Archaeal RNase P
Ribonuclease P (RNase P) is a ribonuclease, present in all cells, that removes 5' leader sequences from tRNA precursor transcripts. RNase P is composed of an RNA of ca. 400 nucleotides and a single protein in Bacteria or 9-12 proteins in the eukaryotic nucleus. The RNA, rather than any protein, is the catalytic subunit; RNase P is a ribozyme. RNase P and other ribozymes are thought to be remnants of the 'RNA World', a stage in the emergence of life before the evolutionary invention of protein or DNA.
The key to understanding differences between Bacteria and eukaryotes, and the origin of eukaryotic systems generally, are the Archaea. RNase P in Archaea has properties of both the bacterial and eukaryotic forms of this enzyme. We have found that the RNA subunit of archaeal RNase P is remarkably like that of Bacteria, and quite different that that of eukaryotes. However, there are at least 4 proteins associated with this RNA, unlike the single small protein in Bacteria, and these proteins are homologs of 4 of the eukaryotic nuclear RNase P proteins and not that of the Bacteria. An understanding of the proteins and their role in RNase P function in Archaea will provide insight into the origin of both the bacterial and eukaryotic systems.
What to know more? Go through the RNase P in Archaea Webinar.
RNA Structure Alignment Ontology
Multiple sequence alignments are powerful tools for understanding the structures, functions, and evolutionary histories of biological macromolecules. Multiple sequence alignments are traditionally two-dimensional matrices, with rows representing individual sequences and columns identifying corresponding (usually homologous) residues from different sequences. This simple paradym has proven very useful, but severly limits the the kind of information that can be represented in an alignment.
Large alignments of complex RNAs suffer from a variety of weaknesses, but perhaps the most fundamental is that the only element of structure that can be aligned are nucleotides, and every nucleotide must be aligned whether this is meaningful or not. Recognizing that an "alignment" is really the assignment of a relationship between parts of a molecule, we have defined a relationship "Corresponds to" as part of the RNA Ontology that can be assigned to any element of a collection of RNA structures. This relationship is assigned specifically and explicitly, rather than wholesale and implicitly as is the case in traditionl alignments, and applies to nucleotides, basepairs, blocks (collections of nucleotides), and stems (collections of basepairs) in an RNA structure. We are currently implementing these terms in OWL, creating example alignments, and developing an ontology of RNA secondary structure as a basis for ontology-centric RNA structure alignments.
The RNase P Database
The RNase P Database is a web resource compiling RNase P RNA and protein sequences, sequence alignments, secondary structures, 3-dimensional models, and links to taxonomic and sequence data at the NCBI. The data is organized phylogenetically, and secondary structures (the focus of the database) are available in a variety of machine and human readable forms. The RNase P Database has been available on the web since 1994, and before that was provided on paper as "The Book of P" beginning in 1991. The RNase P Database has served as a model for the now-common "cottage industry" databases in the world of RNA research. The database is currently not being updated.
Want to know more? Visit the RNase P Database.