How is Transcription Terminated in Prokaryotes?

In prokaryotes, transcription termination is primarily achieved through two mechanisms: intrinsic termination and rho-dependent termination.

1. Intrinsic Termination: Intrinsic termination is the most common mechanism for transcription termination in prokaryotes. It relies on specific DNA sequences in the transcribed RNA molecule and does not require any additional factors. The termination sequence in the DNA template is usually composed of two key elements:

a. Termination (or stop) codon: This sequence consists of a series of adenine (A) bases followed by a complementary uracil (U) sequence in the mRNA. The stop codon is usually encoded as UAA, UAG, or UGA in the mRNA.

b. Termination hairpin (or stem-loop) structure: Following the stop codon, there is a region in the mRNA sequence that forms a stable hairpin structure due to complementary base pairing. This hairpin structure is formed by a series of inverted repeats, which cause the RNA polymerase to pause and destabilize the transcription complex.

The formation of the termination hairpin structure leads to the dissociation of the mRNA from the DNA template and the release of the RNA polymerase. This occurs because the hairpin structure destabilizes the RNA-DNA hybrid, causing the RNA polymerase to lose its grip on the template DNA.

2. Rho-dependent Termination: Rho-dependent termination is an alternative mechanism that requires the presence of a protein called Rho factor (ρ). The rho gene is located separate from the genes being transcribed. The termination process involves the following steps:

a. Rho factor binding: Rho factor recognizes specific DNA sequences known as rut (rho utilization) sites on the mRNA. The rho protein binds to the rut site in the mRNA molecule.

b. RNA-Rho interaction: As the RNA polymerase synthesizes the mRNA, it encounters the rut site. The rho protein moves along the mRNA in the 5′ to 3′ direction, catching up with the elongating RNA polymerase.

c. Termination: When the RNA polymerase encounters a termination signal, it pauses. At this point, the interaction between the rho factor and the RNA polymerase leads to the termination of transcription. Rho factor possesses helicase activity, which helps unwind the RNA-DNA hybrid, releasing the mRNA transcript from the RNA polymerase and terminating transcription.

It is important to note that while intrinsic termination is a common mechanism employed by prokaryotes, rho-dependent termination is less prevalent and occurs only in specific genes or under certain conditions.

In summary, prokaryotes employ two main mechanisms for transcription termination: intrinsic termination, which relies on specific DNA sequences and the formation of termination hairpin structures, and rho-dependent termination, which requires the involvement of the rho factor protein. These termination mechanisms ensure the proper release of mRNA transcripts and the termination of transcription at appropriate sites in prokaryotic genomes.