Wietz Matthias, Millán-Aguiñaga Natalie, Jensen Paul R
Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.
BMC Genomics. 2014 Oct 25;15(1):936. doi: 10.1186/1471-2164-15-936.
Prokaryotic CRISPR-Cas systems confer resistance to viral infection and thus mediate bacteria-phage interactions. However, the distribution and functional diversity of CRISPRs among environmental bacteria remains largely unknown. Here, comparative genomics of 75 Salinispora strains provided insight into the diversity and distribution of CRISPR-Cas systems in a cosmopolitan marine actinomycete genus.
CRISPRs were found in all Salinispora strains, with the majority containing multiple loci and different Cas array subtypes. Of the six subtypes identified, three have not been previously described. A lower prophage frequency in S. arenicola was associated with a higher fraction of spacers matching Salinispora prophages compared to S. tropica, suggesting differing defensive capacities between Salinispora species. The occurrence of related prophages in strains from distant locations, as well as spacers matching those prophages inserted throughout spacer arrays, indicate recurring encounters with widely distributed phages over time. Linkages of CRISPR features with Salinispora microdiversity pointed to subclade-specific contacts with mobile genetic elements (MGEs). This included lineage-specific spacer deletions or insertions, which may reflect weak selective pressures to maintain immunity or distinct temporal interactions with MGEs, respectively. Biogeographic patterns in spacer and prophage distributions support the concept that Salinispora spp. encounter localized MGEs. Moreover, the presence of spacers matching housekeeping genes suggests that CRISPRs may have functions outside of viral defense.
This study provides a comprehensive examination of CRISPR-Cas systems in a broadly distributed group of environmental bacteria. The ubiquity and diversity of CRISPRs in Salinispora suggests that CRISPR-mediated interactions with MGEs represent a major force in the ecology and evolution of this cosmopolitan marine actinomycete genus.
原核生物的CRISPR-Cas系统赋予对病毒感染的抗性，从而介导细菌与噬菌体的相互作用。然而，CRISPRs在环境细菌中的分布和功能多样性仍 largely未知。在这里，对75株盐孢菌菌株的比较基因组学研究为一个世界性海洋放线菌属中CRISPR-Cas系统的多样性和分布提供了见解。
在所有盐孢菌菌株中都发现了CRISPRs，大多数菌株含有多个位点和不同的Cas阵列亚型。在鉴定出的六个亚型中，有三个此前未被描述。与热带盐孢菌相比，沙地盐孢菌中较低的原噬菌体频率与更高比例的与盐孢菌原噬菌体匹配的间隔序列相关，这表明盐孢菌不同物种之间的防御能力存在差异。来自遥远地点的菌株中相关原噬菌体的出现，以及与插入整个间隔序列阵列中的那些原噬菌体匹配的间隔序列，表明随着时间的推移，与广泛分布的噬菌体反复相遇。CRISPR特征与盐孢菌微观多样性的关联指向与移动遗传元件（MGEs）的亚分支特异性接触。这包括谱系特异性的间隔序列缺失或插入，分别可能反映了维持免疫的弱选择压力或与MGEs的不同时间相互作用。间隔序列和原噬菌体分布中的生物地理模式支持盐孢菌物种遇到局部MGEs的概念。此外，与管家基因匹配的间隔序列的存在表明CRISPRs可能具有病毒防御之外的功能。
本研究全面考察了一组广泛分布的环境细菌中的CRISPR-Cas系统。盐孢菌中CRISPRs的普遍性和多样性表明，CRISPR介导的与MGEs的相互作用是这个世界性海洋放线菌属生态和进化中的主要力量。
