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Genome-wide analysis of the rice and Arabidopsis non-specific lipid transfer protein (nsLtp) gene families and identification of wheat nsLtp genes by EST data mining.

Boutrot F, Chantret N, Gautier MF - BMC Genomics (2008)

Bottom Line: We identified 156 putative wheat nsLtp genes, among which 91 were found in the 'Chinese Spring' cultivar.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: UMR1098 Développement et Amélioration des Plantes, INRA, F-34060 Montpellier, France. freddy.boutrot@sainsbury-laboratory.ac.uk

ABSTRACT

Background: Plant 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.

Results: In 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.

Conclusion: Our 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.

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Diversity of the eight cysteine motif in rice, arabidopsis and wheat nsLTP types. The consensus motif of each nsLTP type was deduced from the analysis of the matures sequences of the 52 rice nsLTPs, the 49 arabidopsis nsLTPs and the 156 wheat nsLTPs presented in Table 1, Table 2, and Additional file 2, respectively. AtLTPII.8 that appears to be more distantly related to other type II sequences (see the phylogenetic analysis) was excluded. The values allowing direct identification of the nsLTP type are grey boxed. a cysteine residue number 6 is missing in AtLTPII.10. b cysteine residue number 7 is missing in TaLTPVIa.5. c cysteine residue number 8 is missing in AtLTPI.1. d AtLTPII.10, OsLTPVI.1, OsLTPVI.2, OsLTPVI.4, and TaLTPVIa subfamily members harbor an extra cysteine residue. All type VI contain a Val 4 aa before Cys7 and a Met 10 aa before Cys7 allowing a distinction between type IV and type VI. e AtLTPII.6 harbors an extra cysteine residue. f TaLTPIVc.1 and TaLTPIVa subfamily members harbor an extra cysteine residue. g 12 amino acid residues were counted for the TaLTPIVd.1 that displays no CXC motif. h OsLTPVII.1 and TaLTPVIIa.1 subfamily members harbor an extra cysteine residue.
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Figure 5: Diversity of the eight cysteine motif in rice, arabidopsis and wheat nsLTP types. The consensus motif of each nsLTP type was deduced from the analysis of the matures sequences of the 52 rice nsLTPs, the 49 arabidopsis nsLTPs and the 156 wheat nsLTPs presented in Table 1, Table 2, and Additional file 2, respectively. AtLTPII.8 that appears to be more distantly related to other type II sequences (see the phylogenetic analysis) was excluded. The values allowing direct identification of the nsLTP type are grey boxed. a cysteine residue number 6 is missing in AtLTPII.10. b cysteine residue number 7 is missing in TaLTPVIa.5. c cysteine residue number 8 is missing in AtLTPI.1. d AtLTPII.10, OsLTPVI.1, OsLTPVI.2, OsLTPVI.4, and TaLTPVIa subfamily members harbor an extra cysteine residue. All type VI contain a Val 4 aa before Cys7 and a Met 10 aa before Cys7 allowing a distinction between type IV and type VI. e AtLTPII.6 harbors an extra cysteine residue. f TaLTPIVc.1 and TaLTPIVa subfamily members harbor an extra cysteine residue. g 12 amino acid residues were counted for the TaLTPIVd.1 that displays no CXC motif. h OsLTPVII.1 and TaLTPVIIa.1 subfamily members harbor an extra cysteine residue.

Mentions: The multiple alignment of the cysteine motifs of rice, arabidopsis and wheat nsLTPs also revealed a variable number of inter-cysteine amino acid residues (summarized in Figure 5). The AtLTPII.8 which is phylogenetically distant from all other type II nsLtp genes (see the phylogenetic analysis below) was not taken into consideration. In this way, seven nsLTP types can be identified through typical spacings for this motif. For example, type I nsLTPs contain 19 residues between the conserved Cys4 and Cys5 residues while types III, VII and VIII contain respectively 12, 27 and 25 residues between the conserved Cys6 and Cys7 residues. Similarly, types II, V and IX can be described with respectively 7, 14 and 13 residues between the conserved Cys1 and Cys2 residues. Only types IV and VI can not be distinguished based on this simple feature. A closer analysis of the sequences indicates that type VI nsLTPs are always characterized by a methionine and a valine residue present 10 and 4 aa before Cys7, respectively (Figures 2, 3, 4). At these positions, these two aa are always different in type IV nsLTPs and allow the direct distinction of type IV and VI nsLTPs.


Genome-wide analysis of the rice and Arabidopsis non-specific lipid transfer protein (nsLtp) gene families and identification of wheat nsLtp genes by EST data mining.

Boutrot F, Chantret N, Gautier MF - BMC Genomics (2008)

Diversity of the eight cysteine motif in rice, arabidopsis and wheat nsLTP types. The consensus motif of each nsLTP type was deduced from the analysis of the matures sequences of the 52 rice nsLTPs, the 49 arabidopsis nsLTPs and the 156 wheat nsLTPs presented in Table 1, Table 2, and Additional file 2, respectively. AtLTPII.8 that appears to be more distantly related to other type II sequences (see the phylogenetic analysis) was excluded. The values allowing direct identification of the nsLTP type are grey boxed. a cysteine residue number 6 is missing in AtLTPII.10. b cysteine residue number 7 is missing in TaLTPVIa.5. c cysteine residue number 8 is missing in AtLTPI.1. d AtLTPII.10, OsLTPVI.1, OsLTPVI.2, OsLTPVI.4, and TaLTPVIa subfamily members harbor an extra cysteine residue. All type VI contain a Val 4 aa before Cys7 and a Met 10 aa before Cys7 allowing a distinction between type IV and type VI. e AtLTPII.6 harbors an extra cysteine residue. f TaLTPIVc.1 and TaLTPIVa subfamily members harbor an extra cysteine residue. g 12 amino acid residues were counted for the TaLTPIVd.1 that displays no CXC motif. h OsLTPVII.1 and TaLTPVIIa.1 subfamily members harbor an extra cysteine residue.
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Figure 5: Diversity of the eight cysteine motif in rice, arabidopsis and wheat nsLTP types. The consensus motif of each nsLTP type was deduced from the analysis of the matures sequences of the 52 rice nsLTPs, the 49 arabidopsis nsLTPs and the 156 wheat nsLTPs presented in Table 1, Table 2, and Additional file 2, respectively. AtLTPII.8 that appears to be more distantly related to other type II sequences (see the phylogenetic analysis) was excluded. The values allowing direct identification of the nsLTP type are grey boxed. a cysteine residue number 6 is missing in AtLTPII.10. b cysteine residue number 7 is missing in TaLTPVIa.5. c cysteine residue number 8 is missing in AtLTPI.1. d AtLTPII.10, OsLTPVI.1, OsLTPVI.2, OsLTPVI.4, and TaLTPVIa subfamily members harbor an extra cysteine residue. All type VI contain a Val 4 aa before Cys7 and a Met 10 aa before Cys7 allowing a distinction between type IV and type VI. e AtLTPII.6 harbors an extra cysteine residue. f TaLTPIVc.1 and TaLTPIVa subfamily members harbor an extra cysteine residue. g 12 amino acid residues were counted for the TaLTPIVd.1 that displays no CXC motif. h OsLTPVII.1 and TaLTPVIIa.1 subfamily members harbor an extra cysteine residue.
Mentions: The multiple alignment of the cysteine motifs of rice, arabidopsis and wheat nsLTPs also revealed a variable number of inter-cysteine amino acid residues (summarized in Figure 5). The AtLTPII.8 which is phylogenetically distant from all other type II nsLtp genes (see the phylogenetic analysis below) was not taken into consideration. In this way, seven nsLTP types can be identified through typical spacings for this motif. For example, type I nsLTPs contain 19 residues between the conserved Cys4 and Cys5 residues while types III, VII and VIII contain respectively 12, 27 and 25 residues between the conserved Cys6 and Cys7 residues. Similarly, types II, V and IX can be described with respectively 7, 14 and 13 residues between the conserved Cys1 and Cys2 residues. Only types IV and VI can not be distinguished based on this simple feature. A closer analysis of the sequences indicates that type VI nsLTPs are always characterized by a methionine and a valine residue present 10 and 4 aa before Cys7, respectively (Figures 2, 3, 4). At these positions, these two aa are always different in type IV nsLTPs and allow the direct distinction of type IV and VI nsLTPs.

Bottom Line: We identified 156 putative wheat nsLtp genes, among which 91 were found in the 'Chinese Spring' cultivar.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: UMR1098 Développement et Amélioration des Plantes, INRA, F-34060 Montpellier, France. freddy.boutrot@sainsbury-laboratory.ac.uk

ABSTRACT

Background: Plant 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.

Results: In 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.

Conclusion: Our 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.

Show MeSH