Dr Samuel Furse » 2015 » March

 A Search for the Origins of Life: Protocells and the Emergence of Lipids Tuesday, Mar 31 2015 


The Origins of Life on Earth is a topic that has an impressive resonance. It comes from an innate human desire to belong: almost everyone wonders where they came from. Anyone who has been to a Natural History Museum, and many who have not, wonder what the world must have been like when the dinosaurs were around. Almost everyone fortunate enough to have had a decent science teacher will have been put in the way of wondering what life was like before any kind of multi-celled organism. Geologists and palaeontologists have pieced together evidence from their respective fields to give a time line of the Earth’s history (Figure 1).

Figure 1. A time line of the geological and palaeontological events that we understand of the Earth’s history. This figure courtesy of Astrobiology Magazine, original credit: Dan Brennan/UW-Madison News Graphic

In the 1950s, two biological chemists took this curiosity a step further. Stanley Miller and Harold Urey tested the understanding of the early Earth by recreating the molecular components and conditions of the period, in the lab. They put ammonia, water, methane and hydrogen in a flask and simulated the conditions of an electrical storm (one with lightning) for a week [1, 2] (Figure 2). What they found amazed them. One thing was amino acids—the monomers that comprise proteins, the machinery of cells. The second, a bit further downstream, was evidence for ribose sugars. These are the precursors for nucleic acids, the basic units of the blueprints of life, RNA and DNA. At a stroke, there was evidence for prebiotic synthesis of two of the principal molecular species of terrestrial living systems.

Miller-Urey_experiment kit

Figure 2. The equipment set-up used by Miller and Urey to explore the chemistry of the early Earth’s atmosphere. It was with this that they showed that amino acids and perhaps riboses could form essentially spontaneously under these conditions. Diagram courtesy of Wiki commons, drawing credit here.

A subtle conclusion to this striking result is that the chemistry that drove the production of some of the basic molecular units of life is so simple that in terrestrial terms, it happens spontaneously. This provides an attractive explanation for the how the first batches of two major sets of biomolecules were made. It is not clear whether these spontaneous syntheses happened in rapid succession, as the Miller-Urey experiments suggest, or whether several molecular contributions and variations occurred over years or even millennia. What is clear is that stocks of these molecules could have built up well before they became part of living organisms—there was no ‘Frankenstein moment’ when life was suddenly conferred to a pool of chemicals on the Earth.

It is not a huge step of imagination from the riboses and simple amino acids we understand may have existed in this period, to the blueprints and machinery of the cells of which we too are made. What is missing from these experiments is the emergence of the boundary species, the molecular component(s) that separated the cell from its surroundings. What we have yet to pin down is the origin of lipids.

The emergence of lipids has a particular importance in the origins of life. Without such molecular species, it is not possible to construct even the most basic form of cell as we know it. The simplest requirement of a cell, alongside it being able to replicate, is that it can manage its internal environment. In fact, if it cannot control its internal environment, in practice, it cannot reproduce. An indispensable part of this is the barrier between the inside and the outside—in our cells, the lipid bilayer. Thus, lipids are required in order for cells as we know them to exist.

This need to explain the preparation of the earliest lipids presents several immediate problems in explaining how life as we know it got going. The theory and evidence we have is quite convincing from single cells up to mammals (any decent biology text book above a certain level will explain this lucidly), and the Miller-Urey experiments [1,2] give a significant insight into where amino acids and perhaps nucleic acid polymers came from. Work over the last decade shows that the genetics behind early cells is becoming clearer [3,4], indicating that some of the replication machinery of early cells is being better understood. But how do we get from the early Earth’s atmosphere and weather, to molecules that can spontaneously self-assemble into a primitive membrane that allows cells to divide? Moreover, how can this happen as spontaneously as amino acids form when lightning strikes the ammonia-methane-water-hydrogen cocktail?

A recent paper by Patel et al. begins to provide a possible answer [5]. They show that compounds such as prussic acid (hydrogen cyanide), in the presence of copper ions and hydrogen sulfide (also known as hydrogen sulphide, understood to have been released by volcanic activity early on in the Earth’s existence), can form precursors for nucleic acids, amino acids and, importantly, lipids.

The crucial part of the spontaneous formation of lipids is how polymers of methane the order of 16 or 18 carbon atoms formed, with oxidation probably only at one end, and how enough of these formed in close enough physical and chronological proximity to assemble into a bilayer. Sadly, this has yet to be explained; a Miller-Urey type experiment that results in fatty acids or anything similar, has yet to be reported*.

It is an experiment that many lipid chemists and lipid biologists would give a great deal to stumble upon. What I predict as a more likely progress to the answer is a meeting in the middle. Several experiments have shown that self-assemblies of simple fatty acids are sufficient to provide a boundary for RNA replication [4]. Such experiments have the potential to inform us about some of the limits of what is required for this to take place, e.g. What the shortest length of fatty acid is required for such a boundary, or whether or not fatty acids with oxygen or nitrogen functionality in the middle or at both termini (such as in archaea) are more energetically favoured. At the other end, the design of compartmentalised systems in which conditions such as pH may be controlled [6] tells us the minimum requirements for basic homeostasis. The (proto-)fatty acids that fall into both categories, ones that are easily made spontaneously and ones that can make a boundary, are prime candidates for being called the first lipids.

References

*I hardly need tell you that if I had a shed, I would be doing this sort of experiment in it.

[1] S. L. Miller, H. C. Urey, Science, 1953, 117, 528–9. DOI:10.1126/science.117.3046.528.

[2] S. L. Miller, H. C. Urey, Science, 1959, 130, 245–51. DOI:10.1126/science.130.3370.245.

[3] D. G. Gibson, J. I. Glass, C. Lartigue, V. N. Noskov, R. Y. Chuang, M. A. Algire, G. A. Benders, M. G. Montague, L. Ma, M. M. Moodie, C. Merryman, S. Vashee, R. Krishnakumar, N. Assad-Garcia, C. Andrews-Pfannkoch, Evgeniya A. Denisova, L. Young, Z. Q. Qi, T. H. Segall-Shapiro, C. H. Calvey, P. P. Parmar, C. A. Hutchison, Hamilton O. Smith, J. Craig Venter, Science, 2010, 329, 52-56. DOI: 10.1126/science.1190719

[4] J. C. Blain and J. W. Szostak, Annual Reviews in Biochemistry, 2014, 83, 615–40. DOI: 10.1146/annurev-biochem-080411-124036

[5] Bhavesh H. Patel, Claudia Percivalle, Dougal J. Ritson, Colm D. Duffy and John D. Sutherland, Nature Chemistry, 2015, 7, 301-307. DOI: 10.1038/NCHEM.2202

[6] D. Miller, P. J. Booth, J. M. Seddon, R.H. Templer, R. V. Law, R. Woscholski, O. Ces, L.M. C. Barter, Journal of the Royal Society, Interface, 2013, 10, 20130496. DOI 10.1098/rsif.2013.0496
 

 

 Phosphatidylethanolamine: The Renaissance in a Lipid Sunday, Mar 1 2015 


If I told you that a lack of lipids were responsible for causing ageing in yeast but too many is associated with insulin resistance in humans, and that although lipids dominate the membrane of the cell envelope in E. coli, they may not be essential, and if I added that lipids could be used to make fluorescent molecules that could be used to probe cellular systems, can be a raw material for making secondary messengers and also be a sort of chemical exchanger to repair other molecules, what would you say?

You might tell me, gently, that you have read The Lipid Chronicles before and so of course I am going to tell you that lipids are the renaissance–how on Earth would anyone be able to write 50 blog posts about a subject that did not have a bit of sparkle?

And you would be right, but perhaps in a crook. All of these things are not the responsibility of lipids, they are the responsibility of one lipid. Phosphatidylethanolamine, PE (structure shown in the figure).

DOPE

Figure. The structure of phosphatidyl ethanolamine (PE). The head group and glyceryl moiety are shown in red and the lipophilic part is shown in blue. The NH3+ is the primary amine group, that exists in this protonated form at physiological pH.

No one would have expected PE to be a renaissance man. It is rather ordinary in many ways, old and a bulk lipid to boot. It makes up >70% of the phospholipid fraction of E. coli and does not really form membranes in its pure form. But in my opinion, therein lies much of the scope for the variety: what we see is that small changes can shift the behaviour of this lipid over the line in one direction or another, showing lots of different guises. This multi-guise idea is strengthened by another contributor, the nucleophilic primary amine group –NH2, that is at the top of the head group. This functionality is the principle difference between PE and phosphatidylcholine (PC) in practice, as well as being a precursor for it. This gives PE a distinct ‘feel’ with respect to other lipids, especially other bulk lipids with a similar structure. This uniqueness gives rise to the ready identification of PE as responsible for its actions.

There is evidence that a lack of PE appears to be responsible for premature ageing in yeast [1]. This comes from a study by Rockenfeller et al. in which the production of PE was stopped at a genetic level*. This switching off of PE production accelerated the production of molecular species that cause age-related damage to cells, and thus eventually cell death. When the PE production machinery has not been switched off, cells can recognise when this damage is happening and engage in a process called autophagy, that removes damaged components and replaces them.

This is rather a contrast to what appears to happen in humans, in a condition where there is too much PE. Obesity-induced insulin resistance, the principle form of type II diabetes, correlates with a shift in the lipid profile in erythrocytes [2], including an increase in PE. The amount of PE is reduced upon exercise-induced weight loss. It is not clear from the study whether underweight mammals have too little PE, but there is evidence that autophagy is stronger when PE is higher in mammalian cells [1]. There is clearly a balance to be struck between too much and too little PE.

This balance may not exist for all species, however. PE typically makes up >70% of the phospholipid fraction of the cell envelope of E. coli cells, and so one might think that it is really rather important. However, there is evidence that although growth is not as strong as in normal E. coli, it is possible for cultures to grow with membranes consisting of only the other lipids that would usually be there, phosphatidyl glycerol (PG) and cardiolipin (CL)[3, 4]. The only absolute requirement in this situation is for the presence of divalent cations (doubly-positively-charged ions) such as calcium and magnesium (Ca++ and Mg++) in the growth medium [3]. This is because in the presence of the cations, the CL causes the membrane to curve in the same way the PE would make it do. Thus, the job of the PE as a lipid that elicits membrane curvature, is replaced. However, I think that the fact that the cells grow poorly despite this suggests that this lipid has other functions in E. coli than merely a bulk lipid.

This is certainly the case in mammalian retina cells. The primary amine group in PE is used in the management of de-oxidation of 11-cis-retinal [5]. PE forms an imine with the aldehyde group, that anchors the retinal to the membrane. Various drugs have been tested that mimic this activity, providing some hope for patients with blinding illnesses [6] (and also features in an earlier post).

Aside from this more chemical use of PE, it can also be used as a raw material for a biological action. It can be used as a carrier of ethanolamine, for producing a signalling molecule, N-acyl ethanolamine. The steps in this process are (i) PE is acylated with a fatty acid, (ii) the phosphate di-ester to is hydrolysed to give phosphatidic acid (PA) and the signal, the acylated ethanolamine. When the fatty acid is arachidonic acid, the final signal is called anandamide. The second step is carried out by a phospholipase D (PLD) enzyme [7].

This rather bewildering set of studies invites a number of general conclusions. PE can be, and is, used for some quite different functions, that controlling it is important, and that it has distinct chemical, biological and physical roles. The remaining question is whether this is the end for research into this lipid, or the beginning. Have we found out all there is to find out, of shock value at least, or are there other secrets—is this the tip of the iceberg?

It certainly seems that iceberg lettuce is no way to improve your PE levels, at least for snails. At least two species of snail show that those fed hen’s eggs have higher PE levels by about 40% than those fed only lettuce [8, 9]. Let us hope that the pace of finding out more about this exciting lipid proceeds faster than the average snail.

References

* The gene that codes for the enzyme that produces PE from its precursor, phosphatidylserine, was removed from the organism

[1] P. Rockenfeller, M. Koska, F. Pietrocola, N. Minois, O. Knittelfelder, V. Sica, J. Franz, D. Carmona-Gutierrez, G. Kroemer and F. Madeo, Cell Death Differ, 2015, 22, 499-508. 10.1038/cdd.2014.219.

[2] M. Younsi, D. Quilliot, N. Al-Makdissy, I. Delbachian, P. Drouin, M. Donner and O. Ziegler, Metabolism, 2002, 51, 1261-1268. 10.1053/meta.2002.35184.

[3] J. A. Killian, M. C. Koorengevel, J. A. Bouwstra, G. Gooris, W. Dowhan and B. de Kruijff, Biochimica et Biophysica Acta , 1994, 1189, 225-232. http://dx.doi.org/10.1016/0005-2736(94)90069-8.

[4] A. DeChavigny, P. N. Heacock and W. Dowhan, Journal of Biological Chemistry, 1991, 266, 5323-5332.

[5] M. Zhong, L. L. Molday and R. S. Molday, Journal of Biological Chemistry, 2009, 284, 3640-3649. 10.1074/jbc.M806580200.

[6] A. Maeda, M. Golczak, Y. Chen, K. Okano, H. Kohno, S. Shiose, K. Ishikawa, W. Harte, G. Palczewska, T. Maeda and K. Palczewski, Nat Chem Biol, 2012, 8, 170-178. 10.1038/nchembio.759.

[7] Y. Okamoto, J. Morishita, K. Tsuboi, T. Tonai and N. Ueda, Journal of Biological Chemistry, 2004, 279, 5298-5305. 10.1074/jbc.M306642200.

[8] J. L. Schneck, B. Fried and J. Sherma, Veliger, 2003, 46, 325-328.

[9] K. R. Sousa, B. Fried and J. Sherma, Journal of Liquid Chromatography, 1990, 13, 3963-3972. 10.1080/01483919008049582.