Highly efficient primed spacer acquisition from targets destroyed by the Escherichia coli type I-E CRISPR-Cas interfering complex.
Prokaryotic clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR associated (Cas) immunity relies on adaptive acquisition of spacers-short fragments of foreign DNA. For the type I-E CRISPR-Cas system from Escherichia coli, efficient "primed" adaptation requires Cas effector proteins and a CRISPR RNA (crRNA) whose spacer partially matches a segment (protospacer) in target DNA. Primed adaptation leads to selective acquisition of additional spacers from DNA molecules recognized by the effector-crRNA complex. When the crRNA spacer fully matches a protospacer, CRISPR interference-that is, target destruction without acquisition of additional spacers-is observed. We show here that when the rate of degradation of DNA with fully and partially matching crRNA targets is made equal, fully matching protospacers stimulate primed adaptation much more efficiently than partially matching ones. The result indicates that different functional outcomes of CRISPR-Cas response to two kinds of protospacers are not caused by different structures formed by the effector-crRNA complex but are due to the more rapid destruction of targets with fully matching protospacers.
Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854;
Ekaterina
E
Semenova
Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia; Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia;
Ekaterina
E
Savitskaya
Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia; Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia;
Olga
O
Musharova
Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854; Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia; Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia; Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia;
Alexandra
A
Strotskaya
Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854; Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia; Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia;
Daria
D
Vorontsova
Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907;
Kirill A
KA
Datsenko
M.V. Lomonosov Moscow State University, Moscow 119991, Russia.
Maria D
MD
Logacheva
Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854; Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia; Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia; Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia; severik@waksman.rutgers.edu.
Konstantin
K
Severinov
D000220:Adaptation, Biological; D064130:CRISPR-Associated Proteins / Q000378:metabolism; D064113:CRISPR-Cas Systems; D021901:DNA, Intergenic; D004706:Endodeoxyribonucleases / Q000378:metabolism; D004720:Endonucleases / Q000378:metabolism; D004926:Escherichia coli / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000378:metabolism
D064130:CRISPR-Associated Proteins; D021901:DNA, Intergenic; D029968:Escherichia coli Proteins; C000591054:Cas2 protein, E coli; D004706:Endodeoxyribonucleases; D004720:Endonucleases; C557650:YgbT protein, E coli
CRISPR interference; CRISPR-Cas; primed CRISPR adaptation