Bacteria and archaea are engaged in a constant arms race to defend against the ever-present threats of viruses and invasion by mobile genetic elements. The most flexible weapons in the prokaryotic defense arsenal are the CRISPR-Cas adaptive immune systems, which are capable of selective identification and neutralization of foreign elements. CRISPR-Cas systems rely on stored genetic memories to facilitate target recognition. Thus, to keep pace with a changing pool of hostile invaders, the CRISPR memory banks must be regularly updated by the addition of new information, through a process termed adaptation. In this review, we outline the recent advances in our understanding of the molecular mechanisms governing adaptation and highlight the diversity between systems.

Clustered regularly interspaced short palindromic repeats (CRISPR), in combination with CRISPR associated (cas) genes, constitute CRISPR-Cas bacterial adaptive immune systems. To generate immunity, these systems acquire short sequences of nucleic acids from foreign invaders and incorporate these into their CRISPR arrays as spacers. This adaptation process is the least characterized step in CRISPR-Cas immunity. Here, we used Pectobacterium atrosepticum to investigate adaptation in Type I-F CRISPR-Cas systems. Pre-existing spacers that matched plasmids stimulated hyperactive primed acquisition and resulted in the incorporation of up to nine new spacers across all three native CRISPR arrays. Endogenous expression of the cas genes was sufficient, yet required, for priming. The new spacers inhibited conjugation and transformation, and interference was enhanced with increasing numbers of new spacers. We analyzed ∼350 new spacers acquired in priming events and identified a 5′-protospacer-GG-3′ protospacer adjacent motif. In contrast to priming in Type I-E systems, new spacers matched either plasmid strand and a biased distribution, including clustering near the primed protospacer, suggested a bi-directional translocation model for the Cas1:Cas2–3 adaptation machinery. Taken together these results indicate priming adaptation occurs in different CRISPR-Cas systems, that it can be highly active in wild-type strains and that the underlying mechanisms vary.

SummaryCRISPR-Cas systems adapt their immunological memory against their invaders by integrating short DNA fragments into clustered regularly interspaced short palindromic repeat (CRISPR) loci. While Cas1 and Cas2 make up the core machinery of the CRISPR integration process, various class I and II CRISPR-Cas systems encode Cas4 proteins for which the role is unknown. Here, we introduced the CRISPR adaptation genes cas1, cas2, and cas4 from the type I-D CRISPR-Cas system of Synechocystis sp. 6803 into Escherichia coli and observed that cas4 is strictly required for the selection of targets with protospacer adjacent motifs (PAMs) conferring I-D CRISPR interference in the native host Synechocystis. We propose a model in which Cas4 assists the CRISPR adaptation complex Cas1-2 by providing DNA substrates tailored for the correct PAM. Introducing functional spacers that target DNA sequences with the correct PAM is key to successful CRISPR interference, providing a better chance of surviving infection by mobile genetic elements.

Highlights d 20 Cascade complexes are required to provide 50% protection d Cascade spends equal time probing DNA (30 ms) and diffusing to a next site d Cas8e dynamically associates with Cascade in cells d CRISPR target search and invader replication compete in a kinetic ''arms race''

Microbes have the unique ability to acquire immunological memories from mobile genetic invaders to protect themselves from predation. To confer CRISPR resistance, new spacers need to be compatible with a targeting requirement in the invader's DNA called the protospacer adjacent motif (PAM). Many CRISPR systems encode Cas4 proteins to ensure new spacers are integrated that meet this targeting prerequisite. Here we report that a gene fusion between cas4 and cas1 from the Geobacter sulfurreducens I-U CRISPR–Cas system is capable of introducing functional spacers carrying interference proficient TTN PAM sequences at much higher frequencies than unfused Cas4 adaptation modules. Mutations of Cas4-domain catalytic residues resulted in dramatically decreased naïve and primed spacer acquisition, and a loss of PAM selectivity showing that the Cas4 domain controls Cas1 activity. We propose the fusion gene evolved to drive the acquisition of only PAM-compatible spacers to optimize CRISPR interference.

150) 28CRISPR-Cas systems encode RNA-guided surveillance complexes to find and cleave 29 invading DNA elements. While it is thought that invaders are neutralized minutes after cell 30 entry, the mechanism and kinetics of target search and its impact on CRISPR protection levels 31 have remained unknown. Here we visualized individual Cascade complexes in a native type I 32 CRISPR-Cas system. We uncovered an exponential relationship between Cascade copy 33 number and CRISPR interference levels, pointing to a time-driven arms race between invader 34 replication and target search, in which 20 Cascade complexes provide 50% protection. Driven 35 by PAM-interacting subunit Cas8e, Cascade spends half its search time rapidly probing DNA 36 (~30 ms) in the nucleoid. We further demonstrate that target DNA transcription and CRISPR 37 arrays affect the integrity of Cascade and impact CRISPR interference. Our work establishes 38 the mechanism of cellular DNA surveillance by Cascade that allows the timely detection of 39 invading DNA in a crowded, DNA-packed environment. 40 41 42

CRISPR-Cas systems are able to acquire immunological memories (spacers) from bacteriophages and plasmids in order to survive infection, however this often occurs at low frequency within a population making it difficult to detect. Here we have developed CAPTURE (CRISPR Adaptation PCR Technique Using Re-amplification and Electrophoresis) a versatile and adaptable protocol to detect spacer acquisition events by electrophoresis imaging, with a sensitivity that can identify spacer acquisition in 1 in 10 5 cells. Our method harnesses two simple PCR steps, separated by automated electrophoresis and extraction of size-selected DNA amplicons, allowing the removal of unexpanded arrays from the sample pool, and enabling a 1000 times more sensitive detection of new spacers than existing PCR protocols. CAPTURE is a straightforward method requiring only one day to enable detection of spacer acquisition in all native CRISPR systems and facilitate studies aimed both at unravelling the mechanism of spacer integration and more sensitive tracing of integration events in natural ecosystems.

The blood selenium (Se) concentrations of New Zealand children were lower than those reported for children living in other countries. This low blood Se was primarily determined by the low dietary intake of the children which, in turn, reflects the low Se content of New Zealand soils. Blood Se also varied geographically, with age, and with differences in quantities and types of food eaten. Children with phenylketonuria and maple syrup urine disease on synthetic diets had low Se intakes and blood Se concentrations compared with children on normal diets, and blood Se was seen to decrease with the length of time on these diets. A strong correlation (r = 0.62, P less than 0.001) was found between the blood Se levels and glutathione peroxidase activities for 107 children. Glutathione peroxidase activities of the children were lower than activities observed in New Zealand adults, refelecting their lower blood Se concentrations.