Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes.

Abstract

Active transport across the vacuolar components of the eukaryotic endomembrane system is energized by a specific vacuolar H+-ATPase. The amino acid sequences of the 70-and 60-kDa subunits of the vacuolar H+-ATPase are -25% identical to the .8 and a subunits, respectively, of the eubacterial-type FOFj-ATPases. We now report that the same vacuolar H+-ATPase subunits are -50% identical to the a and 13 subunits, respectively, of the sulfur-metabolizing Sulfolobus acidocaldarius, an archaebacterium (Archaeobacterium). Moreover, the homologue of an 88-amino acid stretch near the amino-terminal end of the 70-kDa subunit is absent from the FOFj-ATPase P subunit but is present in the a subunit of Sulfolobus. Since the two types of subunits (a and 13 subunits; 60-and 70-kDa subunits) are homologous to each other, they must have arisen by a gene duplication that occurred prior to the last common ancestor of the eubacteria, eukaryotes, and Sulfolobus. Thus, the phylogenetic tree of the subunits can be rooted at the site where the gene duplication occurred. The inferred evolutionary tree contains two main branches: a eubacterial branch and an eocyte branch that gave rise to Sulfolobus and the eukaryotic host cell. The implication is that the vacuolar H+-ATPase of eukaryotes arose by the internalization of the plasma membrane H+-ATPase of an archaebacterial-like ancestral cell.Recently, attention has focused on the evolutionary relationships among the H+-ATPases, particularly the F0F1-ATPases (F-type) and vacuolar (V-type) H+-ATPases. F-and VATPases exhibit a number of structural and functional similarities (1-4). Both are large, multisubunit enzymes (=500 kDa) composed of a water-soluble catalytic sector and an integral membrane proton channel complex. Each hydrophilic sector contains three copies of the catalytic subunit (F-ATPase (3 subunit or V-ATPase 70-kDa subunit), three copies of a regulatory subunit (F-ATPase a subunit or V-ATPase 60-kDa subunit), and one copy each of several minor subunits (4). Sequences obtained for several eukaryotic V-ATPase 70-and 60-kDa subunits confirmed that the Fand V-type H+-ATPases are indeed homologous (5-9). However, the low overall similarity (25%) and the presence of a large stretch of nonhomologous sequence in the 70-kDa subunit (5) suggest that they diverged early in evolution. Consistent with this view, sequences obtained for the two major subunits of the membrane H+-ATPase of Sulfolobus acidocaldarius, an archaebacterium (Archaeobacterium), indicated that the "archaebacterial-type" H+-ATPase is only distantly related to the eubacterial-type F-ATPases (10, 11). In this joint communication from four of the laboratories involved, we show that the H+-ATPase of S. acidocaldarius belongs in the V-ATPase class of proton pumps. The implications for the origin of eukaryotes are discussed. MATERIALS AND METHODSTo determine the evolutionary relationships among the different H+-ATPases, protein or DNA sequences coding for the two major subunits or parts of these subunits were aligned, ...

5. Prebiotic Chemistry – Biochemistry – Emergence of Life (4.4–2 Ga)

“…This is supported by recent phylogenetic analyses of the enzymes involved suggesting that the cenancestor synthesized phospholipids via a non-stereospecific pathway (Pereto´et al, 2004). In addition, the occurrence of universally conserved membrane-bound proteins, such as the protonpump ATPases (Gogarten et al, 1989) and the signal recognition particle, SRP (Gribaldo and Cammarano 1998) fully supports the hypothesis of a cenancestor endowed with lipid membranes.…”

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

“…I am sure that it is wrong. The other classical example of the ATPase α-and β-subunits (Gogarten et al, 1989) is markedly worse ; in that case, the length of the neomuran stem is about seven times that of the branches in the eubacterial crown. Since the fossil record shows unambiguously that the latter represents at least 3n5 Gy, a believer in the molecular clock would have to argue that the evolutionary phase represented by the neomuran stem endured about 25 Gy, twice the age of the universe !…”

The vacuolar H+-ATPase: a universal proton pump of eukaryotes

“…Both Vma5p and Vma13p may be peripheral to the core V 1 complex. Cross-linking studies on the coated vesicle enzyme indicate that Vma4p (4), Vma5p (5) and Vma8p (8) are in contact with the 16 kDa proteolipid of V o (3). V o (subunits shown in light pink) comprises a core formed from a hexameric complex of the 16 kDa proteolipid Vma3p (3) which contains, at least in part, the pathway of proton translocation.…”

“…This naive model represents a synthesis of data relating primarily to the yeast enzyme and also inferred from studies on other systems (see sections [2][3][4]. The functional core of V 1 contains three copies each of polypeptides Vma1p (1) and Vma2p (2) (shown in dark pink and dark grey respectively) and one each of Vma4p (4) and Vma8p (8) (shown in light grey).…”

“…They also have different mechanisms of ATP hydrolysis, not having a phospho-enzyme intermediate characteristic of the Ptype. The V-and F-ATPases are thought to have a common ancestral origin [3,4] and most, possibly all, of the subunits of the two ATPases have been identified and the genes cloned from a variety of organisms. As might be expected, the subunits of the the two display identity with one another.…”