Transposable elements

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
Transposable elements are mobile segments of DNA that relocate in the genome occasionally.
+
[Editorial note: The information on this page pertains to bacteria and primarily ''Escherichia coli''.  If you're interested in adding information on transposable elements in other organisms, please move the contents of this page to [[Transposable elements/Bacteria]].]
 +
 
 +
==Overview==
 +
'''Transposable elements''' or '''transpososns''' are mobile segments of DNA that relocate in the genome occasionally. '''Transposition''' refers to the movement of these segements.  Transposons must encode a '''tranposase''': an enzyme which makes two single-stranded breaks in the target DNA which is a necessary step for transposition.
 +
 
 +
==Nomenclature==
 +
Transposons are named by the abbreviation Tn followed by a number (like Tn''1'', Tn''2'', Tn''3'' and so on).  Genes on transposons are referred to by their genotypic name (like Tn1(''ampR'')).  The transposons that were first  identified did not carry any host genes and were called '''insertion sequences''' or '''IS elements''' (labelled IS''1'', IS''2'' and so on).  When transposons occur within genes, they are designated by the name of the gene, the allele number, two colons and the transposon name (like ''lacZ87''::Tn''3''). 
 +
 
 +
==Classification==
 +
 
 +
There are 4 classes of transposons ...
 +
 
 +
#Insertion sequences or IS elements
 +
#*don't contain any host genes
 +
#*termini have inverted repeat sequences
 +
#*can frequently contain transcription-stop signals or chain termination mutations in all reading frames
 +
#*contain two coding sequences
 +
#Composite transposons or composite type-I transposons
 +
#*an antibiotic resistance gene flanked by two highly similar copies of an IS element (either direct or inverted repeats)
 +
#*sometimes the terminal IS elements can transpose alone
 +
#*transposons in plasmids can act as two transposons
 +
#The Tn3 transposon family
 +
#*~5000bp
 +
#*contains β-lactamase (for ampicillin resistance), a transposase and a resolvase (for transposition)
 +
#*contain short inverted repeats but are not flanked by IS elements
 +
#The transposable phages
 +
#*Mu and D108 phages use tranposition in their life cycles (for DNA replication)
 +
 
 +
===Insertion elements===
 +
 
 +
{|{{table}}
 +
|-
 +
!align="center" style="background:#f0f0f0;"|Element
 +
!align="center" style="background:#f0f0f0;"|Number and copies and location
 +
!align="center" style="background:#f0f0f0;"|Length
 +
!align="center" style="background:#f0f0f0;"|Genbank Accession
 +
|-
 +
|IS''1''
 +
|5-8 in chromosome
 +
|768
 +
|
 +
|-
 +
|IS''2''
 +
|5 in chromosome; 1 in F
 +
|1327
 +
|
 +
|-
 +
|IS''3''
 +
|5 in chromosome; 2 in F
 +
|1258
 +
|
 +
|-
 +
|IS''4''
 +
|1 or 2 in chromosome
 +
|1426
 +
|
 +
|-
 +
|IS''5''
 +
|Unknown
 +
|1195
 +
|
 +
|-
 +
|Tn''1000'' (γδ)
 +
|1 or more in chromosome; 1 in F
 +
|5980
 +
|
 +
|-
 +
|}
 +
 
 +
==Why do I care?==
 +
Transposable elements can hop into your plasmids with out warning.  Note that this can happen not just during cloning but also when transforming intact plasmid into cells.  [[Tom Knight]], [[Jason Kelly]] and [[Reshma Shetty]] have each observed this phenomenon. 
==References==
==References==

Revision as of 14:03, 24 August 2006

[Editorial note: The information on this page pertains to bacteria and primarily Escherichia coli. If you're interested in adding information on transposable elements in other organisms, please move the contents of this page to Transposable elements/Bacteria.]

Contents

Overview

Transposable elements or transpososns are mobile segments of DNA that relocate in the genome occasionally. Transposition refers to the movement of these segements. Transposons must encode a tranposase: an enzyme which makes two single-stranded breaks in the target DNA which is a necessary step for transposition.

Nomenclature

Transposons are named by the abbreviation Tn followed by a number (like Tn1, Tn2, Tn3 and so on). Genes on transposons are referred to by their genotypic name (like Tn1(ampR)). The transposons that were first identified did not carry any host genes and were called insertion sequences or IS elements (labelled IS1, IS2 and so on). When transposons occur within genes, they are designated by the name of the gene, the allele number, two colons and the transposon name (like lacZ87::Tn3).

Classification

There are 4 classes of transposons ...

  1. Insertion sequences or IS elements
    • don't contain any host genes
    • termini have inverted repeat sequences
    • can frequently contain transcription-stop signals or chain termination mutations in all reading frames
    • contain two coding sequences
  2. Composite transposons or composite type-I transposons
    • an antibiotic resistance gene flanked by two highly similar copies of an IS element (either direct or inverted repeats)
    • sometimes the terminal IS elements can transpose alone
    • transposons in plasmids can act as two transposons
  3. The Tn3 transposon family
    • ~5000bp
    • contains β-lactamase (for ampicillin resistance), a transposase and a resolvase (for transposition)
    • contain short inverted repeats but are not flanked by IS elements
  4. The transposable phages
    • Mu and D108 phages use tranposition in their life cycles (for DNA replication)

Insertion elements

Element Number and copies and location Length Genbank Accession
IS1 5-8 in chromosome 768
IS2 5 in chromosome; 1 in F 1327
IS3 5 in chromosome; 2 in F 1258
IS4 1 or 2 in chromosome 1426
IS5 Unknown 1195
Tn1000 (γδ) 1 or more in chromosome; 1 in F 5980

Why do I care?

Transposable elements can hop into your plasmids with out warning. Note that this can happen not just during cloning but also when transforming intact plasmid into cells. Tom Knight, Jason Kelly and Reshma Shetty have each observed this phenomenon.

References

  1. isbn:0-86720-248-3. [MicrobialGenetics]
Personal tools