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Originally published In Press as doi:10.1074/jbc.M010975200 on January 16, 2001

J. Biol. Chem., Vol. 276, Issue 14, 10913-10920, April 6, 2001
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Three RNA Polymerase II Carboxyl-terminal Domain Kinases Display Distinct Substrate Preferences*

Y. RamanathanDagger §, Sanjay M. RajparaDagger §, Syed M. RezaDagger , Emma Lees||, Stewart Shuman**, Michael B. MathewsDagger , and Tsafi Pe'eryDagger Dagger Dagger

From the Dagger  Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, the || Department of Cell Signaling, DNAX Research Institute, Palo Alto, California 94304-1104, and the ** Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021

CDK7, CDK8, and CDK9 are cyclin-dependent kinases (CDKs) that phosphorylate the C-terminal domain (CTD) of RNA polymerase II. They have distinct functions in transcription. Because the three CDKs target only serine 5 in the heptad repeat of model CTD substrates containing various numbers of repeats, we tested the hypothesis that the kinases differ in their ability to phosphorylate CTD heptad arrays. Our data show that the kinases display different preferences for phosphorylating individual heptads in a synthetic CTD substrate containing three heptamer repeats and specific regions of the CTD in glutathione S-transferase fusion proteins. They also exhibit differences in their ability to phosphorylate a synthetic CTD peptide that contains Ser-2-PO4. This phosphorylated peptide is a poor substrate for CDK9 complexes. CDK8 and CDK9 complexes, bound to viral activators E1A and Tat, respectively, target only serine 5 for phosphorylation in the CTD peptides, and binding to the viral activators does not change the substrate preference of these kinases. These results imply that the display of different CTD heptads during transcription, as well as their phosphorylation state, can affect their phosphorylation by the different transcription-associated CDKs.

* This work was supported by National Institutes of Health Grant AI31802.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

§ Both authors contributed equally to this work.

Present address: Center for Applied Genomics, New Jersey Medical School-UMDNJ, MSB A-901, 185 S. Orange Ave., Newark, NJ 07103.

Dagger Dagger To whom correspondence should be addressed: Dept. of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103. Tel.: 973-972-8763; Fax: 973-972-5594; E-mail: peeryts@umdnj.edu.

Copyright © 2001 by The American Society for Biochemistry and Molecular Biology, Inc.


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