Transposons
Chapter 21
高雄醫學大學
生物醫學暨環境生物學系
張學偉 助理教授
Email: changhw@kmu.edu.tw 分機: 2691
21.1 Introduction
Evolution of genomes via:
1. Acquisition of new sequences- horizontal
transfer of genetic material between genomes by
extrachromosomal elements
2. Rearrangements of existing sequencestransfer within the genome
2
1. Acquisition of new sequences- horizontal transfer
of genetic material between genomes by extrachromosomal elements
a) Bacteria- plasmids move by conjugation (F plasmid,
Hfr)
b) Phages – spread by infection (transduction)
c) Both can transfer host genome with its own replicon
3
2. Rearrangements of existing sequencestransfer within the genome
a) Unequal recombination- mispairing in homologous
recombination
b) Nonreciprocal recombination- results in duplication
of loci; one copy- original function, the other- evolves
c) Transposable elements (transposons)
4
Figure 21.1
5
Transposons (transposable elements)
definition
“discrete sequences in the genome that are
mobile- able to transport themselves to
other locations within the genome.”
6
Basic concept for Transposons
1. Move directly from one site in the genome to
another (do not need other vectors)
2. not rely on any relationship between sequences at
the donor and recipient sites- Non-homologous
recombination.
3. Internal counterpart to vectors that move
sequences between genomes (phages & plasmids).
May provide a major source of mutations in the
genome.
4. Two classes: a) DNA transposon; b) Retroviruses
& retroposons
5. Transposons found in both prokaryotes and
eukaryotes.
7
Bacterial vs. Eukaryotic Tranaposons
Bacterial transposons carry genes that
transpose themselves.
Eukaryotes
• Although many are defective (lost ability to
transpose independently) and rely on the
enzymes from a few functional transposons.
• Many number and variety of transposons
included.
8
Transposable elements can promote
rearrangement of the genome directly or indirectly:
• directly (Tn itself)
1.cause deletions or inversions or
2.lead to movement of host sequences to new
locations.
• indirectly
1.serve as substrates for cellular recombination
systems as “portable regions of homology”
2.two copies-sometimes on different
chromosomes in eukaryotes- provide sites for
reciprocal recombination.
3.These types of exchanges lead to deletions,
insertions, inversions, or translocations.
9
Natural selection view for Transposons
Neither advantage nor disadvantage on the
phenotype.
But the selfish DNA concerned only with its
own propagation (parasite to the genome;
yet-selective advantage)
Is an independent entity that residues in the
genome.
10
Good comment for Transposons
• Any transposition event conferring a
selective advantage, e.g., genetic
rearrangement.
• It will lead to preferential survival
11
Other features of Transposon
1. Transposons are DNA elements that
transpose to different places on the DNA.
2. Transposition is the movement of the
transposon.
3. It requires special protein factors
particularly to cut and ligate the DNA
 transposase
4. NO homology is required between the
transposon and the target sequence.
5. First identified in bacterial operonspontaneous silencing.
12
21.2 Insertion Sequences Are Simple
Transposition Modules
KEY CONCEPT
• An insertion sequence is a transposon that
codes for the enzyme(s) needed for
transposition flanked by short inverted
terminal repeats (IR, ITR).
• is closely related rather than identical
• at the ends of transposon
• are autonomous unit- sponsors its own
transposition
• Recognition of the ends (IR)- critical in transposition;
point mutations abort it
13
• IR (inverted terminal
repeat)
KEY CONCEPT
• The target site is
 random, hotspots, or
preferred (bent DNA;
DR
IR
consensus sequence;
inactive region).
 duplicated during insertion
forms DR (direct repeat).
• The length of the DR is:
– characteristic for any particular
transposon
Figure 21.2
KEY CONCEPT
14
Rate comparison
1. Rate of transposition:
~10-3-10-4 per element per generation
2. Rate of spontaneous mutation:
~10-5-10-7 per generation
3. Rate of reversion (by precise excision of the IS
element)
~10-6-10-10 per generation
~103 times less frequent than insertion
15
21.3 Composite Transposons Have IS Modules
IS-L
IS-R
KEY CONCEPT
• Composite transposons have a central
region flanked by an IS element at each end.
• Central region carry other genes (antibiotic
resistance or other markers).
• IS elements only carry enzymes needed for
transposition (transposase, resolvase).
16
KEY CONCEPT
• Either one or both of the
IS elements of a
composite transposon
may transposition.
• A functional IS module
can transpose either
itself (Fig.21.2) or the
entire transposon
DR
• An active IS element at
either end may also
transpose independently.
IR
NOT identical but close related
17
Figure 21.3
Mobility frequency:
IS10 > Tn10
Transposition frequency declines
with distance between IS10.
 length-depend factor
determines the size of common
composite Tn.
With marker
 high freq. under selection > IS10
Inside-out
Figure 21.04: IS elements can mobilize other sequences.
19
Summary on Transposons
1. The smallest transposons are called insertion
sequences (IS elements).
2. IS elements have inverted repeats at either end and
a transposase gene in between; they do NOT have any
resistance or other markers.
3. Transpoase is responsible for:
(1) creating a target site (random, or consensus seq);
(2) recognize the ends (IS) of the transposon.
4. Two IS elements flanking a marker gene(s) form a
composite transposon.
20
21.4 Transposition Occurs by Both Replicative and
Nonreplicative Mechanisms
KEY CONCEPT
All transposons
use a common
mechanism
1
The stagger between
the cuts determines the
length of the direct
repeats.
2
ATGCA
TACGT
corrected
3
The target repeat is
characteristic of each
transposon; reflects the
geometry of the cutting
enzyme
21
Figure 21.5
KEY CONCEPT
• The order of events and exact nature of the
connections between transposon and target DNA
determine whether transposition is:
– Replicative & Nonreplicative (cut-and-paste)
The use of staggered ends is common to all
transpositions: three types
• Replicative [R] TnA
• Nonreplicative [N] IS, Tn10 and Tn5
• Conservative [C] (nonreplicative)
• Some Tn use only one type
• Others multiple types: R and N/C  IS1, IS903,
R or N/C  phage Mu
22
Animation
23
Replicative
Figure 21.6
Transposon is duplicated; a copy of the original element is
made at a recipient site (TnA); donor keeps original copy
Transposition- an increase in the number of Tn copies
ENZs: transposase (acts on the ends of original Tn) and
resolvase (acts on the duplicated copies)
24
Nonreplicative
Figure 21.7 Nonreplicative transposition
a) Transposon moves from one site to another and is conserved;
breaks in donor required host repair system.
b) IS, Tn10 and Tn5 use this mechanism; no Tn copy increase
c) ENZs: only transposase
25
Conservative (nonreplicative)
P.851
Epiosome: is a plasmid able to
integrate into bacterial DNA
Figure 21.08: Movement conserves bonds.
a) Tn excised from donor and inserted in target –
• every nucleotide bond is conserved like in lambda
integration (Site-Specific Recombination)
• large elements (episomes?)
b) ENZs: transposase (related to l integrase family)
26
21.5 Transposons Cause Rearrangement of DNA
KEY CONCEPT
• Homologous recombination between multiple
copies of a transposon causes rearrangement
of host DNA. [deletion, inversion]
• Homologous recombination between the
repeats of a transposon may lead to precise or
imprecise excision.
27
IS1L
Step 1
IS1R
Recombination using
cellular enzymes
Tn inserts a copy at a
second site near its
original location
Step 2
Lost from
the cell
Single copy on
chromosome
Reciprocal recombination
between two copies of the
transposon
•recombination between two elements
in same orientation (DR)
Figure 21.09: Direct repeats recombine to excise material.
28
(A)
(B)
(B)
 not relies on Tncoded function
(A)
(B)
Recombination
using cellular
enzymes
(A)
•recombination between two
elements in opposite
orientation (IR)
Figure 21.10: Inverted repeat recombination inverts material.
P859
Excisions not supported by Tn’s:
Precise excision - removes transposon & one copy of duplicated sequence;
rare Tn10= ~10-9; recombination between 5-9 bp duplicated target sequences
Imprecise excision - leaves a remnant of the transposon; Tn10= ~10-6.
P854
sufficient to prevent target gene reactivation.
29
recombination between 24 bp IS-modules of a composite Transposon
21.6 Common Intermediates for Transposition
Both replicative and non-replicative transposition
use a common mechanism:
IS elements, prokaryotic & eukaryotic transposons,
and bacteriophage Mu, retroviral DNA and the first
stages of immunoglobulin recombination use the
similar mechanism.
KEY CONCEPT
• Transposition starts by forming a strand
transfer complex.
– The transposon is connected to the target site
through one strand at each end. (1 x 2)
30
Joining transposon to its targetcommon pathway
1. Synapsis stage- two ends of
transposon are brought together
[shown after cleavage but actually occurs previously]
2. Transposon nicked at both ends;
target nicked at both strands
3. Nicked ends joined crosswise;
covalent connection between the
transposon and the target
31
KEY CONCEPT
•
1
MuA
tetramer
2
The Mu transposase forms
the complex by:
1. synapsing the ends of Mu DNA
2. followed by nicking
3. then a strand transfer RX
Next step differs and determines the
type of transposition:
Replicative transposition follows if the
complex is replicated.
3
Nonreplicative transposition follows if it
is repaired.
Animation show the detail
Figure 21.12
32
• Mu integrates by nonreplicative transposition;
1
MuA also
binds to
internal siteneeded for
complex
formation
but not
strand
cleavage
2
• during lytic cycle- number of copies amplified
by replicative transposition
A Mu transposon passes through 3
stable stages:
- MuA binds to ends as tetramer
forming a synapsis.
- MuA subunits act in trans to cut
next to R1 and L1 (coordinately; two active
sites to manipulate DNA).
cuts in
trans
3
transfers
in trans
- MuA acts in trans to cut the
target site DNA and mediate in
trans strand transfer
33
Figure 21.12
1
2
In strand transfer complex
transposon is connected to the target
site through one strand at each end
cuts in
trans
3
transfers
in trans
34
Figure 21.12
The MuB protein chooses targets;
1
Mu Tn moves >10-15 kb away from
original site (target immunity).
2
MuB binds to the MuA-Mu DNA
complex; MuA causes MuB to
hydrolize ATP; MuB released from the
donor DNA.
3
MuB binds nonspecifically to the
target DNA and stimulates the
recombination activity of MuA in
transposition complex.
MuA clears MuB from the donor gives preference for transposition to
35
the target.
Figure 21.12
21.7 Replicative Transposition Proceeds through a
Cointegrate
KEY CONCEPT
•
Replication of a strand
transfer complex
generates a cointegrate:
– A fusion of the donor and
target replicons.
•
(homolgous recombination)
by resolvase
The cointegrate has two
copies of the transposon.
– They lie between the
original replicons.
36
Figure 21.13
KEY CONCEPT
• Recombination between the transposon copies
regenerates the original replicons, but the
recipient has gained a copy of the transposon.
• The recombination reaction is catalyzed by a
resolvase coded by the transposon.
37
Figure 21.14: Mu transposition uses a
crossover intermediate.
38
21.8 Nonreplicative Transposition Proceeds by Breakage and
Reunion
KEY CONCEPT
• Nonreplicative transposition results if:
– a crossover structure is nicked on the unbroken pair of
donor strands and
– the target strands on either side of the transposon are
ligated
donor
target
39
Figure 21.15
KEY CONCEPT
• Two pathways for nonreplicative transposition
differ according to whether:
– the first pair of transposon strands are joined to the
target before the second pair are cut (Tn5), or
– whether all four strands are cut before joining to the
target (Tn10)
40
KEY CONCEPT
• Two pathways for
nonreplicative transposition
differ according to :
– whether all four strands
are cut before joining to
the target (Tn10) or
– whether the first pair of transposon
strands are joined to the target
before the second pair are cut (Tn5),
41
Figure 21.16: Transposition can use cleavage and ligation.
• Two pathways for
nonreplicative transposition
differ according to :
1. nicking
2.interstrand Rx
3
4. cleavage
– whether all four strands are cut
before joining to the target (Tn10) or
– whether the first pair of
transposon strands are
joined to the target before
the second pair are cut
(Tn5),
Figure 21.17: Tn5 is cleaved from flanking DNA.
42
dimer
Tn 5 and Tn 10 transposases
both function as dimers.
Figure 21.18: Transposon ends are joined.
43
21.9 TnA Transposition Requires Transposase and
Resolvase
KEY CONCEPT
• Replicative transposition of TnA requires:
– a transposase to form the cointegrate structure
– a resolvase to release the two replicons
• The action of the resolvase resembles lambda Int
protein.
• It belongs to the general family of topoisomerase-like
site-specific recombination (SSR) reactions.
– They pass through an intermediate in which the protein is
44
covalently bound to the DNA.
(38bp)
Internal res site
Transposase
Limiting factor
in transposition
feedback
Dual role
• Resolvase
• Repressor
(mutant ↗ Tn freq)
Control regions
Figure 21.19: TnA transposon organization is conserved.
TnA features
•Replicative Tn,
•Non-IS-dependent,
•DR (~5bp) generated
at target sites.
Res
1. Can be replaced by RecA-mediated general recombination, but less efficient.
2. 15-20 bp of res site are identical to att.
3. But protein mechanism is different: res- intramolecular resolution.
Att- intermolecular resolution
45
21.10 Transposition of Tn10 Has Multiple Controls
inactive
IS10L
Promoter
RNA stable
strong
weak
OUT RNA function as
an antisense RNA.
One copy  no effect
5 copies  significant
Figure 21.20: Tn10 has two promoters.
KEY CONCEPT
• Multicopy inhibition reduces the rate of transposition of any one
copy of a transposon when other copies of the same
46
transposon are introduced into the genome
Tn must maintain min freq to
survive, but too great freq
may damage the host cells.
Figure 21.21
KEY CONCEPT
• Multiple mechanisms affect the rate of transposition.
47
21.11 Controlling Elements in
Maize Cause Breakage and
Rearrangements
KEY CONCEPT
• Transposition in maize was
discovered because of the
effects of chromosome
breaks.
– The breaks were generated
by transposition of
“controlling elements
(Transposon)- Ds element.”
48
Figure 21.22: Transpositions are clonally inherited.
KEY CONCEPT
dominant
(site for chr. breakage)
recessive
Figure 21.23. A break at controlling element
causes loss of an acentric fragment
• The break generates
one chromosome that
has:
– a centromere
– a broken end
– one acentric fragment
• The acentric fragment
is lost during mitosis;
– detected by the
disappearance of
dominant alleles in a
heterozygote.
49
KEY CONCEPT
• Fusion between the broken ends of
the chromosome generates
dicentric chromosomes.
– These undergo further cycles of
breakage and fusion.
• The breakage-fusion-bridge cycle
is responsible for the occurrence of
somatic variegation.
Figure 21.24 Ds provides a site to initiate the
chromatid breakage-fusion-bridge cycle.
50
21.12 Controlling Elements Form Families of
Transposons
KEY CONCEPT
Common feature
Each family of controlling
elements in maize has two
classes: autonomous and
nonautonomous
Specific feature
The numbers, types, and
locations of the control
elements are characteristic
for each maize strain.
Note! Ds = Dt
51
Figure 21.25
Mutator transposon is one of the simplest elements
MuDR (autonomous element) code for genes:
• mudrA codes for MURA transposase
• mudrB codes for nonessential accessory protein
In MuDR, de-methylation of the terminal repeats
increases transposase experssion.
52
May code for a repressor
Ac element of transposition
transposase
Ds elements have internal deletions.
That inactivate the transacting transposase
Ds is an incomplete
version of Ac itself
Figure 21.26: The Ac element gas five exons that code for a transposase;
Ds element have internal deletions.
•Ds alone could not induce the breakage. (need Ac)
•Transposition of Ac/Ds occurs by a non-replicative mechanism.
53
•Phage using Ac/Ds results in DNA methylation change.
KEY CONCEPT
• Autonomous controlling elements code for proteins
that enable them to transpose.
[note! Ds is coded for deleted form of transpoase; Ac is complete functional;
that is why always written in Ac/Ds system]
• Nonautonomous controlling elements have mutations
that eliminate their capacity to catalyze transposition
(internal sequences).
– They can transpose when an autonomous element provides
the necessary proteins via trans-acting transpoase.
• Autonomous controlling elements have changes of
phase (reversible), when their properties alter as a
result of changes in the state of methylation.
54
Transposable elements in eukaryotes:
Barbara McClintock (1902-1992)
Cold Spring Harbor Laboratory, NY
Nobel Prize in Physiology and Medicine 1983
“for her discovery of mobil genetic elements”
•
Studied transposable elements in corn (Zea mays) 1940s-1950s
(formerly identified as mutator genes by Marcus Rhoades 1930s)
Nonautonomous DNA tn (Ds) require the activator (Ac) to be in the
same cells.
55
21.13 Spm Elements Influence Gene Expression
KEY CONCEPT
• Spm elements affect gene expression at
their sites of insertion, when the TnpA
protein binds to its target sites at the ends
of the transposon.
• Spm elements are inactivated by
methylation.
56
defective
dSpm
Figure 21.27: Spm/En has two genes. tnpA a spliced 2500-bp mRNA
(Exon1-11); tnpB 6000-bp mRNA (containing ORF1+ORF2)
57
21.14 The Role of Transposable Elements in Hybrid
Dysgenesis
KEY CONCEPT
• P elements are transposons that are carried in
P strains of Drosophila melanogaster (fly), but
not in M strains.
• When a P male is crossed with an M female,
transposition is activated.
[Note! M male x P female, transposition is inactivated]
 hybrid dysgenesis
p853
58
• The insertion of P elements at new sites in these
crosses:
– inactivates many genes
– makes the cross infertile
• Dysgenesis is principally a
phenomenon of the germ
cells.
• P-specific sequences can
induce dysgenesis by
insertional inactivation.
• P-specific seq are many
(30-50 copies) and locate in
different chr., but not in M
strain.
= infertile
59
Figure 21.28 Hybrid dysgenesis is asymmetrical
21.15 P Elements Are Activated in the Germline
KEY CONCEPT
31bp
IR
Generate DR of target DNA (~8bp)
• P elements are activated in
the germline of P male x M
female crosses.
• This is because a tissuespecific splicing event
removes one intron (somatic
expression).
– This generates the coding
sequence for the
transposase.
60
Figure 21.29 Pelement has four exons; the first three are spliced together in somatic expression; all four are
spliced together in germline expression
KEY CONCEPT
No repressor
• The P element also
produces a
repressor of
transposition.
– It is inherited
maternally in the
cytoplasm.
Figure 21.30
•The presence of the repressor explains why M male x P female crosses remain fertile.
61
Retroviruses and Retroposons
Retro-transposons
Chapter 22
高雄醫學大學
生物醫學暨環境生物學系
張學偉 助理教授
Email: changhw@kmu.edu.tw 分機: 2691
Like a lysogenic bacteriphage
22.1 Introduction
Retroposons are confined
to an intracellular cycle.
Single strand
• Retrovirus Transposition involved RNA
intermediate is unique to
eukaryotes.
RNA  DNA  RNA
• Retroposon Transposition through RNA
intermediate. (similar)
Itself no transposition
activity but with active
element sequence
[with help from retrovirus]
63
Figure 22.1 Reproductive cycles (continuous) of retroviruses and retroposons.
22.2 The Retrovirus Life Cycle Involves
Transposition-Like Events
KEY CONCEPT
• A retrovirus has two copies of its genome
of single-stranded RNA.
• An integrated provirus is a doublestranded DNA sequence.
64
• A retrovirus generates a provirus by reverse
transcription of the retroviral genome.
Long terminal repeat
integrase
Figure 22.2
65
22.3 Retroviral Genes Codes for Polyproteins
A typical retrovirus has three genes
R seqment
gag & pol in different frame: gap >> gag-pol
polyA
5-cap
Continued
Env proteins
gap-pol
66
Figure 22.3
KEY CONCEPT
• Gag and Pol proteins are translated from a fulllength transcript of the genome.
• Translation of Pol requires a frameshift by the
ribosome.
• Env is translated from a separate mRNA that is
generated by splicing.
• Each of the three protein products is processed by
proteases to give multiple proteins.
67
比較
Viron- physical virus particles p.866
Viroid- small infected nucleic acids
without protein coats.
A process that is
reversed during infection
Figure 22.04: HIV buds from the membrane.
Photo courtesy of Matthew A. Gonda, Ph.D., Chief Executive Officer,
International Medical Innovations, Inc.
68
22.4 Viral DNA Is Generated by Reverse
Transcription
• Retroviruses are called Plus (+) strand
viruses because the viral RNA itself codes for
the protein products.
• Complementary DNA of Virus RNA called minus
(-) strand DNA.
•  another strand in duplex DNA called plus (+)
strand DNA.
• RNase H degrade the RNA part of RNA-DNA
hybrid.
69
22.4 Viral DNA Is Generated by Reverse
Transcription
KEY CONCEPT
R segment
A short sequence
(R) is direct
repeated at
each end of
the viral RNA.
– The 5’ and 3’
ends are RU5 and U3-R,
respectively.
70 in
Figure 22.5 Retrovirial RNA ends in direct repeat (R), the free linear DNA ends
LTR and the provirus ends in LTRs that are shortened by two bases each.
KEY CONCEPT
(+)
• Reverse transcriptase
starts synthesis when a
tRNA primer binds to a
site 100 to 200 bases
from the 5’ end.
(-)
(-)
Figure 22.6-a
71
KEY CONCEPT
•When the enzyme reaches
the end, the 5’-terminal bases
of RNA are degraded.
(-)
–This exposes the 3’ end of the
DNA product.
(-)
(-)
Figure 22.6-b
•The exposed 3’ end base
pairs with the 3’ terminus of
another RNA genome.
• Synthesis continues, generating
a product in which the 5’ and 3’
regions are repeated.
–This gives each end the
structure U3-R-U5.
72
KEY CONCEPT
DNA (-)
• Similar strand switching
events occur when reverse
transcriptase uses the DNA
product to generate a
complementary strand.
RNA
DNA (+)
DNA (-)
Figure 22.7 Synthesis of plus-strand DNA requires a 73
second
jump.
KEY CONCEPT
DNA (-)
RNA (+)
Strand switching is an
example of the copy
choice mechanism of
recombination.
copy choice p869
A type of recombination
used by RNA virus, in
which the RNA polymerase
switches from one template
to another during synthesis
74
Figure 22.8
22.5 Viral DNA Integrates into the Chromosome at radom sites.
KEY CONCEPT
Two base pairs of DNA are
lost from each end of the
retroviral sequence during
the integration reaction.
Linear DNA is inserted
directly into the host
chromosome by the
retroviral integrase enzyme.
Cp. Fig22.5
Figure 22.9
The organization of proviral DNA
in a chromosome is the same
as a transposon.
– The provirus is flanked by short
direct repeats (DR) of a
75
sequence at the target site.
U3 carries promoter
Left LTR
Response for initiating
transcription of provirus
Right LTR
Sometimes (rarely) sponsor
transcription of host seq
near integration site.
LTR also carries an enhancer that acts on cellular and viral seq.
Part of Fig. 22.5
76
22.6 Retroviruses May Transduce Cellular Sequences
Onc = Oncogenesis,
transform ability
From spliced RNA copies
of cellular seq. c-onc
Figure 22.10: Replicative-defective transforming viruses
have a cellular seq substituted for parial viral seq.
c-onc usually interrupted by introns
v-onc is un-interrupted
77
Helper virus
Figure 22.11
Transforming retroviruses are generated by a recombination event:
78
A cellular RNA sequence replaces part of the retroviral RNA.
22.7 Yeast Ty Elements Resemble Retroviruses
Ty = Transposon yeast
• interspersed repeat DNA
• Same transpose mechanism
to retrovirus
• Freq < bacterial Tn
• Two major classes:
Ty1 (30 copies)
Ty917 (6 copies)
•ps: d, 100 copies,
considerable heterogeneity
Figure 22.12: Ty elements have two genes.
79
KEY CONCEPT
• Ty elements are classic
retroposons, with a reverse
transcriptase activity.
– They transpose via an RNA
intermediate.
Ty elements does not give rise
to infectious particles, but viruslike particles (VLPs)
accumulate within the cells.
80
Figure 22.13
Endogenous retroviruses
http://en.wikipedia.org/wiki/Endogenous_retrovirus
• Ty transposons have a similar organization to
endogenous retroviruses. KEY CONCEPT
• endogenous retroviruses are retroviruses
derived from ancient infections of germ cells in
humans, mammals and other vertebrates; as
such their proviruses are passed on to the next
generation and now remain in the genome.
• Most retroviruses (such as HIV-1) infect somatic
cells, but some can also infect germline cells
(cells that make eggs and sperm)
81
22.8 Many Transpable Elements Reside in D.
melanogaster.
• copia is a retroposon that
is abundant in D.
melanogaster.
82
Figure 22.15
22.9 Retroposons Fall into Three Classes
1
2
3
LTR
Figure 22.16
KEY CONCEPT
Retroposons of the viral superfamily are transposons that
mobilize via an RNA that does not form an infectious particle.
83
KEY CONCEPT
• Some retroposons directly resemble retroviruses in their use of
LTRs. - Others do not have LTRs.
• Other elements can be found that were generated by an RNAmediated transposition event;
– But they do not themselves code for enzymes that can catalyze
transposition.
– [Just need help]
Plant
•contain another type of
small mobile element, called
MITE (miniature invertedrepeat transposable element)
•No relationship to SINE,
LINE
Figure 22.17
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KEY CONCEPT
• Transposons and retroposons constitute almost half of
the human genome.
Figure 22.18
Only one SINE have been active in the human lineage:
the common Alu element
85
86
22.10 The Alu Family Has Many Widely Dispersed
Members
KEY CONCEPT
• A major part of repetitive DNA in
mammalian genomes consists of repeats
of a single family:
– organized like transposons
– derived from RNA polymerase III transcripts
•Individual members of the Alu family are related rather than
identical.
•Alu sequence is related to 7SL RNA, a compartment of the
signal recognition particle.
87
22.11 Processed Pseudogenes Originated as
Substrates for Transposition
KEY CONCEPT
• A processed pseudogene is derived from an mRNA
sequence by reverse transcription.
RNA polmerase II
DR
DR
No intron
Figure 22.19
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Evidence:
1. many of the poly-A retroposons that have been
detected by large-scale genomic sequencing are
truncated elelments.
 most of these are missing region from 5’end.
 lost the ability to transpose.
2. Processed pseudogenes
 not expressed by cell due to lack of promoter, intron or
truncate near 5’end. (many cellular gene had been truncated
at 5’end)
 these pseudogenes are often flanked by short repeat
 this is structure of LINE-promoted transposition of cellular
mRNA.
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Summary
processed pseudogenes
• do not carry any information used to transposition.
• do not carry out reverse transcription of RNA.
• A dead ends of evolution.
Active LINE element
• provides most of the RTase activity
• Acts for transposition on: (1) its own
(2) SINE
• For generating processed pseudogenes.
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22.12 LINES Use an Endonuclease to Generate a
Priming End
RT-ase
5’ 3’
endonuclease
DNA-binding protein
5’
KEY CONCEPT
• LINES do not have LTRs.
• They require the retroposon to code
for an endonuclease that generates a
nick to prime reverse transcription.
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Figure 22.20
Note
• Although transposition of cellular RNA can
occur, it is a rare event.
• LINE-encoded protein (ORF1&2) bind
immediately to their own RNA during
translation
 show highly preference to its own RNA
rather than the cellular RNA.
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•Reverse transcription often
does not proceed fully to the
end, so the copy is inactive.
•Original from RNA pol II lacks
of promoter are necessary
inactive.
Figure 22.21: LINES proteins are cis-acting.
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Figure 22.22: Autonomous act on nonautonomous elements.
For transposition to survive, they must occur in the germline.94