Download RNA Viruses

RNA VIRUSES
ALL SORTS OF STRATEGIES
RNA Viruses
• All synthesize through
a double stranded
intermediate - RI replication
intermediate
• RNA dependent RNA
polymerase of viral
origin but may need
host factors
• Termini contain
recognition signals for
replicase
Positive strand viruses
• Begin with translation to
produce replicase
• Makes more positive than
negative strand
– Limiting factor or rapid
packaging so can’t act
as template
• Poliovirus uses VPg
linked to nucleotides as
“primer” - like Ad
Negative Strand Viruses
• Contain enzymes for transcription in virion
• Make mRNA prior to antigenome
– Message gets capped; genome does not
• Plus strand is template for minus strand genome
• Makes more minus than plus strand
dsRNA viruses - conservative
replication
• Uncoating activates
enzymes that produce
mRNA
• + RNA also gets packaged
• Then complementary RNA is produced
• No dsRNA free in cell
• Protects against IF
induction
Transcription challenges
• Less temporal control than
in DNA viruses
• Monogenic problem
– Segmented genomes
usually have individual
genes
– Polyprotein cleavage
• What would expect to see
on gel in early stages of
infection? As infection
progresses?
• What if you performed a
pulse-chase experiment?
Translation challenges: Recognition by ribosomes
and competition from host
• Synthesize own cap
(Reo in cytoplasm)
• Steal from host
(Influenza in
nucleus)
• Use host enzymes
• IRES
Transcription strategies: Togaviruses
• NS at 5’ end - S at 3’
• In vitro only synthesize
NS proteins; stop signal
leads to polyprotein
• In vivo get shorter mRNA
only after minus strand
synthesis that codes for S
polyprotein
• Internal transcription site
on minus strand
• Minus is template for
mRNA and for genome
• S message is more
abundant than NS as
genome gets packaged
Coronaviruses: frame-shifts and subgenomic
RNAs
• Genome translated into
replicase
• Antigenome produced
• Subgenomic mRNAs represent
a nested set of RNAs - all share
short 5’ sequence and a 7 base
sequence but have unique AUG
site and share 3’ end of genome
• May be produced by jumping
polymerase - 7 base sequence in
various parts of genome
– Get recombinant viruses
with mixed infections
– DI particles are common
Influenza virus - segmented negative strand
antigenic drift (mutations) vs shift (reassortment)
Influenza - negative strand virus
• Replication in nucleus
using viral enzymes but
need host RNA-P to
function
• Virion enzyme cleaves cap
from host mRNA and uses
it to extend; adds poly A
tail
• One gene per segment
except for two segments
producing spliced mRNAs
in two different reading
frames yielding two
proteins
Ambisense genomes
• Bunyaviridae such as
Hantavirus
• Genome is used to make
short positive mRNA
• Genome is replicated and
antigenome (plus strand)
is used to make second
mRNA
• Antigenome does not act
as message
Nonsegmented negative strand viruses:
Mononegavirales (rhabdo, filo, paramyxo)
• Hypothesis: Start-stop
• Template 3’ end start point for
virion L (RNA_P) and goes to
termination signal and mRNA
release - then cap and poly A
added
• Some polymerase reinitiates at
next initiation signal and goes
to termination; process repeats
• Each subsequent RNA may be
produced at a lower frequency
(20-30% less)
• Replication requires N capsid
and NS proteins to read through
to complete copy
Retroviruses: diploid ssRNA with
repeats at ends
• RT needs a primer - uses tRNA
at primer binding site
• Synthesized to end and jumps
to 3’ end of strand
• Uses PPT as template for
second strand
• Makes another jump
• Results in dsDNA with Long
Terminal Repeats
– Needed for integration
– Contains promotor and
regulatory regions
– Poly A site
Transcription occurs after integration
• Uses host RNA-P
• May require host factors
to enhance (cell tropism)
• Polyprotein and splicing
strategies
HIV is a more complex retrovirus
• Transactivator protein
(TAT) needed for high
level of transcription
• TAT binds to TAR RNA
and causes readthrough
beyond 5’ region
REV binds to REV Response Element
(RRE) in message
• Early messages are highly
spliced and produce
mainly TAT, REV and Nef
• When REV increases and
binds to message, there is
less splicing
• Leads to synthesis of gag,
pol, env
•