Viral Pathogens: Classification, Biology, Diseases I Flashcards
How varying are viral structures?
Various different viral structures with varying genomes (RNA/DNA)
How does structure effect viral function?
Adenoviruses and influenza viruses cause significant respiratory disease in humans although they differ greatly in structure, pathogenesis and their molecular biology
Outline the various configurations of viral genomes
- Single-stranded RNA (ssRNA)
- Double-stranded RNA (dsRNA)
- Single-stranded DNA (ssDNA)
- Double-stranded RNA (dsDNA)
What maintains the double stranded genomes?
Double-stranded genomes have complementary base pairing
Describe the structure of RNA genomes
RNA genomes can be linear and segmented i.e. more than one RNA per capsid
What is the structures of DNA viral genomes?
DNA genomes can be linear or circular.
What is Baltimore classification?
Viruses are grouped together by the way their genomes are grouped together (RNA/DNA)
Which nucleic acid do all viruses produce?
All viruses produce RNA which can be transcribed into protein to make new viruses
Describe HIV structure
Contains 2 RNA strands encapsulated by a protein capsid all covered by a lipid bilayer gathered by the virus as it emerges from the cell
What is the role of surface glycoproteins?
Protein sites / protein envelope glycoproteins on the cell surface mediate entry into the cell
Name the enzymes in HIV
HIV also houses integrase, reverse transcriptase and protease enzymes
Describe the outer structure of mature HIV
The outer envelope of HIV consists of a lipid bilayer with protruding Env spikes (heterotrimers of SU3TM3).
What structures lie within the envelope of mature HIV?
Inside the envelope lie shells of Gag proteins
In the immature particle, Gag itself forms a single shell
How is the mature HIV conical capsid formed?
MA (matrix protein) associates around the membrane CA (capsid protein) to form the conical capsid
What is the role of the nucleocapsid?
Nucleocapsid coats the viral RNA genome and bridges the interaction between the genome and the capsid as the variant forms
What are the 3 polyproteins synthesised by retroviruses?
- Gag
- Pol
- Env
What is contained within the HIV core?
The core contains two genomic RNA strands (plus strand) that the nucleosome binds, as well as tRNALys3, and ~50 copies of each viral enzyme (PR, RT, and IN).
What is the gag protein?
Gag; group specific antigen; viral core proteins; MA (matrix), CA (capsid), NC (nucleocapsid)
What is the Pol protein?
Pol; viral enzymes; protease (PR), reverse transcriptase (RT) and integrase (IN)
What is the Env protein?
Env; envelope glycoprotein; gp120 SU (surface); gp41 TM (transmembrane)
Name the accessory / regulatory HIV proteins present
- Tat
- Rev
- Vif
- Nef
- Vpu
- Vpr
Involved in immunoregulation to interact and try overcome complex human immune system
What is the role of the Tat accessory protein?
Potent activator of viral transcription
What is the role of the vpr protein?
Cell cycle, virus nuclear import (?)
What is the role of the regulatory Vpu protein?
immune modulator, virus release
What is the role of the Nef protein?
Immune modulator, T-cell activation, virus spread (?)
Describe the role of the regulatory Vif protein
Critical regulator of virus infectivity
Outline the role of the regulatory Rev protein in HIV
Mediates unspliced RNA nuclear export
What mechanism do retroviruses use to organise their genome?
Mechanism of Retroviruses: RNA is brought into cells via viruses and reverse transcribed into DNA
How is HIV RNA differentiated?
HIV RNA is split into different RNA structures that are recognised for different functions
What is the effect of reverse transcription in HIV?
Reverse transcription produces DNA version of the genes to be transcribed to produce all the protein products required as well as back into RNA
Describe the HIV outer envelope structure
HIV-1 Env consists of a trimer of gp41 and gp120 peptide subunits and is covered with glycans
These glycoproteins are large globular structures
How does HIV entry into cells differ from other retroviruses?
HIV entry at cell surface triggered by conformation changes driven by Env/receptor interactions
Contrasts with pH-dependent entry of adenovirus, influenza virus, etc
How does HIV gain entry into cells?
HIV-1 entry requires two membrane proteins:
CD4 (T-cells) and a chemokine receptor (CCR5/CXCR4)
How does HIV infection lead to immunodeficiency?
HIV-1 is tropic for CD4 expressing cells such as helper T cells and macrophages; the loss
of which results in immunodeficiency (& AIDS)
Outline how HIV interacts with CD4 T cells
- HIV specifically binds to CD4 receptor on T cells
- Allows interaction with specific coreceptors CCR5 and
CXCR4 - Produces 6-Helix bundle formation
- Envelope meshes viral and cellular plasma membranes
together allowing entry into cell
How does HIV travel through the cell?
HIV doesn’t travel passively through the cell, but alters it genome along the way
Outline the first alterations HIV undergoes once inside the host cell
- Uncoating step: Lose capsid, exposing RNA genome covered by enzymes and nucleocapsid protein
- HIV moves down microtubules towards microtubule organising complex to allow directionality
- Undergoes intracellular trafficking to get into nuclear membrane
What is the role of HIV degenerate nuclear entry pathways?
Intracellular trafficking pathways (e.g. microtubules) allows efficient movement of viruses through host cells
What is the role of HIV degenerate nuclear entry pathways?
Each microtubule pathway has a different result that the virus selects
How does HIV decide which pathway to take?
Molecules of capsid that enter cells with the virus help select which microtubule and destination on the cell nuclear membrane is used
Outline the most efficient microtubular pathway to the nucleus
Most efficient pathway involves the capsid molecule directing the virus through cytoplasm to NPC (nuclear pore complex) used by virus to gain entry into nuclear space
Outline the structure of reverse transcriptase (RT)
RT is a heterodimer of p66 and p51 subunits
What are the roles of the 2 RT dimers?
Catalytic properties are in p66 subunit, p51 serves structural role and lacks RNAse H domain
What are the 3 enzymatic activities of RT?
RT displays three distinct enzymatic activities:
- RNA-dependent DNA polymerase
- RNAse H (cleaves RNA from RNA/DNA hybrid)
- DNA-dependent DNA polymerase
How does reverse transcriptase bind to Viral RNA?
RNA with smaller intrinsic RNA structures is recognised by RT
RT finds specificity within those structures and binds to it
How does reverse transcriptase initially form more RNA?
RNA structure produced by RNA polymerase part of RT as well as an RNA primer which is moved to the other end of the genome (unknown reason) to enable even more RNA production
How is DNA formed from RT?
DNA is primed as DNA Pol. component of RT takes over
The DNA primer is then used to produce more copies of DNA
What is the significance of HIV RT?
HIV Reverse transcriptase contains both RNA and DNA polymerase functions together
⇒ produce DNA version of RNA genome
Why must HIV integrate into the host cell DNA?
Cell nucleus is a highly regulated structure; In order to access nuclear components HIV requires to replicate, HIV DNA genome (provirus) is integrated into host chromosomes
How is viral DNA integrated into the host cell?
DNA break repair enzymes are present in the genome. These find specific sequences and break them apart to insert new DNA in them to be copied - mechanism of Viral integrase enzyme
Outline how integrase anneals viral DNA to cellular DNA
- Integrase loops target DNA
- Brings termini sequences into physical contact with the viral genome
- Integrase now has ability through chelation (use of divalent cations) to break open DNA
- One strand at a time anneals viral DNA to cellular DNA
What is LEDGF/P75
LEDGF/P75 is a protein that binds HIV-1 integrase and facilitates targeting to chromatin
LEDGF/P75 isn’t a HIV viral protein but is picked up along the way
How does LEDGF/P75 aid chromatin targeting?
As virus addresses nuclear membrane, LEDGF is bound by virus
Enables it through nuclear pore
LEDGF also allows integrase to recognise specific target sequences within host cell DNA
How is viral transcription mediated?
Viral transcription is regulated by the binding of various Transcription Factors (TF) to the viral DNA in order to recruit polymerases
Why are there so many transcription factors (TF) in HIV?
HIV contains many TF binding sites to ensure transcription will occur in any circumstance
How is CD4 specificity aided by TF?
The HIV-1 promoter contains binding sites for transcription factors that are present in T-lymphocytes
What is the purpose of the Tar-Tat complex?
The TAR RNA binds the Tat protein; TAR-Tat interaction is thought to preferentially bring RNA pol. to the viral genome and enhances elongation of RNA pol II
How are viral proteins formed when HIV transcription occurs
The HIV-1provirus generates different mRNAs for the viral proteins via splicing
How are different viral proteins made from the same HIV?
Splicing alters coding regions of the RNA to produce different proteins with varying functions
What is the fate of the genomic viral RNA transcribed?
Nuclear export of unspliced retrovirus RNA (genomic RNA)
What are the products of viral transcription?
Full length virus and primary transcripts of polyproteins (Gag / pol) produced
What enables the formation of accessory viral proteins?
Splicing occurs to form Env protein which goes on to make further viral proteins
How do the viral proteins produced help export the viral genome?
Virus produces advantageous Rev protein that interacts with RRE structure to bring other cellular proteins along to preferentially export genomic and spliced RNA out the cell
What is the role of the HIV-1 Rev protein?
The HIV-1 Rev protein mediates nuclear export of unspliced and singly spliced viral RNA
What is the significance of the HIV-1 Rev protein?
HIV Rev is essential for the nuclear export of intron-containing viral mRNAs
When is Genomic RNA exported from the host cell?
The long genomic RNA contains introns and is only removed from the the cell when HIV-1 Rev protein interacts with Crm1 and the RRE RNA
How is genomic RNA export mediated?
Regulated by the fact the cell doesn’t contain any machinery enabling intron containing RNA to leave the nucleus
Why does the viral proteins and RNA assemble at the host cell membrane?
The virus assembles at the plasma membrane so it has less distance to travel
Describe the different RNA products present at assembly
The unspliced HIV-1 RNA is the mRNA for Gag and Gag-Pol proteins. Spliced full length RNA genome has 2 copies in the virus
What mechanism enables the virus to leave the cell?
Interaction of the 2 RNA genomes occurs surrounded by protein causing the virus to be pushed out of the host cell
Outline how RNA interaction leads to exportation of the virus
Kissing loop complexes in SL1 and SL4 domains of side structures allows interaction of the 2 RNA genomes at the membrane
Dimerisation of unspliced viral RNA allows packing of two genomes
What proteins are formed from the viral polyproteins gag and pol?
Gag and Gag-Pol proteins assemble viral particles
- Gag produces structural proteins
- Pol produces viral enzymes
- Env produces envelope glycoproteins
How are various polyproteins formed?
Long genomic RNA undergoes slippery sequence translation to form different polyproteins
What is slippery sequence?
Slippery sequence is when ribosome misreads RNA causing a frameshift to produce different polyproteins
Describe the translation slippery sequence that occurs to form gag and pol
Gag-pol protein is generated by -1 ribosomal frameshifting induced by a ‘slippery’ sequence and an RNA hairpin structure
What is myristolation?
Myristoylation is a post-translational modification that proteins undergo enabling them to interact with the plasma membrane
What modification process allows Gag to interact with plasma mebrane?
Myristoylation (Myr) of Glycines in MA domain of Gag mediates association with plasma membrane
Which structures are involved in HIV budding?
The HIV-1 PT(S)AP motif is required for virus budding and mediates binding of the host Tsg101 protein
Myr binding shows interaction with the membrane
What is the role of the P6 protein in viral budding?
P6 protein responsible for pushing out virus from cells; used in cytokinesis of daughter cells
part of ESCRT machinery
How is ESCRT machinary altered in HIV?
The ESCRT machinery is hijacked by HIV to perform membrane abscission during viral release; P6 binds Tsg101 protein to push out virus
Why are polyproteins cleaved at the membrane?
Polyproteins at the membrane get cleaved by protease to produce individual proteins that form the capsid
How does protease form viral capsids?
Protease releases the individual proteins from Gag and Gag-Pol polyproteins
Describe the immature structure of virion?
The immature virion contains ordered arrays of polyproteins (green) surrounded by membrane
Outline the structure of a mature virion
Mature virion has viral protease (Pr) encoded in Gag-Pol polyprotein to digest immature polyproteins to produce individual proteins that come together to form the mature virion
Envelope glycoprotein produces 2 glycoprotein spikes (yellow) that are already at membrane and taken up as virion is pushed out
