Transcription in Prokaryotes

Transcription is a highly regulated process that converts genetic information into RNA molecules. The transcription cycle is divided into three key stages: initiation, elongation, and termination, each driven by specific molecular mechanisms.

Initiation of Transcription

In bacteria, transcription begins when the RNA polymerase core enzyme associates with a sigma factor to form a holoenzyme. For example, the E. coli sigma factor called σ70 forms a holoenzyme, which recognizes the -10 (Pribnow box) and -35 regions upstream of the transcription start site. When binding to the promoter, the RNA polymerase holoenzyme can position on the DNA correctly, and localized unwinding at the -10 region exposes the template strand. Once a few nucleotides are incorporated into the nascent RNA, the sigma factor dissociates, leaving the core RNA polymerase to proceed with elongation.

In archaea, the process is mediated by a TATA-binding protein (TBP), which binds to the TATA box, and transcription factor B (TFB), which recognizes the B recognition element (BRE). These factors recruit RNA polymerase to the transcription initiation site in a manner reminiscent of eukaryotic transcription initiation.

Elongation of the RNA Strand

During elongation, the RNA polymerase synthesizes RNA in the 5' to 3' direction by adding ribonucleotides complementary to the DNA template strand. The polymerase moves along the DNA, unwinding it ahead of the transcription bubble and rewinding it behind, ensuring continuous RNA synthesis.

Termination Mechanisms

Transcription termination in bacteria involves two primary mechanisms. In intrinsic termination, the RNA transcript forms a stem-loop structure followed by a series of uracil residues, destabilizing the RNA-DNA hybrid and causing RNA polymerase to dissociate. Alternatively, Rho-dependent termination involves the Rho protein, which binds to specific RNA sequences and moves along the transcript to displace RNA polymerase.

In archaea, termination is generally intrinsic, relying on stem-loop structures in the RNA transcript to release the RNA polymerase. Unlike bacterial Rho-dependent termination, archaeal transcription does not involve additional protein factors.