CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes
CRISPR Spacers Indicate Preferential Matching of Specific Virioplankton Genes
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DOI：
10.1128/mbio.02651-18
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发表时间：
2018-12
期刊：
影响因子：
6.4
通讯作者：
Daniel J. Nasko;Barbra D. Ferrell;Ryan M. Moore;Jaysheel D. Bhavsar;Shawn W. Polson;K. E. Wommack
中科院分区：
文献类型：
--
作者：
Daniel J. Nasko;Barbra D. Ferrell;Ryan M. Moore;Jaysheel D. Bhavsar;Shawn W. Polson;K. E. Wommack
CRISPR-Cas系统是细菌和古细菌种群抵御病毒感染的一种手段，病毒感染导致海洋中20%至50%的细胞死亡。我们测试了一种假设，即某些病毒基因是CRISPR-Cas系统对病毒基因组的初始攻击的优先目标。利用CASC，一个CRISPR间隔序列发现管道，以及来自海洋微生物和病毒的宏基因组数据，我们发现了一个明确的病毒基因子集，与CRISPR间隔序列具有高匹配频率。此外，我们观察到间隔物和病毒基因之间存在多对多的关系。这些高匹配的病毒基因参与核苷酸代谢、DNA甲基化和病毒结构。CRISPR间隔序列匹配可能是一种进化算法，指向那些对维持感染和裂解最重要的病毒基因。研究这些基因可以促进对自然界病毒-宿主相互作用的理解，并为在有益微生物中利用CRISPR-Cas系统提供新技术。病毒感染对海洋微生物施加了选择压力，因为病毒诱导的细胞裂解导致20%至50%的细胞死亡，导致生物量流入海洋溶解的有机物。古生菌和细菌群体可以利用聚集的规则间隔短回文重复（CRISPR）相关（Cas）系统来防御病毒感染，该系统依赖于间隔序列和病毒基因之间的特定匹配。如果CRISPR间隔序列与病毒基因组内的任何基因匹配都能同样有效地防止裂解，那么任何病毒基因都不应优先与CRISPR间隔序列匹配。然而，如果有效性存在差异，某些病毒基因可能会表现出更高的CRISPR间隔匹配频率。事实上，浮游细菌CRISPR间隔序列与浮游细菌序列的同源性搜索分析显示，复制蛋白、核酸结合蛋白和病毒结构蛋白具有优先匹配性。有效的病毒防御的积极选择压力是对这些观察结果的一个简洁的解释。来自浮游生物宏基因组的CRISPR间隔序列优先匹配浮游生物序列中的甲基转移酶和噬菌体整合酶基因。这些vivi浮游生物CRISPR间隔物可以帮助被感染的宿主细胞防御竞争噬菌体。分析还显示，一半与间隔序列匹配的病毒基因是未知的，一些基因与几个间隔序列匹配，一些间隔序列与多个基因匹配，这是一种多对多的关系。因此，CRISPR间隔序列匹配可能是一种进化算法，在严格的选择压力下未知地识别那些基因，以维持病毒感染和裂解。研究这一病毒基因子集可以揭示病毒与宿主相互作用所必需的遗传机制，并为优化有益微生物的CRISPR防御提供新技术。CRISPR-Cas系统是细菌和古细菌种群抵御病毒感染的一种手段，病毒感染导致海洋中20%至50%的细胞死亡。我们测试了一种假设，即某些病毒基因是CRISPR-Cas系统对病毒基因组的初始攻击的优先目标。利用CASC，一个CRISPR间隔序列发现管道，以及来自海洋微生物和病毒的宏基因组数据，我们发现了一个明确的病毒基因子集，与CRISPR间隔序列具有高匹配频率。此外，我们观察到间隔物和病毒基因之间存在多对多的关系。这些高匹配的病毒基因参与核苷酸代谢、DNA甲基化和病毒结构。CRISPR间隔序列匹配可能是一种进化算法，指向那些对维持感染和裂解最重要的病毒基因。研究这些基因可以促进对自然界病毒-宿主相互作用的理解，并为在有益微生物中利用CRISPR-Cas系统提供新技术。
The CRISPR-Cas system is one means by which bacterial and archaeal populations defend against viral infection which causes 20 to 50% of cell mortality in the ocean. We tested the hypothesis that certain viral genes are preferentially targeted for the initial attack of the CRISPR-Cas system on a viral genome. Using CASC, a pipeline for CRISPR spacer discovery, and metagenome data from oceanic microbes and viruses, we found a clear subset of viral genes with high match frequencies to CRISPR spacers. Moreover, we observed a many-to-many relationship of spacers and viral genes. These high-match viral genes were involved in nucleotide metabolism, DNA methylation, and viral structure. It is possible that CRISPR spacer matching is an evolutionary algorithm pointing to those viral genes most important to sustaining infection and lysis. Studying these genes may advance the understanding of virus-host interactions in nature and provide new technologies for leveraging CRISPR-Cas systems in beneficial microbes. ABSTRACT Viral infection exerts selection pressure on marine microbes, as virus-induced cell lysis causes 20 to 50% of cell mortality, resulting in fluxes of biomass into oceanic dissolved organic matter. Archaeal and bacterial populations can defend against viral infection using the clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) system, which relies on specific matching between a spacer sequence and a viral gene. If a CRISPR spacer match to any gene within a viral genome is equally effective in preventing lysis, no viral genes should be preferentially matched by CRISPR spacers. However, if there are differences in effectiveness, certain viral genes may demonstrate a greater frequency of CRISPR spacer matches. Indeed, homology search analyses of bacterioplankton CRISPR spacer sequences against virioplankton sequences revealed preferential matching of replication proteins, nucleic acid binding proteins, and viral structural proteins. Positive selection pressure for effective viral defense is one parsimonious explanation for these observations. CRISPR spacers from virioplankton metagenomes preferentially matched methyltransferase and phage integrase genes within virioplankton sequences. These virioplankton CRISPR spacers may assist infected host cells in defending against competing phage. Analyses also revealed that half of the spacer-matched viral genes were unknown, some genes matched several spacers, and some spacers matched multiple genes, a many-to-many relationship. Thus, CRISPR spacer matching may be an evolutionary algorithm, agnostically identifying those genes under stringent selection pressure for sustaining viral infection and lysis. Investigating this subset of viral genes could reveal those genetic mechanisms essential to virus-host interactions and provide new technologies for optimizing CRISPR defense in beneficial microbes. IMPORTANCE The CRISPR-Cas system is one means by which bacterial and archaeal populations defend against viral infection which causes 20 to 50% of cell mortality in the ocean. We tested the hypothesis that certain viral genes are preferentially targeted for the initial attack of the CRISPR-Cas system on a viral genome. Using CASC, a pipeline for CRISPR spacer discovery, and metagenome data from oceanic microbes and viruses, we found a clear subset of viral genes with high match frequencies to CRISPR spacers. Moreover, we observed a many-to-many relationship of spacers and viral genes. These high-match viral genes were involved in nucleotide metabolism, DNA methylation, and viral structure. It is possible that CRISPR spacer matching is an evolutionary algorithm pointing to those viral genes most important to sustaining infection and lysis. Studying these genes may advance the understanding of virus-host interactions in nature and provide new technologies for leveraging CRISPR-Cas systems in beneficial microbes.