Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems
- Stanford University, United States
- Universidad de Murcia, Spain
- University of Otago, New Zealand
- Stanford University School of Medicine, United States
Abstract
CRISPR-Cas-mediated defense utilizes information stored as spacers in CRISPR arrays to defend against genetic invaders. We define the mode of target interference and role in antiviral defense for two CRISPR-Cas systems in Marinomonas mediterranea. One system (type I-F) targets DNA. A second system (type III-B) is broadly capable of acquiring spacers in either orientation from RNA and DNA, and exhibits transcription-dependent DNA interference. Examining resistance to phages isolated from Mediterranean seagrass meadows, we found that the type III-B machinery co-opts type I-F CRISPR-RNAs. Sequencing and infectivity assessments of related bacterial and phage strains suggests an "arms race" in which phage escape from the type I-F system can be overcome through use of type I-F spacers by a horizontally-acquired type III-B system. We propose that the phage-host arms race can drive selection for horizontal uptake and maintenance of promiscuous type III interference modules that supplement existing host type I CRISPR-Cas systems.
Data availability
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CRISPR targeting and spacer acquisition in M. mediterranea mutants, and associated environmental investigationsPublicly accessible at NCBI Sequence Read Archive (accession no. SRP103952).
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total RNA (> 200 nt) sequencing from MMB-1 strains over-expressing RT-Cas1, Cas2, and Marme_0670 - replicate 1Publicly accessible at NCBI Sequence Read Archive (accession no. SRR2914032).
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total RNA (> 200 nt) sequencing from MMB-1 strains over-expressing RT-Cas1, Cas2, and Marme_0670 - replicate 2Publicly accessible at NCBI Sequence Read Archive (accession no. SRR2914033).
Article and author information
Author details
Patricia Lucas-Elio
Funding
National Institutes of Health (R01-GM37706)
- Andrew Z Fire
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2017, Silas et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems
eLife 6:e27601.
https://doi.org/10.7554/eLife.27601
Further reading
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- Microbiology and Infectious Disease
The persistence of latent viral reservoirs remains the major obstacle to eradicating human immunodeficiency virus (HIV). We herein found that ICP34.5 can act as an antagonistic factor for the reactivation of HIV latency by herpes simplex virus type I (HSV-1), and thus recombinant HSV-1 with ICP34.5 deletion could more effectively reactivate HIV latency than its wild-type counterpart. Mechanistically, HSV-ΔICP34.5 promoted the phosphorylation of HSF1 by decreasing the recruitment of protein phosphatase 1 (PP1α), thus effectively binding to the HIV LTR to reactivate the latent reservoirs. In addition, HSV-ΔICP34.5 enhanced the phosphorylation of IKKα/β through the degradation of IκBα, leading to p65 accumulation in the nucleus to elicit NF-κB pathway-dependent reactivation of HIV latency. Then, we constructed the recombinant HSV-ΔICP34.5 expressing simian immunodeficiency virus (SIV) env, gag, or the fusion antigen sPD1-SIVgag as a therapeutic vaccine, aiming to achieve a functional cure by simultaneously reactivating viral latency and eliciting antigen-specific immune responses. Results showed that these constructs effectively elicited SIV-specific immune responses, reactivated SIV latency, and delayed viral rebound after the interruption of antiretroviral therapy (ART) in chronically SIV-infected rhesus macaques. Collectively, these findings provide insights into the rational design of HSV-vectored therapeutic strategies for pursuing an HIV functional cure.
