Transposable Elements: Meaning, Nomenclature and Classes | Genetics

In this article we will discuss about:- 1. Meaning of Transposable Elements 2. Nomenclature of Transposable Elements 3. Classes.

Meaning of Transposable Elements:

For a long time it was assumed that the genes have fixed chromosomal locations. Genetic recombination is a common process of a cell within which exchange between the homologous DNA sequences takes place. Over the past few decades some information’s of gene rearrangement have come forth that results from illegitimate crossing over between incomplete homologous DNA sequences.

In 1940s, McClintock Barbara in her genetic experiment with maize found that certain genetic elements regularly jump to new locations, and thereby affect gene expression. Therefore, kernels of maize ear show variation in colours. Her work was followed even after 30 years by the recognition that the bacteria contain mobile DNA sequence.

The genetic segments moving from one location to the other were also discovered in bacteria well during 1970s but the frequency was quite low (10^-7 – 10^-2 per generation). Several apparent random mutations disrupting gene function in E.coli were found to occur due to insertion of a large DNA segments.

Many of these sequences had the jumping properties similar to maize elements. Later on the properties of such genes of E. coli could be known at molecular levels through the method of gene cloning and DNA sequencing.

These moving genetic elements have been called with different names such as jumping genes, movable genes, transposons and transposable elements. For consistent work on maize and discovery of jumping genes, McClintock Barbara was awarded Nobel Prize in 1983.

Genome evolves by acquiring new sequences and by rearrangement of existing sequences. The sudden introduction of new sequences results from the ability of a factor to carry information between genome loci. The extra chromosomal element provides information’s by transferring a small DNA segment.

In bacteria plasmids move through conjugation, whereas phages transfer through infection. Both phages and plasmids occasionally transfer host genes along with their own replication. In some bacteria direct transfer of DNA occurs by transformation. In addition, the retroviruses can transfer DNA segment during infection cycle in eukaryotes.

However, gene rearrangement in genome may form new sequences by placing them in new regulatory situation. Rearrangement occurs either from recombination under taken by the cellular system for homologous recombination and repair, or from the transportation induced by transposons. Movement of transposable element from one chromosome site to another is shown in Fig. 8.30.

Generally, the mobile segments of temperate phages (e.g. λ and Mu phages) which resemble insertion sequences are called transposable elements, and the mobile sequence, of bacterial system are called transposons. Thus, the transposable elements have been defined as Dm sequences which can insert into several sites in a genome.

Transposable elements are recognised by the presence of inverted repeat DNA sequences at their ends. These sequences are necessary for the DNA between them to be transposed by a particular enzyme (transposase) associated with the transposable element.

Nomenclature of Transposable Elements:

Campbell (1977) have described the nomenclature of transposable elements in prokaryotes. The transposons which were discovered first did not contain any known host genes. Therefore, for historical reasons these were called insertion sequences or IS elements and designated as IS1, IS2, IS3, etc.

Transposons contain easily recognizable bacterial genes especially for antibiotic resistance. The members of this class are designated by the abbreviation, Tn followed by a number such as Tn1, Tn2, Tn3, etc.

The number distinguishes different transposons. When it is necessary to refer the genes carried on transposons, these are represented by standard genotypical designations such as Tn1 (amp^r), where amp’ refers that the transposon carries the genetic locus for ampicillin resistance.

Moreover transposon present within a particular gene creates mutation in that gene. For example if mutation occurs at position 135 in galT gene by transposon 4, the notation is designated as galT 135::Tn4. Transposons have occasionally been designated in non-standard way also, for example ү, δ which is an element present in F plasmid.

However in eukaryotes no definite pattern of naming of transposable elements is used. For example the transposable elements in Drosophila are named Copia, 497 and P, transposable elements of yeast as Ty1 and transposable element of maize as dissociation element and activator.

Classes of Transposable Elements:

Transposable elements of prokaryotes are generally called transposons.

Mainly three classes of transposable elements have been categorized:

(i) Insertion sequences or IS elements also called simple transposons which contain no genetic information except the DNA sequences necessary for transposition, and also lack host gene,

(ii) Transposons which contains antibiotic resistance genes and may or may not be flanked by two identical copies of IS elements, and

(iii) The transposable phages which are lysogenic phages and employ transposition as a way of life.

(i) Insertion Sequences (IS Elements):

For the first time transposable elements were identified in the form of spontaneous insertions in bacterial operons. Such insertions inhibited the transcription and/or translation of genes in which it was inserted. These simplest transposable elements were called insertion sequences and designated by the prefix IS followed by numbers of each type e.g. IS1, IS2, IS3, etc.

The IS elements are the normal constituents of bacterial chromosome and plasmids. A typical strain of E. coli contains more than 10 copies of at least one of the common IS elements. The properties of some IS elements are given in Table 8.3.

The IS elements are the autonomous units each of which codes only for proteins required for its own transposition. Each IS element differs in sequence size but resemble in several ways in organization (Table 8.3). Mostly all of them are of about 1000 bp long ending with inverted terminal repeats of about 10-40 bp long. Structure of an IS elements before and after insertion at a target site is shown in Fig. 8.31.

The inverted terminal repeat has two copies of repeats which are closely related. For example the same sequence of inverted terminal repeat (ITR) of 9 bp (e.g. 987654321 bp long) is encountered from the flanking DNA on either side of it after proceeding towards the elements. The terminal repeats are believed to serve as recognition sequence for transposition enzymes, the transposes in their role of fusing the ends of IS elements with the target DNA.

Besides IS1, all the IS elements possess a single long coding sequence that starts just inside at one end of ITR and terminate just before or within inverted repeat at the other end. This codes for the transposase. However, IS1 consists of a more complex organisation with two reading frames. The transposase is produced by making a frame shift translation to allow both reading frames to be used.

After transposition by IS element, a sequence of target site of host DNA at the site of insertion is duplicated. The duplicated segment is known as direct repeat. It is repeated in the same orientation.

This duplication of sequence of target site is revealed upon compares before and after insertion of IS element. Therefore, after transposition one copy of sequence of target i.e. direct repeat is present on both the ends of transposon (Fig. 8.31).

However, a transposon results in different sequences of direct repeats, the length of any IS element remains almost constant that is 9 bp. Within a host DNA insertion of most of IS elements occur at a variety of sites. Study of a large number of bacterial transposable elements indicates that each element encodes at least two proteins.

The insertion sequences can be detected in two ways:

(i) They interact and inactivates, genes into which they insert, and

(ii) They may contain promoters which allow RNA polymerase to transcribe and thus turn on adjacent genes. They do not perform any function in bacterial cells except that they may act as natural agent of genetic change by bringing about structure and function.

Many structural variations have been observed in IS element regarding the source and host range of IS elements.

Two generalizations, can be made:

(i) The same kind of IS element such as IS1 can be found on plasmid, phage genome and chromosome of different bacteria, and

(ii) Several IS elements can function efficiently in bacteria that do not contain the same IS element in their chromosome. For example IS 10 is active in both E. coli K12 and Salmonella typhimurium, although their chromosome do not contain IS 10 sequence. Several copies of IS elements may be found on bacterial genome. For example, 8 copies of IS1 and about 5 copies of IS2 are found in E. coli chromosome.