Promoter sites for initiation of transcription in prokaryotes
The binding sites for RNA polymerase enzyme lie within the promoter sequence and may be 41 to 44 base pairs in length in E. coli, where more than 100 promoters have already been sequenced. There is hardly any long conserved sequence over majority of the promoter regions, although short sequences within the promoters are conserved. The start point is a purine in over 90% cases and upstream from this start point is a 6 bp region (TATAAT), which is called Pribnow box and is available in almost all promoters. The conservation of these six bases varies from 45% to 96% as represented by the subscripts in the following sequence (the Pribnow box for lac operon in E. coli is TATGTTG; see next main topic).
The centre of Pribnow ,box lies usually 10 bp upstream and therefore it is sometimes described as -10 sequence (although the actual centre varies from -18 to -12). There is another sequence (T82T84C78A65C54A45) lying -35 bases upstream and is called recognition region. Although details of binding reaction are not known, typical promoters in E. coli use -35 and -10 sequences to be recognized by RNA polymerase (Fig. 32.5). It is obvious thus, that a typical promoter in bacteria has three components : (i) consensus sequence at -10 bp; (ii) consensus sequence at -35 bp, and (iii). start point.
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