Recognition of Prokaryotic Promoters and Role of S-Factors

In prokaryotic RNA polymerases, the σ-factor is required for promoter recognition and binding. It is loosely bound to the core complex and released after the nascent RNA chain becomes 8–9 nucleotides long. The core polymerase with σ-factor has a high affinity for nonspecificDNA. The σ-factor alters the conformation of the holoenzyme so that its affinity for nonspecificDNAis reduced and the specific binding affinity for the promoter is significantly enhanced.

More than one type of σ-factor is present in E. coli, and more such factors are present in other bacteria. These different factors may have specialized functions in altered growth conditions, cause a global change in transcriptional initiation due to their recognition of distinct —35 and —10 sequence elements, and have a preference for different promoters.

RNA chain termination in bacteria occurs by two mechanisms, one with assistance of a protein factor rho (ρ) and the other without need of a protein. In both cases, termination occurs at a specific terminator sequence in the gene, at which the RNA polymerase stops adding nucleotides to the growing RNA chain, which is then released from the template. The terminator sequence often has a “hairpin” structure which results from intramolecular base pairing in a palindromic sequence. It is likely that such hairpins at the end of RNApromote its dissociation from DNA. Termination can be prevented by an anti-terminator protein, which allows the polymerase to ignore the terminator signal.

A unique distinction between prokaryotic and eukaryoticRNAsynthesis is the temporal relationship between its synthesis and utilization in information transfer. Prokaryotic transcription of mRNA is linked to its reading on the ribosome for protein synthesis. Thus, even before transcription is terminated, the 5´ terminal region of the nascentmRNAis complexed with a ribosome for initiation and propagation of protein synthesis. In the case of eukaryotes, transcription occurs in the nucleus, from which the RNA has to be transported to the endoplasmic reticulum with ribosomes in the cytoplasm. Two sequence motifs that are common constituents of promoters in prokaryotic genomes and are nominally referred to as −35 and −10 sequences signify that the midpoint of these sequences are located 35 and 10 bp 5´ of the start site of transcription. However, the exact distance is somewhat variable for different genes. The consensus −35 sequence is TTGACA, and the consensus of −10 is TATAAT. However, both of the sequences are also somewhat variable. The strength of a promoter, i.e., how efficiently it is recognized for transcriptional initiation, depends on the exact sequence of the −35 and −10 sequences and possibly the intervening “spacer” sequences as well. The promoter strength can vary widely among genes, and mutations in the −35 or −10 sequence in a particular gene can dramatically affect its promoter strength.