Background on Protein Protein Interaction Network Evolution

نویسندگان

  • Steffen Brasch
  • Lars Linsen
  • Georg Fuellen
چکیده

Proteins are linear polymers built from 20 building blocks called amino acids. Parts of a protein that are found conserved in many other proteins are called domains; these domains are usually responsible for the protein-protein interactions. Protein-protein interactions (PPIs) are transient or permanent connections between proteins, and they are important for many biological phenomena such as signaling, transcriptional regulation, and multi-enzyme complexes. They are explained by molecular adhesive forces between parts of the proteins (domains) which in turn can be tracked down to the atomic level. Interaction networks evolve by the loss and gain of nodes (proteins) and links (interactions). Biologists assume that the complex networks interconnecting the components of an organism such as a human being are, like all of life, the result of a more or less gradual evolutionary process of descent with modification. Emergence of biological complexity is nevertheless poorly understood, and a deeper understanding is of utmost importance. The most simple kind of evolutionary scenario yielding a complex interaction network is depicted in Figure I. A single protein without any interaction partners except itself is the most simple network (Figure I a). This protein is duplicated (by duplication of the underlying genomic material, i.e. the gene), and we observe two identical proteins that interact with each other (Figure I b). Evolution goes on, and the proteins become gradually different in shape and function, and we observe a small network of two distinct proteins related by duplication; they are called paralogs, and inherited interactions are called paralogous. Further duplications give rise to a more complex network of paralogs (Figure I c); note that some interactions were lost after duplication. Assume that we have followed the evolution of our proteins and their network up to the common ancestor of, for example, human and fly. After speciation, entities evolve differently in the two lineages of descent that yield the two different species (Figure I d and d’). The proteins related by speciation are called orthologs and the inherited interactions and the networks themselves are called orthologous. Conservation of PPIs across species has been observed in many cases [1, 2, 3], for example for the transcriptional network which regulates the development of the heart. It is regulated by interactions which have been conserved at least since the last common ancestor of human and fly [4]. By comparing the networks of many species,

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تاریخ انتشار 2009