ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria

Abstract

ICEberg (http://db-mml.sjtu.edu.cn/ICEberg/) is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. We propose that ICEberg will facilitate efficient, multi-disciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community.

Figure 1.

An overview of ICEberg datasets and outputs using the SLP1 ICE element in Streptomyces coelicolor A3(2) as an example. (a) List of five identified ICEs in S. coelicolor A3(2), one of which has been experimentally verified (30), while the remaining four have been presently and/or previously predicted by in silico approaches (4). (b) A circular representation of the linear chromosome of S. coelicolor A3(2) generated by ICEberg-integrated CGview showing locations and sizes of ICEs within this replicon. (c) An overview of the features of SLP1: size, GC content, insertion site, known or predicted function(s), additional compatible hosts and replicon coordinates. Hyperlinks to NCBI are provided as appropriate, as is a link that allows for visualization of the gene content of the element by Gbrowse. (d) A complete gene list of SLP1 with links to NCBI, UniprotKB and KEGG. The three distinct core ICE modules that mediate integration and excision, conjugation and regulation have been sought, examined and highlighted using different colours. SCO4631 has recently been reported by us to encode a type IV restriction endonuclease, ScoA3McrA, that can cleave phosphorothioated and Dcm-methylated DNA (31).