Structural Biochemistry/The Evolution of Membranes

Cellular membranes are highly complex biological machines, responsible for regulating the import and export of metabolites and polymers.

Metabolic network of the Arabidopsis thaliana citric acid cycle. Enzymes and metabolites are shown as red squares and the interactions between them as black lines.

The Interdependency of Lipid Membranes and Membrane Proteins

The cell membrane contains various types of proteins, including ion channel proteins, proton pumps, G proteins, and enzymes. These membrane proteins function cooperatively to allow ions to penetrate the lipid bilayer. The interdependency of lipid membranes and membrane proteins suggests that lipid bilayers and membrane proteins co-evolved together with membrane bioenergetics.

Ideas About The Earliest Membranes

Several hypotheses of the origin of cellular membranes exist:

• Evolution subsequently took place in vesicles, which were formed by the accumulation of abiogenically formed amphiphilic molecules. The vesicles then transformed into envelopes, likely reminiscent of viral envelopes.
• Proto-cells evolved from the folding of vesicles, upon which the first life forms existed.

A viral envelope.

From Water-Soluble Proteins to Integral Membrane Proteins

Water-soluble proteins evolved gradually into highly hydrophobic membrane proteins. Primordial membranes initially contained pores, which enabled ions, small molecules, and polymers to be exchanged passively between protocells and their environment. In contrast, modern membrane proteins must be inserted into the membrane by membrane protein complexes. Membrane protein complexes could not have logically existed prior to the existence of membrane proteins. Although a single α-helix is thermodynamically unfavorable, one model explains how increasingly complex membrane proteins were derived from a stand-alone hydrophobic α-helix. Molecular dynamics was used to show that an α-helix spontaneously dimerizes on the membrane surface upon entrance, and then oligomerizes within the membrane.

Top view of the α-helix. Four carbonyl groups are pointing upwards towards the viewer, spaced roughly 100° apart on the circle, corresponding to 3.6 amino-acid residues per turn of the helix.

The Co-Evolution of Lipid Bilayers, Membrane Bioenergetics, and Membrane Proteins

In order to maintain proper bioenergetics, cells meticulously regulate the flow of matter and therefore energy through the cellular membrane. There is an inverse relationship between membrane permeability and the number of enzymatic pathways present in a cell.

The Domains of Life.

LUCA and Early Membranes

The first major split between the domains of life is between archaea and bacteria. Yet, there are essential genes that are still common between the two domains that lead to the concept of the LUCA, or last universal common ancestor. Based on the standard model of evolution, the LUCA was based on DNA and led to the three domains of life and existed approximately 3.5 to 3.8 billion years ago. Archaea and bacteria, however, differ greatly in their biogenesis pathways as well as in the hydrophobic chains contained in the membrane structure. The fact that both archaea and bacteria contain membrane-embedded molecular machines such as ATP synthases strongly indicates that the LUCA contained some derivative of membranes, though perhaps not as complex and structured.

It is seemingly impossible to have the formation of impermeable membranes without membrane proteins and translocases to shuttle essential materials in and out of the cell. Consequently, it is also unlikely that very specialized membrane proteins were able to form without a membrane initially present. It is hypothesized that the development of a permeable, porous membrane eventually integrated evolving proteins, to later evolve into a highly specialized and efficient impermeable membrane.

ATPases as Basis of Membrane/Membrane-Protein Co-evolution

F-type ATPases are found in eukaryotic and bacteria mitochondria and chloroplasts, while A-type ATPases around found in archaea (and some bacteria). V-type ATPases are found in eukaryotic cells, particularly in vacuole membranes.

Na⁺/K⁺ATPase

From ‘Pore’ to ATPase

F- and A/V- type ATPases are membrane-embedded proteins and were feasibly present in the LUCA (last universal common ancestor) due to their omnipresence in modern cellular life. These ATPases function as efficient ATP synthases through the completion of a reaction cycle with a physical rotation of a ‘rotor.’ However a proton gradient is required for this function, and therefore an ion-imperable membrane is necessary.

In prokaryotes, sodium ions as well as proton translocations are found in both F- and V- type ATPases. However the ‘rotor’ base, or c-oligomer, in sodium ion translocating F- and V- type ATPases are found to contain almost identical sets of amino acids which serve as sodium ion binding sites. This shows that the last ancestor containing ATPases also contained a sodium ion binding site.

The c-oligomers in the F- and V- ATPases are homologous in their sub-units of composition, which are all unrelated. However, the ‘rotors’ or stalks of the ATPases are not. Based on this information, it is proposed that the F- and V- ATPases evolved from a protein translocase that is ATP dependent, which initially served as the ‘rotor’ or stalk. Membrane components of these ATPases function as membrane ion translocases. They do not function as channels, as the ion binding sites are not accessible from both sides of the membrane at the same time. The c-oligomers that form the base of the rotating stalk/rotor are ~2-3 nm in internal diameter, large enough to allow for transport of materials in and out of a cell membrane. Combining this diameter, along with the ion transport function and potential acquisition of an ATP dependent protein to form the stalk, lend strongly to the idea that ATPases could have once functioned as pores in the membrane.

Birth of Bioenergetics: Beginning of ATP Synthesis and Sodium Tight Membranes

ATPases potentially evolved from a sodium binding pore/protein combination. During the transition phase from porous to ion-tight membranes, there still could have been a demand for sodium binding.

Inside the cell, there is a higher concentration of proteins and polynucleotides, which are negatively charged. Such components could have potentially led to the beginning of a transmembrane electric potential. The Donnan effect shows that this can equate to an electric potential of up to 50mV. Additionally, because of this negative potential inside the semi-porous cell, positive portions of outside proteins tend to insert themselves positive end-first into the cell membranes.

In the Archean era, sodium ion concentration was already 1M in the ocean compared to approximately .01M inside the cell. With the combination of increased ocean salinity (and subsequent sodium ion gradient) and the transmembrane potential, there was enough drive present to turn the ATP dependent rotor/stalk proteins from hydrolyzing ATP into synthesizing ATP. Proposed here is the first membrane bioenergetics: the coupling of outward sodium ion pumps with ATP synthases and dependence on a sodium ion gradient.

Annual mean sea surface salinity for the World Ocean. Data from the World Ocean Atlas 2005.

Sodium-Based Bioenergetics

As the salinity of the ocean continues to increase, evolving cells must constantly remain in ionic-homeostasis. Therefore, sodium-tight membranes are required to prevent solute from entering or exiting the modern cell freely. Additionally, the evolution of membrane pumps was integral for the active expunction of excess Na+ out of the cell.

Proton-Based Bioenergetics

The cellular regulation of proton movement through lipid bilayers requires a significantly more advanced control mechanism than the regulation of sodium, and thus requires more advanced cellular machinery. The necessity of more stringent regulation arises from the chemical fact that proton transfer can be coupled to oxidation-reduction (redox) reactions. Furthermore, lipid bilayers are more conductive to protons than to sodium ions, and protons can integrate into hydrocarbon chains by dissolving in trapped water molecules.

The transition to proton-tight membranes is particularly more complicated because of the fact that lipid bilayers are much more conductive to protons than to sodium ions. Protons can easily enter into bunches of water molecules that are nestled in between chains of lipid hydrocarbons, while sodium ions cannot. The rate-limiting step of trans-membrane conduction of protons is the jumping from one bunch of water molecules to the next. This method of proton transfer can be stopped in two ways: increasing the density of the hydrocarbons, (limiting the bunches of water molecules), or by lowering the mobility of the lipids.

Different organisms have various solutions to the problem of passive proton transfer through the cell membrane:

• Archea form single C40 membrane-spanning lipid molecules by the fusing of two diether lipids.
• Bacteria incorporate additional steric hindrance by attaching bulky compounds such as cyclohexane and cycloheptane to the terminus of membrane fatty acids.

The steric effect makes reactions difficult.

The Hypothesized Co-Evolutionary Scheme of Membranes, Membrane Proteins, and Bioenergetics

Primordial cellular membranes were undoubtedly non-existent in pre-cellular life forms. The earliest cellular life forms contained leaky and inefficient cellular membranes, amphiphilic membrane proteins, and characteristically simple bioenergetics. In contrast, modern cells are carefully regulated by proton-tight membranes, highly hydrophobic membrane proteins, and complex bioenergetics.

References

1. Mulkidjanian A, et al. Co-evolution of primordial membranes and membrane proteins. Trends Biochem Sci. 2009 Apr;34(4):206-15. Epub 2009 Mar 18.
2. Eisenberg D (2003). "The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins". Proc. Natl. Acad. Sci. U.S.A. 100 (20): 11207–10. doi:10.1073/pnas.2034522100. PMC 208735. PMID 12966187. {{cite journal}}: Unknown parameter |month= ignored (help)