Springer Protocols: Abstract: Characterization of Protein-Protein Interactions: Application to the Understanding of Peroxisome Biogenesis

Characterization of Protein-Protein Interactions: Application to the Understanding of Peroxisome Biogenesis

By: Sebastien Leon², Ivet Suriapranata², Mingda Yan², Naganand Rayapuram², Amar Patel², Suresh Subramani²

Abstract

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With the approaching completion of the Pichia pastoris genome, a greater emphasis will have to be placed on the proteome and the protein-protein interactions between its constituents. This chapter discusses methods that have been used for the study of such interactions among both soluble and membrane-associated proteins in peroxisome biogenesis. The procedures are equally applicable to other cellular processes.

Affiliation(s): (2) Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA

Book Title: Pichia Protocols

Series: Methods in Molecular Biology | Volume: 389 | Pub. Date: Aug-08-2007 | Page Range: 219-237 | DOI: 10.1007/978-1-59745-456-8_16

Subject: Biotechnology

Key Words: Protein complexes - protein interactions - yeast two-hybrid, co-immunoprecipitation - tandem affinity purification - TAP-tag - mass spectrometry - membrane protein complexes - soluble protein complexes

References

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1.	Faber, K. N., Heyman, J. A., and Subramani, S. (1998) Two AAA family peroxins, PpPex1p and PpPex6p, interact with each other in an ATP-dependent manner and are associated with different subcellular membranous structures distinct from peroxisomes. Mol Cell Biol 18, 936–943.

2.	Snyder, W. B., Koller, A., Choy, A. J., and Subramani, S. (2000) The peroxin Pex19p interacts with multiple, integral membrane proteins at the peroxisomal membrane. J Cell Biol 149, 1171–1177.

3.	Hazra, P. P., Suriapranata, I., Snyder, W. B., and Subramani, S. (2002) Peroxisome remnants in pex3Δ cells and the requirement of Pex3p for interactions between the peroxisomal docking and translocation subcomplexes. Traffic 3, 560–74.

4.	Graham, T. T. (2004) Unit 8: Protein labeling and immunoprecipitation. 8.5 Immunoprecipitation. In Short protocols in cell biology: a compendium of methods from Current Protocols in Cell Biology (ed. Bonifacio, J.S., Dasso, M., Harford, M., Lippincott-Schwartz, J., and Yamada, K.M., eds.), pp. 8–17. John Wiley & Sons, Hoboken, NJ, USA, pp. 8–17.

5.	Gavin, A. C., Bosche, M., Krause, R., et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147.

6.	Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M., and Séraphin, B. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17, 1030–1032.

7.	Puig, O., Caspary, F., Rigaut, G., et al. (2001) The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24, 218–229.

8.	Higgins, D. R., Busser, K., Comiskey, J., Whittier, P. S., Purcell, T. J., and Hoeffler, J. P. (1998) Small vectors for expression based on dominant drug resistance with direct multicopy selection. Methods Mol. Biol. 103, 41–53.

9.	Miller, J. and Stagljar, I. (2004) Using the yeast two-hybrid system to identify interacting proteins. Methods Mol. Biol. 261, 247–262.

10.	McAlister-Henn, L., Gibson, N., and Panisko, E. (1999) Applications of the yeast two-hybrid system. Methods 19, 330–337.

11.	Hu, J. C., Kornacker, M. G., and Hochschild, A. (2000) Escherichia coli one-and two-hybrid systems for the analysis and identification of protein-protein interactions. Methods 20, 80–94.

12.	Dove, S. L., Joung, J. K., and Hochschild, A. (1997) Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature 386, 627–630.

13.	Joung, J. K., Ramm, E. I., and Pabo, C. O. (2000) A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc. Natl. Acad. Sci. USA 97, 7382–7387.

14.	Karimova, G., Pidoux, J., Ullmann, A., and Ladant, D. (1998) A bacterial twohybrid system based on a reconstituted signal transduction pathway. Proc. Natl. Acad. Sci. USA 95, 5752–5756.

15.	Shaywitz, A. J., Dove, S. L., Kornhauser, J. M., Hochschild, A., and Greenberg, M. E. (2000) Magnitude of the CREB-dependent transcriptional response is determined by the strength of the interaction between the kinase-inducible domain of CREB and the KIX domain of CREB-binding protein. Mol. Cell. Biol. 20, 9409–9422.

16.	Jobling, M. G. and Holmes, R. K. (2000) Identification of motifs in cholera toxin A1 polypeptide that are required for its interaction with human ADP-ribosylation factor 6 in a bacterial two-hybrid system. Proc. Natl. Acad. Sci. USA 97, 14,662–14,667.

17.	Ghys, K., Fransen, M., Mannaerts, G. P., and Van Veldhoven, P. P. (2002) Functional studies on human Pex7p: subcellular localization and interaction with proteins containing a peroxisome-targeting signal type 2 and other peroxins. Biochem. J 365, 41–50.

18.	Fransen, M., Brees, C., Ghys, K., et al. (2002) Analysis of mammalian peroxin interactions using a non-transcription-based bacterial two-hybrid Assay. Mol. Cell. Proteomics 1, 243–252.

19.	Dautin, N., Karimova, G., and Ladant, D. (2003) Human immunodeficiency virus (HIV) type 1 transframe protein can restore activity to a dimerization-deficient HIV protease variant. J. Virol. 77, 8216–8226.

20.	Johnsson, N. and Varshavsky, A. (1994) Split ubiquitin as a sensor of protein interactions in vivo. Proc. Natl. Acad. Sci. USA 91, 10,340–10,344.

21.	Fetchko, M. and Stagljar, I. (2004) Application of the split-ubiquitin membrane yeast two-hybrid system to investigate membrane protein interactions. Methods 32, 349–362.

22.	Thaminy, S., Miller, J., and Stagljar, I. (2004) The split-ubiquitin membrane-based yeast two-hybrid system. Methods Mol. Biol. 261, 297–312.

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