Ligand-dependent protein splicing
Ligand-dependent inteins allow for modulation of a protein's activity in vivo. Upon binding of the ligand to the ligand-dependent intein inserted into the protein of interest, the hybrid protein undergoes protein splicing removing the intein. The activity of the spliced protein is then restored. A 4-hydroxytamoxifen-dependent intein based on the M. tuberculosis RecA intein is prepared and demonstrated in a variety of exteins contexts. The invention provides a system for engineering other ligand-dependent inteins and using them, including the ligand-dependent inteins themselves, hybrid proteins with the inserted ligand-dependent inteins, polynucleotides encoding inteins and hybrid proteins, and engineered cells. Kits with the materials and reagents necessary for preparing and using ligand-dependent inteins are also included.
1. A method of producing and selecting a ligand-dependent intein, the method comprising the steps of:
(a) providing a polynucleotide encoding a hybrid protein comprising a single polypeptide having a target protein with a ligand-dependent intein embedded in the sequence of said target protein, wherein said hybrid protein has the structure:
target(N)-Intein(N)-ligand binding domain-Intein(C)-target(C);
(b) mutating the sequence of the polynucleotide encoding the hybrid protein to generate a plurality of mutated polynucleotides;
(c) transforming the polynucleotides produced in step (b) into cells;
(d) selecting those cells having ligand-dependent intein activity based on the activity of the ligand-dependent intein in the presence of an appropriate ligand that binds the ligand binding domain, wherein a positive selection is based on the ability of the ligand-binding intein to excise itself from the target protein upon ligand binding and produce a functional target protein; and
(e) optionally isolating the polynucleotides produced from the cells identified in step (d).
2. The method of claim 1 , wherein the cells are bacterial cells.
3. The method of claim 1 , wherein the cells are yeast cells.
4. The method of claim 1 , wherein the cells are mammalian cells.
5. The method of claim 1 , wherein the target protein without the ligand-dependent intein confers antibiotic resistance.
6. The method of claim 1 , wherein the target protein without the ligand-dependent intein confers an ability to grow on a medium lacking a nutrient.
7. The method of claim 1 , wherein the target protein without the ligand-dependent intein is fluorescent.
8. The method of claim 1 , wherein the target protein without the ligand-dependent intein is an aminoglycoside phosphorylase.
9. The method of claim 1 , wherein target protein without the ligand-dependent intein is β-galactosidase.
10. The method of claim 1 , wherein the ligand is a small molecule.
11. The method of claim 1 , wherein the ligand is 4-hydroxytamoxifen.
12. The method of claim 1 , wherein the step of mutating comprises mutating polynucleotide sequence that encodes the ligand-dependent intein.
13. The method of claim 1 , wherein the step of mutating comprises mutating the polynucleotide by error-prone polymerase chain reaction (PCR).
14. The method of claim 1 , wherein the steps of mutating, transforming, and selecting are repeated to produce a ligand-dependent intein.
15. The method of claim 1 , wherein the step of selecting is based on antibiotic resistance.
16. The method of claim 1 , wherein the ligand-dependent intein has the structure:
intein(N-terminus)-ligand binding domain-intein (C-terminus)
whereby when the intein is inserted into a protein sequence, the intein exhibits minimal protein splicing activity in the absence of ligand.
17. The method of claim 1 , wherein the ligand is selected from the group consisting of a small molecule, a peptide, a protein, a polynucleotide, an amino acid, a nucleotide, and combinations thereof.
18. The method of claim 1 , wherein the ligand binding domain is derived from the ligand binding domain of the estrogen receptor.
19. The method of claim 1 , wherein the N- and C-terminal portions of the intein are derived from the RecA intein of Mycobacterium tuberculosis.
20. The method of claim 1 , wherein the N- and C-terminal portions of the intein are derived from the VMA intein of Saccharomyces cerevisiae.
21. The method of claim 1 , wherein the intein has the primary amino acid sequence:
(SEQ ID NO: 1)
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFD
QGTRDVIGLRIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAGPGGSG
NSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRE
LVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLL
FAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIIL
LNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQR
LAQLLLILSHIRHMSNKRMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAGG
SGASRVQAFADALDDKFLHDMLAEELRYSVIREVLPTRRARTFDLEVEEL
HTLVAEGVVVHN.
22. The method of claim 1 , wherein the intein is at least 90% homologous to the sequence:
(SEQ ID NO: 1)
LAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFDQ
GTRDVIGLRIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAGPGGSGN
SLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADREL
VHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLF
APNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILL
NSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRL
AQLLLILSHIRHMSNKRMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAGGS
GASRVQAFADALDDKFLHDMLAEELRYSVIREVLPTRRARTFDLEVEELH
TLVAEGVVVHN.
23. The method of claim 1 , wherein the intein is at least 95% homologous to the sequence:
(SEQ ID NO: 1)
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFD
QGTRDVIGLRIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAGPGGSG
NSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRE
LVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLL
FAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIIL
LNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQR
LAQLLLILSHIRHMSNKRMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAGG
SGASRVQAFADALDDKFLHDMLAEELRYSVIREVLPTRRARTFDLEVEEL
HTLVAEGVVVHN.
24. The method of claim 1 , wherein the intein is at least 98% homologous to the sequence:
(SEQ ID NO: 1)
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFD
QGTRDVIGLRIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAGPGGSG
NSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRE
LVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLL
FAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIIL
LNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQR
LAQLLLILSHIRHMSNKRMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAGG
SGASRVQAFADALDDKFLHDMLAEELRYSVIREVLPTRRARTFDLEVEEL
HTLVAEGVVVHN.
25. The method of claim 1 , wherein the intein has the primary amino acid sequence selected from the group consisting of:
1-1:
(SEQ ID NO: 7)
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFD
QGTRDVIGLRIAGGAILWATPDHKVLTEYGWRAAGELRKGDRVAGPGGSG
NSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRE
LVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLL
FAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIIL
LNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQR
LAQLLLILSHIRHMSNKRMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAGG
SGASRVQAFADALDDKFLHDMLAEELRYSVIREVLPTRRARTFDLEVEEL
HTLVAEGVVVHN;
1-5:
(SEQ ID NO: 8)
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFD
QGTRDVIGLRIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAGPGGSG
NSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRE
LVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLL
FAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIIL
LNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQR
LAQLLLILSHIRHMSNKRMEHLYSMKCKNEVPLHDLLLEMLDAHRLHAGG
SGASRVQAFADALDDKFLHDMLAEELRYSVIREVLPTRRARTFDLEVEEL
HTLVAEGVVVHN;
1-14:
(SEQ ID NO: 9)
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFD
QGTRDVIGLRIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAGPGGSG
NSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRE
LVHMINWAKRVPGFVDLTLHDQAHLLECAWLEILMIGLVWRSMEHPGKLL
FAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIIL
LNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQR
LAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAGG
SGASRVQAFADALDDKFLHDMLAEELRYSVIREVLPTRRARTFDLEVEEL
HTLVAEGVVVHN
1-16:
(SEQ ID NO: 10)
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLHARPVVSWFD
QGTRDVIGLRIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAGPGGSG
NSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRE
LVHMINWAKRVPGFVDLTLHDQAHLLECAWLEILMIGLVWRSMEHPGKLL
FAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIIL
LNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQR
LAQLLLILSHIRHMSNKRMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAGG
SGASRVQAFADALDDRFQHDMLAEELRYSVIREVLPTRRARTFDLEVEEL
HTLVAEGVVVHN;
2-4:
(SEQ ID NO: 11)
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAAAKDGTLLARPVVSWFD
QGTRDVIGLRIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAGPGGSG
NSLALSLTADQMVSALLDAEPPILYSEYDPTSPFSEASMMGLLTNLADRE
LVHMINWAKRVPGFVDLTLHDQAHLLECAWLEILMIGLVWRSMEHPGKLL
FAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIIL
LNSGVYTFLSSTLKSLEEKDHIHRALDKITDTLIHLMAKAGLTLQQQHQR
LAQLLLILSHIRHMSNKGMEHLYSMKYKNVVPLYDLLLEMLDAHRLHAGG
SGASRVQAFADALDDKFLHDMLAEELRYSVIREVLPTRRARTFDLEVEEL
HTLVAEGVVVHN;
2-5:
(SEQ ID NO: 12)
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHMVAAAKDGTLHARPVVSWFD
QGTRDVIGLRIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAGPGGSG
NSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRE
LVHMINWAKRVPGFVDLTLHDQAHLLECAWLEILMIGLVWRSMEHPGKLL
FAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIIL
LNSGVYTFLSSTLKPLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQR
LAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAGG
SGASRVQAFADALDDKFLHDMLAEELRYSVIREVLPTLRARTFDLEVEEL
HTLVAEGVVVHN;
3-2:
(SEQ ID NO: 13)
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAVAKDGTLLARPVVSWFD
QGTRDVIGLRIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAGPGGSG
NSLALSLTADQMVSALLDAEPPILYSEYDPTSPFSEASMMGLLTNLADRE
LVHMINWAKRVPGFVDLTLHDQAHLLECAWLEILMIGLVWRSMEHPGKLL
FAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIIL
LNSGVYTFLSSTLKSLEEKDHIHRALDKITDTLIHLMAKAGLTLQQQHQR
LAQLLLILSHIRHMSNKGMEHLYSMKYTNVVPLYDLLLEMLDAHRLHAGG
SGASRVQAFADALDDKFLHDMLAEELRYSVIREVLPTRRARTFDLEVEEL
HTLVAEGVVVHN;
and
Min. 3-2:
(SEQ ID NO: 14)
CLAEGTRIFDPVTGTTHRIEDVVDGRKPIHVVAVAKDGTLLARPVVSWFD
QGTRDVIGLRIAGGAIVWATPDHKVLTEYGWRAAGELRKGDRVAGPGGSG
NSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRE
LVHMINWAKRVPGFVDLTLHDQAHLLECAWLEILMIGLVWRSMEHPGKLL
FAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIIL
LNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQR
LAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAGG
SGASRVQAFADALDDKFLHDMLAEELRYSVIREVLPTRRARTFDLEVEEL
HTLVAEGVVVHN.