We developed a transcript profiling methodology to elucidate expression patterns of the cyanobacterium Synechocystis sp. strain PCC 6803 and used the technology to investigate changes in gene expression caused by irradiation with either intermediate-wavelength UV light (UV-B) or high-intensity white light. Several families of transcripts were altered by UV-B treatment, including mRNAs specifying proteins involved in light harvesting, photosynthesis, photoprotection, and the heat shock response. In addition, UV-B light induced the stringent response in Synechocystis, as indicated by the repression of ribosomal protein transcripts and other mRNAs involved in translation. High-intensity white light-and UV-B-mediated expression profiles overlapped in the down-regulation of photosynthesis genes and induction of heat shock response but differed in several other transcriptional processes including those specifying carbon dioxide uptake and fixation, the stringent response, and the induction profile of the high-light-inducible proteins. These two profile comparisons not only corroborated known physiological changes but also suggested coordinated regulation of many pathways, including synchronized induction of D1 protein recycling and a coupling between decreased phycobilisome biosynthesis and increased phycobilisome degradation. Overall, the gene expression profile analysis generated new insights into the integrated network of genes that adapts rapidly to different wavelengths and intensities of light.While sunlight provides the energy for life, intermediatewavelength UV light (UV-B) and long-wavelength UV light (UV-A) injure many organisms. UV-B (280-to 320-nm-wavelength) light generates radicals that damage proteins, nucleic acids, lipids, and the photosynthetic apparatus. The latter damage appears in the form of impaired photosystems I and II, decreased oxygen evolution and CO 2 fixation, inactivation of ATPase activity, reduction in chlorophyll content, and decreased biomass (33). Notably, the D1 protein of the light energy converting complex photosystem II is quite sensitive to UV-B light (10). Although less harmful than UV-B irradiation, UV-A irradiation (320-to 400-nm-wavelength light) also damages proteins, nucleic acids, lipids, and photosystems (11). UV-A irradiation leads to the intramolecular cross-linking of several tRNA species (2), which results in poor aminoacylation and triggering of the stringent response-a phenomenon that reduces the rate of stable RNA, ribosome, and translation factor synthesis, thus arresting growth (32). Higher fluxes of white light also cause a loss of photosynthetic productivity (photoinhibition) (30).In cyanobacteria, more than 99% of UV-B is absorbed by chlorophyll-binding proteins and the light-harvesting complexes (phycobilisomes) (20). Carotenoids protect cells against photooxidative damage by absorbing triplet state energy from chlorophyll and quenching singlet state oxygen (15). In response to changes in light quantity or quality, cyanobacteria modulate the abundance of ch...