CRISPR–Cas in mobile genetic elements: counter-defence and beyond

Faure, Guilhem; Shmakov, Sergey; Yan, Wang‐Ji; Cheng, David R.; Scott, David; Peters, Joseph E.; Makarova, Kira S.; Koonin, Eugene V.

doi:10.1038/s41579-019-0204-7

Cited by 206 publications

(238 citation statements)

References 68 publications

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“…Moreover, subtype IV-A loci encode a DinG family helicase (Csf4), a type IV-specific Cas6-like protein (Csf5), and they typically colocate with a CRISPR array. In contrast, subtype IV-B loci lack dinG, csf5 and an associated CRISPR array but they encode a putative "small subunit" (Cas11) and they often neighbour a cysH gene 7,8 . A recent structural and biochemical analysis of a subtype IV-A CRISPR-Cas system demonstrated the essential role of the Cas6-like enzyme in both the maturation of crRNAs and in the subsequent formation of a Cascade-like crRNA-guided effector complex, composed of Csf1, Csf3, Csf5 and multiple copies of Csf2 9 .…”

Section: Introductionmentioning

confidence: 99%

“…In summary, it is plausible that subtype IV-A systems perform a defensive role, although the apparent absence of an effector nuclease suggests that the mechanism of interference differs significantly from those of other CRISPR-Cas systems. Consistent with this view, alternative functions have been suggested for type IV systems, including their involvement in plasmid propagation mechanisms, and in the enhancement of recombination events with other nucleic acids 7,9 . In particular, the absence of CRISPR arrays linked to the minimal subtype IV-B system provides support for the effector module machinery participating in alternative cellular functions 7 . In the present study we have undertaken a comparative genomics approach to survey all publicly available bacterial and archaeal genomes for type IV CRISPR-Cas systems.…”

Section: Introductionmentioning

confidence: 99%

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Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids

Pinilla‐Redondo

Mayo-Muñoz

Russel

et al. 2019

Preprint

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CRISPR-Cas systems provide prokaryotes with adaptive immune functions against viruses and other genetic parasites by leveraging small non-coding RNAs for nuclease-dependent degradation of their nucleic acid targets. In contrast to all other types of CRISPR-Cas systems, the mechanisms and biological roles of type IV systems have remained largely overlooked.Here, we describe a previously uncharted diversity of type IV gene cassettes, distributed across diverse prokaryotic genome backgrounds, and propose their classification into subtypes and variants. Congruent with recent findings, type IV modules were primarily found on plasmid-like elements. Remarkably, via a comprehensive analysis of their CRISPR spacer content, these systems were found to exhibit a strong bias towards the targeting of other plasmids. Our data indicate that the functions of type IV systems have diverged from those of other host-related CRISPR-Cas immune systems to adopt a yet unrecognised role in mediating conflicts between plasmids that compete to monopolize their hosts. Furthermore, we find evidence for cross-talk between certain type IV and type I CRISPR-Cas systems that co-exist intracellularly, thus providing an answer to the enigmatic absence of adaptation modules in these systems. Collectively, our results lead to the expansion and reclassification of type IV systems and provide novel insights into the biological function and evolution of these elusive systems.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids

Pinilla‐Redondo

Mayo-Muñoz

Russel

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…). Phylogenetic analysis indicated that the entire distinct Cas12k (formally type V‐U5) sub type is exclusively found in this specific type of transposon (Shmakov et al , ; Faure et al , ). As in the case of the variant I‐F and I‐B systems, the effector complex was not proficient for cleavage, in this system because it lacked residues that normally allow Cas12 cleavage in type V elements.…”

Section: Tn7‐like Elements Recruited Crispr/cas Systems On Multiple Smentioning

confidence: 99%

“…The evolution of CRISPR/Cas systems is interwoven with that of transposons and other mobile genetic elements in multiple ways (Faure et al, 2019). The Cas1 protein involved in spacer acquisition was originally derived from the transposase of a group of elements now known as casposons (Krupovic et al, 2014;Krupovic et al, 2017).…”

Section: Other Evolutionary Relationships Between Crispr/cas Systems mentioning

confidence: 99%

Targeted transposition with Tn7 elements: safe sites, mobile plasmids, CRISPR/Cas and beyond

Peters

2019

Molecular Microbiology

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Summary Transposon Tn7 is notable for the control it exercises over where transposition events are directed. One Tn7 integration pathways recognizes a highly conserved attachment (att) site in the chromosome, while a second pathway specifically recognizes mobile plasmids that facilitate transfer of the element to new hosts. In this review, I discuss newly discovered families of Tn7‐like elements with different targeting pathways. Perhaps the most exciting examples are multiple instances where Tn7‐like elements have repurposed CRISPR/Cas systems. In these cases, the CRISPR/Cas systems have lost their canonical defensive function to destroy incoming mobile elements; instead, the systems have been naturally adapted to use guide RNAs to specifically direct transposition into these mobile elements. The new families of Tn7‐like elements also include a variety of novel att sites in bacterial chromosomes where genome islands can form. Interesting families have also been revealed where proteins described in the prototypic Tn7 element are fused or otherwise repurposed for the new dual activities. This expanded understanding of Tn7‐like elements broadens our view of how genetic systems are repurposed and provides potentially exciting new tools for genome modification and genomics. Future opportunities and challenges to understanding the impact of the new families of Tn7‐like elements are discussed.

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“…The randomized pathway is prone to target other mobile genetic elements, such as exogenous plasmids, maximizing its ability to horizontally transfer. Recent bioinformatics analyses uncovered that a set of Tn7‐like transposons contain CRISPR‐Cas systems . These CRISPR‐Cas systems are seemed to be “minimal,” i.e., neither do they have the Cas proteins for acquiring new spacers into their CRISPR array nor the effector complex to cleave a target, implying these “minimal” CRISPR‐Cas system may function as a guide for the Tn7‐like transposon .…”

Section: Genome Integration By Crispr‐guided Transpositionmentioning

confidence: 99%

Strategies for Developing CRISPR‐Based Gene Editing Methods in Bacteria

Wang

Zhang

et al. 2019

Small Methods

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Gene editing is a fundamental technique for the identification of the linkages from genetic determinants to significant biological phenotypes, and the engineering of industrial strains to produce fine chemicals. Recently, the primitive bacterial immunity systems, clustered regularly interspaced short palindromic repeat (CRISPR)‐Cas systems, have been engineered as programmable nucleases to deliver double‐strand breaks (DSBs) at user‐defined loci. The DSB is repaired via either homology‐direct repair or the non‐homologous end joining pathway, generating a mutant in various organisms, and leading a revolution in the field of gene editing. This paper reviews the structural and molecular details of CRISPR‐Cas systems, describing their applications and challenges of genome targeting in bacterial cells. Moreover, the DSB repair pathways in bacteria are summarized and a guideline for selecting repair machines and maximizing the recombination efficiency is presented. In addition, the plasmid curing approaches in bacteria are outlined for iterative gene editing or downstream biological applications. Furthermore, CRISPR‐based transcriptional regulation, base editing, and transposition are also introduced. Finally, this paper prospects the future directions for improving CRISPR‐based gene editing methods in bacteria.

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CRISPR–Cas in mobile genetic elements: counter-defence and beyond

Cited by 206 publications

References 68 publications

Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids

Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids

Targeted transposition with Tn7 elements: safe sites, mobile plasmids, CRISPR/Cas and beyond

Strategies for Developing CRISPR‐Based Gene Editing Methods in Bacteria

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