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J. Biol. Chem., Vol. 279, Issue 47, 49367-49383, November 19, 2004

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New Functions of the Thylakoid Membrane Proteome of Arabidopsis thaliana Revealed by a Simple, Fast, and Versatile Fractionation Strategy^*

Jean-Benoit Peltier, A. Jimmy Ytterberg, Qi Sun¶, and Klaas J. van Wijk||

From the Department of Plant Biology and the ^¶Computational Biology Service Unit, Cornell University, Ithaca, New York 14853

Identification of membrane proteomes remains challenging. Here, we present a simple, fast, and scalable off-line procedure based on three-phase partitioning with butanol to fractionate membrane proteomes in combination with both in-gel and in-solution digestions and mass spectrometry. This should help to further accelerate the field of membrane proteomics. Using this new strategy, we analyzed the salt-stripped thylakoid membrane of chloroplasts of Arabidopsis thaliana. 242 proteins were identified, at least 40% of which are integral membrane proteins. The functions of 86 proteins are unknown; these include proteins with TPR, PPR, rhodanese, and DnaJ domains. These proteins were combined with all known thylakoid proteins and chloroplast (associated) envelope proteins, collected from primary literature, resulting in 714 non-redundant proteins. They were assigned to functional categories using a classification developed for MapMan (Thimm, O., Blasing, O., Gibon, Y., Nagel, A., Meyer, S., Kruger, P., Selbig, J., Muller, L. A., Rhee, S. Y., and Stitt, M. (2004) Plant J. 37, 914–939), updated with information from primary literature. The analysis elucidated the likely location of many membrane proteins, including 190 proteins of unknown function, holding the key to better understanding the two membrane systems. The three-phase partitioning procedure added a new level of dynamic resolution to the known thylakoid proteome. An automated strategy was developed to track possible ambiguous identifications to more than one gene model or family member. Mass spectrometry search results, ambiguities, and functional classifications can be searched via the Plastid Proteome Database.

Received for publication, June 17, 2004 , and in revised form, August 19, 2004.

^* This work was supported by National Science Foundation Grant MCB 0090942 and NYSTAR (to K. J. v. W.). All modeling research was conducted using the resources of the Cornell Theory Center, which is supported by Cornell University. 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 Tables 1 and 2.

Both authors contributed equally to this work.

^|| To whom correspondence should be addressed: Dept. of Plant Biology, Emerson Hall, Rm. 332, Tower Rd., Cornell University, Ithaca, NY 14853. Tel.: 607-255-3664; Fax: 607-255-5407; E-mail: kv35{at}Cornell.edu.

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