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J. Biol. Chem., Vol. 280, Issue 21, 20894-20901, May 27, 2005

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Comprehensive Proteomic Analysis of Saccharomyces cerevisiae Cell Walls

IDENTIFICATION OF PROTEINS COVALENTLY ATTACHED VIA GLYCOSYLPHOSPHATIDYLINOSITOL REMNANTS OR MILD ALKALI-SENSITIVE LINKAGES^*

Qing Yuan Yin, Piet W. J. de Groot, Henk L. Dekker, Luitzen de Jong, Frans M. Klis¶, and Chris G. de Koster

From the Laboratory for Mass Spectrometry of Biomacromolecules and ^¶Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands

The cell wall of yeast contains proteins that are covalently bound to the glycan network. These cell wall proteins (CWPs) mediate cell-cell interactions and may be involved in cell wall biosynthesis. Using tandem mass spectrometry, we have identified 19 covalently bound CWPs of Saccharomyces cerevisiae. Twelve of them are shown for the first time to be covalently incorporated into the cell wall. The identified proteins include 12 predicted glycosylphosphatidylinositol-modified CWPs, all four members of the Pir protein family, and three additional proteins (Scw4p, Scw10p, and Tos1p) that are, like Pir proteins, connected to the cell wall glycan network via an alkali-sensitive linkage. However, Scw4p, Scw10p, and Tos1p do not contain internal repeat sequences shown to be essential for Pir protein incorporation and may represent a separate class of CWPs. Strikingly, seven of the identified proteins (Gas1p, Gas3p, Gas5p, Crh1p, Utr2p, Scw4p, and Scw10p) are classified as glycoside hydrolases. Phenotypic analysis of deletion mutants lacking the corresponding CWP-encoding genes indicated that most of them have altered cell wall properties, which reinforces the importance of the identified proteins for proper cell wall formation. In particular, gas1 and ecm33 were highly sensitive to Calcofluor White and high temperature, whereas gas1, scw4, and tos1 were highly resistant to incubation with -1,3-glucanase. The CWP identification method developed here relies on directly generating tryptic peptides from isolated cell walls and is independent of the nature of the covalent linkages between CWPs and cell wall glycans. Therefore, it will probably be equally effective in many other fungi.

Received for publication, January 10, 2005 , and in revised form, February 28, 2005.

^* This work was supported by the European Commission (QLK2-2000-00795; "Galar Fungail Consortium"). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains Supplemental Table I.

To whom correspondence should be addressed: Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands. Tel.: 31-20-525-7053; Fax: 31-20-525-7056; E-mail: pgroot{at}science.uva.nl.

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