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Acta Biotheor. 2019 Jul 16. doi: 10.1007/s10441-019-09352-0. [Epub ahead of print]

Phylogeny and Sequence Space: A Combined Approach to Analyze the Evolutionary Trajectories of Homologous Proteins. The Case Study of Aminodeoxychorismate Synthase.

Author information

1
Univ. Grenoble Alpes, INES, 73375, Le Bourget du Lac, France.
2
Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium.
3
Department of Biology, Laboratory of Functional Plant Biology, Ghent University, K.L Ledeganckstraat 35, 9000, Ghent, Belgium.
4
Department of Botany and Plant Biology, Laboratory of Plant Biochemistry and Physiology, University of Geneva, Quai E. Ansermet 30, 1211, Geneva, Switzerland.
5
Univ. Grenoble Alpes, CEA, CNRS, INRA, BIG-LPCV, 38000, Grenoble, France.
6
Univ. Grenoble Alpes, CEA, CNRS, INRA, BIG-LPCV, 38000, Grenoble, France. olivier.bastien@cea.fr.
7
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@cea.fr.

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:

ADC synthase; Multi-dimensional scaling; Phylogenetic method; Phylogenetic tree; Sequence space

PMID:
31312977
DOI:
10.1007/s10441-019-09352-0

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