Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families.
Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families.
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DOI：
10.1093/nar/gkq054
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发表时间：
2010-06
影响因子：
14.9
通讯作者：
Storz G
中科院分区：
文献类型：
--
作者：
Fozo EM;Makarova KS;Shabalina SA;Yutin N;Koonin EV;Storz G
被称为I型毒素-抗毒素模块的小的疏水蛋白的合成受到小rna （sRNAs）的抑制，它们最初是在质粒上发现的，它们调节质粒的稳定性，但随后在一些细菌染色体上发现。我们使用详尽的PSI-BLAST和TBLASTN在774个细菌基因组中进行搜索，以确定已知I型毒素的同源物。这些搜索极大地扩展了预测的I型毒素的集合，揭示了Ldr和Fst毒素的同源性，并表明I型毒素-抗毒素位点不通过水平基因转移传播。为了发现新的I型毒素-抗毒素系统，我们基于已知基因座的特征开发了一套搜索参数，包括串联重复序列的存在以及短蛋白c端含有预测跨膜区域的带电和大体积氨基酸簇。我们从肠出血性大肠杆菌和枯草芽孢杆菌中检测了三种预测毒素的sRNAs，并表明其中两种蛋白质在过表达时确实是有毒的。我们还证明了RNA折叠的局部自由能最小值可以用来检测sRNA基因的位置。我们的研究结果表明，I型毒素-抗毒素模块在细菌中的分布比以前所认识的要广泛得多。
Small, hydrophobic proteins whose synthesis is repressed by small RNAs (sRNAs), denoted type I toxin–antitoxin modules, were first discovered on plasmids where they regulate plasmid stability, but were subsequently found on a few bacterial chromosomes. We used exhaustive PSI-BLAST and TBLASTN searches across 774 bacterial genomes to identify homologs of known type I toxins. These searches substantially expanded the collection of predicted type I toxins, revealed homology of the Ldr and Fst toxins, and suggested that type I toxin–antitoxin loci are not spread by horizontal gene transfer. To discover novel type I toxin–antitoxin systems, we developed a set of search parameters based on characteristics of known loci including the presence of tandem repeats and clusters of charged and bulky amino acids at the C-termini of short proteins containing predicted transmembrane regions. We detected sRNAs for three predicted toxins from enterohemorrhagic Escherichia coli and Bacillus subtilis, and showed that two of the respective proteins indeed are toxic when overexpressed. We also demonstrated that the local free-energy minima of RNA folding can be used to detect the positions of the sRNA genes. Our results suggest that type I toxin–antitoxin modules are much more widely distributed among bacteria than previously appreciated.
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影响因子：
14.9
作者：
Shabalina, Svetlana A.;Ogurtsov, Aleksey Y.;Spiridonov, Nikolay A.
通讯作者：
Spiridonov, Nikolay A.
影响因子：
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作者：
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通讯作者：
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DOI：
10.1073/pnas.0808832106
发表时间：
2009-01-20
影响因子：
11.1
作者：
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通讯作者：
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影响因子：
5.5
作者：
Makarova KS;Wolf YI;Koonin EV
通讯作者：
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影响因子：
14.9
作者：
Schäffer, AA;Aravind, L;Altschul, SF
通讯作者：
Altschul, SF