Friday, 21 September 2018

LUCA


All life comes in the form of cells. This immediately raises the question: why? Why should all life have this unique design in common? It might seem plausible that the evolution from chemistry to life would have explored many pathways not involving a cellular architecture whose descendants should be observed to this day. It seems plausible that we should observe a near continuity of strategies for achieving life, yet we observe only a single fundamental, highly evolved, strategy for life.  

This simple but surprising fact implies that proto-life evolved in a specialized environment over a long period of time. Only after evolving many fitness-conferring adaptations in that environment did it emerge and move on to colonize almost the entire planet. The long list of sophisticated adaptations shared by all life implies a universal common ancestor which possessed those adaptations. It implies that all subsequent forms of life inherited their cellular architecture and long list of common biochemical adaptations in a direct line of descent from this last universal common ancestor (LUCA).
Indeed, this reasoning, has led to a near consensus that all existing life has descended from a ‘last universal common ancestor’ or LUCA. It is posited that this distant ancestor possessed the full list of life’s characteristics and all subsequent life has evolved from LUCA and retains those fundamental characteristics (1)

As the good regulator theorem reminds us, any complex system, such as LUCA, forms a model of the system it is regulating (2). This simple understanding provides insights that may help to identify the particular niche in which LUCA evolved; likely niches are those which reflect or mirror the architecture of LUCA and which provide a suitable environment for the evolution of its many adaptations.

‘Origins of life is’ an extremely active area of research and many scenarios have been considered. Among these, Wikipedia suggests alkaline oceanic vents as perhaps the most likely niche in which LUCA evolved from chemistry (1):

The cell probably lived in conditions found in deep sea vents caused by ocean water interacting with magma beneath the ocean floor.

Indeed, the hydrothermal vent hypothesis is perhaps nearing consensus among current research as the most likely origin of life scenario (3). Essentially this hypothesis notes that porous rocks lining the boundary of alkaline hydrothermal vents provides cell-like niches supporting many pre-biotic chemical requirements. These include an energy gradient across pore walls due to alkaline vent flows on one side and more ambient ocean conditions on the other. Such rocky cells provide a rich niche where the chemical precursors of life could become more concentrated than in other more typical oceanic environments (4).

A most surprising thing about LUCA is the advanced state of its evolutionary development. LUCA was a not a simple chemical-like mechanism composing only a few rudimentary adaptations. Rather it was a sophisticated bundle of adaptation fine-tuned to its rocky-vent habitat. This implies that a long period of evolution occurred within the hydrothermal vent environment leading to LUCA and that life evolved beyond LUCA only when it finally inferred how to exist in the wider oceanic environment.

We should understand that LUCA was extremely well adapted for life within the hydrothermal vent niche. We can describe this adaptation both in Darwinian terms and in terms of the free energy principle. The FEP perspective asserts that LUCA had developed a genetic model of a survival strategy in this niche and that it acted to carry out this strategy as accurately as possible. Life before LUCA evolved to produce adaptations that could take advantage of the potential for existence offered by the hydrothermal vent niche. In a sense LUCA and the rocky pores of hydrothermal vents became mirrors of each other minimizing free energy. 

Undoubtedly, as LUCA more fully filled this niche, additional resources and suitable niches became scarce and new forms evolved to make use of a wider range including marginal resources and niches. There is little existing evidence of these experimental forms other than the two forms which ultimately colonized the wider oceanic environment and became the ancestral forms of all life beyond LUCA: bacteria and archaea, more technically named eubacteria and archaebacteria.
These two forms differ somewhat from LUCA. The greatest differences might be summarized as their possession of a cell wall and possessing a new type of chemical machinery for duplicating their genomes. In both instances the detailed chemical machinery, including all the enzymes involved, are quite different in bacteria and archaea – strongly suggesting that these adaptations where achieved through separate evolutionary trajectories.

These significant differences should not obscure their otherwise overwhelming similarity. Both bacteria and archaea share all the trademark characteristics inherited from LUCA. Specifically, their morphology is almost the same; under the microscope they look identical and may be identified only through sophisticated biochemical analysis. Crucially, their overwhelming similarity is in their overall architecture – their cellular structure. 

An obvious evolutionary source of this similarity is LUCA’s adaptations to its niche in pores of the rocks forming the boundaries of hydrothermal vents.

 Figure 9: Taken from (5). A 360 Myr old hydrothermally formed iron sulphide chimney from Silvermines, Ireland, (Boyce et al. 1983). Pores in this rock form chemically active compartments with dimensions comparable to biological cells.

As recent research indicates (5; 6), bacteria and archaea are likely to have become free living organisms in the wider oceanic environment by independently reconstructing their cellular architecture through the evolution of cell walls:

All life is organized as cells…
The naturally arising, three-dimensional compartmentation observed within fossilized seepage-site metal sulphide precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes found in free-living prokaryotes.

Indeed, detailed explanations of plausible evolutionary routes leading from LUCA to bacteria and archaea have been suggested whose main feature is the evolution of cell walls able to provide a chemical habitat closely mimicking the pores of hydrothermal vents to which LUCA was well adapted. 

 
Figure 10:  From (5) A model for the origin of membrane-bounded prokaryotic cells from iron monosulphide compartments within which the chemoautotrophic origin of life could have occurred.

At this point we might step back a little and consider an important implication of this scenario. LUCA was probably the product of several hundred million years of biochemical evolution taking place within the rocky pores of hydrothermal vents and all its adaptations were to this one niche. Obviously, the wider ocean environment offered a good deal of potential for any variant of LUCA able to exist there but how could existence be achieved when all LUCA’s adaptations were to a cellular niche?

Bacteria and archaea both inferred the same successful strategy: reconstruct cellular niches through the invention and construction of cell walls. This is an example of the well-known biological mechanism of niche construction (7) where organisms, such as beavers, evolve the ability to construct niches through mechanisms such as building dams, niches to which their non-dam-building ancestors were already adapted.

At the core of biological evolution is the increased fitness of the organism to its environment or in terms of the FEP, the reduction of the prediction error of organism’s genome. Niche construction represents a dual to this usual understanding by noting that fitness may also be increased if the organism acts to alter its niche in order to achieve a better fit to its existing adaptations.

References

1. Wikipedia. Last universal common ancestor. Wikipedia. [Online] [Cited: June 9, 2018.] https://en.wikipedia.org/wiki/Last_universal_common_ancestor.
2. Every good regulator of a system must be a model of that system. Conant, RC and Ashby, RW. s.l. : Int. J. Systems Sci., 1970, Int. J. Systems Sci., pp. 89–97.
3. Lane, Nick. The vital question. s.l. : Profile Books, 2015.
4. Acetyl Phosphate as a Primordial Energy Currency. Whicher, Alexandra , et al. s.l. : Orig Life Evol Biosph, 2018. https://doi.org/10.1007/s11084-018-9555-8.
5. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Martin, William and Russell, Michael J. s.l. : Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2002, Vol. 258 1429.
6. Early bioenergetic evolution. Sousa FL, Thiergart T, Landan G, Nelson-Sathi S, Pereira AC, Allen JF, Martin WF. s.l. : Phil Trans R Soc B, 2013, Vol. 368: 20130088. http://dx.doi.org/10.1098/rstb.2013.0088.
7. A variational approach to niche construction. Constant, Axel, et al. s.l. : Journal of the Royal Society Interface, 2018.