Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems

Abstract
Data availability
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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

The following data sets were generated

(2017) CRISPR targeting and spacer acquisition in M. mediterranea mutants, and associated environmental investigations
Publicly accessible at NCBI Sequence Read Archive (accession no. SRP103952).

https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP103952

The following previously published data sets were used

1. Silas S
2. Mohr G
3. Sidote DJ
4. Markham LM
5. Sanchez-Amat A
6. Bhaya D
7. Lambowitz AM
8. Fire AZ
(2016) total RNA (> 200 nt) sequencing from MMB-1 strains over-expressing RT-Cas1, Cas2, and Marme_0670 - replicate 1
Publicly accessible at NCBI Sequence Read Archive (accession no. SRR2914032).

https://www.ncbi.nlm.nih.gov/sra/?term=SRR2914032
1. Silas S
2. Mohr G
3. Sidote DJ
4. Markham LM
5. Sanchez-Amat A
6. Bhaya D
7. Lambowitz AM
8. Fire AZ
(2016) total RNA (> 200 nt) sequencing from MMB-1 strains over-expressing RT-Cas1, Cas2, and Marme_0670 - replicate 2
Publicly accessible at NCBI Sequence Read Archive (accession no. SRR2914033).

https://www.ncbi.nlm.nih.gov/sra/?term=SRR2914033

Article and author information

Author details

Sukrit Silas

Chemical and Systems Biology, Stanford University, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
Patricia Lucas-Elio

Genetics and Microbiology, Universidad de Murcia, Murcia, Spain

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-7182-1189
Simon A Jackson

Microbiology and Immunology, University of Otago, Dunedin, New Zealand

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4512-3093
Alejandra Aroca-Crevillén

Genetics and Microbiology, Universidad de Murcia, Murcia, Spain

Competing interests
The authors declare that no competing interests exist.
Loren L Hansen

Pathology, Stanford University, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
Peter C Fineran

Microbiology & Immunology, University of Otago, Dunedin, New Zealand

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4639-6704
Andrew Z Fire

Pathology and Genetics, Stanford University School of Medicine, Stanford, United States

For correspondence
afire@stanford.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-6217-8312
Antonio Sánchez-Amat

Genetics and Microbiology, Universidad de Murcia, Murcia, Spain

For correspondence
antonio@um.es

Competing interests
The authors declare that no competing interests exist.

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

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.