Abstract

Posttranscriptionally modified nucleotides in RNA are generally conserved and phylogenetically distinct, although knowledge of distribution and sequence locations is restricted to relatively few organisms. Progress in recent years has begun to unfold the functional roles of modifications, including maintenance of reading frame during protein synthesis, stabilization of RNA secondary and tertiary structure and influence on RNA-protein interactions. We propose to apply techniques based on electrospray ionization mass spectrometry directly combined with liquid chromatography, recently developed in this laboratory to expand knowledge in selected areas concerning the identities and potential functions of RNA modifications. Of particular interest are tRNA modifications resulting from novel biosynthetic pathways, e.g., the action of aminoacyl tRNA synthetase paralogs and modifications which influence amino acid charging of tRNAs. ? ?

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM029812-30
Application #
7047853
Study Section
Special Emphasis Panel (ZRG1-BECM (01))
Program Officer
Edmonds, Charles G
Project Start
1978-05-01
Project End
2007-03-31
Budget Start
2006-04-01
Budget End
2007-03-31
Support Year
30
Fiscal Year
2006
Total Cost
$204,381
Indirect Cost

  Institution

Name
University of Utah
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
009095365
City
Salt Lake City
State
UT
Country
United States
Zip Code
84112

  Publications

Guymon, Rebecca; Pomerantz, Steven C; Ison, J Nicholas et al. (2007) Post-transcriptional modifications in the small subunit ribosomal RNA from Thermotoga maritima, including presence of a novel modified cytidine. RNA 13:396-403
Guymon, Rebecca; Pomerantz, Steven C; Crain, Pamela F et al. (2006) Influence of phylogeny on posttranscriptional modification of rRNA in thermophilic prokaryotes: the complete modification map of 16S rRNA of Thermus thermophilus. Biochemistry 45:4888-99
Del Campo, Mark; Recinos, Claudia; Yanez, Giscard et al. (2005) Number, position, and significance of the pseudouridines in the large subunit ribosomal RNA of Haloarcula marismortui and Deinococcus radiodurans. RNA 11:210-9
Cleary, Michael D; Meiering, Christopher D; Jan, Eric et al. (2005) Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay. Nat Biotechnol 23:232-7
Chen, Peng; Crain, Pamela F; Nasvall, S Joakim et al. (2005) A ""gain of function"" mutation in a protein mediates production of novel modified nucleosides. EMBO J 24:1842-51
Pomerantz, Steven C; McCloskey, James A (2005) Detection of the common RNA nucleoside pseudouridine in mixtures of oligonucleotides by mass spectrometry. Anal Chem 77:4687-97
McCloskey, James A; Rozenski, Jef (2005) The Small Subunit rRNA Modification Database. Nucleic Acids Res 33:D135-8
Zhou, Shaolian; Sitaramaiah, Devarasetty; Noon, Kathleen R et al. (2004) Structures of two new ""minimalist"" modified nucleosides from archaeal tRNA. Bioorg Chem 32:82-91
Zhou, Shaolian; Sitaramaiah, Devarasetty; Pomerantz, Steven C et al. (2004) Tandem mass spectrometry for structure assignments of wye nucleosides from transfer RNA. Nucleosides Nucleotides Nucleic Acids 23:41-50
Douthwaite, Stephen; Crain, Pamela F; Liu, Mingfu et al. (2004) The tylosin-resistance methyltransferase RlmA(II) (TlrB) modifies the N-1 position of 23S rRNA nucleotide G748. J Mol Biol 337:1073-7

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