[4b] Genome Replication

• There is no RdRp yet identified in cells
• Viral genome diversity:

  • DNA, RNA
  • Linear, Circular
  • Double-stranded, single-stranded
• Location of genome replication:

  • Cytoplasm
  • Some dsDNA viruses
  • dsRNA viruses
  • + RNA viruses
  • -RNA viruses (non-segmented)
  • Retroviruses and pararetroviruses
  • RNA->DNA part
  • Nucleus
  • Some dsDNA viruses
  • ssDNA viruses
  • -RNA viruses (segmented genomes)
  • Influenza
  • Retroviruses and pararetroviruses 
  • DNA->RNA synthesis part
• Primer is synthesized by primase (RNA polymerase)
• Open up the template strand


  Helicases
• Bind Okazaki fragments

  Ligases
• Phenomenon where linear DNA shortens over time

  End replication problem
• Telomerases have a polymerase activity (reverse transcribing) with RNA primer
• RNA polymerase that can synthesize a shortened oligonucleotide primer

  Primase
• Primers than can be used:

  1. RNA
  2. DNA
  3. Proteins (Serine, Tyrosine)
• Organism that can initiate DNA synthesis without primers

  NRS1 phage
• 2 Mechanisms of synthesis

  1. Replication fork
  2. Strand displacement
• In strand displacement, the primer is not an RNA like in a normal replication fork

  • Often a protein or hairpin initiates synthesis
  • Complementary strand displaced
• Theta model

  1. Starts at origin
  2. Semi-conservative replication
  3. Products can be concatemerized, solved by topoisomerases
• Sigma rolling circle model:

  1. Enzyme produces a nick, revealing 3'OH
  2. 5' extended from the genome
• Undergo rolling hairpin replication

  Parvoviruses
• Parvoviruses are replicated in the nucleus, where it is recognized as ssDNA

  • DNA repair enzymes convert it to dsDNA
  • Viral nuclease exposes 3'OH
• Undergoes protein primer initiated replication

  Adenovirus
• Regulation of DNA synthesis:

  1. Rb protein inhibits deacetylases, binds to transcription factors
  2. Adenoviral proteins can sequester Rb, turning on gene expression
• The E6 and E7 proteins bind to Rb to induce cyclin E transcription

  • Gene products sequester p53 (tumor supressor), leading to transcription
• Problem for RNA Viruses:

  • There has to be a switch from mRNA synthesis to RNA for genomes
• All RNA are linear
• Types of initiation

  1. De novo
  2. Internal
  3. Protein-initiated
• Vesicular stomatitis is negative-strand RNA which carries its own polymerase
• In vesicular stomatitis, intergenic sequences are coated with protein so full length RNA can be synthesized
• Proteins that coat intergenic sequences

  N and P proteins
• N and P protein products which bind to the template RNA allows polymerase to skip through the Poly-adenylation and termination signals

  • Results in a full-length complementary RNA that can act as a template for the new strands
• RdRp can recognize and cleave host RNA to steal the 5' cap
• Genomic RNA synthesis for the template is not primed
• +RNA genomes

  • Immediately expressed as proteins
  • Or can serve as templates for negative RNA synthesis that act as templates for more mRNA synthesis or for new genomes

  -RNA genomes

  • Synthesis of +RNA that can serve as templates for mRNA or for new genomes
• Most RNA is cleared of ribosomes before it acts as a template

  • Spatial rather than temporal regulation