Summary of replies on cellular fractionation of Arabidopsis:
Several people suggested the following reference as a place to start:
"Subcellular localization of ubiquitin and ubiquinated proteins in
Arabidopsis thaliana" (Beers et al., JBC 267:15432-39, 1992).
And D. Galbraith sent a reference for fractionation of tobacco protoplasts:
"Biosynthesis, processing and targeting of G-protein of vesicular
stomatitis virus in tobacco protoplasts" (Galbraith et al., Planta
Thanks for the suggestions.