Spacer Acquisition Rates Determine the Immunological Diversity of the Type II CRISPR-Cas Immune Response

Robert Heler; Addison V Wright; Marija Vucelja; Jennifer A Doudna; Luciano A Marraffini

doi:10.1016/j.chom.2018.12.016

Spacer Acquisition Rates Determine the Immunological Diversity of the Type II CRISPR-Cas Immune Response

Cell Host Microbe. 2019 Feb 13;25(2):242-249.e3. doi: 10.1016/j.chom.2018.12.016. Epub 2019 Jan 29.

Authors

Robert Heler¹, Addison V Wright², Marija Vucelja³, Jennifer A Doudna⁴, Luciano A Marraffini⁵

Affiliations

¹ Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA.
² Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
³ Department of Physics, University of Virginia, Charlottesville, VA 22904, USA.
⁴ Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
⁵ Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA. Electronic address: marraffini@rockefeller.edu.

Abstract

CRISPR-Cas systems provide acquired immunity in prokaryotes. Upon infection, short sequences from the phage genome, known as spacers, are inserted between the CRISPR repeats. Spacers are transcribed into small RNA molecules that guide nucleases to their targets. The forces that shape the distribution of newly acquired spacers, which is observed to be uneven, are poorly understood. We studied the spacer patterns that arise after phage infection of Staphylococcus aureus harboring the Streptococcus pyogenes type II-A CRISPR-Cas system. We observed that spacer patterns are established early during the CRISPR-Cas immune response and correlate with spacer acquisition rates, but not with spacer targeting efficiency. The rate of spacer acquisition depended on sequence elements within the spacer, which in turn determined the abundance of different spacers within the adapted population. Our results reveal how the two main forces of the CRISPR-Cas immune response, acquisition and targeting, affect the generation of immunological diversity.

Keywords: CRISPR; Cas9; bacteriophage; immunity; spacer acquisition; staphylococcus.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

CRISPR-Cas Systems*
DNA, Intergenic / genetics*
DNA, Viral / genetics*
Evolution, Molecular*
Staphylococcus Phages / genetics
Staphylococcus Phages / growth & development*
Staphylococcus aureus / enzymology*
Staphylococcus aureus / genetics*
Streptococcus pyogenes / enzymology
Streptococcus pyogenes / genetics

Substances

DNA, Intergenic
DNA, Viral

Grants and funding

DP1 GM128184/GM/NIGMS NIH HHS/United States