Assimilation of C, N, and S into organic compounds requires effective and flexible cooperation among the energy-converting, tightly coupled, thylakoid-bound processes and stromal metabolism. Fluctuations of light, temperature, and changing concentrations of the various reducible substrates pose unique regulatory problems to photoautotrophic plant cells. Covalent redox modification of enzyme proteins as mediated by the ferredoxin/thiore-doxin-system is suited to provide short-term adaptation of various enzymatic activities in the chloroplast. This mode of regulation is based on the continuous turnover of interconvertible enzyme forms, as in the systems driven by protein phosphorylation/dephosphorylation, but is particularly adapted to the unique conditions of a compartment performing oxygenic photosynthesis by depending on the simultaneous presence of reducing power and of oxygen. Individual fine control of each of the enzymes subjected to redox modification is achieved by specific metabolites acting as additional positive or negative effectors of the reductive (and/or oxidative) modification reaction. The biochemical prerequisite for such a control is the presence of regulatory (extra) sequences carrying cysteine residues which are subjected to reversible redox changes. Although no common amino acid sequence has yet been identified among the known regulatory peptides, in all cases the evolution of autotrophy should be related to the presence of extrasequences in otherwise very conserved enzyme molecules.