We report more than 1400 proteins of the secretory-pathway proteome and provide spatial information on the relative presence of each protein in the rough and smooth ER Golgi cisternae and Golgi-derived COPI vesicles. The data support a role for COPI vesicles in recycling and cisternal maturation, showing that Golgi-resident proteins are present at a higher concentration than secretory cargo. Of the 1400 proteins, 345 were identified as previously uncharacterized. Of these, 230 had their subcellular location deduced by proteomics. This study provides a comprehensive catalog of the ER and Golgi proteomes with insight into their identity and function.

The mass-spectrometry-based identification of proteins has created opportunities for the study of organelles, transport intermediates and large subcellular structures. Traditional cell-biology techniques are used to enrich these structures for proteomics analyses, and such analyses provide insights into the biology and functions of these structures. Here, we review the state-of-the-art proteomics techniques for the analysis of subcellular structures and discuss the biological insights that have been derived from such studies.

Proteins containing PDZ domains are involved in a large number of biological functions, including protein scaffolding, organization of ion channels, and signal transduction. We recently identified a novel PDZ domaincontaining protein, PDZK1, that is selectively expressed in normal tissues, where it is associated and colocalized with MAP17, a small 17-kDa membrane-associated protein; cMOAT, an organic anion transporter implicated in multidrug resistance; and the type IIa Na/Pi cotransporter. The protein cluster formed by PDZK1, MAP17, and cMOAT is upregulated in a significant number of human carcinomas originating in the colon, breast, lung, and kidney. In order to better define the function of PDZK1 in the protein cluster and its potential role in the organization of ion channels, we generated a PDZK1 knockout mouse. While PDZK1-deficient mice developed normally, did not display any gross phenotypic abnormalities, and were fecund, lack of PDZK1 resulted in modulation of expression of selective ion channels in the kidney, as well as increased serum cholesterol levels. However, no significant redistribution of proteins known to interact with PDZK1, such as MAP17, cMOAT, and the type IIa Na/Pi cotransporter, was observed. The absence of a more significant phenotype in PDZK1-deficient mice may be due to functional compensation by other PDZ domain-containing proteins, which could be instrumental in determining the location of interacting proteins such as ion channels and other membrane-associated proteins in defined areas of the plasma membrane. PDZK1, a recently described protein containing four PDZ domains, belongs to a cluster of proteins including MAP17 and cMOAT (7-10). All three proteins are upregulated in human carcinomas arising in the kidney, lung, colon, and breast. Although the exact function of PDZK1 is unknown, it has been postulated that it plays a role in multidrug resistance through its interaction with the organic anion transporter cMOAT, also known as MRP2, the multidrug resistance-associated protein (9,11,12,14,24). More recently, PDZK1 has been found to interact with the type IIa Na/Pi cotransporter and therefore may participate in the apical sorting of ion channels (4). Furthermore, PDZK1 is overexpressed in estrogen receptor-positive breast carcinomas compared to estrogen-negative tumors, suggesting a role for PDZK1 in tissue response to ␤-estradiol (3). PDZ domains were originally recognized as structural motifs in the mammalian postsynaptic density protein PSD-95 (1), the Drosophila disk large tumor suppressor Dlg (26), and the tight junction protein ZO-1 (25). Such domains, typically 80 to 120 amino acids, bind to well-defined consensus sequences and have been described in a number of proteins associated with specialized areas of the plasma membrane (2, 22). PDZ domain-containing proteins are involved in synaptic organization, control of cell proliferation, and cell differentiation (1,6,13,20,26). Some of these proteins contain several PDZ domains and, as a result, promote the clustering of a...

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