A1 Journal article (refereed)
Cooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting System (2021)

Hoikkala, V., Ravantti, J., Díez-Villaseñor, C., Tiirola, M., Conrad, R. A., McBride, M. J., Moineau, S., & Sundberg, L.-R. (2021). Cooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting System. Mbio, 12(2), Article e03338-20. https://doi.org/10.1128/mbio.03338-20

JYU authors or editors

Hoikkala, Ville
Diez Villaseñor, César
Tiirola, Marja
Sundberg, Lotta-Riina

Publication details

All authors or editors: Hoikkala, Ville; Ravantti, Janne; Díez-Villaseñor, César; Tiirola, Marja; Conrad, Rachel A.; McBride, Mark J.; Moineau, Sylvain; Sundberg, Lotta-Riina

Journal or series: Mbio

ISSN: 2161-2129

eISSN: 2150-7511

Publication year: 2021

Publication date: 30/03/2021

Volume: 12

Issue number: 2

Article number: e03338-20

Publisher: American Society for Microbiology

Publication country: United States

Publication language: English

DOI: https://doi.org/10.1128/mbio.03338-20

Publication open access: Openly available

Publication channel open access: Open Access channel

Publication is parallel published (JYX): https://jyx.jyu.fi/handle/123456789/74936

Abstract

CRISPR-Cas immune systems adapt to new threats by acquiring new spacers from invading nucleic acids such as phage genomes. However, some CRISPR-Cas loci lack genes necessary for spacer acquisition despite variation in spacer content between microbial strains. It has been suggested that such loci may use acquisition machinery from cooccurring CRISPR-Cas systems within the same strain. Here, following infection by a virulent phage with a double-stranded DNA (dsDNA) genome, we observed spacer acquisition in the native host Flavobacterium columnare that carries an acquisition-deficient CRISPR-Cas subtype VI-B system and a complete subtype II-C system. We show that the VI-B locus acquires spacers from both the bacterial and phage genomes, while the newly acquired II-C spacers mainly target the viral genome. Both loci preferably target the terminal end of the phage genome, with priming-like patterns around a preexisting II-C protospacer. Through gene deletion, we show that the RNA-cleaving VI-B system acquires spacers in trans using acquisition machinery from the DNA-cleaving II-C system. Our observations support the concept of cross talk between CRISPR-Cas systems and raise further questions regarding the plasticity of adaptation modules.

Keywords: bacteria; bacteriophages; immune system; evolution; horizontal gene transfer; DNA; RNA