Summary: Reverse transcriptase (RNA-dependent DNA polymerase)
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Reverse transcriptase Edit Wikipedia article
(RNA-dependent DNA polymerase)
|SCOPe||1hmv / SUPFAM|
|RNA-directed DNA polymerase|
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / QuickGO|
A reverse transcriptase (RT) is an enzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription. Reverse transcriptases are used by retroviruses to replicate their genomes, by retrotransposon mobile genetic elements to proliferate within the host genome, by eukaryotic cells to extend the telomeres at the ends of their linear chromosomes, and by some non-retroviruses such as the hepatitis B virus, a member of the Hepadnaviridae, which are dsDNA-RT viruses.
Retroviral RT has three sequential biochemical activities: RNA-dependent DNA polymerase activity, ribonuclease H, and DNA-dependent DNA polymerase activity. Collectively, these activities enable the enzyme to convert single-stranded RNA into double-stranded cDNA. In retroviruses and retrotransposons, this cDNA can then integrate into the host genome, from which new RNA copies can be made via host-cell transcription. The same sequence of reactions is widely used in the laboratory to convert RNA to DNA for use in molecular cloning, RNA sequencing, polymerase chain reaction (PCR), or genome analysis.
Reverse transcriptases were discovered by Howard Temin at the University of Wisconsinâ€“Madison in Rous sarcoma virions and independently isolated by David Baltimore in 1970 at MIT from two RNA tumour viruses: murine leukemia virus and again Rous sarcoma virus. For their achievements, they shared the 1975 Nobel Prize in Physiology or Medicine (with Renato Dulbecco).
Well-studied reverse transcriptases include:
- HIV-1 reverse transcriptase from human immunodeficiency virus type 1 ( ) has two subunits, which have respective molecular weights of 66 and 51 kDa.
- M-MLV reverse transcriptase from the Moloney murine leukemia virus is a single 75 kDa monomer.
- AMV reverse transcriptase from the avian myeloblastosis virus also has two subunits, a 63 kDa subunit and a 95 kDa subunit.
- Telomerase reverse transcriptase that maintains the telomeres of eukaryotic chromosomes.
Function in viruses
The enzymes are encoded and used by viruses that use reverse transcription as a step in the process of replication. Reverse-transcribing RNA viruses, such as retroviruses, use the enzyme to reverse-transcribe their RNA genomes into DNA, which is then integrated into the host genome and replicated along with it. Reverse-transcribing DNA viruses, such as the hepadnaviruses, can allow RNA to serve as a template in assembling and making DNA strands. HIV infects humans with the use of this enzyme. Without reverse transcriptase, the viral genome would not be able to incorporate into the host cell, resulting in failure to replicate.
Process of reverse transcription
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 Î´, mistaking the viral DNA-RNA for a primer and synthesizing a double-stranded DNA by similar mechanism as in primer removal, where the newly synthesized DNA displaces the original RNA template.
The process of reverse transcription is extremely error-prone, and it is during this step that mutations may occur. Such mutations may cause drug resistance.
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 positive-sense single-stranded RNA with a 5' cap and 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 as a series of these steps:
- 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 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 5â€™ end of the RNA.
- The tRNA primer then "jumps" to the 3â€™ 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.
Retroviral RNA is arranged in 5â€™ terminus to 3â€™ terminus. The site where the primer is annealed to viral RNA is called the primer-binding site (PBS). The RNA 5â€™end to the PBS site is called U5, and the RNA 3â€™ 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 5â€™ terminus of viral RNA is unusual because reverse transcriptase synthesize DNA from 3â€™ end of the primer in the 5â€™ to 3â€™ direction (with respect to the newly synthesized DNA strand). Therefore, the primer and reverse transcriptase must be relocated to 3â€™ 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.
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 cDNA strand into an antisense DNA to form a double-stranded viral DNA intermediate (vDNA).
In cellular life
Self-replicating stretches of eukaryotic genomes known as retrotransposons utilize reverse transcriptase to move from one position in the genome to another via an RNA intermediate. They are found abundantly in the genomes of plants and animals. Telomerase is another reverse transcriptase found in many eukaryotes, including humans, which carries its own RNA template; this RNA is used as a template for DNA replication.
Initial reports of reverse transcriptase in prokaryotes came as far back as 1971 (Beljanski et al., 1971a, 1972). These have since been broadly described as part of bacterial Retrons, distinct sequences that code for reverse transcriptase, and are used in the synthesis of msDNA. In order to initiate synthesis of DNA, a primer is needed. In bacteria, the primer is synthesized during replication.
Valerian Dolja of Oregon State argues that viruses, due to their diversity, have played an evolutionary role in the development of cellular life, with reverse transcriptase playing a central role.
The reverse transcriptase employs a "right hand" structure similar to that found in other viral nucleic acid polymerases. In addition to the transcription function, retroviral reverse transcriptases have a domain belonging to the RNase H family, which is vital to their replication. By degrading the RNA template, it allows the other strand of DNA to be synthesized. Some fragments from the digestion also serves as the primer for the DNA polymerase (either the same enzyme or a host protein), responsible for making the other (plus) strand.
There are three different replication systems during the life cycle of a retrovirus. First of all, the reverse transcriptase synthesizes viral DNA from viral RNA, and then from newly made complementary DNA strand. The second replication process occurs when host cellular DNA polymerase replicates the integrated viral DNA. Lastly, RNA polymerase II transcribes the proviral DNA into RNA, which will be packed into virions. Therefore, mutation can occur during one or all of these replication steps.
Reverse transcriptase has a high error rate when transcribing RNA into DNA since, unlike most other DNA polymerases, it has no proofreading ability. This high error rate allows mutations to accumulate at an accelerated rate relative to proofread forms of replication. The commercially available reverse transcriptases produced by Promega are quoted by their manuals as having error rates in the range of 1 in 17,000 bases for AMV and 1 in 30,000 bases for M-MLV.
Other than creating single-nucleotide polymorphisms, reverse transcriptases have also been shown to be involved in processes such as transcript fusions, exon shuffling and creating artificial antisense transcripts. It has been speculated that this template switching activity of reverse transcriptase, which can be demonstrated completely in vivo, may have been one of the causes for finding several thousand unannotated transcripts in the genomes of model organisms.
As HIV uses reverse transcriptase to copy its genetic material and generate new viruses (part of a retrovirus proliferation circle), specific drugs have been designed to disrupt the process and thereby suppress its growth. Collectively, these drugs are known as reverse-transcriptase inhibitors and include the nucleoside and nucleotide analogues zidovudine (trade name Retrovir), lamivudine (Epivir) and tenofovir (Viread), as well as non-nucleoside inhibitors, such as nevirapine (Viramune).
Reverse transcriptase is commonly used in research to apply the polymerase chain reaction technique to RNA in a technique called reverse transcription polymerase chain reaction (RT-PCR). The classical PCR technique can be applied only to DNA strands, but, with the help of reverse transcriptase, RNA can be transcribed into DNA, thus making PCR analysis of RNA molecules possible. Reverse transcriptase is used also to create cDNA libraries from mRNA. The commercial availability of reverse transcriptase greatly improved knowledge in the area of molecular biology, as, along with other enzymes, it allowed scientists to clone, sequence, and characterise RNA.
Reverse transcriptase has also been employed in insulin production. By inserting eukaryotic mRNA for insulin production along with reverse transcriptase into bacteria, the mRNA could be inserted into the prokaryote's genome. Large amounts of insulin can then be created, sidestepping the need to harvest pig pancreas and other such traditional sources. Directly inserting eukaryotic DNA into bacteria would not work because it carries introns, so would not translate successfully using the bacterial ribosomes. Processing in the eukaryotic cell during mRNA production removes these introns to provide a suitable template. Reverse transcriptase converted this edited RNA back into DNA so it could be incorporated in the genome.
- cDNA library
- DNA polymerase
- Reverse transcribing virus
- RNA polymerase
- Retrotransposon marker
- "Structural basis of HIV-1 resistance to AZT by excision". Nature Structural & Molecular Biology. 17 (10): 1202â€“9. doi:10.1038/nsmb.1908. PMC 2987654. PMID 20852643. ; Tu X, Das K, Han Q, Bauman JD, Clark AD, Hou X, Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH, Sarafianos SG, Arnold E (October 2010).
- Baltimore D (June 1970). "RNA-dependent DNA polymerase in virions of RNA tumour viruses". Nature. 226 (5252): 1209â€“11. doi:10.1038/2261209a0. PMID 4316300.
- Temin HM, Mizutani S (June 1970). "RNA-dependent DNA polymerase in virions of Rous sarcoma virus". Nature. 226 (5252): 1211â€“3. doi:10.1038/2261211a0. PMID 4316301.
- Ferris AL, Hizi A, Showalter SD, Pichuantes S, Babe L, Craik CS, Hughes SH (April 1990). "Immunologic and proteolytic analysis of HIV-1 reverse transcriptase structure" (PDF). Virology. 175 (2): 456â€“64. doi:10.1016/0042-6822(90)90430-y. PMID 1691562.
- Konishi A, Yasukawa K, Inouye K (July 2012). "Improving the thermal stability of avian myeloblastosis virus reverse transcriptase Î±-subunit by site-directed mutagenesis" (PDF). Biotechnology Letters. 34 (7): 1209â€“15. doi:10.1007/s10529-012-0904-9. PMID 22426840.
- Bio-Medicine.org - Retrovirus Retrieved on 17 Feb, 2009
- Telesnitsky A, Goff SP (1993). "Strong-stop strand transfer during reverse transcription". In Skalka MA, Goff SP (eds.). Reverse transcriptase (1st ed.). New York: Cold Spring Harbor. p. 49. ISBN 978-0-87969-382-4.
- Bernstein A, Weiss R, Tooze J (1985). "RNA tumor viruses". Molecular Biology of Tumor Viruses (2nd ed.). Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory.
- Moelling K, Broecker F (April 2015). "The reverse transcriptase-RNase H: from viruses to antiviral defense". Annals of the New York Academy of Sciences. 1341: 126â€“35. doi:10.1111/nyas.12668. PMID 25703292.
- Kaiser GE (January 2008). "The Life Cycle of HIV". Doc Kaiser's Microbiology Home Page. Community College of Baltimore Count. Archived from the original on 2010-07-26.
- Krieger M, Scott MP, Matsudaira PT, Lodish HF, Darnell JE, Zipursky L, Kaiser C, Berk A (2004). Molecular cell biology. New York: W.H. Freeman and CO. ISBN 978-0-7167-4366-8.
- Hurwitz J, Leis JP (January 1972). "RNA-dependent DNA polymerase activity of RNA tumor viruses. I. Directing influence of DNA in the reaction". Journal of Virology. 9 (1): 116â€“29. PMC 356270. PMID 4333538.
- Arnold C (17 July 2014). "Could Giant Viruses Be the Origin of Life on Earth?". National Geographic. Retrieved 29 May 2016.
- Sarafianos SG, Marchand B, Das K, Himmel DM, Parniak MA, Hughes SH, Arnold E (January 2009). "Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition". Journal of Molecular Biology. 385 (3): 693â€“713. doi:10.1016/j.jmb.2008.10.071. PMC 2881421. PMID 19022262.
- Hansen JL, Long AM, Schultz SC (August 1997). "Structure of the RNA-dependent RNA polymerase of poliovirus". Structure. 5 (8): 1109â€“22. doi:10.1016/S0969-2126(97)00261-X. PMID 9309225.
- Schultz SJ, Champoux JJ (June 2008). "RNase H activity: structure, specificity, and function in reverse transcription". Virus Research. 134 (1â€“2): 86â€“103. doi:10.1016/j.virusres.2007.12.007. PMC 2464458. PMID 18261820.
- Bbenek K, Kunkel AT (1993). "The fidelity of retroviral reverse transcriptases". In Skalka MA, Goff PS (eds.). Reverse transcriptase. New York: Cold Spring Harbor Laboratory Press. p. 85. ISBN 978-0-87969-382-4.
- "Promega kit instruction manual" (PDF). 1999. Archived from the original (PDF) on 2006-11-21.
- Houseley J, Tollervey D (August 2010). "Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro". PLOS ONE. 5 (8): e12271. doi:10.1371/journal.pone.0012271. PMC 2923612. PMID 20805885.
- Zeng XC, Wang SX (June 2002). "Evidence that BmTXK beta-BmKCT cDNA from Chinese scorpion Buthus martensii Karsch is an artifact generated in the reverse transcription process". FEBS Letters. 520 (1â€“3): 183â€“4, author reply 185. doi:10.1016/S0014-5793(02)02812-0. PMID 12044895.
- van Bakel H, Nislow C, Blencowe BJ, Hughes TR (2011). "Response to "The Reality of Pervasive Transcription"". PLoS Biology. 9 (7): e1001102. doi:10.1371/journal.pbio.1001102. PMC 3134445.
- RNA+Transcriptase at the US National Library of Medicine Medical Subject Headings (MeSH)
- animation of reverse transcriptase action and three reverse transcriptase inhibitors
- Molecule of the month (September 2002) at the RCSB PDB
- HIV Replication 3D Medical Animation. (Nov 2008). Video by Boehringer Ingelheim.
- Goodsell DS. "Molecule of the Month: Reverse Transcriptase (Sep 2002)". Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB). Retrieved 2013-01-13.
- PDBe-KB provides an overview of all the structure information available in the PDB for Human immunodeficiency virus Reverse transcriptase
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Reverse transcriptase (RNA-dependent DNA polymerase) Provide feedback
A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.
Internal database links
|SCOOP:||DUF6451 Exo_endo_phos MatK_N RdRP_1 RT_RNaseH RT_RNaseH_2 RVT_2 Transposase_22|
|Similarity to PfamA using HHSearch:||RdRP_1|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000477
The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons. The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) ( EC ). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns [ PUBMED:12758069 ], bacterial msDNAs, hepadnaviruses, and caulimoviruses.
Retroviral reverse transcriptase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [ PUBMED:8828137 ].
Several crystal structures of the reverse transcriptase (RT) domain have been determined [ PUBMED:1377403 ].
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This clan represents the replicative RNA dependent RNA polymerase. from a variety of RNA viruses .
The clan contains the following 11 members:Birna_RdRp DUF6451 Flavi_NS5 Mitovir_RNA_pol RdRP_1 RdRP_2 RdRP_3 RdRP_4 RVT_1 RVT_2 Viral_RdRp_C
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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|Seed source:||Published_alignment and HMM_iterative_training|
|Previous IDs:||rvt; RVT;|
|Number in seed:||69|
|Number in full:||95116|
|Average length of the domain:||170.60 aa|
|Average identity of full alignment:||16 %|
|Average coverage of the sequence by the domain:||25.45 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||29|
|Download:||download the raw HMM for this family|
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The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the RVT_1 domain has been found. There are 866 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.