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TitleGenome expansion by a CRISPR trimmer-integrase.
Journal, issue, pagesNature, Vol. 618, Issue 7966, Page 855-861, Year 2023
Publish dateJun 14, 2023
AuthorsJoy Y Wang / Owen T Tuck / Petr Skopintsev / Katarzyna M Soczek / Gary Li / Basem Al-Shayeb / Julia Zhou / Jennifer A Doudna /
PubMed AbstractCRISPR-Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity. CRISPR systems ...CRISPR-Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity. CRISPR systems maintain genome integrity and avoid autoimmunity by distinguishing between self and non-self, a process for which the CRISPR/Cas1-Cas2 integrase is necessary but not sufficient. In some microorganisms, the Cas4 endonuclease assists CRISPR adaptation, but many CRISPR-Cas systems lack Cas4. Here we show here that an elegant alternative pathway in a type I-E system uses an internal DnaQ-like exonuclease (DEDDh) to select and process DNA for integration using the protospacer adjacent motif (PAM). The natural Cas1-Cas2/exonuclease fusion (trimmer-integrase) catalyses coordinated DNA capture, trimming and integration. Five cryo-electron microscopy structures of the CRISPR trimmer-integrase, visualized both before and during DNA integration, show how asymmetric processing generates size-defined, PAM-containing substrates. Before genome integration, the PAM sequence is released by Cas1 and cleaved by the exonuclease, marking inserted DNA as self and preventing aberrant CRISPR targeting of the host. Together, these data support a model in which CRISPR systems lacking Cas4 use fused or recruited exonucleases for faithful acquisition of new CRISPR immune sequences.
External linksNature / PubMed:37316664 / PubMed Central
MethodsEM (single particle)
Resolution2.91 - 4.1 Å
Structure data

29561

8fy9

EMDB-29561, PDB-8fy9:
Cryo-EM structure of Cas1:Cas2-DEDDh:PAM-deficient prespacer complex
Method: EM (single particle) / Resolution: 3.1 Å

29562

8fya

EMDB-29562, PDB-8fya:
Cryo-EM structure of Cas1:Cas2-DEDDh:PAM-containing prespacer complex
Method: EM (single particle) / Resolution: 2.91 Å

29563

8fyb

EMDB-29563, PDB-8fyb:
Cryo-EM structure of Cas1:Cas2-DEDDh:half-site integration complex
Method: EM (single particle) / Resolution: 3.1 Å

29564

8fyc

EMDB-29564, PDB-8fyc:
Cryo-EM structure of Cas1:Cas2-DEDDh:half-site integration complex linear CRISPR repeat conformation
Method: EM (single particle) / Resolution: 4.1 Å

29565

8fyd

EMDB-29565, PDB-8fyd:
Cryo-EM structure of Cas1:Cas2-DEDDh:half-site integration complex bent CRISPR repeat conformation
Method: EM (single particle) / Resolution: 3.9 Å

Source
  • megasphaera (bacteria)
KeywordsDNA BINDING PROTEIN/DNA / CRISPR / integrase / CRISPR adaptation module / PAM / prespacer / exonuclease / DNA binding protein-DNA complex / enzyme / ribonucleoprotein

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