State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. postal 510-3, Cuernavaca, 62250, Morelos, Mexico.
ISME J. 2020 Jun;14(6):1479-1493. doi: 10.1038/s41396-020-0623-5. Epub 2020 Mar 4.
CRISPR-Cas systems are considered as barriers to horizontal gene transfer (HGT). However, the influence of such systems on HGT within species is unclear. Also, little is known about the impact of CRISPR-Cas systems on bacterial evolution at the population level. Here, using Bacillus cereus sensu lato as model, we investigate the interplay between CRISPR-Cas systems and HGT at the population scale. We found that only a small fraction of the strains have CRISPR-Cas systems (13.9% of 1871), and most of such systems are defective based on their gene content analysis. Comparative genomic analysis revealed that the CRISPR-Cas systems are barriers to HGT within this group, since strains harboring active systems contain less mobile genetic elements (MGEs), have lower fraction of unique genes and also display limited environmental distributions than strains without active CRISPR-Cas systems. The introduction of a functional CRISPR-Cas system into a strain lacking the system resulted in reduced adaptability to various stresses and decreased pathogenicity of the transformant strain, indicating that B. cereus group strains could benefit from inactivating such systems. Our work provides a large-scale case to support that the CRISPR-Cas systems are barriers to HGT within species, and that in the B. cereus group the inactivation of CRISPR-Cas systems correlated with acquisition of MGEs that could result in better adaptation to diverse environments.
CRISPR-Cas 系统被认为是水平基因转移 (HGT) 的障碍。然而，这些系统对种内 HGT 的影响尚不清楚。此外，人们对 CRISPR-Cas 系统对细菌在种群水平上进化的影响知之甚少。在这里，我们使用 Bacillus cereus sensu lato 作为模型，研究了 CRISPR-Cas 系统与种群水平上 HGT 之间的相互作用。我们发现，只有一小部分菌株具有 CRISPR-Cas 系统（在 1871 个菌株中占 13.9%），并且根据它们的基因含量分析，大多数此类系统存在缺陷。比较基因组分析表明，CRISPR-Cas 系统是该群体内 HGT 的障碍，因为携带活性系统的菌株含有较少的可移动遗传元件 (MGEs)，具有较低比例的独特基因，并且与没有活性 CRISPR-Cas 系统的菌株相比，其环境分布也有限。将功能性 CRISPR-Cas 系统引入缺乏该系统的菌株中，导致该转化菌株对各种应激的适应性降低，致病性降低，表明 B. cereus 组菌株可能受益于使此类系统失活。我们的工作提供了一个大规模的案例来支持 CRISPR-Cas 系统是种内 HGT 的障碍，并且在 B. cereus 组中，CRISPR-Cas 系统的失活与可移动遗传元件的获得相关，这可能导致更好地适应不同的环境。
