Skip to main content

Protein Splicing: From the Foundations to the Development of Biotechnological Applications

  • Protocol
  • First Online:
Expressed Protein Ligation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2133))

Abstract

Expressed protein ligation is a simple and powerful method in protein engineering to introduce sequences of unnatural amino acids, posttranslational modifications, and biophysical probes into proteins of any size. This methodology has been developed based on the knowledge obtained from protein splicing. Protein splicing is a multistep biochemical reaction that includes the concomitant cleavage and formation of peptide bonds carried out by self-processing domains named inteins. The natural substrates of protein splicing are essential proteins found in intein-containing organisms; inteins are also functional in nonnative frameworks and can be used to alter nearly any protein’s primary amino acid sequence. Accordingly, different reactivity features of inteins have been largely exploited to manipulate proteins in countless methods encompassing fields from biochemical research to the development of biotechnological applications including the study of disease progression and validation of potential drug candidates. Here, we review almost three decades of research to uncover the chemical and biochemical enigmas of protein splicing and the development of inteins as potent protein engineering tools.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Kane PM, Yamashiro CT, Wolczyk DF, Neff N, Goebl M, Stevens TH (1990) Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H(+)-adenosine triphosphatase. Science 250(4981):651–657

    Article  CAS  Google Scholar 

  2. Hirata R, Ohsumk Y, Nakano A, Kawasaki H, Suzuki K, Anraku Y (1990) Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae. J Biol Chem 265(12):6726–6733

    CAS  PubMed  Google Scholar 

  3. Perler FB (2002) InBase: the Intein Database. Nucleic Acids Res 30(1):383–384

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  5. Porter JA, Ekker SC, Park WJ, von Kessler DP, Young KE, Chen CH, Ma Y, Woods AS, Cotter RJ, Koonin EV, Beachy PA (1996) Hedgehog patterning activity: role of a lipophilic modification mediated by the carboxy-terminal autoprocessing domain. Cell 86(1):21–34

    Article  CAS  Google Scholar 

  6. Hall TM, Porter JA, Young KE, Koonin EV, Beachy PA, Leahy DJ (1997) Crystal structure of a Hedgehog autoprocessing domain: homology between Hedgehog and self-splicing proteins. Cell 91(1):85–97

    Article  CAS  Google Scholar 

  7. Varjosalo M, Taipale J (2008) Hedgehog: functions and mechanisms. Genes Dev 22(18):2454–2472. https://doi.org/10.1101/gad.1693608

    Article  CAS  PubMed  Google Scholar 

  8. Perler FB (1998) Protein splicing of inteins and hedgehog autoproteolysis: structure, function, and evolution. Cell 92(1):1–4

    Article  CAS  Google Scholar 

  9. Pietrokovski S (1998) Modular organization of inteins and C-terminal autocatalytic domains. Protein Sci 7(1):64–71. https://doi.org/10.1002/pro.5560070106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Perler FB (1999) A natural example of protein trans-splicing. Trends Biochem Sci 24(6):209–211

    Article  CAS  Google Scholar 

  11. Chevalier BS, Stoddard BL (2001) Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res 29(18):3757–3774

    Article  CAS  Google Scholar 

  12. Giriat I, Muir TW, Perler FB (2001) Protein splicing and its applications. Genet Eng (NY) 23:171–199

    Article  CAS  Google Scholar 

  13. Chong S, Williams KS, Wotkowicz C, Xu MQ (1998) Modulation of protein splicing of the Saccharomyces cerevisiae vacuolar membrane ATPase intein. J Biol Chem 273(17):10567–10577

    Article  CAS  Google Scholar 

  14. Chong S, Xu MQ (1997) Protein splicing of the Saccharomyces cerevisiae VMA intein without the endonuclease motifs. J Biol Chem 272(25):15587–15590

    Article  CAS  Google Scholar 

  15. Caspi J, Amitai G, Belenkiy O, Pietrokovski S (2003) Distribution of split DnaE inteins in cyanobacteria. Mol Microbiol 50(5):1569–1577

    Article  CAS  Google Scholar 

  16. 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. https://doi.org/10.1093/nar/gkp095

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. 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. https://doi.org/10.1074/jbc.M112.372680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Thiel IV, Volkmann G, Pietrokovski S, Mootz HD (2014) An atypical naturally split intein engineered for highly efficient protein labeling. Angew Chem Int Ed Engl 53(5):1306–1310. https://doi.org/10.1002/anie.201307969

    Article  CAS  PubMed  Google Scholar 

  19. Bachmann AL, Mootz HD (2015) An unprecedented combination of serine and cysteine nucleophiles in a split intein with an atypical split site. J Biol Chem 290(48):28792–28804. https://doi.org/10.1074/jbc.M115.677237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Tori K, Dassa B, Johnson MA, Southworth MW, Brace LE, Ishino Y, Pietrokovski S, Perler FB (2010) Splicing of the mycobacteriophage Bethlehem DnaB intein: identification of a new mechanistic class of inteins that contain an obligate block F nucleophile. J Biol Chem 285(4):2515–2526. https://doi.org/10.1074/jbc.M109.069567

    Article  CAS  PubMed  Google Scholar 

  21. Xu MQ, Perler FB (1996) The mechanism of protein splicing and its modulation by mutation. EMBO J 15(19):5146–5153

    Article  CAS  Google Scholar 

  22. Sun P, Ye S, Ferrandon S, Evans TC, Xu MQ, Rao Z (2005) Crystal structures of an intein from the split dnaE gene of Synechocystis sp. PCC6803 reveal the catalytic model without the penultimate histidine and the mechanism of zinc ion inhibition of protein splicing. J Mol Biol 353(5):1093–1105. https://doi.org/10.1016/j.jmb.2005.09.039

    Article  CAS  PubMed  Google Scholar 

  23. Du Z, Zheng Y, Patterson M, Liu Y, Wang C (2011) pK(a) coupling at the intein active site: implications for the coordination mechanism of protein splicing with a conserved aspartate. J Am Chem Soc 133(26):10275–10282. https://doi.org/10.1021/ja203209f

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Frutos S, Goger M, Giovani B, Cowburn D, Muir TW (2010) Branched intermediate formation stimulates peptide bond cleavage in protein splicing. Nat Chem Biol 6(7):527–533. https://doi.org/10.1038/nchembio.371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M, Kretz K, Lin X, Mathur E, Ni J, Podar M, Richardson T, Sutton GG, Simon M, Soll D, Stetter KO, Short JM, Noordewier M (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A 100(22):12984–12988. https://doi.org/10.1073/pnas.1735403100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Choi JJ, Nam KH, Min B, Kim SJ, Soll D, Kwon ST (2006) Protein trans-splicing and characterization of a split family B-type DNA polymerase from the hyperthermophilic archaeal parasite Nanoarchaeum equitans. J Mol Biol 356(5):1093–1106. https://doi.org/10.1016/j.jmb.2005.12.036

    Article  CAS  PubMed  Google Scholar 

  27. Southworth MW, Benner J, Perler FB (2000) An alternative protein splicing mechanism for inteins lacking an N-terminal nucleophile. EMBO J 19(18):5019–5026. https://doi.org/10.1093/emboj/19.18.5019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Chong S, Shao Y, Paulus H, Benner J, Perler FB, Xu MQ (1996) Protein splicing involving the Saccharomyces cerevisiae VMA intein. The steps in the splicing pathway, side reactions leading to protein cleavage, and establishment of an in vitro splicing system. J Biol Chem 271(36):22159–22168

    Article  CAS  Google Scholar 

  29. Paulus H (2000) Protein splicing and related forms of protein autoprocessing. Annu Rev Biochem 69:447–496. https://doi.org/10.1146/annurev.biochem.69.1.447

    Article  CAS  PubMed  Google Scholar 

  30. Muir TW (2003) Semisynthesis of proteins by expressed protein ligation. Annu Rev Biochem 72:249–289. https://doi.org/10.1146/annurev.biochem.72.121801.161900

    Article  CAS  PubMed  Google Scholar 

  31. Mootz HD, Muir TW (2002) Protein splicing triggered by a small molecule. J Am Chem Soc 124(31):9044–9045

    Article  CAS  Google Scholar 

  32. Vila-Perello M, Muir TW (2010) Biological applications of protein splicing. Cell 143(2):191–200. https://doi.org/10.1016/j.cell.2010.09.031

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  34. Muir TW (1995) A chemical approach to the construction of multimeric protein assemblies. Structure 3(7):649–652

    Article  CAS  Google Scholar 

  35. Giriat I, Muir TW (2003) Protein semi-synthesis in living cells. J Am Chem Soc 125(24):7180–7181. https://doi.org/10.1021/ja034736i

    Article  CAS  PubMed  Google Scholar 

  36. Cheriyan M, Perler FB (2009) Protein splicing: a versatile tool for drug discovery. Adv Drug Deliv Rev 61(11):899–907. https://doi.org/10.1016/j.addr.2009.04.021

    Article  CAS  PubMed  Google Scholar 

  37. Noren CJ, Wang J, Perler FB (2000) Dissecting the chemistry of protein splicing and its applications. Angew Chem Int Ed Engl 39(3):450–466

    Article  CAS  Google Scholar 

  38. Oeemig JS, Aranko AS, Djupsjobacka J, Heinamaki K, Iwai H (2009) Solution structure of DnaE intein from Nostoc punctiforme: structural basis for the design of a new split intein suitable for site-specific chemical modification. FEBS Lett 583(9):1451–1456. https://doi.org/10.1016/j.febslet.2009.03.058

    Article  CAS  PubMed  Google Scholar 

  39. Ludwig C, Schwarzer D, Zettler J, Garbe D, Janning P, Czeslik C, Mootz HD (2009) Semisynthesis of proteins using split inteins. Methods Enzymol 462:77–96. https://doi.org/10.1016/S0076-6879(09)62004-8

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  41. 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. https://doi.org/10.1007/s00018-012-1120-4

    Article  CAS  PubMed  Google Scholar 

  42. Elleuche S, Poggeler S (2010) Inteins, valuable genetic elements in molecular biology and biotechnology. Appl Microbiol Biotechnol 87(2):479–489. https://doi.org/10.1007/s00253-010-2628-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work has been supported by grants BIO2013-43517, from MINECO (Spain) and SING12/0 from UdG. V.G. acknowledges her fellowship from the Universitat de Girona.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Marc Ribó .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Romero-Casañas, A., Gordo, V., Castro, J., Ribó, M. (2020). Protein Splicing: From the Foundations to the Development of Biotechnological Applications. In: Vila-Perelló, M. (eds) Expressed Protein Ligation. Methods in Molecular Biology, vol 2133. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0434-2_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-0434-2_2

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0433-5

  • Online ISBN: 978-1-0716-0434-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics