成簇的规则间隔的短回文重复序列及其相关蛋白(CRISPR-Cas)系统广泛存在于原核生物中,以识别和破坏遗传入侵者。内源性CRISPR-Cas系统的系统整理和表征有助于我们对这种自然遗传机制的理解和潜在利用。在这项研究中,我们使用组合策略筛选了39个完整和692个不完整的粘细菌基因组,以处理删节的基因组信息,并揭示了至少19个CRISPR-Cas亚型,其分布具有分类学差异,并且通常在种内菌株中随机丢失。每个亚型中的cas基因在进化上聚集,但分离得很深,而大多数CRISPR根据重复序列的基序特征分为四种类型。粘细菌CRISPR中记录的间隔区具有较高的GC含量,匹配大量的噬菌体,少量的质粒,and,令人惊讶的是,巨大的有机基因组。我们通过实验证明了黄花粘球菌DK1622中三个内源性系统对人工遗传入侵者的免疫和自靶免疫活性,并揭示了微同源性介导的末端连接机制,用于免疫诱导的DNA修复,而不是同源定向修复。全景视图和免疫活动意味着内源性CRISPR-Cas机制的潜在全能免疫功能和应用。
目标:作为适应性免疫系统,成簇的规则间隔的短回文重复序列及其相关蛋白(CRISPR-Cas)使原核生物能够抵御外部遗传物质的入侵。粘细菌是一群革兰氏染色阴性掠食性细菌的集合,其特征是复杂的多细胞社会行为。对其内在CRISPR-Cas系统的深入分析有利于我们理解宿主细胞在其环境生态位内采用的生存策略。此外,本研究中提出的实验发现不仅表明CRISPR-Cas在粘细菌中具有强大的免疫功能,而且还表明其潜在的应用。
The clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) system widely occurs in prokaryotic organisms to recognize and destruct genetic invaders. Systematic collation and characterization of endogenous CRISPR-Cas systems are conducive to our understanding and potential utilization of this natural genetic machinery. In this study, we screened 39 complete and 692 incomplete genomes of
myxobacteria using a combined strategy to dispose of the abridged genome information and revealed at least 19 CRISPR-Cas subtypes, which were distributed with a taxonomic difference and often lost stochastically in intraspecies strains. The cas genes in each subtype were evolutionarily clustered but deeply separated, while most of the CRISPRs were divided into four types based on the motif characteristics of repeat sequences. The spacers recorded in myxobacterial CRISPRs were in high G+C content, matching lots of phages, tiny amounts of plasmids, and, surprisingly, massive organismic genomes. We experimentally demonstrated the immune and self-target immune activities of three endogenous systems in Myxococcus xanthus DK1622 against artificial genetic invaders and revealed the microhomology-mediated end-joining mechanism for the immunity-induced DNA repair but not homology-directed repair. The panoramic view and immune activities imply potential omnipotent immune functions and applications of the endogenous CRISPR-Cas machinery.
OBJECTIVE: Serving as an adaptive immune system, clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) empower prokaryotes to fend off the intrusion of external genetic materials.
Myxobacteria are a collective of swarming Gram-stain-negative predatory bacteria distinguished by intricate multicellular social behavior. An in-depth analysis of their intrinsic CRISPR-Cas systems is beneficial for our understanding of the survival strategies employed by host cells within their environmental niches. Moreover, the experimental findings presented in this study not only suggest the robust immune functions of CRISPR-Cas in
myxobacteria but also their potential applications.