Rho factor 495236 226019988 2008-07-16T13:51:07Z Boghog2 2428506 /* External links */ added group abbreviation to TF navbox template {{Refimprove|date=March 2007}} {{Cleanup|date=March 2007}} {{too many links}} A '''ρ factor''' ('''rho factor''') is a [[protein]] found in [[prokaryotes]], especially '''''[[E. coli]]''''', involved in the [[termination factor|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 [[transcription|transcribed]] into [[RNA]], the start point. From this point, [[RNA polymerase]] moves along the [[template]], [[synthesis|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 factor|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 [[rho 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 [[Adenosine triphosphate|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 analyzed 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]]. ==See also== * [[RNA polymerase]] * [[Transcription (genetics)|Transcription]] * ==External links== * {{MeshName|Rho+Factor}} {{Transcription factors|g0}} [[Category:Proteins]]