title: Structural implications of novel diversity in eucaryal RNase P RNA.
abstract: Previous eucaryotic RNase P RNA secondary structural models have been based on limited diversity, representing only two of the approximately 30 phylogenetic kingdoms of the domain Eucarya. To elucidate a more generally applicable structure, we used biochemical, bioinformatic, and molecular approaches to obtain RNase P RNA sequences from diverse organisms including representatives of six additional kingdoms of eucaryotes. Novel sequences were from acanthamoeba (Acathamoeba castellanii, Balamuthia mandrillaris, Filamoeba nolandi), animals (Caenorhabditis elegans, Drosophila melanogaster), alveolates (Theileria annulata, Babesia bovis), conosids (Dictyostelium discoideum, Physarum polycephalum), trichomonads (Trichomonas vaginalis), microsporidia (Encephalitozoon cuniculi), and diplomonads (Giardia intestinalis). An improved alignment of eucaryal RNase P RNA sequences was assembled and used for statistical and comparative structural analysis. The analysis identifies a conserved core structure of eucaryal RNase P RNA that has been maintained throughout evolution and indicates that covariation in size occurs between some structural elements of the RNA. Eucaryal RNase P RNA contains regions of highly variable length and structure reminiscent of expansion segments found in rRNA. The eucaryal RNA has been remodeled through evolution as a simplified version of the structure found in bacterial and archaeal RNase P RNAs.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Room A3B40, Boulder, CO 80309-0347, USA.
authors.forename: Steven M
authors.initials: SM
authors.lastname: Marquez
authors.forename: J Kirk
authors.initials: JK
authors.lastname: Harris
authors.forename: Scott T
authors.initials: ST
authors.lastname: Kelley
authors.forename: James W
authors.initials: JW
authors.lastname: Brown
authors.forename: Scott C
authors.initials: SC
authors.lastname: Dawson
authors.forename: Elisabeth C
authors.initials: EC
authors.lastname: Roberts
authors.forename: Norman R
authors.initials: NR
authors.lastname: Pace
mesh_terms: D048248:Acanthamoeba castellanii / Q000201:enzymology / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D016384:Consensus Sequence / Q000235:genetics; D030541:Databases, Genetic; D005057:Eukaryotic Cells / Q000145:classification / Q000201:enzymology / Q000378:metabolism*; D019143:Evolution, Molecular; D023281:Genomics; D016829:Giardia lamblia / Q000201:enzymology / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012313:RNA / Q000737:chemistry* / Q000235:genetics* / Q000302:isolation & purification; D043262:Ribonuclease P / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D012313:RNA; D043262:Ribonuclease P