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, or a variant thereof, and when aminoacylated with serine the Ser-tRNA Sec is a substrate for SelA or a variant thereof,
wherein the tRNA Sec is a variant of SEQ ID NO:1 wherein one or more base pairs selected from the group consisting of C7•G66, G49•U65, and C50•G64 are mutated,
wherein when aminoacylated with seleocysteine the Sec-tRNA Sec is recognized by EF-Tu, and
wherein the anticodon of the non-naturally occurring tRNA Sec hybridizes to a stop codon.
2. The isolated nucleic acid of claim 1 further comprising a heterologous expression control sequence.
3. An expression vector comprising the isolated nucleic acid of claim 2 .
4. A host cell comprising the isolated nucleic acid of claim 1 .
5. The host cell of claim 4 wherein the host cell is a prokaryote, archaeon, or eukaryote.
6. The host cell of claim 5 wherein the prokaryotic cell is E. coli.
7. The host cell of claim 6 wherein the endogenous E. coli genes encoding selA, selB, and selC, or combinations thereof have been deleted or mutated to reduce or prevent expression of SelA, SelB, or SelC protein.
8. The host cell of claim 4 wherein the host cell express one or more of the proteins selected from the group consisting of SerRS, EF-Tu, and SelA.
9. The host cell of claim 4 wherein the host cell expresses SerRS, EF-Tu, and SelA.
10. A method of making a recombinant selenocysteine containing protein comprising co-expressing a non-naturally occurring tRNA Sec encoded by the nucleic acid of claim 1 in a host cell also expressing SerRS, EF-Tu, and SelA, with a polynucleotide comprising a codon that hybridizes with the anticodon of the non-naturally occurring tRNA Sec .
11. The method of claim 10 wherein the codon of the polynucleotide that hybridizes with the anticodon of the non-naturally occurring tRNA Sec was substituted for a codon encoding a cysteine in a reference sequence at least 90% identical to the polynucleotide sequence.
12. The method of claim 11 wherein the polynucleotide encodes an enzyme, cofactor or an antibody.
13. The method of claim 10 further comprising purifying the recombinant selenocysteine containing protein by chromatography comprising an activated thiol sepherose.
14. A non-naturally occurring tRNA Sec encoded by the nucleic acid of claim 1 .
15. The host cell of claim 4 wherein the nucleic acid is integrated into the host cell's genome.
16. A tRNA Sec comprising at least 90% sequence identity to SEQ ID NO:1, wherein one or more nucleotides selected from group consisting of 8, 67, 68, 82, 83, and 84 are substituted relative to SEQ ID NO:1, wherein the anticodon of nucleotides 35-37 of SEQ ID NO:1 are CUA (amber), UCA (opal), or UUA (ochre), and wherein the tRNA Sec is a substrate for EF-Tu when aminoacylated.
17. A nucleic acid encoding a tRNA Sec comprising at least 90% sequence identity to SEQ ID NO:1, wherein one or more nucleotides selected from group consisting of 8, 67, 68, 82, 83, and 84 are substituted relative to SEQ ID NO:1, wherein the anticodon of nucleotides 35-37 of SEQ ID NO:1 are CUA (amber), UCA (opal), or UUA (ochre), and wherein the tRNA Sec is a substrate for EF-Tu when aminoacylated.
18. The nucleic acid of claim 17 further comprising a heterologous expression control sequence.
19. An expression vector comprising the nucleic acid of claim 17 .
20. A host cell comprising the nucleic acid of claim 17 .