Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR–Cas effector complexes

Marnix Vlot, Joep Houkes, Silke J.A. Lochs, Daan C. Swarts, Peiyuan Zheng, Tim Kunne, Prarthana Mohanraju, Carolin Anders, Martin Jinek, John Van Der Oost, Mark J. Dickman, Stan J.J. Brouns*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

12 Citations (Scopus)

Abstract

Prokaryotes encode various host defense systems that provide protection against mobile genetic elements. Restriction–modification (R–M) and CRISPR–Cas systems mediate host defense by sequence specific targeting of invasive DNA. T-even bacteriophages employ covalent modifications of nucleobases to avoid binding and therefore cleavage of their DNA by restriction endonucleases. Here, we describe that DNA glucosylation of bacteriophage genomes affects interference of some but not all CRISPR–Cas systems. We show that glucosyl modification of 5-hydroxymethylated cytosines in the DNA of bacteriophage T4 interferes with type I-E and type II-A CRISPR–Cas systems by lowering the affinity of the Cascade and Cas9–crRNA complexes for their target DNA. On the contrary, the type V-A nuclease Cas12a (also known as Cpf1) is not impaired in binding and cleavage of glucosylated target DNA, likely due to a more open structural architecture of the protein. Our results suggest that CRISPR–Cas systems have contributed to the selective pressure on phages to develop more generic solutions to escape sequence specific host defense systems.
Original languageEnglish
Pages (from-to)873-885
JournalNucleic acids research
Volume46
Issue number2
DOIs
Publication statusPublished - 25 Jan 2018

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Bacteriophages
DNA
T-Phages
Interspersed Repetitive Sequences
Bacteriophage T4
Deoxyribonuclease I
Cytosine
DNA Restriction Enzymes
Genome
Proteins

Cite this

Vlot, Marnix ; Houkes, Joep ; Lochs, Silke J.A. ; Swarts, Daan C. ; Zheng, Peiyuan ; Kunne, Tim ; Mohanraju, Prarthana ; Anders, Carolin ; Jinek, Martin ; Van Der Oost, John ; Dickman, Mark J. ; Brouns, Stan J.J. / Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR–Cas effector complexes. In: Nucleic acids research. 2018 ; Vol. 46, No. 2. pp. 873-885.
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abstract = "Prokaryotes encode various host defense systems that provide protection against mobile genetic elements. Restriction–modification (R–M) and CRISPR–Cas systems mediate host defense by sequence specific targeting of invasive DNA. T-even bacteriophages employ covalent modifications of nucleobases to avoid binding and therefore cleavage of their DNA by restriction endonucleases. Here, we describe that DNA glucosylation of bacteriophage genomes affects interference of some but not all CRISPR–Cas systems. We show that glucosyl modification of 5-hydroxymethylated cytosines in the DNA of bacteriophage T4 interferes with type I-E and type II-A CRISPR–Cas systems by lowering the affinity of the Cascade and Cas9–crRNA complexes for their target DNA. On the contrary, the type V-A nuclease Cas12a (also known as Cpf1) is not impaired in binding and cleavage of glucosylated target DNA, likely due to a more open structural architecture of the protein. Our results suggest that CRISPR–Cas systems have contributed to the selective pressure on phages to develop more generic solutions to escape sequence specific host defense systems.",
author = "Marnix Vlot and Joep Houkes and Lochs, {Silke J.A.} and Swarts, {Daan C.} and Peiyuan Zheng and Tim Kunne and Prarthana Mohanraju and Carolin Anders and Martin Jinek and {Van Der Oost}, John and Dickman, {Mark J.} and Brouns, {Stan J.J.}",
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Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR–Cas effector complexes. / Vlot, Marnix; Houkes, Joep; Lochs, Silke J.A.; Swarts, Daan C.; Zheng, Peiyuan; Kunne, Tim; Mohanraju, Prarthana; Anders, Carolin; Jinek, Martin; Van Der Oost, John; Dickman, Mark J.; Brouns, Stan J.J.

In: Nucleic acids research, Vol. 46, No. 2, 25.01.2018, p. 873-885.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR–Cas effector complexes

AU - Vlot, Marnix

AU - Houkes, Joep

AU - Lochs, Silke J.A.

AU - Swarts, Daan C.

AU - Zheng, Peiyuan

AU - Kunne, Tim

AU - Mohanraju, Prarthana

AU - Anders, Carolin

AU - Jinek, Martin

AU - Van Der Oost, John

AU - Dickman, Mark J.

AU - Brouns, Stan J.J.

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AB - Prokaryotes encode various host defense systems that provide protection against mobile genetic elements. Restriction–modification (R–M) and CRISPR–Cas systems mediate host defense by sequence specific targeting of invasive DNA. T-even bacteriophages employ covalent modifications of nucleobases to avoid binding and therefore cleavage of their DNA by restriction endonucleases. Here, we describe that DNA glucosylation of bacteriophage genomes affects interference of some but not all CRISPR–Cas systems. We show that glucosyl modification of 5-hydroxymethylated cytosines in the DNA of bacteriophage T4 interferes with type I-E and type II-A CRISPR–Cas systems by lowering the affinity of the Cascade and Cas9–crRNA complexes for their target DNA. On the contrary, the type V-A nuclease Cas12a (also known as Cpf1) is not impaired in binding and cleavage of glucosylated target DNA, likely due to a more open structural architecture of the protein. Our results suggest that CRISPR–Cas systems have contributed to the selective pressure on phages to develop more generic solutions to escape sequence specific host defense systems.

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