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Marine Synechococcus spp. are extremely sensitive to copper toxicity. Some strains have been shown to produce high-affinity, extracellular ligands of unknown structure which form complexes with free cupric ion. They are also known to produce metallothioneins (MT) in response to cadmium and zinc stress. In the present study, marine Synechococcus PCC 73109 (Agmenellum quadruplicatum BG-1) (Van Baalen) was exposed to three concentrations of CuSO4 for various times. Size exclusion chromatography, atomic absorption spectrophotometry, and reverse phase HPLC were used to isolate an intracellular copper binding ligand of low molecular weight (< 6,500 Da). The ligand was detected after exposure to ≥ 8 μM CuSO4 for 2 hr in BG-11 medium. The intracellular ligand was characterized by electrospray mass spectrometry, amino acid analysis and a universal assay for siderophores. The ligand was not MT, phytochelatin or a siderophore. It is not a peptide but it contains lysine and an unidentified UV 254-absorbing constituent. This compound is a novel copper-binding ligand previously not reported in Synechococcus spp.