J Theor Biol. 2003 May 21;222(2):199-210.

Evolving protein interaction networks through gene duplication.

Source

Dept. de Fisica, FEN, Universitat Politècnica de Catalunya, Campus Nord B4, 08034 Barcelona, Spain.

Abstract

The topology of the proteome map revealed by recent large-scale hybridization methods has shown that the distribution of protein-protein interactions is highly heterogeneous, with many proteins having few edges while a few of them are heavily connected. This particular topology is shared by other cellular networks, such as metabolic pathways, and it has been suggested to be responsible for the high mutational homeostasis displayed by the genome of some organisms. In this paper we explore a recent model of proteome evolution that has been shown to reproduce many of the features displayed by its real counterparts. The model is based on gene duplication plus re-wiring of the newly created genes. The statistical features displayed by the proteome of well-known organisms are reproduced and suggest that the overall topology of the protein maps naturally emerges from the two leading mechanisms considered by the model.

PMID:: 12727455; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

Proteome

LinkOut - more resources

Full Text Sources

Supplemental Content

Save items

Related citations in PubMed

Modeling protein network evolution under genome duplication and domain shuffling. [BMC Syst Biol. 2007]
Modeling protein network evolution under genome duplication and domain shuffling.
Evlampiev K, Isambert H. BMC Syst Biol. 2007 Nov 13; 1:49. Epub 2007 Nov 13.
Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins. [Biol Direct. 2007]
Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins.
Axelsen JB, Yan KK, Maslov S. Biol Direct. 2007 Nov 26; 2:32. Epub 2007 Nov 26.
Conservation and topology of protein interaction networks under duplication-divergence evolution. [Proc Natl Acad Sci U S A. 2008]
Conservation and topology of protein interaction networks under duplication-divergence evolution.
Evlampiev K, Isambert H. Proc Natl Acad Sci U S A. 2008 Jul 22; 105(29):9863-8. Epub 2008 Jul 16.
Review Innovation from reduction: gene loss, domain loss and sequence divergence in genome evolution. [Appl Bioinformatics. 2003]
Review Innovation from reduction: gene loss, domain loss and sequence divergence in genome evolution.
Braun EL. Appl Bioinformatics. 2003; 2(1):13-34.
Review Evolution in protein interaction networks: co-evolution, rewiring and the role of duplication. [Biochem Soc Trans. 2009]
Review Evolution in protein interaction networks: co-evolution, rewiring and the role of duplication.
Robertson DL, Lovell SC. Biochem Soc Trans. 2009 Aug; 37(Pt 4):768-71.

See reviews... See all...

Cited by 41 PubMed Central articles

Biological robustness: paradigms, mechanisms, and systems principles. [Front Genet. 2012]
Biological robustness: paradigms, mechanisms, and systems principles.
Whitacre JM. Front Genet. 2012; 3:67. Epub 2012 May 11.
Network evolution: rewiring and signatures of conservation in signaling. [PLoS Comput Biol. 2012]
Network evolution: rewiring and signatures of conservation in signaling.
Sun MG, Sikora M, Costanzo M, Boone C, Kim PM. PLoS Comput Biol. 2012 Mar; 8(3):e1002411. Epub 2012 Mar 15.
Evidence for network evolution in an Arabidopsis interactome map. [Science. 2011]
Evidence for network evolution in an Arabidopsis interactome map.
Arabidopsis Interactome Mapping Consortium. Science. 2011 Jul 29; 333(6042):601-7.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.
Cited in Books
NCBI Bookshelf books that cite the current articles.

Recent activity

Clear Turn Off Turn On

Evolving protein interaction networks through gene duplication.
Evolving protein interaction networks through gene duplication.
J Theor Biol. 2003 May 21 ;222(2):199-210.

PubMed
Properties of purified recombinant human polyamine oxidase, PAOh1/SMO.
Properties of purified recombinant human polyamine oxidase, PAOh1/SMO.
Biochem Biophys Res Commun. 2003 May 16 ;304(4):605-11.

PubMed
Quality of life of growth hormone (GH) deficient young adults during discontinua...
Quality of life of growth hormone (GH) deficient young adults during discontinuation and restart of GH therapy.
Psychoneuroendocrinology. 2003 Jul ;28(5):612-26.

PubMed
Emerging roles for E2F: beyond the G1/S transition and DNA replication.
Emerging roles for E2F: beyond the G1/S transition and DNA replication.
Cancer Cell. 2003 Apr ;3(4):311-6.

PubMed
Hydantoin-5-propionic aciduria in folic acid nondependent formiminoglutamic acid...
Hydantoin-5-propionic aciduria in folic acid nondependent formiminoglutamic aciduria observed in two siblings.
Pediatr Res. 1976 Apr ;10(4):215-9.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: