The long term objective of this grant proposal is to gain a greater understanding of the catalytic role of ribosomal RNA in protein synthesis. Particular functions have already been assigned to many regions of both 16S and 23S rRNAs in E. coli.
The aim of this project is to define these regions in greater detail, deciphering both the higher order structure and function, by utilizing a combination of powerful genetic, biochemical, biophysical and phylogenetic techniques. The recent discovery of a conformational switch in 16S rRNA affecting the mRNA pathway in the decoding region demonstrates the remarkable, dynamic nature of the ribosome. This encourages one to look for additional evidence of interactive relationships between different regions of rRNA within the subunits and between the subunits. The primary approach will involve rRNA mutagenesis of a plasmid-borne rrnB operon. Different host strains and plasmid vectors are available to permit even lethal mutations to be expressed. The technique of second site suppressor mutagenesis (or accelerated evolution) will be utilized to identify essential nucleotides comprising functional motifs and uncover more distant contacts representative of dynamic interactions. Sites of covariation and base triples identified by phylogenetic analysis will be mutagenized to further define three-dimensional structures such as the peptidyl transferase region. It is anticipated that these studies will further our understanding of the functional role of rRNA during all steps of translation (decoding, peptide bond formation and translocation) as they reveal the complex nature of the higher order structure and the multitude of dynamic processes which together define protein synthesis.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM019756-27
Application #
2770878
Study Section
Physiological Chemistry Study Section (PC)
Project Start
1975-09-01
Project End
2001-08-31
Budget Start
1998-09-01
Budget End
1999-08-31
Support Year
27
Fiscal Year
1998
Total Cost
Indirect Cost
Name
Brown University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
001785542
City
Providence
State
RI
Country
United States
Zip Code
02912
Carr, Jennifer F; Danziger, Michael E; Huang, Athena L et al. (2015) Engineering the genome of Thermus thermophilus using a counterselectable marker. J Bacteriol 197:1135-44
Carr, Jennifer F; Gregory, Steven T; Dahlberg, Albert E (2015) Transposon mutagenesis of the extremely thermophilic bacterium Thermus thermophilus HB27. Extremophiles 19:221-8
Demirci, Hasan; Murphy 4th, Frank V; Murphy, Eileen L et al. (2014) Structural analysis of base substitutions in Thermus thermophilus 16S rRNA conferring streptomycin resistance. Antimicrob Agents Chemother 58:4308-17
Demirci, Hasan; Murphy 4th, Frank; Murphy, Eileen et al. (2013) A structural basis for streptomycin-induced misreading of the genetic code. Nat Commun 4:1355
Demirci, Hasan; Wang, Leyi; Murphy 4th, Frank V et al. (2013) The central role of protein S12 in organizing the structure of the decoding site of the ribosome. RNA 19:1791-801
Demirci, Hasan; Sierra, Raymond G; Laksmono, Hartawan et al. (2013) Serial femtosecond X-ray diffraction of 30S ribosomal subunit microcrystals in liquid suspension at ambient temperature using an X-ray free-electron laser. Acta Crystallogr Sect F Struct Biol Cryst Commun 69:1066-9
Cantara, William A; Murphy 4th, Frank V; Demirci, Hasan et al. (2013) Expanded use of sense codons is regulated by modified cytidines in tRNA. Proc Natl Acad Sci U S A 110:10964-9
Monshupanee, Tanakarn; Johansen, Shanna K; Dahlberg, Albert E et al. (2012) Capreomycin susceptibility is increased by TlyA-directed 2'-O-methylation on both ribosomal subunits. Mol Microbiol 85:1194-203
Demirci, Hasan; Murphy 4th, Frank; Belardinelli, Riccardo et al. (2010) Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function. RNA 16:2319-24
Demirci, Hasan; Larsen, Line H G; Hansen, Trine et al. (2010) Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus. RNA 16:1584-96

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