Linking enzyme studies to bioinformatics: The genome profile for the
             substrates of an RNA processing enzyme

                           Tao Pan
       Department of Biochemistry and Molecular Biology
                   The University of Chicago
  
Transfer RNAs are adaptors in the translation of a messenger RNA to a
protein. tRNAs are initially transcribed from the DNA genome as a precursor
form: it has extra nucleotides at the 5' and 3' ends. The RNA processing
enzyme ribonuclease P (RNase P) is the only enzyme required to produce the
mature 5' end of all tRNAs through a site-specific endonucleolytic cleavage
reaction. In bacteria, RNase P is composed of a large RNA (P RNA, ~125 kD)
and a small protein (P protein, ~14 kD). The bacterial RNase P comes in two
distinct types (A and B) on the basis of the secondary structure of the P
RNA. Interestingly, a type B RNase P (e.g. from Bacillus subtilis) is a
dimer, i.e. it contains two P RNA and two P protein subunits, whereas a
type A RNase P (e.g. from E. coli) is a monomer, i.e. it contains one P RNA
and one P protein. This structural difference also correlates with the
vastly different tRNA gene organization in these two bacteria. More than
60% of the tRNA genes in Bacillus is organized in specific clusters, an
arrangement completely absent in E. coli. Furthermore in Bacillus, the tRNA
genes present in these clusters code for distinct amino acids compared to
the tRNAs genes that are not in these clusters. I will present the results
of our enzymatic studies on this RNA processing enzyme and discuss how
bioinformatics can be applied to the genome analysis of transfer RNA and
RNase P genes.