During the development of the endosymbiotic relationship between the invading ‘plastid’ and the recipient prokaryotic cell through the course of evolution, many changes occurred to the invading ‘plastid’. As we have seen, one major change has been the extensive movement of genetic information from the plastid's own genome into the nuclear genome. As a result of these events, the cell is faced with a major problem; namely, how those proteins now encoded by the cell's nucleus get back into the correct place within the plastid in order to allow the plastid to function effectively. Since around 95% of the proteins that are present in the mature chloroplast in the cells of present-day plants are encoded by genes in the nucleus, this problem becomes significantly more than just routing the occasional protein and it constitutes a major flow of protein trafficking within the cell. Plastids import much more than proteins. In all cells, plastids play a major role in metabolic biochemistry and synthesise many important molecules, which are utilised in other parts of the cell (see Chapter 7). Thus a wide variety of molecules other than proteins are imported and exported by the plastid in its normal course of biochemical function. Foremost amongst these are the end products of photosynthesis as well as lipids, amino acids and various other intermediates in biochemical pathways.

A complication which has to be overcome in trafficking molecules into and out of the plastid is that the boundary of the plastid is a double membrane, composed of the outer envelope membrane and the inner envelope membrane, with a distinct compartment in between; the envelope lumen.