Microbial  Recombination and Plasmids:

Transposable Elements
The chromosomes of bacteria, viruses, and eucaryotic cells contain pieces of DNA that move around the genome. Such movement
is called transposition. DNA segments that carry the genes required  for  this  process  and  consequently  move  about  chromosomes are transposable elements or transposons.Unlike other
processes that reorganize DNA, transposition does not require extensive areas of homology between the transposon and its destination site. Transposons behave somewhat like lysogenic prophages
 except that they originate in one chromosomal
location and can move to a different location in the same chromosome. Transposable elements differ from phages in lacking a virus
life  cycle  and  from  plasmids  in  being  unable  to  reproduce  autonomously and to exist apart from the chromosome. They were
first discovered in the 1940s by Barbara McClintock during her
studies  on  maize  genetics  (a  discovery  that  won  her  the  Nobel
prize in 1983). They have been most intensely studied in bacteria.
The simplest transposable elements are insertion sequences
or IS elements . An IS element is a short sequence
of DNA (around 750 to 1,600 base pairs [bp] in length) containing only the genes for those enzymes required for its transposition and bounded at both ends by identical or very similar sequences of nucleotides in reversed orientation known as inverted
repeats . Inverted repeats are usually about 15 to 25
base pairs long and vary among IS elements so that each type of
IS  has  its  own  characteristic  inverted  repeats.  Between  the  inverted repeats is a gene that codes for an enzyme called transposase(and sometimes a gene for another essential protein). This
enzyme is required for transposition and accurately recognizes
the ends of the IS. Each type of element is named by giving it the

prefix IS followed by a number. In E. coli several copies of different IS elements have been observed; some of their properties.
Transposable  elements  also  can  contain  genes  other  than
those  required  for  transposition  (for  example, antibiotic  resistance or toxin genes). These elements often are called composite
transposons or elements. Complete agreement about the nomenclature of transposable elements has not yet been reached. Sometimes  transposable  elements  are  called  transposons  when  they
have extra genes, and insertion sequences when they lack these.
Composite transposons often consist of a central region containing the extra genes, flanked on both sides by IS elements that are  identical or very similar in sequence.Many composite transposons are simpler in organization. They are bounded
by  short  inverted  repeats, and  the  coding  region  contains  both
transposition genes and the extra genes. It is believed that composite transposons are formed when two IS elements associate
with a central segment containing one or more genes. This association could arise if an IS element replicates and moves only a
gene or two down the chromosome. Composite transposon names
begin with the prefix Tn.
  The process of transposition in procaryotes involves a series of
events, including self-replication and recombinational processes.
Typically  in  bacteria, the  original  transposon  remains  at  the
parental site on the chromosome, while a replicated copy inserts at
the target DNA. This is called replicative transposition. Target sites are specific sequences about five to nine base pairs
long. When a transposon inserts at a target site, the target sequence
is duplicated so that short, direct-sequence repeats flank the transposon’s terminal inverted repeats. This can be seen where the five base pair target sequence moves to both
ends of the transposon and retains the same orientation.
The transposition of the Tn3 transposon is a well-studied example of replicative transposition. In the first stage the plasmid containing the Tn3 transposon fuses with the target plasmid to form a cointegrate molecule.
This process requires the Tn3 transposon enzyme coded for by the tnpA gene. Note
that the cointegrate has two copies of the Tn3transposon. In the
second stage the cointegrate is resolved to yield two plasmids, each
with a copy of the transposon. Resolution involves a crossover at the two ressites and is catalyzed by
a resolvase enzyme coded for by the tnp Rgene. 
Transposable elements produce a variety of important effects.
They can insert within a gene to cause a mutation or stimulate
DNA rearrangement, leading to deletions of genetic material. If a
transposon insertion produces an obvious phenotypic change, the
gene can be tracked by following this altered phenotype. One can
fragment the genome and isolate the mutated fragment, thereby
partially purifying the gene. Thus transposons may be used to purify genes and study their functions. Because some transposons
carry stop codons or termination sequences, they may block translation or transcription. Other elements carry promoters and thus
activate genes near the point of insertion. Eucaryotic genes as well
as procaryotic genes can be turned on and off by transposon movement. Transposons also are located within plasmids and participate in such processes as plasmid fusion and the insertion of F

plasmids into the E. coli chromosome.

In the previous discussion of plasmids, it was noted that an R
plasmid can carry genes for resistance to several drugs. Transposons
have antibiotic resistance genes and play a major role in generating

these plasmids. Consequently the existence of these elements causes serious problems in the treatment of disease. Since plasmids can contain  several  different  target  sites, transposons  will  move  between
them; thus plasmids act as both the source and the target for transposons with resistance genes. In fact, multiple drug resistance plasmids probably often arise from transposon accumulation on a single
plasmid. Because  transposons  also  move  between
plasmids and primary chromosomes, drug resistance genes can exchange between plasmids and chromosomes, resulting in the further
spread of antibiotic resistance.
Some transposons bear transfer genes and can move between  bacteria  through  the  process  of  conjugation, as  discussed in the next section. A well-studied example of such a
conjugative  transposon is  Tn916 from Enterococcus  faecalis.Although Tn916 cannot replicate autonomously, it will
transfer itself from E. faecalisto a variety of recipients and integrate into their chromosomes. Because it carries a gene for
tetracycline  resistance, this  conjugative  transposon  also
spreads drug resistance.

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