Tuesday, October 02, 2007

Transposons: Part I

 
Transposons are segments of DNA that can move (transpose) within the genome. They are also known as mobile genetic elements, transposable elements, jumping genes, or selfish DNA. Transposons often encode the enzymes necessary to catalyze their relocation and duplication in the genome. They don't usually have any function other than replicating themselves and jumping around in the genome. That's why they're sometimes called "selfish DNA." Selfish DNA is not the same as the "selfish genes" of Richard Dawkins. Those are real genes that perpetuate themselves through a beneficial effect on the organism they inhabit.

There are many different types of transposon. The best characterized ones are found in bacterial genomes where they are called insertion elements (IS). An example is shown below.
This example exhibits most of the characteristics of simple transposons. The grey bars at each end represent the genomic DNA into which the transposon is inserted. The yellow bars indicate a short stretch (~5 bp) of genomic DNA that's repeated on either side of the insertion element. This short repeat is almost always associated with insertion and excision of the transposon and it's a diagnostic feature of mobile genetic elements.

The red bars are inverted repeats at the ends of the transposon. This is another feature that's common to most transposons and it is required for copying and insertion/excision. This particular example contains a gene for the enzyme "transposase" (green).

The mechanism of transposition is shown in the figure below. Transposase catalyzes the excision of the transposon from the genome. It also cuts the DNA at the target site creating staggered ends with single-strand extensions, much like the cleavage sites of some restriction endonucleases [Restriction, Modification, and Epigenetics].


The excised transposon is integrated into the DNA that has been cut at the target site, then the single-stranded gaps are filled in by DNA polymerase and sealed by DNA ligase. The result is an integrated transposon with a short stretch of duplicated genomic DNA at each end.

In this case, the transposon can really be said to "jump" from one location to another. The original site is completely restored and the transposon moves to another location.

Many bacteria contain composite transposons that contain additional genes. The best known ones are those that carry genes for drug resistance, such as tetracycline resistance (transposon Tn10) or chloramphenicol resistance (Tn9). One of the reasons why drug resistance spreads in bacterial populations is because the resistance gene is on a mobile genetic element that can integrate into foreign DNA or into a plasmid that can be readily transferred.

There are usually not many transposons in a typical bacterial genome. This is because there are not many sites of integration that aren't lethal. In most cases when a transposon jumps it lands in a gene and inactivates it. This is usually lethal. Thus, most bacterial transposons reside in parts of the genome that are non-essential and there isn't much of that in bacteria.

Genomes that contain lots of non-essential DNA (junk) are likely to carry many transposons.

5 comments :

  1. There are usually not many transposons in a typical bacterial genome. This is because there are not many sites of integration that aren't lethal. In most cases when a transposon jumps it lands in a gene and inactivates it. This is usually lethal. Thus, most bacterial transposons reside in parts of the genome that are non-essential and there isn't much of that in bacteria.

    This seems like a chicken-egg issue. I'd argue that the lack of TEs in bacterial genomes is an issue of population size -- large bacterial population sizes allow for selection to purge these slightly deleterious insertions.

    Also, are you going to discuss Class I TEs? Class II TEs aren't selfish elements within a genome b/c copy number remains constant. Class I TEs can increase in copy number within a genome.

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  2. rpm, no I'm going to skip right to retrotransposons. It's too difficult to explain replicative transposition.

    BTW, aren't you mixing up class I and class II? I thought Tn3 was a class II transposon?

    Mu is the only class III transposon, right?

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  3. It's not correct, RPM. Even though Class II elements, also known as cut-and-paste or DNA transposons, use a conservative mechanism of transposition, they can still multiply and proliferate in the genome. One way by which this can happen is through repair of the gap left at the site of transposon excision via homologous recombination. The result is a net gain of one copy of the transposon. Another strategy, used by bacterial and some eukaryotic elements, is to jump during DNA replication from a replicated site to an as yet non-replicated site. The result is that the transposon is replicated twice, again increasing its copy number by one copy.

    Although the amplification dynamic of class 2 transposons is not as explosive as for class 1 elements, class 2 elements can reach fairly high copy numbers. For example, in your genome (and also mine and Larry's), there are approximately 350,000 class 2 transposons per haploid genome. Human DNA transposons group in about 125 families with copy numbers up to 30,000 per family.

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