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The Ocelloid

The Ocelloid

Through the eye of a microbe

The Lost Eukaryote: an introduction to cellular evolution

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The most fundamental divide in the diversity of living creatures is arguably the one between prokaryotes (=bacteria*) and eukaryotes (the tiny island of cumbersomely complex cells that consists of protists. And a couple insignificant lineages that are hardly worth talking about). Much of the earth's biota seems perfectly content with small, streamlined genomes and similarly small, streamlined cell architecture. All but one group, that for some odd reason ended up with a membrane-bound package of a junky genome we call the nucleus. The nucleus, in turn, is but a spokesperson-organelle for the massive changes in cellular architecture that occurred in the transition from prokaryotic to eukaryotic forms -- a feature that most likely arose with the changes rather than initiating them. The most prominent features present in all eukaryotes are the actin and tubulin cytoskeleton, endomembrane trafficking (enabling phagocytosis) and mitochondria or some form thereof. Unfortunately (or fortunately, as it keeps us employed?), most of these features appear to have been already present and well-developed in the last common ancestor of all known eukaryotes, thereby depriving us of a convenient grade from which to infer how these structures actually evolved. Once upon a time, it was thought that some anaerobic eukaryotes lacked mitochondria and diverged from the aerobes before the mitochondrion was 'enslaved' through endosymbiosis in the latter (oddly enough, early ribosomal DNA trees even supported that, but that's a story for another day). However, it later turned out that even the mitochondrion was already present in the last common ancestor, and thus when we work our way back to reconstruct the evolution of the eukaryotic cell, we are stuck with a fairly modern cell that seemingly erupts spontaneously from a bacterial sea. Odd and unsettling to say the least.

*Yeah, yeah, Archaea included, we can argue about that later...

As a protistologist and some sort of a cell biologist by modest training, I am particularly interested in cellular evolution. In other words, while some focus on the evolution of macroscopic structures like wings and organs, and others look at molecular evolution of proteins and DNA sequences, I am especially fascinated by the in-between, or how subcellular structures themselves evolve. Unlike molecular biologists, we don't have the luxury of compressing the bulk of our data into sequences, and unlike developmental biologists, we can't really fiddle with gene expression patterns and play with a variety of well-established mutants, both natural (visible diversity) and lab-generated. This is partly why there's a chance you probably never heard of evolutionary cell biology as a field. The other big problem is that much of cellular diversity is, in fact, microbial, and microbial eukaryotes are barely studied (yeasts excluded -- but they're secondarily unicellular anyway, and really, really weird). It is in the unicellular protist realm where the cell is at its finest, for it cannot cower behind the multitudes of defective cell types of a multicellular organism to get by, and must be largely self-sufficient. (This is illustrated further by the higher average complexity (diversity of cell parts) in a unicellular cell than that of multicellular organisms (McShea 2002 Evolution)) Not only are these unicellular organisms cellularly complicated, they're also quite diverse. Bacteria most definitely have a cell biology of their own, but that has become recognised only recently, with the advent of fluorescent, and now super-resolution, light microscopy -- where one can finally track labelled proteins in a living cell. Thus, for the moment, evolutionary cell biology is ultimately the cell biology of protists in light of evolution.

Of course, just comparing cell structures and marvelling at their diversity isn't really all there is to exploring the evolution of something. Even reconstructing ancestral states is just the beginning. Evolutionary biology ultimately pursues mechanisms -- the more general, the better. We could simply assume evolution is adaptation  and make up stories as we go along (not entirely unpopular in some circles), but that wouldn't be good science. Evolution involves introduction of variation through mutation (with its own associated biases) as well as sorting thereof nor only through selection, but also by drift and migration.

Furthermore, heritability is a key required component in evolutionary change, and here we may even get something interesting: transmission of information from one cell to the next (generationally) is not only genomic (or genetic), but also depends on a spatial component. If you simply express a genome in a lipid vesicle, the proteins will not magically self-assemble into a working cell. A chunk of necessary information is directed by the patterning in the cell preceding the division. Extra-nuclear (or extra-genomic) cellular inheritance is not a mere figment of speculative imagination -- it has been demonstrated in ciliates in a landmark experiment by Tracy Sonneborn and Janine Beisson: a row of cilia was inverted surgically (presumably without affecting the genome, of course) in a Paramecium, and this strain with a backwards row of cilia persists to this very day, despite multiple genetic outcrossings (Beisson & Sonneborn 1965 PNAS)! Several of Sonneborn's deciples have continued the work on cytoplasmic inheritance in ciliates, with some fascinating results. However, molecular work on poorly-established model organisms is difficult and frustrating, and until recently bordered on insanity.  Unfortunately, just as the tools for doing molecular and cell biology on more obscure organisms are greatly improving (10 years ago, you couldn't just sequence a genome on a whim...), the field has largely...retired.

If there is a channel of inheritance that occurs in parallel with classical genetics, this opens up a whole new jungle of tantalising questions and models waiting to be described and later discarded in favour of better ones. While classical quantitative genetics (which studies the inheritance of visible, measurable traits from generation to generation) is a fairly established and well-studied field at this point, a parallel epigenetic system of heritability would call for expansion of the field to include non-genomic quantitative genetics, where it gets rather tricky due to lack of direct digital coding sequences. Of course, if such a thing were to be pursued and studied, it would have to be in unicellular organisms, for they don't have that pesky bottleneck where the entire multi-million celled creature has to fit through a fertilised egg or seed for later re-patterning. Essentially, this would call for an evolutionary developmental biology of the single cell. While all cells go through something resembling classical development in principle in at least some stage of their lives, we don't typically think of development on a cellular level. We really should.

Enough with the long-winded theoretical introduction. What, if anything, can we say about the grandest scale of eukaryotic cellular evolution, or that nagging question of how eukaryotes evolved? Unfortunately, as mentioned above, the picture is a little unsettling. That last common ancestor of ours was simply too complex! (creationist quotemining in 3...2...1)

[caption id="attachment_131" align="aligncenter" width="734" caption="It appears that the last eukaryotic common ancestor (LECA), of all currently known living eukaryotes, has been a fairly sophisticated cell with a nucleus and a mitochondrion, as well as elaborate cytoskeletal and membrane trafficking systems. Presumably, the first eukaryotic common ancestor was drastically less complicated, but its nature remains elusive, and all but one of its descendants...lost. (Also see Field & Dacks 2009 Curr Op Cell Biol)(abbreviations are for major eukaryotic supergroups, in no particular order: Ex - Excavates; Op - Opisthokonts; Am - Amoebozoans; SAR - Stramenopile-Alveolate-Rhizaria clade; Arch - Archaeplastids; Ha - "Hacrobia")"]The last common ancestor is not the same as the first common ancestor...![/caption]

Not only does LECA appear to possess a mitochondrion and a modern nucleus, but it already has a sophisticated membrane trafficking system, a cytoskeleton, capacity to devour prey by phagocytosis, a eukaryotic cell cycle regulation system, meiotic sex, and even a flagellum. Not only does it have modern-looking structures, but it seems to have already used many of the same molecular components used in a variety of living eukaryotes today. As an aside, you may perhaps recall having learned cell biology going structure by structure: there's an endoplasmic reticulum for making proteins and moving them, a Golgi for sorting them, vacuoles and lysosomes for storage and digestion, a nucleus for DNA... but it's perhaps more productive, and less confusing even, to think of the cell as a network of systems (like the human body), the key ones being metabolic pathways, the genome, cell cycle, the membrane trafficking system and the cytoskeleton, with the rest of the cell emerging from them. (this list is by no means meant to be definitive)

Of course, the first eukaryote-like thing, FECA*, presumably emerged from the bacterial realm. Somehow in the interim, between FECA and LECA, our lineage lost many of its bacterial features (such as a murein wall -- think Gram staining) and picked up all sorts of eukaryotic traits. One would imagine it not being a case where a single proto-eukaryote population just sits around and gradually eukaryifies until it becomes LECA and then explodes into a ton of supergroups -- the pre-LECA eukaryotes were probably diverse and had numerous long-lost offshoots. But somehow, it appears that only one lineage survived to rapidly diversify into modern extant eukaryotes. What where those enigmatic lost eukaryotes? Why did only one lineage survive to bind them all in mystery?

* We could call it them the Lost Eukaryotic Common Ancestors, but the acronym would be confusing...

Unfortunately, where we have a sample size of one in the form of a single phylogenetic event, we are left with little else but mere speculation (the question of the origin of sex falls under the same category). We might be tempted to think the presence of a mitochondrion or its relics in every known eukaryote may allude to mitochondrial symbiosis doing something important. Perhaps a massive selective sweep because this new organelle was that damn awesome. While this may sound reasonable, we have no clear evidence pointing either way. If we knew roughly when eukaryotes arose, we could speculate on some massive environmental change, perhaps a mass extinction where just by chance a single lineage survived. But our estimates for the origin of eukaryotes range from 0.8-3.5 billion years ago, in the wildest estimates. The likeliest time period in my irrelevant opinion, based on fossils and molecular clocks, would be the early Mesoproterozoic or the late Paleoproterozoic (~1.2-1.8 billion years) -- a time period still poorly understood. Hell, at times we can hardly tell whether a microfossil is even biotic in origin, let alone discern what made it!

I have probably convinced you by now that both the question of how cells evolve and the issue of the very origin of eukaryotes are thoroughly impossible to address. Usually when people write about science, the story works towards gradually clarifying one conundrum or another. Yes, there is often the occasional setback and an annoyingly unfitting data point that rudely asserts its foul presence in the midst of your otherwise beautiful hypothesis. But the topic of eukaryotic evolution is a whole other type of story -- in fact, while the protistan phylogeny has been clearing up over the past decade, the question of how they got there in the first place slipped further and further away. And the recent adventures in protistan genomes and proteomes only make it worse -- by rendering the Last Eukaryotic Common Ancestor unbearably complex.

But there is hope, and it lies in the bewildering diversity of eukaryotic cells -- as protists. We can still learn how eukaryotic cells evolve, and work on those general principles and models that are the holy grail of evolutionary biology (as much as anything can be holy in science, but we try!). We could perhaps even extrapolate those principles back in time and use the few subtle clues we have to uncover some of the FECA's descendents' path to eukaryocy (fine, eukaryote-hood). In fact, in the next post we'll look at once such case in the evolution of membrane trafficking machinery. We still have a vastness of post-LECA diversity and evolution to address.

Anywhere there is heritable diversity, there is an evolutionary system awaiting attention. Like culture and language, cells are no exception.

The views expressed are those of the author and are not necessarily those of Scientific American.

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