Retroviruses L26-28

Question 1

Retroviruses have ___1___ genomes.
But they are unique in that they convert their genomic ___1___ into dsDNA.
Reverse transcription, catalysed by ___2___.

Answer 1

1. RNA

2. Reverse Transcriptase

Question 2

Name the 3 classes of Retroviruses.

Answer 2

• Ocornaviruses
• Lentiviruses
• Spumaviruses

Question 3

What is the protein/function of the retrovirus gene gag?

Answer 3

• Precursor to internal structural proteins

Question 4

What is the protein/function of the retrovirus gene pro?

Answer 4

• Viral protease (PR)

Question 5

What is the protein/function of the retrovirus gene pol?

Answer 5

• Precursor to Integrase (IN) & reverse transcriptase (RT)

Question 6

What is the protein/function of the retrovirus gene env?

Answer 6

• Precursor to envelope glycoprotein

Question 7

Describe the retroviral genome.

3

Answer 7

• Positive sense genome between 7-10 Kb
• The genomic RNA is capped and polyadenylated
• The retrovirion contains two copies of the genomic RNA

Question 8

Describe Retroviral replication:

Initiation of Infection.

Answer 8

• Mechanisms of entry into the cells depend upon the retrovirus
• For lentiviruses infection is initiated by interaction of viral Env proteins with specific cell surface receptors.
• This is followed by fusion of viral and cellular envelopes and entry of the capsid into cytoplasm

Question 9

Describe Retroviral replication:

Generation of cDNA.

Answer 9

• Virion RNA is converted to cDNA by reverse transcriptase (RT) while the virion is in the cytoplasm

(Read much more on slides)

Question 10

Describe Retroviral replication:

Migration of the cDNA into the nucleus.

Answer 10

• cDNAs migrate to the nucleus in a complex with INTEGRASE (IN). This is produced by proteolytic
  cleavage of from a precursor poly peptide produced from the pol gene
• However the process of migration differs in lentivirus and oncornavirus infections
• During oncornavirus infections migration requires a proliferating cell and the breakdown of the nuclear
  membrane allows access of cDNA to chromatin
• During lentivirus infection cDNA along with the IN enzyme are transported through the nuclear pore

Question 11

Describe Retroviral replication:

Integration of cDNA into the host genome.

Answer 11

• IN cleaves 2 nucleotides from
  the 3’ end of the cDNA
• IN cleaves host genomic DNA:
  IN separates the breaks by
  several base pairs, forming a jagged cut
• IN ligates host DNA to the 3’ of the retroviral cDNA
• Host proteins fill in the gaps and ligate the retroviral cDNA to the host
• The target site is duplicated

Question 12

Describe Retroviral replication:

Expression of viral mRNA and RNA genomes.

Answer 12

• Following integration the 5’ LTR serves as promoter for RNA polymerase II and the 3’ LTR serves as polyadenylation/transcription stop signal
• The full length RNA is transported to the cytoplasm for translation or encapsidation into virions (ie. to function as a new RNA genome).
• Some RNA is spliced in the nucleus to generate mRNA that can then serve for as a template for Env and other accessory proteins

Question 13

Describe Retroviral replication:

Splicing and Translation.

Answer 13

• Full length mRNA is transported to the cytoplasm for translation or encapsidation into virions (ie. to function as a new RNA genome)
• Unspliced mRNA serves as a template for translation of the gag pro and pol genes
• This has some unusual features. gag is always followed by suppressible (leaky) stop codon
• pro and pol may be in different reading frames to gag
  This is because the RNA around the stop codon forms a secondary structure that can cause ribosome skipping (frameshifting)
• gag translation can sometimes start with an unusual CUG codon upstream from the normal AUG. This leads to the production of a variant protein that serves as the matrix protein
• Some RNA is spliced in the nucleus to generate mRNA that can then serve for as a template for Env and other accessory proteins

Question 14

Describe Retroviral replication:

Capsid Assembly and Maturation.

Answer 14

• Maturation of capsids takes place as the virion buds from the infected cell
• In most cases the maturation process is only completed after the release of the immature virion
• The Gag-Pol precursor is cleaved in the capsid to yield free protease (PR)
• The free protease then releases active RT and IN
• As a result little free RT is expressed in the infected cell, which prevents further integration into the host genome

Question 15

What is HIV?

Answer 15

HIV is a lentivirus that infect humans and cause acquired immune deficiency syndrome (AIDS).

Question 16

Name and describe the 2 types of HIV.

Answer 16

• HIV-1, responsible for the global AIDs pandemic. HIV-1 strains can be divided into several groups that were independently transmitted to humans from chimpanzees
• HIV-2, less pathogenic and primarily found in West Africa. HIV-2 is closely relayed to simian immunodeficiency virus (SIV)
  found in sooty mangabeys

Question 17

HIV-1 is a lentivirus and is capable of infecting non dividing cells.

Like most lentiviruses it infects macrophages.

It is a complex retrovirus and in addition to the core retroviral genes it has six accessory genes:
NAME THEM.

Answer 17

• vif
• vpr
• tat
• rev
• vpu
• nef