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

• Published in: PeerJ (San Francisco, CA) CA), 2019-08, Vol.7, p.e7504-e7504, Article e7504
• Main Authors: Fleury, Cécile, Gracy, Jérôme, Gautier, Marie-Françoise, Pons, Jean-Luc, Dufayard, Jean-François, Labesse, Gilles, Ruiz, Manuel, de Lamotte, Frédéric
• Format: Article
• Language: English
• Subjects: Amino acid sequence; Amino acids; Analysis; Biochemistry; Biochemistry, Molecular Biology; Bioinformatics; Case studies; Computational biology; Computational Science; Computer Science; Defense mechanisms; Divergence; Evolution (Biology); Gene expression; Genomes; Handedness; Life Sciences; Lipid transfer proteins; Lipids; Localization; Molecular modeling; Multigenic family; nsLTP; Peptides; Phylogenetics; Phylogeny; Physiological aspects; Plant; Plant breeding; Plant Science; Protein structure; Proteins; Seeds; Structure-function relationships; Superhelix; Tobacco; Vegetal Biology
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.7504

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. 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. 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.