Question

Why does the promoter efficiency tend to decrease with the number of G-C base pairs in the -10 region of a prokaryotic gene?

Answer 1

The promoter is a consensus and evolutionarily conserved sequence of DNA found upstream the start codon in a gene. The consensus sequence is highly specific in nature and the extent of its conservation is extremely important in nature. The RNA polymerase identifies these upstream signals in the DNA which tend to be sensitive as close as a single nucleotide. Hence, a change in sequence of these upstream regulators by a single codon will lead to failure of binding of RNA polymerase or loosening of binding. Comparative studies have shown that these upstream regulator sequences largely contain patches of nucleotides such as TATA box, poly-GC sequences etc. Further, the strength of binding of the RNA polymerase then depends upon the number and conservation of these sequences i.e. TATA box and GC base pairs upstream the start site. Consequently, any sequential change in these sequences will be detrimental for the gene expression since the binding of sigma factor as well as RNA polymerase would be highly compromised in nature as these molecular entities will fail to identify the consensus sequences.

This is why mutational changes in the upstream regulators are highly detrimental for gene expression both in prokaryotes and eukaryotes.