title: Evolutionary primacy of sodium bioenergetics.
abstract: BACKGROUND
  The F- and V-type ATPases are rotary molecular machines that couple translocation of protons or sodium ions across the membrane to the synthesis or hydrolysis of ATP. Both the F-type (found in most bacteria and eukaryotic mitochondria and chloroplasts) and V-type (found in archaea, some bacteria, and eukaryotic vacuoles) ATPases can translocate either protons or sodium ions. The prevalent proton-dependent ATPases are generally viewed as the primary form of the enzyme whereas the sodium-translocating ATPases of some prokaryotes are usually construed as an exotic adaptation to survival in extreme environments.
  
  
  RESULTS
  We combine structural and phylogenetic analyses to clarify the evolutionary relation between the proton- and sodium-translocating ATPases. A comparison of the structures of the membrane-embedded oligomeric proteolipid rings of sodium-dependent F- and V-ATPases reveals nearly identical sets of amino acids involved in sodium binding. We show that the sodium-dependent ATPases are scattered among proton-dependent ATPases in both the F- and the V-branches of the phylogenetic tree.
  
  
  CONCLUSIONS
  Barring convergent emergence of the same set of ligands in several lineages, these findings indicate that the use of sodium gradient for ATP synthesis is the ancestral modality of membrane bioenergetics. Thus, a primitive, sodium-impermeable but proton-permeable cell membrane that harboured a set of sodium-transporting enzymes appears to have been the evolutionary predecessor of the more structurally demanding proton-tight membranes. The use of proton as the coupling ion appears to be a later innovation that emerged on several independent occasions.
authors.affiliation: School of Physics, University of Osnabrück, D-49069 Osnabrück, Germany. amulkid@uos.de
authors.forename: Armen Y
authors.initials: AY
authors.lastname: Mulkidjanian
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Galperin
authors.forename: Kira S
authors.initials: KS
authors.lastname: Makarova
authors.forename: Yuri I
authors.initials: YI
authors.lastname: Wolf
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001419:Bacteria / Q000201:enzymology; D027682:Cation Transport Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004734:Energy Metabolism / Q000502:physiology*; D019143:Evolution, Molecular; D010802:Phylogeny; D021122:Protein Subunits / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012964:Sodium / Q000378:metabolism*; D000254:Sodium-Potassium-Exchanging ATPase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013329:Structure-Activity Relationship; D025262:Vacuolar Proton-Translocating ATPases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D027682:Cation Transport Proteins; D021122:Protein Subunits; D012964:Sodium; D000251:Adenosine Triphosphatases; D025262:Vacuolar Proton-Translocating ATPases; C021838:sodium-translocating ATPase; D000254:Sodium-Potassium-Exchanging ATPase