Abstract
BackgroundNon-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.MethodsIn 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.ResultsFollowing 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.
Highlights
Since the work of Kader, Julienne & Vergnolle (1984) and Kader (1996), numerous proteins capable of transferring lipids have been annotated as non-specific lipid transfer proteins
These studies involve a limited number of sequences and/or species: a total of 15 Non-specific Lipid Transfer Proteins (nsLTPs) identified in Arabidopsis (Arondel et al, 2000), restricted to Poaceae (Jang et al, 2007), Solanaceae (Liu et al, 2010; D’Agostino et al, 2019), or Gossypium (Li et al, 2016; Meng et al, 2018)
In all, including the wheat, rice and Arabidopsis sequences previously identified by Boutrot, Chantret & Gautier (2008), 797 non-redundant mature amino acid sequences belonging to more than 120 plant species were kept for analysis
Summary
Since the work of Kader, Julienne & Vergnolle (1984) and Kader (1996), numerous proteins capable of transferring lipids have been annotated as non-specific lipid transfer proteins (nsLTPs) Their primary sequences are characterized by a conserved 8-Cysteine Motif (8CM) (C-Xn-C-Xn-CC-Xn-CXC-Xn-C-Xn-C), which plays an important role in their structural scaffold (José-Estanyol, Gomis-Rüth & Puigdomènech, 2004). Plant nsLTPs are ubiquitous proteins encoded by multigene families, as reported in different phylogenetic studies. In comparison to previous studies, we computed the most extensive phylogenetic analysis, sampling 797 nsLTP sequences from 123 different species This allows to enrich the phylogenic tree of many evolutionary events that would have been hidden with more restrictive species choices. This work allows a better representation of the diversity of plant nsLTPs in terms of sequence, structure and function
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