1. TRANSPOSABLE GENETIC ELEMENTS I

2. At the end of this chapter you should…
Understand the structure, function and mechanism underlying known transposons in bacteria.
Describe the structure, function and mechanisms of transposition of transposable elements in eukaryotes.
Explain the nature of retrotransposons and how they relate to the other transposable elements.
Understand the genetic implications of transposable elements and their role in evolution.

3. Chapter outline
Transposable elements (TEs) are discrete DNA sequences that move from one location to another within the genome. They are found in nearly all species that have been studied and constitute a large fraction of some genomes, including that of Homo sapiens.
TEs are potent broad-spectrum mutator elements that are responsible for generating variation in the host genome and have a role as key players in the ecology of the genome.
TEs comprise a group of distinct DNA segments with the capacity to move, or transpose, between many nonhomologous (unrelated ) sites in the genome. The properties of these elements provide them with the capacity to mutate the DNA of the host organisms in which they reside in many different ways.

4. Historical Sidelight – Barbara McClintock.
Credit: Used with permission of Marjorie M. Bhavnani, photo from Cold Spring Harbor Laboratory Archives.
Historical Sidelight – Barbara McClintock.
Historical Sidelight – Barbara McClintock.
© 2003 John Wiley and Sons Publishers

5. Colour variation among kernels of maize
Colour variation among kernels of maize. Studies of the genetic basis of this variation led to the discovery of transposable elements.

6. Barbara McClintock first published her transposon findings in 1948
Barbara McClintock first published her transposon findings in In 1949 she showed that the change of unstable recessive alleles to the dominant form in maize was due to the movement of a short segment of a chromosome.
She first named these segments “controlling elements” because of her emphasis on their role in gene expression.
The discovery of transposition was important in providing a new concept of genomes as fluid and dynamic entities.
It was not well received initially for various reasons.
During the ’60’s and ’70’s more evidence for the existence of transposons came to light.
In 1983, McClintock was awarded the Nobel prize.

7. Transposable elements: an overview
Over 40% of our human genome is composed of TEs indicating they have played a major role in shaping the structure of chromosomes and our genome.
Geneticists have been particularly interested in the application of TEs as tools useful in research and phylogenetic analysis.
Structural molecular biologists have an interest in TEs because of their homologies with virus replication machinery, transcription factors, and bindings proteins.
TEs have the potential to be of particular interest to evolutionary biologists because of the interactions with their hosts.

8. They can be classified into three classes based how they transpose.
In one, a transposase encoded by the transposon itself excises the element from the genome and catalyzes its insertion elsewhere – transposition by cut-and-paste transposons.
In the second, called replicative transposition by replicative transposons, the transposase interacts with the element and its new site of insertion including replication of the element and subsequent insertion; the replicated copy remains at the original site.
In the third, retrotransposition by the retrotransposons encode a reverse transcriptase to make a DNA copy from the element’s RNA template which then insert into new sites; such elements are related to retroviruses and are called retroviruslike elements.

10. Note…Key Points
A cut-and-paste transposon is excised from one genomic position and inserted into another by an enzyme, the transposase, which is usually encoded by the transposon itself.
A replicative transposon is copied during the process of transposition.
A retrotransposon produces RNA molecules that are reverse transcribed into DNA molecules; these DNA molecules are subsequently inserted into new genomic positions.

11. Transposable elements in bacteria
Transposable elements in bacteria were the first to be studied at the molecular level.
Bacterial transposons move within and between the bacterial chromosome and various types of plasmids.
There are three main types :
1. the insertion sequences, or IS elements.
2. the composite transposons, and
3. the Tn3 elements.
These three types of transposons differ in size and structure.

12. Three main types:
IS elements are the simplest: contain only genes whose products are involved in promoting or regulating transposition, including transposase
Composite transposons: 2 IS elements insert near each other allowing the DNA between them to become transposable
Tn3 elements: larger than IS elements and contain genes other than those required for retrotransposition and behave as IS elements.
Composite transposons and Tn3 elements containing some genes that encode products unrelated to the transposition process.

13. IS Elements
The insertion sequences or IS elements are the simplest transposons they may insert at many different sites in the bacterial chromosome, are –2.5 Kb in length, contain inverted terminal repeats of 9-40 bp in length, and many encode a transposition enzyme or transposase.
The smallest, IS1, is 768 bp long.
A bacterial chromosome may contain several copies of a particular type of IS elements. For example, 6 to 10 copies of IS1 are found in the E. coli chromosome.
Plasmid may also contain IS elements.
When a particular IS element resides in both a plasmid and a chromosome, it creates the opportunity for homologous recombination between different DNA molecules.
Such recombination appears to be responsible for the integration of the F plasmid into E. coli chromosome.

14. The enzyme – transposase – seems to bind at or near the ends of the element, cuts both strands of the DNA. Cleavage of the DNA at these sites excises the element from the chromosome or plasmid, so that it can be inserted at a new position in the same or a different DNA molecule.
IS elements are therefore cut-and-paste transposons.
The bacterial chromosome may contain many copies of a particular IS element.
The F plasmid has two different IS elements which allows homologous recombination between the plasmid and the same IS elements in the chromosome.

17. Composite Transposons
Composite transposons are denoted by Tn and are created when two IS elements insert near each other which captures the DNA sequence between them and can thereby promote their movement.
Next slides give three examples.
1st slide - In Tn9, the flanking IS elements are in the same orientation with respect to each other.
2nd and 3rd slide - In Th5 and Tn10 , the orientation is inverted.
The best studied examples contain antibiotic resistance genes between the elements.
In some cases, the IS elements flanking the interior DNA are not identical but at least one encodes a transposase that enables transposition.

21. Composite Transposons
Tn5 illustrates another feature of the composite transposons: their movement is regulated. When a bacterial cell is infected with a nonlytic bacteriophage that carriers Tn5 on its chromosome, the frequency of Tn5 transposition is dramatically reduced if the infected cell already carriers a copy of Tn5.
This reduction implies that the resident transposon inhibits the transposition of an incoming transposons, possibly by synthesizing a represor.

24. Tn3 Elements
Tn3 are larger than the IS elements, and usually contain genes that are not necessary for transposition.
TN3 elements do not have IS elements at each of their ends, they have simple inverted repeats 38 to 40 bp long at their termini.
Tn3 is unusual in that it contains three genes specifying a transposase (tnpA), a resolvase (tnpR) and an enzyme called beta lactamase (bla) confers resistance to the antibiotic ampicillin, and the other two proteins play important roles in transposition.
The transposition of Tn3 occurs in two stages.