Reverse transcriptase

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Reverse transcriptase-related cellular gene
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Reverse transcriptase
(RNA-dependent DNA polymerase)
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RNA-directed DNA polymerase
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A reverse transcriptase (RT) is an

telomeres at the ends of their linear chromosomes. Contrary to a widely held belief, the process does not violate the flows of genetic information as described by the classical central dogma, as transfers of information from RNA to DNA are explicitly held possible.[2][3][4]

Retroviral RT has three sequential biochemical activities: RNA-dependent

RNA sequencing, polymerase chain reaction (PCR), or genome analysis
.

History

Reverse transcriptases were discovered by

MIT from two RNA tumour viruses: murine leukemia virus and again Rous sarcoma virus.[6] For their achievements, they shared the 1975 Nobel Prize in Physiology or Medicine (with Renato Dulbecco
).

Well-studied reverse transcriptases include:

Function in viruses

RNase H active site and the polymerase
active site are shown in ball-and-stick form.

The enzymes are encoded and used by viruses that use reverse transcription as a step in the process of replication. Reverse-transcribing

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.[citation needed
]

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 removal, where the newly synthesized DNA displaces the original RNA template.[citation needed
]

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

drug resistance
.

Retroviral reverse transcription

Mechanism of reverse transcription in HIV. Step numbers will not match up.

HTLV). Creation of double-stranded DNA occurs in the cytosol[10]
as a series of these steps:

  1. tRNA
    acts as a primer and hybridizes to a complementary part of the virus RNA genome called the primer binding site or PBS.
  2. 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.
  3. A domain on the reverse transcriptase enzyme called
    RNAse H
    degrades the U5 and R regions on the 5’ end of the RNA.
  4. 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.
  5. The complementary DNA (cDNA) added in (2) is further extended.
  6. The majority of viral RNA is degraded by RNAse H, leaving only the PP sequence.
  7. Synthesis of the second DNA strand begins, using the remaining PP fragment of viral RNA as a primer.
  8. The tRNA primer leaves and a "jump" happens. The PBS from the second strand hybridizes with the complementary PBS on the first strand.
  9. 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.[11]

Retroviral RNA is arranged in 5’ terminus to 3’ terminus. The site where the

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.[12][13]

The HIV reverse transcriptase also has

DNA-dependent DNA polymerase activity that copies the sense cDNA strand into an antisense DNA to form a double-stranded viral DNA intermediate (vDNA).[14] The HIV viral RNA structural elements regulate the progression of reverse transcription.[15]

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.[16]

Initial reports of reverse transcriptase in prokaryotes came as far back as 1971 in France (Beljanski et al., 1971a, 1972) and a few years later in the USSR (Romashchenko 1977[17]). 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.[18]

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.[19]

Structure

The reverse transcriptase employs a "right hand" structure similar to that found in other

RNase H family, which is vital to their replication. By degrading the RNA template, it allows the other strand of DNA to be synthesized.[22] Some fragments from the digestion also serve as the primer for the DNA polymerase (either the same enzyme or a host protein), responsible for making the other (plus) strand.[20]

Replication fidelity

There are three different replication systems during the life cycle of a retrovirus. The first process is the reverse transcriptase synthesis of viral DNA from viral RNA, which then forms newly made complementary DNA strands. 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. Mutation can occur during one or all of these replication steps.[23]

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.[24]

Other than creating

antisense transcripts.[25][26] 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.[27]

Template switching

Two RNA genomes are packaged into each retrovirus particle, but, after an infection, each virus generates only one provirus.[28] After infection, reverse transcription is accompanied by template switching between the two genome copies (copy choice recombination).[28] There are two models that suggest why RNA transcriptase switches templates. The first, the forced copy-choice model, proposes that reverse transcriptase changes the RNA template when it encounters a nick, implying that recombination is obligatory to maintaining virus genome integrity. The second, the dynamic choice model, suggests that reverse transcriptase changes templates when the RNAse function and the polymerase function are not in sync rate-wise, implying that recombination occurs at random and is not in response to genomic damage. A study by Rawson et al. supported both models of recombination.[28] From 5 to 14 recombination events per genome occur at each replication cycle.[29] Template switching (recombination) appears to be necessary for maintaining genome integrity and as a repair mechanism for salvaging damaged genomes.[30][28]

Applications

The molecular structure of zidovudine (AZT), a drug used to inhibit reverse transcriptase

Antiviral drugs

Further information: Reverse-transcriptase inhibitor

As

tenofovir (Viread), as well as non-nucleoside inhibitors, such as nevirapine (Viramune).[citation needed
]

Molecular biology

Further information: Reverse transcription polymerase chain reaction

Reverse transcriptase is commonly used in research to apply the

enzymes
, it allowed scientists to clone, sequence, and characterise RNA.

See also

References

  1. PMID 20852643
    .
  2. S2CID 4164029
    .
  3. ^ Sarkar S (1996). The Philosophy and History of Molecular Biology: New Perspectives. Dordrecht: Kluwer Academic Publishers. pp. 187–232.
  4. S2CID 67861162
    .
  5. S2CID 4187764
    .
  6. S2CID 4222378
    .
  7. PMID 1691562
    .
  8. ^
    S2CID 207096569
    .
  9. PMID 16756500
    .
  10. ^ Bio-Medicine.org - Retrovirus Retrieved on 17 Feb, 2009
  11. ISBN 978-0-87969-382-4
    .
  12. ^ 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.
  13. S2CID 42378727
    .
  14. ^ 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.
  15. S2CID 221636459
    .
  16. ISBN 978-0-7167-4366-8
    .
  17. ^ Romashchenko AG, et al. (1977). "Otdelenie ot preparatov DNK-polimeraz I RNK-zavisimoy DNK-polimeraz; oshistka i svoystva fermenta". Proceedings of the USSR Academy of Sciences. 233: 734–737.
  18. PMID 4333538
    .
  19. ^ Arnold C (17 July 2014). "Could Giant Viruses Be the Origin of Life on Earth?". National Geographic. Archived from the original on July 18, 2014. Retrieved 29 May 2016.
  20. ^
    PMID 19022262
    .
  21. PMID 9309225
    .
  22. PMID 18261820
    .
  23. ISBN 978-0-87969-382-4
    .
  24. ^ "Promega kit instruction manual" (PDF). 1999. Archived from the original (PDF) on 2006-11-21.
  25. PMID 20805885
    .
  26. S2CID 24619868
    .
  27. PMC 3134445
    .
  28. ^
    PMID 30307534
    .
  29. S2CID 20086739
    .
  30. PMID 1700865
    .

External links
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