In-Depth Notes on RNA Viruses and Retroviruses

RNA Viruses and Gene Expression

  • General Features of RNA Viruses

    • Utilize the host's macromolecule synthesizing machinery.
    • Synthesize only essential enzymes not present in the host.
    • Example: Sars-Cov-2 has a (+) RNA genome (Class 1) that is immediately translated.
    • Eukaryotic viruses leverage eukaryotic host machinery; prokaryotic viruses utilize prokaryotic host machinery.
    • RNA viruses require synthesizing RNA-directed RNA polymerase (replicase); retroviruses employ reverse transcriptase.

  • RNA Viral Genome

    • The (+) strand of RNA codes for proteins.

Retroviruses

  • Process of Reverse Transcription in Retroviruses
    • Reverse transcriptase catalyzes:
    • RNA-directed DNA synthesis
    • RNA degradation (via RNase H domain of reverse transcriptase)
    • DNA-directed DNA synthesis

Retroviral Life Cycle

  • Overview of the Retroviral Life Cycle
    • Begins with reverse transcribing the RNA genome into duplex DNA.
    • Integrated into the host genome, then transcribed into RNA.
    • RNA Genome Enzyme: reverse transcriptase
    • LTR (long terminal repeat) facilitates integration and transcription.
    • Viral RNA serves dual functions: both genomic and mRNA.
    • Provirus is transcribed into RNA alongside host RNA; some viral RNA functions as mRNA, while others are packaged as genomic RNA.
    • New virions bud from the plasma membrane, often leading to cell apoptosis.

Fidelity and Variability of Retroviral Replication

  • Low Fidelity of Reverse Transcriptase
    • Lacks 3’ to 5’ exonuclease activity and other fidelity checks.
    • Error Rates:
    • Reverse transcriptase: ~1 in 10^5
    • High-fidelity replicative DNA polymerases: ~1 in 10^9 to 10^10
    • High recombination rate between non-identical (+) RNA genomes leads to significant variability and potential drug resistance.

Expression of Retroviral Genes

  • Polyproteins and Processing
    • Retroviral genes expressed as polyproteins that undergo processing via protein splicing (using protease).
    • Various strategies used to generate multiple proteins from limited genomic material.
    • Monocistronic mRNA structure includes introns that must be spliced for proper protein synthesis.

Nonsense Mutations and Suppressor tRNAs

  • Nonsense Mutations
    • Can lead to unwanted STOP codons, leading to truncated proteins.
    • Suppressed by mutant tRNAs recognizing STOP codons, inserting amino acids instead.
    • Approx. 11% of genetic diseases are due to nonsense mutations.

Caps and Translation Initiation

  • 5’ Caps
    • Added to mRNAs, preventing degradation, enhancing translation.
    • Methylation occurs on the cap, influencing stability and recognition by ribosomes.

Intron Splicing

  • Process of Intron Splicing
    • Involves removal of introns and splicing together of exons.
    • Alternative intron splicing allows for different protein products from the same pre-mRNA, critical for viruses like retroviruses.

Frameshifting Mechanisms

  • Pseudoknots and Ribosomal Frameshifting
    • Pseudoknots induce ribosomal pausing, causing frameshifting at slippery sequences.
    • This allows viruses to produce different ratios of proteins based on ribosome behavior.

Viral Integration into Host DNA

  • Mechanism of Integration
    • Integrase, a viral protein, catalyzes integration of viral DNA into the host genome.
    • U3 regions enhance transcription from integrated virus DNA, which can activate uncontrolled cell division, resulting in tumorigenesis.

Transforming Viruses

  • Replication-Defective Transforming Viruses
    • May substitute parts of their sequences with cellular sequences, requiring helper viruses for replication.
    • V-onc genes (viral oncogenes) can trigger oncogenic transformations by activating cell division signals.