A dual function of the CRISPR–Cas system in bacterial antivirus immunity and DNA repair

Babu, M. Madan; Beloglazova, Natalia; Flick, Robert; Graham, Chris; Skarina, T.; Nocek, B.; Gagarinova, Alla; Pogoutse, Oxana; Brown, Greg; Binkowski, Andrew; Phanse, Sadhna; Joachimiak, Andrzej; Koonin, Eugene V.; Savchenko, Alexei; Emili, Andrew; Greenblatt, Jack; Edwards, A.M.; Yakunin, Alexander F.

doi:10.1111/j.1365-2958.2010.07465.x

Cited by 242 publications

(260 citation statements)

References 93 publications

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“…1d, Supplementary Tables S3 and S4). Cells lacking cas2, or producing Cas1 point mutant lacking nucleolytic activity 24 , did not acquire spacers (Fig. 1d).…”

Section: Resultsmentioning

confidence: 94%

Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system

et al. 2012

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“…1d, Supplementary Tables S3 and S4). Cells lacking cas2, or producing Cas1 point mutant lacking nucleolytic activity 24 , did not acquire spacers (Fig. 1d).…”

Section: Resultsmentioning

confidence: 94%

Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system

et al. 2012

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“…These primers, all annealing to plasmid sequences, were selected based on similar melting temperatures to minimize PCR variations. As a control, we used the same primers to test acquisition on cultures harboring pCas1 D221A +2, a plasmid encoding a point mutation that renders Cas1 nonfunctional (11,22). In all instances, PCR amplification was evident in cultures harboring the functional Cas1 but not in those with the altered Cas1, indicating that the assay specifically detects acquisition events (Fig.…”

Section: Resultsmentioning

confidence: 99%

DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array

Yosef

Shitrit

Goren

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins constitute a recently identified prokaryotic defense system against invading nucleic acids. DNA segments, termed protospacers, are integrated into the CRISPR array in a process called adaptation. Here, we establish a PCR-based assay that enables evaluating the adaptation efficiency of specific spacers into the type I-E Escherichia coli CRISPR array. Using this assay, we provide direct evidence that the protospacer adjacent motif along with the first base of the protospacer (5′-AAG) partially affect the efficiency of spacer acquisition. Remarkably, we identified a unique dinucleotide, 5′-AA, positioned at the 3′ end of the spacer, that enhances efficiency of the spacer's acquisition. Insertion of this dinucleotide increased acquisition efficiency of two different spacers. DNA sequencing of newly adapted CRISPR arrays revealed that the position of the newly identified motif with respect to the 5′-AAG is important for affecting acquisition efficiency. Analysis of approximately 1 million spacers showed that this motif is overrepresented in frequently acquired spacers compared with those acquired rarely. Our results represent an example of a short nonprotospacer adjacent motif sequence that affects acquisition efficiency and suggest that other as yet unknown motifs affect acquisition efficiency in other CRISPR systems as well.defense mechanism | phage-host interaction | acquisition step C lustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) comprise an important prokaryotic defense system against horizontally transferred DNA (1-3) and RNA (4). This system shows remarkable analogies to the mammalian immune system (5, 6) and to eukaryotic RNA-interference mechanisms (7, 8). Three major types and 10 subtypes of CRISPR/Cas systems (9) have been found across ∼90% of archaeal genomes and ∼50% of bacterial genomes. All types consist of a CRISPR array-short repeated sequences called "repeats" flanking short sequences called "spacers." The array is usually preceded by a leader, AT-rich DNA sequence that drives CRISPR array expression and is important for acquiring new spacers into the array (10, 11). A cluster of CRISPR-associated (cas) genes encoding proteins that process the transcript, interfere with foreign nucleic acids, and acquire new spacers usually lies adjacent to the CRISPR array (12)(13)(14). RNA transcribed from the CRISPR array (crRNA) is processed by Cas proteins into RNA-based spacers flanked by partial repeats. These crRNAs specifically direct Cas interfering proteins to target nucleic acids matching the spacers. The spacers are acquired from these targeted sequences, termed "protospacers." Spacer acquisition into the CRISPR array consequently results in guiding the system to cleave DNA molecules harboring the corresponding protospacers. This feature renders the system competent in adaptively and specifically targeting invaders.Spacer acquisition into a CRISPR array...

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“…In M. xanthus, the formation of fruiting bodies following starvation involves Cas proteins (311,312). Moreover, in E. coli, one of the most conserved Cas proteins is a nuclease that physically interacts with DNA repair proteins (313). This protein and its CRISPR array have been proposed to have an important role in DNA repair and chromosomal segregation following DNA damage.…”

Section: Genetic Elements Controlling the Stability Of Mobile Elementsmentioning

confidence: 99%

Bacterial Genome Instability

Darmon

Leach

2014

Microbiol Mol Biol Rev

337

289

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SUMMARY Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.

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A dual function of the CRISPR–Cas system in bacterial antivirus immunity and DNA repair

Cited by 242 publications

References 93 publications

Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system

Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system

DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array

Bacterial Genome Instability

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