title: Further perspective on the catalytic core and secondary structure of ribonuclease P RNA.
abstract: Phylogenetic comparative analyses of RNase P RNA-encoding gene sequences from Chlorobium limicola, Chlorobium tepidum, Bacteroides thetaiotaomicron, and Flavobacterium yabuuchiae refine the secondary structure model of the general (eu)bacterial RNase P RNA and show that a highly conserved feature of that RNA is not essential. Two helices, comprised of 2 base pairs each, are added to the secondary structure model and form part of a cruciform in the RNA. Novel sequence variations in the B. thetaiotaomicron and F. yabuuchiae RNA indicate the likelihood that all secondary structure resulting from canonical base-pairing has been detected: there are no remaining unpaired, contiguous, canonical complementarities in the structure model common to all bacterial RNase P RNAs. A nomenclature for the elements of the completed secondary structure model is proposed. The Chlorobium RNase P RNAs lack a stem-loop structure that is otherwise universally present and highly conserved in structure in other (eu)bacterial RNase P RNAs. The Chlorobium RNAs are nevertheless catalytic, with kinetic properties similar to those of RNase P RNAs of Escherichia coli and other Bacteria. Removal of this stem-loop structure from the E. coli RNA affects neither its affinity for nor its catalytic rate for cleavage of a precursor transfer RNA substrate. These results show that this structural element does not play a direct role in substrate binding or catalysis.
authors.affiliation: Department of Biology, Indiana University, Bloomington 47405.
authors.forename: E S
authors.initials: ES
authors.lastname: Haas
authors.forename: J W
authors.initials: JW
authors.lastname: Brown
authors.forename: C
authors.initials: C
authors.lastname: Pitulle
authors.forename: N R
authors.initials: NR
authors.lastname: Pace
mesh_terms: D001419:Bacteria; D001439:Bacteroides; D001483:Base Sequence; D002384:Catalysis; D003001:Cloning, Molecular; D004722:Endoribonucleases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins; D005417:Flavobacterium; D005798:Genes, Bacterial; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D016337:RNA, Catalytic / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D043262:Ribonuclease P; D012689:Sequence Homology, Nucleic Acid
chemical_list: D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; D016337:RNA, Catalytic; D004722:Endoribonucleases; D043262:Ribonuclease P; C470865:ribonuclease P, E coli