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Nucleic Acids Res. 2013 Jan;41(Database issue):D660-5. doi: 10.1093/nar/gks1248.

SecReT4: a web-based bacterial type IV secretion system resource.

Bi D, Liu L, Tai C, Deng Z, Rajakumar K*, Ou HY*.

 Link to PubMed

SecReT4 ( http://db-mml.sjtu.edu.cn/SecReT4/) is an integrated database providing comprehensive information of type IV secretion systems (T4SSs) in bacteria. T4SSs are versatile assemblages that promote genetic exchange and/or effector translocation with consequent impacts on pathogenesis and genome plasticity. T4SSs have been implicated in conjugation, DNA uptake and release and effector translocation. The effectors injected into eukaryotic target cells can lead to alteration of host cellular processes during infection. SecReT4 offers a unique, highly organized, readily exploreable archive of known and putative T4SSs and cognate effectors in bacteria. It currently contains details of 10 752 core components mapping to 808 T4SSs and 1884 T4SS effectors found in representatives of 289 bacterial species, as well as a collection of more than 900 directly related references. A broad range of similarity search, sequence alignment, phylogenetic, primer design and other functional analysis tools are readily accessible via SecReT4. We propose that SecReT4 will facilitate efficient investigation of large numbers of these systems, recognition of diverse patterns of sequence-, gene- and/or functional conservation and an improved understanding of the biological roles and significance of these versatile molecular machines. SecReT4 will be regularly updated to ensure its ongoing maximum utility to the research community.

News in Chinese

2013年1月初,国际分子生物学刊物《核酸研究 (Nucleic Acids Research)》正式发表了我组的研究论文 “SecReT4: 细菌四型分泌系统开放知识库” (http://db-mml.sjtu.edu.cn/SecReT4/)。我组2010级直博生毕德玺与2011级硕士生刘林梦为该论文共同第一作者。围绕细菌基因组岛的识别和功能解析,我组先后提出了岛识别策略 (Ou, et al. NAR 2007),开发了基因组快速比对工具 (Shao, et al. NAR 2010),探讨了岛遗传稳定性与细菌毒II型素-抗毒素系统关系(Shao, et al. NAR 2011),和分析了整合性接合元件等典型岛 (Bi, et al.NAR 2012)。刚刚发表的这篇研究论文则侧重分析了与岛转移相关的四型分泌系统。

四型分泌系统 (type IV secretion system, T4SS) 是一种在革兰氏阴性菌和革兰氏阳性菌中均广泛存在的多功能、多组分的跨膜通道结构。与细菌中已发现的其它分泌系统不同,T4SS形成的管道既能通过蛋白质 又能通过DNA,因此T4SS能够介导细菌接合转移、DNA释放和摄取以及效应蛋白分泌等功能。其中,T4SS所介导的接合转移是基因水平转移的重要机制 之一,多数接合型质粒和整合性接合元件都依靠它们自身编码的T4SS进行接合转移,进而散播它们所携带的生物学性状,如耐药性和致病性等重要性状。该研究 工作通过文献深度挖掘和生物信息学精确预测,在五百多株已测序细菌基因组中识别出八百多个T4SS,对一万多个T4SS组分和接近两千个效应蛋白进行了功 能描述,建立了开放知识库SecReT4。通过比较分析对T4SS进行了系统分类,扩充了已报道的T4SS类别。此外,对T4SS关键组分的进化分析为建 立统一和定量的T4SS分类标准提供了新的参考。

Figure 1. (A) Inferred phylogenetic relationships of the VirB4 components of 828 T4SSs. Amino acid  sequences  were  aligned  using MUSCLE  and  the  tree  was  generated  by  MEGA5.05 with the neighbor-joining  method. Four  T4SS  types  (Type  IVA - Type  IVD)  are  marked  in different colors. (B) The highlighted VirB4 components of 18 T4SS representatives .


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