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...

Functional compartmentalization of cells is a universal strategy for segregating processes that require specific components, undergo regulation by modulating concentrations of those components, or that would be detrimental to other processes. Primary cilia are hair-like organelles that project from the apical plasma membranes of epithelial cells where they serve as exclusive compartments for sensing physical and chemical signals in the environment. As such, molecules involved in signal transduction are enriched within cilia and regulating their ciliary concentrations allows adaptation to the environmental stimuli. The highly efficient organization of primary cilia has been co-opted by major sensory neurons, olfactory cells and the photoreceptor neurons that underlie vision. The mechanisms underlying compartmentalization of cilia are an area of intense current research. Recent findings have revealed similarities and differences in molecular mechanisms of ciliary protein enrichment and its regulation among primary cilia and sensory cilia. Here we discuss the physiological demands on photoreceptors that have driven their evolution into neurons that rely on a highly specialized cilium for signaling changes in light intensity. We explore what is known and what is not known about how that specialization appears to have driven unique mechanisms for photoreceptor protein and membrane compartmentalization.

The Ess1 prolyl isomerase from Saccharomyces cerevisiae and its human ortholog, Pin1, play critical roles in transcription by regulating RNA polymerase II. In human cells, Pin1 also regulates a variety of signaling proteins, and Pin1 misexpression is linked to several human diseases. To gain insight into Ess1/Pin1 function, we carried out a synthetic genetic array screen to identify novel targets of Ess1 in yeast. We identified potential targets of Ess1 in transcription, stress, and cell-cycle pathways. We focused on the cell-cycle regulators Swi6 and Whi5, both of which show highly regulated nucleocytoplasmic shuttling during the cell cycle. Surprisingly, Ess1 did not control their transcription but instead was necessary for their nuclear localization. Ess1 associated with Swi6 and Whi5 in vivo and bound directly to peptides corresponding to their nuclear localization sequences in vitro. Binding by Ess1 was significant only if the Swi6 and Whi5 peptides were phosphorylated at Ser-Pro motifs, the target sites of cyclin-dependent kinases. On the basis of these results, we propose a model in which Ess1 induces a conformational switch (cis-trans isomerization) at phospho-Ser-Pro sites within the nuclear targeting sequences of Swi6 and Whi5. This switch would promote nuclear entry and/or retention during late M and G1 phases and might work by stimulating dephosphorylation at these sites by the Cdc14 phosphatase. This is the first study to identify targets of Ess1 in yeast other than RNA polymerase II.

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