Chromatophore genome sequence of Paulinella sheds light on acquisition of photosynthesis by eukaryotes

Background: It is commonly accepted that a single primary endosymbiosis gave rise to the photosynthetic organelles of plants, the plastids. Recently, we presented evidence that photosynthetic inclusions, termed chromatophores, present in the filose thecamoeba Paulinella chromatophora originated from an independent, more recent primary endosymbiotic event. To clarify metabolic capabilities of the chromatophore and its state of integration into the host, we present here the complete genome sequence of the chromatophore. Results: Our data reveal a fundamental reduction of the chromatophore genome. The single, circular chromosome of 1.02 Mb encodes 867 protein-coding genes and is, therewith, the smallest cyanobacterial genome reported to date. Compared to Synechococcus WH5701, a free-living relative of the chromatophore, only 26% of the genes were retained. Eleven putative pseudogenes were identified, indicating that reductive genome evolution is ongoing. Although the chromatophore genome contains a complete set of photosynthesis genes, it lacks not only genes thought to be dispensable for an intracellular lifestyle but also genes of essential pathways for amino acid and cofactor synthesis. Conclusions: Our data characterize the chromatophore as a photosynthetic entity that is absolutely dependent on its host for growth and survival. Thus, the chromatophores of P. chromatophora are the only known cyanobacterial descendants besides plastids with a significantly reduced genome that confer photosynthesis to their eukaryotic host. Their comparison with plastids and bacterial endosymbionts of invertebrates sheds light on early steps of the integration of a photosynthetic prokaryote into a eukaryotic cell.