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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

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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.

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Acknowledgements

This work was supported by the French National Research Agency (ANR-10-LABEX-04 GRAL Labex, Grenoble Alliance for Integrated Structural Cell Biology; ANR-11-BTBR-0008 Océanomics; ANR-15-IDEX-02 GlycoAlps and “Origin Of Life” Cross Disciplinary Projects of the Univ. Grenoble-Alpes; ANR-17-EURE-0003).

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Authors and Affiliations

  1. Univ. Grenoble Alpes, INES, 73375, Le Bourget du Lac, France

    Sylvain Lespinats & Benoît Colange

  2. Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium

    Olivier De Clerck

  3. Department of Biology, Laboratory of Functional Plant Biology, Ghent University, K.L Ledeganckstraat 35, 9000, Ghent, Belgium

    Vera Gorelova & Dominique Van Der Straeten

  4. Department of Botany and Plant Biology, Laboratory of Plant Biochemistry and Physiology, University of Geneva, Quai E. Ansermet 30, 1211, Geneva, Switzerland

    Vera Gorelova

  5. Univ. Grenoble Alpes, CEA, CNRS, INRA, BIG-LPCV, 38000, Grenoble, France

    Delphine Grando, Eric Maréchal, Fabrice Rébeillé & Olivier Bastien

  6. Laboratoire de Physiologie Cellulaire Végétale, Département Réponse et Dynamique Cellulaire, CEA Grenoble, UMR 5168, CNRS-CEA-INRA-Université J. Fourier, 17 rue des Martyrs, 38054, Grenoble Cedex 09, France

    Olivier Bastien

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  1. Sylvain Lespinats
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Lespinats, S., De Clerck, O., Colange, B. et al. Phylogeny and Sequence Space: A Combined Approach to Analyze the Evolutionary Trajectories of Homologous Proteins. The Case Study of Aminodeoxychorismate Synthase. Acta Biotheor 68, 139–156 (2020). https://doi.org/10.1007/s10441-019-09352-0

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