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Publication    
Nucleic Acids Research, 2012, 40, D621-D626.

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

D. Bi, Z. Xu, E. Harrison, C. Tai, Y. Wei, X. He, S. Jia, Z. Deng, K. Rajakumar* and H.Y. Ou*

 Link to PubMed
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.

News in Chinese

细菌整合型接合元件数据库ICEberg对外开放

近日,国际分子生物学刊物《Nucleic Acids Research》在线发表了我组2010级博士生毕德玺为第一作者的论文“ICEberg: 基于web的细菌整合型接合元件资源”。

亲缘细菌的染色体骨架通常相对保守,但有些菌株通过拥有某些特异的可移动遗传元件,如原噬菌体、插入序列、转座子、整合子和基因组岛等,维持或增强它们在 强大选择压力下的竞争优势和稳定遗传。有些基因组岛由整合型接合元件组成,展示出位点特异整合、切出环化和接合等典型的自行转移特性。整合性接合元件 (integrative and conjugative elements, ICEs) 广泛存在于细菌中,是基因水平转移的一种有效途径,在细菌进化中具有重要意义;但目前所发现的ICEs仅如冰山一角。整合性接合元件资源库ICEberg 通过生物信息学预测和文献挖掘,系统地识别了上百个细菌中400多个ICEs,提出了ICEs家族分类方法,比较分析了位点特异整合、切出环化、接合转移 和精细调控等典型的自行转移特性。
 
Figure 1. ICE patterns.

 


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