Evolutionary conservation of motif constituents in the yeast protein interaction network

By S. Wuchty, Zoltn Oltvai, Albert-László Barabási. Nature Genetics, 2003

458 citations recorded by the source corpus.

Understanding why some cellular components are conserved across species but others evolve rapidly is a key question of modern biology. Here we show that in Saccharomyces cerevisiae, proteins organized in cohesive patterns of interactions are conserved to a substantially higher degree than those that do not participate in such motifs. We find that the conservation of proteins in distinct topological motifs correlates with the interconnectedness and function of that motif and also depends on the structure of the overall interactome topology. These findings indicate that motifs may represent evolutionary conserved topological units of cellular networks molded in accordance with the specific biological function in which they participate.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/279c7d0f8cce4f71a6e15b847e249d583160d7f2

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Citations in the corpus

Protein interaction networks from yeast to human. (2004, background): “In addition to the study of the global topology of interaction networks, the existence of recurring local topological features, known as network motifs, has been shown first in transcriptional networks [53] and later in protein networks [54].”
Bio::Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping (2011, background): “It has been shown that the connectivity of well-conserved proteins in PPI networks is negatively correlated with their rate of evolution [53,54] and, as a consequence, more connected proteins evolve at lower rate because they are subject to higher pressure to co-evolve with interacting proteins.”
Integrative approaches for finding modular structure in biological networks (2013, background): “Biological networks undergo substantial rewiring through evolutionary time, concomitant with gains, losses or modifications of gene functions 107–110 .”
Network biology: understanding the cell's functional organization (2004, background): “The high degree of evolutionary conservation of motif constituents within the yeast protein interaction networ”
Analyzing and modeling real-world phenomena with complex networks: a survey of applications (2007, background): “They observed that some motifs are conserved from simple organisms to more complex ones [340].”
Interaction network containing conserved and essential protein complexes in Escherichia coli (2005, background): “χ also bound PriA (primosomal DNA helicase), b1808 (putative ATP-dependent helicase) and TopA (DNA topoisomerase I), along with three conserved replication factors that act coordinately in vitro”
Binding properties and evolution of homodimers in protein–protein interaction networks (2005, background): “In support of this conclusion, we note that self-interacting proteins also have about twice as many interaction partners compared with non-dimers (Table 1). Indeed, the number of interaction partners of a protein was shown before to be positively correlated with its probability to be essential for t”
Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network (2004, background): “The high degree of evolutionary conservation of the motif constituents within the yeast protein interaction network [6], and the convergent evolution observed in the transcriptional regulatory network of diverse species towards the same motif types [7,8] suggest that motifs are indeed of direct biol”
Network analyses in systems pharmacology (2009, background): “These have shed light onto the information processing capabilities of the network and suggested mechanisms of network evolution (Barabasi and Albert 1999; Ma'ayan et al., 2005; Muller et al., 2008; Wuchty et al., 2003).”
Identifying gene-disease associations using centrality on a literature mined gene-interaction network (2008, methodology): “To our knowledge, this is the first effort of building a gene-interaction network by automatic literature mining and applying network centrality to predict genedisease associations on that network.”
A human protein-protein interaction network: a resource for annotating the proteome. (2005, unknown): “Therefore, Y2H interactions that are present in three- and four-protein-interaction loop motifs (Goldberg and Roth, 2003; Wuchty et al., 2003; Yeger-Lotem et al., 2004) were identified.”
Comparative Genomics in Eukaryotes (2005, background): “, 2002) or when they are part of relatively densely connected motifs (Wuchty et al., 2003).”
Scale-free networks in cell biology (2005, background): “, 2003) and evolutionarily conserved (Wuchty et al., 2003), partly because of their enrichment in protein complexes.”
Online Predicted Human Interaction Database (2005, unknown): “While these predictions should be thought of as hypotheses until experimentally validated, there is increasing evidence that PPIs are conserved through evolution (Pagel et al. , 2004; Wuchty et al. , 2003).”
Functional and evolutionary inference in gene networks: does topology matter? (2006, background): “Another notable recent contribution is the work of Wuchty et al. (2003), who demonstrated greater evolutionary conservation of proteins participating in particular motifs in the yeast protein-interaction network.”
Analysis of Biological Networks (2008, background): “In one of the seminal papers of complex network theory, Watts and Strogatz proposed a model for coexistence of local structure on the one hand, and a small average path length on the other hand [72].”