CDK11 in TREX/THOC Regulates HIV mRNA 3' End Processing

Abstract

Transcriptional cyclin-dependent kinases play important roles in eukaryotic gene expression. CDK7, CDK9 (P-TEFb), and CDK13 are also critical for HIV replication. However, the function of CDK11 remained enigmatic. In this report, we determined that CDK11 regulates the cleavage and polyadenylation (CPA) of all viral transcripts. CDK11 was found associated with the TREX/THOC, which recruited this kinase to DNA. Once at the viral genome, CDK11 phosphorylated serines at position 2 in the CTD of RNAPII, which increased levels of CPA factors at the HIV 3' end. In its absence, cleavage of viral transcripts was greatly attenuated. In contrast, higher levels of CDK11 increased the length of HIV poly(A) tails and the stability of mature viral transcripts. We conclude that CDK11 plays a critical role for the cotranscriptional processing of all HIV mRNA species.

Figure 1. CDK11 associates with TREX/THOC in 293 T cells

A. A schematic representation of CDK11 and CycL2. CDK11 contains 782 residues and migrates with an apparent molecular mass of 110 kDa. CycL2 contains 520 residues with an apparent molecular mass of 58 kDa. White ovals depict regions rich in glutamic acids (pE), the kinase domain of CDK11, cyclin boxes and the arginine-serine (RS)-rich domain in CycL2. B. Dendrogram of the CDK11 proteome. Mass spectrometry of proteins that co-immunoprecipitated with CDK11 identified TREX/THOC (blue circles), EJC (brown circles) and various OTHER (yellow circles) proteins. C. Co-immunoprecipitations of f:CDK11-interacting proteins. Immunoprecipitation of FLAG epitope-tagged CDK11 protein (f:CDK11) was followed by western blotting with anti-FLAG, UAP56, THOC1, CycL2, RBM8A, SAP18 and SCAMP2 antibodies. Lanes contain the following: lane 1, input; lane 2, co-immunoprecipitated proteins; lane 3, IgG control. D. Co-immunoprecipitations between endogenous proteins. Immunoprecipitation of the endogenous CDK11 protein (CDK11) was followed by western blotting with anti-UAP56, THOC5, THOC1 and RBM8A antibodies (lanes 3–7). Lanes are as in panel C.

Figure 2. CDK11 increases HIV gene expression and replication in 293 T cells

A. Schematic representation of NL4-3.Luc and LTR.Luc plasmid targets, respectively. NL4-3.Luc does not express Env (crossed lines) and contains the luciferase gene in the place of Nef. B. CDK11 activates NL4-3.luc and LTR.Luc. Luciferase activity was measured in lysates of cells co-expressing f:CDK11 or the empty plasmid vector and LTR.Luc or pNL4-3.Luc. Error bars represent mean ± SE, n = 3. Western blots of f:CDK11 and actin as the loading control are presented below the bar graph. See also Figures S1 and S2. C. CDK11 increases the production of new viral particles. Presented is the HIV p24 ELISA of supernatants from cells that co-expressed f:CDK11 and NL4-3.Luc. Error bars are as in panel B. D. CDK11 increases the production of HIV structural proteins. Presented is a western blot of HIV Gag levels in cells expressing f:CDK11 and NL4-3.Luc or plasmid vector control. Amounts of plasmid effectors are presented above the western blot. Lanes 1 and 4, 2 and 5 and 3 and 6 should be compared. Below this panel are western blots of f:CDK11 and actin, as in panel C.

Figure 3. CDK11 regulates levels of all HIV transcripts in 293T cells

A. Schematic representation of HIV transcripts. The three main viral mRNA species are represented: unspliced (US), singly spliced (SS) and multiply spliced (MS) HIV transcripts. Arrows indicate the direction and location of primers. B. CDK11 increases levels of all HIV transcripts. RT-qPCR of HIV RNA from cells that co-expressed f:CDK11 or plasmid vector and pNL4-3.Luc. Primers were designed to detect unspliced (US) genomic, singly spliced (SS) and multiply spliced (MS) HIV transcripts. Error bars represent mean ± SE, n = 3. C. CDK11 depletion decreases HIV mRNA splicing. CDK11-depleted cells co-expressed the same plasmids as in panel B. Presented are RT-qPCR data with errors as in panel B. Western blots of CDK11 and actin are presented below the bar graph. See also Figure S3.

Figure 4. CK2 does not contribute to CTD phosphorylation by CDK11

Kinase assays were performed with the immunoprecipitated f:CDK11 protein and GST-CTD using cold ATP, followed by western blotting with anti-Ser2P and Ser5P antibodies. Lane 3 contains reactions with the immunoprecipitated f:CDK11 protein from CK2-depleted cells. The western blot for the depletion of CK2 is presented at the bottom.

Figure 5. Knockdown of CDK11 decreases levels of Ser2P and CPA factors at the HIV 3’ end in HeLaP4 cells

A. Schematic representation of the NL4-3.Luc. Horizontal lines beneath the gene represent regions amplified by qPCR after ChIPs. B, C, D, E, F, H. Effects of CDK11 depletion and THOC1 depletion (G) on levels of RNAPII, Ser2P, Ser5P, CDK11, CstF77 and PAP at the HIV gene. ChIPs were performed using indicated antibodies in cells expressing the NL4-3.Luc and treated with siCDK11 or siTHOC1 (black diamonds and lines) and compared to those treated with siScr RNA (gray circles and lines). Sequences corresponding to the HIV 5’ end, Pol, and 3’ end were amplified by qPCR. Values represent percentage of input normalized to IgG levels. See also Figure S4. I. Confirmation of depleted proteins. Presented are western blots of CDK11, THOC1, CstF77 and PAP in cell lysates, where actin represents the loading control.

Figure 6. Knockdown of CDK11 or THOC1 increases HIV 3’end read through transcription in HeLa P4 and J-Lat 9.2 cells

A. Schematic representation of primers used for the HIV 3’ end read through assay. Note that position 1 corresponds to position 9530 from the 5’ HIV LTR. Locations of polyA and cleavage sites are depicted by arrows. Fw and Rv are forward and reverse primers, respectively. B. Knockdown of CDK11 or THOC1 increases read through of HIV transcripts. Black bars represent fold-increased read-through over WT cells. Error bars represent the mean +/− SE, n = 3. Western blots of CDK11 and THOC1 with actin as the loading control are presented below the bar graph. C. Schematic representation of the PP5 gene and the integrated HIV in J-Lat 9.2 cells. Two different capped (black circles) transcripts are diagrammed below the gene, those that terminate in the 5’ HIV LTR and those that read through into the viral coding sequences. PCR primers for RT-qPCR are presented below primary transcripts. D. CDK11 depletion increases read through transcription past the 5’ HIV LTR in J-Lat 9.2 cells. Black bar and error bars are as in panel B. Western blots of CDK11 with actin as the loading control are presented below the bar graph. See also Figure S5.

Figure 7. CDK11 increases length of polyA tails and stability of HIV transcripts in HeLa P4 cells

A. Schematic representation of extreme 3’ RACE using the All Tail kit for polyA tail length, with indicated primer sets. Position 1 was assigned arbitrarily to the beginning of the forward primer (Fw). It is 9571 nucleotides removed from the 5’ end of the unsplised (US) genomic NL4.3.Luc transcript. Note that the ligated primer (in red) measures 20 nucleotides. Steps in the reaction are depicted in red. Rv, reverse primer. B. Length of HIV polyA tails. HIV polyA tails in HeLa P4 cells co-expressing siCDK11, vector or f:CDK11 and pNL4-3.Luc were amplified by RT-qPCR and separated by a 2.5% agarose gel electophoresis. C. CDK11 increases the stability of HIV transcripts. Measured was the stability of HIV genomic transcripts in cells co-expressing f:CDK11 and pNL4-3.Luc. After 24 hours, cells were treated with Actinomycin D and RNA was extracted at different time points. RT-qPCR was performed in duplicate. Error bars represent mean ± SE, n =3.