publication . Article . 2018

Synchronous birth is a dominant pattern in receptor-ligand evolution

Grandchamp, Anna; Monget, Philippe;
Open Access English
  • Published: 01 Aug 2018 Journal: BMC Genomics, volume 19 (eissn: 1471-2164, Copyright policy)
  • Publisher: BioMed Central
Abstract
Background Interactions between proteins are key components in the chemical and physical processes of living organisms. Among these interactions, membrane receptors and their ligands are particularly important because they are at the interface between extracellular and intracellular environments. Many studies have investigated how binding partners have co-evolved in genomes during the evolution. However, little is known about the establishment of the interaction on a phylogenetic scale. In this study, we systematically studied the time of birth of genes encoding human membrane receptors and their ligands in the animal tree of life. We examined a total of 553 pai...
Subjects
free text keywords: Research Article, Ligand, Receptor, Phylogeny, Co-appearance, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], TP248.13-248.65, QH426-470, Ligand;Receptor;Phylogeny;Co-appearance, Biotechnology, Genetics, Phylogenetics, Intracellular, Evolutionary biology, Phylogenetic tree, Cell surface receptor, Gene, Biology, Extracellular
66 references, page 1 of 5

1. Andreani J, Guerois R. Evolution of protein interactions: from Interactomes to interfaces. Arch Biochem Biophys. 2014;554:65-75. [OpenAIRE]

2. Lynch M, Hagner K. Evolutionary meandering of intermolecular interactions along the drift barrier. Proc Natl Acad Sci. 2015;112(1):E30-8.

3. Fraser HB, Hirsh AE, Wall DP, Eisen MB. Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A. 2004;101(24):9033-8.

4. Rand DM, Haney RA, Fry AJ. Cytonuclear coevolution: the genomics of cooperation. Trends Ecol Evol. 2004;19(12):645-53. Schlesinger, K. J., Stromberg, S. P., & Carlson, J. M. (2014). Coevolutionary immune system dynamics driving pathogen speciation. PLoS One, 9(7), e102821.

5. Lewis AC, Saeed R, Deane CM. Predicting protein-protein interactions in the context of protein evolution. Mol BioSyst. 2010;6(1):55-64.

6. Bloom JD, Wilke CO, Arnold FH, Adami C. Stability and the evolvability of function in a model protein. Biophys J. 2004;86(5):2758-64.

7. Williams PD, Pollock DD, Goldstein RA. Evolution of functionality in lattice proteins. J Mol Graph Model. 2001;19(1):150-6.

8. Wuchty S, Oltvai ZN, Barabási A-L. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet. 2003; 35(2):176-9.

9. Lovell SC, Robertson DL. An integrated view of molecular coevolution in protein-protein interactions. Mol Biol Evol. 2010;27(11):2567-75.

10. Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science. 2015;348(6237):921-5.

11. Mintseris J, Weng Z. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci U S A. 2005; 102(31):10930-5. [OpenAIRE]

12. Jack BR, Meyer AG, Echave J, Wilke CO. Functional sites induce long-range evolutionary constraints in enzymes. PLoS Biol. 2016;14(5):e1002452.

13. Echave J, Wilke CO. Biophysical models of protein evolution: Understanding the patterns of evolutionary sequence divergence. Annu Rev Biophys. 2017; 46:85-103.

14. Innan H, Kondrashov F. The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet. 2010;11(2):97-108.

15. Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405(6784):299-304. [OpenAIRE]

66 references, page 1 of 5
Abstract
Background Interactions between proteins are key components in the chemical and physical processes of living organisms. Among these interactions, membrane receptors and their ligands are particularly important because they are at the interface between extracellular and intracellular environments. Many studies have investigated how binding partners have co-evolved in genomes during the evolution. However, little is known about the establishment of the interaction on a phylogenetic scale. In this study, we systematically studied the time of birth of genes encoding human membrane receptors and their ligands in the animal tree of life. We examined a total of 553 pai...
Subjects
free text keywords: Research Article, Ligand, Receptor, Phylogeny, Co-appearance, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], TP248.13-248.65, QH426-470, Ligand;Receptor;Phylogeny;Co-appearance, Biotechnology, Genetics, Phylogenetics, Intracellular, Evolutionary biology, Phylogenetic tree, Cell surface receptor, Gene, Biology, Extracellular
66 references, page 1 of 5

1. Andreani J, Guerois R. Evolution of protein interactions: from Interactomes to interfaces. Arch Biochem Biophys. 2014;554:65-75. [OpenAIRE]

2. Lynch M, Hagner K. Evolutionary meandering of intermolecular interactions along the drift barrier. Proc Natl Acad Sci. 2015;112(1):E30-8.

3. Fraser HB, Hirsh AE, Wall DP, Eisen MB. Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A. 2004;101(24):9033-8.

4. Rand DM, Haney RA, Fry AJ. Cytonuclear coevolution: the genomics of cooperation. Trends Ecol Evol. 2004;19(12):645-53. Schlesinger, K. J., Stromberg, S. P., & Carlson, J. M. (2014). Coevolutionary immune system dynamics driving pathogen speciation. PLoS One, 9(7), e102821.

5. Lewis AC, Saeed R, Deane CM. Predicting protein-protein interactions in the context of protein evolution. Mol BioSyst. 2010;6(1):55-64.

6. Bloom JD, Wilke CO, Arnold FH, Adami C. Stability and the evolvability of function in a model protein. Biophys J. 2004;86(5):2758-64.

7. Williams PD, Pollock DD, Goldstein RA. Evolution of functionality in lattice proteins. J Mol Graph Model. 2001;19(1):150-6.

8. Wuchty S, Oltvai ZN, Barabási A-L. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet. 2003; 35(2):176-9.

9. Lovell SC, Robertson DL. An integrated view of molecular coevolution in protein-protein interactions. Mol Biol Evol. 2010;27(11):2567-75.

10. Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science. 2015;348(6237):921-5.

11. Mintseris J, Weng Z. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci U S A. 2005; 102(31):10930-5. [OpenAIRE]

12. Jack BR, Meyer AG, Echave J, Wilke CO. Functional sites induce long-range evolutionary constraints in enzymes. PLoS Biol. 2016;14(5):e1002452.

13. Echave J, Wilke CO. Biophysical models of protein evolution: Understanding the patterns of evolutionary sequence divergence. Annu Rev Biophys. 2017; 46:85-103.

14. Innan H, Kondrashov F. The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet. 2010;11(2):97-108.

15. Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405(6784):299-304. [OpenAIRE]

66 references, page 1 of 5
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