The nondiazotrophic cyanobacterium Synechococcus sp. strain PCC 7942 responds to nitrogen deprivation by differentiating into nonpigmented resting cells able to survive prolonged periods of starvation. The degradation of photosynthetic pigments, termed chlorosis, proceeds in an ordered manner in which the light-harvesting phycobiliproteins are degraded prior to chlorophyll. Here, we show that the function of the global transcription activator of nitrogen-regulated genes, NtcA, is required for the sequential pigment degradation and cell survival. The P(II) protein, known to signal the nitrogen status of the cells, is most probably not involved in the perception of the nitrogen-starvation-specific signal since in a mutant lacking P(II), chlorosis proceeded in the same manner as in the wild type. Inhibition of glutamine synthetase with l-methionine sulfoximine led to a rapid decrease of apc mRNA and to an increase of nblA mRNA levels, which is characteristic for nitrogen deprivation, suggesting that nitrogen starvation is sensed by a metabolic signal connected to glutamine synthetase activity. However, l-methionine sulfoximine treatment did not induce phycobiliprotein degradation, but led to an immediate cessation of this proteolytic process after its induction by nitrogen deprivation. This suggests that the proteolytic activity elicited by the expression of nblA has to be supported by glutamine synthetase activity.