IS4 family goes genomic.

BMC Evolutionary Biology
Daniel De PalmenaerJ Mahillon

Abstract

Insertion sequences (ISs) are small, mobile DNA entities able to expand in prokaryotic genomes and trigger important rearrangements. To understand their role in evolution, accurate IS taxonomy is essential. The IS4 family is composed of approximately 70 elements and, like some other families, displays extremely elevated levels of internal divergence impeding its classification. The increasing availability of complete genome sequences provides a valuable source for the discovery of additional IS4 elements. In this study, this genomic database was used to update the structural and functional definition of the IS4 family. A total of 227 IS4-related sequences were collected among more than 500 sequenced bacterial and archaeal genomes, representing more than a three fold increase of the initial inventory. A clear division into seven coherent subgroups was discovered as well as three emerging families, which displayed distinct structural and functional properties. The IS4 family was sporadically present in 17 % of analyzed genomes, with most of them displaying single or a small number of IS4 elements. Significant expansions were detected only in some pathogens as well as among certain extremophiles, suggesting the probable involvemen...Continue Reading

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Datasets Mentioned

BETA
CU179680

Methods Mentioned

BETA
protein folding
X-ray

Software Mentioned

BLASTN
ACLAME
Clustal W
Parallel PRRN
wEMBOSS
Clustal
Tribe
Dialign
Jalview
Muscle

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