Evolutionarily conserved motifs and modules in mitochondrial protein-protein interaction networks.

Advances in organelle interactomics have led to new insights into organelle functions. In this study, we considered the common mitochondrial PIN of four evolutionarily distant eukaryotic species, namely Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans. By comparative interactomics analysis of mitochondrial PINs in these organisms, five conserved modules were identified. Modules comprise the main mitochondrial tasks, including proteins involved in translation process, mitochondrial import inner membrane proteins, TCA cycle enzymes, mitochondrial electron transport chain, and metabolic enzymes. Furthermore, we reemphasize that subgraphs of network, i.e., motifs and themes, may represent evolutionarily conserved topological units which are biologically significant.

[1]  Damian Szklarczyk,et al.  The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored , 2010, Nucleic Acids Res..

[2]  Z N Oltvai,et al.  Evolutionary conservation of motif constituents in the yeast protein interaction network , 2003, Nature Genetics.

[3]  Sebastian Bonhoeffer,et al.  The Evolution of Connectivity in Metabolic Networks , 2005, PLoS biology.

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

[5]  Zhongming Zhao,et al.  Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana , 2008, Cell Research.

[6]  Antonio del Sol,et al.  Topology of small-world networks of protein?Cprotein complex structures , 2005, Bioinform..

[7]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[8]  William R. Penuel,et al.  The ‘New’ Science of Networks and the Challenge of School Change , 2007 .

[9]  Mathieu Bastian,et al.  Gephi: An Open Source Software for Exploring and Manipulating Networks , 2009, ICWSM.

[10]  Bill Doult,et al.  On with the new. , 1996, Nursing standard (Royal College of Nursing (Great Britain) : 1987).

[11]  Erich Bornberg-Bauer,et al.  The Evolution of Protein Interaction Networks in Regulatory Proteins , 2004, Comparative and functional genomics.

[12]  Falk Schreiber,et al.  Analysis of Biological Networks , 2008 .

[13]  G. Shadel,et al.  Expanding the mitochondrial interactome , 2007, Genome Biology.

[14]  Zhi Wang,et al.  Correction: In Search of the Biological Significance of Modular Structures in Protein Networks , 2007, PLoS Comput. Biol..

[15]  Joshua M. Stuart,et al.  A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules , 2003, Science.

[16]  Ernesto Estrada.  Quantifying network heterogeneity. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[17]  H. Hirt,et al.  Protein networking: insights into global functional organization of proteomes , 2008, Proteomics.

[18]  Jun Dong,et al.  Understanding network concepts in modules , 2007, BMC Systems Biology.

[19]  W. Martin,et al.  Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes , 2012, Microbiology and Molecular Reviews.

[20]  Dennis P Wall,et al.  A simple dependence between protein evolution rate and the number of protein-protein interactions , 2003, BMC Evolutionary Biology.

[21]  C. Cannings,et al.  On the structure of protein-protein interaction networks. , 2003, Biochemical Society transactions.

[22]  Peer Bork,et al.  Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle , 2006, PLoS genetics.

[23]  D. Ingber,et al.  High-Betweenness Proteins in the Yeast Protein Interaction Network , 2005, Journal of biomedicine & biotechnology.

[24]  E. Shoubridge,et al.  SURF1, encoding a factor involved in the biogenesis of cytochrome c oxidase, is mutated in Leigh syndrome , 1998, Nature Genetics.

[25]  David H Perlman,et al.  Software tool for researching annotations of proteins: open-source protein annotation software with data visualization. , 2009, Analytical chemistry.

[26]  Ioannis Xenarios,et al.  DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..

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

[28]  Peter Grindrod,et al.  Review of uses of network and graph theory concepts within proteomics , 2004, Expert review of proteomics.

[29]  Trey Ideker,et al.  Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..

[30]  G. Cesareni,et al.  Comparative interactomics: comparing apples and pears? , 2007, Trends in biotechnology.

[31]  A. Venkatakrishnan,et al.  MitoInteractome: Mitochondrial protein interactome database, and its application in 'aging network' analysis , 2009, BMC Genomics.

[32]  S. L. Wong,et al.  Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network , 2005, Journal of biology.

[33]  Peter Donnelly,et al.  Superfamilies of Evolved and Designed Networks , 2004 .

[34]  A. E. Hirsh,et al.  Protein dispensability and rate of evolution , 2001, Nature.

[35]  Falk Schreiber,et al.  MAVisto: a tool for the exploration of network motifs , 2005, Bioinform..

[36]  A. Wagner,et al.  Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications , 2002, BMC Evolutionary Biology.