Comparative analysis of related biosynthetic gene clusters can provide new insights into the versatility of these pathways and allow the discovery of new natural products. The freshwater cyanobacterium Microcystis aeruginosa NIES298 produces the cytotoxic peptide microcyclamide. Here, we provide evidence that the cyclic hexapeptide is formed by a ribosomal pathway through the activity of a set of processing enzymes closely resembling those recently shown to be involved in patellamide biosynthesis in cyanobacterial symbionts of ascidians. Besides two subtilisin-type proteases and a heterocyclization enzyme, the gene cluster discovered in strain NIES298 encodes six further open reading frames, two of them without similarity to enzymes encoded by the patellamide gene cluster. Analyses of genomic data of a second cyanobacterial strain, M. aeruginosa PCC 7806, guided the discovery and structural elucidation of two novel peptides of the microcyclamide family. The identification of the microcyclamide biosynthetic genes provided an avenue by which to study the regulation of peptide synthesis at the transcriptional level. The precursor genes were strongly and constitutively expressed throughout the growth phase, excluding the autoinduction of these peptides, as has been observed for several peptide pheromone families in bacteria.Cyanobacteria are known as a prolific source of secondary metabolites exhibiting unique structural features and biological activities. Various cyanobacterial compounds (e.g., curacin A, aeruginosin, and cryptophycin) have great potential for drug development (33, 36). However, due to their adverse effects on higher organisms, several cyanobacterial metabolites are regarded as health-threatening toxins and have caused serious concern among water authorities worldwide. A majority of these compounds, in particular, those that were isolated from planktonic freshwater cyanobacteria belonging to the genera Microcystis, Planktothrix, Nostoc, and Anabaena, can be classified as peptides or possess peptidic substructures often comprising highly modified amino acid moieties. Several of these peptides, such as the hepatotoxin microcystin or the protease inhibitors aeruginosin and anabaenopeptolide, were shown to be produced by nonribosomal peptide synthetase assembly lines (13,27,34).The recent characterization of the patellamide biosynthetic pathway from the as-yet-nonculturable cyanobacterial symbiont of the ascidian Lissoclinum patella has revealed that there are biosynthetic pathways independent from nonribosomal peptide synthetase systems capable of producing modified and cyclic peptide structures in cyanobacteria (29). The patellamide family of cyclic pseudosymmetrical octapeptides is characterized by the presence of thiazole and oxazole moieties. Although nonribosomal biosynthesis was anticipated for the formation of these peptides, heterologous expression of a microcin-like gene cluster discovered in the genome of the symbiotic cyanobacterium Prochloron didemni unambiguously showed that these peptide...