Rho factor

A ρ factor (rho factor) is a protein found in prokaryotes, especially E. coli, involved in the termination of transcription. This is done by dissociating the ternary transcription complex at the termination of a gene.

Transcription 

Transcription involves synthesis of an RNA chain representing one strand of a DNA duplex. By "representing" we mean that the RNA is identical in sequence with one strand of the DNA, which is called the coding strand. It is complementary to the other strand, which provides the template strand for RNA synthesis.

RNA synthesis is catalyzed by the enzyme RNA polymerase. Transcription starts when RNA polymerase binds to a special region, the promoter, at the start of the gene. The promoter surrounds the first base pair that is transcribed into RNA, the startpoint. From this point, RNA polymerase moves along the template, synthesizing RNA, until it reaches a terminator sequence. This action defines a transcription unit that extends from the promoter to the terminator.

Once RNA polymerase has started transcription, the enzyme moves along the template, synthesizing RNA, until it meets a terminator (t) sequence. At this point, the enzyme stops adding nucleotides to the growing RNA chain, releases the completed product, and dissociates from the DNA template. Termination requires that all hydrogen bonds holding the RNA-DNA hybrid together must be broken, after which the DNA duplex reforms.

Terminators vary widely in their efficiencies of termination. At some terminators, the termination event can be prevented by specific ancillary factors that interact with RNA polymerase. Antitermination causes the enzyme to continue transcription past the terminator sequence, an event called readthrough

Terminators are distinguished in E. coli according to whether RNA polymerase requires any additional factors to terminate in vitro: A core enzyme can terminate in vitro at certain sites in the absence of any other factor. These sites are called intrinsic terminators. Rho-dependent terminators are defined by the need for addition of Rho factor in vitro; and mutations show that the factor is involved in termination in vivo ( Mutations in a ρ factor may cause the RNA polymerase to read through from one operon to the next, creating longer RNA molecules. This is usually lethal to the cell as production of the excess RNA imposes a large metabolic demand on the cell).

Rho factor is an essential protein in E. coli. It functions solely at the stage of termination. In E. coli, it is a ~275 kD hexamer of identical subunits. The 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 acid through the hole in the middle of the hexamer formed from the RNA-binding domains of the subunits. Rho functions as an ancillary factor for RNA polymerase. Rho-dependent terminators account for about half E. coli terminators. They were discovered in phage genomes.

An individual Rho factor acts processively on a single 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 (many such sequences have been discovered. But no consensus is available among these, but the different sequences each seem specific, in that small changes in the sequence does not cause termination). 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 analysed or verified. This is sometimes called the Hot Pursuit Model of Rho Termination.

A nonsense mutation in one gene of a transcription unit (here, an operon; all operons are transcription units, but not vice versa always) prevents the expression (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 ribosomes prevent Rho from reaching RNA polymerase. But a nonsense mutation releases the ribosomes, 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.

Note: In prokaryotes (like E. coli), Since DNA is transcribed (DNA-> RNA) and translated (RNA->protein) simultaneously, RNA is not usually referred to as mRNA. The term mRNA is used in eukaryotes to distinguish it from other types of RNA and also to refer to the fact that RNA produced in nucleus is processed before being sent to cytosol for translation.