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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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Multiple sequence alignment of rice nsLTPs. Amino acid sequences were deduced from nsLtp genes identified from the TIGR Rice Pseudomolecules release 4 (Table 1). Sequences were aligned using HMMERalign to maximize the eight-cysteine motif alignment, and manually refined. The conserved cysteine residues are black boxed and additional cysteine residues grey boxed.
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Figure 2: Multiple sequence alignment of rice nsLTPs. Amino acid sequences were deduced from nsLtp genes identified from the TIGR Rice Pseudomolecules release 4 (Table 1). Sequences were aligned using HMMERalign to maximize the eight-cysteine motif alignment, and manually refined. The conserved cysteine residues are black boxed and additional cysteine residues grey boxed.

Mentions: Since it allows all the cysteine residues to be maintained in a conserved position, the HMMalign program was preferred to ClustalW and was thus used to perform the multiple alignments of rice (Figure 2), arabidopsis (Figure 3) and wheat (Figure 4) nsLTPs. Based on the identity matrix (data not shown) calculated from the multiple sequence alignments and the nomenclature criteria that group mature proteins sharing more than 30% identity in a type [32], 49 out of the 52 rice nsLTPs, 45 out of the 49 arabidopsis nsLTPs and the 122 wheat nsLTPs were found to be clustered in nine types. The majority (147 out of 223) of the rice, arabidopsis and wheat nsLtp genes encode proteins that belong to the type I and type II nsLTPs. Fourteen rice, 15 arabidopsis and 34 wheat proteins described six new nsLTP types named types IV to IX. Three rice proteins and four arabidopsis proteins display less than 30% identity between themselves or with other nsLTPs to either make a type by themselves or be integrated in an already identified type. Therefore, these proteins were named OsLTPY.1 to OsLTPY.3 and AtLTPY.1 to AtLTPY.4.


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)

Multiple sequence alignment of rice nsLTPs. Amino acid sequences were deduced from nsLtp genes identified from the TIGR Rice Pseudomolecules release 4 (Table 1). Sequences were aligned using HMMERalign to maximize the eight-cysteine motif alignment, and manually refined. The conserved cysteine residues are black boxed and additional cysteine residues grey boxed.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2277411&req=5

Figure 2: Multiple sequence alignment of rice nsLTPs. Amino acid sequences were deduced from nsLtp genes identified from the TIGR Rice Pseudomolecules release 4 (Table 1). Sequences were aligned using HMMERalign to maximize the eight-cysteine motif alignment, and manually refined. The conserved cysteine residues are black boxed and additional cysteine residues grey boxed.
Mentions: Since it allows all the cysteine residues to be maintained in a conserved position, the HMMalign program was preferred to ClustalW and was thus used to perform the multiple alignments of rice (Figure 2), arabidopsis (Figure 3) and wheat (Figure 4) nsLTPs. Based on the identity matrix (data not shown) calculated from the multiple sequence alignments and the nomenclature criteria that group mature proteins sharing more than 30% identity in a type [32], 49 out of the 52 rice nsLTPs, 45 out of the 49 arabidopsis nsLTPs and the 122 wheat nsLTPs were found to be clustered in nine types. The majority (147 out of 223) of the rice, arabidopsis and wheat nsLtp genes encode proteins that belong to the type I and type II nsLTPs. Fourteen rice, 15 arabidopsis and 34 wheat proteins described six new nsLTP types named types IV to IX. Three rice proteins and four arabidopsis proteins display less than 30% identity between themselves or with other nsLTPs to either make a type by themselves or be integrated in an already identified type. Therefore, these proteins were named OsLTPY.1 to OsLTPY.3 and AtLTPY.1 to AtLTPY.4.

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