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  • Rob Stadler

There Is No Such Thing as a "Proto-membrane" or a "Proto-cell"


Origin-of-life researchers have a lot of explaining to do. In the last 70 years, our appreciation for the required complexity of the simplest forms of life has grown exponentially, while prebiotically plausible explanations for life’s required components remain elusive. One possible exception involves the formation of cell membranes. The basic structure of all cell membranes is a phospholipid bilayer. Phospholipids (or more generally, amphiphilic molecules) naturally form into spherical bilayers when placed in water under the right conditions.[1]

Do cell membranes really form by purely natural processes? Cell membranes are essential for life because they actively maintain homeostasis, providing a consistent environment inside the cell despite varying conditions outside the cell. To accomplish this, they must be actively and selectively permeable – passing essential nutrients into the cell and pushing waste products out of the cell.

A simple membrane composed only of phospholipids is too tight – it does not allow adequate transportation across the membrane, thus converting the inner contents to a tomb for decaying components and accumulation of waste. Some researchers have therefore suggested that early “proto-membranes” were leaky, composed of simpler amphiphilic molecules.[2] But simple leaky membranes are no better at maintaining homeostasis than simple tight membranes.

In life, membranes face conflicting requirements such as keeping very small items out while allowing substantially larger items in. For example, membranes pump protons out and must not allow the protons to pass freely back in, but they must also transfer larger nutrient molecules like histidine into the cell. The challenge is that histidine is about 700,000 times the size of a proton. Cells must also allow water to enter, but water facilitates free flow of protons and cells cannot allow protons to flow freely. No degree of “leakiness” in a membrane will succeed in keeping protons out while allowing histidine and water in.

How can any membrane meet such dramatically conflicting requirements? All cellular life employs a variety of highly specialized protein channels and active transport systems in the membrane. Mycoplasma genitalium, one of the simplest forms of single-celled life, produces about 140 different proteins that serve these functions within the cell membrane.[3] Of all the known proteins produced by living organisms, about 1/3 operate within membranes.[4] To maintain homeostasis, these protein channels must be highly specific, allowing only particular molecules to pass in a particular direction. A phospholipid bilayer that incorporates 140 different complex proteins bears almost no resemblance to the simple “membranes” that can be produced by prebiotic processes.

Whereas complex cells can manufacture essential nutrients from simple feedstock molecules, simpler cells must import more of the necessary nutrients. Therefore, transportation of a variety of molecules across the membrane actually becomes more important in simpler cells. The majority of the required protein channels consume energy (in the form of ATP).[5] A recent study proposed that membrane transport accounts for approximately 20% of energy consumption in one of the simplest known cells, JVCI Syn3A.[6]

Another layer of required complexity of cell membranes is the fundamental asymmetry of the bilayer: the inner (cytoplasmic) leaflet contains different lipids and protein orientations than the outer (extracellular) leaflet.[7] For example, glycolipids are always found in the outer leaflet. No prebiotic natural process can produce this type of asymmetric lipid bilayer.

The very simple “membranes” produced by placing amphiphilic molecules in water are more like soap bubbles or lava lamps than actual cell membranes. Suggesting that cell membranes are easy to produce in prebiotic conditions demonstrates a fundamental ignorance of the function of cell membranes. To sustain life, membranes must have been complex from the very start – actively and selectively permeable. Yes, origin-of-life researchers have a lot of explaining to do, even when it comes to cell membranes.

As we uncover layer after layer of the astounding complexity of even the simplest forms of life, the origin-of-life research community increasingly relies upon their trump card: imaginary protocells that existed long ago and were dramatically simpler than existing life. As the story goes, modern life may indeed be very complex, but protocells used to be much simpler, and there was plenty of time for the complexity to develop.

Protocells conveniently fill the uncomfortably large gap between the simple molecules that can be produced by prebiotic processes and the staggering complexity of all extant life. But there are three major problems with the concept of protocells. The three major problems are all backed by strong empirical support, in sharp contrast to the concept of protocells.

First, scientists have been working for decades to simplify existing life, trying to arrive at a minimal viable life form by jettisoning anything that is not essential from the simplest extant cells. The success of Craig Venter’s group is well known. Building off their efforts to produce synthetic life (“Synthia” or “Mycoplasma labritorium”) in 2010,[8,9] they introduced the current record holder for the simplest autonomously reproducing cell (JVCI Syn3.0) in 2016.[10] With a genome of only 473 genes and 520,000 base pairs of DNA, JVCI Syn3.0 can reproduce autonomously, but it certainly isn’t robust. Keeping it alive requires a coddled environment – essentially a life-support system. To arrive at a slightly more stable and robust organism that reproduced faster, the team later added back 19 genes to arrive at JVCI Syn3A.[11] When combined, this work provides an approximate boundary for the simplest possible self-replicating life. We are clearly approaching the limit of viable cell simplicity. It seems safe to conclude that at least 400 genes (and approximately 500,000 base pairs of DNA) are the minimum requirements to produce a self-replicating cell.

Second, we know that the process of simplifying an existing cell by removing some of its functionality doesn’t actually simplify the overall problem – it only exports the required complexity to the environment. A complex, robust cell can survive in changing conditions with varying food sources. A simplified cell becomes dependent on the environment to provide a constant, precise stream of the required nutrients. In other words, the simplified cell has reduced ability to maintain homeostasis, so the cell can only remain alive if the environment takes on the responsibility for homeostasis. Referring to JVCI Syn3A, Thornberg et al. conclude “Unlike most organisms, which have synthesis pathways for most of its building blocks, Syn3A has been reduced to the point where it relies on having to transport them in,”[12] implying that the environment must provide a continuous supply of more specific and complex nutrients. The only energy source that JVCI Syn3A can process is glucose,[11] so the environment must provide a continuous supply of its only tolerable food. Intelligent humans can provide such a coddled, life-support environment, but a prebiotic Earth could not. Protocells would therefore place untenable requirements on their environment, and the requirements would have to be consistently met for millions of years.

Third, we know that existing microbes are constantly trying to simplify themselves, to the extent that their environment will allow. In Richard’s Lenski’s famous E. coli experiment, the bacteria simplified themselves by jettisoning their ribose operons after a few thousand generations, because they didn’t need to metabolize ribose and they could replicate 2% faster without it, providing a selective advantage.[13] Furthermore, Kuo and Ochman studied the well-established preference of prokaryotes to minimize their own DNA, concluding: “deletions outweigh insertions by at least a factor of 10 in most prokaryotes”[14] This means that existing life has been trying since life began to be as simple as possible. Therefore, it is likely that extant life has already reached something close to the simplest possible life, unless experimenters like Richard Lenski provide a coddled environment for a long duration that allows further simplification. But such a coddled environment requires the intervention of intelligent humans to provide just the right ingredients, at the right concentrations, and at the right time. No prebiotic environment could do this. Therefore, scientists need not try to simplify existing life – we already have good approximations of the simplest form. Indeed, Mycoplasma genitalium has a genome of 580,000 base pairs and 468 genes [15] whereas Craig Venter’s minimal “synthetic cell” JVCI Syn3.0 has a comparable genome of 520,000 base pairs and 473 genes.[10]

The data provides a clear picture: the surprising complexity of even the simplest forms of existing life – 500,00 base pairs of DNA – cannot be avoided and cannot be reduced unless intelligent agents provide a complex life-support environment. Because protocells would have had to survive and reproduce in a harsh and otherwise lifeless planet, protocells are not a viable concept. Protocells place origin-of-life researchers in a rather awkward position: relying upon an imaginary entity to sustain their belief that only matter and energy exist.


References

1. Lombard J, Lopez-Garcia P, Moreira D. The early evolution of lipid membranes and the three domains of life. Nature Reviews Microbiology 2012. 10; 507-515.

2. Mansy SS et al. Template-directed synthesis of a genetic polymer in a model protocell. Nature. 2008; 454: 122-125.

3. Fraser CM et al. The minimal gene complement of Mycoplasma genitalium. Science. 1995; 270; 397-403.

4. Poetsch A, Wolters D. Bacterial membrane proteomics. Proteomics. 2008; 8: 4100-4122.

5. Santos, JA et al. Functional and structural characterization of an ECF-type ABC transporter for vitamin B12. eLife. 2018; 7: e35828.

6. Thornburg ZR et al. Fundamental behaviors emerge from simulations of a living minimal cell. Cell 2022; 185: 345-360.

7. Dingjan T, Futerman AH. The fine-tuning of cell membrane lipid bilayers accentuates their compositional complexity. BioEssays 2021; 43: 2100021. DOI: 10.1002/bies.202100021.

8. Gibson DG et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 2010; 329:52–56.

9. Gibson DG et al. Synthetic Mycoplasma mycoides JCVI-syn1.0 clone sMmYCp235-1, complete sequence. 2010. NCBI Nucleotide. Identifier: CP002027.1.

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