mediated activation of gene transcription in the human pathogen Neisseria gonorrhoeae
    • Yu, C. & Genco, C. A. Fur-mediated activation of gene transcription in the human pathogen Neisseria gonorrhoeae. J. Bacteriol. 194, 1730-1742 (2012).
    • (2012) J. Bacteriol. , vol.194 , pp. 1730-1742
    • Yu, C.1    Genco, C.A.2
  • 23
    • 34548598563 scopus 로고    scopus 로고
    • Structure and function of the Escherichia coli protein YmgB: A protein critical for biofilm formation and acid-resistance
    • Lee, J. et al. Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance. J. Mol. Biol. 373, 11-26 (2007).
    • (2007) J. Mol. Biol. , vol.373 , pp. 11-26
    • Lee, J.1
  • 24
    • 84876877656 scopus 로고    scopus 로고
    • Genome-wide identification of Bacillus subtilis CodY-binding sites at single-nucleotide resolution
    • Belitsky, B. R. & Sonenshein, A. L. Genome-wide identification of Bacillus subtilis CodY-binding sites at single-nucleotide resolution. Proc. Natl Acad. Sci. USA 110, 7026-7031 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 7026-7031
    • Belitsky, B.R.1    Sonenshein, A.L.2
  • 25
    • 0036837766 scopus 로고    scopus 로고
    • Recognition of DNA by Fur: A reinterpretation of the fur box consensus sequence
    • Baichoo, N. & Helmann, J. D. Recognition of DNA by Fur: a reinterpretation of the Fur box consensus sequence. J. Bacteriol. 184, 5826-5832 (2002).
    • (2002) J. Bacteriol. , vol.184 , pp. 5826-5832
    • Baichoo, N.1    Helmann, J.D.2
  • 26
    • 84866937220 scopus 로고    scopus 로고
    • Inferring direct DNA binding from ChIP-seq
    • Bailey, T. L. & Machanick, P. Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res. 40, e128 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. e128
    • Bailey, T.L.1    MacHanick, P.2
  • 27
    • 83255164884 scopus 로고    scopus 로고
    • Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
    • Rhee, H. S. & Pugh, B. F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147, 1408-1419 (2011).
    • (2011) Cell , vol.147 , pp. 1408-1419
    • Rhee, H.S.1    Pugh, B.F.2
  • 28
    • 47249152834 scopus 로고    scopus 로고
    • The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions
    • Shimada, T., Ishihama, A., Busby, S. J. & Grainger, D. C. The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acids Res. 36, 3950-3955 (2008).
    • (2008) Nucleic Acids Res. , vol.36 , pp. 3950-3955
    • Shimada, T.1    Ishihama, A.2    Busby, S.J.3    Grainger, D.C.4
  • 29
    • 33750203381 scopus 로고    scopus 로고
    • Genetic regulation of fluxes: Iron homeostasis of Escherichia coli
    • Semsey, S. et al. Genetic regulation of fluxes: iron homeostasis of Escherichia coli. Nucleic Acids Res. 34, 4960-4967 (2006).
    • (2006) Nucleic Acids Res. , vol.34 , pp. 4960-4967
    • Semsey, S.1
  • 30
    • 67349095027 scopus 로고    scopus 로고
    • Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA
    • Desnoyers, G., Morissette, A., Prevost, K. & Masse, E. Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA. EMBO J. 28, 1551-1561 (2009).
    • (2009) EMBO J. , vol.28 , pp. 1551-1561
    • Desnoyers, G.1    Morissette, A.2    Prevost, K.3    Masse, E.4
  • 31
    • 38049188050 scopus 로고    scopus 로고
    • Combinatorics of feedback in cellular uptake and metabolism of small molecules
    • Krishna, S., Semsey, S. & Sneppen, K. Combinatorics of feedback in cellular uptake and metabolism of small molecules. Proc. Natl Acad. Sci. USA 104, 20815-20819 (2007).
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 20815-20819
    • Krishna, S.1    Semsey, S.2    Sneppen, K.3
  • 32
    • 79953850801 scopus 로고    scopus 로고
    • The alternative aerobic ribonucleotide reductase of Escherichia coli, NrdEF, is a manganese-dependent enzyme that enables cell replication during periods of iron starvation
    • Martin, J. E. & Imlay, J. A. The alternative aerobic ribonucleotide reductase of Escherichia coli, NrdEF, is a manganese-dependent enzyme that enables cell replication during periods of iron starvation. Mol. Microbiol. 80, 319-334 (2011).
    • (2011) Mol. Microbiol. , vol.80 , pp. 319-334
    • Martin, J.E.1    Imlay, J.A.2
  • 33
    • 84885367114 scopus 로고    scopus 로고
    • Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
    • O'Brien, E. J. et al. Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol. Syst. Biol. 9, 693 (2013).
    • (2013) Mol. Syst. Biol. , vol.9 , pp. 693
    • O'Brien, E.J.1
  • 34
    • 33748043648 scopus 로고    scopus 로고
    • Staphylococcus aureus redirects central metabolism to increase iron availability
    • Friedman, D. B. et al. Staphylococcus aureus redirects central metabolism to increase iron availability. PLoS Pathog. 2, e87 (2006).
    • (2006) PLoS Pathog. , vol.2 , pp. e87
    • Friedman, D.B.1
  • 35
    • 60849099323 scopus 로고    scopus 로고
    • IscR controls iron-dependent biofilm formation in Escherichia coli by regulating type i fimbria expression
    • Wu, Y. & Outten, F. W. IscR controls iron-dependent biofilm formation in Escherichia coli by regulating type I fimbria expression. J. Bacteriol. 191, 1248-1257 (2009).
    • (2009) J. Bacteriol. , vol.191 , pp. 1248-1257
    • Wu, Y.1    Outten, F.W.2
  • 36
    • 84860735686 scopus 로고    scopus 로고
    • The small RNA RybA regulates key-genes in the biosynthesis of aromatic amino acids under peroxide stress in E. Coli
    • Gerstle, K., Klatschke, K., Hahn, U. & Piganeau, N. The small RNA RybA regulates key-genes in the biosynthesis of aromatic amino acids under peroxide stress in E. coli. RNA. Biol. 9, 458-468 (2012).
    • (2012) RNA. Biol. , vol.9 , pp. 458-468
    • Gerstle, K.1    Klatschke, K.2    Hahn, U.3    Piganeau, N.4
  • 37
    • 84898620711 scopus 로고    scopus 로고
    • The iron stimulon and fur regulon of Geobacter sulfurreducens and their role in energy metabolism
    • Embree, M. et al. The iron stimulon and fur regulon of Geobacter sulfurreducens and their role in energy metabolism. Appl. Environ. Microbiol. 80, 2918-2927 (2014).
    • (2014) Appl. Environ. Microbiol. , vol.80 , pp. 2918-2927
    • Embree, M.1
  • 38
    • 84891448799 scopus 로고    scopus 로고
    • The transcriptional landscape of Campylobacter jejuni under iron replete and iron limited growth conditions
    • Butcher, J. & Stintzi, A. The transcriptional landscape of Campylobacter jejuni under iron replete and iron limited growth conditions. PLoS One 8, e79475 (2013).
    • (2013) PLoS One , vol.8 , pp. e79475
    • Butcher, J.1    Stintzi, A.2
  • 39
    • 84882709338 scopus 로고    scopus 로고
    • Global transcriptional response of Caulobacter crescentus to iron availability
    • da Silva Neto, J. F., Lourenco, R. F. & Marques, M. V. Global transcriptional response of Caulobacter crescentus to iron availability. BMC Genomics 14, 549 (2013).
    • (2013) BMC Genomics , vol.14 , pp. 549
    • Da Silva Neto, J.F.1    Lourenco, R.F.2    Marques, M.V.3
  • 40
    • 79961063576 scopus 로고    scopus 로고
    • Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation
    • Davies, B. W., Bogard, R. W. & Mekalanos, J. J. Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation. Proc. Natl Acad. Sci. USA 108, 12467-12472 (2011).
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 12467-12472
    • Davies, B.W.1    Bogard, R.W.2    Mekalanos, J.J.3
  • 41
    • 77956340995 scopus 로고    scopus 로고
    • Comprehensive comparative analysis of strand-specific RNA sequencing methods
    • Levin, J. Z. et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7, 709-715 (2010).
    • (2010) Nat. Methods , vol.7 , pp. 709-715
    • Levin, J.Z.1
  • 42
    • 84892777715 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the sigma factor network in Escherichia coli: Topology and functional states
    • Cho, B. K. et al. Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states. BMC Biol. 12, 4 (2014).
    • (2014) BMC Biol. , vol.12 , pp. 4
    • Cho, B.K.1
  • 43
    • 84879002382 scopus 로고    scopus 로고
    • Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli
    • McCloskey, D., Palsson, B. O. & Feist, A. M. Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol. Syst. Biol. 9, 661 (2013).
    • (2013) Mol. Syst. Biol. , vol.9 , pp. 661
    • McCloskey, D.1    Palsson, B.O.2    Feist, A.M.3
  • 44
    • 33644945692 scopus 로고    scopus 로고
    • PCR-based tandem epitope tagging system for Escherichia coli genome engineering
    • Cho, B. K., Knight, E. M. & Palsson, B. O. PCR-based tandem epitope tagging system for Escherichia coli genome engineering. Biotechniques 40, 67-72 (2006).
    • (2006) Biotechniques , vol.40 , pp. 67-72
    • Cho, B.K.1    Knight, E.M.2    Palsson, B.O.3
  • 45
    • 33747333128 scopus 로고    scopus 로고
    • A set of recombineering plasmids for Gram-negative bacteria
    • Datta, S., Costantino, N. & Court, D. L. A set of recombineering plasmids for Gram-negative bacteria. Gene 379, 109-115 (2006).
    • (2006) Gene , vol.379 , pp. 109-115
    • Datta, S.1    Costantino, N.2    Court, D.L.3
  • 46
    • 84873020117 scopus 로고    scopus 로고
    • ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy
    • Chapter 21, Unit 21 24
    • Rhee, H. S. & Pugh, B. F. ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy. Curr. Protoc. Mol. Biol. Chapter 21, Unit 21 24 (2012).
    • (2012) Curr. Protoc. Mol. Biol
    • Rhee, H.S.1    Pugh, B.F.2
  • 47
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome. Biol. 10, R25 (2009).
    • (2009) Genome. Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 48
    • 67849122320 scopus 로고    scopus 로고
    • MEME SUITE: Tools for motif discovery and searching
    • Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202-W208 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. W202-W208
    • Bailey, T.L.1
  • 49
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 50
    • 40549120596 scopus 로고    scopus 로고
    • The RAST Server: Rapid annotations using subsystems technology
    • Aziz, R. K. et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9, 75 (2008).
    • (2008) BMC Genomics , vol.9 , pp. 75
    • Aziz, R.K.1


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