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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
Modeling protein network evolution under genome duplication and domain shuffling.
Kirill Evlampiev1, Hervé Isambert
1RNA dynamics and Biomolecular Systems Lab, CNRS UMR168, Institut Curie, Section de Recherche, 11 rue P, & M, Curie, 75005 Paris, France. kirill.evlampiev@curie.fr
BMC Systems Biology
|November 15, 2007
Summary
Genome duplication drives protein-protein interaction network evolution, creating scale-free topologies through asymmetric gene divergence and domain conservation. This explains network structure across eukaryotes.
Area of Science:
- Evolutionary biology
- Systems biology
- Bioinformatics
Background:
- Eukaryotic genomes have undergone successive whole genome duplications.
- These duplications significantly influence the evolution of protein-protein interaction (PPI) networks.
- Previous models focused on linear network growth, not accounting for exponential duplication events.
Purpose of the Study:
- To develop and solve a mathematical model for PPI network evolution under successive genome duplications.
- To demonstrate the intrinsic link between evolutionary conservation, scale-free topology, and genome duplication.
- To investigate the role of asymmetric gene duplicate divergence in PPI network formation.
Main Methods:
- Mathematical modeling of PPI network evolution.
- Analysis of gene duplication and divergence dynamics.
- Numerical simulations using S. cerevisiae PPI network data.
Main Results:
- Genome duplication leads to exponential network growth and scale-free topology.
- Asymmetric divergence of gene duplicates, particularly at protein-binding sites, is crucial.
- PPI network topology is robust to domain shuffling and detailed evolutionary parameters.
- The model accurately reproduces large-scale features of S. cerevisiae PPI networks.
Conclusions:
- Genome duplication is a primary driver of PPI network conservation and topology across eukaryotes.
- Scale-free network properties arise from conserved protein-binding domains and asymmetric duplication/divergence.
- Domain shuffling does not disrupt the fundamental scale-free nature of PPI networks.
Related Concept Videos
02:26Conservation of Protein Domains Over Different Proteins
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
02:26Conservation of Protein Domains
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
02:32Exon Recombination
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Exon shuffling follows “splice frame rules.” Each exon has three reading...
03:21Genome Size and the Evolution of New Genes
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.