TY - JOUR
T1 - Regulation through the secondary channel - Structural framework for ppGpp-DksA synergism during transcription
AU - Perederina, Anna
AU - Svetlov, Vladimir
AU - Vassylyeva, Marina N.
AU - Tahirov, Tahir H.
AU - Yokoyama, Shigeyuki
AU - Artsimovitch, Irina
AU - Vassylyev, Dmitry G.
N1 - Funding Information:
We are grateful to Drs. R. Landick and T. Santangelo for critical reading of the manuscript and helpful suggestions for its improvement and Dr. R. Gourse for communicating information prior to publication. We thank Drs. N. Igarashi, N. Matsugaki, and M. Suzuki from the laboratory of Prof. S. Wakatsuki (Photon Factory, Tsukuba, Japan) for the assistance in data collection at the NW12 Synchrotron beam line. This work was supported in part by grant from the National Institutes of Health (to I.A.) and by RIKEN to S.Y. and D.G.V.
PY - 2004/8/6
Y1 - 2004/8/6
N2 - Bacterial transcription is regulated by the alarmone ppGpp, which binds near the catalytic site of RNA polymerase (RNAP) and modulates its activity. We show that the DksA protein is a crucial component of ppGpp-dependent regulation. The 2.0 Å resolution structure of Escherichia coli DksA reveals a globular domain and a coiled coil with two highly conserved Asp residues at its tip that is reminiscent of the transcript cleavage factor GreA. This structural similarity suggests that DksA coiled coil protrudes into the RNAP secondary channel to coordinate a ppGpp bound Mg2+ ion with the Asp residues, thereby stabilizing the ppGpp-RNAP complex. Biochemical analysis demonstrates that DksA affects transcript elongation, albeit differently from GreA; augments ppGpp effects on initiation; and binds directly to RNAP, positioning the Asp residues near the active site. Substitution of these residues eliminates the synergy between DksA and ppGpp. Thus, the secondary channel emerges as a common regulatory entrance for transcription factors.
AB - Bacterial transcription is regulated by the alarmone ppGpp, which binds near the catalytic site of RNA polymerase (RNAP) and modulates its activity. We show that the DksA protein is a crucial component of ppGpp-dependent regulation. The 2.0 Å resolution structure of Escherichia coli DksA reveals a globular domain and a coiled coil with two highly conserved Asp residues at its tip that is reminiscent of the transcript cleavage factor GreA. This structural similarity suggests that DksA coiled coil protrudes into the RNAP secondary channel to coordinate a ppGpp bound Mg2+ ion with the Asp residues, thereby stabilizing the ppGpp-RNAP complex. Biochemical analysis demonstrates that DksA affects transcript elongation, albeit differently from GreA; augments ppGpp effects on initiation; and binds directly to RNAP, positioning the Asp residues near the active site. Substitution of these residues eliminates the synergy between DksA and ppGpp. Thus, the secondary channel emerges as a common regulatory entrance for transcription factors.
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U2 - 10.1016/j.cell.2004.06.030
DO - 10.1016/j.cell.2004.06.030
M3 - Article
C2 - 15294156
AN - SCOPUS:4043108470
SN - 0092-8674
VL - 118
SP - 297
EP - 309
JO - Cell
JF - Cell
IS - 3
ER -