The polypeptide composition of the phycobilisome, the major light-harvesting 
complex of prokaryotic cyanobacteria and certain eukaryotic algae, can be 
modulated by different light qualities in cyanobacteria exhibiting chromatic 
adaptation. We have identified genomic fragments encoding a cluster of 
phycobilisome polypeptides (phycobiliproteins) from the chromatically adapting 
cyanobacterium Fremyella diplosiphon using previously characterized DNA 
fragments of phycobiliprotein genes from the eukaryotic alga Cyanophora paradoxa 
and from F. diplosiphon. Characterization of two lambda-EMBL3 clones containing 
overlapping genomic fragments indicates that three sets of phycobiliprotein 
genes--the alpha- and beta-allophycocyanin genes plus two sets of alpha- and 
beta-phycocyanin genes--are clustered within 13 kilobases on the cyanobacterial 
genome and transcribed off the same strand. The gene order 
(alpha-allophycocyanin followed by beta-allophycocyanin and beta-phycocyanin 
followed by alpha-phycocyanin) appears to be a conserved arrangement found 
previously in a eukaryotic alga and another cyanobacterium. We have reported 
that one set of phycocyanin genes is transcribed as two abundant red 
light-induced mRNAs (1600 and 3800 bases). We now present data showing that the 
allophycocyanin genes and a second set of phycocyanin genes are transcribed into 
major mRNAs of 1400 and 1600 bases, respectively. These transcripts are present 
in RNA isolated from cultures grown in red and green light, although lower 
levels of the 1600-base phycocyanin transcript are present in cells grown in 
green light. Furthermore, a larger transcript of 1750 bases hybridizes to the 
allophycocyanin genes and may be a precursor to the 1400-base species.