Integrative and Conjutative Elements (ICEs) |
Integrative and conjugative elements (ICEs) are a diverse group of mobile genetic elements found in both Gram-positive and Gram-negative bacteria. ICEs are self-transmissible elements that encode a full complement of machinery for conjugation as well as intricate regulatory systems to control excision from the chromosome and onward conjugative transfer [Wozniak and Waldor, 2010]. These multi-talented entities can promote their own mobilization and potentially that of other 'hitch-hiking' genetic elements and thus contribute to horizontal transfer of virulence determinants, antibiotic-resistance genes and other bacterial traits [Hastings. et al., 2004]. ICEs are being identified in increasing numbers as sequenced genome databases expand exponentially [Burrus et al., 2002]. At present only a few have been classified into ICE families, amongst the best characterized of which is the ![]() ![]() ![]() We are collating available experimental and bioinformatics analyses data and literature about known and putative ICEs in bacteria as a PostgreSQL-based database called ICEberg. As its name implies we expect that ICEberg will continue to grow from its currently visible tiny 'tip' representing presently known ICEs to a very substantial database as more and more of these entities are revealed. |
Fig. 1. The type IV restriction endonuclease ScoA3McrA (SCO4631), encoded by the Streptomyces coelicolor M145
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ICEberg, a database for ICE |
A few mobile genetic element-focused web-based recourses such as
IS finder (
![]() ![]() ![]() Users can create maps of ICEs, investigate gene loci of interest with GBrowse, search ICEberg by ICE name, ICE family or organism name and are able to blast a query sequence against ICEberg to identify potential homologs. The multiple sequence alignment tool MUSCLE and Jalview are also readily accessible to allow for user-directed analyses focused on diverse ICE-borne genes to facilitate individualized directions of research. Ultimately, we envisage an ICE-specific resource to facilitate efficient investigation of large numbers of these elements, recognition of less than obvious ICE-associated patterns of sequence-, gene- and/or functional conservation and an improved understanding of the biological significance of these entities in diverse host organisms. As its name implies we expect that ICEberg will continue to grow from its currently visible tiny 'tip' representing presently known ICEs to a very substantial database as more and more of these entities are revealed. We expect that ICEberg will prove to be of major interest to a broad community of researchers. |