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

Abstract

The Ess1 prolyl isomerase in Saccharomyces cerevisiae regulates RNA polymerase II (pol II) by isomerizing peptide bonds within the pol II carboxy-terminal domain (CTD) heptapeptide repeat (YSPTSPS). Ess1 preferentially targets the Ser5-Pro6 bond when Ser5 is phosphorylated. Conformational changes in the CTD induced by Ess1 control the recruitment of essential cofactors to the pol II complex and may facilitate the ordered transition between initiation, elongation, termination, and RNA processing. Here, we show that Ess1 associates with the phospho-Ser5 form of polymerase in vivo, is present along the entire length of coding genes, and is critical for regulating the phosphorylation of Ser7 within the CTD. In addition, Ess1 represses the initiation of cryptic unstable transcripts (CUTs) and is required for efficient termination of mRNA transcription. Analysis using strains lacking nonsense-mediated decay suggests that as many as half of all yeast genes depend on Ess1 for efficient termination. Finally, we show that Ess1 is required for trimethylation of histone H3 lysine 4 (H3K4). Thus, Ess1 has direct effects on RNA polymerase transcription by controlling cofactor binding via conformationally induced changes in the CTD and indirect effects by influencing chromatin modification. P eptidyl-prolyl isomerases (PPIases) are enzymes that noncovalently modify target proteins by catalyzing the rotation of the peptide bond preceding proline residues. PPIases catalyze both cis¡trans and trans¡cis peptide bond isomerizations. The resulting changes in protein conformation can have profound functional consequences, such as altering protein-protein interactions, protein stability, or the suitability of a protein as a target for further modifications, e.g., phosphorylation/dephosphorylation (46,47,56).Three classes of PPIases have been identified (5). The parvulin family of PPIases, of which Ess1 (essential 1) protein in Saccharomyces cerevisiae is the founding eukaryotic member, is distinct from the well-studied cyclophilin and FK506-binding protein (FKBP) families, which are targets of immunosuppressive drugs. In yeast, Ess1 is required for growth (20), and its human homolog, Pin1, complements yeast ess1 mutants (32). 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). In vitro, Ess1 binds and isomerizes phosphorylated Ser5-Pro6 (pSer5-Pro6) within the heptad repeat about 5-fold better than pSer2-Pro3 (17). Ess1 stimulates pSer5-Pro6 isomerization within peptide substrates fr...

A Redox 2-Cys Mechanism Regulates the Catalytic Activity of Divergent Cyclophilins

“…In Saccharomyces cerevisiae, the heptad repeats of the CTD are the targets of Ess1 and Cpr1, two prolylisomerases that affect the progress of transcription and gene silencing (Arévalo-Rodríguez et al, Wu et al, 2000;Ma et al, 2012). We showed that CsCyp complements the function of both Ess1 and Cpr1 and that PthA inhibits its PPIase activity (Domingues et al, 2012).…”

The Ess1 prolyl isomerase: Traffic cop of the RNA polymerase II transcription cycle

“…First, defects in transcription in the ts -mutants are apparent even at permissive temperature, especially for the ess1 H164R allele [128,129]. This is probably why genetic interactions can be observed at semi-permissive (34 °C) and permissive temperatures (25°, 30 °C) [85,95,118,122].…”

“…While some examples of mRNAs readthrough transcription were observed, the majority of effects were on small non-coding RNAs (discussed below). It was not until the use of genetic backgrounds in which mRNA decay pathways were inactivated that transcription readthrough in ess1 mutants was revealed to be wide-spread [128]. About half of the fourteen genes examined in ess1 H164R cells that also carried a deletion of the UPF1 gene showed significant readthrough transcription.…”

“…Indeed ess1 H164R upf1 Δ double mutants showed synthetic growth defects. This was interpreted [128] to indicate that in double mutant cells the accumulation of readthrough transcripts might contribute to their demise, whereas in ess1 H164R UPF1 + cells, where the NMD decay pathway is operational, aberrant transcripts are rapidly degraded [131,132]. …”

“…Both function in RNA processing and in destruction of aberrant RNAs [133,134]. While no genome-wide analysis of ess1 H164R mutants has been done in mRNA decay-deficient backgrounds, based on experiments done thus far it is likely that 47/;50% of all mRNA genes will re quire Ess1 for efficient transcription termination/3′-end processing [128]. …”