Adenosine nucleobase editors and uses thereof
The disclosure provides adenosine deaminases that are capable of deaminating adenosine in DNA. The disclosure also provides fusion proteins comprising a Cas9 (e.g., a Cas9 nickase) domain and adenosine deaminases that deaminate adenosine in DNA. In some embodiments, the fusion proteins further comprise a nuclear localization sequence (NLS), and/or an inhibitor of base repair, such as, a nuclease dead inosine specific nuclease (dISN).
1. An adenosine deaminase comprising an amino acid sequence that is at least 90% identical to the amino acid sequence of SEQ ID NOs: 1, 8, 9, 371, 372, 373, 374, or 375 with the exception of one or more substitutions at positions selected from the group consisting of amino acid residues corresponding to positions 8, 17, 18, 23, 34, 36, 45, 48, 51, 56, 59, 84, 85, 94, 95, 102, 104, 106, 107, 108, 110, 118, 123, 127, 138, 142, 146, 147, 149, 151, 152, 153, 154, 155, 156, and 157 of the amino acid sequence of SEQ ID NO: 1, wherein said adenosine deaminase deaminates adenine in deoxyribonucleic acid (DNA).
2. A base editor for modifying a base within a nucleic acid sequence, wherein said base editor comprises:
a nucleic acid programmable DNA binding protein (napDNAbp) domain, wherein said napDNAbp domain when in conjunction with a bound nucleic acid, site specifically binds a nucleic acid sequence; and
the adenosine deaminase of claim 1 .
3. The base editor of claim 2 , wherein said napDNAbp domain comprises a Cas9 domain, a Cpf1 domain, a CasX domain, a CasY domain, a C2c1 domain, a C2c2 domain, or a C2c3domain.
4. The base editor of claim 3 , wherein said napDNAbp domain comprises a Cas9 domain.
5. The base editor of claim 4 , wherein said Cas9 domain comprises a nuclease dead Cas9 (dCas9), a Cas9 nickase (nCas9), or a nuclease active Cas9.
6. The base editor of claim 5 , wherein said Cas9 domain comprises a nuclease dead Cas9 (dCas9).
7. The base editor of claim 5 , wherein said Cas9 domain comprises a Cas9 nickase (nCas9 ).
8. The base editor of claim 2 , wherein said base editor further comprises an inhibitor of nucleic acid repair.
9. The base editor of claim 8 , wherein said inhibitor of nucleic acid repair is an inhibitor of base excision repair.
10. The base editor of claim 8 , wherein said inhibitor of nucleic acid repair comprises a protein that binds inosine.
11. The base editor of claim 8 , wherein said inhibitor of nucleic acid repair comprises a catalytically inactive inosine-specific nuclease.
12. The base editor of claim 11 , wherein said catalytically inactive inosine-specific nuclease comprises the amino acid sequence set forth in SEQ ID NO: 32 or SEQ ID NO: 33.
13. A method for editing a nucleobase of a DNA sequence, the method comprising:
(a) contacting said DNA sequence with the adenosine deaminase of claim 1 ; and
(b) converting a first nucleobase of said DNA sequence to a second nucleobase.
14. The method of claim 13 , wherein said first nucleobase is adenine.
15. The method of claim 13 , wherein said second nucleobase is inosine.
16. The method of claim 13 , wherein a third nucleobase complementary to said first nucleobase is replaced by a fourth nucleobase complementary to said second nucleobase.
17. The method of claim 13 , further comprising replacing said second nucleobase with a fifth nucleobase that is complementary to said fourth nucleobase.
18. The method of claim 17 , wherein said fifth nucleobase is guanine.
19. The adenosine deaminase of claim 1 , wherein said adenosine deaminase comprises the amino acid sequence of SEQ ID NO: 1 with the exception of the one or more substitutions at positions selected from the group consisting of amino acid residues corresponding to positions 8, 17, 18, 23, 34, 36, 45, 48, 51, 56, 59, 84, 85, 94, 95, 102, 104, 106, 107, 108, 110, 118, 123, 127, 138, 142, 146, 147, 149, 151, 152, 153, 154, 155, 156, and 157 of the amino acid sequence of SEQ ID NO: 1.
20. The base editor of claim 2 , wherein said adenosine deaminase comprises the amino acid sequence of SEQ ID NO: 1 with the exception of the one or more substitutions at positions selected from the group consisting of amino acid residues corresponding to positions 8, 17, 18, 23, 34, 36, 45, 48, 51, 56, 59, 84, 85, 94, 95, 102, 104, 106, 107, 108, 110, 118, 123, 127, 138, 142, 146, 147, 149, 151, 152, 153, 154, 155, 156, and 157 of the amino acid sequence of SEQ ID NO: 1.
21. The method of claim 13 , wherein said adenosine deaminase comprises the amino acid sequence of SEQ ID NO: 1 with the exception of the one or more substitutions at positions selected from the group consisting of amino acid residues corresponding to positions 8, 17, 18, 23, 34, 36, 45, 48, 51, 56, 59, 84, 85, 94, 95, 102, 104, 106, 107, 108, 110, 118, 123, 127, 138, 142, 146, 147, 149, 151, 152, 153, 154, 155, 156, and 157 of the amino acid sequence of SEQ ID NO: 1.
22. The adenosine deaminase of claim 1 , wherein said one or more substitutions are at positions selected from the group consisting of amino acid residues corresponding to positions 23, 36, 48, 51, 84, 106, 108, 123, 142, 146, 147, 152, 155, 156, and 157 of the amino acid sequence of SEQ ID NO: 1.
23. The adenosine deaminase of claim 22 , wherein said one or more substitutions are substitutions selected from the group consisting of W23R, W23L, H36L, P48S, P48A, R51L, L84F, A106V, D108N, H123Y, A142N, S146C, D147Y, R152P, E155V, I156F, and K157N of the amino acid sequence of SEQ ID NO: 1.
24. The adenosine deaminase of claim 22 , wherein said one or more substitutions comprise a group of substitutions at positions selected from the group of substitutions at positions consisting of:
(i) W23, H36, P48, R51, L84, A106, D108, H123, A142, S146, D147, R152, E155, I156, and K157;
(ii) W23, H36, P48, R51, L84, A106, D108, H123, S146, D147, R152, E155, I156, and K157;
(iii) H36, P48, R51, L84, A106, D108, H123, A142, S146, D147, E155, I156, and K157;
(iv) H36, P48, R51, L84, A106, D108, H123, S146, D147, E155, I156, and K157;
(v) H36, R51, L84, A106, D108, H123, S146, D147, E155, I156, and K157;
(vi) L84, A106, D108, H123, D147, E155, and I156;
(vii) A106, D108, D147, and E155;
(viii) A106, and D108; and
(ix) D108; of the amino acid sequence of SEQ ID NO: 1.
25. The adenosine deaminase of claim 22 , wherein said one or more substitutions comprise a group of substitutions selected from the groups of substitutions consisting of:
(i) W23L, H36L, P48A, R51L, L84F, A106V, D108N, H123Y, A142N, S146C, D147Y, R152P, E155V, I156F, and K157N;
(ii) W23R, H36L, P48A, R51L, L84F, A106V, D108N, H123Y, S146C, D147Y, R152P, E155V, I156F, and K157N;
(iii) H36L, P48S, R51L, L84F, A106V, D108N, H123Y, A142N, S146C, D147Y, E155V, I156F, and K157N;
(iv) H36L, P48S, R51L, L84F, A106V, D108N, H123Y, S146C, D147Y, E155V,I156F, and K157N;
(v) H36L, R51L, L84F, A106V, D108N, H123Y, S146C, D147Y, E155V, I156F, and K157N;
(vi) L84F, A106V, D108N, H123Y, D147Y, E155V, and 156F;
(vii) A106V, D108N, D147Y, and E155V;
(viii) A106V, and D108N; and
(ix) D108N; of the amino acid sequence of SEQ ID NO: 1.
26. The base editor of claim 2 further comprising a second adenosine deaminase.
27. The base editor of claim 26 , wherein said second adenosine deaminase is a TadA adenosine deaminase.
28. The base editor of claim 26 , wherein said second adenosine deaminase comprises an amino acid sequence that is at least 90% identical to the amino acid sequence of SEQ ID NO: 1.
29. The base editor of claim 26 , wherein said second adenosine deaminase comprises the amino acid sequence of SEQ ID NO: 1.
30. The adenosine deaminase as in any one of claims 1 , 19 , and 22 - 25 , wherein said at least 90% amino acid sequence identity is based on an alignment against SEQ ID NO: 1, 8, 9, 371, 372, 373, 374, or 375 by NCBI Constraint-based Multiple Alignment Tool (COBALT), and
wherein said COBALT is used with the following parameters:
alignment parameters: Gap penalties-11,-1 and End-Gap penalties-5,-1, CDD Parameters: Use RPS BLAST on; Blast E-value 0.003; Find Conserved columns and Recompute on, and
Query Clustering Parameters: Use query clusters on; Word Size 4; Max cluster distance 0.8; Alphabet Regular.
31. The base editor as in any one of claims 2 - 12 , 20 , and 26 - 29 , wherein said at least 90% amino acid sequence identity is based on an alignment against SEQ ID NO: 1, 8, 9, 371, 372, 373, 374, or 375 by NCBI Constraint-based Multiple Alignment Tool (COBALT), and
wherein said COBALT is used with the following parameters:
alignment parameters: Gap penalties-11,-1 and End-Gap penalties-5,-1, CDD Parameters: Use RPS BLAST on; Blast E-value 0 . 003 ; Find Conserved columns and Recompute on, and
Query Clustering Parameters: Use query clusters on; Word Size 4; Max cluster distance 0.8; Alphabet Regular.
32. The method as in any one of claims 13 - 18 , and 21 , wherein said at least 90% amino acid sequence identity is based on an alignment against SEQ ID NO: 1, 8, 9, 371, 372, 373, 374, or 375 by NCBI Constraint-based Multiple Alignment Tool (COBALT), and
wherein said COBALT is used with the following parameters:
alignment parameters: Gap penalties-11,-1 and End-Gap penalties-5,-1, CDD Parameters: Use RPS BLAST on; Blast E-value 0.003; Find Conserved columns and Recompute on, and
Query Clustering Parameters: Use query clusters on; Word Size 4; Max cluster distance 0.8; Alphabet Regular.