What causes termination of RNA synthesis near the end of a coding sequence in prokaryotic cells?

In prokaryotic cells, the termination of RNA synthesis, specifically in protein-coding genes, is primarily facilitated by a specific DNA sequence called the terminator or termination signal. The termination signal consists of two essential elements: the termination site and a downstream sequence known as the rho-independent terminator or intrinsic terminator.

The termination site typically contains an inverted repeat sequence in the DNA template strand, which leads to the formation of an RNA hairpin structure in the nascent RNA molecule. This RNA hairpin structure is followed by a stretch of adenine nucleotides in the RNA molecule. The formation of the RNA hairpin and the adenine-rich stretch destabilizes the RNA-DNA hybrid, causing the RNA polymerase to pause or stall during transcription.

At this point, the RNA polymerase encounters a weak interaction between the nascent RNA and the DNA template strand, leading to the dissociation of the RNA-DNA hybrid. The weak interaction occurs because the RNA hairpin structure destabilizes the RNA polymerase’s grip on the DNA template. As a result, the RNA polymerase is released from the DNA template, terminating RNA synthesis.

This termination mechanism is called rho-independent termination because it does not require the assistance of the rho protein, which is an additional termination factor found in some prokaryotes. Rho protein-dependent termination involves the rho protein binding to the RNA transcript and moving along it, eventually causing the dissociation of the RNA polymerase from the DNA template.

In summary, the presence of specific termination signals in the DNA template leads to the formation of an RNA hairpin structure, destabilizing the RNA-DNA hybrid and ultimately causing the termination of RNA synthesis in prokaryotic cells.