Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome

Abstract

Prochlorococcus marinus, the dominant photosynthetic organism in the ocean, is found in two main ecological forms: high-light-adapted genotypes in the upper part of the water column and low-light-adapted genotypes at the bottom of the illuminated layer. P. marinus SS120, the complete genome sequence reported here, is an extremely low-light-adapted form. The genome of P. marinus SS120 is composed of a single circular chromosome of 1,751,080 bp with an average G+C content of 36.4%. It contains 1,884 predicted protein-coding genes with an average size of 825 bp, a single rRNA operon, and 40 tRNA genes. Together with the 1.66-Mbp genome of P. marinus MED4, the genome of P. marinus SS120 is one of the two smallest genomes of a photosynthetic organism known to date. It lacks many genes that are involved in photosynthesis, DNA repair, solute uptake, intermediary metabolism, motility, phototaxis, and other functions that are conserved among other cyanobacteria. Systems of signal transduction and environmental stress response show a particularly drastic reduction in the number of components, even taking into account the small size of the SS120 genome. In contrast, housekeeping genes, which encode enzymes of amino acid, nucleotide, cofactor, and cell wall biosynthesis, are all present. Because of its remarkable compactness, the genome of P. marinus SS120 might approximate the minimal gene complement of a photosynthetic organism.

Fig. 1.

Schematic organization of a P. marinus SS120 cell showing the main metabolic pathways and transporters. Gene identifiers are shown by numbers in blue. Genes with uncertain annotation are shown with a question mark. Reactions for which no candidate enzyme was confidently predicted are indicated by dashed arrows. Pathways that involve multiple reactions are shown by double arrows. Final biosynthetic products are indicated as follows: light blue, amino acids; dark yellow, nucleotides; brown, sugars; pink, cofactors. Chl cycle is based on ref. . Cyt, cytochrome; Flvd, flavodoxin; FNR, ferredoxin:NADP⁺ oxidoreductase; PQ, plastoquinone.