Identification of the genes encoding Mn2+-dependent RNase I-III and Mg2+-dependent RNase HIII from Bacillus subtilis: Classification of RNases H intothree families

Database searches indicated that the genome of Bacillus subtilis contains t hree different genes encoding RNase H homologues. The ypdQ gene encodes an RNase HI homologue with 132 amino acid residues, whereas the rnh and ysgB g enes encode RNase HII homologues with 255 and 313 amino acid residues, resp ectively. RNases HI and HII show no significant sequence similarity. These genes were individually expressed in Escherichia coli; the recombinant prot eins were purified, and their enzymatic properties were compared with those of E. coli RNases HI and HII. We found that the ypdQ gene product showed n o RNase H activity. The 2.2 kb pair genomic DNA containing this gene did no t suppress the RNase H deficiency of an E, coli rnhA mutant, indicating tha t this gene product shows no RNase H activity in vivo as well. In contrast, the rnh (rnhB) gene product (RNase HII) showed a preference for Mn2+, as d id E. coli RNase HII, whereas the ysgB (mhC) gene product (RNase HIII) exhi bited a Mg2+-dependent RNase H activity. Oligomeric substrates digested wit h these enzymes indicate similar recognition of these substrates by B. subt ilis and E. coli RNases HII. Likewise, B. subtilis RNase HIII and E. coli R Nase HI have generated similar products. These results suggest that B. subt ilis RNases HII and HIII may be functionally similar to E, coli RNases HII and HI, respectively. We propose that Mn2+-dependent RNase HII is universal ly present in various organisms and Mg2+-dependent RNase HIII, which may ha ve evolved from RNase HII, functions as a substitute for RNase HI.