title: Footprinting analysis of interactions between the largest eukaryotic RNase P/MRP protein Pop1 and RNase P/MRP RNA components.
abstract: Ribonuclease (RNase) P and RNase MRP are closely related catalytic ribonucleoproteins involved in the metabolism of a wide range of RNA molecules, including tRNA, rRNA, and some mRNAs. The catalytic RNA component of eukaryotic RNase P retains the core elements of the bacterial RNase P ribozyme; however, the peripheral RNA elements responsible for the stabilization of the global architecture are largely absent in the eukaryotic enzyme. At the same time, the protein makeup of eukaryotic RNase P is considerably more complex than that of the bacterial RNase P. RNase MRP, an essential and ubiquitous eukaryotic enzyme, has a structural organization resembling that of eukaryotic RNase P, and the two enzymes share most of their protein components. Here, we present the results of the analysis of interactions between the largest protein component of yeast RNases P/MRP, Pop1, and the RNA moieties of the enzymes, discuss structural implications of the results, and suggest that Pop1 plays the role of a scaffold for the stabilization of the global architecture of eukaryotic RNase P RNA, substituting for the network of RNA-RNA tertiary interactions that maintain the global RNA structure in bacterial RNase P.
authors.affiliation: Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Fagerlund
authors.affiliation: Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Perederina
authors.affiliation: Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Igor
authors.initials: I
authors.lastname: Berezin
authors.affiliation: Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Andrey S
authors.initials: AS
authors.lastname: Krasilnikov
mesh_terms: D004722:Endoribonucleases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D023302:Protein Footprinting / Q000379:methods*; D016337:RNA, Catalytic / Q000737:chemistry; D012331:RNA, Fungal / Q000737:chemistry; D043262:Ribonuclease P / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012260:Ribonucleases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012261:Ribonucleoproteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: C089992:POP1 protein, S cerevisiae; C484542:POP4 protein, S cerevisiae; D016337:RNA, Catalytic; D012331:RNA, Fungal; D012261:Ribonucleoproteins; D029701:Saccharomyces cerevisiae Proteins; D004722:Endoribonucleases; D012260:Ribonucleases; C058330:mitochondrial RNA-processing endoribonuclease; D043262:Ribonuclease P
keywords: Pop1; RNA folding; RNase MRP; RNase P; Saccharomyces cerevisiae; ribonucleoprotein