Responding to green and red light, certain cyanobacteria change the composition of their light-harvesting pigments, phycoerythrin (PE) and phycocyanin (PC). Although this phenomenon—complementary chromatic adaptation—is well known, the green light–sensing mechanism for PE accumulation is unclear. The filamentous cyanobacterium
Nostoc punctiforme
ATCC
29133 (
N. punctiforme
) regulates PE synthesis in response to green and red light (group II chromatic adaptation). We disrupted the green/red-perceiving histidine-kinase gene (
ccaS
) or the cognate response regulator gene (
ccaR
), which are clustered with several PE and PC genes (
cpeC
-
cpcG2-cpeR1
operon) in
N. punctiforme
. Under green light, wild-type cells accumulated a significant amount of PE upon induction of
cpeC
-
cpcG2
-
cpeR1
expression, whereas they accumulated little PE with suppression of
cpeC
-
cpcG2
-
cpeR1
expression under red light. Under both green and red light, the
ccaS
mutant constitutively accumulated some PE with constitutively low
cpeC
-
cpcG2
-
cpeR1
expression, whereas the
ccaR
mutant accumulated little PE with suppression of
cpeC
-
cpcG2
-
cpeR1
expression. The results of an electrophoretic mobility shift assay suggest that CcaR binds to the promoter region of
cpeC
-
cpcG2
-
cpeR1
, which contains a conserved direct-repeat motif. Taken together, the results suggest that CcaS phosphorylates CcaR under green light and that phosphorylated CcaR then induces
cpeC
-
cpcG2
-
cpeR1
expression, leading to PE accumulation. In contrast, CcaS probably represses
cpeC
-
cpcG2
-
cpeR1
expression by dephosphorylation of CcaR under red light. We also found that the
cpeB-cpeA
operon is partially regulated by green and red light, suggesting that the green light-induced regulatory protein CpeR1 activates
cpeB-cpeA
expression together with constitutively induced CpeR2.