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Remodeling the CTD
- RNA polymerase II and the integration of nuclear events

The RNA polymerase II CTD appears to interact with a number of multiprotein complexes involved in both transcription and pre-mRNA processing to produce the mature mRNA (see Fig. 1). The assembly and disassembly of processing complexes on the CTD likely occurs in a highly dynamic and temporally and spatially regulated manner during the transcription cycle. An important question then is how such transitions might be coordinated. In this regard, two newly discovered proteins, each of which possesses a different class of PPIase domain, are intriguing. PPIases catalyze cis-trans isomerization of the peptide bond on the amino-terminal side of proline residue in peptides and proteins. PPIases are classified into three distinct families. The cyclophilins and the FK506-binding proteins (FKBPs) families are sensitive to the immunosuppressant drugs cyclosporin A (CsA) and FK506, respectively. A third group is the parvulin family, which is not inhibited by those drugs. PPIases are thought to function in protein folding, trafficking, assembly/disassembly, and direct regulation of protein function (for review, see Hunter 1998; Gothel and Marahiel 1999).

Human SRcyp/SCAF10 was originally identified in a yeast two-hybrid screen as a CTD-interacting protein (Bourquin et al. 1997). SRcyp has a cyclophilin-like PPIase domain in its amino terminus and an RS-rich region similar to those found in SR proteins in its carboxy-terminal half, which also contains a CTD-interacting domain (CID; see above). Overall, this domain organization is related to that of the SCAFs, hence the name SCAF10. The rat homolog of the SRcyp, matrin CYP, was shown to possess PPIase activity in vitro (Mortillaro and Berezney 1998). SRcyp and matrin CYP were shown to colocalize in cells with the SR protein splicing factor SC35 and the snRNP protein U1-70K, respectively. Based on these findings, it was suggested that the CTD, via its proline-containing heptad repeats, may be induced to undergo conformational changes by the PPIase activity of SCAF10, and that this may help facilitate the assembly or disassembly of splicing factors on the CTD. Although these properties of SCAF10 are highly suggestive of an interesting role for SCAF10 in linking the RNAPII CTD to splicing, functional support for this idea is not yet available.

Another interesting nuclear PPIase is Ess1/Pin1, which is an evolutionarily conserved member of the parvulin family. Ess1 was initially discovered in yeast and mutations gave rise to defects in cell division (Hanes et al. 1989). The human counterpart of Ess1, Pin1, was discovered in a yeast two-hybrid screen with a cell-cycle kinase, NIMA, and depletion (by antisense) and overexpression in human cells both resulted in cell-cycle defects in G2/M phase (Lu et al. 1996). In keeping with a possible direct role in cell cycle control, Pin1 has been shown to bind in vitro to a number of mitotic regulators (Shen et al. 1998). Ess1/Pin1 possesses two distinct domains: an amino-terminal WW domain, which is involved in protein-protein interactions, and a PPIase catalytic domain. A remarkable feature of the protein is its unique substrate specificity. Ess1/Pin1 dramatically enhances (1000-3000 fold) isomerization of prolines preceded by phosphorylated serine (pSer) or threonine (pThr) compared with a proline preceded by a nonphosphorylated residue (Yaffe et al. 1997; Hani et al. 1999). The WW domain of Pin1 has been shown to be responsible for interacting with pSer/pThr-Pro motifs in target proteins (Lu et al. 1999). Ser/Thr-Pro is the core of the target sequence recognized by cyclin-dependent kinases, which fits nicely with the possibility that Ess/Pin1 functions by binding to and altering the conformation of mitotic regulators phosphorylated on Ser/Thr-Pro.

But compelling evidence also suggests that Ess1/Pin1 functions in mRNA 3'-end formation by linking the processing reaction to transcription (see Fig. 4). As mentioned above, Ess1 was uncovered in a genetic screen for ts mutations affecting proteins that function in mRNA 3'-end formation. The screen was designed to be very specific for 3'-end formation, and indeed mRNAs with unprocessed 3' ends could be detected at the nonpermissive temperature (Hani et al. 1995, 1999). Pointing to a link with the CTD, a biochemical selection employing phosphorylated GST-CTD and a yeast extract identified Ess1 as the major interacting protein (Morris et al. 1999). The interaction is specific for the phosphorylated form of the CTD, and RNAP II0 appears to be the major Ess1/Pin1 interacting protein, in humans (Albert et al. 1999) as well as yeast, likely reflecting the abundance of the pSer-Pro dipeptides in the phosphorylated CTD. Especially given that the genetic screen specifically identified mutants defect in PPIase activity, an attractive model is that Ess1/Pin1 effects a conformational change in the phosphorylated CTD that leads to enhanced efficiency of 3'-end formation. It is also possible that changes in the CTD and/or complexed proteins affect subsequent transcription termination (see below).

The above discussion suggests that Ess1/Pin1 may well be a bifunctional protein, participating directly in cell cycle control and mRNA 3'-end formation. However, it is also conceivable that at least some of the cell cycle arrest phenotype could be indirect, reflecting changes in gene expression as a result of defects in 3'-end formation. For example, mutations in certain splicing factors in fission yeast have been shown to display cell cycle phenotypes (Potashkin et al. 1998), and genetic depletion of the polyadenylation factor CstF-64 in chicken DT40 cells causes cell-cycle arrest (Takagaki and Manley 1998).

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