Heidi H. Luoto

Na+-translocating Membrane Pyrophosphatases Are Widespread in the Microbial World and Evolutionarily Precede H+-translocating Pyrophosphatases

Membrane pyrophosphatases (PPases), divided into K+-dependent and K+-independent subfamilies, were believed to pump H+ across cell membranes until a recent demonstration that some K+-dependent PPases function as Na+ pumps. Here, we have expressed seven evolutionarily important putative PPases in Escherichia coli and estimated their hydrolytic, Na+ transport, and H+ transport activities as well as their K+ and Na+ requirements in inner membrane vesicles. Four of these enzymes (from Anaerostipes caccae, Chlorobium limicola, Clostridium tetani, and Desulfuromonas acetoxidans) were identified as K+-dependent Na+ transporters. Phylogenetic analysis led to the identification of a monophyletic clade comprising characterized and predicted Na+-transporting PPases (Na+-PPases) within the K+-dependent subfamily. H+-transporting PPases (H+-PPases) are more heterogeneous and form at least three independent clades in both subfamilies. These results suggest that rather than being a curious rarity, Na+-PPases predominantly constitute the K+-dependent subfamily. Furthermore, Na+-PPases possibly preceded H+-PPases in evolution, and transition from Na+ to H+ transport may have occurred in several independent enzyme lineages. Site-directed mutagenesis studies facilitated the identification of a specific Glu residue that appears to be central in the transport mechanism. This residue is located in the cytoplasm-membrane interface of transmembrane helix 6 in Na+-PPases but shifted to within the membrane or helix 5 in H+-PPases. These results contribute to the prediction of the transport specificity and K+ dependence for a particular membrane PPase sequence based on its position in the phylogenetic tree, identity of residues in the K+ dependence signature, and position of the membrane-located Glu residue.

Membrane-integral pyrophosphatase subfamily capable of translocating both Na+ and H+

One of the strategies used by organisms to adapt to life under conditions of short energy supply is to use the by-product pyrophosphate to support cation gradients in membranes. Transport reactions are catalyzed by membrane-integral pyrophosphatases (PPases), which are classified into two homologous subfamilies: H+-transporting (found in prokaryotes, protists, and plants) and Na+-transporting (found in prokaryotes). Transport activities have been believed to require specific machinery for each ion, in accordance with the prevailing paradigm in membrane transport. However, experiments using a fluorescent pH probe and 22Na+ measurements in the current study revealed that five bacterial PPases expressed in Escherichia coli have the ability to simultaneously translocate H+ and Na+ into inverted membrane vesicles under physiological conditions. Consistent with data from phylogenetic analyses, our results support the existence of a third, dual-specificity bacterial Na+,H+-PPase subfamily, which apparently evolved from Na+-PPases. Interestingly, genes for Na+,H+-PPase have been found in the major microbes colonizing the human gastrointestinal tract. The Na+,H+-PPases require Na+ for hydrolytic and transport activities and are further activated by K+. Based on ionophore effects, we conclude that the Na+ and H+ transport reactions are electrogenic and do not result from secondary antiport effects. Sequence comparisons further disclosed four Na+,H+-PPase signature residues located outside the ion conductance channel identified earlier in PPases using X-ray crystallography. Our results collectively support the emerging paradigm that both Na+ and H+ can be transported via the same mechanism, with switching between Na+ and H+ specificities requiring only subtle changes in the transporter structure.

Pyrophosphate-Fueled Na+ and H+ Transport in Prokaryotes

SUMMARY In its early history, life appeared to depend on pyrophosphate rather than ATP as the source of energy. Ancient membrane pyrophosphatases that couple pyrophosphate hydrolysis to active H+ transport across biological membranes (H+-pyrophosphatases) have long been known in prokaryotes, plants, and protists. Recent studies have identified two evolutionarily related and widespread prokaryotic relics that can pump Na+ (Na+-pyrophosphatase) or both Na+ and H+ (Na+,H+-pyrophosphatase). Both these transporters require Na+ for pyrophosphate hydrolysis and are further activated by K+. The determination of the three-dimensional structures of H+- and Na+-pyrophosphatases has been another recent breakthrough in the studies of these cation pumps. Structural and functional studies have highlighted the major determinants of the cation specificities of membrane pyrophosphatases and their potential use in constructing transgenic stress-resistant organisms.

Membrane Na+-pyrophosphatases can transport protons at low sodium concentrations

Background: Prokaryotic membrane Na+-PPases couple PPi hydrolysis with active Na+ transport. Results: Na+-PPases can transport both Na+ and H+ at Na+ concentrations <5 mm but only Na+ above this level. Conclusion: Na+-PPases are dual specificity transporters in which H+ transport activity is masked under physiological conditions. Significance: Inherent Na+/H+ promiscuity provides a basis for Na+-PPase evolution to H+-PPase. Membrane-bound Na+-pyrophosphatase (Na+-PPase), working in parallel with the corresponding ATP-energized pumps, catalyzes active Na+ transport in bacteria and archaea. Each ∼75-kDa subunit of homodimeric Na+-PPase forms an unusual funnel-like structure with a catalytic site in the cytoplasmic part and a hydrophilic gated channel in the membrane. Here, we show that at subphysiological Na+ concentrations (<5 mm), the Na+-PPases of Chlorobium limicola, four other bacteria, and one archaeon additionally exhibit an H+-pumping activity in inverted membrane vesicles prepared from recombinant Escherichia coli strains. H+ accumulation in vesicles was measured with fluorescent pH indicators. At pH 6.2–8.2, H+ transport activity was high at 0.1 mm Na+ but decreased progressively with increasing Na+ concentrations until virtually disappearing at 5 mm Na+. In contrast, 22Na+ transport activity changed little over a Na+ concentration range of 0.05–10 mm. Conservative substitutions of gate Glu242 and nearby Ser243 and Asn677 residues reduced the catalytic and transport functions of the enzyme but did not affect the Na+ dependence of H+ transport, whereas a Lys681 substitution abolished H+ (but not Na+) transport. All four substitutions markedly decreased PPase affinity for the activating Na+ ion. These results are interpreted in terms of a model that assumes the presence of two Na+-binding sites in the channel: one associated with the gate and controlling all enzyme activities and the other located at a distance and controlling only H+ transport activity. The inherent H+ transport activity of Na+-PPase provides a rationale for its easy evolution toward specific H+ transport.

Two independent evolutionary routes to Na+/H+ co-transport function in membrane pyrophosphatases

Membrane-bound pyrophosphatases (mPPases) hydrolyze pyrophosphate (PPi) to transport H(+), Na(+) or both and help organisms to cope with stress conditions, such as high salinity or limiting nutrients. Recent elucidation of mPPase structure and identification of subfamilies that have fully or partially switched from Na(+) to H(+) pumping have established mPPases as versatile models for studying the principles governing the mechanism, specificity and evolution of cation transporters. In the present study, we constructed an accurate phylogenetic map of the interface of Na(+)-transporting PPases (Na(+)-PPases) and Na(+)- and H(+)-transporting PPases (Na(+),H(+)-PPases), which guided our experimental exploration of the variations in PPi hydrolysis and ion transport activities during evolution. Surprisingly, we identified two mPPase lineages that independently acquired physiologically significant Na(+) and H(+) cotransport function. Na(+),H(+)-PPases of the first lineage transport H(+) over an extended [Na(+)] range, but progressively lose H(+) transport efficiency at high [Na(+)]. In contrast, H(+)-transport by Na(+),H(+)-PPases of the second lineage is not inhibited by up to 100 mM Na(+) With the identification of Na(+),H(+)-PPase subtypes, the mPPases protein superfamily appears as a continuum, ranging from monospecific Na(+) transporters to transporters with tunable levels of Na(+) and H(+) cotransport and further to monospecific H(+) transporters. Our results lend credence to the concept that Na(+) and H(+) are transported by similar mechanisms, allowing the relative efficiencies of Na(+) and H(+) transport to be modulated by minor changes in protein structure during the course of adaptation to a changing environment.

Role of the potassium/lysine cationic center in catalysis and functional asymmetry in membrane-bound pyrophosphatases.

Membrane-bound pyrophosphatases (mPPases), which couple pyrophosphate hydrolysis to transmembrane transport of H+ and/or Na+ ions, are divided into K+,Na+-independent, Na+-regulated, and K+-dependent families. The first two families include H+-transporting mPPases (H+-PPases), whereas the last family comprises one Na+-transporting, two Na+- and H+-transporting subfamilies (Na+-PPases and Na+,H+-PPases, respectively), and three H+-transporting subfamilies. Earlier studies of the few available model mPPases suggested that K+ binds to a site located adjacent to the pyrophosphate-binding site, but is substituted by the ε-amino group of an evolutionarily acquired lysine residue in the K+-independent mPPases. Here, we performed a systematic analysis of the K+/Lys cationic center across all mPPase subfamilies. An Ala → Lys replacement in K+-dependent mPPases abolished the K+ dependence of hydrolysis and transport activities and decreased these activities close to the level (4-7%) observed for wild-type enzymes in the absence of monovalent cations. In contrast, a Lys → Ala replacement in K+,Na+-independent mPPases conferred partial K+ dependence on the enzyme by unmasking an otherwise conserved K+-binding site. Na+ could partially replace K+ as an activator of K+-dependent mPPases and the Lys → Ala variants of K+,Na+-independent mPPases. Finally, we found that all mPPases were inhibited by excess substrate, suggesting strong negative co-operativity of active site functioning in these homodimeric enzymes; moreover, the K+/Lys center was identified as part of the mechanism underlying this effect. These findings suggest that the mPPase homodimer possesses an asymmetry of active site performance that may be an ancient prototype of the rotational binding-change mechanism of F-type ATPases.