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Living with two extremes: Conclusions from the genome sequence of Natronomonas pharaonis

Max-Planck-Institute of Biochemistry, Department of Membrane Biochemistry, D-82152 Martinsried, Germany

Natronomonas pharaonis is an extremely haloalkaliphilic archaeon that was isolated from salt-saturated lakes of pH 11. We sequenced its 2.6-Mb GC-rich chromosome and two plasmids (131 and 23 kb). Genome analysis suggests that it is adapted to cope with severe ammonia and heavy metal deficiencies that arise at high pH values. A high degree of nutritional self-sufficiency was predicted and confirmed by growth in a minimal medium containing leucine but no other amino acids or vitamins. Genes for a complex III analog of the respiratory chain could not be identified in the N. pharaonis genome, but respiration and oxidative phosphorylation were experimentally proven. These studies identified protons as coupling ion between respiratory chain and ATP synthase, in contrast to other alkaliphiles using sodium instead. Secretome analysis predicts many extracellular proteins with alkaline-resistant lipid anchors, which are predominantly exported through the twin-arginine pathway. In addition, a variety of glycosylated cell surface proteins probably form a protective complex cell envelope. N. pharaonis is fully equipped with archaeal signal transduction and motility genes. Several receptors/transducers signaling to the flagellar motor display novel domain architectures. Clusters of signal transduction genes are rearranged in haloarchaeal genomes, whereas those involved in information processing or energy metabolism show a highly conserved gene order.

¹ Corresponding author.
E-mail oesterhe{at}biochem.mpg.de; fax 49-89-8578-3557.

[Supplemental material is available online at www.genome.org. The Natronomonas genome is accessible through HaloLex (http://www.halolex.mpg.de). The sequence data from this study have been submitted to EMBL under the accession numbers CR936257 (chromosome), CR936258 (plasmid PL131), and CR936259 (plasmid PL23).]

² Pumping of chloride ions into the cell causes a passive cation flow. The relative contribution of the different cations depends on their membrane permeability. The protonophore CCCP selectively increased membrane permeability for protons and accordingly results in increased alkalinization.

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