Rho factor
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A ρ factor (rho factor) is a prokaryotic protein involved in the termination of transcription.
Rho factor is an essential transcription protein in prokaryotes. In Escherichia coli, it is a ~275 kD hexamer of identical subunits. Each subunit has an RNA-binding domain and an ATP-hydrolysis domain. Rho is a member of the family of ATP-dependent hexameric helicases that function by passing nucleic acids through the hole in the middle of the hexamer. Rho functions as an ancillary factor for RNA polymerase. Rho-dependent terminators account for about half of E. coli terminators. Rho-dependent terminators were first discovered in phage genomes.
A Rho factor acts on a RNA substrate. Rho's key function is its helicase activity, for which energy is provided by an RNA-dependent ATP hydrolysis. The initial binding site for Rho is an extended (~70 nucleotides, sometimes 80-100 nucleotides) single-stranded region, rich in cytosine and poor in guanine, in the RNA being synthesised, upstream of the actual terminator sequence. Several rho binding sequences have been discovered. No consensus is found among these, but the different sequences each seem specific, as small mutations in the sequence disrupts its function. Rho binds to RNA and then uses its ATPase activity to provide the energy to translocate along the RNA until it reaches the RNA-DNA helical region, where it unwinds the hybrid duplex structure. It is thought that the RNA polymerase pauses at the termination sequence, which allows Rho factor to catch up. However, the kinetics are quite complex and have not been fully analyzed or verified.
In short, rho factor acts as an ATP-dependent unwinding enzyme, moving along the newly forming RNA molecule towards its 3' end and unwinding it from the DNA template as it proceeds.
A nonsense mutation in one gene of an operon prevents the translation of subsequent genes in the unit. This effect is called polarity. A common cause is the absence of the mRNA corresponding to the subsequent (distal) parts of the unit. Suppose that there are Rho-dependent terminators within the transcription unit, that is, before the terminator that usually is used. Normally these earlier terminators are not used, because the ribosome prevents Rho from reaching RNA polymerase. But a nonsense mutation releases the ribosome, so that Rho is free to attach to and/or move along the RNA, enabling it to act on RNA polymerase at the terminator. As a result, the enzyme is released, and the distal regions of the transcription unit are never transcribed.
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