-
1
-
-
59249092262
-
TraR, a homolog of a RNAP secondary channel interactor, modulates transcription
-
M.D. Blankschien, K. Potrykus, E. Grace, A. Choudhary, D. Vinella, M. Cashel, and C. Herman TraR, a homolog of a RNAP secondary channel interactor, modulates transcription PLoS Genet. 5 2009 e1000345
-
(2009)
PLoS Genet.
, vol.5
, pp. 1000345
-
-
Blankschien, M.D.1
Potrykus, K.2
Grace, E.3
Choudhary, A.4
Vinella, D.5
Cashel, M.6
Herman, C.7
-
2
-
-
52949100970
-
Crystal structure of Escherichia coli Rnk, a new RNA polymerase- interacting protein
-
V. Lamour, S.T. Rutherford, K. Kuznedelov, U.A. Ramagopal, R.L. Gourse, K. Severinov, and S.A. Darst Crystal structure of Escherichia coli Rnk, a new RNA polymerase-interacting protein J. Mol. Biol. 383 2008 367 379
-
(2008)
J. Mol. Biol.
, vol.383
, pp. 367-379
-
-
Lamour, V.1
Rutherford, S.T.2
Kuznedelov, K.3
Ramagopal, U.A.4
Gourse, R.L.5
Severinov, K.6
Darst, S.A.7
-
3
-
-
0346243938
-
Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase
-
O. Laptenko, J. Lee, I. Lomakin, and S. Borukhov Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase EMBO J. 22 2003 6322 6334
-
(2003)
EMBO J.
, vol.22
, pp. 6322-6334
-
-
Laptenko, O.1
Lee, J.2
Lomakin, I.3
Borukhov, S.4
-
4
-
-
4043108470
-
Regulation through the secondary channel - Structural framework for ppGpp-DksA synergism during transcription
-
A. Perederina, V. Svetlov, M.N. Vassylyeva, T.H. Tahirov, S. Yokoyama, I. Artsimovitch, and D.G. Vassylyev Regulation through the secondary channel - structural framework for ppGpp-DksA synergism during transcription Cell 118 2004 297 309
-
(2004)
Cell
, vol.118
, pp. 297-309
-
-
Perederina, A.1
Svetlov, V.2
Vassylyeva, M.N.3
Tahirov, T.H.4
Yokoyama, S.5
Artsimovitch, I.6
Vassylyev, D.G.7
-
5
-
-
35748963229
-
The carboxy-terminal coiled-coil of the RNA polymerase β′-subunit is the main binding site for Gre factors
-
M.N. Vassylyeva, V. Svetlov, A.D. Dearborn, S. Klyuyev, I. Artsimovitch, and D.G. Vassylyev The carboxy-terminal coiled-coil of the RNA polymerase β′-subunit is the main binding site for Gre factors EMBO Rep. 8 2007 1038 1043
-
(2007)
EMBO Rep.
, vol.8
, pp. 1038-1043
-
-
Vassylyeva, M.N.1
Svetlov, V.2
Dearborn, A.D.3
Klyuyev, S.4
Artsimovitch, I.5
Vassylyev, D.G.6
-
6
-
-
45449099933
-
Advances in bacterial promoter recognition and its control by factors that do not bind DNA
-
S.P. Haugen, W. Ross, and R.L. Gourse Advances in bacterial promoter recognition and its control by factors that do not bind DNA Nat. Rev.; Microbiol. 6 2008 507 519
-
(2008)
Nat. Rev.; Microbiol.
, vol.6
, pp. 507-519
-
-
Haugen, S.P.1
Ross, W.2
Gourse, R.L.3
-
7
-
-
79961184265
-
Controlled interplay between trigger loop and Gre factor in the RNA polymerase active centre
-
M. Roghanian, Y. Yuzenkova, and N. Zenkin Controlled interplay between trigger loop and Gre factor in the RNA polymerase active centre Nucleic Acids Res. 39 2011 4352 4359
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 4352-4359
-
-
Roghanian, M.1
Yuzenkova, Y.2
Zenkin, N.3
-
8
-
-
84860380221
-
Transcription initiation factor DksA has diverse effects on RNA chain elongation
-
R. Furman, A. Sevostyanova, and I. Artsimovitch Transcription initiation factor DksA has diverse effects on RNA chain elongation Nucleic Acids Res. 40 2012 3392 3402
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 3392-3402
-
-
Furman, R.1
Sevostyanova, A.2
Artsimovitch, I.3
-
9
-
-
33846604629
-
Effects of DksA, GreA, and GreB on transcription initiation: Insights into the mechanisms of factors that bind in the secondary channel of RNA polymerase
-
S.T. Rutherford, J.J. Lemke, C.E. Vrentas, T. Gaal, W. Ross, and R.L. Gourse Effects of DksA, GreA, and GreB on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of RNA polymerase J. Mol. Biol. 366 2007 1243 1257
-
(2007)
J. Mol. Biol.
, vol.366
, pp. 1243-1257
-
-
Rutherford, S.T.1
Lemke, J.J.2
Vrentas, C.E.3
Gaal, T.4
Ross, W.5
Gourse, R.L.6
-
10
-
-
80052008241
-
Linking RNA polymerase backtracking to genome instability in E. coli
-
D. Dutta, K. Shatalin, V. Epshtein, M.E. Gottesman, and E. Nudler Linking RNA polymerase backtracking to genome instability in E. coli Cell 146 2011 533 543
-
(2011)
Cell
, vol.146
, pp. 533-543
-
-
Dutta, D.1
Shatalin, K.2
Epshtein, V.3
Gottesman, M.E.4
Nudler, E.5
-
11
-
-
77952527102
-
The transcription factor DksA prevents conflicts between DNA replication and transcription machinery
-
A.K. Tehranchi, M.D. Blankschien, Y. Zhang, J.A. Halliday, A. Srivatsan, and J. Peng The transcription factor DksA prevents conflicts between DNA replication and transcription machinery Cell 141 2010 595 605
-
(2010)
Cell
, vol.141
, pp. 595-605
-
-
Tehranchi, A.K.1
Blankschien, M.D.2
Zhang, Y.3
Halliday, J.A.4
Srivatsan, A.5
Peng, J.6
-
12
-
-
22544464455
-
RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription
-
B.W. Trautinger, R.P. Jaktaji, E. Rusakova, and R.G. Lloyd RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription Mol. Cell 19 2005 247 258
-
(2005)
Mol. Cell
, vol.19
, pp. 247-258
-
-
Trautinger, B.W.1
Jaktaji, R.P.2
Rusakova, E.3
Lloyd, R.G.4
-
13
-
-
67649552968
-
Super DksAs: Substitutions in DksA enhancing its effects on transcription initiation
-
M.D. Blankschien, J.H. Lee, E.D. Grace, C.W. Lennon, J.A. Halliday, and W. Ross Super DksAs: substitutions in DksA enhancing its effects on transcription initiation EMBO J. 28 2009 1720 1731
-
(2009)
EMBO J.
, vol.28
, pp. 1720-1731
-
-
Blankschien, M.D.1
Lee, J.H.2
Grace, E.D.3
Lennon, C.W.4
Halliday, J.A.5
Ross, W.6
-
14
-
-
77449093660
-
Role of the RNA polymerase trigger loop in catalysis and pausing
-
J. Zhang, M. Palangat, and R. Landick Role of the RNA polymerase trigger loop in catalysis and pausing Nat. Struct. Mol. Biol. 17 2009 99 104
-
(2009)
Nat. Struct. Mol. Biol.
, vol.17
, pp. 99-104
-
-
Zhang, J.1
Palangat, M.2
Landick, R.3
-
15
-
-
0033551770
-
Mapping interactions of Escherichia coli GreB with RNA polymerase and ternary elongation complexes
-
N. Loizos, and S.A. Darst Mapping interactions of Escherichia coli GreB with RNA polymerase and ternary elongation complexes J. Biol. Chem. 274 1999 23378 23386
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 23378-23386
-
-
Loizos, N.1
Darst, S.A.2
-
16
-
-
0043244877
-
Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase
-
N. Opalka, M. Chlenov, P. Chacon, W.J. Rice, W. Wriggers, and S.A. Darst Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase Cell 114 2003 335 345
-
(2003)
Cell
, vol.114
, pp. 335-345
-
-
Opalka, N.1
Chlenov, M.2
Chacon, P.3
Rice, W.J.4
Wriggers, W.5
Darst, S.A.6
-
17
-
-
78650310283
-
Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein
-
S. Tagami, S. Sekine, T. Kumarevel, N. Hino, Y. Murayama, and S. Kamegamori Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein Nature 468 2010 978 982
-
(2010)
Nature
, vol.468
, pp. 978-982
-
-
Tagami, S.1
Sekine, S.2
Kumarevel, T.3
Hino, N.4
Murayama, Y.5
Kamegamori, S.6
-
18
-
-
84862776860
-
Role of the coiled-coil tip of Escherichia coli DksA in promoter control
-
J.H. Lee, C.W. Lennon, W. Ross, and R.L. Gourse Role of the coiled-coil tip of Escherichia coli DksA in promoter control J. Mol. Biol. 416 2012 503 517
-
(2012)
J. Mol. Biol.
, vol.416
, pp. 503-517
-
-
Lee, J.H.1
Lennon, C.W.2
Ross, W.3
Gourse, R.L.4
-
19
-
-
77957921869
-
Complete structural model of Escherichia coli RNA polymerase from a hybrid approach
-
N. Opalka, J. Brown, W.J. Lane, K.A. Twist, R. Landick, F.J. Asturias, and S.A. Darst Complete structural model of Escherichia coli RNA polymerase from a hybrid approach PLoS Biol. 8 2010 e1000483
-
(2010)
PLoS Biol.
, vol.8
, pp. 1000483
-
-
Opalka, N.1
Brown, J.2
Lane, W.J.3
Twist, K.A.4
Landick, R.5
Asturias, F.J.6
Darst, S.A.7
-
20
-
-
69949098465
-
Escherichia coli DksA binds to Free RNA polymerase with higher affinity than to RNA polymerase in an open complex
-
C.W. Lennon, T. Gaal, W. Ross, and R.L. Gourse Escherichia coli DksA binds to Free RNA polymerase with higher affinity than to RNA polymerase in an open complex J. Bacteriol. 191 2009 5854 5858
-
(2009)
J. Bacteriol.
, vol.191
, pp. 5854-5858
-
-
Lennon, C.W.1
Gaal, T.2
Ross, W.3
Gourse, R.L.4
-
21
-
-
84870522491
-
Direct interactions between the coiled-coil tip of DksA and the trigger loop of RNA polymerase mediate transcriptional regulation
-
In press
-
Lennon, C. W.; Ross, W.; Martin-Tumas, S.; Toulokhonov, I.; Vrentas, C. E.; Rutherford, S. T.; et al. (2012). Direct interactions between the coiled-coil tip of DksA and the trigger loop of RNA polymerase mediate transcriptional regulation. Genes Dev.; In press.
-
(2012)
Genes Dev.
-
-
Lennon C., .W.1
Ross, W.2
Martin-Tumas, S.3
Toulokhonov, I.4
Vrentas C., .E.5
Rutherford S., .T.6
-
22
-
-
79956308538
-
Evolution of two modes of intrinsic RNA polymerase transcript cleavage
-
W. Ruan, E. Lehmann, M. Thomm, D. Kostrewa, and P. Cramer Evolution of two modes of intrinsic RNA polymerase transcript cleavage J. Biol. Chem. 286 2011 18701 18707
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 18701-18707
-
-
Ruan, W.1
Lehmann, E.2
Thomm, M.3
Kostrewa, D.4
Cramer, P.5
-
23
-
-
84866290790
-
Structural and mechanistic basis for the inhibition of Escherichia coli RNA polymerase by T7 Gp2
-
E. James, M. Liu, C. Sheppard, V. Mekler, B. Camara, and B. Liu Structural and mechanistic basis for the inhibition of Escherichia coli RNA polymerase by T7 Gp2 Mol. Cell 47 2012 755 766
-
(2012)
Mol. Cell
, vol.47
, pp. 755-766
-
-
James, E.1
Liu, M.2
Sheppard, C.3
Mekler, V.4
Camara, B.5
Liu, B.6
-
24
-
-
0038823636
-
Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions
-
I. Artsimovitch, V. Svetlov, K.S. Murakami, and R. Landick Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions J. Biol. Chem. 278 2003 12344 12355
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 12344-12355
-
-
Artsimovitch, I.1
Svetlov, V.2
Murakami, K.S.3
Landick, R.4
-
25
-
-
0037020252
-
The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing
-
J. Ederth, I. Artsimovitch, L.A. Isaksson, and R. Landick 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
-
26
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
R.L. Tatusov, N.D. Fedorova, J.D. Jackson, A.R. Jacobs, B. Kiryutin, and E.V. Koonin The COG database: an updated version includes eukaryotes BMC Bioinformatics 4 2003 41
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Kiryutin, B.5
Koonin, E.V.6
-
27
-
-
78751693014
-
Role of a Zn-independent DksA in Zn homeostasis and stringent response
-
C.E. Blaby-Haas, R. Furman, D.A. Rodionov, I. Artsimovitch, and V. de Crecy-Lagard Role of a Zn-independent DksA in Zn homeostasis and stringent response Mol. Microbiol. 79 2011 700 715
-
(2011)
Mol. Microbiol.
, vol.79
, pp. 700-715
-
-
Blaby-Haas, C.E.1
Furman, R.2
Rodionov, D.A.3
Artsimovitch, I.4
De Crecy-Lagard, V.5
-
28
-
-
67649327176
-
FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix
-
M.N. Price, P.S. Dehal, and A.P. Arkin FastTree: computing large minimum evolution trees with profiles instead of a distance matrix Mol. Biol. Evol. 26 2009 1641 1650
-
(2009)
Mol. Biol. Evol.
, vol.26
, pp. 1641-1650
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
29
-
-
84855898808
-
Effects on growth by changes of the balance between GreA, GreB, and DksA suggest mutual competition and functional redundancy in Escherichia coli
-
D. Vinella, K. Potrykus, H. Murphy, and M. Cashel Effects on growth by changes of the balance between GreA, GreB, and DksA suggest mutual competition and functional redundancy in Escherichia coli J. Bacteriol. 194 2012 261 273
-
(2012)
J. Bacteriol.
, vol.194
, pp. 261-273
-
-
Vinella, D.1
Potrykus, K.2
Murphy, H.3
Cashel, M.4
-
30
-
-
79957486892
-
The dksA promoter is negatively feedback regulated by DksA and ppGpp
-
P. Chandrangsu, J.J. Lemke, and R.L. Gourse The dksA promoter is negatively feedback regulated by DksA and ppGpp Mol. Microbiol. 80 2011 1337 1348
-
(2011)
Mol. Microbiol.
, vol.80
, pp. 1337-1348
-
-
Chandrangsu, P.1
Lemke, J.J.2
Gourse, R.L.3
-
31
-
-
39849100395
-
Regulation of the fimB promoter: A case of differential regulation by ppGpp and DksA in vivo
-
A. Aberg, V. Shingler, and C. Balsalobre Regulation of the fimB promoter: a case of differential regulation by ppGpp and DksA in vivo Mol. Microbiol. 67 2008 1223 1241
-
(2008)
Mol. Microbiol.
, vol.67
, pp. 1223-1241
-
-
Aberg, A.1
Shingler, V.2
Balsalobre, C.3
-
32
-
-
34547204502
-
A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing
-
I. Toulokhonov, J. Zhang, M. Palangat, and R. Landick A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing Mol. Cell 27 2007 406 419
-
(2007)
Mol. Cell
, vol.27
, pp. 406-419
-
-
Toulokhonov, I.1
Zhang, J.2
Palangat, M.3
Landick, R.4
-
33
-
-
78650546051
-
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media
-
T.M. Conrad, M. Frazier, A.R. Joyce, B.K. Cho, E.M. Knight, and N.E. Lewis RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media Proc. Natl Acad. Sci. USA 107 2010 20500 20505
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 20500-20505
-
-
Conrad, T.M.1
Frazier, M.2
Joyce, A.R.3
Cho, B.K.4
Knight, E.M.5
Lewis, N.E.6
-
34
-
-
58849139777
-
Allosteric control of Escherichia coli rRNA promoter complexes by DksA
-
S.T. Rutherford, C.L. Villers, J.H. Lee, W. Ross, and R.L. Gourse Allosteric control of Escherichia coli rRNA promoter complexes by DksA Genes Dev. 23 2009 236 248
-
(2009)
Genes Dev.
, vol.23
, pp. 236-248
-
-
Rutherford, S.T.1
Villers, C.L.2
Lee, J.H.3
Ross, W.4
Gourse, R.L.5
-
35
-
-
81155132249
-
Tagetitoxin inhibits RNA polymerase through trapping of the trigger loop
-
I. Artsimovitch, V. Svetlov, S.M. Nemetski, V. Epshtein, T. Cardozo, and E. Nudler Tagetitoxin inhibits RNA polymerase through trapping of the trigger loop J. Biol. Chem. 286 2011 40395 40400
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 40395-40400
-
-
Artsimovitch, I.1
Svetlov, V.2
Nemetski, S.M.3
Epshtein, V.4
Cardozo, T.5
Nudler, E.6
-
36
-
-
34447513771
-
Structural basis for substrate loading in bacterial RNA polymerase
-
D.G. Vassylyev, M.N. Vassylyeva, J. Zhang, M. Palangat, I. Artsimovitch, and R. Landick Structural basis for substrate loading in bacterial RNA polymerase Nature 448 2007 163 168
-
(2007)
Nature
, vol.448
, pp. 163-168
-
-
Vassylyev, D.G.1
Vassylyeva, M.N.2
Zhang, J.3
Palangat, M.4
Artsimovitch, I.5
Landick, R.6
-
37
-
-
28544453415
-
Structural basis for transcription inhibition by tagetitoxin
-
D.G. Vassylyev, V. Svetlov, M.N. Vassylyeva, A. Perederina, N. Igarashi, and N. Matsugaki Structural basis for transcription inhibition by tagetitoxin Nat. Struct. Mol. Biol. 12 2005 1086 1093
-
(2005)
Nat. Struct. Mol. Biol.
, vol.12
, pp. 1086-1093
-
-
Vassylyev, D.G.1
Svetlov, V.2
Vassylyeva, M.N.3
Perederina, A.4
Igarashi, N.5
Matsugaki, N.6
-
38
-
-
0348166026
-
Biochemical assays of Gre factors of Thermus thermophilus
-
O. Laptenko, and S. Borukhov Biochemical assays of Gre factors of Thermus thermophilus Methods Enzymol. 371 2003 219 232
-
(2003)
Methods Enzymol.
, vol.371
, pp. 219-232
-
-
Laptenko, O.1
Borukhov, S.2
-
39
-
-
0033765116
-
RNA polymerases from Bacillus subtilis and Escherichia coli differ in recognition of regulatory signals in vitro
-
I. Artsimovitch, V. Svetlov, L. Anthony, R.R. Burgess, and R. Landick RNA polymerases from Bacillus subtilis and Escherichia coli differ in recognition of regulatory signals in vitro J. Bacteriol. 182 2000 6027 6035
-
(2000)
J. Bacteriol.
, vol.182
, pp. 6027-6035
-
-
Artsimovitch, I.1
Svetlov, V.2
Anthony, L.3
Burgess, R.R.4
Landick, R.5
-
40
-
-
0034691146
-
Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals
-
I. Artsimovitch, and R. Landick Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals Proc. Natl Acad. Sci. USA 97 2000 7090 7095
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 7090-7095
-
-
Artsimovitch, I.1
Landick, R.2
-
41
-
-
34147155174
-
Structural basis for converting a general transcription factor into an operon-specific virulence regulator
-
G.A. Belogurov, M.N. Vassylyeva, V. Svetlov, S. Klyuyev, N.V. Grishin, D.G. Vassylyev, and I. Artsimovitch Structural basis for converting a general transcription factor into an operon-specific virulence regulator Mol. Cell 26 2007 117 129
-
(2007)
Mol. Cell
, vol.26
, pp. 117-129
-
-
Belogurov, G.A.1
Vassylyeva, M.N.2
Svetlov, V.3
Klyuyev, S.4
Grishin, N.V.5
Vassylyev, D.G.6
Artsimovitch, I.7
-
42
-
-
34848915239
-
Allosteric control of the RNA polymerase by the elongation factor RfaH
-
V. Svetlov, G.A. Belogurov, E. Shabrova, D.G. Vassylyev, and I. Artsimovitch Allosteric control of the RNA polymerase by the elongation factor RfaH Nucleic Acids Res. 35 2007 5694 5705
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 5694-5705
-
-
Svetlov, V.1
Belogurov, G.A.2
Shabrova, E.3
Vassylyev, D.G.4
Artsimovitch, I.5
|