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BIOL 3155 Lecture Notes - Rous Sarcoma Virus, Ribonuclease H, Stem-Loop

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BIOL 3155
K.Andrew White

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Chapter 28: Retroviruses
Genome is (+) sensed but not directly translated when it goes into cells
Brief History Table 1.2
o First discovery of retrovirus was by Peyton Rouse (1911). Showed that sarcoma virus
could induce tumor formation in chickens. Won nobel prize is 1966.
o RT in retroviruses discovered by Temin and Baltimore (1971), nobel prize in 1975.
discovered RT, against central dogma.
o Dogma was that flow went from DNA to RNA to protein.
o But, opposite is true for retroviruses with RT (it converts RNA to DNA)
o Cellular oncogenes in retrovirus discovered by Bishop and Varmus, Tumor caused by Rous
sarcoma virus acquiring an altered cellular oncogene
Retroviridae (family)
o Consists of 7 genera
o Grouped based on differences in morphology and genome organization
o Table 28.1
o alpha, beta, gamma, delta, epsilon- retroviruses. Lentivirus causes HIV-1 in humans.
(missed pic, but basically these r the viruses she mentioned).
Do not need to know example of virus, but know host.
Focus on Lentiviruses, example, and host.
General Structure of Virion
o Figure 28.1
o Virus contains envelope.
o Icosahedral or conical for capsid (capsid = HIV).
o Approximately 100 nm across
o Contains RT, integrase (IN) and protease (PR). 3 different enzymes. Protease is outside
particle but inside matrix.
o Virus contains tRNA which is important because it is used as a primer.
o Virus contains two copies of RNA genome. These are diploid and dimerized have
partial base pairing to each other that keeps them together
o Both copies may not be identical. May have single or multiple mutations. This is due to
RNA-RNA interactions.
o Contains transmembrane protein (TM). Surface protein (SU - noncovalently bound to TM).
Matrix protein (MA - under envelope; coats inside of the envelope). Capsid protein (CA;
the one that actually forms the icosahedral capsid). Nucleocapsid protein (NC - directly
coats genome RNA)
General Genome Structure
o Positive sense single stranded RNA. (+)ssRNA
o Approx 7 10 kb
o Figure 28.2
Represents simple retroviral genome (more complex retroviruses will contain more
genes; e.g. HIV-1 is a complex retrovirus)
All retroviruses have 5’ cap and 3’ poly-A tail (virion genome is not translated, however
this is not how they initiate an infection). Not grouped with (+)RNA viruses.
Repeated sequence (R) at 5’ and 3’ ends.

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Unique regions (U5) (contain dimerization RNA hairpin; where the two copies of the
genome will interact for dimerization) and U3
Contains primer binding sequence (PBS) there are tRNAs in particle; these bind to
PBS. tRNA type is virus/strain dependent. this is where the tRNAs bind. the tRNA would
be used as a primer??
There are also splice sites (SS 5’ splice site and 3’ splice site).
There is also a packaging signal (psi) important (must be present)for identifying viral
genome as what needs to be packaged and put into particles.
Polypurine tract (a run of As abd Gs) plays important role during replication cycle.
3 genes involved: (listen here)
Gag (group-specific antigen)
Pol (polymerase) pol genes are expressed by readthrough or frameshift
Env (envelope) env genes are expressed from spliced mRNA
Genes are polyproteins expressed fused to each other. Depending on virus, will have
either a readthrough or frameshift event that will extend Gag into Pol.
we have 3 genes but more than 3 proteins.
Overview of Entry
o Figure 28.3
Binding of SU to the receptor (virus/cell specific). SU is attachment protein.
Fusion at surface (or endocytosis and pH dependent fusion for some viruses). but in both
cases it's mdiated by the black receptor on the pic? Fusion is TM-dependent (TM is
involved in fusion).
Capsid is delivered into cytosol. Often, the capsid is referred to as a core.
RT occurs inside the core (in cytosol). RNAs are never released into cytosol; they are
used as template for RT while in core.
Net result is ssRNA is converted into dsDNA. Entire core is transported into nucleus
through NP (Nuclear pore occurs for Lentiviruses [i.e. HIV]).
For most retroviruses, core can only be transported after nuclear envelope is broken
down. This only occurs during cellular division.
There is then integration (integrase protein is involved with this). dsDNA integrated into
genome; becomes part of host. Can replicated now along with host genome.
Reverse Transcription (whole thing is mediated by Reverse Transcriptase)
o Figure 28.4
o In order for ssRNA genome to be converted into dsDNA, you need RT. RT in its active
form is a dimer.
conversion of viral genome into dsDNA. (vRdDp & vDdDp)
Ribonuclease H (RNase H) will degrade RNA only when it is present in a RNA-DNA
o Viral genome (black) goes from 5’ end (left) to 3’ end (right).
o First, tRNA (present in viral particle) base pairs to PBS. tRNA is serving as a primer (will
provide 3’ hydroxyl group to which additional nucleotides can be added).
o RT will bind to primer and extend it. This is called synthesis of minus-strand strong-stop
DNA. (1st step)
o DNA is shown in black in the figure. (small DNA sequence)
o RNase H now digests RNA in DNA-RNA hybrid. At end of DNA strand, we now have
copy of repeated sequence (R’). (2nd step)
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