Transposable Elements in Genetics

Transposable Elements

• Mobile DNA sequences found in all organisms
• Frequently cause mutations and DNA rearrangements
• Discovered in the 1940s by Barbara McClintock while studying maize genetics

General Characters

• Most generate short, flanking direct repeats at the target site when inserted
• Many possess short terminal inverted repeats
• Flanking direct repeats are 3 to 12 bp long and present on both sides of most transposable elements
  • Not part of the transposable element, they are generated during insertion
• Terminal inverted repeats are 9 to 40 bp long and are inverted complements of one another
  • Found at the ends of many, but not all, transposable elements

Transposition

• Movement of transposable elements from one location to another
• Several different mechanisms are used for transposition in prokaryotic and eukaryotic cells
• All types of transposition have several features in common:
  • Staggered breaks are made in the target DNA
  • The transposable element is joined to single-stranded ends of the target DNA
  • DNA is replicated at the single-strand gaps

Mechanisms of Transposition

• Can occur through a DNA molecule or through the production of an RNA molecule that is then reverse transcribed into DNA
• DNA Transposons (class I transposable elements): transpose as DNA
• Retrotransposons (class II transposable elements): transpose through an RNA intermediate
  • RNA is transcribed from the transposable element (DNA) and then copied back into DNA using reverse transcriptase
• Transposition can be replicative (the element is copied and the copy moves) or non-replicative (the element excises and moves)

Characteristics of Two Major Classes of Transposable Genetic Elements

Class I

• Structure: Short, terminal inverted repeats; short flanking direct repeats at the target site
• Genes encoded: Transposase gene (and sometimes others)
• Transposition: Through DNA (replicative or non-replicative)
• Examples: IS1 (E. coli), Tn3 (E. coli), Ac, Ds (Maize), p elements (Drosophila)

Class II

• Structure: Long, terminal direct repeats; short flanking direct repeats at the target site
• Genes encoded: Reverse transcriptase gene (and sometimes others)
• Transposition: By RNA intermediate
• Examples: Ty (Yeasts), copia (Drosophila), Alu (Human)

Structure of Transposable Elements

Bacteria

• Two major groups:
  • Simple transposable elements (insertion sequences): Carry only the information required for movement
  • More complex transposable elements (composite transposons): Contain DNA sequences not directly related to transposition
• Insertion Sequences:
  • Simplest type of transposable element in bacterial chromosomes and plasmids
  • Carry only the genetic information necessary for their movement
  • Typically 800 to 2000 bp in length and possess terminal inverted repeats and flanking direct repeats at the site of insertion
  • Contain one or two genes that code for transposase
• Composite Transposons
  • Segment of DNA flanked by two copies of an insertion sequence
  • Consists of a central region with extra genes, flanked by identical or very similar IS elements
  • Contain genes other than those required for transposition
  • Lacking insertion sequences are referred to as non-composite transposons
  • Example: Tn3 (5000 bp - Possesses terminal inverted repeats of 38 bp and generates flanking direct repeats that are 5 bp in length)

Effects of Transposable Elements

• Can insert within a gene to cause a mutation or stimulate DNA rearrangement leading to deletions of genetic material
• Used to purify genes and study their function
  • Can fragment the genome and isolate the mutated fragment, purifying the gene
• Can turn on and off eukaryotic and prokaryotic genes
• Located within plasmids and participate in processes like plasmid fusion and the insertion of F plasmids into the E. coli chromosome
• Play an extremely important role in the generation and transfer of new gene combinations

Evolutionary Significance of Transposable Elements

• Cellular-function hypothesis: Suggest that transposable elements provide some important function for the cell
• Genetic-variation hypothesis: Proposes that transposable elements provide evolutionary flexibility by inducing mutations
• Selfish-DNA hypothesis: Suggests that transposable elements do not benefit the cell but are widespread because they can replicate and spread