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Protein interaction maps for model organisms

Nature Reviews Molecular Cell Biology volume 2, pages 55–63 (2001)Cite this article

Abstract

Until recently, classical genetics and biochemistry were the main techniques used to investigate how organisms develop, reproduce, behave and age. But with the availability of complete genome sequences new approaches are emerging. Complete sets of proteins — 'proteomes' — can be predicted from genome sequences and used to characterize protein functions globally. For example, through the large-scale identification of physical protein–protein interactions, comprehensive protein interaction maps are being generated. And these maps might help us to understand the processes that control the biology of living organisms.

Key Points

  • The availability of complete genome sequences for some organisms allows the prediction of complete sets of proteins — proteomes.

  • To characterize protein function on a genome-wide scale, functional genomic approaches are now being taken. These are usually based on conventional assays modified to allow high-throughput or automated settings in which many proteins can be analysed simultaneously.

  • One functional genomic approach consists of the systematic identification of physical protein–protein interactions for a given proteome, with the aim of generating comprehensive protein interaction maps.

  • In classical proteomic approaches, the starting material is a protein extract from the organism. Such approaches are often limited by their inability to identify specific interactions within a complex of interacting proteins. This limitation can potentially be overcome by reverse proteomic approaches.

  • In reverse proteomic approaches, which can be computer-based or experimental, experiments are designed using the predicted proteome.

  • Computer-based approaches can use three assumptions:

  • Proteins encoded by pairs of separate genes functionally interact if their orthologues (proteins that have similar functions in different organisms) are known to be part of a single protein in another organism.

  • There is strong selective pressure for functionally interacting proteins to be inherited together during speciation.

  • Proteins that physically interact in one organism will co-evolve so that their respective orthologues maintain the ability to interact in another organism.

  • The yeast two-hybrid approach allows yeast cells expressing an interacting protein pair (X and Y) to be selected by using fusion tags attached to X and Y that reconstitute a transcription factor upon an interaction between X and Y, leading to the activation of reporter gene expression. This approach can be used to systematically test many possible interacting pairs.

  • Potential interactions can be confirmed by co-purifying or co-immunoprecipitating the partner proteins, examining loss-of-function phenotypes of the genes that encode interaction partners, or examining the effect of a loss of a protein interaction in vivo.

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Figure 1: Protein interactions are crucial in many aspects of biological function.
Figure 2: Two directions for proteomics in protein interaction mapping.
Figure 3: Genetic and physical interactions overlap in the LET-60/Ras pathway involved in vulval development in Caenorhabditis elegans.
Figure 4: Clustering analysis of interactions involving synthetic multivulva proteins in Caenorhabditis elegans suggests the existence of a multiprotein complex.

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Acknowledgements

We thank S. Boulton, L. Matthews and J. Dekker for critical reading of the manuscript. The work from this laboratory is supported by grants from the NHGRI, the NCI and the MGRI awarded to M.V.

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Authors and Affiliations

  1. Dana-Farber Cancer Institute and Department of Genetics Harvard Medical School, 44 Binney Street, Boston , 02115, Massachusetts, USA

    Albertha J. M. Walhout & Marc Vidal

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Related links

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DATABASE LINKS

CED-4

CED-9

Ste5p

topoisomerase II

Gal4p

LIN-12

GLP-1

LAG-1

LET-23

FURTHER INFORMATION

Yeast proteome database

Yeast two-hybrid protein interaction map

In silico protein interaction map

Nematode two-hybrid protein interaction map

ENCYCLOPEDIA OF LIFE SCIENCES

Protein quaternary structure: subunit–subunit interactions

Glossary

ORTHOLOGUES

Genes that belong to different organisms and that have a similar function.

EXPRESSION-PROFILING EXPERIMENTS

One of the first functional genomic approaches developed, in which expression levels of large sets of transcripts are compared under different experimental conditions, or during development of an organism in a large-scale, high-throughput fashion.

PROTEOME

The complete set of (predicted) proteins, by analogy to genome (the complete genetic material).

EPISTASIS ANALYSIS

Epistasis is the masking of a phenotype caused by a mutation in one gene by a mutation in another gene. Epistasis analysis can therefore be used to dissect the order in which genes in a genetic pathway act.

SPLICEOSOME

Molecular machine involved in gene splicing.

TWO-HYBRID MATRIX EXPERIMENTS

The systematic testing of different protein pairs for a two-hybrid interaction phenotype.

CONTIG

Usually refers to an overlapping set of DNA fragments. Here, we use contig in the context of interaction clusters in which contiguous series of interactions can be found.

COMPLEMENTATION GROUP

Independent mutations in a single locus that fail to complement the phenotypes they confer.

CLUSTERING ANALYSIS

By looking for interaction partners that have been found with multiple baits, interaction contigs can be identified.

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Walhout, A., Vidal, M. Protein interaction maps for model organisms. Nat Rev Mol Cell Biol 2, 55–63 (2001). https://doi.org/10.1038/35048107

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