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Chapter
16
Retroviruses
And
retroposons
16.1 Introduction
16.2 The retrovirus life cycle involves transposition-like
events
16.3 Retroviral genes codes for polyproteins
16.4 Viral DNA is generated by reverse transcription
16.5 Viral DNA integrates into the chromosome
16.6 Retroviruses may transduce cellular sequences
16.7 Yeast Ty elements resemble retroviruses
16.8 Many transposable elements reside in D. melanogaster
16.9 Retroposons fall into two classes
16.10 The Alu family has many widely dispersed members
16.1 Introduction
Retroposon is a transposon that mobilizes
via an RNA form; the DNA element is
transcribed into RNA, and then reversetranscribed into DNA, which is inserted at
a new site in the genome.
9.1 Introduction
Figure 16.1 The reproductive
cycles of retroviruses and
retroposons involve
alternation of reverse
transcription from RNA to
DNA with transcription
from DNA to RNA. Only
retroviruses can generate
infectious particles.
Retroposons are confined to
an intracellular cycle.
16.2 The retrovirus life cycle
involves transposition like events
LTR is an abbreviation
for long-terminal repeat.
16.2 The retrovirus
life cycle involves
transposition like
events
Figure 16.2 The
retroviral life cycle
proceeds by reverse
transcribing the RNA
genome into duplex
DNA, which is inserted
into the host genome, in
order to be transcribed
into RNA.
16.2 The retrovirus life cycle involves
transposition like events
Figure 16.3 The genes of the retrovirus are expressed
as polyproteins that are processed into individual
products.
16.2 The retrovirus life cycle involves
transposition like events
Figure 16.4
Retroviruses (HIV)
bud from the
plasma membrane
of an infected cell.
Photograph kindly
provided by
Matthew Gonda.
16.2 The retrovirus life cycle involves transposition like events
Figure 16.5
Retroviral RNA
ends in direct
repeats (R), the
free linear DNA
ends in LTRs,
and the
provirus ends
in LTRs that
are shortened
by two bases
each.
16.2 The retrovirus
life cycle involves
transposition like
events
Figure 16.6 Minus strand
DNA is generated by
switching templates
during reverse
transcription.
16.2 The retrovirus
life cycle involves
transposition like
events
Figure 16.7 Synthesis of
plus strand DNA requires
a second jump.
16.2 The retrovirus life cycle involves
transposition like events
Figure 16.9 Integrase
is the only viral
protein required for
the integration
reaction, in which
each LTR loses 2 bp
and is inserted
between 4 bp repeats
of target DNA.
16.2 The retrovirus life
cycle involves
transposition like events
Figure 16.8 Copy choice
recombination occurs when
reverse transcriptase releases its
template and resumes DNA
synthesis using a new template.
Transfer between template
strands is probably occurs
directly, but is shown here in
separate steps to illustrate the
process.
16.3 Retroviruses may
transduce cellular sequences
Helper virus provides functions
absent from a defective virus,
enabling the latter to complete the
infective cycle during a mixed
infection.
16.3 Retroviruses may transduce cellular sequences
Figure 16.10 Replication-defective transforming viruses
have a cellular sequence substituted for part of the viral
sequence. The defective virus may replicate with the
assistance of a helper virus that carries the wild-type
functions.
16.3 Retroviruses may transduce cellular sequences
Figure 16.11 Replicationdefective viruses may be
generated through
integration and deletion
of a viral genome to
generate a fused viralcellular transcript that is
packaged with a normal
RNA genome.
Nonhomologous
recombination is
necessary to generate
the replication-defective
transforming genome.
16.4 Yeast Ty elements resemble retroviruses
Figure 16.12 Ty
elements terminate in
short direct repeats
and are transcribed
into two overlapping
RNAs. They have two
reading frames, with
sequences related to
the retroviral gag and
pol genes.
16.4 Yeast Ty elements
resemble retroviruses
Figure 16.13 A unique Ty
element, engineered to
contain an intron,
transposes to give copies
that lack the intron. The
copies possess identical
terminal repeats, generated
from one of the termini of
the original Ty element.
16.4 Yeast Ty elements resemble retroviruses
Figure 16.3 The genes of the retrovirus are expressed
as polyproteins that are processed into individual
products.
16.4 Yeast Ty elements resemble retroviruses
Figure 16.4
Retroviruses (HIV)
bud from the
plasma membrane
of an infected cell.
Photograph kindly
provided by
Matthew Gonda.
16.4 Yeast Ty elements resemble retroviruses
Figure 16.5 Retroviral
RNA ends in direct
repeats (R), the free
linear DNA ends in
LTRs, and the
provirus ends in
LTRs that are
shortened by two
bases each.
16.4 Yeast Ty elements
resemble retroviruses
Figure 16.6 Minus strand
DNA is generated by
switching templates
during reverse
transcription.
16.4 Yeast Ty elements resemble retroviruses
Figure 16.14 Ty
elements
generate viruslike particles.
Photograph
kindly provided
by Alan
Kingsman.
16.5 Many
transposable elements
reside in D.
melanogaster
Figure 16.15 Three types
of transposable element
in D. melanogaster have
different structures.
16.5 Many
transposable elements
reside in D.
melanogaster
Figure 16.15 Three types
of transposable element
in D. melanogaster have
different structures.
16.6 Retroposons fall into two classes
Alu family is a set of dispersed, related sequences,
each ~300 bp long, in the human genome. The
individual members have Alu cleavage sites at each
end (hence the name).
Processed pseudogene is an inactive gene copy that
lacks introns, contrasted with the interrupted structure
of the active gene. Such genes presumably originate by
reverse transcription of mRNA and insertion of a
duplex copy into the genome.
16.6 Retroposons fall into two classes
Figure 16.16 Retroposons can be
divided into the viral or nonviral
superfamilies.
16.6 Retroposons fall into two classes
Figure 16.17
Retroposons
of the viral
family have
terminal
repeats and
include open
reading
frames.
16.6
Retroposons fall
into two classes
Figure 16.6 Minus
strand DNA is
generated by
switching
templates during
reverse
transcription.
16.6
Retroposons fall
into two classes
Figure 16.18
Retrotransposition of nonLTR elements occurs by
nicking the target to provide
a primer for cDNA synthesis
on an RNA template.
16.6 Retroposons fall into two classes
Figure 16.19 Pseudogenes could arise by
reverse transcription of RNA to give duplex
DNAs that become integrated into the
genome.
16.6 Retroposons fall into two classes
Figure 23.11 An
intron codes for an
endonuclease that
makes a doublestrand break in
DNA. The
sequence of the
intron is duplicated
and then inserted at
the break.
16.7 Summary
•Reverse transcription is the unifying mechanism
for reproduction of retroviruses and perpetuation of
retroposons.
•Retroviruses have genomes of single-stranded
RNA that are replicated through a double-stranded
DNA intermediate.
•Reverse transcriptase is the major component of
pol, and is responsible for synthesizing a DNA
(minus strand) copy of the viral (plus strand) RNA.
16.7 Summary
•Switches in template during nucleic acid
synthesis allow recombination to occur by
copy choice.
•The integration event generates direct target
repeats (like transposons that mobilize via
DNA).
•Another class of retroposons have the
hallmarks of transposition via RNA, but
have no coding sequences (or at least none
resembling retroviral functions).