A square archaeon, the smallest eukaryote and the largest bacteria

The past 2 months brought significant advances in genome sequencing for all three domains of life. These include the genome sequence of the marine unicellular green alga Ostreococcus tauri that has the smallest cell size (usually 1 mm) of all known eukaryotes, the genome sequence of the square-celled archaeon Haloquadratum walsbyi and its relatives, and a dozen of new bacterial genomes, including some of the largest ones sequenced so far – Myxococcus xanthus and Rhodococcus sp. RHA1 whose genome sizes are more than 9 Mb – and the genome of the oil spill-degrading bacterium Alcanivorax borkumensis (Table 1). Ostreococcus tauri belongs to the family Prasinophyceae, an early branching group of green algae that retains some primitive features of ancestral green plants. Its single cell contains a nucleus with a single nuclear pore and a greatly reduced cytoplasm with one chloroplast and one mitochondrion. It carries a single copy of each of the core cell cycle genes and produces relatively primitive light-harvesting antenna complexes (Robbens et al., 2005; Six et al., 2005). Despite these traits, O. tauri grows very fast and occasionally causes algal blooms in coastal waters. Ostreococcus tauri is a common member of marine phytoplankton; in oligotrophic waters of Atlantic, Indian and Pacific oceans it may account for up to 90% of the autotrophic biomass. The genome of O. tauri consists of 20 chromosomes, ranging in size from 0.16 to 1.07 Mb (Derelle et al., 2006) with the total size of 12.56 Mb. Thus, O. tauri genome is the smallest of any autotrophic eukaryotes sequenced so far and is just a tad larger than the genomes of Saccharomyces cerevisiae and several other yeasts. It contains 8166 predicted open reading frames, which is similar to the protein set of the actinobacterium Streptomyces coelicolor A3(2) and much less than the protein sets of Rhodococcus sp. RHA1 (see below) and of two bacteria with previously sequenced genomes, Burkholderia xenovorans LB400 and Bradyrhizobium japonicum USDA 110. As much as 81% of the O. tauri genome consists of coding DNA, which is the highest number of all sequenced eukaryotic genomes. Overall, this genome shows the signs of compaction (streamlining), similar to those seen in Pelagibacter ubique and Prochlorococcus marinus, other ubiquitous marine autotrophs. It appears that adaptation to the relatively stable marine environment in these entirely different lineages occurred along the same lines and was dominated by massive gene loss. There is no doubt that this sequence will provide a valuable reference point for the comparative analysis of various plant genomes. There is also certain commercial potential: several O. tauri genes have been subject of two patents issued in 2005 and 2006 to BASF Plant Science GmbH (see GenBank accession numbers CS020113 and CS351561 for examples). Two papers published back-to-back in the online journal BMC Genomics describe, respectively, the genome sequence of the haloarchaeon H. walsbyi and the metagenome of the microbial community of a saturated brine (crystallizer) pond, from which this organism was isolated (Bolhuis et al., 2006; Legault et al., 2006). First described as ‘a square bacterium’ in 1980 by Anthony Walsby and referred ever since as ‘Walsby’s square bacterium’ or ‘Walsby’s square archaeon’, H. walsbyi has the shape of a thin rectangle with a side of up to 10 mm but only 0.25 mm thick (Walsby, 2005). This organism has not been cultivated until 2004, when two groups succeeded in growing it in an axenic culture in hypersaline media containing pyruvate (Bolhuis et al., 2004; Burns et al., 2004). Cultivation of H. walsbyi paved the way to the complete genome sequence of this very unusual organism that can survive in the brine containing 3.3 M NaCl and 2 M MgCl2. The genome sequence of H. walsbyi revealed protonand chloride-translocating bacteriorhodopsins and a dihydroxyacetone-specific phosphoenolpyruvatedependent phosphotransferase system (PTS), the first one found in any archaeon. The authors note that dihydroxyacetone is an end-product of glycerol metabolism by Salinibacter ruber, a bacterium that inhabits the same *For correspondence. E-mail galperin@ncbi.nlm.nih.gov; Tel. (+1) 301 435 5910; Fax (+1) 301 435 7793. Environmental Microbiology (2006) 8(10), 1683–1687 doi:10.1111/j.1462-2920.2006.01131.x