Transposable Elements in Genetics

What are Transposable Elements?

• Mobile DNA sequences present in all organisms
• Frequently cause mutations and DNA rearrangements
• Many transposable elements control their own transposition
• Barbara McClintock discovered transposable elements in the 1940s studying maize genetics

Characteristics

• Short flanking direct repeats (3 to 12 bp) are generated during insertion, not part of the element itself
• Many transposable elements have terminal inverted repeats (9 to 40 bp) that are inverted complements of each other

Transposition

• Movement of a transposable element from one location to another
• Several mechanisms are used for transposition in both prokaryotes and eukaryotes
• All transposition types share these features:
  • 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

• Transposition can occur through a DNA molecule or an RNA intermediate
• Transposable elements that transpose as DNA are called DNA transposons or Class I transposable elements
• Transposable elements that transpose through an RNA intermediate are called retrotransposons or Class II transposable elements
• Transposition can be:
  • Replicative: a copy of the transposable element is moved to a new site
  • Non-replicative: the transposable element is excised from the old site and moved to a new site

Characteristics of the Two Major Classes

Class I (DNA Transposons)

• 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 (Retrotransposons)

• 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 and eukaryotes possess a variety of transposable element types with different structures

Transposable Elements in Bacteria

• Two major groups of DNA transposons:
  • Simple transposable elements (insertion sequences): carry only the information needed for movement
  • More complex transposable elements (composite transposons): contain DNA sequences not directly related to transposition

I. Insertion Sequences

• Simplest type of transposable element in bacterial chromosomes and plasmids
• Carry only the genetic information necessary for movement
• Typically 800 to 2000 bp in length
• Possess terminal inverted repeats
• Generate flanking direct repeats at the site of insertion
• Most contain one or two genes that code for transposase

II. Composite Transposons

• Segment of DNA flanked by two copies of an insertion sequence
• Contain genes other than those required for transposition
• Transposable elements lacking insertion sequences are referred to as non-composite transposons
• Example: Tn3 (5000 bp - Possesses terminal inverted repeats of 38 bp and generates 5 bp flanking direct repeats)

Effects of Transposable Elements

• Can insert into a gene, causing mutations or stimulating DNA rearrangements that lead to deletions
• Can be used to purify genes and study their function (fragment the genome and isolate the mutated fragment)
• Can turn eukaryotic and prokaryotic genes on and off
• Located in plasmids and participate in plasmid fusion and insertion of F plasmids into the E. coli chromosome
• Play an important role in the generation and transfer of new gene combinations

Evolutionary Significance of Transposable Elements

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