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Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis.

ABSTRACT: Background:Non-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. Several hundreds of different nsLTP sequences-and counting-have been characterized so far, but their biological functions remain unclear. It has been clear for years that they present a certain interest for agronomic and nutritional issues. Deciphering their functions means collecting and analyzing a variety of data from gene sequence to protein structure, from cellular localization to the physiological role. As a huge and growing number of new protein sequences are available nowadays, extracting meaningful knowledge from sequence-structure-function relationships calls for the development of new tools and approaches. As nsLTPs show high evolutionary divergence, but a conserved common right handed superhelix structural fold, and as they are involved in a large number of key roles in plant development and defense, they are a stimulating case study for validating such an approach. Methods:In this study, we comprehensively investigated 797 nsLTP protein sequences, including a phylogenetic analysis on canonical protein sequences, three-dimensional structure modeling and functional annotation using several well-established bioinformatics programs. Additionally, two integrative methodologies using original tools were developed. The first was a new method for the detection of (i) conserved amino acid residues involved in structure stabilization and (ii) residues potentially involved in ligand interaction. The second was a structure-function classification based on the evolutionary trace display method using a new tree visualization interface. We also present a new tool for visualizing phylogenetic trees. Results:Following this new protocol, an updated classification of the nsLTP superfamily was established and a new functional hypothesis for key residues is suggested. Lastly, this work allows a better representation of the diversity of plant nsLTPs in terms of sequence, structure and function.

SUBMITTER: Fleury C

PROVIDER: S-EPMC6698131 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis.

Fleury Cécile C Gracy Jérôme J Gautier Marie-Françoise MF Pons Jean-Luc JL Dufayard Jean-François JF Labesse Gilles G Ruiz Manuel M de Lamotte Frédéric F

PeerJ 20190814

<h4>Background</h4>Non-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. Several hundreds of different nsLTP sequences-and counting-have been characterized so far, but their biological functions remain unclear. It has been clear for years that they present a certain interest for agronomic and nutritional issues. Deciphering their functions means collecting and analyzing a variety of data from gene sequence to p ...[more]

PMID: 31428542

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Dataset Information

Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis.

Publications

Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis.

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