Skip to main content

PCNA-Dependent Ubiquitination of Cdt1 and p21 in Mammalian Cells

  • Protocol
  • First Online:
Book cover Cell Cycle Control

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1170))

Abstract

PCNA is a DNA clamp, acting on chromatin as a platform for various proteins involved in many aspects of DNA replication-linked processes. Most of these proteins have the PCNA-interaction protein motif (PIP box) that associates with PCNA. Recent works show that PCNA plays an important role as a matchmaker, connecting PCNA-interacting proteins to the ubiquitin ligase CRL4Cdt2 for their degradation. Proteins degraded by CRL4Cdt2 include Cdt1, p21, and Set8 in mammalian cells. These CRL4Cdt2 substrates have a PIP degron that consists of the canonical PIP-box sequence and additional conserved amino acids required for ubiquitination. The degradation of these proteins is triggered when PCNA is loaded onto chromatin at the onset of S phase, and this process is important to prevent re-replication of DNA. These CRL4Cdt2 substrates are also degraded through the same mechanism in response to DNA damage. In this chapter, we describe several approaches to investigate how PIP degron-containing proteins are degraded in a PCNA-dependent manner.

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 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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. Nakayama KI, Nakayama K (2006) Ubiquitin ligases: cell-cycle control and cancer. Nat Rev Cancer 6(5):369–381

    Article  CAS  PubMed  Google Scholar 

  2. Petroski MD, Deshaies RJ (2005) Function and regulation of cullin-RING ubiquitin ligases. Nat Rev Mol Cell Biol 6(1):9–20

    Article  CAS  PubMed  Google Scholar 

  3. Bell SP, Dutta A (2002) DNA replication in eukaryotic cells. Annu Rev Biochem 71:333–374

    Article  CAS  PubMed  Google Scholar 

  4. Nishitani H, Lygerou Z (2002) Control of DNA replication licensing in a cell cycle. Genes Cells 7(6):523–534

    Article  CAS  PubMed  Google Scholar 

  5. Blow JJ, Dutta A (2005) Preventing re-replication of chromosomal DNA. Nat Rev Mol Cell Biol 6(6):476–486

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  6. Ilves I, Petojevic T, Pesavento JJ, Botchan MR (2010) Activation of the MCM2-7 helicase by association with Cdc45 and GINS proteins. Mol Cell 37(2):247–258

    Article  CAS  PubMed  Google Scholar 

  7. Masai H, Matsumoto S, You Z, Yoshizawa-Sugata N, Oda M (2010) Eukaryotic chromosome DNA replication: where, when, and how? Annu Rev Biochem 79:89–130

    Article  CAS  PubMed  Google Scholar 

  8. Machida YJ, Hamlin JL, Dutta A (2005) Right place, right time, and only once: replication initiation in metazoans. Cell 123(1):13–24

    Article  CAS  PubMed  Google Scholar 

  9. Arias EE, Walter JC (2007) Strength in numbers: preventing rereplication via multiple mechanisms in eukaryotic cells. Genes Dev 21(5):497–518

    Article  CAS  PubMed  Google Scholar 

  10. Abbas T, Dutta A (2011) CRL4Cdt2: master coordinator of cell cycle progression and genome stability. Cell Cycle 10(2):241–249

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. Havens CG, Walter JC (2011) Mechanism of CRL4Cdt2, a PCNA-dependent E3 ubiquitin ligase. Genes Dev 25(15):1568–1582

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  12. Waga S, Stillman B (1998) The DNA replication fork in eukaryotic cells. Annu Rev Biochem 67:721–751

    Article  CAS  PubMed  Google Scholar 

  13. Moldovan GL, Pfander B, Jentsch S (2007) PCNA, the maestro of the replication fork. Cell 129(4):665–679

    Article  CAS  PubMed  Google Scholar 

  14. Gulbis JM, Kelman Z, Hurwitz J, O’Donnell M, Kuriyan J (1996) Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA. Cell 87(2):297–306

    Article  CAS  PubMed  Google Scholar 

  15. Arias EE, Walter JC (2006) PCNA functions as a molecular platform to trigger Cdt1 destruction and prevent re-replication. Nat Cell Biol 8(1):84–90

    Article  CAS  PubMed  Google Scholar 

  16. Nishitani H, Sugimoto N, Roukos V, Nakanishi Y, Saijo M, Obuse C, Tsurimoto T, Nakayama KI, Nakayama K, Fujita M, Lygerou Z, Nishimoto T (2006) Two E3 ubiquitin ligases, SCF-Skp2 and DDB1-Cul4, target human Cdt1 for proteolysis. EMBO J 25(5):1126–1136

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  17. Senga T, Sivaprasad U, Zhu W, Park JH, Arias EE, Walter JC, Dutta A (2006) PCNA is a cofactor for Cdt1 degradation by CUL4/DDB1-mediated N-terminal ubiquitination. J Biol Chem 281(10):6246–6252

    Article  CAS  PubMed  Google Scholar 

  18. Havens CG, Walter JC (2009) Docking of a specialized PIP Box onto chromatin-bound PCNA creates a degron for the ubiquitin ligase CRL4Cdt2. Mol Cell 35(1):93–104

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Michishita M, Morimoto A, Ishii T, Komori H, Shiomi Y, Higuchi Y, Nishitani H (2011) Positively charged residues located downstream of PIP box, together with TD amino acids within PIP box, are important for CRL4(Cdt2)-mediated proteolysis. Genes Cells 16(1):12–22

    Article  CAS  PubMed  Google Scholar 

  20. Higa LA, Wu M, Ye T, Kobayashi R, Sun H, Zhang H (2006) CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. Nat Cell Biol 8(11):1277–1283

    Article  CAS  PubMed  Google Scholar 

  21. Hu J, McCall CM, Ohta T, Xiong Y (2004) Targeted ubiquitination of CDT1 by the DDB1-CUL4A-ROC1 ligase in response to DNA damage. Nat Cell Biol 6(10):1003–1009

    Article  CAS  PubMed  Google Scholar 

  22. Jin J, Arias EE, Chen J, Harper JW, Walter JC (2006) A family of diverse Cul4-Ddb1-interacting proteins includes Cdt2, which is required for S phase destruction of the replication factor Cdt1. Mol Cell 23(5):709–721

    Article  CAS  PubMed  Google Scholar 

  23. Sakaguchi H, Takami T, Yasutani Y, Maeda T, Morino M, Ishii T, Shiomi Y, Nishitani H (2012) Checkpoint kinase ATR phosphorylates Cdt2, a substrate receptor of CRL4 ubiquitin ligase, and promotes the degradation of Cdt1 following UV irradiation. PLoS One 7(9):e46480

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  24. Stathopoulou A, Roukos V, Petropoulou C, Kotsantis P, Karantzelis N, Nishitani H, Lygerou Z, Taraviras S (2012) Cdt1 is differentially targeted for degradation by anticancer chemotherapeutic drugs. PLoS One 7(3):e34621

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  25. Raman M, Havens CG, Walter JC, Harper JW (2011) A genome-wide screen identifies p97 as an essential regulator of DNA damage-dependent CDT1 destruction. Mol Cell 44(1):72–84

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Shiomi Y, Hayashi A, Ishii T, Shinmyozu K, Nakayama J, Sugasawa K, Nishitani H (2012) Two different replication factor C proteins, Ctf18 and RFC1, separately control PCNA-CRL4Cdt2-mediated Cdt1 proteolysis during S phase and following UV irradiation. Mol Cell Biol 32(12):2279–2288

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Abbas T, Sivaprasad U, Terai K, Amador V, Pagano M, Dutta A (2008) PCNA-dependent regulation of p21 ubiquitylation and degradation via the CRL4Cdt2 ubiquitin ligase complex. Genes Dev 22(18):2496–2506

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  28. Kim Y, Starostina NG, Kipreos ET (2008) The CRL4Cdt2 ubiquitin ligase targets the degradation of p21Cip1 to control replication licensing. Genes Dev 22(18):2507–2519

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  29. Nishitani H, Shiomi Y, Iida H, Michishita M, Takami T, Tsurimoto T (2008) CDK inhibitor p21 is degraded by a proliferating cell nuclear antigen-coupled Cul4-DDB1Cdt2 pathway during S phase and after UV irradiation. J Biol Chem 283(43):29045–29052

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Abbas T, Shibata E, Park J, Jha S, Karnani N, Dutta A (2010) CRL4(Cdt2) regulates cell proliferation and histone gene expression by targeting PR-Set7/Set8 for degradation. Mol Cell 40(1):9–21

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  31. Centore RC, Havens CG, Manning AL, Li JM, Flynn RL, Tse A, Jin J, Dyson NJ, Walter JC, Zou L (2010) CRL4(Cdt2)-mediated destruction of the histone methyltransferase Set8 prevents premature chromatin compaction in S phase. Mol Cell 40(1):22–33

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  32. Jorgensen S, Eskildsen M, Fugger K, Hansen L, Larsen MS, Kousholt AN, Syljuasen RG, Trelle MB, Jensen ON, Helin K, Sorensen CS (2011) SET8 is degraded via PCNA-coupled CRL4(CDT2) ubiquitylation in S phase and after UV irradiation. J Cell Biol 192(1):43–54

    Article  PubMed Central  PubMed  Google Scholar 

  33. Oda H, Hubner MR, Beck DB, Vermeulen M, Hurwitz J, Spector DL, Reinberg D (2010) Regulation of the histone H4 monomethylase PR-Set7 by CRL4(Cdt2)-mediated PCNA-dependent degradation during DNA damage. Mol Cell 40(3):364–376

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  34. Tardat M, Brustel J, Kirsh O, Lefevbre C, Callanan M, Sardet C, Julien E (2010) The histone H4 Lys 20 methyltransferase PR-Set7 regulates replication origins in mammalian cells. Nat Cell Biol 12(11):1086–1093

    Article  CAS  PubMed  Google Scholar 

  35. Shibata E, Abbas T, Huang X, Wohlschlegel JA, Dutta A (2011) Selective ubiquitylation of p21 and Cdt1 by UBCH8 and UBE2G ubiquitin-conjugating enzymes via the CRL4Cdt2 ubiquitin ligase complex. Mol Cell Biol 31(15):3136–3145

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  36. Nishitani H, Taraviras S, Lygerou Z, Nishimoto T (2001) The human licensing factor for DNA replication Cdt1 accumulates in G1 and is destabilized after initiation of S-phase. J Biol Chem 276(48):44905–44911

    Article  CAS  PubMed  Google Scholar 

  37. Nishitani H, Ohtsubo M, Yamashita K, Iida H, Pines J, Yasudo H, Shibata Y, Hunter T, Nishimoto T (1991) Loss of RCC1, a nuclear DNA-binding protein, uncouples the completion of DNA replication from the activation of cdc2 protein kinase and mitosis. EMBO J 10(6):1555–1564

    CAS  PubMed Central  PubMed  Google Scholar 

  38. Fukuda K, Morioka H, Imajou S, Ikeda S, Ohtsuka E, Tsurimoto T (1995) Structure-function relationship of the eukaryotic DNA replication factor, proliferating cell nuclear antigen. J Biol Chem 270(38):22527–22534

    Article  CAS  PubMed  Google Scholar 

  39. Zhang P, Zhang SJ, Zhang Z, Woessner JF Jr, Lee MY (1995) Expression and physicochemical characterization of human proliferating cell nuclear antigen. Biochemistry 34(34):10703–10712

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was financially supported by JSPS KAKENHI and MEXT KKENHI, Grant in Aid from the Ministry of Education, Culture, Sports, Science, and Technology of Japan.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Hideo Nishitani .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this protocol

Cite this protocol

Hayashi, A., Suenaga, N., Shiomi, Y., Nishitani, H. (2014). PCNA-Dependent Ubiquitination of Cdt1 and p21 in Mammalian Cells. In: Noguchi, E., Gadaleta, M. (eds) Cell Cycle Control. Methods in Molecular Biology, vol 1170. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0888-2_19

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-0888-2_19

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0887-5

  • Online ISBN: 978-1-4939-0888-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics