Functional organization of the yeast proteome by systematic

analysis of protein complexes

Anne-Claude Gavin et al.Anne-Claude Gavin, Markus Bosche, Roland Krause, Paola Grandi, Martina Marzioch, Andreas Bauer, Jorg Schultz, Jens M. Rick, Anne-Marie Michon, Cristina-Maria Cruciat, Marita Remor, Christian Hofert, Malgorzata Schelder, Miro Brajenovic, Heins Ruffner, Alejandro Merino, Karin Klein, Manuela Hudak, David Dickson, Tatjana Rudi, Volker Gnau, Angela Bauch, Sonja Bastuck, Bettina Huhse, Christina Leutwein, Marie-Anne Heurtier, Richard R. Copley, Angela Edelmann, Erich Querfurth, Vladimir Rybin, Gerard Drewes, Manfred Raida, Tewis Bouwmesster, Peer Bork, Bertrand Seraphin, Bernhard Kuster, Gitte Neubauer, and Giulio Superti-Furga (Nature 415. 2002)

Background Information

1.Proteins rarely act alone

2.Comprehensive protein interaction studies thus far:

• two-hybrid systems (ex vivo)

• protein chips (in vitro)

• GST pull-downs (in vivo)

3. Authors used tandem-affinity purification (TAP) and mass spectrometry

Rationale for Using TAP/MS Method

1.Fast purification with high yield

2.In vivo

3.Over-expression of proteins not required

4.Prior knowledge of protein complex not required

5.Purified complex can be used in a variety of studies

The Tandem Affinity Purification Tag

target protein

target protein

TAP Purification Strategy

TAP Purification Strategy

TAP Purification Strategy

TAP Purification Strategy … in detail

1. PCR of the TAP cassette

2. Transformation of yeast cells (homologous recombination)

3. Selection of positive clones

4. Large-scale cultivation

5. Cell lysis Tandem affinity purification

6. One-dimensional SDS-PAGE

7. MALDI-TOF protein identification

8. Bioinformatic data interpretation

The Experiment

Processed 1,739 genes (1,143 human orthologues)

Purified 589 protein assemblies

Annotated 232 multiprotein complexes (98 known, 134 new)

Proposed new/additional cellular roles for 344 proteins (231 new)

Identified 1,440 distinct gene products

The Experiment …cont’d

9% of the 232 TAP complexes had no new component

2-83 components per TAP complex

Assigned cellular roles to complexes according to YPD and literature studies

Nine functional categories

Some Statistics

A Higher-Order Map

http://yeast.cellzome.com

Linked Complexes

Results of the Experiment

• Orthologues tend to interact with orthologues (53% vs 31%)

• Essential genes tend to interact with essential genes (44% vs 17%)

• Existence of “orthologous proteome” for eukaryotes?

Some Faults of the TAP Method

• “Super” unstable protein complexes

• TAP tag may interfere with complex

• Transient interactions

Low stoichiometric complexes

Physiology-specific interactions

Conclusions

•This TAP/MS method is the largest analysis of protein complexes

•Allows efficient identification of low-abundance proteins

•Allows purification of very large complexes

•Can complement other biochemical techniques

•Lower-order maps and higher-order maps provide crucial information

Great Summer Reading

Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol. 17, 1030-1032 (1999).

Puig, O. et al. The tandem affinity purification (tap) method: a general procedure of protien complex purification. Methods 24, 218-229 (2001).