-
2
-
-
0034671288
-
RNA polymerase: Structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II
-
Ebright R.H. RNA polymerase: Structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J. Mol. Biol. 304 (2000) 687-698
-
(2000)
J. Mol. Biol.
, vol.304
, pp. 687-698
-
-
Ebright, R.H.1
-
3
-
-
0032698634
-
Transcription activation by catabolite activator protein (CAP)
-
Busby S., and Ebright R.H. Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293 (1999) 199-213
-
(1999)
J. Mol. Biol.
, vol.293
, pp. 199-213
-
-
Busby, S.1
Ebright, R.H.2
-
5
-
-
0032450673
-
Gene transcription by recruitment
-
Zaman Z., Ansari A.Z., Gaudreau L., Nevado J., and Ptashne M. Gene transcription by recruitment. Cold Spring Harb. Symp. Quant. Biol. 63 (1998) 167-171
-
(1998)
Cold Spring Harb. Symp. Quant. Biol.
, vol.63
, pp. 167-171
-
-
Zaman, Z.1
Ansari, A.Z.2
Gaudreau, L.3
Nevado, J.4
Ptashne, M.5
-
6
-
-
0030960672
-
Transcriptional activation by recruitment
-
Ptashne M., and Gann A. Transcriptional activation by recruitment. Nature 386 (1997) 569-577
-
(1997)
Nature
, vol.386
, pp. 569-577
-
-
Ptashne, M.1
Gann, A.2
-
8
-
-
0023918675
-
Structure and function of bacterial sigma factors
-
Helmann J.D., and Chamberlin M.J. Structure and function of bacterial sigma factors. Annu. Rev. Biochem. 57 (1988) 839-872
-
(1988)
Annu. Rev. Biochem.
, vol.57
, pp. 839-872
-
-
Helmann, J.D.1
Chamberlin, M.J.2
-
9
-
-
0242692671
-
Multiple sigma subunits and the partitioning of bacterial transcription space
-
Gruber T.M., and Gross C.A. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu. Rev. Microbiol. 57 (2003) 441-466
-
(2003)
Annu. Rev. Microbiol.
, vol.57
, pp. 441-466
-
-
Gruber, T.M.1
Gross, C.A.2
-
10
-
-
0037261948
-
The sigma70 family of sigma factors
-
Paget M.S., and Helmann J.D. The sigma70 family of sigma factors. Genome Biol. 4 (2003) 203
-
(2003)
Genome Biol.
, vol.4
, pp. 203
-
-
Paget, M.S.1
Helmann, J.D.2
-
11
-
-
0033912262
-
The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor
-
Buck M., Gallegos M.T., Studholme D.J., Guo Y., and Gralla J.D. The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor. J. Bacteriol. 182 (2000) 4129-4136
-
(2000)
J. Bacteriol.
, vol.182
, pp. 4129-4136
-
-
Buck, M.1
Gallegos, M.T.2
Studholme, D.J.3
Guo, Y.4
Gralla, J.D.5
-
12
-
-
0027770723
-
In a class of its own: The RNA polymerase sigma factor sigma 54 (sigma N)
-
Merrick M.J. In a class of its own: The RNA polymerase sigma factor sigma 54 (sigma N). Mol. Microbiol. 10 (1993) 903-909
-
(1993)
Mol. Microbiol.
, vol.10
, pp. 903-909
-
-
Merrick, M.J.1
-
13
-
-
1842591130
-
The regulation of bacterial transcription initiation
-
Browning D.F., and Busby S.J. The regulation of bacterial transcription initiation. Nature Rev. Microbiol. 2 (2004) 57-65
-
(2004)
Nature Rev. Microbiol.
, vol.2
, pp. 57-65
-
-
Browning, D.F.1
Busby, S.J.2
-
14
-
-
0035066617
-
Transcriptional regulation at a distance in bacteria
-
Xu H., and Hoover T.R. Transcriptional regulation at a distance in bacteria. Curr. Opin. Microbiol. 4 (2001) 138-144
-
(2001)
Curr. Opin. Microbiol.
, vol.4
, pp. 138-144
-
-
Xu, H.1
Hoover, T.R.2
-
15
-
-
0036039734
-
Mechanochemical ATPases and transcriptional activation
-
Zhang X., Chaney M., Wigneshweraraj S.R., Schumacher J., Bordes P., Cannon W., and Buck M. Mechanochemical ATPases and transcriptional activation. Mol. Microbiol. 45 (2002) 895-903
-
(2002)
Mol. Microbiol.
, vol.45
, pp. 895-903
-
-
Zhang, X.1
Chaney, M.2
Wigneshweraraj, S.R.3
Schumacher, J.4
Bordes, P.5
Cannon, W.6
Buck, M.7
-
16
-
-
2142707172
-
ATP-dependent transcriptional activation by bacterial PspF AAA+ protein
-
Schumacher J., Zhang X., Jones S., Bordes P., and Buck M. ATP-dependent transcriptional activation by bacterial PspF AAA+ protein. J. Mol. Biol. 338 (2004) 863-875
-
(2004)
J. Mol. Biol.
, vol.338
, pp. 863-875
-
-
Schumacher, J.1
Zhang, X.2
Jones, S.3
Bordes, P.4
Buck, M.5
-
17
-
-
0032164070
-
Active recruitment of sigma54-RNA polymerase to the Pu promoter of Pseudomonas putida: Role of IHF and alphaCTD
-
Bertoni G., Fujita N., Ishihama A., and de Lorenzo V. Active recruitment of sigma54-RNA polymerase to the Pu promoter of Pseudomonas putida: Role of IHF and alphaCTD. EMBO J. 17 (1998) 5120-5128
-
(1998)
EMBO J.
, vol.17
, pp. 5120-5128
-
-
Bertoni, G.1
Fujita, N.2
Ishihama, A.3
de Lorenzo, V.4
-
18
-
-
0022545682
-
Upstream activator sequences are present in the promoters of nitrogen fixation genes
-
Buck M., Miller S., Drummond M., and Dixon R. Upstream activator sequences are present in the promoters of nitrogen fixation genes. Nature 320 (1986) 374-378
-
(1986)
Nature
, vol.320
, pp. 374-378
-
-
Buck, M.1
Miller, S.2
Drummond, M.3
Dixon, R.4
-
19
-
-
0022446209
-
Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter
-
Reitzer L.J., and Magasanik B. Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter. Cell 45 (1986) 785-792
-
(1986)
Cell
, vol.45
, pp. 785-792
-
-
Reitzer, L.J.1
Magasanik, B.2
-
20
-
-
0036777449
-
FleQ, the major flagellar gene regulator in Pseudomonas aeruginosa, binds to enhancer sites located either upstream or atypically downstream of the RpoN binding site
-
Jyot J., Dasgupta N., and Ramphal R. FleQ, the major flagellar gene regulator in Pseudomonas aeruginosa, binds to enhancer sites located either upstream or atypically downstream of the RpoN binding site. J. Bacteriol. 184 (2002) 5251-5260
-
(2002)
J. Bacteriol.
, vol.184
, pp. 5251-5260
-
-
Jyot, J.1
Dasgupta, N.2
Ramphal, R.3
-
21
-
-
0025035371
-
DNA-looping and enhancer activity: Association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter
-
Su W., Porter S., Kustu S., and Echols H. DNA-looping and enhancer activity: Association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter. Proc. Natl. Acad. Sci. USA 87 (1990) 5504-5508
-
(1990)
Proc. Natl. Acad. Sci. USA
, vol.87
, pp. 5504-5508
-
-
Su, W.1
Porter, S.2
Kustu, S.3
Echols, H.4
-
22
-
-
0025012093
-
The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons
-
Hoover T.R., Santero E., Porter S., and Kustu S. The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons. Cell 63 (1990) 11-22
-
(1990)
Cell
, vol.63
, pp. 11-22
-
-
Hoover, T.R.1
Santero, E.2
Porter, S.3
Kustu, S.4
-
23
-
-
0032992369
-
Role of ArgR in activation of the ast operon, encoding enzymes of the arginine succinyl transferase pathway in Salmonella typhimurium
-
Lu C.D., and Abdelal A.T. Role of ArgR in activation of the ast operon, encoding enzymes of the arginine succinyl transferase pathway in Salmonella typhimurium. J. Bacteriol. 181 (1999) 1934-1938
-
(1999)
J. Bacteriol.
, vol.181
, pp. 1934-1938
-
-
Lu, C.D.1
Abdelal, A.T.2
-
24
-
-
0030931164
-
DNA bending and the initiation of transcription at sigma54-dependent bacterial promoters
-
Carmona M., Claverie-Martin F., and Magasanik B. DNA bending and the initiation of transcription at sigma54-dependent bacterial promoters. Proc. Natl. Acad. Sci. USA 94 (1997) 9568-9572
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 9568-9572
-
-
Carmona, M.1
Claverie-Martin, F.2
Magasanik, B.3
-
25
-
-
0033857305
-
Promoter opening by sigma(54) and sigma(70) RNA polymerases: Sigma factor-directed alterations in the mechanism and tightness of control
-
Guo Y., Lew C.M., and Gralla J.D. Promoter opening by sigma(54) and sigma(70) RNA polymerases: Sigma factor-directed alterations in the mechanism and tightness of control. Genes Dev. 14 (2000) 2242-2255
-
(2000)
Genes Dev.
, vol.14
, pp. 2242-2255
-
-
Guo, Y.1
Lew, C.M.2
Gralla, J.D.3
-
26
-
-
0035793716
-
Regulatory sequences in sigma 54 localise near the start of DNA melting
-
Wigneshweraraj S.R., Chaney M.K., Ishihama A., and Buck M. Regulatory sequences in sigma 54 localise near the start of DNA melting. J. Mol. Biol. 306 (2001) 681-701
-
(2001)
J. Mol. Biol.
, vol.306
, pp. 681-701
-
-
Wigneshweraraj, S.R.1
Chaney, M.K.2
Ishihama, A.3
Buck, M.4
-
27
-
-
4844230879
-
Reorganisation of an RNA polymerase-promoter DNA complex for DNA melting
-
Burrows P.C., Severinov K., Buck M., and Wigneshweraraj S.R. Reorganisation of an RNA polymerase-promoter DNA complex for DNA melting. EMBO J 23 (2004) 4253-4263
-
(2004)
EMBO J
, vol.23
, pp. 4253-4263
-
-
Burrows, P.C.1
Severinov, K.2
Buck, M.3
Wigneshweraraj, S.R.4
-
28
-
-
0011064770
-
Products of nitrogen regulatory genes ntrA and ntrC of enteric bacteria activate glnA transcription in vitro: Evidence that the ntrA product is a sigma factor
-
Hirschman J., Wong P.K., Sei K., Keener J., and Kustu S. Products of nitrogen regulatory genes ntrA and ntrC of enteric bacteria activate glnA transcription in vitro: Evidence that the ntrA product is a sigma factor. Proc. Natl. Acad. Sci. USA 82 (1985) 7525-7529
-
(1985)
Proc. Natl. Acad. Sci. USA
, vol.82
, pp. 7525-7529
-
-
Hirschman, J.1
Wong, P.K.2
Sei, K.3
Keener, J.4
Kustu, S.5
-
29
-
-
0345758482
-
Transcription of glnA by purified Escherichia coli components: Core RNA polymerase and the products of glnF, glnG, and glnL
-
Hunt T.P., and Magasanik B. Transcription of glnA by purified Escherichia coli components: Core RNA polymerase and the products of glnF, glnG, and glnL. Proc. Natl. Acad. Sci. USA 82 (1985) 8453-8457
-
(1985)
Proc. Natl. Acad. Sci. USA
, vol.82
, pp. 8453-8457
-
-
Hunt, T.P.1
Magasanik, B.2
-
30
-
-
0024830930
-
Mutations in genes downstream of the rpoN gene (encoding sigma 54) of Klebsiella pneumoniae affect expression from sigma 54-dependent promoters
-
Merrick M.J., and Coppard J.R. Mutations in genes downstream of the rpoN gene (encoding sigma 54) of Klebsiella pneumoniae affect expression from sigma 54-dependent promoters. Mol. Microbiol. 3 (1989) 1765-1775
-
(1989)
Mol. Microbiol.
, vol.3
, pp. 1765-1775
-
-
Merrick, M.J.1
Coppard, J.R.2
-
31
-
-
0034822014
-
Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli
-
Reitzer L., and Schneider B.L. Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli. Microbiol. Mol. Biol. Rev. 65 (2001) 422-444
-
(2001)
Microbiol. Mol. Biol. Rev.
, vol.65
, pp. 422-444
-
-
Reitzer, L.1
Schneider, B.L.2
-
32
-
-
0034192966
-
The biology of enhancer-dependent transcriptional regulation in bacteria: Insights from genome sequences
-
Studholme D.J., and Buck M. The biology of enhancer-dependent transcriptional regulation in bacteria: Insights from genome sequences. FEMS Microbiol. Lett. 186 (2000) 1-9
-
(2000)
FEMS Microbiol. Lett.
, vol.186
, pp. 1-9
-
-
Studholme, D.J.1
Buck, M.2
-
33
-
-
0034666279
-
Competition among seven Escherichia coli sigma subunits: Relative binding affinities to the core RNA polymerase
-
Maeda H., Fujita N., and Ishihama A. Competition among seven Escherichia coli sigma subunits: Relative binding affinities to the core RNA polymerase. Nucleic Acids Res. 28 (2000) 3497-3503
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 3497-3503
-
-
Maeda, H.1
Fujita, N.2
Ishihama, A.3
-
34
-
-
0029029993
-
Core RNA polymerase and promoter DNA interactions of purified domains of sigma N: bipartite functions
-
Cannon W., Missailidis S., Smith C., Cottier A., Austin S., Moore M., and Buck M. Core RNA polymerase and promoter DNA interactions of purified domains of sigma N: bipartite functions. J. Mol. Biol. 248 (1995) 781-803
-
(1995)
J. Mol. Biol.
, vol.248
, pp. 781-803
-
-
Cannon, W.1
Missailidis, S.2
Smith, C.3
Cottier, A.4
Austin, S.5
Moore, M.6
Buck, M.7
-
35
-
-
0032588981
-
Sequences in sigmaN determining holoenzyme formation and properties
-
Gallegos M.T., and Buck M. Sequences in sigmaN determining holoenzyme formation and properties. J. Mol. Biol. 288 (1999) 539-553
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 539-553
-
-
Gallegos, M.T.1
Buck, M.2
-
36
-
-
0023496357
-
The nucleotide sequence of the sigma factor gene ntrA (rpoN) of Azotobacter vinelandii: Analysis of conserved sequences in NtrA proteins
-
Merrick M., Gibbins J., and Toukdarian A. The nucleotide sequence of the sigma factor gene ntrA (rpoN) of Azotobacter vinelandii: Analysis of conserved sequences in NtrA proteins. Mol. Gen. Genet. 210 (1987) 323-330
-
(1987)
Mol. Gen. Genet.
, vol.210
, pp. 323-330
-
-
Merrick, M.1
Gibbins, J.2
Toukdarian, A.3
-
37
-
-
0025180626
-
Role of eukaryotic-type functional domains found in the prokaryotic enhancer receptor factor sigma 54
-
Sasse-Dwight S., and Gralla J.D. Role of eukaryotic-type functional domains found in the prokaryotic enhancer receptor factor sigma 54. Cell 62 (1990) 945-954
-
(1990)
Cell
, vol.62
, pp. 945-954
-
-
Sasse-Dwight, S.1
Gralla, J.D.2
-
38
-
-
0028316752
-
The domain structure of sigma 54 as determined by analysis of a set of deletion mutants
-
Wong C., Tintut Y., and Gralla J.D. The domain structure of sigma 54 as determined by analysis of a set of deletion mutants. J. Mol. Biol. 236 (1994) 81-90
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 81-90
-
-
Wong, C.1
Tintut, Y.2
Gralla, J.D.3
-
39
-
-
0035937702
-
Roles for the C-terminal region of sigma 54 in transcriptional silencing and DNA binding
-
Wang L., and Gralla J.D. Roles for the C-terminal region of sigma 54 in transcriptional silencing and DNA binding. J. Biol. Chem. 276 (2001) 8979-8986
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 8979-8986
-
-
Wang, L.1
Gralla, J.D.2
-
40
-
-
0033764355
-
Transcription initiation-defective forms of sigma(54) that differ in ability to function with a heteroduplex DNA template
-
Kelly M.T., Ferguson III J.A., and Hoover T.R. Transcription initiation-defective forms of sigma(54) that differ in ability to function with a heteroduplex DNA template. J. Bacteriol. 182 (2000) 6503-6508
-
(2000)
J. Bacteriol.
, vol.182
, pp. 6503-6508
-
-
Kelly, M.T.1
Ferguson III, J.A.2
Hoover, T.R.3
-
41
-
-
0026464921
-
A role for the acidic trimer repeat region of transcription factor sigma 54 in setting the rate and temperature dependence of promoter melting in vivo
-
Wong C., and Gralla J.D. A role for the acidic trimer repeat region of transcription factor sigma 54 in setting the rate and temperature dependence of promoter melting in vivo. J. Biol. Chem. 267 (1992) 24762-24768
-
(1992)
J. Biol. Chem.
, vol.267
, pp. 24762-24768
-
-
Wong, C.1
Gralla, J.D.2
-
42
-
-
0034234457
-
The role of region II in the RNA polymerase sigma factor sigma(N) (sigma(54))
-
Southern E., and Merrick M. The role of region II in the RNA polymerase sigma factor sigma(N) (sigma(54)). Nucleic Acids Res. 28 (2000) 2563-2570
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 2563-2570
-
-
Southern, E.1
Merrick, M.2
-
43
-
-
0032735991
-
The interface of sigma with core RNA polymerase is extensive, conserved, and functionally specialized
-
Sharp M.M., Chan C.L., Lu C.Z., Marr M.T., Nechaev S., Merritt E.W., Severinov K., Roberts J.W., and Gross C.A. The interface of sigma with core RNA polymerase is extensive, conserved, and functionally specialized. Genes Dev. 13 (1999) 3015-3026
-
(1999)
Genes Dev.
, vol.13
, pp. 3015-3026
-
-
Sharp, M.M.1
Chan, C.L.2
Lu, C.Z.3
Marr, M.T.4
Nechaev, S.5
Merritt, E.W.6
Severinov, K.7
Roberts, J.W.8
Gross, C.A.9
-
44
-
-
0034635484
-
Low resolution structure of the sigma54 transcription factor revealed by X-ray solution scattering
-
Svergun D.I., Malfois M., Koch M.H., Wigneshweraraj S.R., and Buck M. Low resolution structure of the sigma54 transcription factor revealed by X-ray solution scattering. J. Biol. Chem. 275 (2000) 4210-4214
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 4210-4214
-
-
Svergun, D.I.1
Malfois, M.2
Koch, M.H.3
Wigneshweraraj, S.R.4
Buck, M.5
-
45
-
-
0033619725
-
Targeted protein footprinting: Where different transcription factors bind to RNA polymerase
-
Traviglia S.L., Datwyler S.A., Yan D., Ishihama A., and Meares C.F. Targeted protein footprinting: Where different transcription factors bind to RNA polymerase. Biochemistry 38 (1999) 15774-15778
-
(1999)
Biochemistry
, vol.38
, pp. 15774-15778
-
-
Traviglia, S.L.1
Datwyler, S.A.2
Yan, D.3
Ishihama, A.4
Meares, C.F.5
-
46
-
-
0034660249
-
Conservation of sigma-core RNA polymerase proximity relationships between the enhancer-independent and enhancer-dependent sigma classes
-
Wigneshweraraj S.R., Fujita N., Ishihama A., and Buck M. Conservation of sigma-core RNA polymerase proximity relationships between the enhancer-independent and enhancer-dependent sigma classes. EMBO J. 19 (2000) 3038-3048
-
(2000)
EMBO J.
, vol.19
, pp. 3038-3048
-
-
Wigneshweraraj, S.R.1
Fujita, N.2
Ishihama, A.3
Buck, M.4
-
47
-
-
0033555643
-
Region I modifies DNA-binding domain conformation of sigma 54 within the holoenzyme
-
Casaz P., and Buck M. Region I modifies DNA-binding domain conformation of sigma 54 within the holoenzyme. J. Mol. Biol. 285 (1999) 507-514
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 507-514
-
-
Casaz, P.1
Buck, M.2
-
48
-
-
0034535611
-
Interaction of sigma factor sigmaN with Escherichia coli RNA polymerase core enzyme
-
Scott D.J., Ferguson A.L., Gallegos M.T., Pitt M., Buck M., and Hoggett J.G. Interaction of sigma factor sigmaN with Escherichia coli RNA polymerase core enzyme. Biochem. J. 352 (2000) 539-547
-
(2000)
Biochem. J.
, vol.352
, pp. 539-547
-
-
Scott, D.J.1
Ferguson, A.L.2
Gallegos, M.T.3
Pitt, M.4
Buck, M.5
Hoggett, J.G.6
-
49
-
-
0028789094
-
Converting Escherichia coli RNA polymerase into an enhancer-responsive enzyme: Role of an NH2-terminal leucine patch in sigma 54
-
Wang J.T., Syed A., Hsieh M., and Gralla J.D. Converting Escherichia coli RNA polymerase into an enhancer-responsive enzyme: Role of an NH2-terminal leucine patch in sigma 54. Science 270 (1995) 992-994
-
(1995)
Science
, vol.270
, pp. 992-994
-
-
Wang, J.T.1
Syed, A.2
Hsieh, M.3
Gralla, J.D.4
-
50
-
-
0034615697
-
Sequences in sigma(54) region I required for binding to early melted DNA and their involvement in sigma-DNA isomerisation
-
Gallegos M.T., and Buck M. Sequences in sigma(54) region I required for binding to early melted DNA and their involvement in sigma-DNA isomerisation. J. Mol. Biol. 297 (2000) 849-859
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 849-859
-
-
Gallegos, M.T.1
Buck, M.2
-
51
-
-
0031028731
-
Isolation and properties of enhancer-bypass mutants of sigma 54
-
Syed A., and Gralla J.D. Isolation and properties of enhancer-bypass mutants of sigma 54. Mol. Microbiol. 23 (1997) 987-995
-
(1997)
Mol. Microbiol.
, vol.23
, pp. 987-995
-
-
Syed, A.1
Gralla, J.D.2
-
52
-
-
0033578493
-
Systematic analysis of sigma54 N-terminal sequences identifies regions involved in positive and negative regulation of transcription
-
Casaz P., Gallegos M.T., and Buck M. Systematic analysis of sigma54 N-terminal sequences identifies regions involved in positive and negative regulation of transcription. J. Mol. Biol. 292 (1999) 229-239
-
(1999)
J. Mol. Biol.
, vol.292
, pp. 229-239
-
-
Casaz, P.1
Gallegos, M.T.2
Buck, M.3
-
53
-
-
0033520123
-
Functions of the sigma(54) region I in trans and implications for transcription activation
-
Gallegos M.T., Cannon W.V., and Buck M. Functions of the sigma(54) region I in trans and implications for transcription activation. J. Biol. Chem. 274 (1999) 25285-25290
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 25285-25290
-
-
Gallegos, M.T.1
Cannon, W.V.2
Buck, M.3
-
54
-
-
0033083794
-
Amino-terminal sequences of sigmaN (sigma54) inhibit RNA polymerase isomerization
-
Cannon W., Gallegos M.T., Casaz P., and Buck M. Amino-terminal sequences of sigmaN (sigma54) inhibit RNA polymerase isomerization. Genes Dev. 13 (1999) 357-370
-
(1999)
Genes Dev.
, vol.13
, pp. 357-370
-
-
Cannon, W.1
Gallegos, M.T.2
Casaz, P.3
Buck, M.4
-
56
-
-
0037123659
-
Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution
-
Murakami K.S., Masuda S., and Darst S.A. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science 296 (2002) 1280-1284
-
(2002)
Science
, vol.296
, pp. 1280-1284
-
-
Murakami, K.S.1
Masuda, S.2
Darst, S.A.3
-
57
-
-
0037071844
-
Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution
-
Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., and Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417 (2002) 712-719
-
(2002)
Nature
, vol.417
, pp. 712-719
-
-
Vassylyev, D.G.1
Sekine, S.2
Laptenko, O.3
Lee, J.4
Vassylyeva, M.N.5
Borukhov, S.6
Yokoyama, S.7
-
58
-
-
0033578701
-
Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution
-
Zhang G., Campbell E.A., Minakhin L., Richter C., Severinov K., and Darst S.A. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98 (1999) 811-824
-
(1999)
Cell
, vol.98
, pp. 811-824
-
-
Zhang, G.1
Campbell, E.A.2
Minakhin, L.3
Richter, C.4
Severinov, K.5
Darst, S.A.6
-
59
-
-
27644590206
-
Structures of multisubunit DNA-dependent RNA polymerases
-
Hodgson D.A., and Thomas C.M. (Eds), Cambridge University Press, Cambridge
-
Finn R.D., Orlova E.V., van Heel M., and Buck M. Structures of multisubunit DNA-dependent RNA polymerases. In: Hodgson D.A., and Thomas C.M. (Eds). "SGM Symposium 61: Signals, Switches, Regulons and Cascades: Control of Bacterial Gene Expression" (2002), Cambridge University Press, Cambridge 73-103
-
(2002)
"SGM Symposium 61: Signals, Switches, Regulons and Cascades: Control of Bacterial Gene Expression"
, pp. 73-103
-
-
Finn, R.D.1
Orlova, E.V.2
van Heel, M.3
Buck, M.4
-
60
-
-
0029822092
-
The RpoN-box motif of the RNA polymerase sigma factor sigma N plays a role in promoter recognition
-
Taylor M., Butler R., Chambers S., Casimiro M., Badii F., and Merrick M. The RpoN-box motif of the RNA polymerase sigma factor sigma N plays a role in promoter recognition. Mol. Microbiol. 22 (1996) 1045-1054
-
(1996)
Mol. Microbiol.
, vol.22
, pp. 1045-1054
-
-
Taylor, M.1
Butler, R.2
Chambers, S.3
Casimiro, M.4
Badii, F.5
Merrick, M.6
-
61
-
-
0026592145
-
The helix-turn-helix motif of sigma 54 is involved in recognition of the -13 promoter region
-
Merrick M., and Chambers S. The helix-turn-helix motif of sigma 54 is involved in recognition of the -13 promoter region. J. Bacteriol. 174 (1992) 7221-7226
-
(1992)
J. Bacteriol.
, vol.174
, pp. 7221-7226
-
-
Merrick, M.1
Chambers, S.2
-
62
-
-
0025771543
-
Cassette mutagenesis implicates a helix-turn-helix motif in promoter recognition by the novel RNA polymerase sigma factor sigma 54
-
Coppard J.R., and Merrick M.J. Cassette mutagenesis implicates a helix-turn-helix motif in promoter recognition by the novel RNA polymerase sigma factor sigma 54. Mol. Microbiol. 5 (1991) 1309-1317
-
(1991)
Mol. Microbiol.
, vol.5
, pp. 1309-1317
-
-
Coppard, J.R.1
Merrick, M.J.2
-
63
-
-
0043032654
-
Mapping sigma 54-RNA polymerase interactions at the -24 consensus promoter element
-
Burrows P.C., Severinov K., Ishihama A., Buck M., and Wigneshweraraj S.R. Mapping sigma 54-RNA polymerase interactions at the -24 consensus promoter element. J. Biol. Chem. 278 (2003) 29728-29743
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 29728-29743
-
-
Burrows, P.C.1
Severinov, K.2
Ishihama, A.3
Buck, M.4
Wigneshweraraj, S.R.5
-
64
-
-
0028335281
-
Identification of a DNA-contacting surface in the transcription factor sigma-54
-
Cannon W., Claverie-Martin F., Austin S., and Buck M. Identification of a DNA-contacting surface in the transcription factor sigma-54. Mol. Microbiol. 11 (1994) 227-236
-
(1994)
Mol. Microbiol.
, vol.11
, pp. 227-236
-
-
Cannon, W.1
Claverie-Martin, F.2
Austin, S.3
Buck, M.4
-
65
-
-
0033988987
-
The amino terminus of Salmonella enterica serovar Typhimurium sigma(54) is required for interactions with an enhancer-binding protein and binding to fork junction DNA
-
Kelly M.T., and Hoover T.R. The amino terminus of Salmonella enterica serovar Typhimurium sigma(54) is required for interactions with an enhancer-binding protein and binding to fork junction DNA. J. Bacteriol. 182 (2000) 513-517
-
(2000)
J. Bacteriol.
, vol.182
, pp. 513-517
-
-
Kelly, M.T.1
Hoover, T.R.2
-
66
-
-
0033168678
-
A fork junction DNA-protein switch that controls promoter melting by the bacterial enhancer-dependent sigma factor
-
Guo Y., Wang L., and Gralla J.D. A fork junction DNA-protein switch that controls promoter melting by the bacterial enhancer-dependent sigma factor. EMBO J. 18 (1999) 3736-3745
-
(1999)
EMBO J.
, vol.18
, pp. 3736-3745
-
-
Guo, Y.1
Wang, L.2
Gralla, J.D.3
-
67
-
-
0030984217
-
Multiple pathways to bypass the enhancer requirement of sigma 54 RNA polymerase: Roles for DNA and protein determinants
-
Wang J.T., Syed A., and Gralla J.D. Multiple pathways to bypass the enhancer requirement of sigma 54 RNA polymerase: Roles for DNA and protein determinants. Proc. Natl. Acad. Sci. USA 94 (1997) 9538-9543
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 9538-9543
-
-
Wang, J.T.1
Syed, A.2
Gralla, J.D.3
-
69
-
-
0033570908
-
Compilation and analysis of sigma(54)-dependent promoter sequences
-
Barrios H., Valderrama B., and Morett E. Compilation and analysis of sigma(54)-dependent promoter sequences. Nucleic Acids Res. 27 (1999) 4305-4313
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 4305-4313
-
-
Barrios, H.1
Valderrama, B.2
Morett, E.3
-
70
-
-
0029123818
-
An early A-signal-dependent gene in Myxococcus xanthus has a sigma 54-like promoter
-
Keseler I.M., and Kaiser D. An early A-signal-dependent gene in Myxococcus xanthus has a sigma 54-like promoter. J. Bacteriol. 177 (1995) 4638-4644
-
(1995)
J. Bacteriol.
, vol.177
, pp. 4638-4644
-
-
Keseler, I.M.1
Kaiser, D.2
-
71
-
-
0022580666
-
Deletion analysis of the Klebsiella pneumoniae nitrogenase promoter: importance of spacing between conserved sequences around positions -12 and -24 for activation by the nifA and ntrC (glnG) products
-
Buck M. Deletion analysis of the Klebsiella pneumoniae nitrogenase promoter: importance of spacing between conserved sequences around positions -12 and -24 for activation by the nifA and ntrC (glnG) products. J. Bacteriol. 166 (1986) 545-551
-
(1986)
J. Bacteriol.
, vol.166
, pp. 545-551
-
-
Buck, M.1
-
72
-
-
0024495733
-
Escherichia coli sigma 54 RNA polymerase recognizes Caulobacter crescentus flbG and flaN flagellar gene promoters in vitro
-
Ninfa A.J., Mullin D.A., Ramakrishnan G., and Newton A. Escherichia coli sigma 54 RNA polymerase recognizes Caulobacter crescentus flbG and flaN flagellar gene promoters in vitro. J. Bacteriol. 171 (1989) 383-391
-
(1989)
J. Bacteriol.
, vol.171
, pp. 383-391
-
-
Ninfa, A.J.1
Mullin, D.A.2
Ramakrishnan, G.3
Newton, A.4
-
73
-
-
0028301602
-
DNA distortion and nucleation of local DNA unwinding within sigma-54 (sigma N) holoenzyme closed promoter complexes
-
Morris L., Cannon W., Claverie-Martin F., Austin S., and Buck M. DNA distortion and nucleation of local DNA unwinding within sigma-54 (sigma N) holoenzyme closed promoter complexes. J. Biol. Chem. 269 (1994) 11563-11571
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 11563-11571
-
-
Morris, L.1
Cannon, W.2
Claverie-Martin, F.3
Austin, S.4
Buck, M.5
-
74
-
-
0032785893
-
Regulation of sigma 54-dependent transcription by core promoter sequences: Role of -12 region nucleotides
-
Wang L., Guo Y., and Gralla J.D. Regulation of sigma 54-dependent transcription by core promoter sequences: Role of -12 region nucleotides. J. Bacteriol. 181 (1999) 7558-7565
-
(1999)
J. Bacteriol.
, vol.181
, pp. 7558-7565
-
-
Wang, L.1
Guo, Y.2
Gralla, J.D.3
-
75
-
-
0031740289
-
Multiple in vivo roles for the -12-region elements of sigma 54 promoters
-
Wang L., and Gralla J.D. Multiple in vivo roles for the -12-region elements of sigma 54 promoters. J. Bacteriol. 180 (1998) 5626-5631
-
(1998)
J. Bacteriol.
, vol.180
, pp. 5626-5631
-
-
Wang, L.1
Gralla, J.D.2
-
76
-
-
0037082415
-
Correlating protein footprinting with mutational analysis in the bacterial transcription factor sigma54 (sigmaN)
-
Wigneshweraraj S.R., Casaz P., and Buck M. Correlating protein footprinting with mutational analysis in the bacterial transcription factor sigma54 (sigmaN). Nucleic Acids Res. 30 (2002) 1016-1028
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1016-1028
-
-
Wigneshweraraj, S.R.1
Casaz, P.2
Buck, M.3
-
77
-
-
0035282873
-
In vitro roles of invariant helix-turn-helix motif residue R383 in sigma(54) (sigma(N))
-
Wigneshweraraj S.R., Ishihama A., and Buck M. In vitro roles of invariant helix-turn-helix motif residue R383 in sigma(54) (sigma(N)). Nucleic Acids Res. 29 (2001) 1163-1174
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 1163-1174
-
-
Wigneshweraraj, S.R.1
Ishihama, A.2
Buck, M.3
-
78
-
-
0032854067
-
The sigma 54 DNA-binding domain includes a determinant of enhancer responsiveness
-
Chaney M., and Buck M. The sigma 54 DNA-binding domain includes a determinant of enhancer responsiveness. Mol. Microbiol. 33 (1999) 1200-1209
-
(1999)
Mol. Microbiol.
, vol.33
, pp. 1200-1209
-
-
Chaney, M.1
Buck, M.2
-
79
-
-
0032578471
-
Promoter opening via a DNA fork junction binding activity
-
Guo Y., and Gralla J.D. Promoter opening via a DNA fork junction binding activity. Proc. Natl. Acad. Sci. USA 95 (1998) 11655-11660
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 11655-11660
-
-
Guo, Y.1
Gralla, J.D.2
-
80
-
-
0033938884
-
Isomerization of a binary sigma-promoter DNA complex by transcription activators
-
Cannon W.V., Gallegos M.T., and Buck M. Isomerization of a binary sigma-promoter DNA complex by transcription activators. Nature Struct. Biol. 7 (2000) 594-601
-
(2000)
Nature Struct. Biol.
, vol.7
, pp. 594-601
-
-
Cannon, W.V.1
Gallegos, M.T.2
Buck, M.3
-
81
-
-
0037474295
-
Multiple roles of the RNA polymerase beta subunit flap domain in sigma 54-dependent transcription
-
Wigneshweraraj S.R., Kuznedelov K., Severinov K., and Buck M. Multiple roles of the RNA polymerase beta subunit flap domain in sigma 54-dependent transcription. J. Biol. Chem. 278 (2003) 3455-3465
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 3455-3465
-
-
Wigneshweraraj, S.R.1
Kuznedelov, K.2
Severinov, K.3
Buck, M.4
-
82
-
-
0037490143
-
Nucleotide-dependent triggering of RNA polymerase-DNA interactions by an AAA regulator of transcription
-
Cannon W., Bordes P., Wigneshweraraj S.R., and Buck M. Nucleotide-dependent triggering of RNA polymerase-DNA interactions by an AAA regulator of transcription. J. Biol. Chem. 278 (2003) 19815-19825
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 19815-19825
-
-
Cannon, W.1
Bordes, P.2
Wigneshweraraj, S.R.3
Buck, M.4
-
84
-
-
0035449829
-
Binding of transcriptional activators to sigma 54 in the presence of the transition state analog ADP-aluminum fluoride: Insights into activator mechanochemical action
-
Chaney M., Grande R., Wigneshweraraj S.R., Cannon W., Casaz P., Gallegos M.T., Schumacher J., Jones S., Elderkin S., Dago A.E., Morett E., and Buck M. Binding of transcriptional activators to sigma 54 in the presence of the transition state analog ADP-aluminum fluoride: Insights into activator mechanochemical action. Genes Dev. 15 (2001) 2282-2294
-
(2001)
Genes Dev.
, vol.15
, pp. 2282-2294
-
-
Chaney, M.1
Grande, R.2
Wigneshweraraj, S.R.3
Cannon, W.4
Casaz, P.5
Gallegos, M.T.6
Schumacher, J.7
Jones, S.8
Elderkin, S.9
Dago, A.E.10
Morett, E.11
Buck, M.12
-
85
-
-
0033607619
-
Suppression analysis of positive control mutants of NifA reveals two overlapping promoters for Klebsiella pneumoniae rpoN
-
Grande R.A., Valderrama B., and Morett E. Suppression analysis of positive control mutants of NifA reveals two overlapping promoters for Klebsiella pneumoniae rpoN. J. Mol. Biol. 294 (1999) 291-298
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 291-298
-
-
Grande, R.A.1
Valderrama, B.2
Morett, E.3
-
86
-
-
0037332383
-
Domain architectures of sigma54-dependent transcriptional activators
-
Studholme D.J., and Dixon R. Domain architectures of sigma54-dependent transcriptional activators. J. Bacteriol. 185 (2003) 1757-1767
-
(2003)
J. Bacteriol.
, vol.185
, pp. 1757-1767
-
-
Studholme, D.J.1
Dixon, R.2
-
87
-
-
0033536573
-
Solution structure of the DNA-binding domain of NtrC with three alanine substitutions
-
Pelton J.G., Kustu S., and Wemmer D.E. Solution structure of the DNA-binding domain of NtrC with three alanine substitutions. J. Mol. Biol. 292 (1999) 1095-1110
-
(1999)
J. Mol. Biol.
, vol.292
, pp. 1095-1110
-
-
Pelton, J.G.1
Kustu, S.2
Wemmer, D.E.3
-
88
-
-
0037106322
-
Secondary structure and DNA binding by the C-terminal domain of the transcriptional activator NifA from Klebsiella pneumoniae
-
Ray P., Smith K.J., Parslow R.A., Dixon R., and Hyde E.I. Secondary structure and DNA binding by the C-terminal domain of the transcriptional activator NifA from Klebsiella pneumoniae. Nucleic Acids Res. 30 (2002) 3972-3980
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 3972-3980
-
-
Ray, P.1
Smith, K.J.2
Parslow, R.A.3
Dixon, R.4
Hyde, E.I.5
-
89
-
-
0028122355
-
The major dimerization determinants of the nitrogen regulatory protein NTRC from enteric bacteria lie in its carboxy-terminal domain
-
Klose K.E., North A.K., Stedman K.M., and Kustu S. The major dimerization determinants of the nitrogen regulatory protein NTRC from enteric bacteria lie in its carboxy-terminal domain. J. Mol. Biol. 241 (1994) 233-245
-
(1994)
J. Mol. Biol.
, vol.241
, pp. 233-245
-
-
Klose, K.E.1
North, A.K.2
Stedman, K.M.3
Kustu, S.4
-
90
-
-
0027391968
-
Effects of insertions and deletions in glnG (ntrC) of Escherichia coli on nitrogen regulator I-dependent DNA binding and transcriptional activation
-
Shiau S.P., Chen P., and Reitzer L.J. Effects of insertions and deletions in glnG (ntrC) of Escherichia coli on nitrogen regulator I-dependent DNA binding and transcriptional activation. J. Bacteriol. 175 (1993) 190-199
-
(1993)
J. Bacteriol.
, vol.175
, pp. 190-199
-
-
Shiau, S.P.1
Chen, P.2
Reitzer, L.J.3
-
91
-
-
4344578623
-
Phosphorylation-independent dimer-dimer interactions by the enhancer-binding activator NtrC of Escherichia coli: A third function for the C-terminal domain
-
Yang X.F., Ji Y., Schneider B.L., and Reitzer L. Phosphorylation-independent dimer-dimer interactions by the enhancer-binding activator NtrC of Escherichia coli: A third function for the C-terminal domain. J. Biol. Chem. 279 (2004) 36708-36714
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 36708-36714
-
-
Yang, X.F.1
Ji, Y.2
Schneider, B.L.3
Reitzer, L.4
-
92
-
-
0033555834
-
In vivo and in vitro activities of the Escherichia coli sigma54 transcription activator, PspF, and its DNA-binding mutant, PspFΔHTH
-
Jovanovic G., Rakonjac J., and Model P. In vivo and in vitro activities of the Escherichia coli sigma54 transcription activator, PspF, and its DNA-binding mutant, PspFΔHTH. J. Mol. Biol. 285 (1999) 469-483
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 469-483
-
-
Jovanovic, G.1
Rakonjac, J.2
Model, P.3
-
93
-
-
0030894489
-
Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein
-
Wyman C., Rombel I., North A.K., Bustamante C., and Kustu S. Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein. Science 275 (1997) 1658-1661
-
(1997)
Science
, vol.275
, pp. 1658-1661
-
-
Wyman, C.1
Rombel, I.2
North, A.K.3
Bustamante, C.4
Kustu, S.5
-
94
-
-
3042733355
-
Helicobacter pylori FlgR is an enhancer-independent activator of sigma54-RNA polymerase holoenzyme
-
Brahmachary P., Dashti M.G., Olson J.W., and Hoover T.R. Helicobacter pylori FlgR is an enhancer-independent activator of sigma54-RNA polymerase holoenzyme. J. Bacteriol. 186 (2004) 4535-4542
-
(2004)
J. Bacteriol.
, vol.186
, pp. 4535-4542
-
-
Brahmachary, P.1
Dashti, M.G.2
Olson, J.W.3
Hoover, T.R.4
-
95
-
-
0033821317
-
Phosphorylation-induced signal propagation in the response regulator ntrC
-
Lee J., Owens J.T., Hwang I., Meares C., and Kustu S. Phosphorylation-induced signal propagation in the response regulator ntrC. J. Bacteriol. 182 (2000) 5188-5195
-
(2000)
J. Bacteriol.
, vol.182
, pp. 5188-5195
-
-
Lee, J.1
Owens, J.T.2
Hwang, I.3
Meares, C.4
Kustu, S.5
-
96
-
-
0029002441
-
Active contribution of two domains to cooperative DNA binding of the enhancer-binding protein nitrogen regulator I (NtrC) of Escherichia coli: Stimulation by phosphorylation and the binding of ATP
-
Chen P., and Reitzer L.J. Active contribution of two domains to cooperative DNA binding of the enhancer-binding protein nitrogen regulator I (NtrC) of Escherichia coli: Stimulation by phosphorylation and the binding of ATP. J. Bacteriol. 177 (1995) 2490-2496
-
(1995)
J. Bacteriol.
, vol.177
, pp. 2490-2496
-
-
Chen, P.1
Reitzer, L.J.2
-
97
-
-
0142091549
-
Regulation of the transcriptional activator NtrC1: Structural studies of the regulatory and AAA+ ATPase domains
-
Lee S.Y., De La Torre A., Yan D., Kustu S., Nixon B.T., and Wemmer D.E. Regulation of the transcriptional activator NtrC1: Structural studies of the regulatory and AAA+ ATPase domains. Genes Dev. 17 (2003) 2552-2563
-
(2003)
Genes Dev.
, vol.17
, pp. 2552-2563
-
-
Lee, S.Y.1
De La Torre, A.2
Yan, D.3
Kustu, S.4
Nixon, B.T.5
Wemmer, D.E.6
-
98
-
-
0035695915
-
Structural insights into the regulation of bacterial signalling proteins containing PRDs
-
van Tilbeurgh H., and Declerck N. Structural insights into the regulation of bacterial signalling proteins containing PRDs. Curr. Opin. Struct. Biol. 11 (2001) 685-693
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 685-693
-
-
van Tilbeurgh, H.1
Declerck, N.2
-
99
-
-
0031943540
-
Antagonistic effects of dual PTS-catalysed phosphorylation on the Bacillus subtilis transcriptional activator LevR
-
Martin-Verstraete I., Charrier V., Stulke J., Galinier A., Erni B., Rapoport G., and Deutscher J. Antagonistic effects of dual PTS-catalysed phosphorylation on the Bacillus subtilis transcriptional activator LevR. Mol. Microbiol. 28 (1998) 293-303
-
(1998)
Mol. Microbiol.
, vol.28
, pp. 293-303
-
-
Martin-Verstraete, I.1
Charrier, V.2
Stulke, J.3
Galinier, A.4
Erni, B.5
Rapoport, G.6
Deutscher, J.7
-
100
-
-
0031262875
-
PAS: A multifunctional domain family comes to light
-
Ponting C.P., and Aravind L. PAS: A multifunctional domain family comes to light. Curr. Biol. 7 (1997) R674-R677
-
(1997)
Curr. Biol.
, vol.7
-
-
Ponting, C.P.1
Aravind, L.2
-
101
-
-
0028208257
-
RocR, a novel regulatory protein controlling arginine utilization in Bacillus subtilis, belongs to the NtrC/NifA family of transcriptional activators
-
Calogero S., Gardan R., Glaser P., Schweizer J., Rapoport G., and Debarbouille M. RocR, a novel regulatory protein controlling arginine utilization in Bacillus subtilis, belongs to the NtrC/NifA family of transcriptional activators. J. Bacteriol. 176 (1994) 1234-1241
-
(1994)
J. Bacteriol.
, vol.176
, pp. 1234-1241
-
-
Calogero, S.1
Gardan, R.2
Glaser, P.3
Schweizer, J.4
Rapoport, G.5
Debarbouille, M.6
-
102
-
-
0035853296
-
Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains
-
Anantharaman V., Koonin E.V., and Aravind L. Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. J. Mol. Biol. 307 (2001) 1271-1292
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 1271-1292
-
-
Anantharaman, V.1
Koonin, E.V.2
Aravind, L.3
-
103
-
-
0029073435
-
The amino-terminal domain of the prokaryotic enhancer-binding protein XylR is a specific intramolecular repressor
-
Perez-Martin J., and De Lorenzo V. The amino-terminal domain of the prokaryotic enhancer-binding protein XylR is a specific intramolecular repressor. Proc. Natl. Acad. Sci. USA 92 (1995) 9392-9396
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 9392-9396
-
-
Perez-Martin, J.1
De Lorenzo, V.2
-
104
-
-
0031945812
-
Aromatic ligand binding and intramolecular signalling of the phenol-responsive sigma54-dependent regulator DmpR
-
O'Neill E., Ng L.C., Sze C.C., and Shingler V. Aromatic ligand binding and intramolecular signalling of the phenol-responsive sigma54-dependent regulator DmpR. Mol. Microbiol. 28 (1998) 131-141
-
(1998)
Mol. Microbiol.
, vol.28
, pp. 131-141
-
-
O'Neill, E.1
Ng, L.C.2
Sze, C.C.3
Shingler, V.4
-
105
-
-
4544275675
-
Bacterial transcriptional regulators for degradation pathways of aromatic compounds
-
Tropel D., and Van Der Meer J.R. Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol. Mol. Biol. Rev. 68 (2004) 474-500
-
(2004)
Microbiol. Mol. Biol. Rev.
, vol.68
, pp. 474-500
-
-
Tropel, D.1
Van Der Meer, J.R.2
-
106
-
-
0036009684
-
Deciphering the action of aromatic effectors on the prokaryotic enhancer-binding protein XylR: A structural model of its N-terminal domain
-
Devos D., Garmendia J., de Lorenzo V., and Valencia A. Deciphering the action of aromatic effectors on the prokaryotic enhancer-binding protein XylR: A structural model of its N-terminal domain. Environ. Microbiol. 4 (2002) 29-41
-
(2002)
Environ. Microbiol.
, vol.4
, pp. 29-41
-
-
Devos, D.1
Garmendia, J.2
de Lorenzo, V.3
Valencia, A.4
-
107
-
-
0034981053
-
New insights into the activation of o-xylene biodegradation in Pseudomonas stutzeri OX1 by pathway substrates
-
Arenghi F.L., Barbieri P., Bertoni G., and de Lorenzo V. New insights into the activation of o-xylene biodegradation in Pseudomonas stutzeri OX1 by pathway substrates. EMBO Rep. 2 (2001) 409-414
-
(2001)
EMBO Rep.
, vol.2
, pp. 409-414
-
-
Arenghi, F.L.1
Barbieri, P.2
Bertoni, G.3
de Lorenzo, V.4
-
108
-
-
0029132191
-
Direct regulation of the ATPase activity of the transcriptional activator DmpR by aromatic compounds
-
Shingler V., and Pavel H. Direct regulation of the ATPase activity of the transcriptional activator DmpR by aromatic compounds. Mol. Microbiol. 17 (1995) 505-513
-
(1995)
Mol. Microbiol.
, vol.17
, pp. 505-513
-
-
Shingler, V.1
Pavel, H.2
-
109
-
-
0030712081
-
The GAF domain: An evolutionary link between diverse phototransducing proteins
-
Aravind L., and Ponting C.P. The GAF domain: An evolutionary link between diverse phototransducing proteins. Trends Biochem. Sci. 22 (1997) 458-459
-
(1997)
Trends Biochem. Sci.
, vol.22
, pp. 458-459
-
-
Aravind, L.1
Ponting, C.P.2
-
110
-
-
3042640724
-
Role of the amino-terminal GAF domain of the NifA activator in controlling the response to the antiactivator protein NifL
-
Martinez-Argudo I., Little R., and Dixon R. Role of the amino-terminal GAF domain of the NifA activator in controlling the response to the antiactivator protein NifL. Mol. Microbiol. 52 (2004) 1731-1744
-
(2004)
Mol. Microbiol.
, vol.52
, pp. 1731-1744
-
-
Martinez-Argudo, I.1
Little, R.2
Dixon, R.3
-
111
-
-
0029874910
-
Identification, nucleotide sequence, and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon
-
Jovanovic G., Weiner L., and Model P. Identification, nucleotide sequence, and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon. J. Bacteriol. 178 (1996) 1936-1945
-
(1996)
J. Bacteriol.
, vol.178
, pp. 1936-1945
-
-
Jovanovic, G.1
Weiner, L.2
Model, P.3
-
112
-
-
0242575006
-
Secretion defects that activate the phage shock response of Escherichia coli
-
Jones S.E., Lloyd L.J., Tan K.K., and Buck M. Secretion defects that activate the phage shock response of Escherichia coli. J. Bacteriol. 185 (2003) 6707-6711
-
(2003)
J. Bacteriol.
, vol.185
, pp. 6707-6711
-
-
Jones, S.E.1
Lloyd, L.J.2
Tan, K.K.3
Buck, M.4
-
113
-
-
0035154988
-
The psp locus of Yersinia enterocolitica is required for virulence and for growth in vitro when the Ysc type III secretion system is produced
-
Darwin A.J., and Miller V.L. The psp locus of Yersinia enterocolitica is required for virulence and for growth in vitro when the Ysc type III secretion system is produced. Mol. Microbiol. 39 (2001) 429-444
-
(2001)
Mol. Microbiol.
, vol.39
, pp. 429-444
-
-
Darwin, A.J.1
Miller, V.L.2
-
114
-
-
0036293607
-
Mechanism of action of the Escherichia coli phage shock protein PspA in repression of the AAA family transcription factor PspF
-
Elderkin S., Jones S., Schumacher J., Studholme D., and Buck M. Mechanism of action of the Escherichia coli phage shock protein PspA in repression of the AAA family transcription factor PspF. J. Mol. Biol. 320 (2002) 23-37
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 23-37
-
-
Elderkin, S.1
Jones, S.2
Schumacher, J.3
Studholme, D.4
Buck, M.5
-
115
-
-
0033986477
-
The PspA protein of Escherichia coli is a negative regulator of sigma(54)-dependent transcription
-
Dworkin J., Jovanovic G., and Model P. The PspA protein of Escherichia coli is a negative regulator of sigma(54)-dependent transcription. J. Bacteriol. 182 (2000) 311-319
-
(2000)
J. Bacteriol.
, vol.182
, pp. 311-319
-
-
Dworkin, J.1
Jovanovic, G.2
Model, P.3
-
116
-
-
1542275423
-
Organization of the AAA(+) adaptor protein PspA is an oligomeric ring
-
Hankamer B.D., Elderkin S.L., Buck M., and Nield J. Organization of the AAA(+) adaptor protein PspA is an oligomeric ring. J. Biol. Chem. 279 (2004) 8862-8866
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 8862-8866
-
-
Hankamer, B.D.1
Elderkin, S.L.2
Buck, M.3
Nield, J.4
-
117
-
-
2442690436
-
Purification and characterization of the AAA+ domain of Sinorhizobium meliloti DctD, a sigma54-dependent transcriptional activator
-
Xu H., Gu B., Nixon B.T., and Hoover T.R. Purification and characterization of the AAA+ domain of Sinorhizobium meliloti DctD, a sigma54-dependent transcriptional activator. J. Bacteriol. 186 (2004) 3499-3507
-
(2004)
J. Bacteriol.
, vol.186
, pp. 3499-3507
-
-
Xu, H.1
Gu, B.2
Nixon, B.T.3
Hoover, T.R.4
-
118
-
-
0032969563
-
AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes
-
Neuwald A.F., Aravind L., Spouge J.L., and Koonin E.V. AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res. 9 (1999) 27-43
-
(1999)
Genome Res.
, vol.9
, pp. 27-43
-
-
Neuwald, A.F.1
Aravind, L.2
Spouge, J.L.3
Koonin, E.V.4
-
119
-
-
0034885052
-
AAA+ superfamily ATPases: Common structure-diverse function
-
Ogura T., and Wilkinson A.J. AAA+ superfamily ATPases: Common structure-diverse function. Genes Cells 6 (2001) 575-597
-
(2001)
Genes Cells
, vol.6
, pp. 575-597
-
-
Ogura, T.1
Wilkinson, A.J.2
-
120
-
-
0032557498
-
Association states of the transcription activator protein NtrC from E. coli determined by analytical ultracentrifugation
-
Rippe K., Mucke N., and Schulz A. Association states of the transcription activator protein NtrC from E. coli determined by analytical ultracentrifugation. J. Mol. Biol. 278 (1998) 915-933
-
(1998)
J. Mol. Biol.
, vol.278
, pp. 915-933
-
-
Rippe, K.1
Mucke, N.2
Schulz, A.3
-
121
-
-
20144366027
-
Structure and mechanism of "energy coupling" in bacterial enhancer-binding proteins
-
Rappas M., Schumacher J., Beuron F., Niwa H., Bordes P., Wigneshweraraj S.R., Keetch C., Robinson C., Buck M., and Zhang X. Structure and mechanism of "energy coupling" in bacterial enhancer-binding proteins. Science 307 (2005) 1972-1975
-
(2005)
Science
, vol.307
, pp. 1972-1975
-
-
Rappas, M.1
Schumacher, J.2
Beuron, F.3
Niwa, H.4
Bordes, P.5
Wigneshweraraj, S.R.6
Keetch, C.7
Robinson, C.8
Buck, M.9
Zhang, X.10
-
122
-
-
0027340543
-
The sigma 54 bacterial enhancer-binding protein family: Mechanism of action and phylogenetic relationship of their functional domains
-
Morett E., and Segovia L. The sigma 54 bacterial enhancer-binding protein family: Mechanism of action and phylogenetic relationship of their functional domains. J. Bacteriol. 175 (1993) 6067-6074
-
(1993)
J. Bacteriol.
, vol.175
, pp. 6067-6074
-
-
Morett, E.1
Segovia, L.2
-
123
-
-
0036830121
-
New roles for conserved regions within a sigma 54-dependent enhancer-binding protein
-
Lew C.M., and Gralla J.D. New roles for conserved regions within a sigma 54-dependent enhancer-binding protein. J. Biol. Chem. 277 (2002) 41517-41524
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 41517-41524
-
-
Lew, C.M.1
Gralla, J.D.2
-
124
-
-
0037418230
-
The ATP hydrolyzing transcription activator phage shock protein F of Escherichia coli: Identifying a surface that binds sigma 54
-
Bordes P., Wigneshweraraj S.R., Schumacher J., Zhang X., Chaney M., and Buck M. The ATP hydrolyzing transcription activator phage shock protein F of Escherichia coli: Identifying a surface that binds sigma 54. Proc. Natl. Acad. Sci. USA 100 (2003) 2278-2283
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 2278-2283
-
-
Bordes, P.1
Wigneshweraraj, S.R.2
Schumacher, J.3
Zhang, X.4
Chaney, M.5
Buck, M.6
-
125
-
-
0028839628
-
Protein crosslinking studies suggest that Rhizobium meliloti C4-dicarboxylic acid transport protein D, a sigma 54-dependent transcriptional activator, interacts with sigma 54 and the beta subunit of RNA polymerase
-
Lee J.H., and Hoover T.R. Protein crosslinking studies suggest that Rhizobium meliloti C4-dicarboxylic acid transport protein D, a sigma 54-dependent transcriptional activator, interacts with sigma 54 and the beta subunit of RNA polymerase. Proc. Natl. Acad. Sci. USA 92 (1995) 9702-9706
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 9702-9706
-
-
Lee, J.H.1
Hoover, T.R.2
-
126
-
-
0030609128
-
A conserved region in the sigma54-dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation
-
Wang Y.K., Lee J.H., Brewer J.M., and Hoover T.R. A conserved region in the sigma54-dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation. Mol. Microbiol. 26 (1997) 373-386
-
(1997)
Mol. Microbiol.
, vol.26
, pp. 373-386
-
-
Wang, Y.K.1
Lee, J.H.2
Brewer, J.M.3
Hoover, T.R.4
-
127
-
-
0025740385
-
TyrR protein of Escherichia coli and its role as repressor and activator
-
Pittard A.J., and Davidson B.E. TyrR protein of Escherichia coli and its role as repressor and activator. Mol. Microbiol. 5 (1991) 1585-1592
-
(1991)
Mol. Microbiol.
, vol.5
, pp. 1585-1592
-
-
Pittard, A.J.1
Davidson, B.E.2
-
128
-
-
0041355268
-
RNA polymerase subunit requirements for activation by the enhancer-binding protein Rhodobacter capsulatus NtrC
-
Richard C.L., Tandon A., Sloan N.R., and Kranz R.G. RNA polymerase subunit requirements for activation by the enhancer-binding protein Rhodobacter capsulatus NtrC. J. Biol. Chem. 278 (2003) 31701-31708
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 31701-31708
-
-
Richard, C.L.1
Tandon, A.2
Sloan, N.R.3
Kranz, R.G.4
-
130
-
-
0037123602
-
Structural basis of transcription initiation: An RNA polymerase holoenzyme-DNA complex
-
Murakami K.S., Masuda S., Campbell E.A., Muzzin O., and Darst S.A. Structural basis of transcription initiation: An RNA polymerase holoenzyme-DNA complex. Science 296 (2002) 1285-1290
-
(2002)
Science
, vol.296
, pp. 1285-1290
-
-
Murakami, K.S.1
Masuda, S.2
Campbell, E.A.3
Muzzin, O.4
Darst, S.A.5
-
131
-
-
12144288236
-
A regulator that inhibits transcription by targeting an intersubunit interaction of the RNA polymerase holoenzyme
-
Gregory B.D., Nickels B.E., Garrity S.J., Severinova E., Minakhin L., Urbauer R.J., Urbauer J.L., Heyduk T., Severinov K., and Hochschild A. A regulator that inhibits transcription by targeting an intersubunit interaction of the RNA polymerase holoenzyme. Proc. Natl. Acad. Sci. USA 101 (2004) 4554-4559
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 4554-4559
-
-
Gregory, B.D.1
Nickels, B.E.2
Garrity, S.J.3
Severinova, E.4
Minakhin, L.5
Urbauer, R.J.6
Urbauer, J.L.7
Heyduk, T.8
Severinov, K.9
Hochschild, A.10
-
132
-
-
0038001440
-
Characterization of the interactions between the bacteriophage T4 AsiA protein and RNA polymerase
-
Simeonov M.F., Bieber Urbauer R.J., Gilmore J.M., Adelman K., Brody E.N., Niedziela-Majka A., Minakhin L., Heyduk T., and Urbauer J.L. Characterization of the interactions between the bacteriophage T4 AsiA protein and RNA polymerase. Biochemistry 42 (2003) 7717-7726
-
(2003)
Biochemistry
, vol.42
, pp. 7717-7726
-
-
Simeonov, M.F.1
Bieber Urbauer, R.J.2
Gilmore, J.M.3
Adelman, K.4
Brody, E.N.5
Niedziela-Majka, A.6
Minakhin, L.7
Heyduk, T.8
Urbauer, J.L.9
-
133
-
-
0036469062
-
A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition
-
Kuznedelov K., Minakhin L., Niedziela-Majka A., Dove S.L., Rogulja D., Nickels B.E., Hochschild A., Heyduk T., and Severinov K. A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition. Science 295 (2002) 855-857
-
(2002)
Science
, vol.295
, pp. 855-857
-
-
Kuznedelov, K.1
Minakhin, L.2
Niedziela-Majka, A.3
Dove, S.L.4
Rogulja, D.5
Nickels, B.E.6
Hochschild, A.7
Heyduk, T.8
Severinov, K.9
-
134
-
-
0344413496
-
The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination
-
Toulokhonov I., and Landick R. The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination. Mol. Cell 12 (2003) 1125-1136
-
(2003)
Mol. Cell
, vol.12
, pp. 1125-1136
-
-
Toulokhonov, I.1
Landick, R.2
-
135
-
-
0031456021
-
A mutant RNA polymerase that forms unusual open promoter complexes
-
Severinov K., and Darst S.A. A mutant RNA polymerase that forms unusual open promoter complexes. Proc. Natl. Acad. Sci. USA 94 (1997) 13481-13486
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 13481-13486
-
-
Severinov, K.1
Darst, S.A.2
-
136
-
-
0034682813
-
Dissection of two hallmarks of the open promoter complex by mutation in an RNA polymerase core subunit
-
Nechaev S., Chlenov M., and Severinov K. Dissection of two hallmarks of the open promoter complex by mutation in an RNA polymerase core subunit. J. Biol. Chem. 275 (2000) 25516-25522
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 25516-25522
-
-
Nechaev, S.1
Chlenov, M.2
Severinov, K.3
-
137
-
-
0028270742
-
A non-essential domain of Escherichia coli RNA polymerase required for the action of the termination factor Alc
-
Severinov K., Kashlev M., Severinova E., Bass I., McWilliams K., Kutter E., Nikiforov V., Snyder L., and Goldfarb A. A non-essential domain of Escherichia coli RNA polymerase required for the action of the termination factor Alc. J. Biol. Chem. 269 (1994) 14254-14259
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 14254-14259
-
-
Severinov, K.1
Kashlev, M.2
Severinova, E.3
Bass, I.4
McWilliams, K.5
Kutter, E.6
Nikiforov, V.7
Snyder, L.8
Goldfarb, A.9
-
138
-
-
0037020252
-
The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing
-
Ederth J., Artsimovitch I., Isaksson L.A., and Landick R. The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing. J. Biol. Chem. 277 (2002) 37456-37463
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 37456-37463
-
-
Ederth, J.1
Artsimovitch, I.2
Isaksson, L.A.3
Landick, R.4
-
139
-
-
0033022148
-
Inhibition of Escherichia coli RNA polymerase by bacteriophage T7 gene 2 protein
-
Nechaev S., and Severinov K. Inhibition of Escherichia coli RNA polymerase by bacteriophage T7 gene 2 protein. J. Mol. Biol. 289 (1999) 815-826
-
(1999)
J. Mol. Biol.
, vol.289
, pp. 815-826
-
-
Nechaev, S.1
Severinov, K.2
-
140
-
-
0036300776
-
Beta subunit residues 186-433 and 436-445 are commonly used by Esigma54 and Esigma70 RNA polymerase for open promoter complex formation
-
Wigneshweraraj S.R., Nechaev S., Severinov K., and Buck M. Beta subunit residues 186-433 and 436-445 are commonly used by Esigma54 and Esigma70 RNA polymerase for open promoter complex formation. J. Mol. Biol. 319 (2002) 1067-1083
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 1067-1083
-
-
Wigneshweraraj, S.R.1
Nechaev, S.2
Severinov, K.3
Buck, M.4
-
141
-
-
9144244886
-
Regulated communication between the upstream face of RNA polymerase and the beta' subunit jaw domain
-
Wigneshweraraj S.R., Burrows P.C., Necheav S., Zenkin N., Severinov K., and Buck M. Regulated communication between the upstream face of RNA polymerase and the beta' subunit jaw domain. EMBO J 23 (2004) 4264-4274
-
(2004)
EMBO J
, vol.23
, pp. 4264-4274
-
-
Wigneshweraraj, S.R.1
Burrows, P.C.2
Necheav, S.3
Zenkin, N.4
Severinov, K.5
Buck, M.6
-
142
-
-
33645871158
-
-
Wigneshweraraj, S. R., Burrows, P. C., Zakeyeva, I., Severinov, K., and Buck, M. In press. Contribution of the beta' Jaw domain to sigma54-RNA polymerase dependent transcription.
-
-
-
-
143
-
-
0242693109
-
Bacteriophage-induced modifications of host RNA polymerase
-
Nechaev S., and Severinov K. Bacteriophage-induced modifications of host RNA polymerase. Annu. Rev. Microbiol. 57 (2003) 301-322
-
(2003)
Annu. Rev. Microbiol.
, vol.57
, pp. 301-322
-
-
Nechaev, S.1
Severinov, K.2
-
144
-
-
0029166594
-
The bacterial enhancer-binding protein NTRC is a molecular machine: ATP hydrolysis is coupled to transcriptional activation
-
Wedel A., and Kustu S. The bacterial enhancer-binding protein NTRC is a molecular machine: ATP hydrolysis is coupled to transcriptional activation. Genes Dev. 9 (1995) 2042-2052
-
(1995)
Genes Dev.
, vol.9
, pp. 2042-2052
-
-
Wedel, A.1
Kustu, S.2
-
145
-
-
4344602493
-
Nucleotide-dependent interactions between a fork junction-RNA polymerase complex and an AAA+ transcriptional activator protein
-
Cannon W.V., Schumacher J., and Buck M. Nucleotide-dependent interactions between a fork junction-RNA polymerase complex and an AAA+ transcriptional activator protein. Nucleic Acids Res. 32 (2004) 4596-4608
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 4596-4608
-
-
Cannon, W.V.1
Schumacher, J.2
Buck, M.3
-
147
-
-
0032897503
-
Involvement of the FtsH (HflB) protease in the activity of sigma 54 promoters
-
Carmona M., and de Lorenzo V. Involvement of the FtsH (HflB) protease in the activity of sigma 54 promoters. Mol. Microbiol. 31 (1999) 261-270
-
(1999)
Mol. Microbiol.
, vol.31
, pp. 261-270
-
-
Carmona, M.1
de Lorenzo, V.2
-
148
-
-
33645895752
-
-
Shingler, V., personal communication.
-
-
-
-
149
-
-
0037155137
-
Transcriptional activation of a heat-shock gene, lonD, of Myxococcus xanthus by a two component histidine-aspartate phosphorelay system
-
Ueki T., and Inouye S. Transcriptional activation of a heat-shock gene, lonD, of Myxococcus xanthus by a two component histidine-aspartate phosphorelay system. J. Biol. Chem. 277 (2002) 6170-6177
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 6170-6177
-
-
Ueki, T.1
Inouye, S.2
|