ICEberg
ICEberg
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 link SXT/R391 family of Vibrio cholerae. In addition, several elements discovered more than a decade ago which had previously been classified as plasmids or conjugative transposons, such as link pSAM2 (1984) and link Tn916 (1995), have now been defined as ICEs. ICEs typically exhibit a number of features that are of interest to researchers in the fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. These include high levels of functional diversity, foreign and frequently patchwork origins and sparse experimental data on these entities.

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 link SLP1 ICE element, is able to cleave phosphorothioated and Dcm-methylated DNA [Liu, et al. (2010) PLoS Genetics, 6, e1001253].
  

ICEberg, a database for ICE
A few mobile genetic element-focused web-based recourses such as IS finder (link Reference centre for bacterial Insertion Sequences ), PAIDB (link Pathogenicity island database) and ACLAME (link A Classification of Genetic Mobile Elements) are already available. However, well-organized and comprehensive data for ICEs are at present unavailable to potential users. As such, 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. ICEberg now contains details of more than two hundred ICEs found in representatives of approximately one hundred Bacteria species. These ICEs have been manually curated and are cataloged in ICEberg along with more than two hundred directly relevant references. This database contains detailed information on all archived ICEs and the genes carried by each entity, including unique identifiers, species details and hyperlink-paths to other public databases, like NCBI, UniprotKB and KEGG. Of particular note, the three distinct modules of ICEs which mediate (i) integration and excision, (ii) conjugation and (iii) regulation of these foreign elements have been sought, examined and highlighted in the database.

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.