Modular organization in the reductive evolution of protein-protein interaction networks

BackgroundThe variation in the sizes of the genomes of distinct life forms remains somewhat puzzling. The organization of proteins into domains and the different mechanisms that regulate gene expression are two factors that potentially increase the capacity of genomes to create more complex systems. High-throughput protein interaction data now make it possible to examine the additional complexity generated by the way that protein interactions are organized.ResultsWe have studied the reduction in genome size of Buchnera compared to its close relative Escherichia coli. In this well defined evolutionary scenario, we found that among all the properties of the protein interaction networks, it is the organization of networks into modules that seems to be directly related to the evolutionary process of genome reduction.ConclusionIn Buchnera, the apparently non-random reduction of the modular structure of the networks and the retention of essential characteristics of the interaction network indicate that the roles of proteins within the interaction network are important in the reductive process.

[1]  P. Bourgine,et al.  Topological and causal structure of the yeast transcriptional regulatory network , 2002, Nature Genetics.

[2]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[3]  Kimberly Van Auken,et al.  WormBase: a multi-species resource for nematode biology and genomics , 2004, Nucleic Acids Res..

[4]  M. Hattori,et al.  Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. , 2001, DNA research : an international journal for rapid publication of reports on genes and genomes.

[5]  Jon R. Armstrong,et al.  Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[6]  R. Guimerà,et al.  Functional cartography of complex metabolic networks , 2005, Nature.

[7]  H. Herzel,et al.  Is there a bias in proteome research? , 2001, Genome research.

[8]  S. Oliver,et al.  Chance and necessity in the evolution of minimal metabolic networks , 2006, Nature.

[9]  Martin Kuiper,et al.  BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks , 2005, Bioinform..

[10]  M. Gerstein,et al.  Genomic analysis of regulatory network dynamics reveals large topological changes , 2004, Nature.

[11]  A. Wagner.  How the global structure of protein interaction networks evolves , 2002, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[12]  M. Hattori,et al.  Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS , 2000, Nature.

[13]  S. Kanaya,et al.  Large-scale identification of protein-protein interaction of Escherichia coli K-12. , 2006, Genome research.

[14]  S. Shen-Orr,et al.  Networks Network Motifs : Simple Building Blocks of Complex , 2002 .

[15]  A. Emili,et al.  Interaction network containing conserved and essential protein complexes in Escherichia coli , 2005, Nature.

[16]  M E J Newman,et al.  Modularity and community structure in networks. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[17]  P. Bork,et al.  Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.

[18]  Christian von Mering,et al.  STRING: known and predicted protein–protein associations, integrated and transferred across organisms , 2004, Nucleic Acids Res..

[19]  Alfonso Valencia,et al.  Reductive genome evolution in Buchnera aphidicola , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[20]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[21]  U. Alon,et al.  Spontaneous evolution of modularity and network motifs. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[22]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[23]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[24]  Jürgen Gadau,et al.  The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[25]  M E J Newman,et al.  Finding and evaluating community structure in networks. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[26]  Hyunsoo Kim,et al.  Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae , 2006, BMC Bioinformatics.

[27]  Hidemi Watanabe,et al.  Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia , 2002, Nature Genetics.

[28]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Alexander Rives,et al.  Modular organization of cellular networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Nicola J. Rinaldi,et al.  Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.

[31]  James R. Knight,et al.  A Protein Interaction Map of Drosophila melanogaster , 2003, Science.