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Phylogeny and sequence space : a combined approach to analyze the evolutionary trajectories of homologous proteins : the case study of aminodeoxychorismate synthase

(2020) ACTA BIOTHEORETICA. 68(1). p.139-156
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Abstract
During the course of evolution, variations of a protein sequence is an ongoing phenomenon however limited by the need to maintain its structural and functional integrity. Deciphering the evolutionary path of a protein is thus of fundamental interest. With the development of new methods to visualize high dimension spaces and the improvement of phylogenetic analysis tools, it is possible to study the evolutionary trajectories of proteins in the sequence space. Using the data-driven high-dimensional scaling method, we show that it is possible to predict and represent potential evolutionary trajectories by representing phylogenetic trees into a 3D projection of the sequence space. With the case of the aminodeoxychorismate synthase, an enzyme involved in folate synthesis, we show that this representation raises interesting questions about the complexity of the evolution of a given biological function, in particular concerning its capacity to explore the sequence space.
Keywords
Phylogenetic method, Multi-dimensional scaling, Sequence space, ADC synthase, Phylogenetic tree, FITNESS LANDSCAPES, ALIGNMENT, BIOSYNTHESIS, PERFORMANCE, DATABASE, ENCODES, POINTS, PLANTS, GENE

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MLA
Lespinats, Sylvain, et al. “Phylogeny and Sequence Space : A Combined Approach to Analyze the Evolutionary Trajectories of Homologous Proteins : The Case Study of Aminodeoxychorismate Synthase.” ACTA BIOTHEORETICA, vol. 68, no. 1, 2020, pp. 139–56, doi:10.1007/s10441-019-09352-0.
APA
Lespinats, S., De Clerck, O., Colange, B., Gorelova, V., Grando, D., Marechal, E., … Bastien, O. (2020). Phylogeny and sequence space : a combined approach to analyze the evolutionary trajectories of homologous proteins : the case study of aminodeoxychorismate synthase. ACTA BIOTHEORETICA, 68(1), 139–156. https://doi.org/10.1007/s10441-019-09352-0
Chicago author-date
Lespinats, Sylvain, Olivier De Clerck, Benoit Colange, Vera Gorelova, Delphine Grando, Eric Marechal, Dominique Van Der Straeten, Fabrice Rebeille, and Olivier Bastien. 2020. “Phylogeny and Sequence Space : A Combined Approach to Analyze the Evolutionary Trajectories of Homologous Proteins : The Case Study of Aminodeoxychorismate Synthase.” ACTA BIOTHEORETICA 68 (1): 139–56. https://doi.org/10.1007/s10441-019-09352-0.
Chicago author-date (all authors)
Lespinats, Sylvain, Olivier De Clerck, Benoit Colange, Vera Gorelova, Delphine Grando, Eric Marechal, Dominique Van Der Straeten, Fabrice Rebeille, and Olivier Bastien. 2020. “Phylogeny and Sequence Space : A Combined Approach to Analyze the Evolutionary Trajectories of Homologous Proteins : The Case Study of Aminodeoxychorismate Synthase.” ACTA BIOTHEORETICA 68 (1): 139–156. doi:10.1007/s10441-019-09352-0.
Vancouver
1.
Lespinats S, De Clerck O, Colange B, Gorelova V, Grando D, Marechal E, et al. Phylogeny and sequence space : a combined approach to analyze the evolutionary trajectories of homologous proteins : the case study of aminodeoxychorismate synthase. ACTA BIOTHEORETICA. 2020;68(1):139–56.
IEEE
[1]
S. Lespinats et al., “Phylogeny and sequence space : a combined approach to analyze the evolutionary trajectories of homologous proteins : the case study of aminodeoxychorismate synthase,” ACTA BIOTHEORETICA, vol. 68, no. 1, pp. 139–156, 2020.
@article{8626232,
  abstract     = {During the course of evolution, variations of a protein sequence is an ongoing phenomenon however limited by the need to maintain its structural and functional integrity. Deciphering the evolutionary path of a protein is thus of fundamental interest. With the development of new methods to visualize high dimension spaces and the improvement of phylogenetic analysis tools, it is possible to study the evolutionary trajectories of proteins in the sequence space. Using the data-driven high-dimensional scaling method, we show that it is possible to predict and represent potential evolutionary trajectories by representing phylogenetic trees into a 3D projection of the sequence space. With the case of the aminodeoxychorismate synthase, an enzyme involved in folate synthesis, we show that this representation raises interesting questions about the complexity of the evolution of a given biological function, in particular concerning its capacity to explore the sequence space.},
  author       = {Lespinats, Sylvain and De Clerck, Olivier and Colange, Benoit and Gorelova, Vera and Grando, Delphine and Marechal, Eric and Van Der Straeten, Dominique and Rebeille, Fabrice and Bastien, Olivier},
  issn         = {0001-5342},
  journal      = {ACTA BIOTHEORETICA},
  keywords     = {Phylogenetic method,Multi-dimensional scaling,Sequence space,ADC synthase,Phylogenetic tree,FITNESS LANDSCAPES,ALIGNMENT,BIOSYNTHESIS,PERFORMANCE,DATABASE,ENCODES,POINTS,PLANTS,GENE},
  language     = {eng},
  number       = {1},
  pages        = {139--156},
  title        = {Phylogeny and sequence space : a combined approach to analyze the evolutionary trajectories of homologous proteins : the case study of aminodeoxychorismate synthase},
  url          = {http://dx.doi.org/10.1007/s10441-019-09352-0},
  volume       = {68},
  year         = {2020},
}

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