-
1
-
-
50649098819
-
Redox-active antibiotics control gene expression and community behavior in divergent bacteria
-
doi:10.1126/science.1160619
-
Dietrich LEP, Teal TK, Price-Whelan A, Newman DK (2008) Redox-active antibiotics control gene expression and community behavior in divergent bacteria. Science 321: 1203-1206. doi:10.1126/science.1160619.
-
(2008)
Science
, vol.321
, pp. 1203-1206
-
-
Dietrich, L.E.P.1
Teal, T.K.2
Price-Whelan, A.3
Newman, D.K.4
-
2
-
-
0026784249
-
Two-stage control of an oxidative stress regulon: The Escherichia coli SoxR protein triggers redox-inducible expression of the soxS regulatory gene
-
Nunoshiba T, Hidalgo E, Amábile-Cuevas CF, Demple B (1992) Two-stage control of an oxidative stress regulon: the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS regulatory gene. J Bacteriol 174: 6054-6060.
-
(1992)
J Bacteriol
, vol.174
, pp. 6054-6060
-
-
Nunoshiba, T.1
Hidalgo, E.2
Amábile-Cuevas, C.F.3
Demple, B.4
-
3
-
-
14944340675
-
Activation of SoxR-dependent transcription in Pseudomonas aeruginosa
-
DOI 10.1093/jb/mvh168
-
Kobayashi K, Tagawa S (2004) Activation of SoxR-dependent transcription in Pseudomonas aeruginosa. J Biochem 136: 607-615. doi:10.1093/jb/mvh168. (Pubitemid 40364183)
-
(2004)
Journal of Biochemistry
, vol.136
, Issue.5
, pp. 607-615
-
-
Kobayashi, K.1
Tagawa, S.2
-
4
-
-
33845411514
-
Agrobacterium tumefaciens soxR is involved in superoxide stress protection and also directly regulates superoxide-inducible expression of itself and a target gene
-
DOI 10.1128/JB.00856-06
-
Eiamphungporn W, Charoenlap N, Vattanaviboon P, Mongkolsuk S (2006) Agrobacterium tumefaciens soxR is involved in superoxide stress protection and also directly regulates superoxide-inducible expression of itself and a target gene. J Bacteriol 188: 8669-8673. doi:10.1128/JB.00856-06. (Pubitemid 44894069)
-
(2006)
Journal of Bacteriology
, vol.188
, Issue.24
, pp. 8669-8673
-
-
Eiamphungporn, W.1
Charoenlap, N.2
Vattanaviboon, P.3
Mongkolsuk, S.4
-
5
-
-
78649647804
-
Expression of the Streptomyces coelicolor SoxR regulon is intimately linked with actinorhodin production
-
doi:10.1128/JB.00916-10
-
Dela Cruz R, Gao Y, Penumetcha S, Sheplock R, Weng K, et al. (2010) Expression of the Streptomyces coelicolor SoxR regulon is intimately linked with actinorhodin production. J Bacteriol 192: 6428-6438. doi:10.1128/JB.00916-10.
-
(2010)
J Bacteriol
, vol.192
, pp. 6428-6438
-
-
Dela Cruz, R.1
Gao, Y.2
Penumetcha, S.3
Sheplock, R.4
Weng, K.5
-
6
-
-
78650114522
-
Activation of the SoxR regulon in Streptomyces coelicolor by the extracellular form of the pigmented antibiotic actinorhodin
-
doi:10.1128/JB.00965-10
-
Shin J-H, Singh AK, Cheon D-J, Roe J-H (2011) Activation of the SoxR regulon in Streptomyces coelicolor by the extracellular form of the pigmented antibiotic actinorhodin. J Bacteriol 193: 75-81. doi:10.1128/JB.00965-10.
-
(2011)
J Bacteriol
, vol.193
, pp. 75-81
-
-
Shin, J.-H.1
Singh, A.K.2
Cheon, D.-J.3
Roe, J.-H.4
-
7
-
-
84855891357
-
Novel roles of SoxR, a transcriptional regulator from Xanthomonas campestris, in sensing redox-cycling drugs and regulating a protective gene that have overall implications for bacterial stress physiology and virulence on a host plant
-
doi:10.1128/JB.05603-11
-
Mahavihakanont A, Charoenlap N, Namchaiw P, Eiamphungporn W, Chattrakarn S, et al. (2012) Novel roles of SoxR, a transcriptional regulator from Xanthomonas campestris, in sensing redox-cycling drugs and regulating a protective gene that have overall implications for bacterial stress physiology and virulence on a host plant. J Bacteriol 194: 209-217. doi:10.1128/JB.05603- 11.
-
(2012)
J Bacteriol
, vol.194
, pp. 209-217
-
-
Mahavihakanont, A.1
Charoenlap, N.2
Namchaiw, P.3
Eiamphungporn, W.4
Chattrakarn, S.5
-
8
-
-
0030844766
-
Cysteine-to-alanine replacements in the Escherichia coli SoxR protein and the role of the [2Fe-2S] centers in transcriptional activation
-
DOI 10.1093/nar/25.8.1469
-
Bradley TM, Hidalgo E, Leautaud V, Ding H, Demple B (1997) Cysteine-to-alanine replacements in the Escherichia coli SoxR protein and the role of the [2Fe-2S] centers in transcriptional activation. Nuc Acids Res 25: 1469-1475. doi:10.1093/nar/25.8.1469. (Pubitemid 27302902)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.8
, pp. 1469-1475
-
-
Bradley, T.M.1
Hidalgo, E.2
Leautaud, V.3
Ding, H.4
Demple, B.5
-
9
-
-
84872424732
-
Species-specific residues calibrate SoxR sensitivity to redox-active molecules
-
doi:10.1111/mmi.12101
-
Sheplock R, Recinos DA, Mackow N, Dietrich LEP, Chander M (2013) Species-specific residues calibrate SoxR sensitivity to redox-active molecules. Mol Microbiol 87: 368-381. doi:10.1111/mmi.12101.
-
(2013)
Mol Microbiol
, vol.87
, pp. 368-381
-
-
Sheplock, R.1
Recinos, D.A.2
Mackow, N.3
Dietrich, L.E.P.4
Chander, M.5
-
10
-
-
0025078495
-
Positive control of a global antioxidant defense regulon activated by superoxide-generating agents in Escherichia coli
-
doi:10.1073/pnas.87.16.6181
-
Greenberg JT, Monach P, Chou JH, Josephy PD, Demple B (1990) Positive control of a global antioxidant defense regulon activated by superoxide-generating agents in Escherichia coli. Proc Natl Acad Sci USA 87: 6181-6185. doi:10.1073/pnas.87.16.6181.
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 6181-6185
-
-
Greenberg, J.T.1
Monach, P.2
Chou, J.H.3
Josephy, P.D.4
Demple, B.5
-
11
-
-
0025369726
-
soxR, a locus governing a superoxide response regulon in Escherichia coli K-12
-
Tsaneva IR, Weiss B (1990) soxR, a locus governing a superoxide response regulon in Escherichia coli K-12. J Bacteriol 172: 4197-4205. (Pubitemid 20236706)
-
(1990)
Journal of Bacteriology
, vol.172
, Issue.8
, pp. 4197-4205
-
-
Tsaneva, I.R.1
Weiss, B.2
-
12
-
-
0025816912
-
Molecular characterization of the soxRS genes of Escherichia coli: Two genes control a superoxide stress regulon
-
Amábile-Cuevas CF, Demple B (1991) Molecular characterization of the soxRS genes of Escherichia coli: two genes control a superoxide stress regulon. Nuc Acids Res 19: 4479-4484. doi:10.1093/nar/19.16.4479. (Pubitemid 21912827)
-
(1991)
Nucleic Acids Research
, vol.19
, Issue.16
, pp. 4479-4484
-
-
Amabile-Cuevas, C.F.1
Demple, B.2
-
13
-
-
0025809949
-
Two divergently transcribed genes, soxR and soxS, control a superoxide response regulon of Escherichia coli
-
Wu J, Weiss B (1991) Two divergently transcribed genes, soxR and soxS, control a superoxide response regulon of Escherichia coli. J Bacteriol 173: 2864-2871.
-
(1991)
J Bacteriol
, vol.173
, pp. 2864-2871
-
-
Wu, J.1
Weiss, B.2
-
14
-
-
0034977251
-
Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
-
DOI 10.1128/JB.183.13.3890-3902.2001
-
Pomposiello PJ, Bennik MH, Demple B (2001) Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate. J Bacteriol 183: 3890-3902. doi:10.1128/JB.183.13.3890-3902.2001. (Pubitemid 32565468)
-
(2001)
Journal of Bacteriology
, vol.183
, Issue.13
, pp. 3890-3902
-
-
Pomposiello, P.J.1
Bennik, M.H.J.2
Demple, B.3
-
15
-
-
17644408447
-
Pseudomonas aeruginosa SoxR does not conform to the archetypal paradigm for SoxR-dependent regulation of the bacterial oxidative stress adaptive response
-
DOI 10.1128/IAI.73.5.2958-2966.2005
-
Palma M, Zurita J, Ferreras JA, Worgall S, Larone DH, et al. (2005) Pseudomonas aeruginosa SoxR does not conform to the archetypal paradigm for SoxR-dependent regulation of the bacterial oxidative stress adaptive response. Infect Immun 73: 2958-2966. doi:10.1128/IAI.73.5.2958-2966.2005. (Pubitemid 40570364)
-
(2005)
Infection and Immunity
, vol.73
, Issue.5
, pp. 2958-2966
-
-
Palma, M.1
Zurita, J.2
Ferreras, J.A.3
Worgall, S.4
Larone, D.H.5
Shi, L.6
Campagne, F.7
Quadri, L.E.N.8
-
16
-
-
30944437009
-
Regulation of superoxide stress in Pseudomonas putida KT2440 is different from the SoxR paradigm in Escherichia coli
-
DOI 10.1016/j.bbrc.2005.12.142, PII S0006291X05029013
-
Park W, Peña-Llopis S, Lee Y, Demple B (2006) Regulation of superoxide stress in Pseudomonas putida KT2440 is different from the SoxR paradigm in Escherichia coli. Biochem Biophys Res Commun 341: 51-56. doi:10.1016/j.bbrc.2005.12.142. (Pubitemid 43117385)
-
(2006)
Biochemical and Biophysical Research Communications
, vol.341
, Issue.1
, pp. 51-56
-
-
Park, W.1
Pena-Llopis, S.2
Lee, Y.3
Demple, B.4
-
17
-
-
33747082622
-
The phenazine pyocyanin is a terminal signalling factor in the quorum sensing network of Pseudomonas aeruginosa
-
DOI 10.1111/j.1365-2958.2006.05306.x
-
Dietrich LEP, Price-Whelan A, Petersen A, Whiteley M, Newman DK (2006) The phenazine pyocyanin is a terminal signalling factor in the quorum sensing network of Pseudomonas aeruginosa. Mol Microbiol 61: 1308-1321. doi:10.1111/j.1365-2958.2006.05306.x. (Pubitemid 44215429)
-
(2006)
Molecular Microbiology
, vol.61
, Issue.5
, pp. 1308-1321
-
-
Dietrich, L.E.P.1
Price-Whelan, A.2
Petersen, A.3
Whiteley, M.4
Newman, D.K.5
-
18
-
-
84888345885
-
Comparative study of SoxR activation by redox-active compounds
-
doi:10.1111/mmi.12410
-
Singh AK, Shin J-H, Lee K-L, Imlay JA, Roe J-H (2013) Comparative study of SoxR activation by redox-active compounds. Mol Microbiol 90: 983-996. doi:10.1111/mmi.12410.
-
(2013)
Mol Microbiol
, vol.90
, pp. 983-996
-
-
Singh, A.K.1
Shin, J.-H.2
Lee, K.-L.3
Imlay, J.A.4
Roe, J.-H.5
-
19
-
-
0037439266
-
The structure of ActVA-Orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis
-
DOI 10.1093/emboj/cdg031
-
Sciara G, Kendrew SG, Miele AE, Marsh NG, Federici L, et al. (2003) The structure of ActVA-Orf6, a novel type of monooxygenase involved in actinorhodin biosynthesis. EMBO J 22: 205-215. doi:10.1093/emboj/cdg031. (Pubitemid 36119426)
-
(2003)
EMBO Journal
, vol.22
, Issue.2
, pp. 205-215
-
-
Sciara, G.1
Kendrew, S.G.2
Miele, A.E.3
Marsh, N.G.4
Federici, L.5
Malatesta, F.6
Schimperna, G.7
Savino, C.8
Vallone, B.9
-
20
-
-
0035576880
-
Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays
-
DOI 10.1101/gad.943401
-
Huang J, Lih CJ, Pan KH, Cohen SN (2001) Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 15: 3183-3192. doi:10.1101/gad.943401. (Pubitemid 33115681)
-
(2001)
Genes and Development
, vol.15
, Issue.23
, pp. 3183-3192
-
-
Huang, J.1
Lih, C.-J.2
Pan, K.-H.3
Cohen, S.N.4
-
21
-
-
0003869903
-
-
Norwich, England: The John Innes Foundation
-
Kieser T, Bibb MJ, Buttner MJ, Chater KF, Hopwood DA (2000) Practical Streptomyces genetics. Norwich, England: The John Innes Foundation.
-
(2000)
Practical Streptomyces Genetics
-
-
Kieser, T.1
Bibb, M.J.2
Buttner, M.J.3
Chater, K.F.4
Hopwood, D.A.5
-
22
-
-
0037046560
-
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
-
DOI 10.1038/417141a
-
Bentley SD, Chater KF, Cerdeño-Tárraga A-M, Challis GL, Thomson NR, et al. (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417: 141-147. doi:10.1038/417141a. (Pubitemid 34506788)
-
(2002)
Nature
, vol.417
, Issue.6885
, pp. 141-147
-
-
Bentley, S.D.1
Chater, K.F.2
Cerdeno-Tarraga, A.-M.3
Challis, G.L.4
Thomson, N.R.5
James, K.D.6
Harris, D.E.7
Quail, M.A.8
Kieser, H.9
Harper, D.10
Bateman, A.11
Brown, S.12
Chandra, G.13
Chen, C.W.14
Collins, M.15
Cronin, A.16
Fraser, A.17
Goble, A.18
Hidalgo, J.19
Hornsby, T.20
Howarth, S.21
Huang, C.-H.22
Kieser, T.23
Larke, L.24
Murphy, L.25
Oliver, K.26
O'Neil, S.27
Rabbinowitsch, E.28
Rajandream, M.-A.29
Rutherford, K.30
Rutter, S.31
Seeger, K.32
Saunders, D.33
Sharp, S.34
Squares, R.35
Squares, S.36
Taylor, K.37
Warren, T.38
Wietzorrek, A.39
Woodward, J.40
Barrell, B.G.41
Parkhill, J.42
Hopwood, D.A.43
more..
-
23
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
doi:10.1093/bioinformatics/btp324
-
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760. doi:10.1093/ bioinformatics/btp324.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
24
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
doi:10.1093/bioinformatics/btq033
-
Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842. doi:10.1093/ bioinformatics/btq033.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
25
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
DOI 10.1101/gr.4086505
-
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res 15: 1451-1455. doi:10.1101/gr.4086505. (Pubitemid 41400913)
-
(2005)
Genome Research
, vol.15
, Issue.10
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
Burhans, R.4
Elnitski, L.5
Shah, P.6
Zhang, Y.7
Blankenberg, D.8
Albert, I.9
Taylor, J.10
Miller, W.11
Kent, W.J.12
Nekrutenko, A.13
-
26
-
-
75949108066
-
Galaxy: A web-based genome analysis tool for experimentalists
-
doi:10.1002/0471142727.mb1910s89
-
Blankenberg D, Kuster von G, Coraor N, Ananda G, Lazarus R, et al. (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol Chapter 19: 19.10.1-.10.21. doi:10.1002/0471142727.mb1910s89.
-
(2010)
Curr Protoc Mol Biol Chapter
, vol.19
-
-
Blankenberg, D.1
Von Kuster, G.2
Coraor, N.3
Ananda, G.4
Lazarus, R.5
-
27
-
-
77955801615
-
Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Galaxy Team doi:10.1186/gb-2010-11-8-r86
-
Goecks J, Nekrutenko A, Taylor J, Galaxy Team (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11: R86-R86. doi:10.1186/gb-2010-11-8-r86.
-
(2010)
Genome Biol
, vol.11
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
28
-
-
77958471357
-
Differential expression analysis for sequence count data
-
doi:10.1186/gb-2010-11-10-r106
-
Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106. doi:10.1186/gb-2010-11-10-r106.
-
(2010)
Genome Biol
, vol.11
-
-
Anders, S.1
Huber, W.2
-
29
-
-
0025183708
-
Basic local alignment search tool
-
doi:10.1016/S0022-2836(05)80360-2
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410. doi:10.1016/S0022-2836(05)80360- 2.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
30
-
-
0033990048
-
Primer3 on the WWW for general users and for biologist programmers
-
Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
-
(2000)
Methods Mol Biol
, vol.132
, pp. 365-386
-
-
Rozen, S.1
Skaletsky, H.2
-
31
-
-
65649092976
-
Biopython: Freely available Python tools for computational molecular biology and bioinformatics
-
doi:10.1093/bioinformatics/btp163
-
Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422-1423. doi:10.1093/bioinformatics/btp163.
-
(2009)
Bioinformatics
, vol.25
, pp. 1422-1423
-
-
Cock, P.J.A.1
Antao, T.2
Chang, J.T.3
Chapman, B.A.4
Cox, C.J.5
-
32
-
-
0029762312
-
afsR is a pleiotropic but conditionally required regulatory gene for antibiotic production in Streptomyces coelicolor A3(2)
-
Floriano B, Bibb M (1996) afsR is a pleiotropic but conditionally required regulatory gene for antibiotic production in Streptomyces coelicolor A3(2). Mol Microbiol 21: 385-396. doi:10.1046/j.1365-2958.1996.6491364.x. (Pubitemid 26291543)
-
(1996)
Molecular Microbiology
, vol.21
, Issue.2
, pp. 385-396
-
-
Floriano, B.1
Bibb, M.2
-
33
-
-
0037066712
-
Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies
-
DOI 10.1074/jbc.M110968200
-
Rigali S, Derouaux A, Giannotta F, Dusart J (2002) Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. J Biol Chem 277: 12507-12515. doi:10.1074/jbc.M110968200. (Pubitemid 34952608)
-
(2002)
Journal of Biological Chemistry
, vol.277
, Issue.15
, pp. 12507-12515
-
-
Rigali, S.1
Derouaux, A.2
Giannotta, F.3
Dusart, J.4
-
34
-
-
78651271733
-
Integrative genomics viewer
-
doi:10.1038/nbt.1754
-
Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, et al. (2011) Integrative genomics viewer. Nat Biotechnol 29: 24-26. doi:10.1038/nbt.1754.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
Thorvaldsdottir, H.2
Winckler, W.3
Guttman, M.4
Lander, E.S.5
-
35
-
-
84875634162
-
Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
-
doi:10.1093/bib/bbs017
-
Thorvaldsdottir H, Robinson JT, Mesirov JP (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinformatics 14: 178-192. doi:10.1093/bib/bbs017.
-
(2013)
Brief Bioinformatics
, vol.14
, pp. 178-192
-
-
Thorvaldsdottir, H.1
Robinson, J.T.2
Mesirov, J.P.3
|