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Small cytoplasmic RNA (scRNA) is a member of an evolutionarily conserved signal-recognition-particle-like RNA family. Using a DNA fragment of Bacillus subtilis scRNA gene as a probe, we cloned and characterized a Clostridium perfringens gene encoding the scRNA. Mapping the 5' and 3' ends of scRNA revealed that C. perfringens scRNA consists of 269 nucleotides: the sequence has about 70% primary sequence homology with B. subtilis scRNA. The predicted secondary structure appeared to be similar to that of B. subtilis scRNA, indicating that there are domains I and II in C. perfringens scRNA, in addition to domain IV. Functional analysis showed that C. perfringens scRNA could compensate for vegetative growth and allow the formation of heat-resistant spores in an scRNA-depleted B. subtilis strain, whereas Escherichia coli 4.5S RNA could not maintain sporulation. Since both E. coli 4.5S RNA and C. perfringens scRNA have the same binding specificity to B. subtilis Ffh protein, the difference in complementation activity reflects the function of domains I and II.

Small cytoplasmic RNA (scRNA) gene from Clostridium perfringens can replace the gene for the Bacillus subtilis scRNA in both growth and sporulation