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Mobile Genetic Elements in Eukaryotes

In this mobile genetic elements in eukaryotes post we have briefly explained about mobile DNA, how do mobile genetic elements work?, and major types of mobile genetic elements.

The second type of repetitious DNA in eukaryotic genomes, termed interspersed repeats (also known as moderately repeated DNA, or intermediate-repeat DNA).

They are composed of a very large number of copies of relatively few sequence families. These sequences, which are interspersed throughout mammalian genomes, make up ≈25– 50 percent of mammalian DNA (≈45 percent of human DNA).

Because moderately repeated DNA sequences have the unique ability to “move” in the genome, they are called mobile DNA elements (or transposable elements).

Although mobile genetic elements, ranging from hundreds to a few thousand base pairs in length, originally were discovered in eukaryotes, they also are found in prokaryotes. The process by which these sequences are copied and inserted into a new site in the genome is called transposition.

Mobile genetic elements (or simply mobile elements) are essentially molecular symbionts and have no specific function in the biology of their host organisms, but exist only to maintain themselves, For this reason, Francis Crick referred to them as “selfish DNA.”

When transposition of eukaryotic mobile elements occurs in germ cells, the transposed sequences at their new sites can be passed on to succeeding generations. In this way, mobile elements have multiplied and slowly accumulated in eukaryotic genomes over evolutionary time.

Since mobile elements are eliminated from eukaryotic genomes very slowly, they now constitute a significant portion of the genomes of many eukaryotes. Transposition also may occur within a somatic cell; in this case the transposed sequence is transmitted only to the daughter cells derived from that cell.

In rare cases, this may lead to a somatic-cell mutation with detrimental phenotypic effects, for example, the inactivation of a tumor suppressor gene.

Mobile Genetic Elements

Barbara McClintock discovered the first mobile genetic elements in maize (corn) during the 1940s. She characterized genetic entities that could move into and back out of genes, changing the phenotype of corn kernels. Her theories were very controversial until similar mobile genetic elements were discovered in bacteria, where they were characterized as specific DNA sequences, and the molecular basis of their transposition was deciphered.

Mobile genetic elements are classified into two categories: (1) those that transpose directly as DNA and (2) those that transpose via an RNA intermediate transcribed from the mobile element by an RNA polymerase and then converted back into double-stranded DNA by a reverse transcriptase.

Mobile genetic elements that transpose through a DNA intermediate are generally referred to as DNA transposons. Mobile genetic elements that transpose to new sites in the genome via an RNA intermediate are called retrotransposons because their movement is analogous to the infectious process of retroviruses. Indeed, retroviruses can be thought of as retrotransposons that evolved genes encoding viral coats, thus allowing them to transpose between cells.

Mobile DNA

Mobile Genetic Elements

Types of Mobile Genetic Elements

Most mobile genetic elements in bacteria transpose directly as DNA. Most mobile genetic elements in eukaryotes are retrotransposons, but eukaryotic DNA transposons also occur.

Bacterial Insertion Sequences

Certain E.coli mutations caused by the spontaneous insertion of a DNA sequence, ≈1–2 kb long, into the middle of a gene. These inserted stretches of DNA are called insertion sequences, or IS elements. So far, more than 20 different IS elements have been found in E. coli and other bacteria. Transposition of an IS element is a very rare event, occurring in only one in 105107 cells per generation, depending on the IS element.

Many transpositions inactivate essential genes, killing the host cell and the IS elements it carries. Therefore, higher rates of transposition would probably result in too great a mutation rate for the host cell to survive. However, since IS elements transpose more or less randomly, some transposed sequences enter nonessential regions of the genome (e.g., regions between genes), allowing the cell to survive.

At a very low rate of transposition, most host cells survive and therefore propagate the symbiotic IS element. IS elements also can insert into plasmids or lysogenic viruses, and thus be transferred to other cells. When this happens, IS elements can transpose into the chromosomes of virgin cells. An inverted repeat, usually containing ≈50 base pairs, invariably is present at each end of an insertion sequence. In an inverted repeat the 5’→ 3’sequence on one strand is repeated on the other strand, as

Between the inverted repeats is a region that encodes transposase, an enzyme required for transposition of the IS elements.

Viral retrotransposons

Mobile DNA

5 and 3 direct repeats typical of all mobile genetic elements. The central protein-coding region is flanked by two long terminal repeats (LTRs) 250- to 600-bp, which are element-specific direct repeats.

LTRs, the hallmark of these mobile genetic elements, also are present in retroviral DNA. LTRs are characteristic of integrated retroviral DNA and are critical to the life cycle of retroviruses.

Like other mobile genetic elements, integrated retrotransposons have short target-site direct repeats at their 3 and 5 ends. The protein-coding region constitutes 80 percent or more of a retrotransposon.

Mobile DNA

Viral retrotransposons

The short direct repeat sequences (light blue) of target-site DNA are generated during integration of the retroviral DNA into the host-cell genome. The left LTR directs cellular RNA polymerase II to initiate transcription at the first nucleotide of the left R region. The resulting primary transcript extends beyond the right LTR.

The right LTR, now present in the RNA primary transcript, directs cellular enzymes to cleave the primary transcript at the last nucleotide of the right R region and to add a poly(A) tail, yielding a retroviral RNA genome.

The genomic RNA is packaged in the virion with a retrovirus-specific cellular tRNA hybridized to a complementary sequence near its 5 end called the primer-binding site (PBS).

The retroviral RNA has a short direct-repeat terminal sequence (R) at each end. The overall reaction is catalyzed by reverse transcriptase, which catalyzes polymerization of deoxyribonucleotides and digestion of the RNA strand in a DNA-RNA hybrid.

The entire process yields a double-stranded DNA molecule that is longer than the template RNA and has a long terminal repeat (LTR) at each end.

The PBS and R regions are actually much shorter than the U5 and U3 regions, and the central coding region is very much longer (7500 nucleotides) than the other regions.

Mobile DNA

Retroviral genomic RNA

Further Readings

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