Novel tonoplast transporters identified using a proteomic approach with vacuoles isolated from cauliflower buds.

Young meristematic plant cells contain a large number of small vacuoles, while the largest part of the vacuome in mature cells is composed by a large central vacuole, occupying 80% to 90% of the cell volume. Thus far, only a limited number of vacuolar membrane proteins have been identified and characterized. The proteomic approach is a powerful tool to identify new vacuolar membrane proteins. To analyze vacuoles from growing tissues we isolated vacuoles from cauliflower (Brassica oleracea) buds, which are constituted by a large amount of small cells but also contain cells in expansion as well as fully expanded cells. Here we show that using purified cauliflower vacuoles and different extraction procedures such as saline, NaOH, acetone, and chloroform/methanol and analyzing the data against the Arabidopsis (Arabidopsis thaliana) database 102 cauliflower integral proteins and 214 peripheral proteins could be identified. The vacuolar pyrophosphatase was the most prominent protein. From the 102 identified proteins 45 proteins were already described. Nine of these, corresponding to 46% of peptides detected, are known vacuolar proteins. We identified 57 proteins (55.9%) containing at least one membrane spanning domain with unknown subcellular localization. A comparison of the newly identified proteins with expression profiles from in silico data revealed that most of them are highly expressed in young, developing tissues. To verify whether the newly identified proteins were indeed localized in the vacuole we constructed and expressed green fluorescence protein fusion proteins for five putative vacuolar membrane proteins exhibiting three to 11 transmembrane domains. Four of them, a putative organic cation transporter, a nodulin N21 family protein, a membrane protein of unknown function, and a senescence related membrane protein were localized in the vacuolar membrane, while a white-brown ATP-binding cassette transporter homolog was shown to reside in the plasma membrane. These results demonstrate that proteomic analysis of highly purified vacuoles from specific tissues allows the identification of new vacuolar proteins and provides an additional view of tonoplastic proteins.

Starvation-induced expression of autophagy-related genes in Arabidopsis.

BACKGROUND INFORMATION: Autophagy is a catabolic process for degradation of cytoplasmic components in the vacuolar apparatus. A genome-wide survey recently showed evolutionary conservation among autophagy genes in yeast, mammals and plants. To elucidate the molecular and subcellular machinery responsible for the sequestration and subsequent digestion of intracellular material in plants, we utilized a combination of morphological and molecular methods (confocal laser-scanning microscopy, transmission electron microscopy and real-time PCR respectively). RESULTS: Autophagy in Arabidopsis thaliana suspension-cultured cells was induced by carbon starvation, which triggered an immediate arrest of cell growth together with a rapid degradation of cellular proteins. We followed the onset of these responses and, in this report, provide a clear functional classification for the highly polymorphic autophagosomes by which the cell sequesters and degrades a portion of its own cytoplasm. Quantification of autophagy-related structures shows that cells respond to the stress signal by a rapid and massive, but transient burst of autophagic activity, which adapts to the stress signal. We also monitored the real-time expressions of AtATG3, AtATG4a, AtATG4b, AtATG7 and AtATG8a-AtATG8i genes, which are orthologues of yeast genes involved in the Atg8 ubiquitination-like conjugation pathway and are linked to autophagosome formation. We show that these autophagy-related genes are transiently up-regulated in a co-ordinated manner at the onset of starvation. CONCLUSIONS: Sucrose starvation induces autophagy and up-regulates orthologues of the yeast Atg8 conjugation pathway genes in Arabidopsis cultured cells. The AtATG3, AtATG4a, AtATG4b, AtATG7 and AtATG8a-AtATG8i genes are expressed in successive waves that parallel the biochemical and cytological remodelling that takes place. These genes thus serve as early markers for autophagy in plants.