Biology Reference
In-Depth Information
9.3
Interactomes, Bionetworks, and IDSs
Since the yeast two-hybrid (Y2H) method of measuring protein-protein interactions
was introduced by Fields and Song (1989), a variety of derivative methods has
been devised to study protein-protein and protein-drug interactions in many differ-
ent species of organisms, leading to the emergence of the field of interactomes
(Ito et al. 2001; Suter et al. 2008). The term interactome was coined by French
scientists Bernard Jacq and his colleagues in 1999 to indicate the whole set of
molecular interactions that go on in living cells. The term is a natural extension
of genome (the whole set of genes in an organism), transcriptome (the whole set
of RNAs encoded in a genome), proteome (the whole set of proteins encoded in
agenome), chemoreactome (the whole set of chemical reactions catalyzed by
enzymes in a cell), and phenome (the whole set of phenotypes exhibited by a cell).
Since the cell is a hierarchically organized system of genome, transcriptome, prote-
ome, chemoreactome, and phenome, we can represent the cell interactome algebrai-
cally as:
Interactome
Genome
Transcriptome
Proteome
¼
þ
þ
Chemoactome
Phenome
(9.3)
þ
þ
Of the five subcellular interactomes appearing in Eq. 9.3 , the protein interactome
(also called interative proteome ) has been best studied because of the availability
of the Y2H method that allows biologists to measure protein-protein interactions
directly. Table 9.2 summarizes the current knowledge of the protein-protein
interactomes from several species (Stumpf et al. 2008).
The cell interactome can be graphically represented as amultilayered hypernetwork
such as the p53 hypernetwork shown inFig. 9.2 . “Interactome” defined as the totality of
molecular interactions in cells ( http://en.wikipedia.org/wiki/Interactome ) and higher
organisms has a significant overlap in meanings with bionetworks (Sect. 2.4.1 ).
Bionetworks emphasizes the static connections among the nodes while interactomes
focus on the dynamic interactions among nodes. The relation between bionetworks
and interactomes may be akin to the relation between kinematics and dynamics in
physics (Sect. 2.3.5 ) and hence Bohr's kinematics-dynamics complementarity may be
applicable to both physics and biology as indicated in Table 9.3 . In other words,
Table 9.2 The estimated protein-protein interactome sizes of various organisms (Stumpf et al.
2008)
Organisms Nodes Edges Interactome size a
1. Saccharomyces cerevisiae 4,959 17,229 25,229
2. Drosophila melanogaster 7,451 17,226 74,336
3. Caenorhabditis elegans 2,638 3,970 240,544
4. Homo sapiens 1,085 1,346 672,918
a The total number of the edges of the whole protein-protein interactome theoretically predicted
based on the data obtained from partial or sub-interactomes
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