Skip to main content

Tools to Study SUMO Conjugation in Caenorhabditis elegans

  • Protocol
  • First Online:
SUMO

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1475))

Abstract

The cell biology of sumoylation has mostly been studied using transformed cultured cells and yeast. In recent years, genetic analysis has demonstrated important roles for sumoylation in the biology of C. elegans. Here, we expand the existing set of tools making it possible to address the role of sumoylation in the nematode C. elegans using a combination of genetics, imaging, and biochemistry. Most importantly, the dynamics of SUMO conjugation and deconjugation can be followed very precisely both in space and time within living worms. Additionally, the biochemistry of SUMO conjugation and deconjugation can be addressed using recombinant purified components of the C. elegans sumoylation machinery, including E3 ligases and SUMO proteases. These tools and reagents will be useful to gain insights into the biological role of SUMO in the context of a multicellular organism.

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 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
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. Nacerddine K, Lehembre F, Bhaumik M et al (2005) The SUMO pathway is essential for nuclear integrity and chromosome segregation in mice. Dev Cell 9(6):769–779

    Article  CAS  PubMed  Google Scholar 

  2. Wang L, Wansleeben C, Zhao S et al (2014) SUMO2 is essential while SUMO3 is dispensable for mouse embryonic development. EMBO Rep 15(8):878–885

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Fernandez AG, Gunsalus KC, Huang J et al (2005) New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones. Genome Res 15(2):250–259

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Jones D, Crowe E, Stevens TA et al (2002) Functional and phylogenetic analysis of the ubiquitylation system in Caenorhabditis elegans: ubiquitin-conjugating enzymes, ubiquitin-activating enzymes, and ubiquitin-like proteins. Genome Biol 3(1):research0002–research0002.0015

    PubMed  Google Scholar 

  5. Kamath RS, Fraser AG, Dong Y et al (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421(6920):231–237

    Article  CAS  PubMed  Google Scholar 

  6. Rual JF, Ceron J, Koreth J et al (2004) Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res 14(10B):2162–2168

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Flotho A, Melchior F (2013) Sumoylation: a regulatory protein modification in health and disease. Annu Rev Biochem 82:357–385

    Article  CAS  PubMed  Google Scholar 

  8. Gareau JR, Lima CD (2010) The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nat Rev Mol Cell Biol 11(12):861–871

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Yunus AA, Lima CD (2009) Structure of the Siz/PIAS SUMO E3 ligase Siz1 and determinants required for SUMO modification of PCNA. Mol Cell 35(5):669–682

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Johnson ES, Gupta AA (2001) An E3-like factor that promotes SUMO conjugation to the yeast septins. Cell 106(6):735–744

    Article  CAS  PubMed  Google Scholar 

  11. Zhao X, Blobel G (2005) A SUMO ligase is part of a nuclear multiprotein complex that affects DNA repair and chromosomal organization. Proc Natl Acad Sci U S A 102(13):4777–4782

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Hay RT (2007) SUMO-specific proteases: a twist in the tail. Trends Cell Biol 17(8):370–376

    Article  CAS  PubMed  Google Scholar 

  13. Mukhopadhyay D, Dasso M (2007) Modification in reverse: the SUMO proteases. Trends Biochem Sci 32(6):286–295

    Article  CAS  PubMed  Google Scholar 

  14. Holway AH, Kim SH, La Volpe A et al (2006) Checkpoint silencing during the DNA damage response in Caenorhabditis elegans embryos. J Cell Biol 172(7):999–1008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ward JD, Bojanala N, Bernal T et al (2013) Sumoylated NHR-25/NR5A regulates cell fate during C. elegans vulval development. PLoS Genet 9(12):e1003992

    Article  PubMed  PubMed Central  Google Scholar 

  16. Broday L, Kolotuev I, Didier C et al (2004) The small ubiquitin-like modifier (SUMO) is required for gonadal and uterine-vulval morphogenesis in Caenorhabditis elegans. Genes Dev 18(19):2380–2391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Kim SH, Michael WM (2008) Regulated proteolysis of DNA polymerase eta during the DNA-damage response in C. elegans. Mol Cell 32(6):757–766

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Kaminsky R, Denison C, Bening-Abu-Shach U et al (2009) SUMO regulates the assembly and function of a cytoplasmic intermediate filament protein in C. elegans. Dev Cell 17(5):724–735

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Zhang H, Smolen GA, Palmer R et al (2004) SUMO modification is required for in vivo Hox gene regulation by the Caenorhabditis elegans Polycomb group protein SOP-2. Nat Genet 36(5):507–511

    Article  CAS  PubMed  Google Scholar 

  20. Pelisch F, Sonneville R, Pourkarimi E et al (2014) Dynamic SUMO modification regulates mitotic chromosome assembly and cell cycle progression in Caenorhabditis elegans. Nat Commun 5:5485. doi:10.1038/ncomms6485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Sapir A, Tsur A, Koorman T et al (2014) Controlled sumoylation of the mevalonate pathway enzyme HMGS-1 regulates metabolism during aging. Proc Natl Acad Sci U S A 111(37):E3880–E3889

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Tsur A, Bening Abu-Shach U, Broday L (2015) ULP-2 SUMO protease regulates E-cadherin recruitment to adherens junctions. Dev Cell 35(1):63–77

    Article  CAS  PubMed  Google Scholar 

  23. Green RA, Audhya A, Pozniakovsky A et al (2008) Expression and imaging of fluorescent proteins in the C. elegans gonad and early embryo. Methods Cell Biol 85:179–218

    Article  CAS  PubMed  Google Scholar 

  24. Frokjaer-Jensen C, Davis MW, Hopkins CE et al (2008) Single-copy insertion of transgenes in Caenorhabditis elegans. Nat Genet 40(11):1375–1383

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Dickinson DJ, Pani AM, Heppert JK et al (2015) Streamlined genome engineering with a self-excising drug selection cassette. Genetics 200(4):1035–1049

    Article  PubMed  PubMed Central  Google Scholar 

  26. Ward JD (2015) Rapid and precise engineering of the Caenorhabditis elegans genome with lethal mutation co-conversion and inactivation of NHEJ repair. Genetics 199(2):363–377

    Article  PubMed  Google Scholar 

  27. Kamath RS, Martinez-Campos M, Zipperlen P et al (2001) Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans. Genome Biol 2(1):research0002.0001–research0002.0010

    Google Scholar 

  28. Shen L, Tatham MH, Dong C et al (2006) SUMO protease SENP1 induces isomerization of the scissile peptide bond. Nat Struct Mol Biol 13(12):1069–1077

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Tatham MH, Hay RT (2009) FRET-based in vitro assays for the analysis of SUMO protease activities. Methods Mol Biol 497:253–268

    Article  CAS  PubMed  Google Scholar 

  30. McCarter J, Bartlett B, Dang T et al (1999) On the control of oocyte meiotic maturation and ovulation in Caenorhabditis elegans. Dev Biol 205(1):111–128

    Article  CAS  PubMed  Google Scholar 

  31. Soderberg O, Gullberg M, Jarvius M et al (2006) Direct observation of individual endogenous protein complexes in situ by proximity ligation. Nat Methods 3(12):995–1000

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by the Wellcome Trust (grant 098391/Z/12/7), Cancer Research UK (grant C434/A13067), BBSRC (grant BB/J015199/1), and a Marie Curie Fellowship (grant 297881). Some nematode strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). R.T.H. is a Senior Investigator of the Wellcome Trust. Wellcome Trust grant 097045/B/11/Z provided infrastructure support. The author(s) would like to acknowledge networking support by the Proteostasis COST action (BM1307).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Federico Pelisch .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media New York

About this protocol

Cite this protocol

Pelisch, F., Hay, R.T. (2016). Tools to Study SUMO Conjugation in Caenorhabditis elegans . In: Rodriguez, M. (eds) SUMO. Methods in Molecular Biology, vol 1475. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6358-4_17

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6358-4_17

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6356-0

  • Online ISBN: 978-1-4939-6358-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics