Cell Cycle-Dependent Transcription: The Cyclin Dependent Kinase Cdk1 Is a Direct Regulator of Basal Transcription Machineries

Abstract

The cyclin-dependent kinase Cdk1 is best known for its function as master regulator of the cell cycle. It phosphorylates several key proteins to control progression through the different phases of the cell cycle. However, studies conducted several decades ago with mammalian cells revealed that Cdk1 also directly regulates the basal transcription machinery, most notably RNA polymerase II. More recent studies in the budding yeast Saccharomyces cerevisiae have revisited this function of Cdk1 and also revealed that Cdk1 directly controls RNA polymerase III activity. These studies have also provided novel insight into the physiological relevance of this process. For instance, cell cycle-stage-dependent activity of these complexes may be important for meeting the increased demand for various proteins involved in housekeeping, metabolism, and protein synthesis. Recent work also indicates that direct regulation of the RNA polymerase II machinery promotes cell cycle entry. Here, we provide an overview of the regulation of basal transcription by Cdk1, and we hypothesize that the original function of the primordial cell-cycle CDK was to regulate RNAPII and that it later evolved into specialized kinases that govern various aspects of the transcription machinery and the cell cycle.

Keywords: Cdk1; RNA polymerase; cell cycle; cyclin-dependent kinase; transcription.

Figure 1

The cell cycle and the transcription cycle in S. cerevisiae. (A) The four phases of the cell cycle (left), which are regulated by Cdk1 in complex with nine different cyclins that fluctuate throughout the cell cycle (right). (B) The four main phases of the transcription cycle. Created with Biorender.com.

Figure 2

CTD phosphorylation. (A) Kinases that phosphorylate the CTD in vertebrates (top) and in S. cerevisiae (bottom). Additional CTD kinases have been described but are not depicted here for simplicity. For clarity, only a single heptad repeat is shown. (B) Relative levels of the different CTD residues along the body of genes in S. cerevisiae. Created with BioRender.com.

Figure 3

Stages of transcription by RNAPII. (A) During the preinitiation stage, upstream activation sequences (UAS) recruit specific transcription factors (‘sTF’), which bind the Mediator complex. Mediator recruits hypophosphorylated RNAPII to form the PIC. (B,C) Kin28 phosphorylates Ser5 and Ser7 when RNAPII initiates transcription, resulting in recruitment of the capping machinery and capping of the nascent mRNA. (D) During the elongation stage, Bur1 and Ctk1 phosphorylate Ser2, leading to binding of elongation factors. (E) When the polymerase reaches the polyadenylation signal in the gene, polyadenylation and cleavage factors that recognize phosphorylated Ser2 then cleave and polyadenylate the mRNA, followed by dissociation of the RNAPII complex. For clarity, only a single heptad repeat is shown in this figure. Created with Biorender.com.

Figure 4

Regulation of RNAPII by cell/cycle CDKs in mammalian cells. (A) In M phase, Cdk1 inhibits transcription by phosphorylating RNAPII on Ser5, thereby preventing its incorporation into the PIC. Cdk1 also phosphorylates and thereby inhibits the Cdk7 subunit of TFIIH as well as multiple components of TFIID. (B) In contrast, during G1/S phase the cell-cycle CDK Cdk2 activates transcription in HIV/infected cells. Here, the Tat protein recruits Cdk7, which enhances Ser5 phosphorylation, but Tat also recruits Cdk2, which subsequently phosphorylates Ser2 to promote transcriptional elongation. For clarity, only a single heptad repeat is shown in this figure. Created with Biorender.com.

Figure 5

Cdk1 directly controls RNAPII by phosphorylating CTD-Ser5 in budding yeast. (A) Regulation of RNAPII by Cdk1 at housekeeping genes. Cdk1 localizes to highly expressed genes, such as PMA1, where it phosphorylates Ser5 to promote transcription and recruitment of the capping machinery [103]. Cdk1 synergizes with Kin28 in this process [103], and we have previously hypothesized that priming of RNAPII by Kin28 results in recruitment of Cdk1, potentially through binding of its cyclin partner to phosphorylated Ser5, which then phosphorylates additional Ser5 residues in the CTD [109]. (B) Regulation of RNAPII by Cdk1 at cell cycle genes. During late G1, Cln3-Cdk1 is recruited to SBF target genes where it directly promotes transcription by phosphorylating CTD-Ser5 to promote cell cycle entry. Created with Biorender.com.

Figure 6

Regulation of RNAPI. (A) Overview of rDNA gene transcription by RNAPI (budding yeast nomenclature). (B) In mammalian cells, during M phase Cyclin B-Cdk1 phosphorylates TAF1C, TBP, and upstream binding factor, which prevents binding of Selective factor to the promoter. Dephosphorylation by the phosphatase Cdc14 allows for reactivation of transcription (not depicted here). Created with Biorender.com.

Figure 7

Regulation of RNAPIII. (A) tRNA genes have an internal promoter that consists of an A box and a B box, which is bound by TFIIIC. TFIIIC interacts with TFIIIB, leading to recruitment of RNAPIII and transcription. (B) Cdk1 is recruited to tRNA genes by the cyclin Clb5, although it is unknown which protein is recognized by Clb5. Cdk1 then phosphorylates Bdp1, which promotes its interaction with TFIIIC, resulting in increased tRNA synthesis.