ICEberg 2.0: an updated database of bacterial integrative and conjugative elements

Abstract

ICEberg 2.0 (http://db-mml.sjtu.edu.cn/ICEberg/) is an updated database that provides comprehensive information about bacterial integrative and conjugative elements (ICEs). Compared with the previous version, three major improvements were made. First, with the aid of text mining and manual curation, it now recorded the details of 1032 ICEs, including 270 with experimental supports and 762 from bioinformatics prediction. Second, as increasing evidence has shown that ICEs frequently mobilize the so-called 'hitchhikers', such as integrative and mobilizable elements (IMEs) and cis-mobilizable elements (CIMEs), 83 known transfer interactions between 49 IMEs and 7 CIMEs with 19 ICEs taken from the literature were included and illustrated with visually intuitive directed graphs. An expanded collection of 260 chromosome-borne IMEs and 235 CIMEs was also added. At last, ICEberg 2.0 provides an online tool ICEfinder to predict ICEs or IMEs in bacterial genome sequences. It combines a similarity search for the integrase, relaxase and/or type IV secretion system and the co-localization of these corresponding homologous genes. With the recent updates, ICEberg 2.0 might provide better support for understanding the biological traits of ICEs, especially as their interaction with cognate mobilizable elements may further promote horizontal gene flow.

Figure 1.

The updated web interface of ICEberg 2.0 using the SXT(MO10) in Vibrio cholerae O139 MO10 as an example. (A) The browse modules of ICEberg on the home page, consisting of three sections (ICEs, IMEs and CIMEs). (B) An overview of the feature of SXT(MO10) with the newly added putative oriT region (oriT coordinates, the corresponding link of most related oriT in oriTDB and the detailed sequences) and relaxase gene (coordinates, locus tag and MOB family). (C) Detailed information on the mobile interactions between ICEs and IMEs or CIMEs in both graph and table format. (D) A graphical display of ICE genetic modules was constructed using a local Perl script. AR: acquired antibiotic resistance genes; T4SS, type IV secretion system.