The action of<i>Escherichia coli</i>CRISPR–Cas system on lytic bacteriophages with different lifestyles and development strategies

Strotskaya, Alexandra; Savitskaya, Ekaterina; Metlitskaya, Anastasia; Morozova, Natalia; Datsenko, Kirill A.; Semenova, Ekaterina; Severinov, Konstantin

doi:10.1093/nar/gkx042

Cited by 67 publications

(102 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Distinguishing between these two approaches is important as it affects the interpretation of parameters obtained from experiments. For example, a CRISPR-Cas system can remain active in doomed or dead cells, resulting in lower viral burst size and fewer secondary infections [31]. Our analysis based on [31] resulted in the estimate of the CRISPR failure probability around 30% compared to 10 −5 in [21].…”

Section: Comparison With Existing Resultsmentioning

confidence: 94%

“…If the virus mutation rate is lower and the CRISPR interference efficiency is higher, the presence of an additional viral species will affect the optimal S and δ more strongly. However, relating the model parameters to the experimental results [31], it is unlikely that the CRISPR efficiency in the multivirus environment can be significantly higher in vivo than the numbers shown in Fig. 7.…”

Section: Multiple Viral Speciesmentioning

confidence: 99%

See 1 more Smart Citation

Optimal number of spacers in CRISPR arrays

Martynov

Severinov

Ispolatov

2017

Preprint

Self Cite

View full text Add to dashboard Cite

We estimate the number of spacers in a CRISPR array of a bacterium which maximizes its protection against a viral attack. The optimality follows from a competition between two trends: too few distinct spacers make the bacteria vulnerable to an attack by a virus with mutated corresponding protospacers, while an excessive variety of spacers dilutes the number of the CRISPR complexes armed with the most recent and thus most effective spacers. We first evaluate the optimal number of spacers in a simple scenario of an infection by a single viral species and later consider a more general case of multiple viral species. We find that depending on such parameters as the concentration of CRISPR-CAS interference complexes and its preference to arm with more recently acquired spacers, the rate of viral mutation, and the number of viral species, the predicted optimal array length lies within a range quite reasonable from the viewpoint of recent experiments.Author summary CRISPR-Cas system is an adaptive immunity defense in bacteria and archaea against viruses. It works by accumulating in bacterial genome an array of spacers, or fragments of virus DNA fromND 4.0 International license not peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was . http://dx.doi.org/10.1101/143073 doi: bioRxiv preprint first posted online May. 29, 2017; previous attacks. By matching spacers to corresponding parts of virus DNA called protospacers, CRISPR-Cas system identifies and destroys intruder DNA. Here we theoretically estimate the number of spacers that maximizes bacterial survival. This optimum emerges from a competition between two trends: More spacers allow a bacterium to hedge against mutations in viral protospacers. However, keeping too many spacers makes the older ones inefficient because of accumulation of mutations in corresponding protospacers in viruses. Thus, fewer CRISPR-Cas molecular machines are left armed with more efficient young spacers. We have shown that a higher efficiency of CRISPR-Cas system allows a bacterium to utilize more spacers, increasing the optimal array length. On contrary, a higher viral mutation rate makes older spacers useless and favors shorter arrays. A higher diversity in viral species reduces the efficiency of CRISPR-Cas but does not necessary lead to longer arrays. We think that our study provides a new viewpoint at a huge variety in the observed array lengths and adds relevance to evolutionary models of bacterial-phage coexistence.

show abstract

Section: Comparison With Existing Resultsmentioning

confidence: 94%

Section: Multiple Viral Speciesmentioning

confidence: 99%

Optimal number of spacers in CRISPR arrays

Martynov

Severinov

Ispolatov

2017

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…A second hallmark of primed adaptation is that spacer acquisition occurs in a bidirectional, orientation-dependent manner relative to the PAM of the PPS. In particular, the non-transcribed strand of spacers acquired from the PAM-proximal region (upstream) or PAM-distal region (downstream) is derived from the nontarget strand or target strand, respectively 21 .…”

mentioning

confidence: 99%

Detection of Spacer Precursors Formed In Vivo During Primed CRISPR Adaptation

Shiriaeva

Savitskaya

Datsenko

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Type I CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR associated) loci provide prokaryotes with a nucleic-acid-based adaptive immunity against foreign DNA1. Immunity involves “adaptation,” the integration of ~30-bp DNA fragments into the CRISPR array as “spacer” sequences, and “interference,” the targeted degradation of DNA containing a “protospacer” sequence mediated by a complex containing a spacer-derived CRISPR RNA (crRNA)1–4. Specificity for targeting interference to protospacers, but not spacers, occurs through recognition of a 3-bp protospacer adjacent motif (PAM)5 by the crRNA-containing complex6. Interference-driven DNA degradation of protospacer-containing DNA can be coupled with “primed adaptation,” ill which spacers are acquired from DNA surrounding the targeted protospacer in a bidirectional, orientation-dependent manner2,3,7. Here we construct a robust in vivo model for primed adaptation consisting of an Escherichia coli type I-E CRISPR-Cas “self-targeting” locus encoding a crRNA that targets a chromosomal protospacer. We develop a strand-specific, high-throughput-sequencing method for analysis of DNA fragments, “FragSeq,” and use this method to detect short fragments derived from DNA surrounding the targeted protospacer. The detected fragments have sequences matching spacers acquired during primed adaptation, contain ~3- to 4-nt overhangs derived from excision of genomic DNA within a PAM, are generated in a bidirectional, orientation-dependent manner relative to the targeted protospacer, require the functional integrity of machinery for interference and adaptation to accumulate, and function as spacer precursors when exogenously introduced into cells by transformation. DNA fragments with a similar structure accumulate in cells undergoing primed adaptation in a type I-F CRISPR-Cas self-targeting system. We propose the DNA fragments detected in this work are products of universal steps of spacer precursor processing in type I CRISPR-Cas systems.

show abstract

“…For example, base modifications have been previously shown to block type II (72) and type I (73) immunity, although the type II results seem to depend on the guide RNA design (74). Certain mechanisms of phage injection and replication may also be recalcitrant to CRISPR targeting, as was recently shown for phage T5, which injects its genome gradually such that only ~10% of the DNA is a substrate for effective CRISPR-Cas immunity (73). Additionally, Acr proteins that conduct enzymatic inactivation or destruction of Cas proteins or the crRNA, or transcriptional repression of any component of the CRISPR-Cas system, might sufficiently shift the balance in favor of the phage during infection.…”

Section: Anti-crisprs As Modifiers Of Crispr-cas Functionmentioning

confidence: 99%

The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs

2017

View full text Add to dashboard Cite

Bacteria and archaea use CRISPR-Cas adaptive immune systems to defend themselves from infection by bacteriophages (phages). These RNA-guided nucleases are powerful weapons in the fight against foreign DNA, such as phages and plasmids, as well as a revolutionary gene editing tool. Phages are not passive bystanders in their interactions with CRISPR-Cas systems, however; recent discoveries have described phage genes that inhibit CRISPR-Cas function. More than 20 protein families, previously of unknown function, have been ascribed anti-CRISPR function. Here, we discuss how these CRISPR-Cas inhibitors were discovered and their modes of action elucidated. We also consider the potential impact of anti-CRISPRs on bacterial and phage evolution. Finally, we speculate about the future of this field.

show abstract

The action ofEscherichia coliCRISPR–Cas system on lytic bacteriophages with different lifestyles and development strategies

Cited by 67 publications

References 52 publications

Optimal number of spacers in CRISPR arrays

Optimal number of spacers in CRISPR arrays

Detection of Spacer Precursors Formed In Vivo During Primed CRISPR Adaptation

The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs

Contact Info

Product

Resources

About