A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
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DOI：
10.1186/1745-6150-1-7
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发表时间：
2006-03-16
期刊：
影响因子：
5.5
通讯作者：
Koonin, Eugene V.
中科院分区：
文献类型：
--
作者：
Makarova, Kira S.;Grishin, Nick V.;Koonin, Eugene V.
背景资料：所有古细菌和许多细菌基因组都含有重复的规则间隔短回文重复序列（CRISPR）和CRISPR相关基因（cas）的可变阵列，这些基因先前已经在其蛋白质产物序列的比较分析的基础上参与了一种新形式的DNA修复。然而，CRISPR和cas基因的接近强烈表明，它们具有相关的功能，这是很难调和的修复hypothesis.Results：众多cas基因产物的蛋白质序列被归类为类似的25个不同的蛋白质家族，几个新的功能和结构的预测。CRISPR和cas基因的比较基因组分析导致以下假设：CRISPR-Cas系统（卡斯）是一种防御入侵的质粒和质粒的机制，其功能类似于真核RNA干扰（RNAi）系统。卡斯的几个组成部分和真核RNAi中涉及的蛋白质之间绘制了特定的功能类比，包括双链RNA特异性解旋酶-核酸酶（dicer），切割靶mRNA的内切核酸酶（slicer）和RNA依赖性RNA聚合酶。然而，没有一个卡斯组分与其明显的真核功能对应物是正交的。有人提出，CRISPR的独特插入片段，其中一些与噬菌体和质粒基因的片段同源，通过与靶mRNA的碱基配对并促进其降解或翻译关闭而发挥原核siRNA（psiRNA）的功能。针对预测的原核siRNA系统的功能和具有编码psiRNA的独特插入物的新CRISPR单元的形成开发了具体的假设方案，所述插入物赋予对相应的新遇到的质粒的免疫力。CRISPR中独特的插入片段显示，即使在密切相关的细菌菌株之间也几乎没有相似性，这表明它们在进化规模上的快速更替。这一发现的推论是，即使在密切相关的原核生物中，最常见的细菌和质粒是不同的和/或，占主导地位的细菌和质粒翻转rapid.Conclusion：我们以前提出，Cas蛋白包括一个新的DNA修复系统。cas基因与CRISPR的关联，特别是在CRISPR单元中存在与噬菌体和质粒基因同源的独特插入片段，使我们放弃了这一假设。卡斯似乎最有可能是一种通过RNAi机制发挥功能的原核防御系统。这个系统的功能似乎涉及到整合到古细菌和细菌的染色体产生遗传免疫力，以各自的代理人的外源基因片段。然而，似乎这种遗传在进化尺度上是极其不稳定的，使得即使在密切相关的原核生物中，独特的psiRNAs的库也被完全替换，推测是响应于快速变化的显性质粒和质粒的库。
Background: All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated ( cas) genes that have been previously implicated in a novel form of DNA repair on the basis of comparative analysis of their protein product sequences. However, the proximity of CRISPR and cas genes strongly suggests that they have related functions which is hard to reconcile with the repair hypothesis.Results: The protein sequences of the numerous cas gene products were classified into similar to 25 distinct protein families; several new functional and structural predictions are described. Comparative-genomic analysis of CRISPR and cas genes leads to the hypothesis that the CRISPR-Cas system ( CASS) is a mechanism of defense against invading phages and plasmids that functions analogously to the eukaryotic RNA interference (RNAi) systems. Specific functional analogies are drawn between several components of CASS and proteins involved in eukaryotic RNAi, including the double-stranded RNA-specific helicase-nuclease (dicer), the endonuclease cleaving target mRNAs ( slicer), and the RNA-dependent RNA polymerase. However, none of the CASS components is orthologous to its apparent eukaryotic functional counterpart. It is proposed that unique inserts of CRISPR, some of which are homologous to fragments of bacteriophage and plasmid genes, function as prokaryotic siRNAs (psiRNA), by base-pairing with the target mRNAs and promoting their degradation or translation shutdown. Specific hypothetical schemes are developed for the functioning of the predicted prokaryotic siRNA system and for the formation of new CRISPR units with unique inserts encoding psiRNA conferring immunity to the respective newly encountered phages or plasmids. The unique inserts in CRISPR show virtually no similarity even between closely related bacterial strains which suggests their rapid turnover, on evolutionary scale. Corollaries of this finding are that, even among closely related prokaryotes, the most commonly encountered phages and plasmids are different and/or that the dominant phages and plasmids turn over rapidly.Conclusion: We proposed previously that Cas proteins comprise a novel DNA repair system. The association of the cas genes with CRISPR and, especially, the presence, in CRISPR units, of unique inserts homologous to phage and plasmid genes make us abandon this hypothesis. It appears most likely that CASS is a prokaryotic system of defense against phages and plasmids that functions via the RNAi mechanism. The functioning of this system seems to involve integration of fragments of foreign genes into archaeal and bacterial chromosomes yielding heritable immunity to the respective agents. However, it appears that this inheritance is extremely unstable on the evolutionary scale such that the repertoires of unique psiRNAs are completely replaced even in closely related prokaryotes, presumably, in response to rapidly changing repertoires of dominant phages and plasmids.