Research Summary

RNase P in Archaea

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 an RNA (not protein) enzyme. 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. RNase P is an attractive target for the development of novel antimicrobials; RNase P is a large essential ribonucleoprotein, much like the ribosome, which is the target for a wide range of natural and synthetic antibiotics. It is also highly conserved in Bacteria, so that an inhibitor might be effective against a wide range of pathogens, but very different in eukaryotes (both in the nucleus and mitochondrion), so that an inhibitor of the bacterial enzyme is unlikely to be toxic to humans.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. 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.

Although the RNA subunits of archaeal RNase P RNAs are generally like those of Bacteria, those of Methanococcus and Archaeoglobus are unique; they lack all of the regions of the RNA known to be involved in substrate recognition other than at the cleavage site.Our hypothesis is that a protein or proteins have replaced the substrate recognition functions of the RNA. Identification of protein(s) replacing the absent substrate binding sites in these RNAs would be the first clear case of the evolutionary replacement of a specific RNA structure and function by protein, an important proof of principle for any viable RNA World hypothesis.

A more extreme case is that of the RNase P RNA of Pyrobaculum, in which the entire S-domain is apparently absent. These RNAs contain the entire catalytic domain, and everything known to be essential for substrate recognition, but are nevertheless not acitive in the absence of protein. Pre-tRNA processing may be quite unusual in this organisms; most tRNAs would be predicted to contain only 1-3nt leader sequences. Transfer RNA processing, and RNase P's role in this, is entirely unexplored in this organism.

What to know more? Go through the RNase P in Archaea Webinar.

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. Historically, the RNase P Database has been updated continuously as new sequences became available - it is currently a bit behind as I reconfigure the site to function as a true searchable database using rnaml as the main data format.

Want to know more? Visit the RNase P Database.

RNA Structure Alignment Ontology

Multiple sequence alignments are powerful tools for understanding the structures, functions, and evolutionary histories of linear biological macromolecules (DNA, RNA, and proteins), and for finding homologues in genomic sequences. Multiple sequence alignments are usually shown as two-dimensional matrices, with rows representing individual sequences and columns identifying structurally similar (presumably homologous) residues from different sequences. In accommodating the rapidly growing number of new sequences that are becoming available through high-throughput genomic sequencing, traditional two-dimensional alignments rapidly become unmanageable due to vertical and horizontal expansion. In parallel with large-scale sequencing efforts, progress in structural biology is contributing detailed secondary structures, and atomic-resolution 3D structures of representative molecules of important families of biological molecules. Structural data increase tremendously in value when associated with corresponding multiple sequence alignments. The resolution of alignments in turn increases when 3D data is utilized to establish structural similarity. Solving the expansion and data integration problems requires explicitly stating the fundamental meaning of each portion of the alignment. In short, what is required is an ontology of RNA alignments. The purpose of this ontology is two-fold: first to enable the development of new representations of RNA data and software tools to resolve the expansion problems with current RNA sequence alignments; second, to facilitate the integration of sequence data with secondary and 3D structural as well as other experimental information to create more accurate alignments.

Want to know more? Go through the RNA Alignment Ontology webinar, or visit the RNAML or RNA Ontology Consortium web sites.

BioEdit

BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP.  An intuitive multiple document interface with convenient features  makes alignment and manipulation  of sequences relatively easy on your desktop computer. Several sequence manipulation and analysis options and links to external anaylsis programs facilitate a working environment which allows you to view and manipulate sequences with simple point-and-click operations. BioEdit was written by Tom Hall while he was a Ph.D. stduent in the Brown lab, and although he is now at Ibis Therapeutics, he continiues to maintain BioEdit to some extent. BioEdit is available at no charge, and has become the non-commercial sequence alignment editor of choice for PC users all over the world.

Want to know more? Go to the BioEdit Home Page.