Uncoupling the TFIIH Core and Kinase Modules Leads To Misregulated RNA Polymerase II CTD Serine 5 Phosphorylation

Abstract

TFIIH is an essential transcription initiation factor for RNA polymerase II (RNApII). This multi-subunit complex comprises two modules that are physically linked by the subunit Tfb3 (MAT1 in metazoans). The TFIIH Core Module, with two DNA-dependent ATPases and several additional subunits, promotes DNA unwinding. The TFIIH Kinase Module phosphorylates Serine 5 of the C-terminal domain (CTD) of RNApII subunit Rpb1, a modification that coordinates exchange of initiation and early elongation factors. While it is not obvious why these two disparate activities are bundled into one factor, the connection may provide temporal coordination during early initiation. Here we show that Tfb3 can be split into two parts to uncouple the TFIIH modules. The resulting cells grow slower than normal, but are viable. Chromatin immunoprecipitation of the split TFIIH shows that the Core Module, but not the Kinase, is properly recruited to promoters. Instead of the normal promoter-proximal peak, high CTD Serine 5 phosphorylation is seen throughout transcribed regions. Therefore, coupling the TFIIH modules is necessary to localize and limit CTD kinase activity to early stages of transcription. These results are consistent with the idea that the two TFIIH modules began as independent functional entities that became connected by Tfb3 during early eukaryotic evolution.

Keywords: Biological Sciences: Biochemistry; Genetics.

Fig. 1.. Tfb3 N-term-Linker fusions to other kinase modules can replace Tfb3, but not Kin28.

(A) Schematic of TFIIH structure within the PIC. The domain structure of Tfb3 (green) is shown, connecting the TFIIH Kinase (cyan) and Core (blue) Modules. (B) Schematic of Tfb3 fusions to other kinase modules. (C) The kin28Δ strain YSB744 was transformed with pRS425 (Vector), pRS415-KIN28, pRS425-TFB3-BUR2, pRS425-TFB3-CTK3, or pRS425-TFB3-MPK1. Transformants were tested for the ability to replace a KIN28/URA3 construct by plasmid shuffling. Cells were streaked on -LEU-TRP (center) or -LEU-TRP+5-FOA (right) plates for 3 days at 30°C. (D) pRS315 (Vector), pRS425-TFB3, pRS315/TFB3Δ2 (aa 1–275) (29), pRS425-TFB3-BUR2, pRS425-TFB3-CTK3, and pRS425-TFB3-MPK1 were transformed into tfb3Δ strain SHY907 (22), replacing the plasmid-expressed wild-type gene by plasmid shuffling. Streaks shown were grown on –LEU for 4 days (center) or on -LEU+5-FOA plates (right) for 9 days.

Fig. 2.. Tfb3 can be split into two functional parts.

(A) Schematic of Tfb3 deletion constructs. Note that all constructs retained amino acids 1–11 at the N-terminus for ease of cloning and to avoid differential sensitivity to N-end rule degradation. (B) Plasmid shuffling was used to test pRS424 (Vector), pRS424-TFB3 (WT TFB3), pRS424-TFB3(Δ145–321) (N-term), and pRS424-TFB3 (Δ252–321) (N-term-Linker) for the ability to support growth of tfb3Δ shuffling strain SHY907/YF2456 (22). Streaks shown were grown on -TRP+5-FOA plates for 5 days at 30°C (C) Spot assay for growth. Tfb3 N-term (YSB3704) and N-term-Linker (YSB3722) strains were transformed with pRS425 (Vector), pSH1542 (WT TFB3), pRS315-TFB3(1–11, 238-Stop)-Flag1-TAP (C-term low copy), pRS425-TFB3(1–11, 238-Stop) (C-term high copy), pRS425-TFB3(1–11, 139-Stop), or pLH366 (Linker-C-term high copy). Ten-fold serial dilutions were spotted onto –LEU-TRP plates for 3 days. For comparison to normal growth, an isogenic strain carrying WT TFB3 (YSB3788) was spotted in parallel (top strip).

Fig. 3.. The TFIIH Kinase Module associates with the untethered Tfb3 C-terminal domain.

(A) Whole cell extracts were made from YSB3788 (TFB3 untagged), YSB3723 (TFB3-TAP + N-term), YSB3732 (N-term-Linker + C-term-TAP), and YSB3728 (N-term + Linker-C-term-TAP). Both Input extracts (lanes 1–4) and IgG-Agarose precipitated fractions (lanes 5–8) were resolved by SDS-PAGE and blotting for Tfb3. (B) To probe for other Kinase Module subunits, IgG precipitates were probed with anti-Ccl1 and anti-Kin28 antibodies. In all panels, asterisks mark TAP-tagged Tfb3 derivatives (which also react with secondary antibody due to the protein A component).

Fig. 4.. Splitting Tfb3 uncouples the TFIIH Kinase Module from the Core Module and the PIC.

The same IgG-Agarose precipitates analyzed in Fig. 3 were also probed with the following antibodies against: (A) TFIIH Core Module subunit Tfb1 (note background binding of Tfb1 to beads as seen in lane 1, and non-specific band ^~50 kDa), and (B) TFIIE subunits Tfa1 and Tfa2 (note non-specific band ^~60 kDa), which serves as a marker for the RNApII PIC. In all panels, asterisks mark TAP-tagged Tfb3 derivatives reacting with secondary antibody due to the protein A component.

Figure 5.. Loss of proper Kinase Module and Ser5P promoter localization in split Tfb3 cells.

Crosslinked chromatin was prepared from strains expressing full length Tfb3 (YSB3788), the separated N-term-Linker and C-term derivatives (YSB3731), the N-term and Linker-C-term derivatives (YSB3727), or N-term and C-term with no Linker (YSB3725). Samples were immunoprecipitated and processed for sequencing of crosslinked DNA as described in Methods. Two biological replicates for each antibody were used to generate metagene profiles of (A) TFIIH Core subunit Tfb1, (B) TFIIH Kinase subunit Kin28, (C) Rpb1 CTD Ser5P, (D) RNApII subunit Rpb1, and (E) Ser5P normalized to total Rpb1. The analysis used only those nuclear genes with an average RNApII occupancy greater than 4 reads per million (rpm) and longer than 1 kb (n=95). Individual replicates are shown in Supplemental Fig. S3. To account for the differing lengths of genes, each graph shows 1 kb centered on the transcription start site (TSS) to the left of the dividing line, and 1 kb centered on the polyadenylation site (pA) to the right.

Figure 6.. Split Tfb3 strains are not hyper-sensitive to UV light.

Yeast strains carrying the indicated Tfb3 configurations were plated at various densities and exposed to the indicated dosages of UV light. Surviving colonies were counted after several days. The graph shows the averaged values from multiple replicates, and error bars represent standard deviation. Note that there are two strain backgrounds. The tfb1–101 strain (YSB250, black) is a positive control for an NER-defective strain sensitive to UV light, and its isogenic WT control is YSB207 (yellow). The other five isogenic strains are in a tfb6Δ background, lacking the Tfb6 protein that competes with the TFIIH for Ssl2 binding (33): WT/tfb6Δ (YSB3788, green), N-term (YSB3724, red), N-term-Linker (YSB3729, blue), N-term + Linker-C-term (YSB3727, orange), and N-term-Linker + C-term (YSB3731, slate).

Figure 7.. Model for linkage between the TFIIH Kinase and Core Module functions.

A. In free TFIIH, the Tfb3 linker contacts the Ssl2/XPB subunit to create a “closed” conformation. In this configuration, the translocase, and possibly the kinase, may be inhibited. B. Upon TFIIH incorporation as the final component of the PIC, the Kinase Module engages with both Mediator (not pictured) and the CTD. These interactions may help release the Tfb3/MAT1 linker from Ssl2/XPB, allowing the translocase to access downstream DNA to promote ATP hydrolysis and promoter melting.