The assembly of the photosynthetic apparatus utilizes component protei
ns that are synthesized by two genomes and then targeted into and acro
ss the thylakoid membrane. The emerging picture is one of a remarkably
complex system of protein trafficking, in which at least four distinc
t pathways operate within the chloroplast - two for lumenal proteins a
nd two for integral membrane proteins. Some of the pathways can be tra
ced back to the prokaryotic ancestor of the chloroplast, whereas other
s appear to have arisen more recently - one in response to the transfe
r of genes to the plant nucleus and another, possibly, in response to
the acquisition of new photosynthetic proteins. Remarkably, proteins i
n three of these pathways are synthesized with cleavable signal type p
eptides that are almost identical in overall structure, yet that execu
te entirely different functions. Recent studies have begun to reconcil
e the function of these targeting signals with the nature of the prote
in being targeted.