![]() Expression of CRISPR arrays is constitutive and inducible by promoter elements within the preceding leader sequence ( 5, 6). Acquisition occurs via molecular sampling of foreign genetic elements, from which short sequences, termed “spacers,” are integrated in a polarized fashion into the CRISPR array ( 4). CRISPR-Cas–mediated immunity relies on distinct molecular processes, categorized as acquisition, expression, and interference ( 3). Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (Cas) are an adaptive immune system targeted against invasive genetic elements in bacteria ( 3). Innate immunity includes cell-wall modification, restriction/modification systems, and abortive phage infection ( 2). To cope with the permanent threat of predatory bacteriophages and selfish genetic elements, bacteria have evolved both innate and adaptive immune systems targeting exogenous genetic elements. MGEs encompass genes conferring high rates of dissemination, adaptive advantages to the host, and genomic stability, leading to their nearly universal presence in bacterial genomes. The term “MGE” encompasses plasmids, bacteriophages, transposable elements, genomic islands, and many other specialized genetic elements ( 1). Mobile genetic elements (MGEs) present bacteria with continuous challenges to genomic stability, promoting evolution through horizontal gene transfer. These results established that self-targeting CRISPR-Cas systems may direct significant evolution of bacterial genomes on a population level, influencing genome homeostasis and remodeling. Chimeric insertion sequence footprints were observed at the deletion junctions after targeting all of the four genomic islands, suggesting a common mechanism of deletion via recombination between flanking insertion sequences. Genotyping of Lac − survivors revealed variable deletion events between the flanking insertion-sequence elements, all resulting in elimination of the Lac-encoding island. Targeting lacZ within the largest 102-kbp genomic island was lethal to wild-type cells and resulted in a reduction of up to 2.5-log in the surviving population. In this study, the endogenous CRISPR3 type II system was programmed to target the four islands independently through plasmid-based expression of engineered CRISPR arrays. To investigate the genetic outcomes resulting from CRISPR-Cas targeting of integrated MGEs, in silico prediction revealed four genomic islands without essential genes in lengths from 8 to 102 kbp, totaling 7% of the genome. CRISPR-Cas systems are widespread in streptococci, suggesting that the interplay between CRISPR-Cas systems and MGEs is one of the driving forces governing genome homeostasis in this genus. Clustered regularly interspaced short palindromic repeats–CRISPR-associated genes (CRISPR-Cas), the adaptive immune system in bacteria, limits genetic diversity by targeting MGEs including bacteriophages, transposons, and plasmids. Genomic analysis of Streptococcus thermophilus revealed that mobile genetic elements (MGEs) likely contributed to gene acquisition and loss during evolutionary adaptation to milk.
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