In this article we will discuss about the meaning of transposable elements.
The chromosomes of E. coli and other prokaryotes contain discrete moveable segments of DNA called transposable elements, which can be translocated to other locations. Such DNA sequences can move from one position on a chromosome to another, and from one DNA molecule to another.
They are detected when they are present in the midst of sequences where they were not previously present. They are integrated into DNA by mechanisms that do not require recognition of sequence homology. Transposable elements were first described by McClintock in 1965 in maize (Zea mays) when controlling genes were found to be transposed to different locations.
The controlling action of these genes is evident from their ability to suppress the function of neighbouring genes, known as position effect. For example, the gene A1 which codes for anthocyanin pigment in corn kernels is regulated by two types of controlling genes.
One type regulates the function of gene A1; the other type called signalling gene is present elsewhere, on a different chromosome, and gives the signal for activity to which the regulating gene responds. DNA segments similar to transposable elements are also present in eukaryotes. These elements are involved in the formation of inversions, deletions and fusions of DNA segments.
In fact they appear to be hot spots (vulnerable points) for these chromosomal changes. As such they are efficient tools for the study of mutagenesis. Transposable elements are divided into two general classes, depending on whether they transpose via DNA intermediates, or via RNA intermediates.
Many transposons in bacteria move via DNA intermediates. The simplest transposable elements are the insertion sequences (IS elements), ranging in size from 800 to 2000 nucleotides. Insertion sequences usually encode only the transposase protein required for transposition, and one or more additional proteins that regulate the rate of transposition.
Like many transposable elements in eukaryotes, they possess inverted repeat sequences at their termini. Transposase acts at the site of inverted repeats for recognising and mobilising the IS element. Upon insertion they create a short, direct duplication of the target sequence at each end of the inserted element.
The DNA organisation of the insertion sequence IS50 is shown in Figure below:
Other transposable elements in bacteria are more complex, containing one or more genes unrelated to transposition that can be mobilised along with the transposable element. Such complex transposons consist of two insertion sequences flanking other genes, which move as a unit. Insertion sequences move from one chromosomal site to another without replicating their DNA.
Transposase introduces a staggered break in the target DNA and cleaves at the ends of the transposon inverted repeat sequences. Transposase has high specificity for transposon inverted repeats, but is less specific with respect to the sequence of the target DNA, hence it catalyses the movement of transposons throughout the genome.
Subsequent to the cleavage of transposon and target site DNAs, transposase joins the broken ends of target DNA to the transposable element. The resulting gap in the target-site DNA is repaired by DNA synthesis, followed by ligation to the other strand of the transposon. At the end of this process there is a short direct repeat of the target-site DNA on both sides of the transposable element, indicating transposon integration.
Some other types of transposons move by a more complex mechanism, in which the transposon is replicated accompanying its integration into a new target site. This results in integration of one copy of the transposon into a new position in the genome, while another copy remains at its original location. In yeasts and protozoans, transposition by a replicative mechanism is responsible for programmed DNA rearrangements that regulate gene expression.
In these cases, transposition is initiated by the action of a site-specific nuclease that cleaves a specific target site, at which a copy of the transposable element is then inserted. Thus, transposable elements are capable of moving to non-specific sites throughout the genome. They can also participate in specific gene arrangements that result in programmed changes in gene expression.
Most transposons in eukaryotic cells move via RNA intermediates, the mechanism being similar to the replication of retroviruses. As already described, RNA genomes in retroviruses replicate via synthesis of a DNA pro virus, which is integrated into the chromosomal DNA of infected cells. The enzyme reverse transcriptase catalyses the synthesis of a DNA copy of the viral RNA.
This mechanism leads to the synthesis of a linear DNA molecule that contains direct repeats of several hundred nucleotides at both ends. These repeated sequences called long terminal repeats or LTR or LTR-transposons arise from duplication of sites on viral RNA at which primers bind to initiate DNA synthesis.
Thus, LTR sequences play important roles in reverse transcription, and are also involved in the integration and subsequent transcription of pro-viral DNA. LTR transposons resemble retroviruses, have transcription control sequences, but lack sequences for forming the viral capsid.
The reverse transcriptase synthesizes DNA in the 5′ to 3′ direction yielding a linear DNA with LTRs at both ends. The linear viral DNA integrates into the host cell chromosome by a process similar to the integration of DNA transposable elements, catalysed by a viral integration protein, and occurs at many different target sequences in cellular DNA.
At the end of the process the integrated provirus is flanked by a direct repeat of cell sequences, similar to the repeats that flank DNA transposons. The viral life cycle continues with transcription of the integrated provirus, which produces viral genomic RNA and mRNAs that direct synthesis of viral proteins. The genomic RNA is packaged into viral particles that are released from host cell and can infect a new cell.
Retroviruses have been considered one type of retro-transposon, an element that moves via RNA intermediates. There are other retro-transposons that do not behave like retroviruses, are not packaged into infectious particles. These retro-transposons can move to new chromosomal sites within the same cell via mechanisms similar to those involved in retrovirus replication.
Some retro-transposons present in yeast, Drosophila, mice and plants are structurally similar to retroviruses. They are called class I retro-transposons, have LTR sequences at both ends, encode reverse transcriptase and integration proteins, and transpose via transcription into RNA, synthesise a new copy of DNA by reverse transcriptase, and integrate into cellular DNA.
For example, retro-transposonsnts that are about 5.9 kilo base long and include two directly repeated terminal sequences or LTRs (Figure below).
Each LTR contains a promoter and sequences recognized by transposing enzymes. The Ty elements encode a single 5,700 nucleotide long mRNA that begins at the promoter in LTR at the 5′ end of the element. The mRNA transcript contains two open reading frames (ORFs) designated TyA and TyB that encode two different proteins required for transposition. The number of copies of Ty elements varies between strains, though usually there are 35 in a strain.
The yeast Ty elements are similar to retroviruses that replicate by producing DNA using viral reverse transcriptase. The DNA integrates into host chromosome where it is transcribed to produce progeny RNA viral genomes and mRNAs for viral proteins. Ty elements are similar to retroviruses and are designated retro-transposons.
Some mammals, insects, plants and trypanosomes contain class II retro-transposons which do not have LTR sequences. In mammals most of these retro-transposons consist of highly repetitive long interspersed elements (LINEs), which are repeated about 50,000 times in the genome. Like other transposable elements, LINEs are flanked by short direct repeats of the target-site DNA.
The SINEs that are about 100 to 400 bp long repeated sequences interspersed in the genome also belong to this group. LINEs and SINEs are retro-transposons. LINEs are autonomous elements that encode enzymes required for their own transposition. SINEs are non-autonomous elements that do not encode enzymes for their transposition, but depend upon enzymes encoded by LINEs.
A very abundant SINE family in humans is the Alu family. The Alu sequences constitute a major family of these elements, of which there are a million copies in the genome. These sequences are about 300 bases long, have A-rich tracts at their 3′ end and are flanked by short duplications of target-site DNA sequences.
SINEs arose by reverse transcription of small RNAs, including tRNAs and small cytoplasmic RNAs involved in protein transport. SINEs do not encode functional protein products and represent pseudogenes that arose via RNA-mediated transposition.
The transposition of SINEs and LINEs offers no advantage to the cell in which they are located. They induce mutations when they integrate at a new target site, and are thus harmful for the cell. In fact, mutations resulting from transposition of LINEs and Alu sequences have been associated with some cases of haemophilia, muscular dystrophy and colon cancer.