Compositions and methods for making selenocysteine containing polypeptides
Non-naturally occurring tRNA Sec and methods of using them for recombinant expression of proteins engineered to include one or more selenocysteine residues are disclosed. The non-naturally occurring tRNA Sec can be used for recombinant manufacture of selenocysteine containing polypeptides encoded by mRNA without the requirement of an SECIS element. In some embodiments, selenocysteine containing polypeptides are manufactured by co-expressing a non-naturally occurring tRNA Sec a recombinant expression system, such as E. coli , with SerRS, EF-Tu, SelA, or PSTK and SepSecS, and an mRNA with at least one codon that recognizes the anticodon of the non-naturally occurring tRNA Sec .
1. An isolated nucleic acid comprising a nucleic acid sequence encoding a non-naturally occurring tRNA Sec , wherein the non-naturally occurring tRNA Sec is recognized by SerRS, when aminoacylated with serine the Ser-tRNA Sec is a substrate for SelA, and when aminoacylated with seleocysteine the Sec-tRNA Sec is recognized by EF-Tu,
wherein the non-naturally occurring tRNA Sec comprises at least 80% sequence identity to SEQ ID NO:6, 7, or 8.
2. The isolated nucleic acid of claim 1 , wherein the non-naturally occurring tRNA Sec comprises one or more mutations relative to a parent tRNA Sec , wherein the parent tRNA Sec is a variant of a naturally occurring E. coli tRNA Ser , wherein the acceptor stem of E. coli tRNA Sec is replaced with the acceptor stem of E. coli tRNA Sec .
3. The isolated nucleic acid of claim 1 , wherein the non-naturally occurring tRNA Sec comprises at least 90% sequence identity to SEQ ID NO:6, 7, or 8.
4. The isolated nucleic acid of claim 1 , wherein the non-naturally occurring tRNA Sec exhibits tighter binding with SelA than the tRNA of SEQ ID NO:7, while retaining Ser-tRNA formation by SerRS.
5. The isolated nucleic acid of claim 1 , wherein the non-naturally occurring tRNA Sec comprises one or more mutations at positions U8, G9, or A27 in the core region; A14 or G15 in the D-arm; U21 in the D-loop; A52 or U62 in the T-arm; A59 in the T-loop; U44 or G48 in the variable arm; or a combination thereof relative to SEQ ID NO:6, 7, or 8.
6. The isolated nucleic acid of claim 5 , wherein the non-naturally occurring tRNA Sec comprises substitutions at U8, G9, and A27 in the core region; substitutions at A14 and G15 in the D-arm; deletion of U21 in the D-loop; substitutions at A52 and U62 in the T-arm; a substitution at A59 in the T-loop; and the insertion of residues 44 and 48 in the variable arm relative to SEQ ID NO:6, 7, or 8.
7. The isolated nucleic acid of claim 6 , wherein the non-naturally occurring tRNA Sec comprises the following mutations: U8G, G9U, and A27G in the core region; A14U and G15C in the D-arm; deletion of U21 in the D-loop; A52G and U62C in the T-arm; A59C in the T-loop; and the insertion of residues U44 and G48 in the variable arm relative to SEQ ID NO:6, 7, or 8.
8. The isolated nucleic acid of claim 1 , wherein the non-naturally occurring tRNA Sec comprises the backbone of SEQ ID NO:6, 7, or 8, with one or more mutations selected from the group consisting of (i) nucleotide positions 9 and/or 10 remain unchanged or are substituted; (ii) nucleotides 15 and/or 16 remain unchanged or are substituted; (iii) nucleotide 20 remains unchanged or is deleted; (iv) one or both of nucleotides 25 and 26 remain unchanged, one or both of nucleotides 25 and 26 are substituted, a nucleotide is inserted between nucleotides 25 and 26, or a combination thereof; (v) nucleotide 28 remains unchanged or is substituted; (vi) one or two nucleotides are inserted between nucleotides 45 and 46; (vii) one or two nucleotides are inserted between nucleotides 61 and 62; (viii) nucleotide 65 remains the same or is substituted; (ix) nucleotide 72 remains the same or is substituted; (x) nucleotide 75 remains the same or is substituted, or a combination thereof relative to SEQ ID NO:6, 7, or 8.
9. The isolated nucleic acid of claim 1 , wherein the non-naturally occurring tRNA Sec comprises the sequence of any one of SEQ ID NO:59-85, or a variant thereof with a substituted anticodon.
10. The isolated nucleic acid of claim 1 , wherein the non-naturally occurring tRNA Sec comprises the sequence of SEQ ID NO:59, or a variant thereof with a substituted anticodon.
11. The isolated nucleic acid of claim 1 further comprising a heterologous expression control sequence.
12. An expression vector comprising the isolated nucleic acid of claim 1 operably linked to a heterologous expression control sequence.
13. A host cell comprising the isolated nucleic acid of claim 1 .
14. The host cell of claim 13 , wherein the host cell is a prokaryote, archaeon, or eukaryote.
15. The host cell of claim 14 , wherein the prokaryotic cell is E. coli.
16. The host cell of claim 13 , wherein the nucleic acid is incorporated into the genome of the cell.
17. The host cell of claim 16 , wherein the host cell is a genetically recoded organism.
18. A non-naturally occurring tRNA sec comprising a sequence at least 80% identical to SEQ ID NO:6, 7, or 8, wherein the tRNA sec is recognized by SerRS, when aminoacylated with serine the Ser-tRNA Sec is a substrate for SelA, and when aminoacylated with seleocysteine the Sec-tRNA Sec is recognized by EF-Tu.
19. The non-naturally occurring tRNA sec of claim 18 , wherein the tRNA sec exhibits tighter binding with SelA than the tRNA of SEQ ID NO:7, while retaining Ser-tRNA formation by SerRS.
20. A non-naturally occurring tRNA sec comprising the nucleic acid sequence of any one of SEQ ID NO:59-85, or a variant thereof with a substituted anticodon.