Molecular Genetics

Termination of transcripts at some specific sites requires participation of a protein factor.

Facts

• E. coli lysogenized by lambda phage makes a small lambda RNA.
• In vitro, E. coli RNA polymerase holoenzyme transcribes lambda DNA into a very long RNA.
• The ability of the in vitro reaction to make natural length lambda RNA is restored by the addition of a protein factor, called rho (r) (ref).
• Consensus analysis of termination sites dependent on rho reveals a stem loop structure near the 3' end of the RNA. No U-rich stretch is present.
• Rho binds RNA and can, if provided ATP (which it hydrolyzes), move along the RNA.
• Rho is an ATP-dependent helicase (ref). It works on RNA-RNA and RNA-DNA duplexes.
• Rho can not melt completely double-stranded RNA. It requires a region of about 80 nt of single-stranded RNA to bind and unwinds the rest.

Interpretations

• A model consistent with the data is that rho binds to the nascent RNA at a region devoid of secondary structure. It hydrolyzes ATP and moves 5' to 3', trying to catch up with the RNA polymerase. When polymerase pauses, which happens when secondary structures form near the 3' end of the nascent RNA, rho catches up and melts the RNA-DNA duplex in the replication bubble, causing termination.
• RNA secondary structure plays two roles in rho-dependent termination: it prevents rho from binding the RNA; it causes RNA polymerase to pause during transcription.

Further information

• Transcription termination, in some cases, is rho-independent.
• Termination of transcription can serve a role in regulating gene expression in procaryotes.
• The consensus approach aided in the deduction of features defining terminator sequences (ref).
• Precise mechanisms of termination are still being explored.
• Synthesis of the rho protein is controlled by rho controlling the synthesis of its own full length mRNA (ref).

This is page 2232 of Molecular Genetics by Ulrich Melcher, © 1997, 1998, 2000, 2003