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Coexpression patterns indicate that GPI-anchored non-specific lipid transfer proteins are involved in accumulation of cuticular wax, suberin and sporopollenin

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Abstract

The non-specific lipid transfer proteins (nsLTP) are unique to land plants. The nsLTPs are characterized by a compact structure with a central hydrophobic cavity and can be classified to different types based on sequence similarity, intron position or spacing between the cysteine residues. The type G nsLTPs (LTPGs) have a GPI-anchor in the C-terminal region which attaches the protein to the exterior side of the plasma membrane. The function of these proteins, which are encoded by large gene families, has not been systematically investigated so far. In this study we have explored microarray data to investigate the expression pattern of the LTPGs in Arabidopsis and rice. We identified that the LTPG genes in each plant can be arranged in three expression modules with significant coexpression within the modules. According to expression patterns and module sizes, the Arabidopsis module AtI is functionally equivalent to the rice module OsI, AtII corresponds to OsII and AtIII is functionally comparable to OsIII. Starting from modules AtI, AtII and AtIII we generated extended networks with Arabidopsis genes coexpressed with the modules. Gene ontology analyses of the obtained networks suggest roles for LTPGs in the synthesis or deposition of cuticular waxes, suberin and sporopollenin. The AtI-module is primarily involved with cuticular wax, the AtII-module with suberin and the AtIII-module with sporopollenin. Further transcript analysis revealed that several transcript forms exist for several of the LTPG genes in both Arabidopsis and rice. The data suggests that the GPI-anchor attachment and localization of LTPGs may be controlled to some extent by alternative splicing.

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Acknowledgments

The authors are grateful for the assistance from Muneeswaran Jayachandra Pandiyan during the initial phase of the study. This work was supported by Carl Tryggers Stiftelse.

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Authors and Affiliations

  1. IFM, Linköping University, 581 83, Linköping, Sweden

    Monika M. Edstam, Kristina Blomqvist, Anna Eklöf, Uno Wennergren & Johan Edqvist

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  1. Monika M. Edstam
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  2. Kristina Blomqvist
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  3. Anna Eklöf
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  4. Uno Wennergren
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  5. Johan Edqvist
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Correspondence to Johan Edqvist.

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11103_2013_113_MOESM8_ESM.pdf

Fuzzy C-Means plots for datasets Whole Plant, Biotic Stress, Abiotic Stress and Hormone. The plots illustrate to which probability (from 0 to 1) each AtLTPG belongs to each of three clusters. The genes in module AtI are green, genes in module AtII are red and genes placed in AtIII are blue (PDF 77 kb)

11103_2013_113_MOESM9_ESM.pdf

The expression pattern of members in module AtI after different abiotic stresses in shoot (top) and root (bottom). Each graph represents the expression level of one protein. Standard deviation is shown as error bars (PDF 267 kb)

11103_2013_113_MOESM10_ESM.pdf

The expression pattern of members in module AtI after different biotic stresses. Each graph represents the expression level of one protein. Standard deviation is shown as error bars (PDF 162 kb)

11103_2013_113_MOESM11_ESM.pdf

The expression pattern of members in module AtI after treatment with different chemicals. Each graph represents the expression level of one protein. Standard deviation is shown as error bars (PDF 154 kb)

11103_2013_113_MOESM12_ESM.pdf

The expression pattern of members in module AtII after different abiotic stresses in shoot (top) and root (bottom). Each graph represents the expression level of one protein. Standard deviation is shown as error bars (PDF 328 kb)

11103_2013_113_MOESM13_ESM.pdf

The expression pattern of members in module AtII after different biotic stresses. Each graph represents the expression level of one protein. Standard deviation is shown as error bars (PDF 104 kb)

11103_2013_113_MOESM14_ESM.pdf

The expression pattern of members in module AtII after different hormone treatments. Each graph represents the expression level of one protein. Standard deviation is shown as error bars (PDF 163 kb)

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The expression pattern of members in module AtIII after different abiotic stresses in shoot (top) and root (bottom). Each graph represents the expression level of one protein. Standard deviation is shown as error bars (PDF 380 kb)

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The expression pattern of members in module AtIII after different biotic stresses. Each graph represents the expression level of one protein. Standard deviation is shown as error bars (PDF 230 kb)

Supplementary material 17 (PDF 238 kb)

11103_2013_113_MOESM18_ESM.pdf

The expression pattern of members in module AtIII after different hormone treatments. Each graph represents the expression level of one protein. Standard deviation is shown as error bars (PDF 194 kb)

11103_2013_113_MOESM19_ESM.xls

The expression pattern of members in module AtIII after treatment with different chemicals. Each graph represents the expression level of one protein. Standard deviation is shown as error bars (XLS 52 kb)

Supplementary material 20 (XLS 47 kb)

Supplementary material 21 (XLS 41 kb)

11103_2013_113_MOESM22_ESM.pdf

Control of genomic DNA contamination in the RNA samples used for investigation of alternative splicing. The control is shown for tissues and conditions where alternative splicing was found. (A) The expression of AtLTPG1 in flower during normal growth conditions. Results from the synthesized cDNA (+RT) and the negative control (-RT) is shown. (B) The expression of AtLTPG1 in leaf during constant light. Only the negative control (-RT) is shown. (C) The expression of AtLTPG8 in leaf during normal growth conditions. Only the negative control (-RT) is shown. (D) The expression of AtLTPG8 in flower during constant light. Results from the synthesized cDNA (+RT) and the negative control (-RT) is shown. (E) The expression of AtLTPG11 in leaf during constant light. Only the negative control (-RT) is shown. (F) The expression of AtLTPG29 in flower during normal growth conditions. Results from the synthesized cDNA (+RT) and the negative control (-RT) is shown. (G) The expression of AtLTPG29 in silique during constant light. Only the negative control (-RT) is shown. (PDF 151 kb)

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Edstam, M.M., Blomqvist, K., Eklöf, A. et al. Coexpression patterns indicate that GPI-anchored non-specific lipid transfer proteins are involved in accumulation of cuticular wax, suberin and sporopollenin. Plant Mol Biol 83, 625–649 (2013). https://doi.org/10.1007/s11103-013-0113-5

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