The mcyABCDEFGHIJ gene cluster of Microcystis aeruginosa encodes the mixed polyketide synthase/nonribosomal peptide synthetase (microcystin synthetase) which is responsible for biosynthesis of the potent liver toxin microcystin. The sequence and orientation of the mcy genes have previously been reported, but no transcriptional analysis had been performed prior to this study. The mcyABCDEFGHIJ genes are transcribed as two polycistronic operons, mcyABC and mcyDEFGHIJ, from a central bidirectional promoter between mcyA and mcyD. Two transcription start sites were detected for both mcyA and mcyD when cells were exposed to light intensities of 68 and 16 mol of photons m ؊2 s ؊1 . The start sites, located 206 and 254 bp upstream of the translational start for mcyD under high and low light conditions, respectively, indicate long untranslated leader regions. Putative transcription start sites were also identified for mcyE, mcyF, mcyG, mcyH, mcyI, and mcyJ but not for mcyB and mcyC. A combination of reverse transcription-PCR and rapid amplification of cDNA ends was employed throughout this work, which may have been one of the first transcriptional analyses of a large nonribosomal polyketide gene cluster.Cyanobacteria are known to produce a wide range of bioactive compounds, including nonribosomally made peptides, polyketides, alkaloids, and lipopolysaccharides. Some of these compounds are neuro-or hepatotoxins, and their impact on human and animal health has resulted in concern worldwide. Microcystin is a hepatotoxic heptapeptide produced by several species of the genera Microcystis, Anabaena, Nostoc, and Oscillatoria. More than 65 structural isoforms of microcystins with various toxicities have been identified having the common structure cyclo(Adda-D-Glu-Mdha-D-Ala-L-X-D-MeAsp-L-Z), where X and Z are variable L amino acids, Adda is 3-amino-9-methoxy-2,6,8,-trimethyl-10-phenyl-4,6-decadienoic acid, D-MeAsp is 3-methylaspartic acid, and Mdha is N-methyldehydroalanine (27, 31).Microcystin is synthesized nonribosomally via a mixed polyketide synthase/nonribosomal peptide synthetase system called microcystin synthetase (2,12,23). Recently, the gene cluster encoding the microcystin synthetase complex has been identified and sequenced (25,34). This 55-kb gene cluster consists of six open reading frames (ORFs) with a mixed nonribosomal peptide synthetase/polyketide synthase nature (mcyA to mcyE and mcyG) and four smaller ORFs with putative precursor and tailoring functions (mcyF and mcyH to mcyJ). Catalytic domains in mcyA to mcyE and mcyG are responsible for incorporation of the precursors phenylacetate, malonyl coenzyme A, S-adenosyl-L-methionine, glutamate, serine, alanine, leucine, D-methyl-isoaspartate, and arginine. The smaller ORFs encode monofunctional proteins which are putatively involved in O-methylation (McyJ), epimerization (McyF), dehydration (McyI), and cellular localization (McyH) (24,34).