-
1
-
-
0029983288
-
Transcription activation by the bacteriophage Mu Mor protein: Analysis of promoter mutations in Pm identifies a new region required for promoter function
-
Artsimovitch, I., and Howe, M.M. (1996) Transcription activation by the bacteriophage Mu Mor protein: analysis of promoter mutations in Pm identifies a new region required for promoter function. Nucleic Acids Res 24: 450-457.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 450-457
-
-
Artsimovitch, I.1
Howe, M.M.2
-
2
-
-
0027718102
-
Nucleic acid structure analysis: A users guide to a collection of new analysis programs
-
Babcock, M.S., Pednault, E.P., and Olson, W.K. (1993) Nucleic acid structure analysis: a users guide to a collection of new analysis programs. J Biomol Struct Dyn 11: 597-628.
-
(1993)
J Biomol Struct Dyn
, vol.11
, pp. 597-628
-
-
Babcock, M.S.1
Pednault, E.P.2
Olson, W.K.3
-
3
-
-
0023389549
-
DNA specificity determinants of Escherichia coli tryptophan repressor binding
-
Bass, S., Sugiono, P., Arvidson, D.N., Gunsalus, R.P., and Youderian, P. (1987) DNA specificity determinants of Escherichia coli tryptophan repressor binding. Genes Dev 1: 565-572.
-
(1987)
Genes Dev
, vol.1
, pp. 565-572
-
-
Bass, S.1
Sugiono, P.2
Arvidson, D.N.3
Gunsalus, R.P.4
Youderian, P.5
-
4
-
-
0027146277
-
Operator sequence context influences amino acid-base-pair interactions in 434 repressor-operator complexes
-
Bell, A.C., and Koudelka, G.B. (1993) Operator sequence context influences amino acid-base-pair interactions in 434 repressor-operator complexes. J Mol Biol 234: 542-553.
-
(1993)
J Mol Biol
, vol.234
, pp. 542-553
-
-
Bell, A.C.1
Koudelka, G.B.2
-
5
-
-
0034995688
-
Mutational analysis of the high-affinity BvgA binding site in the fha promoter of Bordetella pertussis
-
Boucher, P.E., Yang, M.S., and Stibitz, S. (2001) Mutational analysis of the high-affinity BvgA binding site in the fha promoter of Bordetella pertussis. Mol Microbiol 40: 991-999.
-
(2001)
Mol Microbiol
, vol.40
, pp. 991-999
-
-
Boucher, P.E.1
Yang, M.S.2
Stibitz, S.3
-
6
-
-
0031026786
-
Transcription activation at class II CAP-dependent promoters
-
Busby, S., and Ebright, R.H. (1997) Transcription activation at class II CAP-dependent promoters. Mol Microbiol 23: 853-859.
-
(1997)
Mol Microbiol
, vol.23
, pp. 853-859
-
-
Busby, S.1
Ebright, R.H.2
-
7
-
-
0032698634
-
Transcription activation by catabolite activator protein (CAP)
-
Busby, S., and Ebright, R.H. (1999) Transcription activation by catabolite activator protein (CAP). J Mol Biol 293: 199-213.
-
(1999)
J Mol Biol
, vol.293
, pp. 199-213
-
-
Busby, S.1
Ebright, R.H.2
-
8
-
-
0036203066
-
Structure of the bacterial RNA polymerase promoter specificity sigma subunit
-
Campbell, E.A., Muzzin, O., Chlenov, M., Sun, J.L., Olson, C.A., Weinman, O., et al. (2002) Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol Cell 9: 527-539.
-
(2002)
Mol Cell
, vol.9
, pp. 527-539
-
-
Campbell, E.A.1
Muzzin, O.2
Chlenov, M.3
Sun, J.L.4
Olson, C.A.5
Weinman, O.6
-
9
-
-
0025746636
-
Genetic analysis of Agrobacterium
-
Cangelosi, G.A., Best, E.A., Martinetti, G., and Nester, E.W. (1991) Genetic analysis of Agrobacterium. Methods Enzymol 204: 384-397.
-
(1991)
Methods Enzymol
, vol.204
, pp. 384-397
-
-
Cangelosi, G.A.1
Best, E.A.2
Martinetti, G.3
Nester, E.W.4
-
10
-
-
33744983319
-
The rcsA promoter of Pantoea stewartii subsp. stewartii features a low-level constitutive promoter and an EsaR quorum-sensing-regulated promoter
-
Carlier, A.L., and von Bodman, S.B. (2006) The rcsA promoter of Pantoea stewartii subsp. stewartii features a low-level constitutive promoter and an EsaR quorum-sensing-regulated promoter. J Bacteriol 188: 4581-4584.
-
(2006)
J Bacteriol
, vol.188
, pp. 4581-4584
-
-
Carlier, A.L.1
von Bodman, S.B.2
-
11
-
-
0018959055
-
In vitro gene fusions that join an enzymatically active betagalactosidase segment to aminoterminal fragments of exogenous proteins: Escherichia coli plasmid vectors for the detection and cloning of translational initiation signals
-
Casadaban, M.J., Chou, J., and Cohen, S.N. (1980) In vitro gene fusions that join an enzymatically active betagalactosidase segment to aminoterminal fragments of exogenous proteins: Escherichia coli plasmid vectors for the detection and cloning of translational initiation signals. J Bacteriol 143: 971-980.
-
(1980)
J Bacteriol
, vol.143
, pp. 971-980
-
-
Casadaban, M.J.1
Chou, J.2
Cohen, S.N.3
-
12
-
-
0027943595
-
Multiple protein-DNA and protein-protein interactions are involved in transcriptional activation by MalT
-
Danot, O., and Raibaud, O. (1994) Multiple protein-DNA and protein-protein interactions are involved in transcriptional activation by MalT. Mol Microbiol 14: 335-346.
-
(1994)
Mol Microbiol
, vol.14
, pp. 335-346
-
-
Danot, O.1
Raibaud, O.2
-
13
-
-
0345639649
-
Identification of the operator of the lux regulon from the Vibrio fischeri strain ATCC7744
-
Devine, J.H., Shadel, G.S., and Baldwin, T.O. (1989) Identification of the operator of the lux regulon from the Vibrio fischeri strain ATCC7744. Proc Natl Acad Sci USA 86: 5688-5692.
-
(1989)
Proc Natl Acad Sci USA
, vol.86
, pp. 5688-5692
-
-
Devine, J.H.1
Shadel, G.S.2
Baldwin, T.O.3
-
14
-
-
0035793714
-
Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis
-
Ducros, V.M., Lewis, R.J., Verma, C.S., Dodson, E.J., Leonard, G., Turkenburg, J.P., et al. (2001) Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis. J Mol Biol 306: 759-771.
-
(2001)
J Mol Biol
, vol.306
, pp. 759-771
-
-
Ducros, V.M.1
Lewis, R.J.2
Verma, C.S.3
Dodson, E.J.4
Leonard, G.5
Turkenburg, J.P.6
-
15
-
-
0035185549
-
Quorum sensing in Vibrio fischeri: Analysis of the LuxR DNA binding region by alanine-scanning mutagenesis
-
Egland, K.A., and Greenberg, E.P. (2001) Quorum sensing in Vibrio fischeri: analysis of the LuxR DNA binding region by alanine-scanning mutagenesis. J Bacteriol 183: 382-386.
-
(2001)
J Bacteriol
, vol.183
, pp. 382-386
-
-
Egland, K.A.1
Greenberg, E.P.2
-
16
-
-
0028352589
-
A LuxR-LuxI type regulatory system activates Agrobacterium Ti plasmid conjugal transfer in the presence of a plant tumor metabolite
-
Fuqua, W.C., and Winans, S.C. (1994) A LuxR-LuxI type regulatory system activates Agrobacterium Ti plasmid conjugal transfer in the presence of a plant tumor metabolite. J Bacteriol 176: 2796-2806.
-
(1994)
J Bacteriol
, vol.176
, pp. 2796-2806
-
-
Fuqua, W.C.1
Winans, S.C.2
-
17
-
-
0032459427
-
The functional and regulatory roles of sigma factors in transcription
-
Gross, C.A., Chan, C., Dombroski, A., Gruber, T., Sharp, M., Tupy, J., and Young, B. (1998) The functional and regulatory roles of sigma factors in transcription. Cold Spring Harb Symp Quant Biol 63: 141-155.
-
(1998)
Cold Spring Harb Symp Quant Biol
, vol.63
, pp. 141-155
-
-
Gross, C.A.1
Chan, C.2
Dombroski, A.3
Gruber, T.4
Sharp, M.5
Tupy, J.6
Young, B.7
-
18
-
-
0031473847
-
SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
-
Guex, N., and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18: 2714-2723.
-
(1997)
Electrophoresis
, vol.18
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
19
-
-
0028500170
-
The small, versatile pPZP family of Agrobacterium binary vectors for plant transformation
-
Hajdukiewicz, P., Svab, Z., and Maliga, P. (1994) The small, versatile pPZP family of Agrobacterium binary vectors for plant transformation. Plant Mol Biol 25: 989-994.
-
(1994)
Plant Mol Biol
, vol.25
, pp. 989-994
-
-
Hajdukiewicz, P.1
Svab, Z.2
Maliga, P.3
-
20
-
-
2642666491
-
Degradation of carboxyterminal tagged cytoplasmic proteins by the Escherichia coli protease HfIB (FtsH)
-
Herman, C., Thévenet, D., Bouloc, P., Walker, G.C., and D'Ari, R. (1998) Degradation of carboxyterminal tagged cytoplasmic proteins by the Escherichia coli protease HfIB (FtsH). Genes Dev 12: 1348-1355.
-
(1998)
Genes Dev
, vol.12
, pp. 1348-1355
-
-
Herman, C.1
Thévenet, D.2
Bouloc, P.3
Walker, G.C.4
D'Ari, R.5
-
21
-
-
0344585344
-
Involvement of region 4 of the sigma70 subunit of RNA polymerase in transcriptional activation of the lux operon during quorum sensing
-
Johnson, D.C., Ishihama, A., and Stevens, A.M. (2003) Involvement of region 4 of the sigma70 subunit of RNA polymerase in transcriptional activation of the lux operon during quorum sensing. FEMS Microbiol Lett 228: 193-201.
-
(2003)
FEMS Microbiol Lett
, vol.228
, pp. 193-201
-
-
Johnson, D.C.1
Ishihama, A.2
Stevens, A.M.3
-
22
-
-
0023187152
-
Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro
-
Koudelka, G.B., Harrison, S.C., and Ptashne, M. (1987) Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro. Nature 326: 886-888.
-
(1987)
Nature
, vol.326
, pp. 886-888
-
-
Koudelka, G.B.1
Harrison, S.C.2
Ptashne, M.3
-
23
-
-
0033988273
-
The replicator of the nopaline-type Ti plasmid pTiC58 is a member of the repABC family and is influenced by the TraR-dependent quorum-sensing regulatory system
-
Li, P.L., and Farrand, S.K. (2000) The replicator of the nopaline-type Ti plasmid pTiC58 is a member of the repABC family and is influenced by the TraR-dependent quorum-sensing regulatory system. J Bacteriol 182: 179-188.
-
(2000)
J Bacteriol
, vol.182
, pp. 179-188
-
-
Li, P.L.1
Farrand, S.K.2
-
24
-
-
0035187731
-
Construction of a derivative of Agrobacterium tumefaciens C58 that does not mutate to tetracycline resistance
-
Luo, Z.Q., Clemente, T.E., and Farrand, S.K. (2001) Construction of a derivative of Agrobacterium tumefaciens C58 that does not mutate to tetracycline resistance. Mol Plant Microbe Interact 14: 98-103.
-
(2001)
Mol Plant Microbe Interact
, vol.14
, pp. 98-103
-
-
Luo, Z.Q.1
Clemente, T.E.2
Farrand, S.K.3
-
25
-
-
0035393302
-
Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
-
Luscombe, N.M., Laskowski, R.A., and Thornton, J.M. (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res 29: 2860-2874.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
26
-
-
0036786677
-
Dimerization allows DNA target site recognition by the NarL response regulator
-
Maris, A.E., Sawaya, M.R., Kaczor-Grzeskowiak, M., Jarvis, M.R., Bearson, S.M., Kopka, M.L., et al. (2002) Dimerization allows DNA target site recognition by the NarL response regulator. Nat Struct Biol 9: 771-778.
-
(2002)
Nat Struct Biol
, vol.9
, pp. 771-778
-
-
Maris, A.E.1
Sawaya, M.R.2
Kaczor-Grzeskowiak, M.3
Jarvis, M.R.4
Bearson, S.M.5
Kopka, M.L.6
-
27
-
-
0003785155
-
-
Cold Spring Harbor, NY: Cold Spring Harbor Laboratory
-
Miller, J. (1972) Experiments in Molecular Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
-
(1972)
Experiments in Molecular Genetics
-
-
Miller, J.1
-
28
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
Olson, W.K., Gorin, A.A., Lu, X.J., Hock, L.M., and Zhurkin, V.B. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA 95: 11163-11168.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 11163-11168
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.J.3
Hock, L.M.4
Zhurkin, V.B.5
-
29
-
-
0034614483
-
Sequence-dependent DNA structure: Dinucleotide conformational maps
-
Packer, M.J., Dauncey, M.P., and Hunter, C.A. (2000) Sequence-dependent DNA structure: dinucleotide conformational maps. J Mol Biol 295: 71-83.
-
(2000)
J Mol Biol
, vol.295
, pp. 71-83
-
-
Packer, M.J.1
Dauncey, M.P.2
Hunter, C.A.3
-
30
-
-
0037512321
-
A LuxR-type regulator from Agrobacterium tumefaciens elevates Ti plasmid copy number by activating transcription of plasmid replication genes
-
Pappas, K.M., and Winans, S.C. (2003) A LuxR-type regulator from Agrobacterium tumefaciens elevates Ti plasmid copy number by activating transcription of plasmid replication genes. Mol Microbiol 48: 1059-1073.
-
(2003)
Mol Microbiol
, vol.48
, pp. 1059-1073
-
-
Pappas, K.M.1
Winans, S.C.2
-
31
-
-
3843091794
-
Chemical communication in proteobacteria: Biochemical and structural studies of signal synthases and receptors required for intercellular signalling
-
Pappas, K.M., Weingart, C.L., and Winans, S.C. (2004) Chemical communication in proteobacteria: biochemical and structural studies of signal synthases and receptors required for intercellular signalling. Mol Microbiol 53: 755-769.
-
(2004)
Mol Microbiol
, vol.53
, pp. 755-769
-
-
Pappas, K.M.1
Weingart, C.L.2
Winans, S.C.3
-
32
-
-
0041935939
-
-
National Institutes of Health, Online, URL
-
Rasband, W.S. (2004) ImageJ. National Institutes of Health. [Online]. URL http://rsb.info.nih.gov/lj/
-
(2004)
ImageJ
-
-
Rasband, W.S.1
-
33
-
-
0030861863
-
Transcription activation at class II CRP-dependent promoters: The role of different activating regions
-
Rhodius, V.A., West, D.M., Webster, C.L., Busby, S.J., and Savery, N.J. (1997) Transcription activation at class II CRP-dependent promoters: the role of different activating regions. Nucleic Acids Res 25: 326-332.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 326-332
-
-
Rhodius, V.A.1
West, D.M.2
Webster, C.L.3
Busby, S.J.4
Savery, N.J.5
-
35
-
-
20544460658
-
Protein-DNA recognition patterns and predictions
-
Sarai, A., and Kono, H. (2005) Protein-DNA recognition patterns and predictions. Annu Rev Biophys Biomol Struct 34: 379-398.
-
(2005)
Annu Rev Biophys Biomol Struct
, vol.34
, pp. 379-398
-
-
Sarai, A.1
Kono, H.2
-
36
-
-
0030932572
-
DNA binding and bending by the human papillomavirus type 16 E2 protein. Recognition of an extended binding site
-
Thain, A., Webster, K., Emery, D., Clarke, A.R., and Gaston, K. (1997) DNA binding and bending by the human papillomavirus type 16 E2 protein. Recognition of an extended binding site. J Biol Chem 272: 8236-8242.
-
(1997)
J Biol Chem
, vol.272
, pp. 8236-8242
-
-
Thain, A.1
Webster, K.2
Emery, D.3
Clarke, A.R.4
Gaston, K.5
-
37
-
-
0037009372
-
The crystal structure of the quorum sensing protein TraR bound to its autoinducer and target DNA
-
Vannini, A., Volpari, C., Gargioli, C., Muraglia, E., Cortese, R., De Francesco, R., et al. (2002) The crystal structure of the quorum sensing protein TraR bound to its autoinducer and target DNA. EMBO J 21: 4393-4401.
-
(2002)
EMBO J
, vol.21
, pp. 4393-4401
-
-
Vannini, A.1
Volpari, C.2
Gargioli, C.3
Muraglia, E.4
Cortese, R.5
De Francesco, R.6
-
38
-
-
27944442272
-
Quorum sensing: Cell-to-cell communication in bacteria
-
Waters, C.M., and Bassler, B.L. (2005) Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol 21: 319-346.
-
(2005)
Annu Rev Cell Dev Biol
, vol.21
, pp. 319-346
-
-
Waters, C.M.1
Bassler, B.L.2
-
39
-
-
22144443530
-
Direct binding of the quorum sensing regulator CepR of Burkholderia cenocepacia to two target promoters in vitro
-
Weingart, C.L., White, C.E., Liu, S., Chai, Y., Cho, H., Tsai, C.S., et al. (2005) Direct binding of the quorum sensing regulator CepR of Burkholderia cenocepacia to two target promoters in vitro. Mol Microbiol 57: 452-467.
-
(2005)
Mol Microbiol
, vol.57
, pp. 452-467
-
-
Weingart, C.L.1
White, C.E.2
Liu, S.3
Chai, Y.4
Cho, H.5
Tsai, C.S.6
-
40
-
-
14844328070
-
Identification of amino acid residues of the Agrobacterium tumefaciens quorum-sensing regulator TraR that are critical for positive control of transcription
-
White, C.E., and Winans, S.C. (2005) Identification of amino acid residues of the Agrobacterium tumefaciens quorum-sensing regulator TraR that are critical for positive control of transcription. Mol Microbiol 55: 1473-1486.
-
(2005)
Mol Microbiol
, vol.55
, pp. 1473-1486
-
-
White, C.E.1
Winans, S.C.2
-
41
-
-
0034830307
-
Promoter specificity elements in Pseudomonas aeruginosa quorum-sensing-controlled genes
-
Whiteley, M., and Greenberg, E.P. (2001) Promoter specificity elements in Pseudomonas aeruginosa quorum-sensing-controlled genes. J Bacteriol 183: 5529-5534.
-
(2001)
J Bacteriol
, vol.183
, pp. 5529-5534
-
-
Whiteley, M.1
Greenberg, E.P.2
-
42
-
-
0030595337
-
Structural classification of HTH DNA-binding domains and protein-DNA interaction modes
-
Wintjens, R., and Rooman, M. (1996) Structural classification of HTH DNA-binding domains and protein-DNA interaction modes. J Mol Biol 262: 294-313.
-
(1996)
J Mol Biol
, vol.262
, pp. 294-313
-
-
Wintjens, R.1
Rooman, M.2
-
43
-
-
0037182879
-
Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA
-
Zhang, R.G., Pappas, T., Brace, J.L., Miller, P.C., Oulmassov, T., Molyneaux, J.M., et al. (2002) Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA. Nature 417: 971-974.
-
(2002)
Nature
, vol.417
, pp. 971-974
-
-
Zhang, R.G.1
Pappas, T.2
Brace, J.L.3
Miller, P.C.4
Oulmassov, T.5
Molyneaux, J.M.6
-
44
-
-
0033609151
-
Autoinducer binding by the quorum-sensing regulator TraR increases affinity for target promoters in vitro and decreases TraR turnover rates in whole cells
-
Zhu, J., and Winans, S.C. (1999) Autoinducer binding by the quorum-sensing regulator TraR increases affinity for target promoters in vitro and decreases TraR turnover rates in whole cells. Proc Natl Acad Sci USA 96: 4832-4837.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 4832-4837
-
-
Zhu, J.1
Winans, S.C.2
-
45
-
-
0035852714
-
The quorum-sensing transcriptional regulator TraR requires its cognate signaling ligand for protein folding, protease resistance, and dimerization
-
Zhu, J., and Winans, S.C. (2001) The quorum-sensing transcriptional regulator TraR requires its cognate signaling ligand for protein folding, protease resistance, and dimerization. Proc Natl Acad Sci USA 98: 1507-1512.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 1507-1512
-
-
Zhu, J.1
Winans, S.C.2
-
46
-
-
0031690671
-
Analogs of the autoinducer 3-oxooctanoyl-homoserine lactone strongly inhibit activity of the TraR protein of Agrobacterium tumefaciens
-
Zhu, J., Beaber, J.W., More, M.I., Fuqua, C., Eberhard, A., and Winans, S.C. (1998) Analogs of the autoinducer 3-oxooctanoyl-homoserine lactone strongly inhibit activity of the TraR protein of Agrobacterium tumefaciens. J Bacteriol 180: 5398-5405.
-
(1998)
J Bacteriol
, vol.180
, pp. 5398-5405
-
-
Zhu, J.1
Beaber, J.W.2
More, M.I.3
Fuqua, C.4
Eberhard, A.5
Winans, S.C.6
|