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A Cassette Approach for the Identification of Intein Insertion Sites

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Split Inteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1495))

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Abstract

Over the past decade split inteins have established themselves as powerful tools for protein engineering, protein semisynthesis, and protein functional control approaches. Their key advantage lies in the protein trans-splicing (PTS) reaction that enables posttranslational protein assembly from two independent, even synthetic, peptide precursors. However, since most split intein applications deal with fragmentation and modification of proteins, various issues can arise, ranging from reduced stability to impairment of protein folding. In this chapter I address how the usage of DNA encoded intein cassettes can streamline and speed up the identification of functional split intein insertion sites in novel proteins of interest (POI).

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References

  1. Gimble FS, Thorner J (1992) Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae. Nature 357(6376):301–306. doi:10.1038/357301a0

    Article  CAS  PubMed  Google Scholar 

  2. Lennard KR, Tavassoli A (2014) Peptides come round: using SICLOPPS libraries for early stage drug discovery. Chemistry 20(34):10608–10614. doi:10.1002/chem.201403117

    Article  CAS  PubMed  Google Scholar 

  3. Mootz HD (2009) Split inteins as versatile tools for protein semisynthesis. Chembiochem 10(16):2579–2589. doi:10.1002/cbic.200900370

    Article  CAS  PubMed  Google Scholar 

  4. Shah NH, Muir TW (2014) Inteins: nature’s gift to protein chemists. Chem Sci 5(1):446–461. doi:10.1039/C3SC52951G

    Article  CAS  PubMed  Google Scholar 

  5. Topilina NI, Mills KV (2014) Recent advances in in vivo applications of intein-mediated protein splicing. Mob DNA 5(1):5. doi:10.1186/1759-8753-5-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Volkmann G, Iwai H (2010) Protein trans-splicing and its use in structural biology: opportunities and limitations. Mol Biosyst 6(11):2110–2121. doi:10.1039/c0mb00034e

    Article  CAS  PubMed  Google Scholar 

  7. Wood DW, Camarero JA (2014) Intein applications: from protein purification and labeling to metabolic control methods. J Biol Chem 289(21):14512–14519. doi:10.1074/jbc.R114.552653

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Perler FB (2002) InBase: the intein database. Nucleic Acids Res 30(1):383–384

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Dassa B, London N, Stoddard BL, Schueler-Furman O, Pietrokovski S (2009) Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family. Nucleic Acids Res 37(8):2560–2573. doi:10.1093/nar/gkp095

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Brenzel S, Kurpiers T, Mootz HD (2006) Engineering artificially split inteins for applications in protein chemistry: biochemical characterization of the split Ssp DnaB intein and comparison to the split Sce VMA intein. Biochemistry 45(6):1571–1578. doi:10.1021/bi051697+

    Article  CAS  PubMed  Google Scholar 

  11. Ludwig C, Pfeiff M, Linne U, Mootz HD (2006) Ligation of a synthetic peptide to the N terminus of a recombinant protein using semisynthetic protein trans-splicing. Angew Chem Int Ed Engl 45(31):5218–5221. doi:10.1002/anie.200600570

    Article  CAS  PubMed  Google Scholar 

  12. Mills KV, Johnson MA, Perler FB (2014) Protein splicing: how inteins escape from precursor proteins. J Biol Chem 289(21):14498–14505. doi:10.1074/jbc.R113.540310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Volkmann G, Mootz HD (2013) Recent progress in intein research: from mechanism to directed evolution and applications. Cell Mol Life Sci 70(7):1185–1206. doi:10.1007/s00018-012-1120-4

    Article  CAS  PubMed  Google Scholar 

  14. Carvajal-Vallejos P, Pallisse R, Mootz HD, Schmidt SR (2012) Unprecedented rates and efficiencies revealed for new natural split inteins from metagenomic sources. J Biol Chem 287(34):28686–28696. doi:10.1074/jbc.M112.372680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Shah NH, Dann GP, Vila-Perello M, Liu Z, Muir TW (2012) Ultrafast protein splicing is common among cyanobacterial split inteins: implications for protein engineering. J Am Chem Soc 134(28):11338–11341. doi:10.1021/ja303226x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Zettler J, Schutz V, Mootz HD (2009) The naturally split Npu DnaE intein exhibits an extraordinarily high rate in the protein trans-splicing reaction. FEBS Lett 583(5):909–914. doi:10.1016/j.febslet.2009.02.003

    Article  CAS  PubMed  Google Scholar 

  17. Mootz HD, Blum ES, Tyszkiewicz AB, Muir TW (2003) Conditional protein splicing: a new tool to control protein structure and function in vitro and in vivo. J Am Chem Soc 125(35):10561–10569. doi:10.1021/ja0362813

    Article  CAS  PubMed  Google Scholar 

  18. Mootz HD, Blum ES, Muir TW (2004) Activation of an autoregulated protein kinase by conditional protein splicing. Angew Chem Int Ed Engl 43(39):5189–5192. doi:10.1002/anie.200460941

    Article  CAS  PubMed  Google Scholar 

  19. Tyszkiewicz AB, Muir TW (2008) Activation of protein splicing with light in yeast. Nat Methods 5(4):303–305. doi:10.1038/nmeth.1189

    CAS  PubMed  Google Scholar 

  20. Selgrade DF, Lohmueller JJ, Lienert F, Silver PA (2013) Protein scaffold-activated protein trans-splicing in mammalian cells. J Am Chem Soc 135(20):7713–7719. doi:10.1021/ja401689b

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Buskirk AR, Ong YC, Gartner ZJ, Liu DR (2004) Directed evolution of ligand dependence: small-molecule-activated protein splicing. Proc Natl Acad Sci U S A 101(29):10505–10510. doi:10.1073/pnas.0402762101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Berrade L, Kwon Y, Camarero JA (2010) Photomodulation of protein trans-splicing through backbone photocaging of the DnaE split intein. Chembiochem 11(10):1368–1372. doi:10.1002/cbic.201000157

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Binschik J, Zettler J, Mootz HD (2011) Photocontrol of protein activity mediated by the cleavage reaction of a split intein. Angew Chem Int Ed Engl 50(14):3249–3252. doi:10.1002/anie.201007078

    Article  CAS  PubMed  Google Scholar 

  24. Zettler J, Eppmann S, Busche A, Dikovskaya D, Dotsch V, Mootz HD, Sonntag T (2013) SPLICEFINDER—a fast and easy screening method for active protein trans-splicing positions. PLoS One 8(9), e72925. doi:10.1371/journal.pone.0072925

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Lee YT, Su TH, Lo WC, Lyu PC, Sue SC (2012) Circular permutation prediction reveals a viable backbone disconnection for split proteins: an approach in identifying a new functional split intein. PLoS One 7(8):e43820. doi:10.1371/journal.pone.0043820

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Sonntag T, Mootz HD (2011) An intein-cassette integration approach used for the generation of a split TEV protease activated by conditional protein splicing. Mol Biosyst 7(6):2031–2039. doi:10.1039/c1mb05025g

    Article  CAS  PubMed  Google Scholar 

  27. Nunn CM, Jeeves M, Cliff MJ, Urquhart GT, George RR, Chao LH, Tscuchia Y, Djordjevic S (2005) Crystal structure of tobacco etch virus protease shows the protein C terminus bound within the active site. J Mol Biol 350(1):145–155. doi:10.1016/j.jmb.2005.04.013

    Article  CAS  PubMed  Google Scholar 

  28. van den Ent F, Lowe J (2006) RF cloning: a restriction-free method for inserting target genes into plasmids. J Biochem Biophys Methods 67(1):67–74. doi:10.1016/j.jbbm.2005.12.008

    Article  CAS  PubMed  Google Scholar 

  29. Silver PA, Chiang A, Sadler I (1988) Mutations that alter both localization and production of a yeast nuclear protein. Genes Dev 2(6):707–717

    Article  CAS  PubMed  Google Scholar 

  30. Gietz D, St Jean A, Woods RA, Schiestl RH (1992) Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res 20(6):1425

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Rose MD, Winston F, Hieter P (1990) Methods in yeast genetics: a laboratory course manual. Cold Spring Harbor, New York

    Google Scholar 

  32. Schiestl RH, Gietz RD (1989) High efficiency transformation of intact yeast cells using single stranded nucleic acids as a carrier. Curr Genet 16(5–6):339–346

    Article  CAS  PubMed  Google Scholar 

  33. Muona M, Aranko AS, Raulinaitis V, Iwai H (2010) Segmental isotopic labeling of multi-domain and fusion proteins by protein trans-splicing in vivo and in vitro. Nat Protoc 5(3):574–587. doi:10.1038/nprot.2009.240

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

I thank the Mootz lab for continuous support and suggestions, in particular Joachim Zettler for his contribution to the PTS project. The author acknowledges funding from the Fonds der Chemischen Industrie, the National Institutes of Health (R01 GM074868 and R01 DK083834), and the Kieckhefer Foundation.

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Correspondence to Tim Sonntag .

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Sonntag, T. (2017). A Cassette Approach for the Identification of Intein Insertion Sites. In: Mootz, H. (eds) Split Inteins. Methods in Molecular Biology, vol 1495. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6451-2_16

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  • DOI: https://doi.org/10.1007/978-1-4939-6451-2_16

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6449-9

  • Online ISBN: 978-1-4939-6451-2

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