Abstract
BackgroundPlant non-specific lipid transfer proteins (nsLTPs) are encoded by multigene families and possess physiological functions that remain unclear. Our objective was to characterize the complete nsLtp gene family in rice and arabidopsis and to perform wheat EST database mining for nsLtp gene discovery.ResultsIn this study, we carried out a genome-wide analysis of nsLtp gene families in Oryza sativa and Arabidopsis thaliana and identified 52 rice nsLtp genes and 49 arabidopsis nsLtp genes. Here we present a complete overview of the genes and deduced protein features. Tandem duplication repeats, which represent 26 out of the 52 rice nsLtp genes and 18 out of the 49 arabidopsis nsLtp genes identified, support the complexity of the nsLtp gene families in these species. Phylogenetic analysis revealed that rice and arabidopsis nsLTPs are clustered in nine different clades. In addition, we performed comparative analysis of rice nsLtp genes and wheat (Triticum aestivum) EST sequences indexed in the UniGene database. We identified 156 putative wheat nsLtp genes, among which 91 were found in the 'Chinese Spring' cultivar. The 122 wheat non-redundant nsLTPs were organized in eight types and 33 subfamilies. Based on the observation that seven of these clades were present in arabidopsis, rice and wheat, we conclude that the major functional diversification within the nsLTP family predated the monocot/dicot divergence. In contrast, there is no type VII nsLTPs in arabidopsis and type IX nsLTPs were only identified in arabidopsis. The reason for the larger number of nsLtp genes in wheat may simply be due to the hexaploid state of wheat but may also reflect extensive duplication of gene clusters as observed on rice chromosomes 11 and 12 and arabidopsis chromosome 5.ConclusionOur current study provides fundamental information on the organization of the rice, arabidopsis and wheat nsLtp gene families. The multiplicity of nsLTP types provide new insights on arabidopsis, rice and wheat nsLtp gene families and will strongly support further transcript profiling or functional analyses of nsLtp genes. Until such time as specific physiological functions are defined, it seems relevant to categorize plant nsLTPs on the basis of sequence similarity and/or phylogenetic clustering.
Highlights
Plant non-specific lipid transfer proteins are encoded by multigene families and possess physiological functions that remain unclear
The Oryza sativa nsLtp gene family is composed of 52 members Based on a conserved 8 CM, non-specific lipid transfer proteins (nsLTPs) remain a structurallyrelated family of proteins
Other proteins were discarded; they consist of three alpha-amylase/trypsin inhibitors which contain 10 cysteine residues engaged in five disulfide bonds [55], three prolamin storage proteins which lack the CXC motif and two 2S albumin storage proteins which present a molecular mass (MM) of about 20 kDa
Summary
Plant non-specific lipid transfer proteins (nsLTPs) are encoded by multigene families and possess physiological functions that remain unclear. The cysteine residues are engaged in four disulfide bonds that stabilize a hydrophobic cavity, which allows the binding of different lipids and hydrophobic compounds in vitro [3] Based on their molecular masses, plant nsLTPs were first separated into two types: type I (9 kDa) and type II (7 kDa) that are distinct both in terms of primary sequence identity (less than 30%) and lipid transfer efficiency [3]. They have different cysteine pairing patterns, type I and type II nsLTPs constitute a structurally related family of proteins. No structural data exists on the lipid transfer ability of type III nsLTPs
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