Functional Interaction of the Ess1 Prolyl Isomerase with Components of the RNA Polymerase II Initiation and Termination Machineries

Abstract

The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a reiterated heptad sequence (Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7) that plays a key role in the transcription cycle, coordinating the exchange of transcription and RNA processing factors. The structure of the CTD is flexible and undergoes conformational changes in response to serine phosphorylation and proline isomerization. Here we report that the Ess1 peptidyl prolyl isomerase functionally interacts with the transcription initiation factor TFIIB and with the Ssu72 CTD phosphatase and Pta1 components of the CPF 3-end processing complex. The ess1 A144T and ess1 H164R mutants, initially described by Hanes and coworkers (Yeast 5:55-72, 1989), accumulate the pSer5 phosphorylated form of Pol II; confer phosphate, galactose, and inositol auxotrophies; and fail to activate PHO5, GAL10, and INO1 reporter genes. These mutants are also defective for transcription termination, but in vitro experiments indicate that this defect is not caused by altering the processing efficiency of the cleavage/polyadenylation machinery. Consistent with a role in initiation and termination, Ess1 associates with the promoter and terminator regions of the PMA1 and PHO5 genes. We propose that Ess1 facilitates pSer5-Pro6 dephosphorylation by generating the CTD structural conformation recognized by the Ssu72 phosphatase and that pSer5 dephosphorylation affects both early and late stages of the transcription cycle.The rigid cyclic structure of the amino acid proline restricts the flexibility of prolyl-containing polypeptides. Peptidyl proline can adopt either the cis or trans conformation, with dramatically different effects on protein secondary structure. Although prolyl cis-trans isomerization can occur spontaneously, uncatalyzed isomerization must overcome large energy of activation barriers (⌬G°), predicted to be 30 kcal ⅐ mol Ϫ1 for trans-to-cis conversion and experimentally determined to range from 14 to 24 kcal ⅐ mol Ϫ1 for cis-to-trans conversion (reviewed in references 32 and 33). Consequently, peptidyl prolyl isomerases (PPIases) have evolved to greatly accelerate the rates of rotation about the peptide bond preceding proline. Accordingly, PPIases are relevant not only for protein folding but also for regulation of dynamic cellular processes (33).PPIases fall into three distinct classes: cyclophilins, FK506 binding proteins, and the parvulins, which include mammalian Pin1 and its budding yeast (Saccharomyces cerevisiae) homolog, Ess1 (2). A unique feature of the Pin1 PPIase is its specific recognition of phosphorylated Ser/Thr-Pro sequences (pSer/ Thr-Pro) (44, 62). Cyclin-dependent protein kinases and type 2A protein phosphatases are specific for the trans isomer of pSer/Thr-Pro. Furthermore, phosphorylation of a Ser/Thr-Pro motif dramatically slows spontaneous prolyl isomerization and prevents other PPIases from working at this prolyl residue (57). Therefore, Pin1 can regulate signaling pathways by controlling the levels of kinase products and phosphat...

The Prolyl Isomerase Pin1 Targets Stem-Loop Binding Protein (SLBP) To Dissociate the SLBP-Histone mRNA Complex Linking Histone mRNA Decay with SLBP Ubiquitination

“…In both yeast and mammals, Pin1 (Ess1 in yeast) regulates the conformation and phosphorylation state of the RNA polymerase (RNAP) II carboxyterminal domain (CTD) (1,41). Ess1 promotes dephosphorylation of Ser-5 of the heptad repeat (Y-S 2 -P-T-S 5 -P-S) in the CTD by interactions with CTD-associated phosphatases Ssu72 and Pcf11, thereby regulating the association of the CTD with components of the 3=-end processing machinery (24,56). Yeast Ess1 is required for transcription termination of small noncoding RNAs such as snoRNAs, cryptic unstable transcripts (CUTs), and upstream regulatory RNAs (uRNAs) via the Nrd1 pathway (51).…”

“…Yeast Ess1 is required for transcription termination of small noncoding RNAs such as snoRNAs, cryptic unstable transcripts (CUTs), and upstream regulatory RNAs (uRNAs) via the Nrd1 pathway (51). Ess1 functionally interacts with the transcription initiation factor TFIIB, Ssu72 phosphatase, and Pta1 components of the 3=-end processing machinery to influence gene looping (24). Besides its effects on transcription, Pin1 has been implicated in the control of mRNA stability of three AU-rich element (ARE)-containing mRNAs, namely, those for granulocye-macrophage colony-stimulating factor (GM-CSF), parathyroid hormone (Pth), and transforming growth factor ␤ (TGF-␤), in the cytoplasm (10,25).…”

Multiple Roles for the Ess1 Prolyl Isomerase in the RNA Polymerase II Transcription Cycle

“…Pin1 has been linked to a number of signaling pathways in human cells and seems to target a wide variety of proteins for isomerization (33,70). In contrast, extensive genetic studies have thus far identified only RNA polymerase II (pol II) as the target of Ess1 in yeast (21,27,65).Within the RNA pol II complex, Ess1 targets the carboxy-terminal domain (CTD) of the largest subunit, Rpb1 (38, 65), which is composed of 26 repeats of the heptapeptide Y 1 S 2 P 3 T 4 S 5 P 6 S 7 (62). Each repeat contains two potential Ess1 substrate binding sites (S-P), where the serines are known to be phosphorylated (24,43).…”

Tissue-specific regulation of alternative polyadenylation represses expression of a neuronal ankyrin isoform in C. elegans epidermal development

“…The dephosphorylation of RNA polymerase II C-terminal domain (CTD) by the yeast homolog Ssu72 could be facilitated by Ess1/Pin1 peptidyl-prolyl cis-trans isomerase (Krishnamurthy et al, 2009;Werner-Allen et al, 2011). Moreover, murine Pin1 can be phosphorylated by death-associated protein kinase 1 (DAPK1), and this phosphorylation alters nuclear localization and enzymatic activity of Pin1 .…”