The m7GpppN cap is a defining feature of eukaryal messenger RNA that is required for mRNA stability and efficient translation. Our long-term goal has been to understand the mechanism of cap formation and how capping is coupled to transcription. Capping entails three enzymatic reactions: (i) the 5'triphosphate end of the pre-mRNA is hydrolyzed to a diphosphate by RNA triphosphatase (TPase);(ii) the diphosphate RNA end is capped with GMP by RNA guanylyltransferase (GTase);and (iii) the GpppN cap is methylated by RNA (guanine-N7) methyltransferase (MTase). The capping enzymes are directed to nascent mRNAs by binding to the phosphorylated carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II), which is composed of a tandem array of heptapeptide repeats (consensus: Y1S2P3T4S5P6S7). The inherently plastic CTD structure is sculpted by dynamic phosphorylation and dephosphorylation of the heptad serine residues. The CTD structure transmits informational cues about the state of the transcription machinery (a CTD code) that is "read" by CTD receptors. Our goal is to understand how CTD information content is specified and conveyed to CTD receptor proteins (especially the capping enzymes). Our genetic dissection of what is essential for fission yeast CTD function is providing new insights to the CTD code, including: (i) structure-activity relations at essential residues;(ii) the distinctive roles of position- specific phosphorylations in sexual differentiation and vegetative growth;and (iii) the ability to bypass "CTD pathologies" caused by S2A and S5A mutations. We've thereby demonstrated that the essential function of the Ser5-P mark in vivo is to recruit the capping enzymes. Capping enzymes also bind to the essential Pol II elongation factor Spt5, which, in conjunction with Spt4, elicits an elongation arrest at promoter-proximal sites that provides a temporal window for capping of nascent mRNAs. Fission yeast Spt5 binds to the capping enzymes via a distinctive "Spt5 CTD" composed of 18 repeats of a nonapeptide motif (consensus: T1P2A3W4N5S6G7S8K9). Genetic studies indicate that the CTDs of fission yeast Pol II and Spt5 play overlapping roles in recruiting the capping enzymes in vivo. This project aims to dissect the functions and structure-activity relations of the Pol II and Spt5 CTDs and the impact of CTD mutations on gene expression. We will determine structures of capping enzymes in complexes with the Pol II and Spt5 CTDs, and then assess genetically the functions of the capping enzyme-CTD interfaces. Capping enzymes discriminate different Pol II CTD phosphorylation arrays, implying that remodeling of the CTD by protein kinases and phosphatases is a means to regulate mRNA processing. Our biochemical and crystallographic studies of S. pombe Fcp1, an essential CTD phosphatase that preferentially hydrolyzes Ser2- PO4, are yielding deep insights to catalysis of CTD dephosphorylation in vitro. In this project, we propose to dissect genetically and biochemically the phosphoprotein substrate specificity of S. pombe Fcp1 and the requirements for Fcp1 function in vivo.

Public Health Relevance

mRNA capping enzymes are attractive targets for anti-infective drug discovery in light of the stark differences in the structures, mechanisms, and pharmacological sensitivities of the capping apparatus in humans versus fungal and protozoan pathogens. CTD phosphorylation dynamics orchestrate eukaryal gene expression. Two of the enzymes we study that modulate CTD structure are implicated in human pathology. A partial deficiency of human CTD phosphatase Fcp1 is associated with the autosomal recessive developmental disorder characterized by cataracts, facial dysmorphism, and peripheral neuropathy. Cdk9 CTD kinase activity is critical for HIV replication and Cdk9 dysregulation is associated with cardiac hypertrophy.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Molecular Genetics B Study Section (MGB)
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Bender, Michael T
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Sloan-Kettering Institute for Cancer Research
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Wang, Zi-Fu; Li, Ming-Hao; Hsu, Shang-Te Danny et al. (2014) Structural basis of sodium-potassium exchange of a human telomeric DNA quadruplex without topological conversion. Nucleic Acids Res 42:4723-33
Jacewicz, Agata; Schwer, Beate; Smith, Paul et al. (2014) Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28. Nucleic Acids Res 42:12885-98
Schwer, Beate; Shuman, Stewart (2014) Structure-function analysis of the Yhc1 subunit of yeast U1 snRNP and genetic interactions of Yhc1 with Mud2, Nam8, Mud1, Tgs1, U1 snRNA, SmD3 and Prp28. Nucleic Acids Res 42:4697-711
Schwer, Beate; Bitton, Danny Asher; Sanchez, Ana M et al. (2014) Individual letters of the RNA polymerase II CTD code govern distinct gene expression programs in fission yeast. Proc Natl Acad Sci U S A 111:4185-90
Schwer, Beate; Chang, Jonathan; Shuman, Stewart (2013) Structure-function analysis of the 5' end of yeast U1 snRNA highlights genetic interactions with the Msl5*Mud2 branchpoint-binding complex and other spliceosome assembly factors. Nucleic Acids Res 41:7485-500
Chang, Jonathan; Schwer, Beate; Shuman, Stewart (2012) Structure-function analysis and genetic interactions of the yeast branchpoint binding protein Msl5. Nucleic Acids Res 40:4539-52
Qiu, Zhicheng R; Schwer, Beate; Shuman, Stewart (2011) Determinants of Nam8-dependent splicing of meiotic pre-mRNAs. Nucleic Acids Res 39:3427-45
Schwer, Beate; Shuman, Stewart (2011) Deciphering the RNA polymerase II CTD code in fission yeast. Mol Cell 43:311-8
Ghosh, Agnidipta; Shuman, Stewart; Lima, Christopher D (2011) Structural insights to how mammalian capping enzyme reads the CTD code. Mol Cell 43:299-310
Qiu, Zhicheng R; Schwer, Beate; Shuman, Stewart (2011) Defining the Mer1 and Nam8 meiotic splicing regulons by cDNA rescue. RNA 17:1648-54

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