Editing Reverse transcriptase (section)

===Process of reverse transcription or retrotranscription===
Reverse transcriptase creates double-stranded DNA from an RNA template.

In virus species with reverse transcriptase lacking DNA-dependent DNA polymerase activity, creation of double-stranded DNA can possibly be done by host-encoded [[DNA polymerase δ]], mistaking the viral DNA-RNA for a primer and synthesizing a double-stranded DNA by a similar mechanism as in [[Primer (molecular biology)#Primer removal|primer removal]], where the newly synthesized DNA displaces the original RNA template.{{citation needed|date=June 2022}}

The process of reverse transcription, also called retrotranscription or retrotras, is extremely error-prone, and it is during this step that mutations may occur. Such mutations may cause [[Resistance to antiviral drugs|drug resistance]].{{cn|date=November 2024}}

==== Retroviral reverse transcription ====
[[Image:Reverse transcription.svg|thumb|300px|Mechanism of reverse transcription in HIV. Step numbers will not match up.]]
[[Retroviruses]], also referred to as class VI [[ssRNA-RT]] viruses, are RNA reverse-transcribing viruses with a DNA intermediate. Their genomes consist of two molecules of [[sense (molecular biology)#RNA sense in viruses|positive-sense]] single-stranded RNA with a [[5' cap]] and [[Polyadenylation|3' polyadenylated tail]]. Examples of retroviruses include the human immunodeficiency virus ([[HIV]]) and the human T-lymphotropic virus ([[HTLV]]). Creation of double-stranded DNA occurs in the [[cytosol]]<ref>[http://www.bio-medicine.org/biology-definition/Retrovirus/ Bio-Medicine.org - Retrovirus] Retrieved on 17 Feb, 2009</ref> as a series of these steps:
# [[lysidine (nucleoside)|Lysyl]] [[tRNA]] acts as a primer and hybridizes to a complementary part of the virus RNA genome called the primer binding site or PBS.
# Reverse transcriptase then adds DNA nucleotides onto the 3' end of the primer, synthesizing [[complementary DNA|DNA complementary]] to the U5 (non-coding region) and R region (a direct repeat found at both ends of the RNA molecule) of the viral RNA.
# A domain on the reverse transcriptase enzyme called [[RNAse H]] degrades the U5 and R regions on the 5' end of the RNA.
# The tRNA primer then "jumps" to the 3' end of the viral genome, and the newly synthesised DNA strands hybridizes to the complementary R region on the RNA.
# The complementary DNA (cDNA) added in (2) is further extended.
# The majority of viral RNA is degraded by RNAse H, leaving only the PP sequence.
# Synthesis of the second DNA strand begins, using the remaining PP fragment of viral RNA as a primer.
# The tRNA primer leaves and a "jump" happens. The PBS from the second strand hybridizes with the complementary PBS on the first strand.
# Both strands are extended to form a complete double-stranded DNA copy of the original viral RNA genome, which can then be incorporated into the host's genome by the enzyme [[integrase]].

Creation of double-stranded DNA also involves ''strand transfer'', in which there is a translocation of short DNA product from initial RNA-dependent DNA synthesis to acceptor template regions at the other end of the genome, which are later reached and processed by the reverse transcriptase for its DNA-dependent DNA activity.<ref>{{cite book |vauthors = Telesnitsky A, Goff SP | veditors = Skalka MA, Goff SP | title = Reverse transcriptase| edition = 1st | publisher = Cold Spring Harbor| location = New York | year = 1993 | chapter =  Strong-stop strand transfer during reverse transcription | page = 49| isbn =978-0-87969-382-4 }}</ref>

Retroviral RNA is arranged in 5' terminus to 3' terminus. The site where the [[primer (molecular biology)|primer]] is annealed to viral RNA is called the primer-binding site (PBS). The RNA 5'end to the PBS site is called U5, and the RNA 3' end to the PBS is called the leader. The tRNA primer is unwound between 14 and 22 [[nucleotides]] and forms a base-paired duplex with the viral RNA at PBS. The fact that the PBS is located near the 5' terminus of viral RNA is unusual because reverse transcriptase synthesize DNA from 3' end of the primer in the 5' to 3'  direction (with respect to the newly synthesized DNA strand). Therefore, the primer and reverse transcriptase must be relocated to 3' end of viral RNA. In order to accomplish this reposition, multiple steps and various enzymes including [[DNA polymerase]], ribonuclease H(RNase H) and polynucleotide unwinding are needed.<ref name="isbn0-87969-167-0">{{cite book |vauthors = Bernstein A, Weiss R, Tooze J | title = Molecular Biology of Tumor Viruses | edition = 2nd| publisher = Cold Spring Harbor Laboratory | location = Cold Spring Harbor, N.Y. | year = 1985 | chapter =  RNA tumor viruses }}</ref><ref name="MoellingBroecker2015">{{cite journal | vauthors = Moelling K, Broecker F | title = The reverse transcriptase-RNase H: from viruses to antiviral defense | journal = Annals of the New York Academy of Sciences | volume = 1341 | issue =  1| pages = 126–35 | date = April 2015 | pmid = 25703292 | doi = 10.1111/nyas.12668 | bibcode = 2015NYASA1341..126M | s2cid = 42378727 }}</ref>

The HIV reverse transcriptase also has [[ribonuclease]] activity that degrades the viral RNA during the synthesis of cDNA, as well as [[DNA-dependent DNA polymerase]] activity that copies the [[Sense (molecular biology)|sense]] cDNA strand into an ''antisense'' DNA to form a double-stranded viral DNA intermediate (vDNA).<ref>{{cite web | first = Gary E. | last = Kaiser | name-list-style = vanc | url = http://student.ccbcmd.edu/courses/bio141/lecguide/unit3/viruses/hivlc.html | work = Doc Kaiser's Microbiology Home Page | title = The Life Cycle of HIV | archive-url = https://web.archive.org/web/20100726222939/http://student.ccbcmd.edu/courses/bio141/lecguide/unit3/viruses/hivlc.html | archive-date = 2010-07-26 | url-status = dead | publisher = Community College of Baltimore Count | date = January 2008 }}</ref> The HIV viral RNA structural elements regulate the progression of reverse transcription.<ref name="pmid32916568">{{cite journal | vauthors = Krupkin M, Jackson LN, Ha B, Puglisi EV | title = Advances in understanding the initiation of HIV-1 reverse transcription | journal = Curr Opin Struct Biol | volume = 65 | pages = 175–183 | date = Dec 2020 | pmid = 32916568 | doi = 10.1016/j.sbi.2020.07.005 | pmc = 9973426 | s2cid = 221636459 }}</ref>