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Transposable Elements: An Overview

Transposable Elements are DNA sequences that are capable of mediating their own movement
(transposition) to new locations within the genome they inhabit, or between different DNA
molecules in the same cell. Barabara McClintock was awarded the Nobel Prize (1983) for her
pioneering discovery of transposable elements in the genome of maize. Transposable elements
of various types are now known to be widely distributed in the genomes of both eukaryotes
and prokaryotes.
The major categories of TEs are distinguished by their transposition mechanisms:

Cut-and-Paste (non-replicative) Transposons - found in prokaryotes and eukaryotes

Insertion Sequence (IS) Elements
Composite Transposons (example, Tn5)

2. Replicative Transposons - prokaryotes only (example, Tn3)

3. Retrotransposons - eukaryotes only
RNA intermediate in transposition/Revrese Transcriptase
some are closely related to retroviruses

Insertion Sequences
Insertion Sequences or IS elements are the simplest form of mobile element in bacteria. They
are normal constituents of many bacterial chromosomes, bacterial plasmids and bacterial
virus genomes.
IS elements consist of a relatively short (700-1500 bp) DNA segment flanked by a 10-40 bp
inverted terminal repeat (ITR) sequence. A complete IS element codes for the protein
(transposase) that catalyses the transposition event. Thus, transposition requires that the IS
element carry a promoter recognized by the RNA polymerase of the host cell. Typically the
gene for the transposase is the only gene within the element.
Molecules of the transposase bind to the ITR sequences at the ends of the IS and bring the
two ends together into a complex, so that the IS element is looped out. Then it cuts both
DNA strands to excise the element. Subsequently, the DNA strands of the vacated site are
re-connected. Molecules of transposase remain attached to both ends of the excised IS
element. Next, the IS element with bound transposase makes staggered cuts in the two
strands of the new target site DNA and the IS element is inserted by ligating one strand of
the element to the target DNA at either end. Finally, the single strand gaps at either end
are filled (by hcellular enzymes) to create the characteristic Direct Terminal Repeat (DTR)
target site duplication that is characteristic of transposable elements.
The transposase is "trans-acting". This means that the transposase expressed from a
complete IS element in one location may mobilize transposition of a defective IS element

elsewhere in the cell which lacks a functional transposase gene; but only if the defective IS
element has an ITR sequence recognized by the transposase produced by the complete
element. The terms "autonomous" and "non-autonomous" are sometimes used to distinguish
complete and defective versions of IS elements.

Composite Transposons
These consist of two copies of the same IS element flanking variable amounts of other DNA
sequences coding for one or several genes with diverse functions, unrelated to transposition.
The best-known transposons carry antibiotic resistance genes.
The diagram below compares the typical structure of the IS50 element with the transposon
Tn5. Tn5 carries 3 antibiotic resistance genes flanked 2 copies of IS50.

Tn3 - a replicative transposon

4.9 kb, flanked by 38-40 bp inverted repeats, NOT by IS elements
transposition involves formation of a COINTEGRATE intermediate and REPLICATION of
the element (transposase) followed by RECOMBINATION between duplicated copies of the
element (resolvase)
resolvase binding to res site also represses transcription of the element; thus Tn3 is a
well-behaved guest in the E. coli genome.

bla: b-lactamase ampicillin resistance

TRANSPOSABLELEMENTS elements participate directly or indirectly in rather bewildering

array of molecular events, in addition to transposition, that alter the genomesthey inhabit.
The multiplicity of transpositional and recombinational events associated with
TEs allows them to unlock the Pandora's box of genome plasticity for bacterial chromosomes
and plasmids in which they are found. The K-12 laboratory strains of E. coli show considerable
variability in the number and location of TEs in their genomes due to transposition events
that have occurred since the parent strain was first isolated in from nature 1922. The most
important genetic consequences of TE activity are insertional inactivation of genes, and as

substrates for homologous recombination.

Insertional Inactivation
Insertion of an IS within a coding sequence generally leads to the loss of gene function (null
Example: IS5 insertion that inactivates gene wbbL in E. coli
4bp target site in wbbL




IS5 [1,195 bp]

(one mismatch)


(Target Site Duplication)

Homologous Recombination
Multiple copies of the same transposable element in the same cell are substrates for
homologous recombination events that may lead to DNA deletions, sequence inversions, or
fusion of separate DNA molecules. For example, homologous recombination between copies of
the same IS element in a conjugal plasmid and the bacterial chromosome leads to formation
of Hfr strains, as shown below.