- Rho factor
A ρ factor (rho factor) is a
proteinfound in prokaryotes, especially " E. coli", involved in the termination of transcription. This is done by dissociatingthe ternarytranscription complex at the termination of a gene.
Transcriptioninvolves synthesis of an RNAchain representing one strand of a DNAduplex. By "representing" we mean that the RNAis 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 strandfor RNA synthesis. RNA synthesisis catalyzedby the enzyme RNA polymerase. Transcriptionstarts when RNA polymerasebinds to a special region, the promoter, at the start of the gene. The promotersurrounds the first base pairthat is transcribed into RNA, the start point. From this point, RNA polymerasemoves along the template, synthesizing RNA, until it reaches a terminatorsequence. This action defines a transcription unit that extends from the promoterto the terminator.
RNA polymerasehas started transcription, the enzymemoves along the template, synthesizing RNA, until it meets a terminator(t) sequence. At this point, the enzymestops adding nucleotidesto the growing RNAchain, releases the completed product, and dissociates from the DNA template. Termination requires that all hydrogen bondsholding the RNA-DNA hybrid together must be broken, after which the DNA duplex reforms. Terminatorsvary widely in their efficiencies of termination. At some terminators, the termination event can be prevented by specific ancillary factors that interact with RNA polymerase. Antiterminationcauses the enzyme to continue transcriptionpast 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 enzymecan terminate in vitroat 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 mutationsshow that the factor is involved in termination " in vivo" ( Mutationsin a rho factormay cause the RNA polymerase to read through from one operonto 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 factoris 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 subunithas 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 acidthrough the hole in the middle of the hexamer formed from the RNA-binding domains of the subunits. Rho functions as an ancillary factorfor RNA polymerase. Rho-dependent terminators account for about half E. coli terminators. They were discovered in phage genomes.
Rho factoracts processively on a single RNA substrate. Rho's key function is its helicaseactivity, 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 Cytosineand 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 ATPaseactivity to provide the energy to translocatealong 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 sequencewhich allows Rho factorto catch up. However, the kineticsare quite complex and have not been fully analyzed or verified. This is sometimes called the Hot Pursuit Model of Rho Termination.
nonsense mutationin one gene of a transcription unit (here, an operon; all operonsare transcription units, but not vice versa always) prevents the expression ( translation) of subsequent genesin the unit. This effect is called polarity. A common cause is the absence of the mRNAcorresponding to the subsequent (distal) parts of the unit. Suppose that there are Rho-dependent terminatorswithin the transcriptionunit, that is, before the terminator that usually is used. Normally these earlier terminators are not used, because the ribosomesprevent Rho from reaching RNA polymerase. But a nonsense mutationreleases 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 enzymeis released, and the distal regions of the transcription unit are never transcribed.
prokaryotes(like " E. coli"), Since DNAis transcribed(DNA-> RNA) and translated(RNA-> protein) simultaneously, RNA is not usually referred to as mRNA. The term mRNA is used in eukaryotesto 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 cytosolfor translation.
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