Research
An evolutionary and functional assessment of regulatory network motifs
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* Corresponding author: Samuel Bottani bottani@paris7.jussieu.fr
1 Laboratoire de Génétique Moléculaire de la Neurotransmission et des Processus Neurodégénératifs CNRS UMR 7091, CERVI La Pitié, 91-105 boulevard de l'Hôpital, 75013 Paris, France
2 Groupe de Modélisation Physique Interfaces Biologie and CNRS-UMR 7057 'Matières et Systèmes Complexes', Université Paris 7, 2 place Jussieu, 75251 Paris Cedex 05, France
3 Unité Génomique des Microorganismes Pathogènes, CNRS URA 2171, Department of the Structure and Dynamics of Genomes, Institut Pasteur, 28 rue du Dr Roux, F-75724 Paris Cedex 15, France
Genome Biology 2005, 6:R35 doi:10.1186/gb-2005-6-4-r35
Published: 24 March 2005Abstract
Background
Cellular functions are regulated by complex webs of interactions that might be schematically represented as networks. Two major examples are transcriptional regulatory networks, describing the interactions among transcription factors and their targets, and protein-protein interaction networks. Some patterns, dubbed motifs, have been found to be statistically over-represented when biological networks are compared to randomized versions thereof. Their function in vitro has been analyzed both experimentally and theoretically, but their functional role in vivo, that is, within the full network, and the resulting evolutionary pressures remain largely to be examined.
Results
We investigated an integrated network of the yeast Saccharomyces cerevisiae comprising transcriptional and protein-protein interaction data. A comparative analysis was performed with respect to Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii and Yarrowia lipolytica, which belong to the same class of hemiascomycetes as S. cerevisiae but span a broad evolutionary range. Phylogenetic profiles of genes within different forms of the motifs show that they are not subject to any particular evolutionary pressure to preserve the corresponding interaction patterns. The functional role in vivo of the motifs was examined for those instances where enough biological information is available. In each case, the regulatory processes for the biological function under consideration were found to hinge on post-transcriptional regulatory mechanisms, rather than on the transcriptional regulation by network motifs.
Conclusion
The overabundance of the network motifs does not have any immediate functional or evolutionary counterpart. A likely reason is that motifs within the networks are not isolated, that is, they strongly aggregate and have important edge and/or node sharing with the rest of the network.