viral replication Flashcards
what does it mean if a cell is susceptible and permissive for a virus?
susceptible: virus can penetrate
permissive: viral genome replication is possible
what is productive infection?
production of infectious virus particles in a cell
what are the types of infection and what are their characteristics?
1.lytic: host cell dies
2.persistent: continous production of viruses because cells survive and limited infection –> balance between virus and host
3.latent: few virus-proteins/RNA are expressed –> no infectious virus is produced due to molecular controls –> external stimuli drive activation
4.transforming: increased cell division rates –> carcinogenesis
5.abortive: reduced proliferation or poor virus/infection ratio (variation in replication-efficiency)
what are the reasons for formation of virus particle?
closed capsid to protect genome
specific entry of defined host
assembly of specific genome
allows budding at specific sites
what are the basic principles of viral replication?
virus entry –> uncoating –> genome replication and protein synthesis –> virus assembly and maturation –> virus release
viral protein synthesis only by host cell machinery
How do eneveloped viruses enter and leave cells?
envelope=lipid bilayer –> entry via membrane fusion and exit via budding
what are the amplification schemes of viruses?
1.eclipse: infectious particles invade and dissociate
2.burst: release of huge numbers of progeny per cell
3.stationary phase: end of viral replication due to death of host cell or limited host factors
what are the effects of virus infection on cell culture?
cytopathic effect
appearance of inclusion bodies
what is tropism and what is it determined by?
host specifity and tissue specifity
determined by:
receptors on cell surface (virus binding)
cell type specific promoter enhancer elements
host factors for entry, gene expression, assembly, transport
entry route in organism, kind of inoculation
what does the viral genome code for and what does it not code for?
it encodes for: particle generation and genome packing, genome replication, regulation of replication cycle, antagonists of celluallar defence mechanism and spread to other cells/organisms
it does not code for:
protein synthesis machinery, enzymes of energy metabolism, factors of membrane biogenesis, telomers and centromers
what forms can a viral genome have?
DNA: single stranded or double stranded (with gap possible)
RNA: positve stranded (=mRNA), negative stranded, double stranded, they can be segmented or non segmented
linear
circular
segmented
what determines the replication pathway?
nature of genome
what strategies are used to copy a RNA genome without loss of information?
-virus encodes RNA-dependent RNA poylmerase or reverse transcriptase
-RNA elements control replication and transcription in cis
-initiation without a Primer for de novo synthesis of RNA
-priming with protein primer
what strategies are used to generate translateable mRNA in RNA viruses?
capping
polyadenylation
cap snatching
IRES elements
give examples of DNA, RNA and enveloped/naked viruses and the form of the genome
enveloped DNA: Pockenviren (dsDNA linear), Herpesviren (ds DNA linear), Hepadna Viren
naked DNA: Adenoviren (ds DNA linear), Papovaviren, Parvoviren (ssDNA)
enveloped RNA: retroviren, Flaviviren, Coronaviren, Filovire, Paramoxyvireb
naked RNA: Reoviren (dsRNA), picornaviren (ssRNA), Caliciviren (ssRNA)
what are limiting factors for genome size?
-time required for genome replication
-capsid size
-RNA stability
-precision of replicase
what is the baltimore scheme?
. +DNA
v
+RNA > -DNA > +-DNA
v
+RNA >-RNA >+mRNA < +-RNA
^-RNA
what are the pathways from genome to mRNA? (!)
the virus genome:
1.serves as mRNA in + strand RNA virus
2.viral RdRp transcribes mRNA in -strand viruses and dsRNA viruses
3.viral RT transcribes genome into dsDNA and cellular DdRp transcribes mRNA in retroviruses
4.cellular DdRp transcribes mRNA in ds DNA viruses
5.viral DdRp transcribes mRNA in Poxviruses
6.replication of genome into dsDNA and transcription by cellular DdRp in ss DNA viruses
where does viral replication take place?
-Poxvirus: Cytoplasm
-RNA viruses dependent on RdRp: cytoplasm
-DNA viruses: nucleus
which Polymerases use Primers?
-no primer: RdRp but specific site
-Primer: DdDp
how are DNA viruses replicated? what are the two mechanism for dsDNA synthesis
1.Replication fork (RNA primer)
2.Strand displacement (never RNA primer)
how is the Polyomavirus replicated?
+-DNA to either +-DNA or mRNA and then to protein. Eventually packed
-replication starts at origin
-genome is complexed with histones
-temporally and quantitatively controlled genome
-SV40 replication
how does the SV40 replicaton work?
highly similar to eukaryotic
1.T-Antigen (hexamer) binds in presence of ATP
2.RPA binds, unwinding of DNA under ATP hydrolysis
3.DNA Pol a-primase binds to each singe strand and synthesizes short pices of RNA (=primers). Interaction between Pol and T-Ag –> Pol-a/Primase replaced by Pol-delta complex
4.Topo I, II, T-ag unwind DNA
5.leading strand is synthezised by pol-delta, RF-c and PCNA
6.lagging strand is synthesized in Okazagi fragments by pol-a and pol-delta, PCNA. RNase removes primers, pol-delat fills gap, ligase ligates fragments
how is the adenovirus replicated?
-protein Primer
-virus encoded replication machinery like DdDp (takes place in nucleus)
-transcription via Pol II and III
-splicing
-all mRNA with identical leader sequence
-synthesis of early proteins (modulate cell cycle, DNA replication, block apoptosis) and late proteins (cell lysis, virion assembly)
-only leading strand, no lagging strand, no RNA primers
what are the 3 main goals of early adenovirus gene expression?
- induce the host cell to tenter the S phase
- set up viral system to protect the infected cell from various antiviral defenses from the host
3.synthesize gene products needed for viral DNA replication and later for synthesis of viral structural proteins
how are dsDNA Herpesviruses replicated? How many ORFs? Where does replication take place?
-differential gene regulation: has immediate early, early and late gene
-84 ORFS
-replication in nucleus
-concatamers
how is the Parvovirus replicated?
+DNA is converted to +-DNA. The +-DNA is converted to mRNA –> then to Protein AND to + DNA and - DNA which is then also packed into the virus
5’ and 3’ hairpins
3’ hairpin serves as primer
5’ covalently bound to viral protein
how is the Hepadna virus (HBV) replicated?
-partially single stranded (part of + strand is missing)
-RT bound to 5’ end of -DNA strand
-plus strand has cap at 5’end
-host enzyme completes + Strand to covalently closed circular (ccc) form
-cellular Pol II transcribes mRNA
-this is used by RT –> synthesizes a partiell dsDNA in capsid
what are the types of polarity of RNA viruses?
+ strand: mRNA polarity
-strand: complementray to mRNA –> no direct transcribtion
ambisense: one RNA serves as both
how is a + strand RNA virus replicated and translated?
translation immediately after infection
replication by viral RdRp in cytoplasm, capping by viral enzymes
how can the coding capacity be enlarged in + Strand RNA viruses?
polyprotein
subgenomic mRNAs
ribosomal frameshifting
nonsense suppression
how is poliovirus replicated?
+ strand
-RNA encodes polyprotein
-proteolytic processing
-protein as primer
-no 5’ cap but IRES for initiation of translation
how are reoviruses replicated?
11 ds RNA segments (+ strand)
each segment is template for monocistronice mRNA
RdRp is packaged into capsid
templates remain in capsid
cotranscriptional export of mRNA from capsid
how are - strand RNA viruses replicated?
-genome serves as template for mRNA synthesis
-always in complex with proteins
-viral RdRp alsways packaged in virion
What is the function of the viral RdRp (in Rhabdovirus)? (!)
-transcribes antigenome/genome
-transcribes 5 monocistronic mRNAs
-capping
-polyadenylation
what are the characteristics of + strand RNA viruses with DNA intermediates (retroviridae)?
diploid: 2 + strand RNAs each complexed with tRNA as primer
serves as template for DNA synthesis
has reverse transcriptase and viral integrase to integrate viral DNA into host cell genome
cellular pol II transcribes mRNAs from integrated viral genome
splicing and frameshifting take place
Which model explains the transition from initiation to elongation for different DNA viruses?
sliding back (jumping back) model
