11 - Transcription, translation and nucleic acid replication of RNA viruses

Question 1

What should be included in the topic?

Answer 1

1. Group III - dsRNA
2. Group IV - +ssRNA
3. Group V - -ssRNA
4. Group VI - viruses using reverse transcriptase
   
   1. Retroviruses
   2. Hepadnavirade
5. Importance of eclipse strategies

Question 2

Group III - dsRNA

Answer 2

• Reoviridae
• Birnaviridae
• Segmented genome
• Capsid within a capsid:
  
  • dsRNA is an alien nucleic acid for the cell → virus protect itself
    
    • Intensive interferon response
    • Partial decapsidation
  • Usually viruses have a double coat
    
    • Outer coat lost
    • Inner capsid contains complete transcription and RNA replication elements
• Transcription:
  
  • The dsRNA is not readable for the ribosomes
  • Viral RdRp - structural!
    
    • Transcription mode → mRNA synthesis
• Translation:
  
  • _​_Monocistronic coding → segment ~ protein
• Replication:
  
  • The mRNA enters into the inner capsid
  • Viral RdRp in replicase mode
  • The mRNA is supplemented with a negative thread
• Late transcription, translation:
  
  • _​_Assembly of progeny virions

Question 3

Group IV - +ssRNA

Answer 3

• Picornaviridae
• Caliciviridae
• Togaviridae
• Coronaviridae
• Arteriviridae
• Astroviridae
• Positive-sense ssRNA viruses (Group IV) have their genome directly utilized as if it were mRNA, producing a single protein which is modified by host and viral proteins to form the various proteins needed for replication. One of these includes RNA-dependent RNA polymerase, which copies the viral RNA to form a double-stranded replicative form, in turn this directs the formation of new virions
• Transcription:
  
  • _​_Genomic RNA ~ mRNA
    
    • 5’ methyl capped, 3’ polyadenylated
    • Directly attaches to the ribosomes
• Translation:
  
  • _​_Polycistronic mRNA
    
    • Precursor polypeptide
    • Protease cleavage
    • Equimolar protein production
  • Monocistronic mRNA:
    
    • Subgenomic mRNA synthesis
      
      • Ndovirales
      • Caliciviridae
      • Togaviridae
      • For structural protein production
      • More accurate synthesis
• Replication:
  
  • _​_Viral replicase (RdRp, non-structural)
  • Replicase intermediate forms:
    
    • dsRNA
    • -ssRNA
  • The -ssRNA is template for the progeny +ssRNA genome
  • Translation from the progeny RNA
  • Finallt the + threads incorporate into the progeny virions

Question 4

Group V - -ssRNA

Answer 4

• Orthomyoxviridae
• Paramyxoviridae
• Bornaviridae
• Filoviridae
• Rhabdoviridae
• Arenaviridae
• Bunyaviridae
• -ssRNA (group V) must have their genome copied by an RNA polymerase to form positive-sense RNA. This means that the virus must bring along with it the RNA-dependent RNA polymerase enzyme. The positive-sense RNA molecule then acts as viral mRNA, which is translated into proteins by the host ribosomes. The resultant protein goes on to direct the synthesis of new virions, such as capsid proteins and RNA replicase, which is used to produce new negative-sense RNA molecules
• Transcription:
  
  • _​_Negative sense RNA (3´→5´)
  • Not readable for the ribosomes → viral RdRp - structural
  • Transcription mode:
    
    • Complementary (+) thread synthesis → mRNA
  • ​Arenaviridae, and certain bunyaviruse have mabisense genome
• Translation:
  
  • _​_Monocistronic
  • Segmented:
    
    • Orthomyxoviriade
    • Arenaviridae
    • Bunyaviridae
  • Short mRNAs:
    
    • Mononegaviriales
• Replication:
  
  • _​_The RdRp in replication mode:
    
    • dsRNA in the nucleocapsid
    • Full length +ssRNA synthesis
    • -ssRNA synthesis
  • Finally the negative threads stay in the progeny virions

Question 5

Group VI - viruses using reverse transcriptase: RNA/DNA

Retroviridae

Answer 5

• +ssRNA (diploid)
• Transcription:
  
  • _​_Genome ~ mRNA, but:
    
    • Reverse transcriptase transcribes to dsDNA
  • The viral dsDNA integrates into the cellular genome → provirus → cell division
  • Cellular transcrpitase: mRNA production
  • Long terminal repeat regions
    
    • Intensive promoter → frequent transcription
• Translation: Polycistronic mRNA - protease clevage
• Replication: = transcription_​_
  
  • The mRNA will finally serves as the genome of the progeny viruses
• Because reverse transcription lacks the usual proofreading of DNA replication, a retrovirus mutates very often. This enables the virus to grow resistant to antiviral pharmaceuticals quickly, and impedes the development of effective vaccines and inhibitors for the retrovirus

Question 6

Group VI - viruses using reverse transcriptase: RNA/DNA

Hepadnaviridae

Answer 6

• ss/dsDNA (circular)
• Hepadnaviruses replicate through an RNA intermediate (which they transcribe back into cDNA using reverse transcriptase).
• Transcription:
  
  • _​_Repair of the gapped genome: viral polymerase
  • Cellular transcriptase: mRNA production → short transcripts ~ proteins
• Translation:
  
  • _​_Monocistronic mRNAs
• Replication:
  
  • Full length transcripts of „mRNA” (cellular enzyme)
  • Complementary DNA thread
  • Circularization, partly completed to dsDNA

Question 7

Importance of eclipse strategies

Answer 7

• Have onsequences on pathogenesis and epidemiology
• Detection of replicative intermediate forms → active virus multiplication
• In vitro protein expression studies
• Anti-viral drug development
  
  • Inhibition of virus-specific enzymes
    
    • HIV:
      
      • Reverse transcriptase inhibitors
      • Protease inhibitors