Lewin Benjamin (ed.) Genes IX
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Oi[Iill
Unequal recombination results from mis-
pairing
by the cellular systems for homologous
recombination. Nonreciprocal recombination
results in
duplication or rearrangement of loci
(see
Section 6.7, Unequal
Crossing-Over
Rearranges Gene Clusters). Duplication of
sequences within a
genome
provides
a
major
source
of new sequences.
One copy of the
sequence can
retain
its original function,
whereas
the other may evolve into
a
new func-
tion. Furthermore, significant
differences
between
individual
genomes
are found at the
molecular level because of
polymorphic
varia-
tions caused
by recombination.
We saw
in
Sec-
tion 6.14,
Minisatellites
Are Useful for Genetic
Mapping, that recombination
between
mini-
satellites adjusts their lengths so that every indi-
vidual
genome
is distinct.
Another major cause of variation is
pro-
vided by transposable elements or trans-
posons:
these are discrete sequences
in
the
genome
that are mobile-they
are able
to trans-
port
themselves
to other locations
within
the
genome.
The mark of a transposon is that
it
does
not utilize an independent form of the element
(such
as
phage
or
plasmid
DNA),
but
moves
directly
from
one site
in
the
genome
to another.
Unlike most otherprocesses involved in
genome
restructuring, transposition does
not rely on
any relationship between the sequences at the
donor and recipient sites. Transposons are
restricted
to moving themselves,
and sometimes
additional sequences, to new sites elsewhere
within the same
genome;
they are, therefore,
an
internal counterpart to the vectors that can
transport sequences
from
one
genome
to
another.
They may
provide
the
major
source
of
mutations in the
genome.
Transposons fall into two
general
classes.
The
groups
of transposons reviewed
in this
chapter exist as sequences of
DNA
coding
for
proteins
that are able directly to
manipulate
DNA so as to
propagate
themselves within
the
genome.
The transposons reviewed in
Chapter 22,
Retroviruses
and
Retroposons,
are
related to retroviruses, and the source
of
their mobility
is
the ability to
make DNA
copies
of their RNA transcripts; the
DNA
copies
then become integrated at
new
sites
in the
genome.
Transposons that
mobilize
via
DNA are
found in both
prokaryotes
and eukaryotes.
Each
bacterial
transposon carries
gene(s)
that code
for the
enzyme activities
required for its own
transposition,
although
it may
also
require
ancillary
functions of the
genome
in
which
it
resides
(such
as
DNA
polymerase
or
DNA
gyrase).
Comparable
systems
exist
in eukary-
otes,
although their
enzymatic
functions are
not so well characterized.
A
genome
may con-
tain both functional
and
nonfunctional
(defec-
tive) elements.
Often
the
majority of
elements
in a eukaryotic
genome are defective,
and
have
Iost the ability
to transpose
independently,
although
they may
still be
recognized
as sub-
strates for transposition
by
the enzymes
pro-
duced by
functional
transposons.
A eukaryotic
genome
contains
a large
number
and variety
of
transposons.
The
fly
genome has
>50
types
of
transposons,
with
a total
of several
hundred
individual elements.
Transposable
elements
can
promote
rearrangements
of the
genome
directly
or
indirectly:
.
The transposition
event
itself
may cause
deletions
or inversions
or lead
to the
movement
of
a host
sequence
to a
new
location.
.
Transposons
serve
as substrates
for
cellular
recombination
systems
by
func-
tioning
as
"portable
regions
of homol-
ogy"; lwo
coPies
of
a transPoson
at
different
locations
(even
on
different
chromosomes)
may
provide
sites
for
reciprocal
recombination.
Such
exchanges
result in deletions,
insertions,
inversions,
or
translocations.
The intermittent
activities'of
a transposon
seem to
provide a somewhat
nebulous
target
f or
natural
selection.
This
concern
has
prompted
suggestions
that
(at
Ieast
some)
transposable
elements
confer
neither advan-
tage
nor disadvantage
on
the
phenotype, but
could constitute
"selfish
DNA"-DNA
con-
cerned only
with
their
own
propagation.
Indeed,
in considering
transposition
as an
event
that is distinct
from
other
cellular
recombina-
tion systems,
we tacitly
accept
the view
that
the transposon
is an
independent
entity
that
resides
in the
genome.
Such a
relationship
of the
transposon
to the
genome
would
resemble
that of
a
parasite
with
its host. Presumably
the
propagation of an ele-
ment
by transposition
is balanced
by
the harm
done
if a transposition
event
inactivates
a nec-
essary
gene,
or
if the
number
of
transposons
becomes
a
burden
on
cellular
systems'
Yet we
must
remember
that
any
transposition
event
conferring
a selective
advantage-for
example,
a
genetic rearrangement-will
lead to
prefer-
ential
survival
of the
genome carrying
the
active
transDoson.
21.1
Introduction
@
Insertion
Sequences
Are
Sim
pLe
Transposition
Modules
.
An insertion
sequence is
a transposon
that codes
for
the enzyme(s)
needed for
transposition
ftanked
by short inverted
terminaI repeats.
r
The
target site at which
a transposon
is inserted is
dupl.icated
during the insertion
process
to form
two repeats in
direct orientation
at
the ends of the
transooson.
o
The
length of the
direct
repeat
is
5 to 9 bp
and
is
characteristic
for
a
ny
particu
[a r
transposo n.
Transposable
elements were
first identified
at
the molecular
level in
the form
of spontaneous
insertions
in
bacterial
operons. Such
an inser-
tion
prevents
transcription
and/or
translation
of
the
gene
in which
it is inserted.
Many
different
types
of transposable
elements
have now
been
characterized.
The
simplest transposons
are called inser-
tion
sequences
(reflecting
the
way in which
FJ{-;ltFil
I
3.} Transposons
have inverted
terminal repeats
and
generate
direct
repeats
of flanking
DNA
at
the target
site. In
this exampte.
the
target is
a 5
bp
sequence.
The
ends
of the transposon
consist
of
inverted
repeati
of 9 bp,
where
the numbers
1
through
9 indjcate
a sequence
of base
pairs.
CHAPTER
2L Transposons
they were detected). Each
type is
given
the
pre-
fix IS, followed
by a number
that identifies
the
type.
(The
original classes were
numbered IS I
to IS4; later
classes have numbers
reflecting
the
history
of their isolation.
but not corresponding
to the total number
of elements
so far isolated!)
The IS
elements are normal
constituents
of
bacterial
chromosomes
and
plasmids.
A standard
strain of E. coli is likely
to contain
several
(<10)
copies of any
one of the more
common IS
ele-
ments. To
describe an insertion
into a
particular
site,
a double colon is
used; so
7,::IS
I
describes
an
IS
I element inserted
into
phage
lambda.
The IS
elements are
autonomous
units,
each
of which
codes only for
the
proteins
needed
to
sponsor its own
transposition. Each
IS
element
is different in
sequence,
but there are
some com-
mon
features in
organization.
The structure
of
a
generic
transposon
before and
after insertion
at a target
site
is
illustrated in FSGiJftr
? 1-F,
which
also summarizes
the details
of some
common IS
elements.
An
IS element
ends in short inverted
ter-
minal repeats;
usually
the two
copies of
the
repeat
are closely related
rather
than identical.
As
illustrated
in the figure,
the
presence
of
the
inverted
terminal repeats
means
that the
same
sequence
is encountered
proceeding
toward
the
element from
the flankine DNA
on
either side
of it.
When
an
IS
element
transposes,
a sequence
of host DNA
at the site
of
insertion
is
duplicated.
The nature
of the
duplication is
revealed
by
comparing
the
sequence of the
target
site before
and
after an insertion
has
occurred. Figure
2I.2
shows
that at the
site of insertion,
the
IS DNA
is
always flanked
by very short
direct repeats.
(In
this context,
"direct"
indicates
that two
copies
of a sequence
are repeated
in the
same
orien-
tation, not
that the repeats
are
adjacent.)
In the
original
gene
(prior
to insertion),
however,
the
target
site has the
sequence
of only one
of these
repeats.
In
the figure, the
target
site consists
of
,
ATGCA
the
sequenc.
i;CGi.
After
rransposirion,
one
copy
of this
sequence is
present
on either
side
of the transposon.
The
sequence
of the
direct repeat
varies
among individual
transposition
events
under-
taken by
a transposon,
but
the Iength
is
con-
stant for any
particular
IS element
(a
reflection
of the mechanism
of transposition).
The
most
common
length
for the
direct repeats
is
9 bp.
An IS
element
therefore
displays
a
charac-
teristic
structure in
which
its ends
are identi-
fied
by the
inverted
terminal
repeats,
whereas
the adjacent
ends of the
flanking
host DNA
are
ai.
|
'123456789
987654321
I
Transposase gene
\
-.+
\
\,u"o
TACGT
TACGT1234s67B9
987654321TACGT
Target
Target
repeat
repeat
Transooson
Target
Inverted
Overall Target
'
repeat
(bp)
repeat (bp)
length
(bp)
setection
ls1
g
23
768
random
lS2
s
41
1927
hotsoots
ls4
1 1-13
18
1428
AAAN2oTTT
lS5
4
16
1195
horspots
lS10R
9
22
1329
NGCTNAGCN
lS50R
I
I
1531
hotspots
15903
I 18 1057
random
524
identified by
the
short direct repeats. When
observed
in a sequence
of
DNA,
this type of
organization is taken to be diagnostic
of
a trans-
poson,
and suggests that the sequence origi-
nated in a transposition event.
Most IS elements insert at a variety of sites
within
host DNA.
Some, though, show
(vary-
ing
degrees
of
)
preference
for
parlicular
hotspots.
The inverted
repeats
define the ends of a
transposon.
Recognition of
the ends
is common
to transposition events sponsored by all types
of transposon.
Cli-acting mutations that
prevent
transposition are
located in
the ends, which are
recognized by
a
protein(s)
responsible for trans-
position.
The
protein
is
called a transposase.
All
the
IS elements except IS I contain a sin-
gle
long coding
region, which
starts
just
inside
the inverted
repeat
at one end and terminates
just
before
or within the inverted repeat at the
other
end. This codes for the transposase.
IS I has
a more complex organization. with
two sepa-
rate reading frames; the transposase
is
produced
by
making a frameshift during translation to
allow both
reading frames to be used.
The lrequency of lransposition
varies among
different elements.
The overall rate of transpo-
sition
is
-I0-l
to
l0a
per
element
per genera-
tion.
Insertions in individual targets occur at a
level comparable
with the
spontaneous
muta-
tion
rate, usually
-
l0-5
to
l0-7
per generation.
Reversion
(by
precise
excision of the IS ele-
ment)
is usually infrequent, with a
range of
rates of
l0-6 to l0-10
per generation,
which
is
-103
times less
frequent
than
insertion.
Composite
Transposons
Have IS Modules
Transposons can carry other
genes
in
addition
to
those coding
for transposition.
Composite
transposons
have a central region
flanked by an
IS
etement at each end.
Either one or
both of the IS etements of a
composite
transposon
may
be abte to undertake
transposition.
A
composite
transposon
may
transpose
as a unit.
but an
active IS element at either end
mav also
transpose
i ndependent[y.
some transposons
carry drug
resistance
(or
other)
markers
in
addition
to the functions con-
cerned
with
transposition.
These transposons
are
named
Tn followed by a number. One
class
of larger transposons
are called cornposite
ele-
ments, because
a central
region
carrying
the
drug marker(s)
is
flanked
on either
side
by
"
arms"
that consist
of IS
elements.
The arms
may be
in either
the
same
or
(more
commonly)
inverted
orientation.
Thus
a composite
transposon
with
arms
that are
direct
repeats has the
structure
If
the
arms are
inverted
repeats, the
struc-
ture is
The arrows
indicate
the
orientation
of
the
arms, which
are identified
as
L
and
R according
to an
(arbitrary)
orientation
of
the
genetic map
of the transposon
from
left
to right.
The structure
of a composite
transposon
is illustrated
in more
detail
in
j'ii.l.i!ii
:r':.:i,
which
also
summarizes
+:j{:1-lIil
:l:i
.;:I
A composite
transposon
has a
centraI
region
carrying
markers
(such
as
drug
resistance)
ftanked by
IS
mod-
utes.
The modules
have
short
jnverted
termjnal
repeats.
If
the modules
themsetves
are
in inverted
orientation,
the short
inverted termina[
repeats
at the
ends
of the
transposon
are
identicat.
21.3
Composite
Transposons
Have IS
Modules
525
New transposon
created
by mobilization
of lS10
modules in
alternative
orientation
transposon moves
again
r:.r:-;iiri,.
i: I ..:
Two
15L0 modules
create a
composite trans-
poson
that can
mobitize
any region
of DNA
that Lies
between
them. When
Tn10 is
part
of a
smatl circular mot-
ecule,
the IS10
repeats
can transpose
ejther side of
the
circ[e.
the
properties
of
some common
composite
transposons.
Arms
consist
of
IS
modules,
and
each mod-
ule
has
the usual
structure
ending
in inverted
repeats;
as a result
the
composite
transposon
also
ends in
the
same
short inverted
repeats.
In
some cases,
the modules
of a composite
transposon
are identical,
such as
Tn9
(direct
repeats
of ISI)
or Tn903
(inverted
repeats
of
IS90l).In
other
cases,
the modules
are
closely
related,
but
not identical.
Thus
we can
distin-
guish
the
L and R
modules
in Tnl0
or
in
Tn5.
A functional
IS module
can transpose
either
itself
or
the entire
transposon.
When
the mod-
ules
of a composite
transposon
are identical,
presumably
either
module
can
sponsor move-
ment
of the
transposon,
as in the
case
of
Tn9
or
Tn903.
When
the modules
are different.
they
may differ
in functional
ability,
so
transposition
CHAPTER
2L
Transposons
can depend
entirely or
principally
on
one of the
modules,
as in the case
of
Tnl0
or Tn5.
we assume
that composite
transposons
evolved
when two originally
independent
mod-
ules associated
with the central
region.
Such a
situation
could arise
when an IS
element trans-
poses
to a recipient
site close to
the donor
site.
The
two identical modules
may
remain identi-
cal or diverge.
The ability
of a single
module
to
transpose
the
entire composite
element
explains
the lack
of selective
pressure
for
both modules
to remain
active.
What is responsible
for
transposing
a com-
posite
transposon
instead
of
just
the individual
module?
This
question
is especially pressing
in
cases where
both the modules
are functional.
In
the example
of
Tn9,
where
the modules
are
IS
I elements,
presumably
each is
active in
its
own right
as well as
on behalf
of the composite
transposon. Why
is
the transposon preserved
as a whole, instead
of each
insertion
sequence
looking
out for itself?
TWo IS
elements in fact
can
transpose
any
sequence residing
between
them, as
well as
themselves.
i:*i.jitl
;l::.ri
shows
that
if Tnl0
resides
on a
circular replicon,
its
two modules
can be
considered
to
flank
either
the
/e/R
gene
of the original
Tnl0 or
the sequence
in the
other
part
of the circle. Thus
a transposition
event
can
involve
either the
original Tnl0
transposon
(marked
by the movement
of rerR)
or the
cre-
ation
of the new
"inside-out"
transposon
with
the alternative
central
region.
Note thatboth
the original
and
"inside-our"
transposons have
inverted
modules,
but these
modules
evidently
can function
in
either
ori-
entation
relative
to the
central region.
The
frequency
of transposition
for
composite
trans-
posons
declines
with
the distance
between
the
modules.
Thus
length
dependence
is
a
factor
in
determining
the sizes
of the
common
compos-
rte transposons.
A major
force
supporting
the transposition
of composite
transposons
is
selection
for
the
marker(s)
carried in
the central
region.
An ISI0
module
is free
to move
around
on its
own, and
mobilizes
an
order of magnitude
more
fre-
quently
than TnI0.
Tnl0
is held
together
by
selection
for tetR,
though,
so
that under
selec-
tive conditions,
the relative
frequency
of intact
Tnl0
transposition
is
much increased.
The
IS elements
code
for transposase
activ-
ities that
are responsible
both for
creating
a tar-
get
site
and for
recognizing
the ends
of
the
transposon.
Only
the ends
are needed
for
a trans-
poson
to
serve
as a substrate
for
transposition.
526
LZ9
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