IS Elements

Description:

Insertion sequence (IS) elements are DNA sequences that are capable of independent transposition. The mechanism of transposition is usually replicative producing IS copies elsewhere in the genome.

The IS elements are grouped into families based on the similarities of their gene products and DNA sequence organization, such as the IS3 family that includes a diverse set of types of IS elements.

The authoritative IS database IS Finder contains IS sequences from many bacteria and archaea, and is a registry for new IS sequence nomenclature and a repository for IS sequences at the CNRS, France, with web-based analytical tools. (Siguier, 2006). IS Finder also has a comprehensive online review of IS sequence and function.

Details:

Transposition is facilitated by IS-encoded transposases, the ins genes, often subject to programmed translational frameshifting to produce a functional transposase. Many IS elements have small terminal inverted repeats (IR) that can be the targets of transposase action. Many of the E. coli K-12 IS elements are active and mutagenic.

Specific instances of IS element types, designated by the addition of letters assigned in EcoGene like IS1A or IS5B, can be identical copies, nearly identical isotypes, or pseudo-element IS' versions (with point mutations, nonsense mutations, insertions of other ISs, or having only partial sequence). The ins genes coded by ISs with multiple insertion sites have been assigned alelle/instance numbers in EcoGene corresponding to the position in the alphabet of its IS instance letter, e.g. IS1A has insA1 and insB1; IS5U has insH21; etc.

IS insertions within or in front of genes affecting function or expression can be selected for in response to natural evolutionary pressure, laboratory domestication, experimental mutant hunts using various selections or screens, or possibly by chance alone without selective pressure.

MG1655(Seq) is the genome-sequenced version of MG1655 represented by Genbank U00096.3 and EcoGene 3.0. MG1655(Seq) has three instances of IS insertion not found in the parental MG1655 strain, presumably acquired in response to selective pressure from laboratory growth and/or maintenance; these have been desugnated as IS1H, IS1I and IS5U in EcoGene (Barker, 2004; Freddolino, 2012).


The 47 instances of IS element insertion in MG1655(Seq) include 13 different types of IS elements or pseudo-elements including IS1(8), IS2(7), IS3(5), IS4(1), IS5(12), IS30(4), IS150(1), IS186(3), IS609(1), IS911'(2), a partially deleted IS600', a partially deleted IS3-like ISX', and a partially deleted IS4-like ISZ' that is closely related to ISEhe3 (Rudd, 1998).

The 47 IS elements contain a total of 68 ins genes including 10 pseudogenes.