Retroviruses and Reverse Transcription
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Questions and Answers

What is the primary function of the HIV Vpu protein?

  • To inhibit virion release from the host cell
  • To increase surface expression of CD4
  • To enhance virus release by degrading tetherin (correct)
  • To facilitate endocytosis of the virus

How does the Nef protein affect immune response?

  • It enhances CD4 expression on T cells
  • It activates antigen-specific T cell responses
  • It increases MHC I surface expression
  • It decreases surface expression of CD4 and MHC I (correct)

What initiates the assembly of the HIV genomic RNA dimer?

  • Direct binding of Gag proteins to CD4
  • Formation of secondary structures that expose the psi signal (correct)
  • Activation of the virion protease
  • Inhibition of the MHC I protein

What role does tetherin play in relation to HIV?

<p>It promotes endocytosis and restricts virus release (D)</p> Signup and view all the answers

What is the role of the ESCRT complexes in HIV maturation?

<p>They transport Gag proteins to the plasma membrane for assembly (C)</p> Signup and view all the answers

What is the first step in the reverse transcription process of retroviruses?

<p>Synthesis of minus-strand strong-stop DNA (C)</p> Signup and view all the answers

Which component acts as a primer for the synthesis of the plus-strand DNA during reverse transcription?

<p>Polypurine tract (ppt) (D)</p> Signup and view all the answers

What is the result of the first strand transfer during reverse transcription?

<p>Hybridization of R sequence with 3' R sequence (C)</p> Signup and view all the answers

What is the role of RNase H in the reverse transcription process?

<p>To digest RNA in RNA:DNA hybrids (D)</p> Signup and view all the answers

What is formed after the synthesis of a full-length minus-strand DNA?

<p>Proviral DNA (A)</p> Signup and view all the answers

What characterizes the polypurine tract (ppt) in the reverse transcription process?

<p>It acts as a primer for plus-strand DNA synthesis (A)</p> Signup and view all the answers

What does the term 'LTR' refer to in the context of retroviral genome?

<p>Long terminal repeat (D)</p> Signup and view all the answers

During the reverse transcription of retroviruses, what happens to the template RNA after copying the full-length genome?

<p>It is completely digested, except for ppt (B)</p> Signup and view all the answers

What role does the HIV-1 protein Vpr play in the viral lifecycle?

<p>Arrests infected cells in G2 stage of the cell cycle (C)</p> Signup and view all the answers

Which factor is necessary for the cytoplasmic transport of unspliced viral mRNAs in HIV-1?

<p>Rev (D)</p> Signup and view all the answers

How does the HIV-1 protein Tat enhance transcription of the viral genome?

<p>By increasing the processivity of RNA polymerase II (A)</p> Signup and view all the answers

What is the primary function of the HIV protein Vif?

<p>Increases virion infectivity by counteracting host antiviral factors (D)</p> Signup and view all the answers

What happens during the transcriptional regulation by transcription factors in the HIV-1 LTR?

<p>They bind to U3 region and are sensitive to cellular stimuli (A)</p> Signup and view all the answers

Which protein is responsible for eliminating the host CD4 protein to enhance virion release?

<p>Vpu (A)</p> Signup and view all the answers

What effect does the absence of Tat have on the transcription process of HIV-1?

<p>Decreases the processivity of RNA polymerase II (D)</p> Signup and view all the answers

What is the function of CRS (cis-acting repressive sequences) in HIV-1?

<p>To inhibit RNA transport to the cytoplasm (D)</p> Signup and view all the answers

What is a consequence of HIV-1 integration into the host genome?

<p>Latent infection that evades immune detection (B)</p> Signup and view all the answers

What does the interaction of Vpr with Gag C-terminal facilitate?

<p>Entry of the preintegration complex into the nucleus (C)</p> Signup and view all the answers

What is the primary reason retroviruses have a high mutation rate?

<p>They lack 3’-5’ exonuclease activity during reverse transcription. (D)</p> Signup and view all the answers

What is the role of integrase in the retroviral life cycle?

<p>It facilitates the cleavage-ligation reaction to integrate proviral DNA into the host genome. (C)</p> Signup and view all the answers

How do retroviruses typically enter the host cell?

<p>Through endocytosis via CD4 and chemokine receptors. (B)</p> Signup and view all the answers

What feature of the retroviral genome enables it to remain latent for extended periods?

<p>Integration into the host genome. (A)</p> Signup and view all the answers

Why are there gaps left in the host DNA after viral integration?

<p>Due to the removal of unpaired nucleotides by integrase. (D)</p> Signup and view all the answers

What is the significance of the U3 region in the viral genome?

<p>It contains sequences that interact with the cellular transcription machinery. (C)</p> Signup and view all the answers

Which step is crucial for the maturation of virions after they bud from the host cell?

<p>Cleavage of Gag/Pol polyproteins by protease. (C)</p> Signup and view all the answers

What is the purpose of the packaging signal (psi) in the retroviral genome?

<p>To bind the NC portion of Gag protein during assembly. (A)</p> Signup and view all the answers

Which component is responsible for the replication of the HIV genome?

<p>Reverse transcriptase. (B)</p> Signup and view all the answers

How can HIV avoid the host's immune response?

<p>By generating small mutations during genome replication. (A)</p> Signup and view all the answers

What are the potential ways of spreading retroviral infections mentioned?

<p>Infection with progeny viruses and cellular division. (B)</p> Signup and view all the answers

What is the function of the Env protein in the retrovirus lifecycle?

<p>It mediates viral entry into the host cell. (A)</p> Signup and view all the answers

Why is a cure for HIV challenging to achieve?

<p>Integrated viral DNA remains in the host genome. (A)</p> Signup and view all the answers

Flashcards

Reverse Transcription

Retroviruses use reverse transcriptase to convert RNA into DNA.

Retrovirus Genome

Retrovirus RNA genomes have repeated sequences, unique regions (U5 and U3), and a primer binding sequence (PBS).

Proviral DNA

The complete, double-stranded DNA copy of the retrovirus RNA genome, integrated into the host cell's DNA.

Reverse Transcriptase (RT)

Enzyme that converts viral RNA into DNA. It performs multiple synthesis steps using specific primers/templates like the tRNA primer

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Integration

The insertion of synthesized proviral DNA into the host cell's genome.

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Long Terminal Repeat (LTR)

Repeated DNA sequences at each end of the proviral DNA.

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RNase H

Enzyme that removes RNA from RNA-DNA hybrid structures.

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5' and 3' ends of Retrovirus RNA

Retrovirus RNA has specific ends ( 5' ends and 3' ends) that are required for reverse transcription.

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Vpu Function

Vpu is a viral protein that helps HIV escape from the host cell by counteracting tetherin, a host protein that tethers the virus to the cell surface.

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Tetherin's Role

Tetherin is a host protein that binds to HIV and other viruses, preventing their release from the cell. It acts like a tether, keeping the virus attached.

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Nef Protein

Nef is a viral protein that helps HIV infect new cells by interfering with CD4 and MHC I, both of which are crucial for immune defense.

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Nef Impact on Immune Response

Nef reduces the expression of CD4 (a receptor for HIV) and MHC I (a protein involved in presenting viral antigens to immune cells), effectively weakening the immune response.

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Genome Packaging Signal (psi)

The genome packaging signal (psi) is a sequence on the HIV genome essential for packaging viral RNA into new virions.

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Retrovirus Reverse Transcription

Retroviruses lack proofreading enzymes, leading to a high mutation rate and a population of diverse variants (quasispecies).

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Retroviral Integration

Integrase enzyme inserts viral DNA into host cell DNA at random spots. This process removes short stretches of DNA and joins the viral and host DNA.

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Preintegration complex

A complex formed by viral proteins and newly synthesized proviral DNA before integration into the host genome.

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Integrase (IN)

Retroviral enzyme that inserts viral DNA into host DNA. It performs cutting and joining of DNA strands

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Retroviral Transcription

Viral genes are transcribed into RNA using cellular machinery and specific sequences within the viral DNA.

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HIV Genome

HIV has a single-stranded RNA genome that is replicated by reverse transcription.

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HIV proteins

HIV has many different capsid proteins (MA, CA, NC...), enzymes (PR, RT), envelope proteins(SU, TM), and regulatory proteins(Vif...).

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HIV Entry

HIV uses CD4 and chemokine receptors (like CCR5 or CXCR4) to enter cells.

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Viral budding

New viruses are produced by pushing through the host cell membrane.

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LTR sequences

Long terminal repeats in retroviral DNA that regulate transcription and polyadenylation by the host cell.

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Quasispecies

A group of very similar viruses with slight mutations in their genetic material.

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Viral Fusion

The process where viral and host membranes fuse to allow viral entry into the cell.

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Proviral DNA replication

Once integrated, the proviral DNA is replicated along with host DNA during cell division.

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HIV Nuclear Entry

Unlike other retroviruses, HIV-1 can infect non-dividing cells by actively transporting proviral DNA into the nucleus, a process driven by viral proteins MA, Vpr, and IN.

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HIV Latency

HIV-1 can integrate into the host genome without immediately producing viral proteins, leading to a latent infection that is difficult to detect and eradicate.

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HIV LTRs Role

Long Terminal Repeats (LTRs) in HIV-1 control the switch between latent and active infection by interacting with cellular transcription factors.

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HIV Tat Protein

The Tat protein is a key activator of HIV-1 transcription, binding to a specific RNA sequence (TAR) to enhance RNA polymerase activity.

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Tat and RNA Polymerase

Tat binds to the nascent RNA, not the DNA, and helps RNA polymerase efficiently transcribe the entire viral genome.

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HIV Rev Protein

The Rev protein helps transport viral mRNAs from the nucleus to the cytoplasm, enabling the production of viral structural proteins.

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HIV Early and Late Proteins

HIV produces early proteins (Tat, Rev, and Nef) from doubly-spliced mRNA before full-length or single-spliced mRNA encoding late proteins is transported.

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HIV Vif Function

Vif protects HIV from a host antiviral factor, APOBEC3G, by inducing its degradation, ensuring the virus's infectivity.

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HIV Vpr Role

Vpr facilitates the entry of the preintegration complex into the nucleus and helps arrest the infected cell in the G2 phase of the cell cycle, potentially benefiting viral transcription.

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HIV Vpu Function

Vpu increases the release of new viruses by triggering the degradation of CD4 protein and counteracting host antiviral factors that tether the virus to the cell surface.

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Study Notes

Retroviruses

  • Retroviruses utilize reverse transcription to convert their RNA genome into DNA.
  • This DNA is then integrated into the host cell's genome.
  • The viral genome has short repeated sequences (R) at the 5' and 3' ends, along with unique regions (U5 and U3).
  • Reverse transcription is initiated by a specific cellular tRNA binding to the genome RNA.
  • Key enzymes involved include reverse transcriptase (RT) and integrase (IN).

Reverse Transcription

  • Reverse transcriptase lacks 3'-5' exonuclease activity, resulting in a high mutation rate in the viral DNA.
  • This leads to the concept of "quasispecies" - a collection of viral variants due to mutations.
  • The process occurs within the viral core, forming a preintegration complex.
  • This complex is too large to pass through nuclear pores, requiring cell division for integration.
  • Template RNA is removed by RNase H throughout the process, with parts acting as primers.
  • The process eventually creates a double-stranded DNA form called proviral DNA, with long terminal repeats (LTRs) at both ends.

Integration

  • Integrase (IN) is a viral enzyme that facilitates the insertion of proviral DNA into the host genome.
  • Integration occurs at random sites in the host DNA.
  • The process involves cleavage and ligation of host and viral DNA.
  • It leaves gaps in the host DNA, which are then repaired by host enzymes.
  • The integrated provirus replicates along with the host cell's DNA, resulting in infection through cell division and potential transmission.

Transcription and Splicing

  • Retroviral DNA can remain latent for a long time, depending on the presence of transcription factors.
  • Specific sequences in the LTR (long terminal repeat) control transcription.
  • Transcription occurs through a TATA box (at U3/R junction) and a poly(A) signal to produce RNA identical to the viral genome RNA.
  • Retroviruses produce at least two mRNAs: unspliced (full-length) and spliced mRNAs for varying viral proteins.

Assembly and Release

  • Virion assembly occurs at the plasma membrane after viral protein synthesis in the late phase of replication.
  • Envelope proteins (Env) are trafficked through the ER and Golgi to the plasma membrane.
  • Gag proteins assemble the viral core, and the Gag/Pol polyproteins are cleaved to mature proteins.
  • The process culminates in budding and release.

Human Immunodeficiency Virus (HIV)

  • HIV is a retrovirus with a positive-sense single-stranded RNA genome.
  • It has specific proteins such as structural proteins (Gag, Pol, Env, Vpr) and non-structural proteins (Vif, Vpu, Tat, Rev, Nef).

HIV - Entry and Replication

  • HIV primarily infects immune system cells via CD4 and chemokine receptors (CCR5 or CXCR4).
  • Viral gp120 binds CD4, triggering conformational changes for co-receptor binding and membrane fusion.
  • Viral core enters the cytoplasm and reverse transcription replicates the viral RNA genome.
  • Unique to HIV, the proviral DNA is transported into the nucleus.

HIV - Latent Infection

  • HIV integration can lead to latent infection due to transcriptional control elements within LTRs.
  • Transcription factors like NF-κB regulate whether the virus is expressed or latent.
  • Viral activity can be responsive to cellular stimuli such as immune cell activation.

HIV - Transcription

  • Tat enhances viral transcription by binding to TAR (Tat-responsive element) on nascent RNA.
  • Tat promotes RNA polymerase II processivity through recruitment of cellular proteins.
  • Specific sequences inhibit RNA export (CRS) needing the Rev protein for export.

HIV - Protein Function

  • Vif: Counteracts APOBEC3G by triggering its degradation, increasing viral infectivity.
  • Vpr: Enhances HIV replication by potentially altering the cell cycle.
  • Vpu: Enhances virion release from infected cells by degrading CD4 and tetherin.
  • Nef: Decreases surface expression of CD4 and MHC I, affecting the immune response.

HIV - Budding and Maturation

  • HIV genome packaging signal causes interaction with the nucleocapsid protein.
  • Gag/Gag-Pol cleavage by protease forms a capsid for virion release.

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Description

Explore the fascinating world of retroviruses and their unique mechanism of reverse transcription. This quiz covers key concepts such as the integration of viral DNA into host genomes, the role of reverse transcriptase, and the implications of high mutation rates in viral populations. Test your knowledge on the important processes and components involved in retroviral replication.

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