Szathmáry recently put forward a scenario of co-evolution of membranes and metabolism, where evolution proceeded through progressive sequestration of protocells from the environment [54
]. Under this model, the gradual build-up of enzymatic pathways inside the protocell should be accompanied by decrease in membrane permeability. Membrane-coupled energy conversion reactions that collectively comprise the membrane bioenergetics (see Box 2
) are an essential part of cell metabolism; unlike other metabolic reactions, these processes are impossible without ion-tight membranes. Here, within the general framework of Szathmáry's model and building upon our previous analysis of the evolution of membrane ATPases [50
], we propose a scenario of co-evolution of membranes and membrane bioenergetics where the gradual decrease in membrane permeability enables the emergence of new energy-converting enzymes ().
The proposed scenario for the evolution of membranes and membrane enzymes - from separate RNA helicases and primitive membrane pores, via membrane RNA and protein translocases, to the F- and V-type ATPases
As discussed above, ATP-driven biopolymer translocases could evolve from a combination of a helicase and a membrane pore (). The primordial translocase could employ sodium cations to crosslink and stabilize the hairpin subunits of the pore (as in Ilyobacter tartaricus
, see ), preventing its destruction by the translocated polymer. Thus, even at the stage of the RNA/protein translocase, when the porous, primordial membranes would be leaky to both Na+
, there could have been a mechanistic demand for Na+
-binding and, accordingly, selection for the corresponding set of amino acid ligands. This scenario seems to be supported by experiments demonstrating a dramatic destabilization of c
-oligomers of Na+
-translocating F-ATPases from I. tartaricus
and Propionigenium modestum
in the absence of Na+
Because the concentration of negatively charged proteins and polynucleotides inside a (proto)cell should be higher than it is outside, even the porous primeval membranes, as argued by Fraústo da Silva and Williams [46
], would maintain transmembrane electric potential difference owing to the Donnan effect (up to 50 mV, negative inside [1
]). This potential could shape the “positive-inside” mechanism of protein insertion into the membrane [67
] and also promote the emergence of voltage-sensitivity in membrane proteins.
The next stage of evolution is envisaged as selection for tighter membranes that would maintain the ionic homeostasis of the evolving cells, a task of ever-increasing importance considering the growing ocean salinity. The primordial ocean emerged from condensation of water vapor [68
] and initially should have low sodium level. However, the sodium concentration in the ocean was high already ~3.5 Gy ago, as judged from the chemical composition of geologically trapped sea water (see [68
] and references therein). The sodium concentration inside all known cells is, on the contrary, low, possibly, because modern cells, in line with the general trend of chemistry conservation [69
], strive to maintain the internal sodium level as low as it was at the emergence of life. The need to keep the internal sodium concentration low should strongly favor evolution of sodium-tight membranes and membrane pumps capable of expunging Na+
out of the cell; selection for mechanisms to keep sodium out could be the driving force behind the above discussed transition from a protein translocase to an ion-translocating membrane ATPase. The key to the transition could be the decrease in the conductivity of the membrane pore. Amino acid replacements leading to increased hydrophobicity on the inside of the pore might cause translocated proteins to get stuck within the translocase. Then, the torque from ATP hydrolysis, transmitted by the stuck substrate polypeptide, would cause rotation of the c
-ring relative to the ex-centric membrane stator. This rotation could eventually be coupled with transmembrane ion translocation along the contact interface, via membrane-embedded, charged amino acid side chains that kept the membrane subunits together (see Box 1
). The transition to the ion translocase could be completed by the ultimate recruitment of unrelated and even structurally dissimilar proteins as central stalks in ancestral archaea and bacteria, as a result of the inclusion of the genes encoding the respective proteins into the operons of the F- and V-type ATPases (see ref. [52
] for details).
Unlike the other Na+
pumps (see Box 2
), the common ancestor of the F- and V-type ATPases, owing to its rotating scaffold, would be potentially able to translocate Na+
ions in both directions. Upon further increase in the ocean salinity, reversal of the rotation would result in the Na+
-driven synthesis of ATP by this primordial rotary machine. Already in Archaean, the concentration of Na+
in the ocean water was approx. 1M [68
], as compared to ~0.01 M inside the cell, that is, the Na+
-gradient, together with the transmembrane voltage, could be powerful enough to cause the switch of the rotary machine from the hydrolysis to the synthesis of ATP. The advent of the ion-gradient driven ATP synthesis can be considered the birth of membrane bioenergetics: together with the ancient outward Na+
pumps, the ancestral F- and V-type ATP synthases would complete the first, sodium-dependent bioenergetic cycle in a cell membrane (; see refs. [50
] for details).
The emergence of the energy-converting, sodium-tight membranes should put constraints on the ion tightness of membrane-embedded translocation systems. Conceivably, simple pores that might have been common at the early stages of membrane evolution, failed to pass this evolutionary bottleneck, and were supplanted by gated ion channels and ion-tight machines of the general protein secretion pathways. The survivors of the primordial machinery seem to be the F- and V-type ATPases with their pores plumbed by lipid, as well as the ATP-driven Type III protein secretion systems and the closely related flagellin secretion systems of bacterial flagella [51
]. Both the catalytic subunits and the subunits of the peripheral stalk of the F-type and V-type ATPases are homologous to the corresponding subunits in these protein secretion systems [51
]. As discussed previously [52
], although the extant Type III secretion systems are limited to bacteria in their spread, they might be direct descendants of the primordial protein translocases that also gave rise to the F- and V-type ATPases.
The final evolutionary step in the present scenario is the transition to proton-tight, elaborate membranes [50
]. The proton-based bioenergetics is more lucrative than the sodium-based bioenergetics because proton transfer can be chemically coupled to redox reactions, especially, those of oxygen and diverse quinones, thus enabling the advent of efficient redox-driven generators of PMF (see Box 2
). However, because of the much higher conductivity of lipid bilayers to protons compared to sodium ions (see Box 2
), creation of a non-leaky membrane capable of maintaining a PMF sufficient to drive ATP synthesis is a harder task than creation of a sodium-tight membrane; representatives of the three domains of life employed distinct solutions to this problem. Protons, unlike sodium ions, easily enter water clusters that are nested between lipid hydrocarbon chains, so that the rate-limiting step of transmembrane proton transfer is proton ‘hopping” from one water cluster to another when these clusters collide [3
]. Thus, proton leakage can be suppressed by decreasing the probability of such hopping by (i) restricting the lipid mobility and/or (ii) increasing the hydrocarbon density in the midplane of the bilayer [71
]. Different organisms utilize radically different means to achieve proton tightness of their membranes. For instance, in some archaea, phytanyl chains of two diether lipids are fused to form single C40 membrane-spanning lipid molecules. In many bacteria, membrane fatty acids have branched termini or terminate with cyclohexane or cycloheptane, resulting in additional molecular crowding at the midplane of the bilayer. In addition, different organisms pack different hydrocarbons in the midplane of their H+
-tight membranes (see [50
] and references therein). The diversity of the mechanisms that ensure proton tightness of membranes is compatible with the hypothesis of independent transitions from sodium to proton bioenergetics in multiple lineages (see above). In addition, the energy-converting enzymes had to develop structural traits that enabled the use of PMF for ATP synthesis by facilitating proton transfer between the generators of PMF and the ATP synthase (see Box 2
). Thus, the transition from the sodium-dependent to the proton-dependent energetics would require substantial “upgrades” to both the lipid bilayer and the energy-converting membrane enzymes.
After such “upgrades” were completed, the more energetically efficient and versatile proton-based bioenergetics could spread over [50
]. Once the membranes could maintain PMF and the first proton pumps emerged, the sodium-binding sites of the F and V-type ATPases became obsolete and, apparently, deteriorated independently on multiple occasions [50
]. The ancestral, less effective sodium bioenergetics persisted in anaerobic thermophiles and alkaliphiles that cannot benefit from proton energetics, as well as in some marine and parasitic bacteria and archaea that exist in high-sodium environments (see Box 2
]). However, apparent traces of the primordial Na+
-based bioenergetics are still seen in the universal distribution of Na+
gradients and Na+
-dependent systems of solute transport in virtually all known cell types. In particular, plasma membranes of animal cells are “sodium membranes” [41
] and, with some exceptions [37
], cannot maintain a proton gradient.
Owing to its nearly ubiquitous presence, proton-based energetics is generally viewed as the primary form of biological energy transduction [3
]. By contrast, the ability of some prokaryotes to utilize sodium gradient for ATP synthesis is usually construed as a later adaptation to survival in extreme environments [40
]. The scenario of the origin of proton-driven ATP synthases from a helicase and a simple membrane pore, via the sequential intermediate stages of RNA/protein translocases and sodium-driven ATPase, respectively (see ), implies (perhaps, counter-intuitively but in accordance with some previous ideas [39
]) that membrane bioenergetics, especially, in its modern version that is centered around transmembrane proton gradients, is a relatively late innovation in the evolution of life.