Identification of functional toxin/immunity genes linked to contact-dependent growth inhibition (CDI) and rearrangement hotspot (Rhs) systems.
Identification of functional toxin/immunity genes linked to contact-dependent growth inhibition (CDI) and rearrangement hotspot (Rhs) systems.
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DOI：
10.1371/journal.pgen.1002217
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发表时间：
2011-08
期刊：
影响因子：
4.5
通讯作者：
Hayes CS
中科院分区：
文献类型：
--
作者：
Poole SJ;Diner EJ;Aoki SK;Braaten BA;t'Kint de Roodenbeke C;Low DA;Hayes CS
细菌接触依赖性生长抑制（CDI）是由CdiA/CdiB家族的双伴侣分泌蛋白介导的。每个CdiA蛋白表现出不同的生长抑制活性，其存在于多态性C-末端区域（CdiA-CT）。CDI+细胞还表达特异性阻断同源CdiA-CT活性的独特CdiI免疫蛋白，从而保护细胞免受自身抑制。在这里，我们表明，许多CDI系统包含多个编码CdiA-CT序列的cdiA基因片段。这些“孤儿”cdiA-CT基因几乎总是与下游cdiI基因结合形成cdiA-CT/cdiI模块。比较基因组分析表明，cdiA-CT/cdiI模块是移动的，并在不同细菌的CDI系统之间交换。在许多情况下，孤儿cdiA-CT/cdiI模块与其他细菌物种中的全长cdiA基因融合。大肠杆菌EC 93、大肠杆菌E. coli EC 869和Dickeya dadantii 3937的克隆，证实这些基因编码功能性毒素/免疫对。此外，当与EC 93 CdiA蛋白的N-末端部分融合时，来自EC 93的孤儿模块在细胞介导的CDI中起作用。生物信息学分析表明，CDI系统的遗传组织与rhs（重排热点）位点的特征相同。Rhs蛋白还含有多态性C末端区域（Rhs-CT），其中一些与CdiA-CT具有显著的序列同一性。所有rhs基因后面都有代表可能的rhsI免疫基因的小ORF，并且几个Rhs系统编码孤儿rhs-CT/rhsI模块。对D. dadantii 3937证明Rhs-CT具有生长抑制活性，其被同源RhsI免疫蛋白特异性阻断。总之，这些结果表明，Rhs在细胞间竞争中发挥作用，孤儿基因模块扩大了CDI和Rhs系统部署的毒性活动的多样性。我们实验室最近的工作表明，许多细菌表达接触依赖性生长抑制（CDI）系统，其中细胞表面上的棒状蛋白质将毒性尖端传递到靶细胞中。在细菌中已经鉴定出超过60种不同的毒性尖端，我们的数据表明每个CDI+细胞表达一种特异性免疫蛋白，该蛋白与其同源毒素结合并使其失活以防止细胞自杀。在这里，我们确定基因的有毒提示，不连接到棒蛋白。这些“孤儿”尖端中的每一个都具有毒性活性，这被其相关的免疫蛋白质阻断。值得注意的是，一些细菌物种的孤儿尖端经常出现在其他物种的棒状蛋白上，这表明细胞装载并传递不同的尖端。我们还报告了一个名为Rhs的系统，该系统编码另一种预测的棒状蛋白，该蛋白也携带可变的提示。我们发现Rhs蛋白的末端是有毒的，并且Rhs系统编码特异性阻断毒素活性的免疫蛋白。CDI和Rhs毒素尖端多样性可能代表了由环境资源竞争驱动的微生物军备竞赛。
Bacterial contact-dependent growth inhibition (CDI) is mediated by the CdiA/CdiB family of two-partner secretion proteins. Each CdiA protein exhibits a distinct growth inhibition activity, which resides in the polymorphic C-terminal region (CdiA-CT). CDI+ cells also express unique CdiI immunity proteins that specifically block the activity of cognate CdiA-CT, thereby protecting the cell from autoinhibition. Here we show that many CDI systems contain multiple cdiA gene fragments that encode CdiA-CT sequences. These “orphan” cdiA-CT genes are almost always associated with downstream cdiI genes to form cdiA-CT/cdiI modules. Comparative genome analyses suggest that cdiA-CT/cdiI modules are mobile and exchanged between the CDI systems of different bacteria. In many instances, orphan cdiA-CT/cdiI modules are fused to full-length cdiA genes in other bacterial species. Examination of cdiA-CT/cdiI modules from Escherichia coli EC93, E. coli EC869, and Dickeya dadantii 3937 confirmed that these genes encode functional toxin/immunity pairs. Moreover, the orphan module from EC93 was functional in cell-mediated CDI when fused to the N-terminal portion of the EC93 CdiA protein. Bioinformatic analyses revealed that the genetic organization of CDI systems shares features with rhs (rearrangement hotspot) loci. Rhs proteins also contain polymorphic C-terminal regions (Rhs-CTs), some of which share significant sequence identity with CdiA-CTs. All rhs genes are followed by small ORFs representing possible rhsI immunity genes, and several Rhs systems encode orphan rhs-CT/rhsI modules. Analysis of rhs-CT/rhsI modules from D. dadantii 3937 demonstrated that Rhs-CTs have growth inhibitory activity, which is specifically blocked by cognate RhsI immunity proteins. Together, these results suggest that Rhs plays a role in intercellular competition and that orphan gene modules expand the diversity of toxic activities deployed by both CDI and Rhs systems. Recent work from our laboratories has shown that many bacteria express contact-dependent growth inhibition (CDI) systems in which stick-like proteins on the cell surface deliver toxic tips into target cells. Over 60 distinct toxic tips have been identified in bacteria, and our data indicate that each CDI+ cell expresses a specific immunity protein that binds to its cognate toxin and inactivates it to prevent cell suicide. Here we identify genes for toxic tips that are not attached to the stick protein. Each of these “orphan” tips has toxic activity, which is blocked by its associated immunity protein. Remarkably, the orphan tips of some bacterial species are often found on the stick proteins in other species, suggesting that cells load and deliver different tips. We also report on a system called Rhs, which encodes another predicted stick-like protein that also carries variable tips. We found that the tips of Rhs proteins are toxic and that Rhs systems encode immunity proteins that specifically block toxin activity. CDI and Rhs toxin tip diversity may represent a microbial arms race, driven by the competition for environmental resources.
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