Transposable Genetic Elements

TEs are ubiquitous throughout the evolutionary tree from microorganisms to mammals. For instance, a bacterial virus called phage MuM (mutator) is characterized as a TE based on similarities with other transposons. Mu integration into the host bacterial chromosome is considered transposition because it can occur nearly anywhere, thereby inactivating host genes and generating insertions and deletions.

Transposons also occur naturally in bacterial genomes. The extensively studied species Escherichia coli (E. coli) contains insertion sequences (IS) and transposons in its genome. IS elements are generally small, have inverted sequence repeats at their ends (important for their mobility), and contain Figure 2. Transmission of transposable elements (TEs). Vertical transmission involves a germ-line TE integration (indicated by the X in the sperm), that is passed on to the next generation. Horizontal transmission involves the transfer of a TE (indicated by the X) across species, possibly via a parasite. an overlapping genetic region encoding a transposase and a repressor. Transposons are larger than IS elements, since they contain additional genes such as drug-resistance genes. These elements are flanked either by inverted repeats or by IS elements. Bacterial transposons undergo conservative transposition, in which the transposon is excised and pasted elsewhere, or replicative transposition, in which it is copied and the copy is inserted elsewhere.

Ty elements in yeast contain retroviral-related sequences (called gag and pol) and include long terminal repeats (LTRs); hence they are considered viral (or viral-like) retrotransposons or LTR retrotransposons. Their activity is replicative: An RNA is transcribed from the gene, reverse-transcribed to DNA (cDNA) and integrated elsewhere in the genome. Since Ty does not contain env genes, which code for encapsulating envelope proteins, it does not yield infectious particles. However, viruslike particles accumulate in cells in which retroposition has been induced.

The African Trypanosome, a parasitic protozoan, contains the ingi (non-LTR) retrotransposons. Ingi may therefore be referred to as a parasite's parasite. Full-length elements are 5.2 kilobase pairs long, have multiple adenine nucleotides at one end (called a "poly A tail"), and DNA sequences similar to reverse transcriptase genes and mammalian LINEs (discussed below). Among insects, the Drosophila genome contains a virtual cornucopia of TEs. Fruit fly transposons include mariner, hobo, and P elements, non-LTR-retrotransposons include I, F, and jockey elements, and LTR-retrotransposons such as gypsyM and copia-like elements. These eukaryotic transposons are similar to bacterial IS elements, but are generally larger due to the presence of introns (noncoding sequences of the genome).

The primary TEs in mammalian genomes include short and long interspersed repetitive elements (SINEs and LINEs, respectively). SINEs represent a group of small retrotransposons (75-500 base pairs) and lack protein-coding sequences. In primates, Alu elements represent the predominant SINE family. More than 1 million copies of Alu are contained in the human genome, representing about 13 percent of the genome. This is truly impressive considering their lack of replicative autonomy. Alu elements are 300 base pairs in length, are rich in adenine sequences both internally and at the 3′ (downstream) end, and internal RNA polymerase III promoter sequences, allowing them to be replicated. L1 elements represent the predominant primate LINE family, contain two open reading frames, adenine-rich 3′ ends, and internal RNA polymerase II promoter sequences. They constitute approximately 20 percent of the human genome. A full-length LINE is about 6.5 kilobase pairs long, although most elements are truncated as a result of incomplete reverse transcription.