Characteristic base sequence patterns of promoter and terminator sites in φX174 and fd phage DNAs

Abstract

In order to elucidate characteristic base sequence patterns of promoter and terminator sites, we investigated the base sequence properties over the entire regions of φX174 and fd nucleotide sequences with an intention of computer matching. The properties investigated here are A+T base distribution, recognition- and firm binding-like sequences, palindromes, symmetrical base sequences and other specific sequences of three to seven bases with low frequency of occurrence. The comparison of the present investigation with in vivo and in vitro experimental data of these phages concludes the rule of transcription that the promoter efficiency, especially of in vitro promoters, is under the influence of the A+ T content in a wide range of about 60 bases around the set of recognition and firm binding sequences and most termination sites are characterized by a homology of the G+C rich palindrome followed by a poly A or T sequence. It is also concluded that the promoter-like sequences overlapping with the palindrome or symmetrical base sequence are much reduced in their promoter efficiency. This rule of promoter and terminator efficiencies may serve to predict possible promoter and terminator loci from a given nucleotide sequence of the prokaryotic type and also provide some insight into the molecular mechanism of both initiation and termination of transcription.