Protein co-evolution, co-adaptation and interactions

Co‐evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host–parasite and predator–prey interactions, symbiosis and mutualism. The extrapolation of the concepts and methodologies developed for the study of species co‐evolution at t...

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Published inThe EMBO journal Vol. 27; no. 20; pp. 2648 - 2655
Main Authors Pazos, Florencio, Valencia, Alfonso
Format Journal Article
LanguageEnglish
Published Chichester, UK John Wiley & Sons, Ltd 22.10.2008
Nature Publishing Group UK
Springer Nature B.V
Nature Publishing Group
Subjects
Animals
Biological Evolution
co-evolution
Escherichia coli - metabolism
Evolution & development
Evolution, Molecular
Genomics
Humans
interactome
mirrortree
Models, Biological
Molecular biology
Mutation
Mutualism
New EMBO Member's Review
Parasites
phylogenetic tree
Phylogeny
Predator-prey interactions
Prey
Protein Interaction Mapping
protein-protein interaction
Proteins
Proteins - chemistry
Proteins - genetics
Proteome
Symbiosis
Systems Biology
protein–protein interaction
phylogenetic tree
interactome
co‐evolution
Online AccessGet full text
ISSN0261-4189
1460-2075
1460-2075
DOI10.1038/emboj.2008.189

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Abstract Co‐evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host–parasite and predator–prey interactions, symbiosis and mutualism. The extrapolation of the concepts and methodologies developed for the study of species co‐evolution at the molecular level has prompted the development of a variety of computational methods able to predict protein interactions through the characteristics of co‐evolution. Particularly successful have been those methods that predict interactions at the genomic level based on the detection of pairs of protein families with similar evolutionary histories (similarity of phylogenetic trees: mirrortree ). Future advances in this field will require a better understanding of the molecular basis of the co‐evolution of protein families. Thus, it will be important to decipher the molecular mechanisms underlying the similarity observed in phylogenetic trees of interacting proteins, distinguishing direct specific molecular interactions from other general functional constraints. In particular, it will be important to separate the effects of physical interactions within protein complexes (‘co‐adaptation’) from other forces that, in a less specific way, can also create general patterns of co‐evolution.
AbstractList Co‐evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host–parasite and predator–prey interactions, symbiosis and mutualism. The extrapolation of the concepts and methodologies developed for the study of species co‐evolution at the molecular level has prompted the development of a variety of computational methods able to predict protein interactions through the characteristics of co‐evolution. Particularly successful have been those methods that predict interactions at the genomic level based on the detection of pairs of protein families with similar evolutionary histories (similarity of phylogenetic trees: mirrortree). Future advances in this field will require a better understanding of the molecular basis of the co‐evolution of protein families. Thus, it will be important to decipher the molecular mechanisms underlying the similarity observed in phylogenetic trees of interacting proteins, distinguishing direct specific molecular interactions from other general functional constraints. In particular, it will be important to separate the effects of physical interactions within protein complexes (‘co‐adaptation’) from other forces that, in a less specific way, can also create general patterns of co‐evolution.
Co-evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host–parasite and predator–prey interactions, symbiosis and mutualism. The extrapolation of the concepts and methodologies developed for the study of species co-evolution at the molecular level has prompted the development of a variety of computational methods able to predict protein interactions through the characteristics of co-evolution. Particularly successful have been those methods that predict interactions at the genomic level based on the detection of pairs of protein families with similar evolutionary histories (similarity of phylogenetic trees: mirrortree ). Future advances in this field will require a better understanding of the molecular basis of the co-evolution of protein families. Thus, it will be important to decipher the molecular mechanisms underlying the similarity observed in phylogenetic trees of interacting proteins, distinguishing direct specific molecular interactions from other general functional constraints. In particular, it will be important to separate the effects of physical interactions within protein complexes (‘co-adaptation') from other forces that, in a less specific way, can also create general patterns of co-evolution.
Co-evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host-parasite and predator-prey interactions, symbiosis and mutualism. The extrapolation of the concepts and methodologies developed for the study of species co-evolution at the molecular level has prompted the development of a variety of computational methods able to predict protein interactions through the characteristics of co-evolution. Particularly successful have been those methods that predict interactions at the genomic level based on the detection of pairs of protein families with similar evolutionary histories (similarity of phylogenetic trees: mirrortree). Future advances in this field will require a better understanding of the molecular basis of the co-evolution of protein families. Thus, it will be important to decipher the molecular mechanisms underlying the similarity observed in phylogenetic trees of interacting proteins, distinguishing direct specific molecular interactions from other general functional constraints. In particular, it will be important to separate the effects of physical interactions within protein complexes ('co-adaptation') from other forces that, in a less specific way, can also create general patterns of co-evolution.Co-evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host-parasite and predator-prey interactions, symbiosis and mutualism. The extrapolation of the concepts and methodologies developed for the study of species co-evolution at the molecular level has prompted the development of a variety of computational methods able to predict protein interactions through the characteristics of co-evolution. Particularly successful have been those methods that predict interactions at the genomic level based on the detection of pairs of protein families with similar evolutionary histories (similarity of phylogenetic trees: mirrortree). Future advances in this field will require a better understanding of the molecular basis of the co-evolution of protein families. Thus, it will be important to decipher the molecular mechanisms underlying the similarity observed in phylogenetic trees of interacting proteins, distinguishing direct specific molecular interactions from other general functional constraints. In particular, it will be important to separate the effects of physical interactions within protein complexes ('co-adaptation') from other forces that, in a less specific way, can also create general patterns of co-evolution.
Co-evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host-parasite and predator-prey interactions, symbiosis and mutualism. The extrapolation of the concepts and methodologies developed for the study of species co-evolution at the molecular level has prompted the development of a variety of computational methods able to predict protein interactions through the characteristics of co-evolution. Particularly successful have been those methods that predict interactions at the genomic level based on the detection of pairs of protein families with similar evolutionary histories (similarity of phylogenetic trees: mirrortree). Future advances in this field will require a better understanding of the molecular basis of the co-evolution of protein families. Thus, it will be important to decipher the molecular mechanisms underlying the similarity observed in phylogenetic trees of interacting proteins, distinguishing direct specific molecular interactions from other general functional constraints. In particular, it will be important to separate the effects of physical interactions within protein complexes ('co-adaptation') from other forces that, in a less specific way, can also create general patterns of co-evolution. [PUBLICATION ABSTRACT]
Author Pazos, Florencio
Valencia, Alfonso
Author_xml – sequence: 1
  givenname: Florencio
  surname: Pazos
  fullname: Pazos, Florencio
  organization: Structure of Macromolecules, Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
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  surname: Valencia
  fullname: Valencia, Alfonso
  email: valencia@cnio.es
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/18818697$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
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DocumentTitleAlternate Protein co-evolution, co-adaptation and interactions
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Issue 20
Keywords protein–protein interaction
phylogenetic tree
interactome
co‐evolution
Language English
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This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation or the creation of derivative works without specific permission.
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Snippet Co‐evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host–parasite and predator–prey...
Co-evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host-parasite and predator-prey...
Co-evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host–parasite and predator–prey...
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pubmed
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wiley
springer
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StartPage 2648
SubjectTerms Animals
Biological Evolution
co-evolution
Escherichia coli - metabolism
Evolution & development
Evolution, Molecular
Genomics
Humans
interactome
mirrortree
Models, Biological
Molecular biology
Mutation
Mutualism
New EMBO Member's Review
Parasites
phylogenetic tree
Phylogeny
Predator-prey interactions
Prey
Protein Interaction Mapping
protein-protein interaction
Proteins
Proteins - chemistry
Proteins - genetics
Proteome
Symbiosis
Systems Biology
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Title Protein co-evolution, co-adaptation and interactions
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https://link.springer.com/article/10.1038/emboj.2008.189
https://onlinelibrary.wiley.com/doi/abs/10.1038%2Femboj.2008.189
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Volume 27
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