Editing Rho factor

{{Short description|Prokaryotic protein}}
{{Infobox nonhuman protein
|image=PDB 1pv4 EBI.jpg|caption=Rho factor homohexamer
|UniProt=P0AG30|Symbol=rho
|Name=Transcription termination factor Rho
|Organism=E. coli
}}
{{Infobox protein family
|Name=Transcription termination factor Rho
|Symbol=Term_rho
|InterPro=IPR004665
}}
A '''ρ factor''' ('''Rho factor''') is a [[bacterial]] [[protein]] involved in the [[termination factor|termination]] of [[Transcription (genetics)|transcription]].<ref name="pmid33243850">{{cite journal | vauthors = Said N, Hilal T, Sunday ND, Khatri A, Bürger J, Mielke T, Belogurov GA, Loll B, Sen R, Artsimovitch I, Wahl MC | display-authors = 6 | title = Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase ρ | journal = Science | volume = 371 | issue = 6524 | date = January 2021 | pmid = 33243850 | doi = 10.1126/science.abd1673 | pmc = 7864586 | hdl = 21.11116/0000-0007-AD1D-7 | hdl-access = free }}
* {{cite web |author=Emily Caldwell |date=November 26, 2020 |title=Study revealing the secret behind a key cellular process refutes biology textbooks |website=Phys.org |url=https://phys.org/news/2020-11-revealing-secret-key-cellular-refutes.html}}</ref> Rho factor binds to the transcription terminator pause site, an exposed region of single stranded RNA (a stretch of 72 nucleotides) after the [[open reading frame]] at C-rich/G-poor sequences that lack obvious secondary structure.<ref name="foster">{{cite book | vauthors = Slonczewski J, Foster JW | title = Microbiology: An Evolving Science | location = New York | publisher = W.W. Norton &, Incorporated | date = 2009 | isbn = 978-0-393-11332-7 }}</ref>

Rho factor is an essential transcription protein in bacteria.<ref>{{cite journal | vauthors = Pradeepkiran JA, Kumar KK, Kumar YN, Bhaskar M | title = Modeling, molecular dynamics, and docking assessment of transcription factor rho: a potential drug target in Brucella melitensis 16M | journal = Drug Design, Development and Therapy | volume = 9 | pages = 1897–912 | date = 2015 | pmid = 25848225 | pmc = 4386771 | doi = 10.2147/DDDT.S77020 | doi-access = free }}</ref> In ''[[Escherichia coli]]'', it is a ~274.6 kD hexamer of identical subunits. Each subunit has an RNA-binding domain and an [[adenosine triphosphate|ATP]]-[[hydrolysis]] domain. Rho is a member of the RecA/SF5 family of ATP-dependent hexameric [[helicase]]s that function by wrapping nucleic acids around a single cleft extending around the entire hexamer. Rho functions as an ancillary factor for [[RNA polymerase]].

There are two types of transcriptional termination in bacteria, rho-dependent termination and [[intrinsic termination]] (also called Rho-independent termination). Rho-dependent terminators account for about half of the ''E. coli'' factor-dependent terminators. Other termination factors discovered in ''E. coli'' include [[Replication terminator Tus family|Tau/Ter/Tus]] and nusA. Rho-dependent terminators were first discovered in [[bacteriophage]] genomes.

== Function ==

A Rho factor acts on an 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]], called the [[Rho utilisation site|'''r'''ho '''ut'''ilisation site]] ('''rut'''), 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. RNA polymerase pauses at the termination sequence, which is because there is a specific site around 100 nt away from the Rho binding site called the Rho-sensitive pause site. So, even though the RNA polymerase is about 40 nt per second faster than Rho, it does not pose a problem for the Rho termination mechanism as the RNA polymerase allows Rho factor to catch up.{{Citation needed|date=July 2019}}

In short, Rho factor acts as an ATP-dependent unwinding enzyme, moving along the newly forming RNA molecule towards its [[Directionality (molecular biology)|3′ end]] and unwinding it from the DNA template as it proceeds.{{cn|date=December 2022}}

== Mutations ==

A [[nonsense mutation]] in one gene of an [[operon]] prevents the translation of subsequent genes in the unit. This effect is called mutational polarity. A common cause is the absence of the [[messenger RNA|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.{{Citation needed|date=July 2019}}

== Evolution ==
Rho factor has not been found in [[Archaea]].<ref>{{cite journal|title=Factor-dependent archaeal transcription termination|journal=PNAS|author1=Julie E. Walker |author2=Olivia Luyties |author3=Thomas J. Santangelo |volume=114|number=33|doi=10.1073/pnas.1704028114|date=July 31, 2017|pages=E6767–E6773 |pmid=28760969 |pmc=5565431 |bibcode=2017PNAS..114E6767W |quote=have not identified any obvious homologs of the well-characterized bacterial termination factors rho|doi-access=free }}</ref>

== See also ==
* [[Termination factor]]
* [[Mutation Frequency Decline]] (Mfd) protein is also capable of dissociating RNA polymerase from the DNA template

== References ==
{{Reflist}}

== External links ==
* {{MeshName|Rho+Factor}}
{{Escherichia coli}}
{{Transcription factors|g0}}
{{Transcription}}

[[Category:Bacterial proteins]]
[[Category:Escherichia coli]]
[[Category:Gene expression]]
[[Category:Helicases]]