The localization of the plant-specific thylakoid-soluble phosphoprotein of 9 kDa, TSP9, within the chloroplast thylakoid membrane of spinach has been established by the combined use of fractionation, immunoblotting, cross-linking, and mass spectrometry. TSP9 was found to be exclusively confined to the thylakoid membranes, where it is enriched in the stacked grana membrane domains. After mild solubilization of the membranes, TSP9 migrated together with the major light-harvesting antenna (LHCII) of photosystem II (PSII) and with PSII-LHCII supercomplexes upon separation of the protein complexes by either native gel electrophoresis or sucrose gradient centrifugation. Studies with a cleavable cross-linking agent revealed the interaction of TSP9 with both major and minor LHCII proteins as identified by mass spectrometric sequencing. Cross-linked complexes that in addition to TSP9 contain the peripheral PSII subunits CP29, CP26, and PsbS, which form the interface between LHCII and the PSII core, were found. Our observations also clearly suggest an interaction of TSP9 with photosystem I (PSI) as shown by both immunodetection and mass spectrometry. Sequencing identified the peripheral PSI subunits PsaL, PsaF, and PsaE, originating from cross-linked protein complexes of around 30 kDa that also contained TSP9. The distribution of TSP9 among the cross-linked forms was found to be sensitive to conditions such as light exposure. An association of TSP9 with LHCII as well as the peripheries of the photosystems suggests its involvement in regulation of photosynthetic light harvesting.Signaling through reversible protein phosphorylation is of great importance for proper functioning in eukaryotic cells. In the thylakoid membranes of plant cells, a large number of proteins are phosphorylated in response to light. The process is under complex regulation (reviewed in Ref. 1), and at least five different kinases (2-5) as well as several phosphatases (6 -8) are believed to participate. Most proteins undergoing protein phosphorylation in the thylakoid membrane are associated with photosystem II (PSII) 2 and its light-harvesting antenna (LHCII) (9, 10). Reversible thylakoid protein phosphorylation is known to be of importance for the maintenance and repair of PSII (11, 12) and in balancing the excitation of the two photosystems in the process called state transition (13-15). However, the identity and exact role for all of the thylakoid phosphoproteins are still not known.A 12-kDa phosphoprotein was for long an enigmatic protein without known identity or function (16, 17). Recently we identified this protein and named it TSP9, thylakoid-soluble phosphoprotein of 9 kDa (18). It is a strongly basic protein that is phosphorylated on three threonine residues in the central part, in contrast to other thylakoid phosphoproteins, which are mainly phosphorylated at their N termini (reviewed in Ref. 1). TSP9 so far appears to be absolutely plant-specific. Searches in available data bases have revealed homologues in 49 different plant species but n...