Regulation of CDK9 activity by phosphorylation and dephosphorylation

Abstract

HIV-1 transcription is regulated by CDK9/cyclin T1, which, unlike a typical cell cycle-dependent kinase, is regulated by associating with 7SK small nuclear ribonuclear protein complex (snRNP). While the protein components of this complex are well studied, the mechanism of the complex formation is still not fully understood. The association of CDK9/cyclin T1 with 7SK snRNP is, in part, regulated by a reversible CDK9 phosphorylation. Here, we present a comprehensive review of the kinases and phosphatases involved in CDK9 phosphorylation and discuss their role in regulation of HIV-1 replication and potential for being targeted for drug development. We propose a novel pathway of HIV-1 transcription regulation via CDK9 Ser-90 phosphorylation by CDK2 and CDK9 Ser-175 dephosphorylation by protein phosphatase-1.

Figure 1

Schematic representation of the HIV-1 transcription regulation by CDK9 phosphorylation and dephosphorylation. The figure depicts a network of Tat-interacting host cell factors that affect CDK9 phosphorylation. Arrows indicate phosphorylation (violet), dephosphorylation (orange), and transition of complex P-TEF and transcription complexes (black). CDK2 phosphorylates CDK9 Ser-90. Iron chelators reduce cellular activity of CDK2/cyclin E and inhibit HIV-1 transcription (indicated by red line). CDK7 phosphorylates CDK9 Thr-186. Dephosphorylation of Thr-186 by PPM1A or PP1 facilitates dissociation of CDK9/cyclin T1 from large P-TEFb complex and recruitment of CDK9/cyclin T1 by Tat or BRD4. BRD4 preferentially binds Ser-175-phosphorylated CDK9. Dephosphorylation of Ser-175 by PP1 activates CDK9 kinase activity and activates HIV-1 transcription. Recruitment of CDK9/cyclin T1 by Tat to TAR RNA leads to phosphorylation of NELF which dissociates and also phosphorylation of DSIF and RNAPII CTD Ser-2 residues, which is facilitated by CTD Ser-7 phosphorylation. CDK7 as part of TFIIH phosphorylates CTD Ser-5 and possibly Ser-7 residues. CDK7 also phosphorylates CDK9 Thr-186 and maintains CDK9 Thr-186 phosphorylation during the elongation of transcription.

Figure 2

Structure of CDK9/cyclin T1/Tat complex (model based on PDB 3MIA). Backbone representation of CDK9 residues present in original PDB structure is shown in green color, cyclin T1—in violet, and Tat—in red. Position of Thr-29, Ser-175, Thr-186, and C-terminal Ser/Thr cluster is indicated. Also shown are ATP-binding site and Zn ions that facilitate Tat-cyclin T1 interaction.