메뉴 건너뛰기




Volumn 6, Issue 2, 2014, Pages 215-223

Essential O2-responsive genes of Pseudomonas aeruginosa and their network revealed by integrating dynamic data from inverted conditions

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; OXYGEN; TRANSCRIPTION FACTOR; TRANSCRIPTOME; BACTERIAL RNA;

EID: 84893193594     PISSN: 17579694     EISSN: 17579708     Source Type: Journal    
DOI: 10.1039/c3ib40180d     Document Type: Article
Times cited : (7)

References (54)
  • 3
    • 82555175381 scopus 로고    scopus 로고
    • Low oxygen induces the type III secretion system in Pseudomonas aeruginosa via modulation of the small RNAs rsmZ and rsmY
    • J. O'Callaghan F. J. Reen C. Adams F. O'Gara Low oxygen induces the type III secretion system in Pseudomonas aeruginosa via modulation of the small RNAs rsmZ and rsmY Microbiology 2011 157 3417 3428
    • (2011) Microbiology , vol.157 , pp. 3417-3428
    • O'Callaghan, J.1    Reen, F.J.2    Adams, C.3    O'Gara, F.4
  • 4
    • 34250620817 scopus 로고    scopus 로고
    • Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration
    • C. Alvarez-Ortega C. S. Harwood Responses of Pseudomonas aeruginosa to low oxygen indicate that growth in the cystic fibrosis lung is by aerobic respiration Mol. Microbiol. 2007 65 153 165
    • (2007) Mol. Microbiol. , vol.65 , pp. 153-165
    • Alvarez-Ortega, C.1    Harwood, C.S.2
  • 5
    • 0037377827 scopus 로고    scopus 로고
    • Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: Effects of growth phase and environment
    • V. E. Wagner D. Bushnell L. Passador A. I. Brooks B. H. Iglewski Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: effects of growth phase and environment J. Bacteriol. 2003 185 2080 2095
    • (2003) J. Bacteriol. , vol.185 , pp. 2080-2095
    • Wagner, V.E.1    Bushnell, D.2    Passador, L.3    Brooks, A.I.4    Iglewski, B.H.5
  • 6
    • 0029020024 scopus 로고
    • Anaerobic activation of the entire denitrification pathway in Pseudomonas aeruginosa requires Anr, an analog of Fnr
    • R. W. Ye D. Haas J. O. Ka V. Krishnapillai A. Zimmermann C. Baird J. M. Tiedje Anaerobic activation of the entire denitrification pathway in Pseudomonas aeruginosa requires Anr, an analog of Fnr J. Bacteriol. 1995 177 3606 3609
    • (1995) J. Bacteriol. , vol.177 , pp. 3606-3609
    • Ye, R.W.1    Haas, D.2    Ka, J.O.3    Krishnapillai, V.4    Zimmermann, A.5    Baird, C.6    Tiedje, J.M.7
  • 7
    • 0025873743 scopus 로고
    • Anaerobic growth and cyanide synthesis of Pseudomonas aeruginosa depend on anr, a regulatory gene homologous with fnr of Escherichia coli
    • A. Zimmermann C. Reimmann M. Galimand D. Haas Anaerobic growth and cyanide synthesis of Pseudomonas aeruginosa depend on anr, a regulatory gene homologous with fnr of Escherichia coli Mol. Microbiol. 1991 5 1483 1490
    • (1991) Mol. Microbiol. , vol.5 , pp. 1483-1490
    • Zimmermann, A.1    Reimmann, C.2    Galimand, M.3    Haas, D.4
  • 8
    • 70350752499 scopus 로고    scopus 로고
    • Comparative transcriptome analyses of Pseudomonas aeruginosa
    • D. Balasubramanian K. Mathee Comparative transcriptome analyses of Pseudomonas aeruginosa Hum. Genomics 2009 3 349 361
    • (2009) Hum. Genomics , vol.3 , pp. 349-361
    • Balasubramanian, D.1    Mathee, K.2
  • 12
    • 84861206347 scopus 로고    scopus 로고
    • Heterogeneity in Pseudomonas aeruginosa biofilms includes expression of ribosome hibernation factors in the antibiotic-tolerant subpopulation and hypoxia-induced stress response in the metabolically active population
    • K. S. Williamson L. A. Richards A. C. Perez-Osorio B. Pitts K. McInnerney P. S. Stewart M. J. Franklin Heterogeneity in Pseudomonas aeruginosa biofilms includes expression of ribosome hibernation factors in the antibiotic-tolerant subpopulation and hypoxia-induced stress response in the metabolically active population J. Bacteriol. 2012 194 2062 2073
    • (2012) J. Bacteriol. , vol.194 , pp. 2062-2073
    • Williamson, K.S.1    Richards, L.A.2    Perez-Osorio, A.C.3    Pitts, B.4    McInnerney, K.5    Stewart, P.S.6    Franklin, M.J.7
  • 14
    • 70449529712 scopus 로고    scopus 로고
    • Reverse engineering and verification of gene networks: Principles, assumptions, and limitations of present methods and future perspectives
    • F. He R. Balling A. P. Zeng Reverse engineering and verification of gene networks: principles, assumptions, and limitations of present methods and future perspectives J. Biotechnol. 2009 144 190 203
    • (2009) J. Biotechnol. , vol.144 , pp. 190-203
    • He, F.1    Balling, R.2    Zeng, A.P.3
  • 16
    • 17644395614 scopus 로고    scopus 로고
    • Expression of the quorum-sensing regulatory protein LasR is strongly affected by iron and oxygen concentrations in cultures of Pseudomonas aeruginosa irrespective of cell density
    • E. J. Kim W. Wang W. D. Deckwer A. P. Zeng Expression of the quorum-sensing regulatory protein LasR is strongly affected by iron and oxygen concentrations in cultures of Pseudomonas aeruginosa irrespective of cell density Microbiology 2005 151 1127 1138
    • (2005) Microbiology , vol.151 , pp. 1127-1138
    • Kim, E.J.1    Wang, W.2    Deckwer, W.D.3    Zeng, A.P.4
  • 17
    • 35748956437 scopus 로고    scopus 로고
    • Functional characterization of the gene PA2384 in large-scale gene regulation in response to iron starvation in Pseudomonas aeruginosa
    • P. Zheng J. Sun R. Geffers A. P. Zeng Functional characterization of the gene PA2384 in large-scale gene regulation in response to iron starvation in Pseudomonas aeruginosa J. Biotechnol. 2007 132 342 352
    • (2007) J. Biotechnol. , vol.132 , pp. 342-352
    • Zheng, P.1    Sun, J.2    Geffers, R.3    Zeng, A.P.4
  • 18
    • 0036772641 scopus 로고    scopus 로고
    • Physiological responses of Pseudomonas aeruginosa PAO1 to oxidative stress in controlled microaerobic and aerobic cultures
    • W. Sabra E. J. Kim A. P. Zeng Physiological responses of Pseudomonas aeruginosa PAO1 to oxidative stress in controlled microaerobic and aerobic cultures Microbiology 2002 148 3195 3202
    • (2002) Microbiology , vol.148 , pp. 3195-3202
    • Sabra, W.1    Kim, E.J.2    Zeng, A.P.3
  • 19
    • 0141814788 scopus 로고    scopus 로고
    • Iron deficiency leads to inhibition of oxygen transfer and enhanced formation of virulence factors in cultures of Pseudomonas aeruginosa PAO1
    • E. J. Kim W. Sabra A. P. Zeng Iron deficiency leads to inhibition of oxygen transfer and enhanced formation of virulence factors in cultures of Pseudomonas aeruginosa PAO1 Microbiology 2003 149 2627 2634
    • (2003) Microbiology , vol.149 , pp. 2627-2634
    • Kim, E.J.1    Sabra, W.2    Zeng, A.P.3
  • 20
    • 0142074779 scopus 로고    scopus 로고
    • Alterations in the formation of lipopolysaccharide and membrane vesicles on the surface of Pseudomonas aeruginosa PAO1 under oxygen stress conditions
    • W. Sabra H. Lunsdorf A. P. Zeng Alterations in the formation of lipopolysaccharide and membrane vesicles on the surface of Pseudomonas aeruginosa PAO1 under oxygen stress conditions Microbiology 2003 149 2789 2795
    • (2003) Microbiology , vol.149 , pp. 2789-2795
    • Sabra, W.1    Lunsdorf, H.2    Zeng, A.P.3
  • 21
  • 27
    • 79953890868 scopus 로고    scopus 로고
    • What does biologically meaningful mean? A perspective on gene regulatory network validation
    • A. J. Walhout What does biologically meaningful mean? A perspective on gene regulatory network validation Genome Biol. 2011 12 109
    • (2011) Genome Biol. , vol.12 , pp. 109
    • Walhout, A.J.1
  • 28
    • 84892376552 scopus 로고    scopus 로고
    • Supervised, semi-supervised and unsupervised inference of gene regulatory networks
    • 10.1093/bib/bbt034
    • S. R. Maetschke P. B. Madhamshettiwar M. J. Davis M. A. Ragan Supervised, semi-supervised and unsupervised inference of gene regulatory networks Briefings Bioinf. 2013 10.1093/bib/bbt034
    • (2013) Briefings Bioinf.
    • Maetschke, S.R.1    Madhamshettiwar, P.B.2    Davis, M.J.3    Ragan, M.A.4
  • 29
    • 0021664042 scopus 로고
    • Pseudomonas aeruginosa mutants affected in anaerobic growth on arginine: Evidence for a four-gene cluster encoding the arginine deiminase pathway
    • C. Vander Wauven A. Pierard M. Kley-Raymann D. Haas Pseudomonas aeruginosa mutants affected in anaerobic growth on arginine: evidence for a four-gene cluster encoding the arginine deiminase pathway J. Bacteriol. 1984 160 928 934
    • (1984) J. Bacteriol. , vol.160 , pp. 928-934
    • Vander Wauven, C.1    Pierard, A.2    Kley-Raymann, M.3    Haas, D.4
  • 30
    • 0029832198 scopus 로고    scopus 로고
    • Anaerobically controlled expression system derived from the arcDABC operon of Pseudomonas aeruginosa: Application to lipase production
    • H. V. Winteler B. Schneidinger K. E. Jaeger D. Haas Anaerobically controlled expression system derived from the arcDABC operon of Pseudomonas aeruginosa: application to lipase production Appl. Environ. Microbiol. 1996 62 3391 3398
    • (1996) Appl. Environ. Microbiol. , vol.62 , pp. 3391-3398
    • Winteler, H.V.1    Schneidinger, B.2    Jaeger, K.E.3    Haas, D.4
  • 32
    • 0031746603 scopus 로고    scopus 로고
    • Three rhamnosyltransferases responsible for assembly of the A-band D-rhamnan polysaccharide in Pseudomonas aeruginosa: A fourth transferase, WbpL, is required for the initiation of both A-band and B-band lipopolysaccharide synthesis
    • H. L. Rocchetta L. L. Burrows J. C. Pacan J. S. Lam Three rhamnosyltransferases responsible for assembly of the A-band D-rhamnan polysaccharide in Pseudomonas aeruginosa: a fourth transferase, WbpL, is required for the initiation of both A-band and B-band lipopolysaccharide synthesis Mol. Microbiol. 1998 28 1103 1119
    • (1998) Mol. Microbiol. , vol.28 , pp. 1103-1119
    • Rocchetta, H.L.1    Burrows, L.L.2    Pacan, J.C.3    Lam, J.S.4
  • 34
    • 84863887694 scopus 로고    scopus 로고
    • Studying and modelling dynamic biological processes using time-series gene expression data
    • Z. Bar-Joseph A. Gitter I. Simon Studying and modelling dynamic biological processes using time-series gene expression data Nat. Rev. Genet. 2012 13 552 564
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 552-564
    • Bar-Joseph, Z.1    Gitter, A.2    Simon, I.3
  • 35
    • 84883547999 scopus 로고    scopus 로고
    • Modeling regulatory cascades using Artificial Neural Networks: The case of transcriptional regulatory networks shaped during the yeast stress response
    • M. E. Manioudaki P. Poirazi Modeling regulatory cascades using Artificial Neural Networks: the case of transcriptional regulatory networks shaped during the yeast stress response Front. Genet. 2013 4 110
    • (2013) Front. Genet. , vol.4 , pp. 110
    • Manioudaki, M.E.1    Poirazi, P.2
  • 36
    • 52749097035 scopus 로고    scopus 로고
    • Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules
    • J. V. Turatsinze M. Thomas-Chollier M. Defrance J. van Helden Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules Nat. Protoc. 2008 3 1578 1588
    • (2008) Nat. Protoc. , vol.3 , pp. 1578-1588
    • Turatsinze, J.V.1    Thomas-Chollier, M.2    Defrance, M.3    Van Helden, J.4
  • 37
    • 0032906547 scopus 로고    scopus 로고
    • The ArgR regulatory protein, a helper to the anaerobic regulator ANR during transcriptional activation of the arcD promoter in Pseudomonas aeruginosa
    • C. D. Lu H. Winteler A. Abdelal D. Haas The ArgR regulatory protein, a helper to the anaerobic regulator ANR during transcriptional activation of the arcD promoter in Pseudomonas aeruginosa J. Bacteriol. 1999 181 2459 2464
    • (1999) J. Bacteriol. , vol.181 , pp. 2459-2464
    • Lu, C.D.1    Winteler, H.2    Abdelal, A.3    Haas, D.4
  • 38
    • 0035104921 scopus 로고    scopus 로고
    • Analysis of promoters recognized by PvdS, an extracytoplasmic-function sigma factor protein from Pseudomonas aeruginosa
    • M. J. Wilson B. J. McMorran I. L. Lamont Analysis of promoters recognized by PvdS, an extracytoplasmic-function sigma factor protein from Pseudomonas aeruginosa J. Bacteriol. 2001 183 2151 2155
    • (2001) J. Bacteriol. , vol.183 , pp. 2151-2155
    • Wilson, M.J.1    McMorran, B.J.2    Lamont, I.L.3
  • 39
    • 39649083564 scopus 로고    scopus 로고
    • Expression of the phytochrome operon in Pseudomonas aeruginosa is dependent on the alternative sigma factor RpoS
    • K. Barkovits A. Harms C. Benkartek J. L. Smart N. Frankenberg-Dinkel Expression of the phytochrome operon in Pseudomonas aeruginosa is dependent on the alternative sigma factor RpoS FEMS Microbiol. Lett. 2008 280 160 168
    • (2008) FEMS Microbiol. Lett. , vol.280 , pp. 160-168
    • Barkovits, K.1    Harms, A.2    Benkartek, C.3    Smart, J.L.4    Frankenberg-Dinkel, N.5
  • 40
    • 0030924138 scopus 로고    scopus 로고
    • A transcriptional activator, FleQ, regulates mucin adhesion and flagellar gene expression in Pseudomonas aeruginosa in a cascade manner
    • S. K. Arora B. W. Ritchings E. C. Almira S. Lory R. Ramphal A transcriptional activator, FleQ, regulates mucin adhesion and flagellar gene expression in Pseudomonas aeruginosa in a cascade manner J. Bacteriol. 1997 179 5574 5581
    • (1997) J. Bacteriol. , vol.179 , pp. 5574-5581
    • Arora, S.K.1    Ritchings, B.W.2    Almira, E.C.3    Lory, S.4    Ramphal, R.5
  • 41
    • 31844452542 scopus 로고    scopus 로고
    • PsrA is a positive transcriptional regulator of the type III secretion system in Pseudomonas aeruginosa
    • D. K. Shen D. Filopon L. Kuhn B. Polack B. Toussaint PsrA is a positive transcriptional regulator of the type III secretion system in Pseudomonas aeruginosa Infect. Immun. 2006 74 1121 1129
    • (2006) Infect. Immun. , vol.74 , pp. 1121-1129
    • Shen, D.K.1    Filopon, D.2    Kuhn, L.3    Polack, B.4    Toussaint, B.5
  • 42
    • 0029898120 scopus 로고    scopus 로고
    • Ferric uptake regulator (Fur) mutants of Pseudomonas aeruginosa demonstrate defective siderophore-mediated iron uptake, altered aerobic growth, and decreased superoxide dismutase and catalase activities
    • D. J. Hassett P. A. Sokol M. L. Howell J. F. Ma H. T. Schweizer U. Ochsner M. L. Vasil Ferric uptake regulator (Fur) mutants of Pseudomonas aeruginosa demonstrate defective siderophore-mediated iron uptake, altered aerobic growth, and decreased superoxide dismutase and catalase activities J. Bacteriol. 1996 178 3996 4003
    • (1996) J. Bacteriol. , vol.178 , pp. 3996-4003
    • Hassett, D.J.1    Sokol, P.A.2    Howell, M.L.3    Ma, J.F.4    Schweizer, H.T.5    Ochsner, U.6    Vasil, M.L.7
  • 43
    • 0029798283 scopus 로고    scopus 로고
    • Ferric uptake regulator mutants of Pseudomonas aeruginosa with distinct alterations in the iron-dependent repression of exotoxin A and siderophores in aerobic and microaerobic environments
    • H. A. Barton Z. Johnson C. D. Cox A. I. Vasil M. L. Vasil Ferric uptake regulator mutants of Pseudomonas aeruginosa with distinct alterations in the iron-dependent repression of exotoxin A and siderophores in aerobic and microaerobic environments Mol. Microbiol. 1996 21 1001 1017
    • (1996) Mol. Microbiol. , vol.21 , pp. 1001-1017
    • Barton, H.A.1    Johnson, Z.2    Cox, C.D.3    Vasil, A.I.4    Vasil, M.L.5
  • 44
    • 0035982906 scopus 로고    scopus 로고
    • GeneChip expression analysis of the iron starvation response in Pseudomonas aeruginosa: Identification of novel pyoverdine biosynthesis genes
    • U. A. Ochsner P. J. Wilderman A. I. Vasil M. L. Vasil GeneChip expression analysis of the iron starvation response in Pseudomonas aeruginosa: identification of novel pyoverdine biosynthesis genes Mol. Microbiol. 2002 45 1277 1287
    • (2002) Mol. Microbiol. , vol.45 , pp. 1277-1287
    • Ochsner, U.A.1    Wilderman, P.J.2    Vasil, A.I.3    Vasil, M.L.4
  • 45
    • 0029966305 scopus 로고    scopus 로고
    • Gene repression by the ferric uptake regulator in Pseudomonas aeruginosa: Cycle selection of iron-regulated genes
    • U. A. Ochsner M. L. Vasil Gene repression by the ferric uptake regulator in Pseudomonas aeruginosa: cycle selection of iron-regulated genes Proc. Natl. Acad. Sci. U. S. A. 1996 93 4409 4414
    • (1996) Proc. Natl. Acad. Sci. U. S. A. , vol.93 , pp. 4409-4414
    • Ochsner, U.A.1    Vasil, M.L.2
  • 46
    • 0033955445 scopus 로고    scopus 로고
    • Genetics and regulation of two distinct haem-uptake systems, phu and has, in Pseudomonas aeruginosa
    • U. A. Ochsner Z. Johnson M. L. Vasil Genetics and regulation of two distinct haem-uptake systems, phu and has, in Pseudomonas aeruginosa Microbiology 2000 146 Pt 1 185 198
    • (2000) Microbiology , vol.146 , Issue.PT 1 , pp. 185-198
    • Ochsner, U.A.1    Johnson, Z.2    Vasil, M.L.3
  • 47
    • 0033874090 scopus 로고    scopus 로고
    • Role of the Pseudomonas aeruginosa oxyR-recG operon in oxidative stress defense and DNA repair: OxyR-dependent regulation of katB-ankB, ahpB, and ahpC-ahpF
    • U. A. Ochsner M. L. Vasil E. Alsabbagh K. Parvatiyar D. J. Hassett Role of the Pseudomonas aeruginosa oxyR-recG operon in oxidative stress defense and DNA repair: OxyR-dependent regulation of katB-ankB, ahpB, and ahpC-ahpF J. Bacteriol. 2000 182 4533 4544
    • (2000) J. Bacteriol. , vol.182 , pp. 4533-4544
    • Ochsner, U.A.1    Vasil, M.L.2    Alsabbagh, E.3    Parvatiyar, K.4    Hassett, D.J.5
  • 48
    • 53849137337 scopus 로고    scopus 로고
    • Loss of the oxidative stress regulator OxyR in Pseudomonas aeruginosa PAO1 impairs growth under iron-limited conditions
    • T. Vinckx S. Matthijs P. Cornelis Loss of the oxidative stress regulator OxyR in Pseudomonas aeruginosa PAO1 impairs growth under iron-limited conditions FEMS Microbiol. Lett. 2008 288 258 265
    • (2008) FEMS Microbiol. Lett. , vol.288 , pp. 258-265
    • Vinckx, T.1    Matthijs, S.2    Cornelis, P.3
  • 51
    • 0017878206 scopus 로고
    • Biosynthesis of exopolysaccharide by Pseudomonas aeruginosa
    • F. A. Mian T. R. Jarman R. C. Righelato Biosynthesis of exopolysaccharide by Pseudomonas aeruginosa J. Bacteriol. 1978 134 418 422
    • (1978) J. Bacteriol. , vol.134 , pp. 418-422
    • Mian, F.A.1    Jarman, T.R.2    Righelato, R.C.3
  • 52
    • 0034039015 scopus 로고    scopus 로고
    • Adaptation of E. Coli cell method for micro-scale nitrate measurement with the Griess reaction in culture media
    • J. Xu X. Xu W. Verstraete Adaptation of E. coli cell method for micro-scale nitrate measurement with the Griess reaction in culture media J. Microbiol. Methods 2000 41 23 33
    • (2000) J. Microbiol. Methods , vol.41 , pp. 23-33
    • Xu, J.1    Xu, X.2    Verstraete, W.3
  • 53
    • 80054873254 scopus 로고    scopus 로고
    • Impact of the spotted microarray preprocessing method on fold-change compression and variance stability
    • J. Ambroise B. Bearzatto A. Robert B. Govaerts B. Macq J. L. Gala Impact of the spotted microarray preprocessing method on fold-change compression and variance stability BMC Bioinf. 2011 12 413
    • (2011) BMC Bioinf. , vol.12 , pp. 413
    • Ambroise, J.1    Bearzatto, B.2    Robert, A.3    Govaerts, B.4    Macq, B.5    Gala, J.L.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.