MPK1/SLT2 Links Multiple Stress Responses with Gene Expression in Budding Yeast by Phosphorylating Tyr1 of the RNAP II CTD

Abstract

The RNA polymerase II largest subunit C-terminal domain consists of repeated YSPTSPS heptapeptides. The role of tyrosine-1 (Tyr1) remains incompletely understood, as, for example, mutating all Tyr1 residues to Phe (Y1F) is lethal in vertebrates but a related mutant has only a mild phenotype in S. pombe. Here we show that Y1F substitution in budding yeast resulted in a strong slow-growth phenotype. The Y1F strain was also hypersensitive to several different cellular stresses that involve MAP kinase signaling. These phenotypes were all linked to transcriptional changes, and we also identified genetic and biochemical interactions between Tyr1 and both transcription initiation and termination factors. Further studies uncovered defects related to MAP kinase I (Slt2) pathways, and we provide evidence that Slt2 phosphorylates Tyr1 in vitro and in vivo. Our study has thus identified Slt2 as a Tyr1 kinase, and in doing so provided links between stress response activation and Tyr1 phosphorylation.

Keywords: Mediator; NNS complex; RNA polymerase II; Slt2 kinase; stress response; transcription termination; tyrosine phosphorylation.

Figure 1. RNAP II CTD Tyr to Phe substitution results in severe growth defects

(A) Tetrad dissection of heterozygous diploid Y1F CTD strain (Y1F). Y1F CTD in haploid tetrads marked with NAT resistance and is present in all small-size tetrads. Yeast spot assay comparing growth of WT, CONS, and two Y1F clones, with serial fivefold dilutions, on rich or synthetic complete (SC) medium at 30°C, or on rich medium at indicated temperature, for indicated number of days. (B) Cell-cycle assay showing unsynchronized cells stained with propidium iodide, the two peaks representing cells in G1/G0 and G2, respectively. (C) Western blot analysis of cell lysates derived from WT and Y1F strains using antibodies recognizing the N-terminus of Rpb1 (y80), unphosphorylated consensus repeats (8WG16), Ser2P (3E10 and H5), Ser5P (3E8), Tyr1P (3D12) and GAPDH as indicated. (D) Western blot analysis of an Rpb1 co-IP (using y-80), probing for Ctk1 interaction (using 3HA tagged Ctk1 and HA antibody) with RNAP II (normalized to Rpb3). 5% inputs shown. All results shown are representative of three independent experiments.

Figure 2. SGA analysis identifies suppressors of Y1F growth defects

(A) List of genes showing synthetic rescue of Y1F strain in two SGA suppressor screens. Genes displaying strongest interactions and involved in RNAP II transcription are shown (refer to Table S2 for a complete list). (B) Confirmation of genetic interaction between Y1F and MED13/CDK8/CYCC and UBP8. Strains of indicated genotypes were generated by recombinant transformation and growth compared by spot assay on rich medium with serial five-fold dilutions. YGL178C showed no interaction with Y1F in SGA screen and serves as a control. (C) ChIP analysis of Cdk8/CycC occupancy at promoter regions of indicated genes, using 3HA-tagged Cdk8/CycC. Data normalized to WT signal at each gene; P values less than 0.05 are indicated (*). ChIP data is represented as mean +/− SE of three independent experiments.

Figure 3. Expression of multiple genes is altered in Y1F

(A) List of enriched GO terms through Gene Ontology analysis. The numbers of significantly altered genes used for GO analysis were 306 up-regulated, 324 down-regulated. (B) RT-PCR analysis confirming changes in RNA levels for indicated genes between WT and Y1F strains. (IMD2 was not detected in RNA-seq analysis). (C) Spot assays comparing growth of WT and Y1F strains, using serial five-fold dilutions, on rich and synthetic media with media containing indicated stress-inducing compounds.

Figure 4. Slt2 phosphorylates Tyr1 in vitro and in vivo

(A) In vitro kinase assay using 3HA-tagged Slt2 and Hog1 extracted and IPed from activated cells. Following incubation with GST-CTD, proteins were resolved by SDS-PAGE and blots probed with the indicated antibodies. Lanes are Slt2-HA (SLT2) and kinase-dead (KD), Hog1-HA (HOG1) and kinase dead (KD), beads and antibody control (BA) and GST-CTD alone (CTD). (B) Western blot of Tyr1P levels after stress induction. DMSO, calcofluor white (CFW) and phleomycin (Phl) are shown. Rpb1, Slt2, Hog1, and Rpb3 were also probed using their respective antibodies. Time points are untreated (Un), 15, 30, 45 and 60 minutes. (C) Quantification of (B). Signals were normalized individually to Rpb3 levels, then collectively to uninduced control. (D) Western blot and quantification of Tyr1P levels in isogenic deletion strains. Protein extracts from strains with either SLT2/HOG1 deletions (SΔ/HΔ; double, SHΔ) or kinase-dead mutations (SM/HM) were blotted using 3D12 and normalized to WT. (E) Western blot of Tyr1P levels after heat stress (37°C); signals normalized as in (B). All results shown are representative of three independent experiments; data are represented as mean +/− SE of three independent experiments.

Figure 5. Differential association of Slt2 with WT and Y1F RNAP II

(A) Western blot analysis of a Rpb1 co-IP (using y-80), probing for Slt2 interaction with RNAP II (normalized to Rpb3). 5% inputs shown. (B) Western blot analysis of a Slt2-3HA co-IP, probing for total Rpb1 (y80), Tyr1-P Rpb1 (3D12) and Ser2-P Rpb1 (3E10), using Rpb3 as control for normalization. Untreated (Un), heat treated (37°C) and kinase dead (KD) shown. All results shown are representative of three independent experiments.

Figure 6. RNAP II Tyr1 and Slt2 affect Nrd1 recruitment to RNAP II and chromatin

(A) Western blot analysis of Nrd1 levels after Rpb1 co-IP (using y-80 antibody), with quantification. Nrd1 interaction with RNAP II quantified using Rpb3. (B) Western blot analysis of Rtt103 levels after Rpb1 co-IP (using y-80 antibody), with quantification. Rtt103 interaction with RNAP II quantified using Rpb3. (C) ChIP analysis of Nrd1 occupancy at promoter regions of indicated genes in WT and Y1F strains. (D) ChIP analysis of Nrd1 occupancy at promoter and body regions of model gene FKS2, before and after heat stress. (E) ChIP analysis of Slt2 occupancy at promoter and body regions of model gene FKS2, before and after heat stress. All data are represented as mean +/− SE of three independent experiments.

Figure 7. Role of CTD Tyr1 and Slt2 kinase in activating transcription of stress-inducible genes

In the absence of activation by a stress-induced signaling cascade, Slt2 is inactive and Tyr1 is not phosphorylated. The Nrd1-containing NNS complex is thus recruited to a primarily Ser5P CTD and transcripts are prematurely terminated and degraded. Activation of Slt2 enables the kinase to associate with RNAP II and Mediator/SBF, promoting Cdk8/CycC degradation and RNAP II Tyr1 phosphorylation. This combination of events facilitates activation and prevents termination factor (e.g., NNS) association with the CTD until the 3′ end, when Tyr1 is dephosphorylated, the transcript 3′ processed and transcription terminated.