Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum

Özcan, Ahsen; Pausch, Patrick; Linden, Andreas; Wulf, Alexander; Schühle, Karola; Heider, Johann; Urlaub, Henning; Heimerl, Thomas; Bange, Gert; Randau, Lennart

doi:10.1038/s41564-018-0274-8

Cited by 78 publications

(84 citation statements)

References 46 publications

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“…If true, and given the vast over-representation of type IV systems in plasmids, it suggests that these systems may have evolved as specialists in subverting chromosomal systems. This is consistent with the observation that these systems frequently lack not only the adaptation machinery but also the enzymes necessary for target cleavage 8 , and in some cases for the processing of crRNAs 49 .…”

Section: Discussionsupporting

confidence: 91%

Co-occurrence of multiple CRISPRs andcasclusters suggests epistatic interactions

Bernheim

Bikard

Touchon

et al. 2019

Preprint

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Prokaryotes use CRISPR-Cas for adaptive immunity, but the reasons for the existence of multiple CRISPR and cas clusters remain poorly understood. We found that more than 40% of the genomes encoding a system show atypical genetic organizations. Their analysis revealed negative and positive epistatic interactions between Cas subtypes. The latter often result in one single complex locus with a shared adaptation module and diverse interference mechanisms, presumably to produce more effective immune systems. We typed CRISPRs that could not be unambiguously associated with a cas cluster and found that such complex loci tend to have unique type I repeats in multiple CRISPRs. In contrast, under-represented co-occurrences caused by functional interference or redundancy may lead to CRISPRs distant from cas genes. To investigate the origin of atypical CRISPR-Cas organizations, we analyzed plasmids and phages. Sets of nearly 2000 phages and 10000 prophages were almost devoid of CRISPR-Cas systems, but a sizeable fraction of plasmids had them. Isolated CRISPRs in plasmids were often compatible with the chromosomal cas clusters, suggesting that plasmids use CRISPRs to subvert host immunity. These results point to an important role for the interactions between multiple CRISPR and Cas in the function and evolution of bacterial immunity.

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Section: Discussionsupporting

confidence: 91%

Co-occurrence of multiple CRISPRs andcasclusters suggests epistatic interactions

Bernheim

Bikard

Touchon

et al. 2019

Preprint

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“…3a, Supplementary Table 4). Intriguingly, this bias was not detected in earlier studies that employed lower numbers of non-redundant spacers and were primarily centred around the matching of spacers against (pro)virus databases 7,9,22,38 . Our additional matching of spacers against PLSDB, a comprehensive database of >16,000 curated plasmid genomes 39 , was key in determining the plasmid targeting bias.…”

Section: Discussionmentioning

confidence: 79%

“…These data suggest that the subtype IV-A effector complexes, as in other CRISPR-Cas systems, survey the cellular environment searching for matching nucleic acid targets. However, the study concluded that the spacers of the associated CRISPR arrays yielded no clear spacer-protospacer matches 9 , but an earlier larger-scale analysis reported putative sequence matches to MGEs of which 72% were reported to be of viral origin 10 .…”

Section: Introductionmentioning

confidence: 93%

“…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 . These data suggest that the subtype IV-A effector complexes, as in other CRISPR-Cas systems, survey the cellular environment searching for matching nucleic acid targets.…”

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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“…The two classes are differentiated based on the effector module; class 1 utilises multi-protein effector Cas complexes, while class 2 utilise a single-protein effector (either Cas9 or Cpf1) 5,6 . All types are confirmed, or expected, to provide immunity against invading DNA, while Type III CRISPR-Cas systems can target both DNA and RNA 7,8 .…”

Section: Introductionmentioning

confidence: 93%

Identification of a Type IV CRISPR-Cas system located exclusively on IncHI1B/IncFIB plasmids in Enterobacteriaceae

Newire

Aydin

Juma

et al. 2019

Preprint

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During an investigation of CRISPR carriage in clinical, multi-drug resistant, Klebsiella pneumoniae, a novel CRISPR-Cas system (which we have designated Type IV-B) was detected on plasmids from two K. pneumoniae isolates from Egypt (isolated in 2002-2003) and a single K. pneumoniae isolate from the UK (isolated in 2017). Sequence analysis of other genomes available in GenBank revealed that this novel Type IV-B CRISPR-Cas system was present on 28 other plasmids from various Enterobacteriaceae hosts and was never found on the chromosome. Type IV-B is found exclusively on IncHI1B/IncFIB plasmids and is associated with multiple putative transposable elements. Type IV-B has a single repeat-spacer array (CRISPR1) upstream of the cas loci with some spacers matching regions of conjugal transfer genes of IncFIIK/IncFIB(K) plasmids suggesting a role in plasmid incompatibility. Expression of the cas loci was confirmed in available clinical isolates by RT-PCR; indicating the system is active. To our knowledge, this is the first report describing a new subtype within Type IV CRISPR-Cas systems exclusively associated with IncHI1B/IncFIB plasmids.ImportanceHere, we report the identification of a novel subtype of Type IV CRISPR-Cas that is expressed and exclusively carried by IncHI1B/IncFIB plasmids in Enterobacteriaceae, demonstrating unique evolutionarily juxtaposed connections between CRISPR-Cas and mobile genetic elements (MGEs). Type IV-B encodes a variety of spacers showing homology to DNA from various sources, including plasmid specific spacers and is therefore thought to provide specific immunity against plasmids of other incompatible groups (IncFIIK/IncFIB(K)). The relationship between Type IV-B CRISPR-Cas and MGEs that surround and interrupt the system is likely to promote rearrangement and be responsible for the observed variability of this type. Finally, the Type IV-B CRISPR-Cas is likely to co-operate with other cas loci within the bacterial host genome during spacer acquisition.

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Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum

Cited by 78 publications

References 46 publications

Co-occurrence of multiple CRISPRs andcasclusters suggests epistatic interactions

Co-occurrence of multiple CRISPRs andcasclusters suggests epistatic interactions

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

Identification of a Type IV CRISPR-Cas system located exclusively on IncHI1B/IncFIB plasmids in Enterobacteriaceae

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