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Genome-wide analysis of cell wall-related genes in Tuber melanosporum

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Abstract

A genome-wide inventory of proteins involved in cell wall synthesis and remodeling has been obtained by taking advantage of the recently released genome sequence of the ectomycorrhizal Tuber melanosporum black truffle. Genes that encode cell wall biosynthetic enzymes, enzymes involved in cell wall polysaccharide synthesis or modification, GPI-anchored proteins and other cell wall proteins were identified in the black truffle genome. As a second step, array data were validated and the symbiotic stage was chosen as the main focus. Quantitative RT-PCR experiments were performed on 29 selected genes to verify their expression during ectomycorrhizal formation. The results confirmed the array data, and this suggests that cell wall-related genes are required for morphogenetic transition from mycelium growth to the ectomycorrhizal branched hyphae. Labeling experiments were also performed on T. melanosporum mycelium and ectomycorrhizae to localize cell wall components.

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Acknowledgments

The Tuber genome sequencing project is a collaborative effort involving the Génoscope-CEA and the Tuber Genome Consortium. The authors would like to thank Emmanuelle Morin and Stefano Ghignone for the bioinformatics support; Elisa Zampieri for the help during the preparation of the manuscript, Michele Buffalini, Paola Ceccaroli and Shwet Kamal for the annotation of some genes cited in the paper. This research was funded by PRIN2007; FS’s fellowship PhD was funded by Università di Torino.

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Authors and Affiliations

  1. Istituto per la Protezione delle Piante del CNR, UOS Torino, Viale Mattioli, 25, 10125, Turin, Italy

    Raffaella Balestrini, Fabiano Sillo, Antonella Faccio & Paola Bonfante

  2. Dipartimento di Biologia Vegetale, UniTO, Turin, Italy

    Raffaella Balestrini, Fabiano Sillo, Antonella Faccio & Paola Bonfante

  3. UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, 54280, Champenoux, France

    Annegret Kohler, Emilie Tisserant & Francis Martin

  4. Bioinformatics Institute, A*Star, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore

    Georg Schneider

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  1. Raffaella Balestrini
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  2. Fabiano Sillo
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  3. Annegret Kohler
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  4. Georg Schneider
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Correspondence to Raffaella Balestrini.

Additional information

Communicated by B. Cormack.

R. Balestrini and F. Sillo equally contributed to the paper.

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Table S1 (DOC 55 kb)

Table S2 (DOC 235 kb)

Table S3 (DOC 38 kb)

294_2012_374_MOESM4_ESM.pdf

Table S4. GPI-prediction by using the fungal-specific big-PI algorithm (Eisenhaber et al. 2004) and checking for a predicted signal peptide (Bendtsen et al. 2004). There is experimental evidence for alternative or secondary GPI-anchor attachment sites (Eisenhaber et al. 1999). As such, the predictor reports a main and a secondary site (1: and 2:), each one classified with a letter (P, predicted; S, twilight zone prediction; I, physical properties are not right, but profile matches; N, neither physical properties nor profile matches). The best hit is shown first and is either P or S: if the first one is P, the second one can be P, S or N, or if the first one is S it can be S, I or N. An additional step to check for potential transmembrane domains (TM) in the mature protein has been performed. (PDF 52 kb)

294_2012_374_MOESM5_ESM.xls

Table S5. Expression data for the GPI-anchored protein subset. The individual sheets contain the array and the Solexa/Illumina data as explained in the Supplemental file. (XLS 36 kb)

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Balestrini, R., Sillo, F., Kohler, A. et al. Genome-wide analysis of cell wall-related genes in Tuber melanosporum . Curr Genet 58, 165–177 (2012). https://doi.org/10.1007/s00294-012-0374-6

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