Following the complete sequencing of the genome of the univellular cyanobacterium, Synechocystis sp. strain PCC6803 within our institute, a protein-gene linkage map of this photosynthetic microorganism was successfully constructed for 130 high abundance proteins present on two-dimensional gels. An additional six proteins were analyzed, but were probably encoded extrachromosomally. In order to demonstrate the usefulness of this protein-gene linkage map, we analyzed the changes that occur in cellular proteins after illumination of PCC6803 cells. The results indicate that this protein-gene linkage map greatly simplifies the identification process of such modulated genes. After illumination, at least three distinctive spots with reduced intensity were detected on two-dimensional gels and the corresponding genes of two of these were successfully identified as chaperonin 2 and a Tortula ruralis rehydrin-related gene. Thus, the combination of the protein-gene linkage map and two-dimensional gel electrophoresis should permit a comprehensive analyses of the proteins encoded by the genome (i.e., "proteome") of this photosynthetic autotroph. This post-genome project represents a productive way of exploiting the information obtained from the sequencing of the cyanobacterium genome.