The Rhodophyta (red algae) and Chlorophyta (green algae) form a natural group of algae in that they have chloroplasts surrounded by only the two membranes of the chloroplast envelope. The endosymbiotic theory of chloroplast evolution, first proposed by Mereschkowsky in 1905, is the one most widely accepted for the evolution of the chloroplast (Fig. III.1). According to this theory, a cyanobacterium was taken up by a phagocytic organism into a food vesicle. Normally the cyanobacterium would be digested by the flagellate, but by chance a mutation occurred, with the flagellate being unable to digest the cyanobacterium. This was probably a beneficial mutation because the cyanobacterium, by virtue of its lack of feedback inhibition, secreted considerable amounts of metabolites to the host flagellate. The flagellate in turn gave the cyanobacterium a protected environment, and the composite organism was probably able to live in an ecological niche where there were no photosynthetic organisms (i.e., a slightly acid body of water where free-living cyanobacteria do not grow; see Chapter 2). Pascher (1914) coined terms for this association; he called the endosymbiotic cyanobacteria cyanelles; the host, a cyanome; and the association between the two, a syncyanosis. In the original syncyanosis, the cyanelle had a wall around it. Because the wall slowed the transfer of compounds from the cyanelle to the host and vice versa, any mutation that resulted in a loss of wall would have been beneficial and selected for in evolution. As evolution progressed, these two membranes became the chloroplast envelope, the cyanome cytoplasm took over the formation of the storage product and the polyhedral bodies containing ribulose-1,5-bisphosphate carboxylase/oxygenase differentiated into the pyrenoid.

Most of the genes from the endosymbiotic cyanobacterium were transferred to the host nucleus while a small number of these genes were maintained in the resulting plastid and gave rise to the plastid genome with its associated proteinsynthesizing system. The products of many of the cyanobacterial genes transferred to the nucleus were then retargeted to the plastid to keep it functional. Approximately 3000 nuclear genes in plants encode plastid proteins, whereas the chloroplast genome contains between 100 and 120 genes. The nucleus is also capable of sensing the state of the chloroplast and to react to maintain chloroplast homeostasis.