Optimized protein linkers and methods of use
The invention relates to peptide linkers and fusion proteins comprising linkers designed for optimizing the activity of the proteins comprised therein, and methods for using the same. The invention further relates to newly designed Cas12a-based cytosine base editors.
1. A polypeptide comprising any one of the amino acid sequences of SEQ ID NOs: 1-24.
2. The polypeptide of claim 1 , further comprising a polypeptide of interest linked to any one of the amino acid sequences of SEQ ID NOs: 1-24.
3. The polypeptide of claim 2 , wherein the polypeptide of interest comprises at least one polypeptide or protein domain having deaminase (deamination) activity, nickase activity, recombinase activity, transposase activity, methylase activity, glycosylase (DNA glycosylase) activity, glycosylase inhibitor activity, demethylase activity, transcription activation activity, transcription repression activity, transcription release factor activity, histone modification activity, nuclease activity, single-strand RNA cleavage activity, double-strand RNA cleavage activity, restriction endonuclease activity, nucleic acid binding activity, methyltransferase activity, DNA repair activity, DNA damage activity, dismutase activity, alkylation activity, depurination activity, oxidation activity, pyrimidine dimer forming activity, integrase activity, transposase activity, polymerase activity, ligase activity, helicase activity, and/or photolyase activity.
4. The polypeptide of claim 1 , further comprising a Cas12a domain linked to any one of the amino acid sequences of SEQ ID NOs: 1-24.
5. A fusion protein comprising the polypeptide of claim 4 , wherein the fusion protein further comprises a polypeptide of interest, wherein the Cas12a domain and the polypeptide of interest are linked to one another via any one of the amino acid sequences of SEQ ID NOs: 1-24.
6. The fusion protein of claim 5 , wherein the polypeptide of interest comprises a cytosine deaminase domain.
7. The fusion protein of claim 6 , wherein the cytosine deaminase domain is an apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) domain.
8. The fusion protein of claim 7 , wherein the APOBEC domain is APOBEC1 or APOBEC3A.
9. A cell comprising the fusion protein of claim 6 .
10. The cell of claim 9 , wherein the cell is from an animal, a plant, a fungus, an archaeon, or a bacterium.
11. A method of modifying a target nucleic acid, comprising contacting the target nucleic acid with the fusion protein of claim 6 , and a guide nucleic acid, thereby modifying a target nucleic acid.
12. A method of editing a target nucleic acid, comprising contacting a cell or a cell free system comprising the target nucleic acid with a polynucleotide encoding the fusion protein of claim 6 , or an expression cassette or vector comprising the same, and a guide nucleic acid, or an expression cassette or vector comprising the same, wherein the cytosine deaminase domain converts a cytosine (C) to a thymine (T) in the target nucleic acid, thereby editing the target nucleic acid.
13. The fusion protein of claim 6 , further comprising a uracil DNA glycosylase inhibitor (UGI) domain, wherein the C-terminus of the cytosine deaminase domain is linked to the N-terminus of the Cas12a domain via any one of the amino acid sequences of SEQ ID NOs:1-5 and the C-terminus of the Cas12a domain is linked to the N-terminus of the UGI domain, or the C-terminus of the Cas12a domain is linked to the N-terminus of the UGI domain via any one of the amino acid sequences of SEQ ID NOs:6-9 and the C-terminus of the cytosine deaminase domain is linked to the N-terminus of the Cas12a domain.
14. The fusion protein of claim 13 , wherein the Cas12a domain comprises a mutation in the nuclease active site.
15. The fusion protein of claim 13 , wherein the cytosine deaminase domain is an apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) domain.
16. The fusion protein of claim 15 , wherein the APOBEC domain is a rat or a human APOBEC domain, optionally wherein the rat APOBEC domain is the amino acid sequence of SEQ ID NO:46 and/or the APOBEC domain is the amino acid sequence of SEQ ID NO:47.
17. A cell comprising the fusion protein of claim 13 .
18. The fusion protein of claim 5 , wherein the polypeptide of interest comprises a uracil-DNA glycosylase inhibitor (UGI).
19. The fusion protein of claim 18 , further comprising a cytosine deaminase domain, wherein the C-terminus of the Cas12a domain is linked to the N-terminus of the UGI domain via any one of the amino acid sequences of SEQ ID NOs:10-12 and the C-terminus of the UGI domain is linked to the N-terminus of the cytosine deaminase domain via any one of the amino acid sequences of SEQ ID NOs:13-16.
20. A cell comprising the fusion protein of claim 19 .
21. The fusion protein of claim 18 , further comprising a cytosine deaminase domain,
wherein the Cas12a domain comprises a mutation in the nuclease active site and
(a) the C-terminus of the UGI domain is linked to the N-terminus of the Cas12a domain via any one of the amino acid sequences of SEQ ID NOs:17-19 and the C-terminus of the Cas12a domain is linked to the N-terminus of the cytosine deaminase domain, or
(b) the C-terminus of the UGI domain is linked to the N-terminus of the Cas12a domain and the C-terminus of the Cas12a domain is linked to the N-terminus of the cytosine deaminase domain via any one of the amino acid sequences of SEQ ID NOs:20-24.
22. A cell comprising the fusion protein of claim 21 .
23. The fusion protein of claim 5 , wherein the fusion protein comprises an amino acid sequence of any one of SEQ ID NOs:49-72 or SEQ ID NOs:91-100, 106, or 107.
24. A complex comprising the fusion protein of claim 5 , and a guide nucleic acid.
25. The complex of claim 24 , wherein the Cas12a domain comprises a mutation in the nuclease active site.
26. The polypeptide of claim 4 , wherein the Cas12a domain comprises a mutation in the nuclease active site.
27. The polypeptide of claim 4 , wherein the Cas12a domain is linked at its C-terminus and/or its N-terminus to any one of the amino acid sequences of SEQ ID NOs: 1-24.
28. An expression cassette or vector comprising a polynucleotide encoding a fusion protein comprising a Cas12a domain and a polypeptide of interest, wherein the Cas12a domain and the polypeptide of interest are linked to one another via any one of the amino acid sequences of SEQ ID NOs: 1-24.
29. A cell comprising the expression cassette or vector of claim 28 .
30. The cell of claim 29 , wherein the cell is from an animal, a plant, a fungus, an archaeon, or a bacterium.