RNA-based enzymes play key roles in a wide range of cellular processes, from RNA processing to splicing to translation. While RNA is their catalytic moiety, cellular RNA-based enzymes are ribonucleoproteins (RNPs). The structural and functional roles of proteins and RNA-protein interactions in RNA-based enzymes and RNPs in general are poorly understood. This proposal focuses on S. cerevisiae Ribonuclease (RNase) P and the closely related RNase MRP as a biologically significant and effective model to understand the roles of proteins and RNA-protein interactions in the structure, function, and evolution of ribonucleoproteins. RNases P/MRP are a family of essential RNA-based enzymes that have their origin in the bacterial RNase P ribozyme. In addition to its catalytic RNA moiety, RNase P has a single protein in bacteria, but nine essential proteins in yeast;the protein content increases from ~10% in bacteria to more than 75% in eukaryotes. The reasons for the increased reliance on proteins in the eukaryotic RNase P are not understood, and the functions of the proteins themselves are not known. RNase MRP is an essential eukaryotic RNP. Yeast RNase MRP has a 340-nucleotide-long catalytic RNA which resembles the RNA component of RNase P and 10 essential protein components, eight of which are shared with RNase P. The structural organization of RNase MRP and the roles of its components are not clear. The large and complex eukaryotic RNase P and, especially, RNase MRP are understudied;this proposal aims to fill the gap in our understanding of these fundamentally important catalytic RNPs, and expand our understanding of RNA- protein interactions in general.
The specific aims of the proposal are: (1) Characterize respective contributions of proteins and RNA to specificities of RNase P and RNase MRP RNPs;(2) Determine roles of proteins and RNA-protein interactions in the structural organizations of RNases P/MRP and catalysis. We will characterize the RNA-protein interactions in RNases P/MRP using biochemical studies and structural analysis, and clarify the roles of the proteins in RNases P/MRP.

Public Health Relevance

to Public Health RNases P/MRP are RNA-based enzymes that are required for the survival of eukaryotic cells. Mutations in RNase MRP in humans cause the development of Cartilage Hair Hypoplasia, a severe multi-systemic disorder resulting in dwarfism and immunodeficiency, and a study of RNases P/MRP has a potential to shed a light on the cause of the disease.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM085149-06A1
Application #
8694771
Study Section
Molecular Genetics A Study Section (MGA)
Program Officer
Bender, Michael T
Project Start
2008-08-01
Project End
2018-05-31
Budget Start
2014-07-10
Budget End
2015-05-31
Support Year
6
Fiscal Year
2014
Total Cost
$313,950
Indirect Cost
$103,950
Name
Pennsylvania State University
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
003403953
City
University Park
State
PA
Country
United States
Zip Code
16802
Krasilnikov, Andrey S (2014) Applying UV crosslinking to study RNA-protein interactions in multicomponent ribonucleoprotein complexes. Methods Mol Biol 1086:193-207
Esakova, Olga; Perederina, Anna; Berezin, Igor et al. (2013) Conserved regions of ribonucleoprotein ribonuclease MRP are involved in interactions with its substrate. Nucleic Acids Res 41:7084-91
Khanova, Elena; Esakova, Olga; Perederina, Anna et al. (2012) Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA-protein interactions. RNA 18:720-8
Esakova, Olga; Perederina, Anna; Quan, Chao et al. (2011) Substrate recognition by ribonucleoprotein ribonuclease MRP. RNA 17:356-64
Perederina, Anna; Khanova, Elena; Quan, Chao et al. (2011) Interactions of a Pop5/Rpp1 heterodimer with the catalytic domain of RNase MRP. RNA 17:1922-31
Perederina, Anna; Esakova, Olga; Quan, Chao et al. (2010) Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain. EMBO J 29:761-9
Esakova, Olga; Krasilnikov, Andrey S (2010) Of proteins and RNA: the RNase P/MRP family. RNA 16:1725-47
Lu, Qiaosheng; Wierzbicki, Sara; Krasilnikov, Andrey S et al. (2010) Comparison of mitochondrial and nucleolar RNase MRP reveals identical RNA components with distinct enzymatic activities and protein components. RNA 16:529-37
Perederina, Anna; Esakova, Olga; Quan, Chao et al. (2010) Crystallization and preliminary X-ray diffraction analysis of the P3 RNA domain of yeast ribonuclease MRP in a complex with RNase P/MRP protein components Pop6 and Pop7. Acta Crystallogr Sect F Struct Biol Cryst Commun 66:76-80