This proposal deals with the unprecedented phenomenon of mRNA capping in the cytoplasm. The 5' ends of all mRNAs have an m7G `cap', and proteins that bind to the cap direct the processing, translation and fate of every transcript. The prevailing view was that caps could only be added to newly synthesized pre-mRNAs in the nucleus, and loss of the cap leads irreversibly to mRNA decay. In contrast, we identified transcripts that are stable in an uncapped state, identified a cytoplasmic complex of proteins that can restore the cap onto these transcripts, and identified a cyclical process of decapping and recapping termed `cap homeostasis' that maintains a subset of the transcriptome in an actively translating state. The process of cytoplasmic capping involves conversion of the 5'-monophosphate end of uncapped RNA to a 5'-diphosphate and the transfer of GMP from capping enzyme onto this recapping substrate. All of the enzymes needed to catalyze cytoplasmic capping are present in a single complex that assembles on Nck1, a cytoplasmic SH2/SH3 adapter protein that is best known as a transducer of tyrosine kinase signaling. The RNA 5'-kinase and capping enzyme are juxtaposed by binding to adjacent SH3 domains, and the presence of cap methyltransferase in the complex completes the list of proteins that are necessary and sufficient to affect cytoplasmic capping. Cytoplasmic capping targets are not random; they encode proteins involved in nucleotide binding, protein localization, RNA localization, and the mitotic cell cycle. The working hypothesis of this proposal is that cytoplasmic capping is a selective post-transcriptional process that functions as an amplifier of transcriptome and proteome complexity.
In Aim 1 in vitro, in vivo and biochemical biological approaches will be used to characterize the 5'-kinase and its function in cytoplasmic capping. Nck1 has 4 functional domains, and classical and `top-down' proteomics and biochemical approaches will be used to identify and characterize proteins that are bound uniquely to the 1st SH3 domain and SH2 domain in the context of the cytoplasmic capping complex.
Aim 2 will map the 5' ends of recapped transcripts and determine their relationship to internal cap sites identified by Capped Analysis of Gene Expression (CAGE). The resulting datasets will be mined to identify sequence and/or structural motifs that determine the location of recapped 5' ends and their role in determining target specificity.
In Aim 3 ribosome profiling will be combined with positional proteomics to determine the relationship of cytoplasmic capping to translation and proteome complexity. The results will be confirmed by top-down proteomics of selected products from internally capped transcripts, and changes in subcellular distribution will be used as an assay for functional effects of downstream capping on protein diversity. In summary this work will determine the organization of the cytoplasmic capping complex, the location of recapped ends within target transcripts, and the impact of cytoplasmic capping on transcriptome and proteome complexity.

Public Health Relevance

The cycling of messenger RNAs between active and inactive states plays a central role in cell growth and differentiation, and is a process that is hijacked b some viruses to promote infection and spread. A `cap' that is added to the first nucleotide of all messenger RNAs plays a key role in their life cycle, and this work will study a newly identified process that controls the location of the cap, how this is regulated and the impact cap location has on proteins expressed in different cell types.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM084177-07
Application #
9234542
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Bender, Michael T
Project Start
2008-04-01
Project End
2019-03-31
Budget Start
2017-04-01
Budget End
2018-03-31
Support Year
7
Fiscal Year
2017
Total Cost
$355,587
Indirect Cost
$118,303
Name
Ohio State University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
832127323
City
Columbus
State
OH
Country
United States
Zip Code
43210
Kiss, Daniel L; Baez, William; Huebner, Kay et al. (2017) Impact of FHIT loss on the translation of cancer-associated mRNAs. Mol Cancer 16:179
Kiss, Daniel L; Waters, Catherine E; Ouda, Iman M et al. (2017) Identification of Fhit as a post-transcriptional effector of Thymidine Kinase 1 expression. Biochim Biophys Acta 1860:374-382
Trotman, Jackson B; Giltmier, Andrew J; Mukherjee, Chandrama et al. (2017) RNA guanine-7 methyltransferase catalyzes the methylation of cytoplasmically recapped RNAs. Nucleic Acids Res 45:10726-10739
Gu, Shan-Qing; Gallego-Perez, Daniel; McClory, Sean P et al. (2016) The human PMR1 endonuclease stimulates cell motility by down regulating miR-200 family microRNAs. Nucleic Acids Res 44:5811-9
Kiss, Daniel L; Oman, Kenji M; Dougherty, Julie A et al. (2016) Cap homeostasis is independent of poly(A) tail length. Nucleic Acids Res 44:304-14
Kiss, Daniel L; Oman, Kenji; Bundschuh, Ralf et al. (2015) Uncapped 5' ends of mRNAs targeted by cytoplasmic capping map to the vicinity of downstream CAGE tags. FEBS Lett 589:279-84
Mukherjee, Chandrama; Bakthavachalu, Baskar; Schoenberg, Daniel R (2014) The cytoplasmic capping complex assembles on adapter protein nck1 bound to the proline-rich C-terminus of Mammalian capping enzyme. PLoS Biol 12:e1001933
Patil, Deepak P; Bakthavachalu, Baskar; Schoenberg, Daniel R (2014) Poly(A) polymerase-based poly(A) length assay. Methods Mol Biol 1125:13-23
Wein, Nicolas; Vulin, Adeline; Falzarano, Maria S et al. (2014) Translation from a DMD exon 5 IRES results in a functional dystrophin isoform that attenuates dystrophinopathy in humans and mice. Nat Med 20:992-1000
Mascarenhas, Roshan; Dougherty, Julie A; Schoenberg, Daniel R (2013) SMG6 cleavage generates metastable decay intermediates from nonsense-containing ?-globin mRNA. PLoS One 8:e74791

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