Class II, type V CRISPR systems
Described herein are methods, compositions, and systems derived from uncultivated microorganisms useful for gene editing.
1. A method of modifying a target polynucleotide, the method comprising contacting the target polynucleotide with an engineered nuclease system comprising:
(a) a class 2, type V Cas endonuclease configured to be selective for a protospacer adjacent motif (PAM) sequence comprising 5′-YYn-3′ (SEQ ID NO:3871), wherein the endonuclease comprises a WED II domain and a PAM-interacting domain having at least 80% sequence identity to a WED II domain and a PAM-interacting domain, respectively, of the amino acid sequence of SEQ ID NO: 215; and
(b) an engineered guide ribonucleic acid, wherein the engineered guide ribonucleic acid is configured to form a complex with the endonuclease and the engineered guide ribonucleic acid comprises a spacer sequence configured to hybridize to a region of the target polynucleotide;
thereby modifying the target polynucleotide.
2. The method of claim 1 , wherein the endonuclease comprises WED II and PAM-interacting domains having at least 90% sequence identity to the WED II and PAM-interacting domains, respectively, of the amino acid sequence of SEQ ID NO: 215.
3. The method of claim 1 , wherein the WED II domain and the PAM-interacting domain of the endonuclease comprise an amino acid sequence having at least 90% sequence identity to amino acid residues 561-730 of the amino acid sequence of SEQ ID NO: 215.
4. The method of claim 1 , wherein the WED II domain of the endonuclease comprises a sequence having at least 90% sequence identity to residues 561-632 of the amino acid sequence of SEQ ID NO: 215.
5. The method of claim 1 , wherein the endonuclease comprises a RuvC domain comprising an amino acid sequence having at least 80% sequence identity to RuvCI, RuvCII, and RuvCIII domains of the amino acid sequence of SEQ ID NO: 215, and wherein the endonuclease comprises catalytic residues G578-W579, K583, K641, D886, E976, or D1229.
6. The method of claim 1 , wherein the endonuclease comprises catalytic residues G578-W579, K583, K641, D886, E976, or D1229.
7. The method of claim 1 , wherein the endonuclease comprises at least one of the following mutations: S168R, E172R, or N577R when an amino acid sequence of the endonuclease is aligned to the amino acid sequence of SEQ ID NO: 215.
8. The method of claim 1 , wherein the endonuclease comprises mutations S168R and E172R when an amino acid sequence of the endonuclease is aligned to the amino acid sequence of SEQ ID NO: 215.
9. The method of claim 1 , wherein the endonuclease comprises mutations N577R when an amino acid sequence of the endonuclease is aligned to the amino acid sequence of SEQ ID NO: 215.
10. The method of claim 1 , wherein the endonuclease comprises mutation S168R when an amino acid sequence of the endonuclease is aligned to the amino acid sequence of SEQ ID NO: 215.
11. The method of claim 10 , wherein the endonuclease does not comprise a mutation of an amino acid residue corresponding to E172 or N577 when an amino acid sequence of the endonuclease is aligned to the amino acid sequence of SEQ ID NO: 215.
12. The method of claim 1 , wherein the endonuclease comprises an amino acid sequence having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 215.
13. The method of claim 12 , wherein the endonuclease comprises an amino acid sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO: 215.
14. The method of claim 13 , wherein the endonuclease comprises the amino acid sequence of SEQ ID NO: 215.
15. The method of claim 1 , wherein the engineered guide ribonucleic acid comprises a nucleotide sequence having at least 80% sequence identity to nucleotides 1-20 of the nucleotide sequence of SEQ ID NO: 3609.
16. The method of claim 15 , wherein the engineered guide ribonucleic acid comprises a nucleotide sequence having at least 90% sequence identity to nucleotides 1-20 of the nucleotide sequence of SEQ ID NO: 3609.
17. The method of claim 16 , wherein the engineered guide ribonucleic acid comprises a nucleotide sequence of the nucleotide sequence of SEQ ID NO: 3609.
18. The method of claim 1 , further comprising contacting the said target polynucleotide with a single- or double-stranded deoxyribonucleic acid repair template comprising from 5′ to 3′: a first homology arm comprising a sequence of at least 20 nucleotides 5′ to a portion of the said target polynucleotide, a synthetic deoxyribonucleic acid sequence of at least 10 nucleotides, and a second homology arm comprising a sequence of at least 20 nucleotides 3′ to the portion of the target polynucleotide.
19. The method of claim 18 , wherein the single- or double-stranded deoxyribonucleic acid repair template comprises a transgene donor.
20. The method of claim 1 , further comprising contacting the target polynucleotide with a deoxyribonucleic acid repair template comprising a double-stranded deoxyribonucleic acid segment flanked by one or two single-stranded deoxyribonucleic acid segments.
21. The method of claim 20 , wherein the single-stranded deoxyribonucleic acid segments are conjugated to 5′ ends or 3′ ends of the double-stranded deoxyribonucleic acid segment.
22. The method of claim 20 , wherein the double-stranded deoxyribonucleic acid segment comprises a barcode, an open reading frame, an enhancer, a promoter, a protein-coding sequence, a micro ribonucleic acid coding sequence, a ribonucleic acid coding sequence, or a transgene.
23. The method of claim 1 , wherein the target polynucleotide is located within a cell.
24. The method of claim 23 , wherein the cell is a mammalian cell.
25. The method of claim 24 , wherein the cell is in vitro or in vivo.
26. The method of claim 1 , wherein the sequence identity is determined by a BLASTP, CLUSTALW, MUSCLE, MAFFT algorithm or a CLUSTALW algorithm with the Smith-Waterman homology search algorithm parameters.
27. The method of claim 26 , wherein the sequence identity is determined by the BLASTP homology search algorithm using parameters of a wordlength (W) of 3, an expectation (E) of 10, and a BLOSUM62 scoring matrix setting gap costs at existence of 11, extension of 1 and using a conditional compositional score matrix adjustment.
28. The method of claim 1 , wherein the PAM-interacting domain of the endonuclease comprises an amino acid sequence having at least 90% sequence identity to amino acid residues 633-730 of the amino acid sequence of SEQ ID NO: 215.