Proteomics versus genomics. What type of structure–function relationship are we looking for?

✍ Scribed by Marc H.V. Van Regenmortel

• Publisher: John Wiley and Sons
• Year: 2001
• Tongue: English
• Weight: 53 KB
• Volume: 14
• Category: Article
• ISSN: 0952-3499
• DOI: 10.1002/jmr.554

✦ Synopsis

It is frequently said that we have entered the post-genomic era and that the hegemony of the gene in biology is a thing of the past. One unexpected result of the unravelling of the human genome has been the downgrading of the gene as an explanatory category for organismic complexity. There is, indeed, no simple relationship between the number of genes in an organism and its overall biological complexity. About 30 000 genes suffice to specify a human being, which is only twice the number of genes required for a fruit fly and only a third more than the number required to specify a nematode worm. Comparing genomes to a set of instructions that can be read like a software is a metaphor that is no longer considered apt for explaining the development of an organism from a fertilized egg (Coen, 1999) Proteins have replaced genes as the entities that need to be catalogued and analysed in order to understand biological complexity. The number of different proteins in an organism is much larger than its number of genes, because of splicing phenomena and post-translational modifications and proteolysis of proteins. The sum total of all the proteins expressed in a cell is known as the proteome and its analysis corresponds to the field of proteomics.

Proteomics consists not only in the identification and quantification of proteins but also involves a study of their structure, localization, modification, interactions, activities and functions (Fields, 2001). It is odd, therefore, that the large-scale determination of protein structures in the postgenomic era has become known as structural genomics (instead of structural proteomics). In a similar vein, the functional analysis of proteins is usually called functional genomics (Teichmann et al., 2001;Anderson et al., 2000;Shapiro and Harris, 2000). Originally the term proteomics was associated with the display on two-dimensional polyacrylamide gels of a large number of proteins from a cellular extract, but the term now also covers the functional analysis of gene products (Pandey and Mann, 2000). There seems to be no good reason why the terms structural and functional genomics should be preferred to structural and functional proteomics.

Recent advances in methods of structural analysis of proteins and the substantial funding of large-scale projects aimed at elucidating new protein structures have led to a buoyant expectation in the structural community that the biological functions of many proteins will soon be made 'crystal clear' (Eisenstein et al., 2000). This optimism may well be exaggerated if the following aspects of current proteomics research are taken into account: