Polynucleotides encoding mutant hydrolase proteins with enhanced kinetics and functional expression

1. An isolated polynucleotide comprising a first sequence encoding a mutant dehalogenase that has dehalogenase activity and forms a covalent bond with a dehalogenase substrate, said mutant dehalogenase having at least 85% amino acid sequence identity to the polypeptide of SEQ ID NO: 1, wherein said mutant dehalogenase further comprises (a) substitutions corresponding to substitutions S58T, D78G, A155T, A172T, K175M, C176G, A224E, P291S, and A292T in SEQ ID NO: 1, and (b) substitutions at positions corresponding to positions 272 and/or 106 of SEQ ID NO: 1.

2. The isolated polynucleotide of claim 1 , wherein said mutant dehalogenase further comprises one or more substitutions at positions corresponding to positions in SEQ ID NO: 1 selected from the group consisting of positions 5, 7, 11, 12, 20, 30, 32, 47, 54, 55, 56, 60, 65, 80, 82, 87, 88, 94, 96, 109, 113, 116, 117, 118, 121, 124, 128, 131, 134, 136, 144, 147, 150, 151, 157, 160, 161, 164, 165, 167, 180, 182, 183, 187, 195, 197, 204, 218, 221, 227, 231, 233, 250, 256, 257, 263, 264, 273, 277, 280, 282, 288, and 294.

3. The isolated polynucleotide of claim 1 , wherein said mutant dehalogenase further comprises 5 or more substitutions at positions corresponding to positions in SEQ ID NO: 1 selected from the group consisting of positions 47, 87, 88, 128, 160, 167, 195, 227, 257, 264, and 273.

4. The isolated polynucleotide of claim 1 , wherein said mutant dehalogenase further comprises substitutions at positions corresponding to positions 47, 87, 88, 128, 160, 167, 195, 227, 257, 264, and 273 of SEQ ID NO: 1.

5. The isolated polynucleotide of claim 1 , wherein said mutant dehalogenase comprises substitutions at positions corresponding to both of positions 106 and 272 of SEQ ID NO: 1.

6. The isolated polynucleotide of claim 1 , wherein said mutant dehalogenase further comprises 20 or more substitutions at positions corresponding to positions in SEQ ID NO: 1 selected from the group consisting of positions 5, 7, 11, 12, 20, 30, 32, 47, 54, 55, 56, 60, 65, 80, 82, 87, 88, 94, 96, 109, 113, 116, 117, 118, 121, 124, 128, 131, 134, 136, 144, 147, 150, 151, 157, 160, 161, 164, 165, 167, 180, 182, 183, 187, 195, 197, 204, 218, 221, 227, 231, 233, 250, 256, 257, 263, 264, 273, 277, 280, 282, 288, and 294 of SEQ ID NO: 1.

7. The polynucleotide of claim 1 , further comprising a second sequence encoding a polypeptide of interest linked in frame to the first sequence, such that expression of the polynucleotide results in a fusion polypeptide comprising the mutant dehalogenase and the polypeptide of interest.

8. The polynucleotide of claim 7 , wherein the polypeptide of interest is at the C-terminus of the fusion polypeptide.

9. The polynucleotide of claim 7 , wherein the polypeptide of interest is at the N-terminus of the fusion polypeptide.

10. The polynucleotide of claim 7 , further comprising a sequence encoding a polypeptide linker linking the polypeptide of interest and the mutant dehalogenase.

11. The polynucleotide of claim 10 , wherein the linker comprises a protease recognition sequence.

12. The polynucleotide of claim 11 , wherein the linker comprises SEQ ID NO:31 (EPTTEDLYFQS/C) or SEQ ID NO: 38 (EPTTEDLYFQS/CDN).

13. A vector comprising a polynucleotide comprising a first sequence encoding a mutant dehalogenase that has dehalogenase activity and forms a covalent bond with a dehalogenase substrate, said mutant dehalogenase having at least 85% amino acid sequence identity to the polypeptide of SEQ ID NO: 1, wherein said mutant dehalogenase further comprises (a) substitutions corresponding to substitutions S58T, D78G, A155T, A172T, K175M, C176G, A224E, P291S, and A292T in SEQ ID NO: 1, and (b) substitutions at positions corresponding to positions 272 and/or 106 of SEQ ID NO: 1.

14. The vector of claim 13 , wherein the polynucleotide is operably linked to a promoter.

15. A kit comprising a compound comprising a dehalogenase substrate and either:

(a) a polynucleotide comprising a first sequence encoding a mutant dehalogenase that has dehalogenase activity and forms a covalent bond with a dehalogenase substrate, said mutant dehalogenase having at least 85% amino acid sequence identity to the polypeptide of SEQ ID NO: 1, wherein said mutant dehalogenase further comprises (i) substitutions corresponding to substitutions S58T, D78G, A155T, A172T, K175M, C176G, A224E, P291S, and A292T in SEQ ID NO: 1, and (ii) substitutions at positions corresponding to positions 272 and/or 106 of SEQ ID NO: 1;

(b) a vector that comprises the polynucleotide of (a); or

(c) a vector that comprises the polynucleotide of (a) operably linked to a promoter.

16. The kit of claim 15 , wherein the compound comprising a dehalogenase substrate has the formula (I):

R-linker-A-X  (I)

wherein the linker is a 3 to 30 atom straight or branched chain comprising C, N, S, and/or O;

wherein A-X is a substrate for a dehalogenase;

wherein X is a halogen; and

wherein R is a functional group selected from the list consisting of a fluorophore, an epitope-recognized ligand, a luminophore, a solid support, a contrast agent, a radionuclide, a chelating agent, a drug, and a toxin.

17. An isolated cell comprising a compound comprising a dehalogenase substrate and either:

(a) a polynucleotide comprising a first sequence encoding a mutant dehalogenase that has dehalogenase activity and forms a covalent bond with a dehalogenase substrate, said mutant dehalogenase having at least 85% amino acid sequence identity to the polypeptide of SEQ ID NO: 1, wherein said mutant dehalogenase further comprises (i) substitutions corresponding to substitutions S58T, D78G, A155T, A172T, K175M, C176G, A224E, P291S, and A292T in SEQ ID NO: 1, and (ii) substitutions at positions corresponding to positions 272 and/or 106 of SEQ ID NO: 1;

(b) a vector that comprises the polynucleotide of (a); or

(c) a vector that comprises the polynucleotide of (a) operably linked to a promoter.