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.