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Chloroplasts are structurally complex organelles containing ~2000-3000 proteins. They are delimited by a double membrane system or envelope, have an inner aqueous compartment called the stroma, and possess a second internal membrane system called the thylakoids. Thus, determining the suborganellar location of a chloroplast protein is vital to understanding or verifying its function. One way in which protein localization can be addressed is through fractionation. Here we present two rapid and simple methods that may be applied sequentially on the same day: (a) The isolation of intact chloroplasts from Arabidopsis thaliana plants that may be used directly (e.g., for functional studies such as protein import analysis), or for further processing as follows; (b) separation of isolated chloroplasts into three suborganellar fractions (envelope membranes, a soluble fraction containing stromal proteins, and the thylakoids). These methods are routinely used in our laboratory, and they provide a good yield of isolated chloroplasts and suborganellar fractions that can be used for various downstream applications.

Original publication





Publication Date





45 - 60


Arabidopsis, Chloroplast isolation, Envelope, Percoll, Stroma, Suborganellar fractionation, Sucrose step gradient, Thylakoid, Arabidopsis, Arabidopsis Proteins, Cell Fractionation, Centrifugation, Density Gradient, Chloroplasts, Culture Media, Intracellular Membranes, Povidone, Seedlings, Seeds, Silicon Dioxide, Sucrose