Molecular mechanisms that regulate carbon flux are poorly understood in algae. The <
i>
?glgC<
/i>
mutant of the cyanobacterium <
i>
Synechocystis<
/i>
sp. PCC 6803 is incapable of glycogen storage and displays an array of physiological responses under nitrogen starvation that are different from wild-type (WT). These include non-bleaching phenotype and the redirection of photosynthetically fixed carbon towards excreted organic acids (overflow metabolism) without biomass growth. To understand the role of gene/protein expression in these responses, we followed the time course of transcripts by genome-scale microarrays and proteins by shotgun proteomics in <
i>
?glgC<
/i>
and WT cells upon nitrogen starvation. Compared to WT, the degradation of phycobilisome rod proteins was delayed and attenuated in the mutant, and the core proteins were less degraded
both contributed to the non-bleaching appearance despite the induction of <
i>
nblA<
/i>
genes, suggesting the presence of a break in regulation of the phycobilisome degradation pathway downstream of <
i>
nblA<
/i>
induction. The mutant displayed NtcA-mediated transcriptional response to nitrogen starvation, indicating that it is able to sense nitrogen status. Furthermore, some responses to nitrogen starvation appear to be stronger in the mutant, as shown by the increases in transcripts for the transcriptional regulator, <
i>
rre37<
/i>
, which regulates central carbon metabolism. Accordingly, multiple proteins involved in photosynthesis, central carbon metabolism, and carbon storage and utilization showed lower abundance in the mutant. Furthermore, these results indicate that the transition in the central carbon metabolism from growth to overflow metabolism in <
i>
?glgC<
/i>
does not require increases in expression of the overflow pathway enzymes
the transition and non-bleaching phenotype are likely regulated instead at the metabolite level.