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 sequences-

transfer within the genome

2
1. Acquisition of new sequences- horizontal transfer
of genetic material between genomes by extra-
chromosomal 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 sequences-
transfer 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 operon-
spontaneous 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;
consensus sequence; inactive
region).
DR IR
 duplicated during insertion
forms DR (direct repeat).

• The length of the DR is:

– characteristic for any particular
transposon
Figure 21.2 14
KEY CONCEPT
 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
DR itself (Fig.21.2) or the entire
transposon
• 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
19
Figure 21.04: IS elements can mobilize other sequences.
 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 The stagger between
mechanism
1 the cuts determines the
length of the direct
repeats.
2

The target repeat is

ATGCA
corrected characteristic of each
TACGT
3 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  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
 Recombination using
cellular enzymes
IS1L Step 1 IS1R
Tn inserts a copy at a
second site near its
original location
Step 2
Reciprocal recombination
Lost from
between two copies of the
the cell
transposon

Single copy on •recombination between two elements

chromosome in same orientation (DR)
28
Figure 21.09: Direct repeats recombine to excise material.
 Recombination
using cellular
(A) (B)
enzymes
(B)
 not relies on Tn-
coded function
(A)
•recombination between two
elements in opposite
orientation (IR)
(B) (A)

Figure 21.10: Inverted repeat recombination inverts material.

Excisions not supported by Tn’s: P859

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 target-
common 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

• The Mu transposase forms

1
the complex by:
1. synapsing the ends of Mu DNA
MuA 2. followed by nicking
tetramer
3. then a strand transfer RX

2
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 32

Figure 21.12
 • Mu integrates by nonreplicative transposition;
MuA also • during lytic cycle- number of copies amplified
binds to
1 internal site-
by replicative transposition
needed for
complex
formation A Mu transposon passes through 3
but not
strand
stable stages:
cleavage
- MuA binds to ends as tetramer
2 forming a synapsis.
- MuA subunits act in trans to cut
next to R1 and L1 (coordinately; two active
sites to manipulate DNA).

cuts in
3
transfers - MuA acts in trans to cut the
trans in trans
target site DNA and mediate in
trans strand transfer
33
Figure 21.12
 1

In strand transfer complex

transposon is connected to the target
site through one strand at each end

cuts in transfers
trans 3 in trans

34
Figure 21.12
 The MuB protein chooses targets;

1
Mu Tn moves >10-15 kb away from
original site (target immunity).
MuB binds to the MuA-Mu DNA
complex; MuA causes MuB to
hydrolize ATP; MuB released from the
2 donor DNA.

MuB binds nonspecifically to the

target DNA and stimulates the
recombination activity of MuA in
3 transposition complex.
MuA clears MuB from the donor -
gives preference for transposition to
the target. 35
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.

• The cointegrate has two

copies of the transposon.
(homolgous recombination)
– They lie between the
by resolvase
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 38
crossover intermediate.
 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
1. nicking
nonreplicative transposition
2.interstrand Rx
differ according to :

3 – whether all four strands are cut

before joining to the target (Tn10) or

4. cleavage – 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
covalently bound to the DNA. 44
 (38bp)

Internal res site

Transposase Dual role
• Resolvase
Limiting factor feedback
• Repressor
in transposition (mutant ↗ Tn freq)

Control regions TnA features

•Replicative Tn,
•Non-IS-dependent,
•DR (~5bp) generated
Figure 21.19: TnA transposon organization is conserved. 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. 45
Att- intermolecular resolution
 21.10 Transposition of Tn10 Has Multiple Controls
inactive
IS10L
Promoter
strong RNA stable
OUT RNA function as
weak 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
transposon are introduced into the genome 46
 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
• The break generates
one chromosome that
(site for chr. breakage)
has:
– a centromere
– a broken end
– one acentric fragment

• The acentric fragment is

recessive
lost during mitosis;
– detected by the
Figure 21.23. A break at controlling element
disappearance of
causes loss of an acentric fragment 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

50
chromatid breakage-fusion-bridge cycle.
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 trans-

acting 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 = infertile
(30-50 copies) and locate in
different chr., but not in M
strain. 59
Figure 21.28 Hybrid dysgenesis is asymmetrical
 21.15 P Elements Are Activated in the Germline
KEY CONCEPT
31bp Generate DR of target DNA (~8bp)
IR

• P elements are activated in

the germline of P male x M
female crosses.

• This is because a tissue-

specific 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

• The P element also

produces a
repressor of
transposition.
– It is inherited
maternally in the
No repressor 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.
• Retrovirus -
Single strand
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 double-

stranded DNA sequence.

64
• A retrovirus generates a provirus by reverse
transcription of the retroviral genome.

Long terminal repeat

integrase

65
Figure 22.2
 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 full-

length 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, 68

International Medical Innovations, Inc.
 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 R-
U5 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.
(-)

•The exposed 3’ end base

(-) pairs with the 3’ terminus of
another RNA genome.

Figure 22.6-b
• 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 (-)

RNA
• Similar strand switching
events occur when reverse
transcriptase uses the DNA
product to generate a
complementary strand.

DNA (-)
DNA (+)

Figure 22.7 Synthesis of plus-strand DNA requires a73

second
jump.
 KEY CONCEPT

DNA (-) Strand switching is an

example of the copy
RNA (+)
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.

The organization of proviral DNA

Cp. Fig22.5
in a chromosome is the same as
a transposon.
– The provirus is flanked by short
direct repeats (DR) of a sequence
75
at the target site.
Figure 22.9
 U3 carries promoter

Right LTR
Left LTR Sometimes (rarely) sponsor
Response for initiating transcription of host seq
transcription of provirus 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

77
v-onc is un-interrupted
 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: , 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 virus-
like 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 RNA-

mediated 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 inverted-
repeat transposable
element)
•No relationship to SINE,
84
LINE Figure 22.17
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 88
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.
89
 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.
90
22.12 LINES Use an Endonuclease to Generate a
Priming End
RT-ase endonuclease

DNA-binding protein
5’ 3’ 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.

91
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.

92
 •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.

93
Figure 22.22: Autonomous act on nonautonomous elements.

For transposition to survive, they must occur in the germline. 94