The characteristics of a phosphoprotein with a relative electrophoretic mobility of 12 kDa have been unknown during two decades of studies on redox-dependent protein phosphorylation in plant photosynthetic membranes. Digestion of this protein from spinach thylakoid membranes with trypsin and subsequent tandem nanospray-quadrupole-time-of-flight mass spectrometry of the peptides revealed a protein sequence that did not correspond to any previously known protein. Sequencing of the corresponding cDNA uncovered a gene for a precursor protein with a transit peptide followed by a strongly basic mature protein with a molecular mass of 8,640 Da. Genes encoding homologous proteins were found on chromosome 3 of Arabidopsis and rice as well as in ESTs from 20 different plant species, but not from any other organisms. The protein can be released from the membrane with high salt and is also partially released in response to light-induced phosphorylation of thylakoids, in contrast to all other known thylakoid phosphoproteins, which are integral to the membrane. On the basis of its properties, this plant-specific protein is named thylakoid soluble phosphoprotein of 9 kDa (TSP9). Mass spectrometric analyses revealed the existence of non-, mono-, di-, and triphosphorylated forms of TSP9 and phosphorylation of three distinct threonine residues in the central part of the protein. The phosphorylation and release of TSP9 from the photosynthetic membrane on illumination favor participation of this basic protein in cell signaling and regulation of plant gene expression in response to changing light conditions. P rotein phosphorylation plays a major regulatory role in all cellular functions, from gene expression to signaling and metabolic control. A unique light-and redox-controlled protein phosphorylation system has evolved in plant thylakoid membranes for regulation of the photosynthetic process (1, 2). Intrinsic protein kinases in chloroplast thylakoid membranes (3-5) are activated by light or reducing conditions and controlled by the reduction of plastoquinone and its binding to the reduced cytochrome bf complex (6, 7). Additional modulation of protein phosphorylation in thylakoid membranes involves the thiol redox state (8, 9) as well as light-modulated conformational changes of substrate proteins (10). Activated thylakoid kinases phosphorylate the membrane proteins of photosystem II (PSII) and its light-harvesting antenna (LHCII) as well as a number of still unidentified protein substrates (2, 11-13). The protein dephosphorylation reactions are catalyzed by both integral thylakoid membrane and soluble chloroplast phosphatases (2, 14). The reversible phosphorylation of LHCII polypeptides helps balance the distribution of absorbed light energy between the two photosystems (1,(15)(16)(17). Phosphorylation of the core subunits of PSII controls their maintenance and turnover, with dephosphorylation of the D1 and D2 proteins being a signal for their proteolytic degradation (18,19). Two other subunits of PSII, the chlorophyll a-binding ...