COMPARATIVE-ANALYSIS OF FUNCTIONAL AND STRUCTURAL FEATURES IN THE PRIMASE-DEPENDENT PRIMING SIGNALS, G-SITES, FROM PHAGES AND PLASMIDS

The primase-dependent priming signals, G sites, are directly recognize d by the Escherichia coli primase (dnaG gene product) and conduct the synthesis of primer RNAs. In nucleotide sequence and secondary structu re, there is no striking resemblance between the phage- and plasmid de rived G sites, except for the limited sequence homology near the start position of primer RNA synthesis. In this study, we analyzed the stru cture and function of a G site of plasmid R100, G site(R100), and disc overed the necessity of the coexistence of two domains (domains I and III), which contains blocks A, B; and C, which are nucleotide sequence s highly conserved among the plasmid-derived G sites. However, neither the internal region, domain II, between domains I and III nor the pot ential secondary structure proposed by Bahk et al. (J. D. Bahk, N. Kio ka, H. Sakai, and T. Komano, Plasmid 20:266-270, 1988) is essential fo r single-stranded DNA initiation activity. Furthermore, chimeric G sit es constructed between a G site of phage G4, G site(G4), and G site(R1 00) maintained significant single-stranded DNA initiation activities. These results strongly suggest that phage- and plasmid-derived G sites have functionally equivalent domains. The primase-dependent priming m echanisms of phage- and plasmid-derived G sites are discussed.