Allosteric interactions between capping enzyme subunits and the RNA polymerase II carboxy-terminal domain

Cho, Eun Jung; Rodriguez, Christine R.; Takagi, Toshimitsu; Buratowski, Stephen

doi:10.1101/gad.12.22.3482

Cited by 92 publications

(167 citation statements)

References 23 publications

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“…6 -10). The 5Ј capping complex is not only localized near the pre-mRNA by direct association with the phospho-CTD (11, 12) but is also allosterically activated by phospho-CTD binding (13,14). A variety of evidence strongly suggests that the phospho-CTD is involved in splicing.…”

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confidence: 99%

The Splicing Factor, Prp40, Binds the Phosphorylated Carboxyl-terminal Domain of RNA Polymerase II

Morris

Greenleaf

2000

Journal of Biological Chemistry

164

165

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We showed previously that the WW domain of the prolyl isomerase, Ess1, can bind the phosphorylated carboxyl-terminal domain (phospho-CTD) of the largest subunit of RNA Polymerase II. Analysis of phospho-CTD binding by four other WW domain-containing Saccharomyces cerevisiae proteins indicates the splicing factor, Prp40, and the RNA polymerase II ubiquitin ligase, Rsp5, can also bind the phospho-CTD. The identification of Prp40 as a phospho-CTD binding protein represents the first demonstration of direct interaction between a documented splicing factor and the phospho-CTD. Domain dissection studies reveal that phospho-CTD binding occurs at multiple locations in Prp40, including sites in both the WW and FF domain regions. Because the conserved repeats of the CTD make it an ideal ligand for multi-site binding events, the implications of multi-site binding are discussed. Our data suggest a mechanism by which the phospho-CTD of elongating RNA polymerase II facilitates commitment complex formation by juxtaposing the 5 and 3 splice sites.The carboxyl-terminal domain (CTD) 1 of the largest subunit of RNA polymerase II (1) plays a central role in mRNA synthesis. The CTD is composed of 26 -52 heptad repeats with the consensus sequence, YSPTSPS. These repeats are extensively phosphorylated in RNA polymerase II actively engaged in transcript elongation (2-5).In the past several years evidence has accumulated indicating that the phosphorylated form of the CTD acts to coordinate pre-mRNA processing events (for review see Refs. 6 -10). The 5Ј capping complex is not only localized near the pre-mRNA by direct association with the phospho-CTD (11, 12) but is also allosterically activated by phospho-CTD binding (13,14). A variety of evidence strongly suggests that the phospho-CTD is involved in splicing. The hyperphosphorylated form of RNA polymerase II colocalizes with splicing factors when transcriptionally active (15, 16) and in the nuclear matrix (17-19). Several phospho-CTD binding proteins have been identified that contain SR and RRM domains as found in many splicing factors (20,21). Fusion proteins with a hyperphosphorylated CTD can inhibit splicing in vivo (22). In addition, transcriptionally unengaged but phosphorylated RNA polymerase II is able to stimulate splicing in vitro (23).Recently, we demonstrated that the prolyl isomerase, Ess1, can bind the phosphorylated form of the CTD and that this binding is mediated by its WW domain (24). Because the prolyl isomerase activity of Ess1 preferentially acts on phospho-SerPro peptide bonds, as are found in abundance in the phospho-CTD, our findings provided a plausible explanation for earlier results implicating Ess1 in pre-mRNA 3Ј end formation (25,26).WW domains, named for two highly conserved tryptophan residues, are small independently folding protein domains consisting of slightly more than 30 amino acids arranged in three anti-parallel ␤ sheets (27, 28). These domains have been shown to bind proline-rich sequences containing several different motifs (29). Of five protei...

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confidence: 99%

The Splicing Factor, Prp40, Binds the Phosphorylated Carboxyl-terminal Domain of RNA Polymerase II

Morris

Greenleaf

2000

Journal of Biological Chemistry

164

165

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“…The S. cerevisiae RNA triphosphatase does not bind to the Pol-II CTD by itself (7), but it does bind to the guanylyltransferase (8 -10). The mammalian capping enzyme (Mce1) is a bifunctional polypeptide composed of an N-terminal RNA triphosphatase domain linked to a Cterminal guanylyltransferase domain.…”

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Interactions between Fission Yeast mRNA Capping Enzymes and Elongation Factor Spt5

Pei

Shuman

2002

Journal of Biological Chemistry

127

136

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Elongating RNA polymerase II is targeted by macromolecular assemblies that regulate mRNA synthesis and processing. The capping apparatus is the first of the assemblies to act on the nascent pre-mRNA. Although recruitment of the capping enzymes to the transcription complex is dependent on phosphorylation of the C-terminal domain of the Rpb1 subunit of polymerase II (Pol-II), there may be additional levels of control that coordinate capping with elongation. Here we show that the triphosphatase (Pct1) and guanylyltransferase (Pce1) enzymes of the fission yeast capping apparatus bind independently to the elongation factor Spt5. The C-terminal domain of the 990-amino acid Schizosaccharomyces pombe Spt5 protein, composed of repeats of a nonapeptide motif (consensus sequence TPAWNSGSK), is necessary and sufficient for binding to the capping enzymes in vivo (in a two-hybrid assay) and in vitro. As few as four nonamer repeats suffice for Spt5 binding to Pct1 in vitro, whereas six repeats are required for Spt5 binding to Pce1. A 116-amino acid fragment of the guanylyltransferase Pce1 suffices for binding to the Spt5 C-terminal domain (CTD) but not for binding to the Pol-II CTD. Pct1 and Pce1 can bind simultaneously to the Spt5 CTD in vitro. We find that Spt5 is essential for viability of S. pombe and that it interacts in vivo with S. pombe Spt4 via a central domain distinct from the Spt5 CTD. We suggest that Spt5-induced arrest of elongation at promoter proximal positions ensures a temporal window for recruitment of the capping enzymes. mRNA capping occurs cotranscriptionally by a series of three enzymatic reactions in which the 5Ј triphosphate terminus of the pre-mRNA is cleaved to a diphosphate by RNA triphosphatase, then capped with GMP by RNA guanylyltransferase, and methylated at the N7 position of guanine by RNA (guanine-7) methyltransferase (1). Targeting of cap formation to transcripts made by RNA polymerase II (Pol-II)

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Section: Deciphering the Ctd Codementioning

confidence: 99%

“…Furthermore, the capping enzyme activity is stimulated by an interaction with the phosphorylated CTD, and in return, enhances early transcription. This is considered to be a mechanism that stimulates the extension of the capped RNA only, by coupling capping and the early transcription (Cho et al, 1998;Ho and Shuman, 1999; Kim et al, 2004a;Schroeder et al, 2004).In contrast to the capping, the splicing machineries contain consensus binding sites on the nascent RNA. Therefore, there is some controversy as to whether co-transcriptional splicing (splicing while transcription is ongoing) is required functionally or is simply linked mechanically (i.e.…”

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RNA polymerase II carboxy-terminal domain with multiple connections

Cho¹

2007

Exp Mol Med

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The largest subunit of eukaryotic RNA polymerase II contains a unique domain at its carboxy-terminus, which is referred to as the carboxy-terminal domain (CTD). The CTD is made up of an evolutionarily conserved heptapeptide repeat (YSPTSPS). Over the past decade, there has been increasing attention on the role of the CTD in transcription regulation in the view of mRNA processing and chromatin remodeling. This paper provides a brief overview of the recent progress in the dynamic changes in CTD phosphorylation and its role in integrating multiple nuclear events.Keywords: carboxy-terminal domain kinase; chromatin; phosphorylation; histones; RNA polymerase II; RNA processing, post-transcriptional IntroductionThe largest subunit of eukaryotic RNA polymerase II (pol II) carboxy-terminal domain (CTD) consists of conserved heptapeptide repeats (Y 1 S 2 P 3 T 4 S 5 P 6 S 7 ) (Dahmus, 1996). Mammalian pol II CTD contains 52 repeats, whereas the yeast Saccharomyces cerevisiae CTD has 26-27. A deletion of the mouse, Drosophila, or yeast CTD is lethal. Therefore, the CTD is essential for the viability of an organism, even though the number of repeats can be reduced.Partial deletions of the CTD result in reduced transcription in vivo, and defective responses to various activators. The CTD acts as a platform to couple the mRNA metabolism and chromatin function to the transcription as it recruits various RNA processing/export and histone modifying factors to the transcription complex (Bentley, 2005;Buratowski, 2005;Phatnani and Greenleaf, 2006). This means that the CTD is very important for organizing various nuclear functions to acquire the proper regulation of gene expression. Those functions often depend on the CTD modification such as phosphorylation. Indeed, the CTD is rich in phosphoacceptor amino acid residues and undergoes reversible phosphorylation during the transcription cycle. Two forms of RNA pol II, which differ in the level of phosphorylation of the CTD, can be distinguished and are believed to have distinct functions in the transcription cycle; RNA pol IIa, with a hypophosphorylated CTD, is the form that assembles into the transcription initiation complexes, whereas pol IIo, with a hyperphosphorylated CTD is associated with the transcription elongation complexes. Phosphorylation occurs mainly at discrete serines (S) within the CTD repeats (S2, S5), which is then recognized by different proteins that interconnect the transcription to various nuclear metabolisms. Accordingly, serine phosphorylation is known as the 'CTD code', in a similar way that the 'histone code' refers to the histone modification (Buratowski, 2003). CTD with the phosphorylation codeEarlier models based on a two-step transcription cycle, in which pol IIa was assembled at the promoter and pol IIo carried out transcription elongation, have evolved to one with a more complex CTD phosphorylation cycle. Different modified forms of pol II dominate different stages of transcription (Komarnisky et al., 2000). Pol II assembled at the promoter is...

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Allosteric interactions between capping enzyme subunits and the RNA polymerase II carboxy-terminal domain

Cited by 92 publications

References 23 publications

The Splicing Factor, Prp40, Binds the Phosphorylated Carboxyl-terminal Domain of RNA Polymerase II

The Splicing Factor, Prp40, Binds the Phosphorylated Carboxyl-terminal Domain of RNA Polymerase II

Interactions between Fission Yeast mRNA Capping Enzymes and Elongation Factor Spt5

RNA polymerase II carboxy-terminal domain with multiple connections

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