Further Perspective on the Catalytic Core and Secondary Structure of Ribonuclease P RNA

• Published in: Proceedings of the National Academy of Sciences - PNAS 1994-03, Vol.91 (7), p.2527-2531
• Main Authors: Haas, Elizabeth S., Brown, James W., Pitulle, Christian, Pace, Norman R.
• Format: Article
• Language: English
• Subjects: Bacteria; Bacteriology; Bacteroides; Bacteroides thetaiotaomicron; Base Sequence; Biochemistry; Biological and medical sciences; Catalysis; Chlorobium; Chlorobium limicola; Chlorobium tepidum; Cloning, Molecular; DNA; Endoribonucleases - chemistry; Endoribonucleases - genetics; Endoribonucleases - metabolism; Escherichia coli; Escherichia coli Proteins; Flavobacterium; Fundamental and applied biological sciences. Psychology; Genes; Genes, Bacterial; Genomics; Kinetics; Metabolism. Enzymes; Microbiology; Molecular Sequence Data; Nucleic Acid Conformation; Nucleic acids; Nucleotides; Plasmids; Ribonuclease P; Ribonucleic acid; RNA; RNA, Bacterial - chemistry; RNA, Bacterial - genetics; RNA, Catalytic - chemistry; RNA, Catalytic - genetics; RNA, Catalytic - metabolism; Sequence Homology, Nucleic Acid; Structural members
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.91.7.2527

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.