Ten years has
elapsed since the publication of the first book on proteomics by the editors of
the present book. Rather than ‘proteomics’, the book was entitled Proteome research: new frontiers in
functional genomics. The idea was to establish a continuity with the
Genome Analysis Project, and especially the sequencing of the human genome
which was under way. However, it was already clear to some of us that a new
revolution in biology was being launched: the introduction of a new paradigm
permitted shifting the focus of investigation from DNA sequences to structures
and functions of proteins, interacting between themselves and with other
molecules, including DNA, in ways not encoded in DNA sequences. After
completion of the sequencing of DNA of human and other species, the picture
became even clearer. As is often the case in the history of science, the
previous paradigm dominated by DNA technologies allowed for discoveries which
turned this paradigm upside down. ‘Proteomics’ – the study of the proteome,
i.e. the complete set of proteins in a cell or tissue – is one of the words
being used today to name the new paradigm, together with the more general
expressions ‘biocomplexity’ and ‘systems biology’. But one should not be
mistaken: proteomics is not a plain continuation of genomics. DNA sequences are
being used now as an indispensable source of data regarding the first level of
protein structures. However, this only marks the beginning of an entirely new
story. Moreover, the same protein may have completely different functions in
different tissues, even in the same cell, depending upon its localization in
the cell and the state of activity of the latter. Expressed DNA sequences do
not tell much about three-dimensional structures of proteins or their
modifications in cellular microenvironments, nor about the dynamics of their
synthesis, activation and inactivation, all of these determining their
functions. Knowledge of the proteome is not limited to the pattern of expressed
proteins identified from DNA sequences in DNA microarrays. This has prompted a
change in the whole of biological thinking. For several decades, after the
extraordinary discoveries of DNA structures and functions in the 1960s,
molecular genetics and genomics were a source for explanations, giving answers to century-old questions regarding
the nature of processes specific to living beings, such as metabolism and
reproduction.
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