Abstract
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.
Highlights
Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated proteins (Cas) systems function
The highest proportion was found in B. cytotoxicus where 86% of the analyzed genomes (14 genomes available) contain CRISPER-Cas elements, while only one B. anthracis strain from a total of 188 B. anthracis genomes analyzed was found to contain CRISPR-Cas elements
In the case of the B. cereus strains, 9% of 862 genomes analyzed showed CRISPER-Cas elements, while regarding to the B. thuringiensis strains, we found that 26% of strains have CRISPR-Cas elements from a total of 445 genomes analyzed (Table 1)
Summary
Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated proteins (Cas) systems function. The CRISPR-Cas systems have been proposed as important factors contributing for the evolution of virulence in several pathogens [11, 14,15,16, 18], but the impact of such systems on bacterial evolution at population level is poorly understood. The increasing availability of sequenced genomes will facilitate the study and understanding of the role interplayed among CRISPR-Cas systems and HGT, and its impact on bacterial evolution within species. The large number of available genomes in this group provides a good model to study the relationship among CRISPR-Cas systems and HGT at the population level. We evaluated the impact of CRISPR-Cas systems at the population level, showing that in B. cereus group the inactivation of such systems correlates with MGEs acquisition that could provide genetic traits for better adaptation to diverse environments
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